WO2010054138A2 - Modulators of atp-binding cassette transporters - Google Patents

Modulators of atp-binding cassette transporters Download PDF

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WO2010054138A2
WO2010054138A2 PCT/US2009/063475 US2009063475W WO2010054138A2 WO 2010054138 A2 WO2010054138 A2 WO 2010054138A2 US 2009063475 W US2009063475 W US 2009063475W WO 2010054138 A2 WO2010054138 A2 WO 2010054138A2
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PCT/US2009/063475
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WO2010054138A3 (en
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Sara S. Hadida Ruah
Peter D.J. Grootenhuis
Mark T. Miller
Jason Mccartney
Fredrick Van Goor
Mehdi Michel Djamel Numa
Jinglan Zhou
Brian Bear
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Vertex Pharmaceuticals, Incorporated
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Priority to UAA201106976A priority Critical patent/UA110192C2/en
Priority to CN2009801539702A priority patent/CN102272128A/en
Priority to NZ592693A priority patent/NZ592693A/en
Priority to AU2009313409A priority patent/AU2009313409A1/en
Priority to CA2742980A priority patent/CA2742980A1/en
Priority to BRPI0921234A priority patent/BRPI0921234B8/en
Priority to EP09795592A priority patent/EP2362874A2/en
Application filed by Vertex Pharmaceuticals, Incorporated filed Critical Vertex Pharmaceuticals, Incorporated
Priority to JP2011535676A priority patent/JP2012508246A/en
Priority to MX2011004834A priority patent/MX2011004834A/en
Priority to RU2011122646/04A priority patent/RU2011122646A/en
Publication of WO2010054138A2 publication Critical patent/WO2010054138A2/en
Publication of WO2010054138A3 publication Critical patent/WO2010054138A3/en
Priority to IL212727A priority patent/IL212727A/en
Priority to ZA2011/03856A priority patent/ZA201103856B/en
Priority to IL233996A priority patent/IL233996A/en

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Definitions

  • the present invention relates to modulators of ATP-Binding Cassette (“ABC”) transporters or fragments thereof, including Cystic Fibrosis Transmembrane Conductance Regulator (“CFTR”), compositions thereof and methods therewith.
  • ABSC ATP-Binding Cassette
  • CFTR Cystic Fibrosis Transmembrane Conductance Regulator
  • the present invention also relates to methods of treating ABC transporter mediated diseases using such modulators.
  • ABC transporters are a family of membrane transporter proteins that regulate the transport of a wide variety of pharmacological agents, potentially toxic drugs, and xenobiotics, as well as anions.
  • ABC transporters are homologous membrane proteins that bind and use cellular adenosine triphosphate (ATP) for their specific activities.
  • Some of these transporters were discovered as multidrug resistance proteins (like the MDRl-P glycoprotein, or the multidrug resistance protein, MRPl), defending malignant cancer cells against chemotherapeutic agents.
  • MRPl multidrug resistance protein
  • 48 ABC Transporters have been identified and grouped into 7 families based on their sequence identity and function.
  • ABC transporters regulate a variety of important physiological roles within the body and provide defense against harmful environmental compounds. Because of this, they represent important potential drug targets for the treatment of diseases associated with defects in the transporter, prevention of drug transport out of the target cell, and intervention in other diseases in which modulation of ABC transporter activity may be beneficial.
  • CFTR cAMP/ATP-mediated anion channel
  • CFTR is expressed in a variety of cells types, including absorptive and secretory epithelia cells, where it regulates anion flux across the membrane, as well as the activity of other ion channels and proteins. In epithelia cells, normal functioning of CFTR is critical for the maintenance of electrolyte transport throughout the body, including respiratory and digestive tissue.
  • CFTR is composed of approximately 1480 amino acids that encode a protein made up of a tandem repeat of transmembrane domains, each containing six transmembrane helices and a nucleotide binding domain. The two transmembrane domains are linked by a large, polar, regulatory (R)-domain with multiple phosphorylation sites that regulate channel activity and cellular trafficking.
  • the most prevalent mutation is a deletion of phenylalanine at position 508 of the CFTR amino acid sequence, and is commonly referred to as ⁇ F508-CFTR. This mutation occurs in approximately 70% of the cases of cystic fibrosis and is associated with a severe disease.
  • CFTR transports a variety of molecules in addition to anions
  • this role represents one element in an important mechanism of transporting ions and water across the epithelium.
  • the other elements include the epithelial Na + channel, ENaC, Na + /2C17K + co-transporter, Na + -K + -ATPaSe pump and the basolateral membrane K + channels, that are responsible for the uptake of chloride into the cell.
  • CFTR activity may be beneficial for other diseases not directly caused by mutations in CFTR, such as secretory diseases and other protein folding diseases mediated by CFTR. These include, but are not limited to, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
  • COPD chronic obstructive pulmonary disease
  • COPD dry eye disease
  • Sjogren's Syndrome Sjogren's Syndrome
  • COPD is characterized by airflow limitation that is progressive and not fully reversible.
  • the airflow limitation is due to mucus hypersecretion, emphysema, and bronchiolitis.
  • Activators of mutant or wild-type CFTR offer a potential treatment of mucus hypersecretion and impaired mucociliary clearance that is common in COPD.
  • increasing anion secretion across CFTR may facilitate fluid transport into the airway surface liquid to hydrate the mucus and optimized periciliary fluid viscosity. This would lead to enhanced mucociliary clearance and a reduction in the symptoms associated with COPD.
  • Dry eye disease is characterized by a decrease in tear aqueous production and abnormal tear film lipid, protein and mucin profiles.
  • Sj ⁇ grens's syndrome is an autoimmune disease in which the immune system attacks moisture-producing glands throughout the body, including the eye, mouth, skin, respiratory tissue, liver, vagina, and gut. Symptoms, include, dry eye, mouth, and vagina, as well as lung disease.
  • the disease is also associated with rheumatoid arthritis, systemic lupus, systemic sclerosis, and polymypositis/dermatomyositis. Defective protein trafficking is believed to cause the disease, for which treatment options are limited. Modulators of CFTR activity may hydrate the various organs afflicted by the disease and help to elevate the associated symptoms.
  • the diseases associated with the first class of ER malfunction are Cystic fibrosis (due to misfolded ⁇ F508-CFTR as discussed above), Hereditary emphysema (due to al -antitrypsin; non Piz variants), Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses (due to Lysosomal processing enzymes), Sandhof/Tay-Sachs (due to ⁇ -Hexosaminidase), Crigler- Najjar type II (due to UDP-glucuronyl-sialyc-transferase), Polyendoc
  • Glycanosis CDG type 1 Hereditary emphysema (due to ⁇ l- Antitrypsin (PiZ variant), Congenital hyperthyroidism, Osteogenesis imperfecta (due to Type I, II, IV procollagen), Hereditary hypofibrinogenemia (due to Fibrinogen), ACT deficiency (due to ⁇ l-Antichymotrypsin), Diabetes insipidus (DI), Neurophyseal DI (due to Vasopvessin hormone/V2-receptor), Neprogenic DI (due to Aquaporin II), Charcot-Marie Tooth syndrome (due to Peripheral myelin protein 22), Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease ( due to ⁇ APP and presenilins), Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick
  • CFTR modulators may be beneficial for the treatment of secretory diarrheas, in which epithelial water transport is dramatically increased as a result of secretagogue activated chloride transport.
  • the mechanism involves elevation of cAMP and stimulation of CFTR.
  • Acute and chronic diarrheas represent a major medical problem in many areas of the world. Diarrhea is both a significant factor in malnutrition and the leading cause of death (5,000,000 deaths/year) in children less than five years old.
  • Diarrhea in barn animals and pets such as cows, pigs and horses, sheep, goats, cats and dogs, also known as scours, is a major cause of death in these animals. Diarrhea can result from any major transition, such as weaning or physical movement, as well as in response to a variety of bacterial or viral infections and generally occurs within the first few hours of the animal's life.
  • ETEC enterotoxogenic E-coli
  • Common viral causes of diarrhea include rotavirus and coronavirus.
  • Other infectious agents include Cryptosporidium, giardia lamblia, and salmonella, among others.
  • Symptoms of rotaviral infection include excretion of watery feces, dehydration and weakness. Coronavirus causes a more severe illness in the newborn animals, and has a higher mortality rate than rotaviral infection. Often, however, a young animal may be infected with more than one virus or with a combination of viral and bacterial microorganisms at one time. This dramatically increases the severity of the disease.
  • R, R 1 , R 2 , R 3 , R 4 , and R 5 are defined below.
  • compositions are useful for treating or lessening the severity of a variety of diseases, disorders, or conditions, including, but not limited to, cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation-fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, diabetes mellitus, laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1,
  • ABS-transporter as used herein means an ABC-transporter protein or a fragment thereof comprising at least one binding domain, wherein said protein or fragment thereof is present in vivo or in vitro.
  • binding domain as used herein means a domain on the ABC-transporter that can bind to a modulator. See, e.g., Hwang, T. C. et al., J. Gen. Physiol. (1998): 111(3), 477-90.
  • CFTR cystic fibrosis transmembrane conductance regulator or a mutation thereof capable of regulator activity, including, but not limited to, ⁇ F508 CFTR and G551D CFTR (see, e.g., http://www.genet.sickkids.on.ca/cftr/, for CFTR mutations).
  • modulating means increasing or decreasing, e.g. activity, by a measurable amount.
  • Compounds that modulate ABC Transporter activity, such as CFTR activity, by increasing the activity of the ABC Transporter, e.g., a CFTR anion channel are called agonists.
  • Compounds that modulate ABC Transporter activity, such as CFTR activity, by decreasing the activity of the ABC Transporter, e.g., CFTR anion channel are called antagonists.
  • An agonist interacts with an ABC Transporter, such as CFTR anion channel, to increase the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding.
  • An antagonist interacts with an ABC Transporter, such as CFTR, and competes with the endogenous ligand(s) or substrate(s) for binding site(s) on the receptor to decrease the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding.
  • an ABC Transporter such as CFTR
  • the phrase "treating or reducing the severity of an ABC Transporter mediated disease” refers both to treatments for diseases that are directly caused by ABC Transporter and/or CFTR activities and alleviation of symptoms of diseases not directly caused by ABC Transporter and/or CFTR anion channel activities.
  • diseases whose symptoms may be affected by ABC Transporter and/or CFTR activity include, but are not limited to, Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1 , Hereditary emphysema
  • compounds of the invention may optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention.
  • aliphatic encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
  • an "alkyl” group refers to a saturated aliphatic hydrocarbon group containing 1-12 (e.g., 1-8, 1-6, or 1-4) carbon atoms.
  • An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl, or 2-ethylhexyl.
  • An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, phospho, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)carbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaral
  • substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkyl-SC> 2 -amino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, or haloalkyl.
  • carboxyalkyl such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl
  • cyanoalkyl hydroxyalkyl, alkoxyalkyl, acylalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (al
  • an "alkenyl” group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-12, 2-6, or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to allyl, isoprenyl, 2-butenyl, and 2-hexenyl.
  • An alkenyl group can be optionally substituted with one or more substituents such as halo, phospho, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)carbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino al
  • substituted alkenyls include cyanoalkenyl, alkoxyalkenyl, acylalkenyl, hydroxyalkenyl, aralkenyl, (alkoxyaryl)alkenyl, (sulfonylamino)alkenyl (such as (alkyl-SO 2 -amino)alkenyl), aminoalkenyl, amidoalkenyl, (cycloaliphatic)alkenyl, or haloalkenyl.
  • an "alkynyl” group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-12, 2-6, or 2-4) carbon atoms and has at least one triple bond.
  • An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl.
  • An alkynyl group can be optionally substituted with one or more substituents such as aroyl, heteroaroyl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, nitro, carboxy, cyano, halo, hydroxy, sulfo, mercapto, sulfanyl [e.g., aliphatic sulfanyl or cycloaliphaticsulfanyl], sulfinyl [e.g., aliphaticsulfinyl or cycloaliphaticsulfinyl], sulfonyl [e.g., aliphatic-SCV, aliphaticamino-SCV, or cycloaliphatic- SO 2 -], amido [e.g., aminocarbonyl, alkylaminocarbonyl, alkylcarbonylamino, cycloalkylaminocarbonyl, hetero
  • an “amido” encompasses both “aminocarbonyl” and “carbonylamino”. These terms when used alone or in connection with another group refer to an amido group such as -N(R X )-C(O)-R Y or -C(O)-N(R X ) 2 , when used terminally, and -C(O)- N(R X )- or -N(R X )-C(O)- when used internally, wherein R x and R ⁇ are defined below.
  • amido groups include alkylamido (such as alkylcarbonylamino or alkylaminocarbonyl), (heterocycloaliphatic)amido, (heteroaralkyl)amido, (heteroaryl) amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido, or cycloalkylamido.
  • an "amino" group refers to -NR X R Y wherein each of R x and R ⁇ is independently hydrogen, aliphatic, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted.
  • amino groups examples include alkylamino, dialkylamino, or arylamino.
  • amino When the term “amino” is not the terminal group (e.g., alkylcarbonylamino), it is represented by -NR X -. R x has the same meaning as defined above.
  • an "aryl” group used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl” refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl) ring systems in which the monocyclic ring system is aromatic or at least one of the rings in a bicyclic or tricyclic ring system is aromatic.
  • the bicyclic and tricyclic groups include benzofused 2-3 membered carbocyclic rings.
  • a benzofused group includes phenyl fused with two or more C 4 _ 8 carbocyclic moieties.
  • An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro
  • Non-limiting examples of substituted aryls include haloaryl [e.g., mono-, di (such as
  • aminoaryl e.g., ((alkylsulfonyl)amino)aryl or ((dialkyl)amino)aryl]; (cyanoalkyl)aryl; (alkoxy)aryl; (sulfamoyl)aryl [e.g., (aminosulfonyl)aryl]; (alkylsulfonyl)aryl; (cyano)aryl; (hydroxyalkyl)aryl; ((alkoxy)alkyl)aryl; (hydroxy)aryl, ((carboxy)alkyl)aryl; (((dialkyl)amino)alkyl)aryl; (nitroalkyl)aryl; (((alkylsulfonyl)amino)alkyl)aryl; ((heterocycloaliphatic)carbonyl)aryl;
  • an "araliphatic” such as an “aralkyl” group refers to an aliphatic group (e.g., a C 1 ⁇ alkyl group) that is substituted with an aryl group.
  • "Aliphatic,” “alkyl,” and “aryl” are defined herein.
  • An example of an araliphatic such as an aralkyl group is benzyl.
  • an "aralkyl” group refers to an alkyl group (e.g., a Ci_ 4 alkyl group) that is substituted with an aryl group. Both “alkyl” and “aryl” have been defined above. An example of an aralkyl group is benzyl.
  • An aralkyl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl, including carboxyalkyl, hydroxyalkyl, or haloalkyl such as trifluoromethyl] , cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, amido [e.g., aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycl
  • a "bicyclic ring system” includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common).
  • Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls.
  • a “carbocycle” or “cycloaliphatic” group encompasses a “cycloalkyl” group and a “cycloalkenyl” group, each of which being optionally substituted as set forth below.
  • a “cycloalkyl” group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms.
  • cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]decyl, bicyclo[2.2.2]octyl, adamantyl, or ((aminocarbonyl)cycloalkyl)cycloalkyl.
  • a "cycloalkenyl” group refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds.
  • Examples of cycloalkenyl groups include cyclopentenyl, 1 ,4-cyclohexa-di-enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, or bicyclo[3.3.1]nonenyl.
  • a cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as phosphor, aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino,
  • heterocycle or “heterocycloaliphatic” encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
  • heterocycloalkyl refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof).
  • heterocycloalkyl group examples include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxolanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octahydrobenzofuryl, octahydrochromenyl, octahydrothiochromenyl, octahydroindolyl, octahydropyrindinyl, decahydroquinolinyl, octahydrobenzo[Z?]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-di
  • a "heterocycloalkenyl” group refers to a mono- or bicylic (e.g., 5- to 10-membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S).
  • Monocyclic and bicyclic heterocycloaliphatics are numbered according to standard chemical nomenclature.
  • a heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as phosphor, aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic)aliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycl
  • a “heteroaryl” group refers to a monocyclic, bicyclic, or tricyclic ring system having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and in which the monocyclic ring system is aromatic or at least one of the rings in the bicyclic or tricyclic ring systems is aromatic.
  • a heteroaryl group includes a benzofused ring system having 2 to 3 rings.
  • a benzofused group includes benzo fused with one or two 4 to 8 membered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[ ⁇ ]furyl, benzo[Z?]thiophenyl, quinolinyl, or isoquinolinyl).
  • heterocycloaliphatic moieties e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[ ⁇ ]furyl, benzo[Z?]thiophenyl, quinolinyl, or isoquinolinyl.
  • heteroaryl examples include azetidinyl, pyridyl, IH- indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo-l,2,5-thiadiazolyl,
  • monocyclic heteroaryls include furyl, thiophenyl, 2H-pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4-thiadiazolyl, 2H-pyranyl, 4-H-pranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl.
  • Monocyclic heteroaryls are numbered according to standard chemical nomenclature.
  • bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H- indolyl, indolinyl, benzo[ ⁇ ]furyl, benzo[Z?]thiophenyl, quinolinyl, isoquinolinyl, indolizinyl, isoindolyl, indolyl, benzo[ ⁇ ]furyl, bexo[ ⁇ ]thiophenyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl.
  • Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
  • a heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)
  • heterocycloaliphatic aliphatic
  • carbonyl or (heteroaraliphatic)carbonyl]
  • sulfonyl e.g., aliphaticsulfonyl or aminosulfonyl
  • sulfinyl e.g., aliphatic sulfinyl
  • sulfanyl e.g., aliphaticsulfanyl
  • a heteroaryl can be unsubstituted.
  • Non- limiting examples of substituted heteroaryls include (halo)heteroaryl [e.g., mono- and di-(halo)heteroaryl]; (carboxy )heteroaryl [e.g., (alkoxycarbonyl)heteroaryl] ; cyanoheteroaryl; aminoheteroaryl [e.g., ((alkylsulfonyl)amino)heteroaryl and ((dialkyl)amino)heteroaryl] ; (amido)heteroaryl [e.g., aminocarbonylheteroaryl, ((alkylcarbonyl)amino)heteroaryl, ((((alkyl)amino)alkyl)aminocarbonyl)heteroaryl, (((heteroaryl)amino)carbonyl)heteroaryl, ((heteroaryl)amino)carbonyl)hetero
  • heteroaralkyl refers to an aliphatic group (e.g., a C 1-4 alkyl group) that is substituted with a heteroaryl group.
  • aliphatic group e.g., a C 1-4 alkyl group
  • heteroaryl e.g., a C 1-4 alkyl group
  • heteroarylkyl refers to an alkyl group (e.g., a Ci_ 4 alkyl group) that is substituted with a heteroaryl group. Both “alkyl” and “heteroaryl” have been defined above.
  • a heteroaralkyl is optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloal
  • cyclic moiety and “cyclic group” refer to mono-, bi-, and tricyclic ring systems including cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been previously defined.
  • bridged bicyclic ring system refers to a bicyclic heterocyclicaliphatic ring system or bicyclic cycloaliphatic ring system in which the rings are bridged.
  • bridged bicyclic ring systems include, but are not limited to, adamantanyl, norbornanyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.2.3]nonyl, 2-oxabicyclo[2.2.2]octyl, l-azabicyclo[2.2.2]octyl, 3- azabicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.0 3 ' 7 ]nonyl.
  • a bridged bicyclic ring system can be optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heter
  • an "acyl” group refers to a formyl group or R X -C(O)- (such as alkyl-C(O)-, also referred to as “alkylcarbonyl”) where R x and "alkyl” have been defined previously.
  • R x and "alkyl” have been defined previously.
  • Acetyl and pivaloyl are examples of acyl groups.
  • an “aroyl” or “heteroaroyl” refers to an aryl-C(O)- or a heteroaryl-C(O)-.
  • the aryl and heteroaryl portion of the aroyl or heteroaroyl is optionally substituted as previously defined.
  • alkoxy refers to an alkyl-O- group where “alkyl” has been defined previously.
  • a "carbamoyl” group refers to a group having the structure -O-CO-NR X R Y or -NR X -CO-O-R Z , wherein R x and R ⁇ have been defined above and R z can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
  • a "carboxy” group refers to -COOH, -COOR X , -OC(O)H, -OC(O)R X , when used as a terminal group; or -OC(O)- or -C(O)O- when used as an internal group.
  • haloaliphatic refers to an aliphatic group substituted with 1-3 halogen.
  • haloalkyl includes the group -CF 3 .
  • mercapto refers to -SH.
  • AAss uusseedd hheerreeiinn aa ""ssulfo" group refers to -SO 3 H or -S ⁇ 3 R x when used terminally or -S(O) 3 - when used internally.
  • a "sulfamide” group refers to the structure -NR X -S(O) 2 -NR Y R Z when used terminally and -NR X -S(O) 2 -NR Y - when used internally, wherein R x , R ⁇ , and R z have been defined above.
  • a "sulfonamide” group refers to the structure -S(O) 2 -NR X R Y or -NR X -S(O) 2 -R Z when used terminally; or -S(O) 2 -NR X - or -NR X -S(O) 2 - when used internally, wherein R x , R ⁇ , and R z are defined above.
  • sulfanyl group refers to -S-R x when used terminally and -S- when used internally, wherein R x has been defined above.
  • sulfanyls include aliphatic-S-, cycloaliphatic-S-, aryl-S-, or the like.
  • a "sulfinyl” group refers to -S(O)-R X when used terminally and - S(O)- when used internally, wherein R has been defined above.
  • exemplary sulfinyl groups include aliphatic-S(O)-, aryl-S(O)-, (cycloaliphatic(aliphatic))-S(O)-, cycloalkyl-S(O)-, heterocycloaliphatic-S(O)-, heteroaryl-S(O)-, or the like.
  • a "sulfonyl” group refers to-S(O) 2 -R x when used terminally and -S(O) 2 - when used internally, wherein R x has been defined above.
  • Exemplary sulfonyl groups include aliphatic-S(O) 2 -, aryl-S(O) 2 -, (cycloaliphatic(aliphatic))-S(O) 2 -, cycloaliphatic-S(O) 2 -, heterocycloaliphatic-S(O) 2 -, heteroaryl-S(O) 2 -, (cycloaliphatic(amido(aliphatic)))-S(O) 2 -or the like.
  • a "sulfoxy" group refers to -O-SO-R X or -SO-O-R X , when used terminally and -0-S(O)- or -S(O)-O- when used internally, where R x has been defined above.
  • halogen or halo group refers to fluorine, chlorine, bromine or iodine.
  • alkoxycarbonyl which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-.
  • alkoxyalkyl refers to an alkyl group such as alkyl-O-alkyl-, wherein alkyl has been defined above.
  • phospho refers to phosphinates and phosphonates.
  • phosphinates and phosphonates include -P(O)(R P ) 2 , wherein R p is aliphatic, alkoxy, aryloxy, heteroaryloxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy aryl, heteroaryl, cycloaliphatic or amino.
  • aminoalkyl refers to the structure (R x ) 2 N-alkyl-.
  • a "cyanoalkyl” refers to the structure (NC)-alkyl-.
  • a "urea” group refers to the structure -NR X -CO-NR Y R Z and a “thiourea” group refers to the structure -NR X -CS-NR Y R Z when used terminally and -NR X - C0-NR Y - or
  • the term "vicinal” refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to adjacent carbon atoms.
  • the term "geminal” refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to the same carbon atom.
  • terminal refers to the location of a group within a substituent.
  • a group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure.
  • Carboxyalkyl i.e., R x O(O)C-alkyl is an example of a carboxy group used terminally.
  • a group is internal when the group is present in the middle of a substituent of the chemical structure.
  • Alkylcarboxy e.g., alkyl-C(O)O- or alkyl-OC(O)-
  • alkylcarboxyaryl e.g., alkyl-C(O)O-aryl- or alkyl-O(CO)-aryl-
  • an "aliphatic chain” refers to a branched or straight aliphatic group (e.g., alkyl groups, alkenyl groups, or alkynyl groups).
  • a straight aliphatic chain has the structure
  • a branched aliphatic chain is a straight aliphatic chain that is substituted with one or more aliphatic groups.
  • a branched aliphatic chain has the structure -[CQQIv- where each Q is independently a hydrogen or an aliphatic group; however, Q shall be an aliphatic group in at least one instance.
  • the term aliphatic chain includes alkyl chains, alkenyl chains, and alkynyl chains, where alkyl, alkenyl, and alkynyl are defined above.
  • Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxo, alkoxy, hydroxy, amino, nitro, aryl, cycloaliphatic, heterocycloaliphatic, heteroaryl, haloalkyl, and alkyl.
  • an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxo, alkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl.
  • the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxy, nitro, haloalkyl, and alkyl.
  • the two alkxoy groups can form a ring together with the atom(s) to which they are bound.
  • substituted refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent.
  • Specific substituents are described above in the definitions and below in the description of compounds and examples thereof.
  • an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position.
  • a ring substituent such as a heterocycloalkyl
  • substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
  • stable or chemically feasible refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein.
  • a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40 0 C or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
  • an "effective amount” is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight, and condition of the patient.
  • Body surface area may be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970).
  • patient refers to a mammal, including a human.
  • structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention.
  • structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
  • compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 13 C- or 14 C-enriched carbon are within the scope of this invention.
  • Such compounds are useful, for example, as analytical tools or probes in biological assays, or as therapeutic agents.
  • Compounds of the present invention are useful modulators of ABC transporters and are useful in the treatment of ABC transporter mediated diseases.
  • the present invention relates to compounds of formula I useful as modulators of ABC transporter activity:
  • Ri is -Z A R 4 , wherein each Z A is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z A are optionally and independently replaced by -CO-, -CS-, -C0NR A -, -C0NR A NR A -, -CO 2 -, -OCO-, - NR A C0 2 -,
  • Each R 4 Is independently R A , halo, -OH, -NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R A is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • R 2 is -Z B R 5 , wherein each Z B is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain wherein up to two carbon units of Z are optionally and independently replaced by -CO-, -CS-, -C0NR B -, -C0NR B NR B -, -CO 2 -, -OCO-, - NR B C0 2 -,
  • Each R 5 is independently R B , halo, -OH, -NH 2 , -NO 2 , -CN, - CF 3 , or -OCF 3 .
  • Each R is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • any two adjacent R 2 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle.
  • Ring A is an optionally substituted 3-7 membered monocyclic ring having 0-3 heteroatoms selected from N, O, and S.
  • Ring B is a group having formula Ia:
  • each R 3 and R' 3 is independently -Z 0 R 6 , where each Z c is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain wherein up to two carbon units of Z c are optionally and independently replaced by -CO-, -CS-, -CONR C -, -CONR C NR C -, -CO 2 -, -OCO-, - NR 0 CO 2 -, -O-,
  • Each R 6 is independently R c , halo, -OH, -NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • any two adjacent R 3 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle.
  • R' 3 and an adjacent R 3 group, together with the atoms to which they are attached form an optionally substituted heterocycle.
  • n is 1-3.
  • ring B when ring A is unsubstituted cyclopentyl, n is 1, R 2 is 4-chloro, and R] is hydrogen, then ring B is not 2-(tertbutyl)indol-5-yl, or (2,6- dichlorophenyl(carbonyl))-3-methyl-lH-indol-5-yl; and when ring A is unsubstituted cyclopentyl, n is 0, and R] is hydrogen, then ring B is not
  • Ri is -Z A R 4 , wherein each Z A is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain wherein up to two carbon units of Z A are optionally and independently replaced by -CO-, -CS-, -C0NR A -, -C0NR A NR A -, -CO 2 -, -OCO-, -
  • Each R 4 is independently R A , halo, -OH, -NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R A is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • R] is -Z A R t , wherein each Z A is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain and each R 4 is hydrogen.
  • R] is -Z A R t , wherein each Z A is a bond and each R 4 is hydrogen.
  • Each R 2 is independently -Z B Rs, wherein each Z B is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain wherein up to two carbon units of Z B are optionally and independently replaced by -CO-, -CS-, -C0NR B -, -C0NR B NR B -, -
  • Each R 5 is independently R B , halo, -OH, -
  • Each R B is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • any two adjacent R 2 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle.
  • R 2 is an optionally substituted aliphatic.
  • R 2 is an optionally substituted branched or straight Ci_ 6 aliphatic chain.
  • R 2 is an optionally substituted branched or straight Ci_ 6 alkyl chain, an optionally substituted branched or straight C 2 _ 6 alkenyl chain, or an optionally substituted branched or straight C 2 _ 6 alkynyl chain.
  • R 2 is a branched or straight Ci_ 6 aliphatic chain that is optionally substituted with 1-3 of halo, hydroxy, cyano, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof.
  • R 2 is a branched or straight Ci_ 6 alkyl that is optionally substituted with 1-3 of halo, hydroxy, cyano, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof.
  • R 2 is a methyl, ethyl, propyl, butyl, isopropyl, or tert-butyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, aryl, heteroaryl, cycloaliphatic, or heterocycloaliphatic.
  • R 2 is a methyl, ethyl, propyl, butyl, isopropyl, or tert-butyl, each of which is unsubstituted.
  • R 2 is an optionally substituted branched or straight Ci_ 5 alkoxy.
  • R 2 is a Ci_s alkoxy that is optionally substituted with 1-3 of hydroxy, aryl, heteroaryl, cycloaliphatic, heterocycloaliphatic, or combinations thereof.
  • R 2 is a methoxy, ethoxy, propoxy, butoxy, or pentoxy, each of which is optionally substituted with 1-3 of hydroxy, aryl, heteroaryl, cycloaliphatic, heterocycloaliphatic, or combinations thereof.
  • R 2 is hydroxy, halo, or cyano.
  • R 2 is -Z B Rs
  • Z B is independently a bond or an optionally substituted branched or straight C 1-4 aliphatic chain wherein up to two carbon units of Z B are optionally and independently replaced by -C(O)-, -O-, -S-, -S(O) 2 -, or -NH-
  • R 5 is R , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3
  • R B is hydrogen or aryl.
  • two adjacent R 2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle.
  • two adjacent R 2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle, either of which is fused to the phenyl of formula I, wherein the carbocycle or heterocycle has formula Ib:
  • Each of Z 1 , Z 2 , Z 3 , Z 4 , and Z 5 is independently a bond, -CRvRV-, -NR 7 -, or -O-; each R 7 is independently -Z 0 R 8 , wherein each Z D is independently an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -C0NR D -, -CO 2 -, -OCO-, -NR 0 CO 2 -, -O-, -NR 0 CONR 0 -, -OCONR 0 -, -NR 0 NR 0 -, -NR 0 CO-, -S-, -SO-, -SO 2 -, -NR°-, -SO 2 NR 0 -, -NR 0 SO 2 -, or -NR 0 SO 2 NR 0 -
  • Each R 8 is independently R°, halo, -OH, -NH 2 , -NO 2 , -CN, - CF 3 , or -OCF 3 .
  • Each R° is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • Each R' 7 is independently hydrogen, optionally substituted C 1-6 aliphatic, hydroxy, halo, cyano, nitro, or combinations thereof.
  • any two adjacent R 7 groups together with the atoms to which they are attached form an optionally substituted 3-7 membered carbocyclic ring, such as an optionally substituted cyclobutyl ring, or any two R 7 and R' 7 groups together with the atom or atoms to which they are attached form an optionally substituted 3-7 membered carbocyclic ring or a heterocarbocyclic ring.
  • two adjacent R 2 groups form an optionally substituted carbocycle.
  • two adjacent R 2 groups form an optionally substituted 5-7 membered carbocycle that is optionally substituted with 1-3 of halo, hydroxy, cyano, oxo, cyano, alkoxy, alkyl, or combinations thereof.
  • two adjacent R 2 groups form a 5-6 membered carbocycle that is optionally substituted with 1-3 of halo, hydroxy, cyano, oxo, cyano, alkoxy, alkyl, or combinations thereof.
  • two adjacent R 2 groups form an unsubstituted 5-7 membered carbocycle.
  • two adjacent R 2 groups form an optionally substituted heterocycle.
  • two adjacent R 2 groups form an optionally substituted 5-7 membered heterocycle having 1-3 heteroatoms independently selected from N, O, and S.
  • two adjacent R 2 groups form an optionally substituted 5-6 membered heterocycle having 1-2 oxygen atoms.
  • two adjacent R 2 groups form an unsubstituted 5-7 membered heterocycle having 1-2 oxygen atoms.
  • two adjacent R 2 groups form a heterocyclic ring selected from:
  • two adjacent R 2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle
  • a third R 2 group is attached to any chemically feasible position on the phenyl of formula I.
  • an optionally substituted carbocycle or an optionally substituted heterocycle, both of which is formed by two adjacent R 2 groups; a third R 2 group; and the phenyl of formula I form a group having formula Ic:
  • each R 2 group is independently selected from hydrogen, halo,
  • R 2 is at least one selected from hydrogen, halo, methoxy, phenylmethoxy, hydroxy, hydroxymethyl, trifluoromethoxy, and methyl.
  • two adjacent R 2 groups together with the atoms to which they are attached, form
  • Ring A is an optionally substituted 3-7 membered monocyclic ring having 0-3 heteroatoms selected from N, O, and S.
  • ring A is an optionally substituted 3-7 membered monocyclic cycloaliphatic.
  • ring A is a cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl, each of which is optionally substituted with 1-3 of halo, hydroxy, Ci_ 5 aliphatic, or combinations thereof.
  • ring A is an optionally substituted 3-7 membered monocyclic heterocycloaliphatic.
  • ring A is an optionally substituted 3-7 membered monocyclic heterocycloaliphatic having 1-2 heteroatoms independently selected from N, O, and S.
  • ring A is tetrahydrofuran-yl, tetrahydro-2H-pyran-yl, pyrrolidone-yl, or piperidine-yl, each of which is optionally substituted.
  • ring A is selected from
  • Each Rg is independently -Z E R 9 , wherein each Z E is independently a bond or an optionally substituted branched or straight C 1-5 aliphatic chain wherein up to two carbon units of Z E are optionally and independently replaced by -CO-, -CS-, -C0NR E -, -CO 2 -, -OCO-, -NR E C0 2 -, -O-, -NR E C0NR E -, -0C0NR E -, -NR E NR E -, -NR E C0-, -S-, -SO-, -SO 2 -, -NR E -, -SO 2 NR 1 S -NR E S0 2 -, or -NR E S0 2 NR E -, each R 9 is independently R E , -OH, -NH 2 , -NO 2 , - CN,
  • Each R E is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • q is 0-5.
  • ring A is one selected from
  • ring A is
  • Ring B is a group having formula Ia:
  • Each R 3 and R' 3 is independently -Z 0 R 6 , where each Z c is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z c are optionally and independently replaced by -CO-, -CS-, -CONR C -, - CONR C NR C -, -CO 2 -,
  • Each R 6 is independently R c , halo, -OH, - NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R c is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • any two adjacent R 3 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle, or R' 3 and an adjacent R 3 , i.e., attached to the 2 position of the indole of formula Ia, together with the atoms to which they are attached form an optionally substituted heterocycle.
  • ring B is
  • each R 2 o is -Z G R 2 i, where each Z° is independently a bond or an optionally substituted branched or straight Ci_s aliphatic chain wherein up to two carbon units of Z G are optionally and independently replaced by -CO-, -CS-, -C0NR G -, -CO2-, - OCO-,
  • Each R 21 is independently R°, halo, -OH, -NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R° is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • ring B is
  • R' 3 is hydrogen and R 3 is attached to the 2, 3, 4, 6, or 7 position of the indole of formula Ia.
  • R 3 is attached to the 2 or 3 position of the indole of formula Ia, and R 3 is independently an optionally substituted aliphatic.
  • R 3 is an optionally substituted acyl group.
  • R 3 is an optionally substituted (alkoxy)carbonyl.
  • R 3 is (methoxy)carbonyl, (ethoxy)carbonyl, (propoxy)carbonyl, or (butoxy)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof.
  • R 3 is an optionally substituted (aliphatic)carbonyl.
  • R 3 is an optionally substituted (alkyl)carbonyl that is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof .
  • R 3 is (methyl)carbonyl, (ethyl)carbonyl, (propyl)carbonyl, or
  • R 3 is an optionally substituted (cycloaliphatic)carbonyl or an optionally substituted (heterocycloaliphatic)carbonyl.
  • R 3 is an optionally substituted (C 3 _ 7 cycloaliphatic)carbonyl.
  • R 3 is a (cyclopropyl)carbonyl, (cyclobutyl)carbonyl, (cyclopentyl)carbonyl, (cyclohexyl)carbonyl, or (cycloheptyl)carbonyl, each of which is optionally substituted with aliphatic, halo, hydroxy, nitro, cyano, or combinations thereof.
  • R 3 is an optionally substituted (heterocycloaliphatic)carbonyl.
  • R 3 is an optionally substituted (heterocycloaliphatic)carbonyl having 1-3 heteroatoms independently selected from N, O, and S.
  • R 3 is an optionally substituted (heterocycloaliphatic)carbonyl having 1-3 heteroatoms independently selected from N and O.
  • R 3 is an optionally substituted 4-7 membered monocyclic (heterocycloaliphatic)carbonyl having 1- 3 heteroatoms independently selected from N and O.
  • R 3 is (piperidine-1- yl,)carbonyl, (pyrrolidine- l-yl)carbonyl, or (morpholine-4-yl)carbonyl, (piperazine-1- yl)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, nitro, or aliphatic.
  • R 3 is optionally substituted (aliphatic)amido such as (aliphatic(amino(carbonyl)) that is attached to the 2 or 3 position on the indole ring of formula Ia.
  • R 3 is an optionally substituted (alkyl(amino))carbonyl that is attached to the 2 or 3 position on the indole ring of formula Ia.
  • R 3 is an optionally substituted straight or branched (aliphatic(amino))carbonyl that is attached to the 2 or 3 position on the indole ring of formula Ia.
  • R 3 is (N,N- dimethyl(amino))carbonyl, (methyl(amino))carbonyl, (ethyl(amino))carbonyl, (propyl(amino))carbonyl, (prop-2-yl(amino))carbonyl, (dimethyl(but-2-yl(amino)))carbonyl, (tertbutyl(amino))carbonyl, (butyl(amino))carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof.
  • R 3 is an optionally substituted (alkoxy)carbonyl.
  • R 3 is (methoxy)carbonyl, (ethoxy)carbonyl, (propoxy)carbonyl, or (butoxy)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof.
  • R 3 is an optionally substituted straight or branched Ci_ 6 aliphatic.
  • R 3 is an optionally substituted straight or branched Ci_ 6 alkyl.
  • R 3 is independently an optionally substituted methyl, ethyl, propyl, butyl, isopropyl, or tertbutyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, nitro, or combination thereof.
  • R 3 is an optionally substituted C 3 - 6 cycloaliphatic. Exemplary embodiments include cyclopropyl, 1-methyl- cycloprop-1-yl, etc.
  • p is 2 and the two R 3 substituents are attached to the indole of formula Ia at the 2,4- or 2,6- or 2,7- positions.
  • Exemplary embodiments include 6- F, 3-(optionally substituted C]_ 6 aliphatic or C 3 _ 6 cycloaliphatic); 7-F-2-(-(optionally substituted Ci_ 6 aliphatic or C 3 _ 6 cycloaliphatic)), 4F-2-(optionally substituted Ci_ 6 aliphatic or C 3 - 6 cycloaliphatic); 7-CN-2-(optionally substituted C 1-6 aliphatic or C 3 - 6 cycloaliphatic); 7- Me-2-(optionally substituted C]_ 6 aliphatic or C 3 _ 6 cycloaliphatic) and 7-OMe-2-(optionally substituted C 1-6 aliphatic or C3-6 cycloaliphatic).
  • R 3 is hydrogen. [00152] In several embodiments, R 3 is one selected from:
  • R' 3 is independently -Z 0 R 6 , where each Z c is independently a bond or an optionally substituted branched or straight Ci_ 6 aliphatic chain wherein up to two carbon units of Z c are optionally and independently replaced by -CO-, - CS-, -C0NR c -,
  • Each R 6 is independently R c , halo, -OH, -NH 2 , -NO 2 , -CN, or -OCF 3 .
  • Each R c is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, or an optionally substituted heteroaryl.
  • each R c is hydrogen, Ci_ 6 aliphatic, or C 3 - O cycloaliphatic, wherein either of the aliphatic or cycloaliphatic is optionally substituted with up to 4 -OH substituents.
  • R c is hydrogen, or Ci_ 6 alkyl optionally substituted with up to 4 -OH substituents.
  • R' 3 is is independently -Z 0 R 6 , where each Z c is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z c are optionally and independently replaced by -C(O)-, -C(O)NR C -, -C(O)O-, -NR c C(0)0-, -O-, -NR 0 S(O) 2 -, or -NR C -.
  • Each R 6 is independently
  • Each R c is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, or an optionally substituted heteroaryl.
  • each R c is hydrogen, Ci_ 6 aliphatic, or C 3 _ 6 cycloaliphatic, wherein either of the aliphatic or cycloaliphatic is optionally substituted with up to 4 -OH substituents.
  • R c is hydrogen, or C 1-6 alkyl optionally substituted with up to 4 -OH substituents.
  • R' 3 is hydrogen or
  • R 3 is H or a C 1-2 aliphatic that is optionally substituted with 1-3 of halo, -
  • R 32 is -L-R 33 , wherein L is a bond, -CH 2 -, -CH 2 O-, -
  • R 33 is hydrogen, or Ci -2 aliphatic, cycloaliphatic, heterocycloaliphatic, or heteroaryl, each of which is optionally subsitututed with 1 of -OH,
  • R 3 is hydrogen and R 32 is Ci_ 2 aliphatic optionally substituted with -OH, -NH 2 , or -CN.
  • R' 3 is independently selected from one of the following: -H, -CH 3 , -CH 2 CH 3 , -C(O)CH 3 , -CH 2 CH 2 OH, -C(O)OCH 3 ,
  • ring B is one selected from:
  • n 1-3.
  • n is 1. In other embodiments, n is 2. In still other embodiments, n is 3.
  • the present invention relates to compounds of formula II useful as modulators of ABC transporter activity:
  • R is H, OH, OCH 3 or two R taken together form -OCH 2 O- or -OCF 2 O-;
  • Ri is H or alkyl;
  • R 2 is H or F;
  • R 3 is H or CN;
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N(CH3)3, or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • the present invention provides compounds of formula II, wherein the compounds set forth below are excluded:
  • two R taken together form -OCF 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCF 2 O-, R] is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 CH 2 N + (CH 3 ) 3 .
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 and R 5 taken together form a five membered ring.
  • two R taken together form -OCH 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • R is OH
  • Ri is H
  • R 2 is H
  • R 3 is H
  • R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH.
  • At least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is H. In another embodiment, at least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • the compound is represented by formula Ha:
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH3)3, or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH, - CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH.
  • R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH; and R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • Exemplary compounds of the present invention include, but are not limited to, those illustrated in Table 1 below.
  • Table 1 Exemplary compounds of the present invention.
  • the present invention relates to a pharmaceutical composition
  • a pharmaceutical composition comprising (i) a compound of the present invention; and (ii) a pharmaceutically acceptable carrier.
  • the composition further comprises an additional agent selected from a mucolytic agent, bronchodialator, an anti-biotic, an anti-infective agent, an anti-inflammatory agent, CFTR corrector, or a nutritional agent.
  • the composition further comprises an additional agent selected from compounds disclosed in U.S. Patent Application Serial No. 11/165,818, published as U.S. Published Patent Application No. 2006/0074075, filed June 24, 2005, and hereby incorporated by reference in its entirety.
  • the composition further comprises N-(5-hydroxy-2,4- ditert-butyl-phenyl)-4-oxo-lH-quinoline-3-carboxamide.
  • These compositions are useful for treating the diseases described below including cystic fibrosis. These compositions are also useful in the kits described below.
  • the present invention relates to a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formula II: II wherein independently for each occurrence:
  • R is H, OH, OCH 3 or two R taken together form -CH 2 CH 2 CH 2 -, -OCH 2 O- or - OCF 2 O-;
  • Ri is H or alkyl
  • R 2 is H or F
  • R 3 is H or CN
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • the ABC transporter is CFTR.
  • two R taken together form -OCF 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 CH 2 N + (CH 3 ) 3 .
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 and R 5 taken together form a five membered ring.
  • two R taken together form -OCH 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • R is OH, Ri is H, R 2 is H, R 3 is H, and R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH.
  • at least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is H.
  • at least one R is OCH 3 , at least two R] are methyl, R 2 is H, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -CH 2 CH 2 CH 2 -
  • Ri is H
  • R 2 is H
  • R 3 is H
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • the compound is represented by formula Ha:
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH, - CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH.
  • R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH; and R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • the compound is selected from Table 1.
  • the present invention relates to a method of treating a condition, disease, or disorder in a patient implicated by ABC transporter activity, comprising the step of administering to said patient a compound having formula II:
  • R is H, OH, OCH 3 or two R taken together form -CH 2 CH 2 CH 2 -, -OCH 2 O- or - OCF 2 O-;
  • Ri is H or alkyl
  • R 2 is H or F
  • R 3 is H or CN
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • two R taken together form -OCF 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 CH 2 N + (CH 3 ) 3 .
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 and R 5 taken together form a five membered ring.
  • two R taken together form -OCH 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • R is OH
  • Ri is H
  • R 2 is H
  • R 3 is H
  • R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH.
  • At least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is H. In another embodiment, at least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -CH 2 CH 2 CH 2 -
  • Ri is H
  • R 2 is H
  • R 3 is H
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • the compound is represented by formula Ha:
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH3)3, or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH, - CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH.
  • R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH; and R 5 is OH, - CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • the compound is selected from Table 1.
  • said condition, disease, or disorder is selected from cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation- fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, diabetes mellitus, laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, hereditary emphysema, congenital hyperthyroidism, osteogenesis imperfecta,
  • R is H, OH, OCH 3 or two R taken together form -CH 2 CH 2 CH 2 -, -OCH 2 O- or - OCF 2 O-;
  • Ri is H or alkyl
  • R 2 is H or F
  • R 3 is H or CN
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring; and (ii) instructions for: a) contacting the composition with the biological sample; and b) measuring activity of said ABC transporter or a fragment thereof.
  • the kit further comprises instructions for a) contacting an additional composition with the biological sample; b) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of said first composition.
  • the kit is used to measure the density of CFTR.
  • two R taken together form -OCF 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is H.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F,
  • R 3 is H, and R 4 is -CH 2 CH 2 N + (CH 3 ) 3 .
  • two R taken together form - OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form -OCF 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 and R 5 taken together form a five membered ring.
  • two R taken together form -OCH 2 O-, Ri is H, and R 2 is F.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, and R 3 is H.
  • two R taken together form -OCH 2 O-, Ri is H, R 2 is F, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • R is OH, Ri is H, R 2 is H, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • At least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is H.
  • at least one R is OCH 3 , at least two Ri are methyl, R 2 is H, R 3 is H, and R 4 is - CH 2 OCH 2 CH(OH)CH 2 OH.
  • two R taken together form - CH 2 CH 2 CH 2 -, Ri is H, R 2 is H, R 3 is H, and R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH.
  • the compound is represented by formula Ha:
  • R 4 is H, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH;
  • R 5 is H, OH, -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 OH, or R 4 and R 5 taken together form a five membered ring.
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or -CH 2 CH 2 OH.
  • R 5 is OH, -CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • R 4 is -CH 2 OCH 2 CH(OH)CH 2 OH, -CH 2 CH 2 N + (CH 3 ) 3 , or - CH 2 CH 2 OH; and R 5 is OH, -CH 2 OCH 2 CH(OH)CH 2 OH, or -CH 2 OH.
  • the compound is selected from Table 1. [00166] III. SUBGENERIC COMPOUNDS OF THE PRESENT INVENTION
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula Id:
  • R 1 , R 2 , and ring A are defined above in formula I, and ring B, R 3 and p are defined in formula Ia. Furthermore, when ring A is unsubstituted cyclopentyl, n is 1, R 2 is 4-chloro, and Ri is hydrogen, then ring B is not 2-(tertbutyl)indol-5-yl, or (2,6- dichlorophenyl(carbonyl))-3-methyl-lH-indol-5-yl; and when ring A is unsubstituted cyclopentyl, n is 0, and Ri is hydrogen, then ring B is not
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula Id:
  • R 1 , R 2 , and ring A are defined above in formula I, and ring B, R 3 and p are defined in formula Ia.
  • each R 3 is independently -Z G Ri 2 , where each Z° is independently a bond or an unsubstituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z° are optionally and independently replaced by -CS-, - C0NR G NR G -, -CO 2 -, -OCO-, -NR 0 CO 2 -, -O-, -NR 0 CONR 0 -, -OCONR 0 -, -NR 0 NR 0 -, -S-, - SO-, -SO 2 -, -NR 0 -,
  • each R 12 is independently R°, halo, -OH, -NH 2 , - NO 2 , -CN, or -OCF 3 , and each R° is independently hydrogen, an unsubstituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an unsubstituted aryl, or an optionally substituted heteroaryl; or any two adjacent R 3 groups together with the atoms to which they are attached form an optionally substituted heterocycle.
  • R 1 , R 2 , and ring A are defined above in formula I; R 3 , R' 3 , and p are defined above in formula Ia; and Z 1 , Z 2 , Z 3 , Z 4 , and Z 5 are defined above in formula Ib.
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula Ha:
  • R 1 , R 2 , and ring A are defined above in formula I; R 3 , R' 3 , and p are defined above in formula Ia; and Z 1 , Z 2 , Z 3 , Z 4 , and Z 5 are defined above in formula Ib.
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula lib:
  • R 1 , R 2 , and ring A are defined above in formula I; R 3 , R' 3 , and p are defined above in formula Ia; and Z 1 , Z 2 , Z 3 , Z 4 , and Z 5 are defined above in formula Ib.
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula Hc:
  • R 1 , R 2 and n are defined above in formula I; and R 3 , R' 3 , and p are defined in formula Ia.
  • Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity.
  • the compound has formula Hd:
  • R' 3 is independently selected from one of the following: -H, -CH 3 , -CH 2 CH 3 , -C(O)CH 3 , -CH 2 CH 2 OH, -C(O)OCH 3 , ⁇ °- NHOOOH, ⁇ COsH HM. C M.
  • each R 3 is independently selected from -H, -CH 3 , -CH 2 OH, -CH 2 CH 3 , -CH 2 CH 2 OH, -CH 2 CH 2 CH 3 , -NH 2 , halo, - OCH 3 , -CN, -CF 3 , -C(O)OCH 2 CH 3 , -S(O) 2 CH 3 , -CH 2 NH 2 , -C(O)NH 2 ,
  • the compounds of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) may be readily synthesized from commercially available or known starting materials by known methods. Exemplary synthetic routes to produce compounds of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) are provided below in Schemes 1-22 below.
  • the acid Ia may be converted to the corresponding acid chloride Ib using thionyl chloride in the presence of a catalystic amount of dimethylformamide. Reaction of the acid chloride with the amine provides compounds of the invention I. Alternatively, the acid Ia may be directly coupled to the amine using known coupling reagents such as, for example, HATU in the presence of triethylamine.
  • the nitrile 2a reacts with a suitable bromochloroalkane in the presence of sodium hydroxide and a phase tranfer catalyst such as butyltriethylammonium chloride to provide the intermediate 2b. Hydrolysis of the nitrile of 2b provides the acid Ia. In some instances, isolation of the intermediate 2b is unnecessary.
  • phenylacetonitriles 2a are commercially available or may be prepared as illustrated in Scheme 3.
  • reaction of an aryl bromide 3a with carbon monoxide in the presence of methanol and tetrakis(triphenylphosphine)palladium (0) provides the ester 3b.
  • Reduction of 3b with lithium aluminum hydride provides the alcohol 3c which is converted to the halide 3d with thionyl chloride.
  • Reaction of 3d with sodium cyanide provides the nitrile 2a.
  • a nitroaniline 6a is converted to the hydrazine 6b using nitrous acid in the presence of HCl and stannous chloride.
  • Reaction of 6b with an aldehyde or ketone CH 3 C(O)R 3 provides the hydrazone 6c which on treatment with phophoric acid in toluene leads to a mixture of nitro indoles 6d and 6e.
  • Catalytic hydrogenation in the presence of palladium on carbon provides a mixture of the amino indoles 6f and 6g which may be separated using know methods such as, for example, chromatography.
  • R 4 -LG base likeCs 2 CC> 3 ;
  • R 4 is alkyl and LG is tosylate;
  • the radical R employed therein is a substituent, e.g., RW as defined hereinabove.
  • RW substituents
  • One of skill in the art will readily appreciate that synthetic routes suitable for various substituents of the present invention are such that the reaction conditions and steps employed do not modify the intended substituents.
  • compositions comprising any of the compounds as described herein, and optionally comprise a pharmaceutically acceptable carrier, adjuvant or vehicle.
  • these compositions optionally further comprise one or more additional therapeutic agents.
  • a pharmaceutically acceptable derivative or a prodrug includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.
  • the term "pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
  • a “pharmaceutically acceptable salt” means any non-toxic salt or salt of an ester of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
  • compositions of this invention include those derived from suitable inorganic and organic acids and bases.
  • Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid
  • organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2- naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate
  • Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N + (Ci_ 4 alkyl) 4 salts.
  • This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersible products may be obtained by such quaternization.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.
  • the pharmaceutically acceptable compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, adjuvant, or vehicle, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • a pharmaceutically acceptable carrier, adjuvant, or vehicle which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980) discloses various carriers used in formulating pharmaceutically acceptable compositions
  • any conventional carrier medium is incompatible with the compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutically acceptable composition, its use is contemplated to be within the scope of this invention.
  • materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylene-polyoxypropylene- block polymers, wool fat, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc
  • the present invention provides a method of treating a condition, disease, or disorder implicated by ABC transporter activity.
  • the present invention provides a method of treating a condition, disease, or disorder implicated by a deficiency of ABC transporter activity, the method comprising administering a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) to a subject, preferably a mammal, in need thereof.
  • the present invention provides a method of treating Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1 , Hereditary emphysema, Congenital hyperthyroidis
  • the present invention provides a method of treating cystic fibrosis comprising the step of administering to said mammal a composition comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd), or a preferred embodiment thereof as set forth above.
  • an "effective amount" of the compound or pharmaceutically acceptable composition is that amount effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler- Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema
  • the compounds and compositions, according to the method of the present invention may be administered using any amount and any route of administration effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay- Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis
  • CDG type 1 Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive
  • the exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like.
  • the compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage.
  • dosage unit form refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
  • the specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts.
  • patient means an animal, preferably a mammal, and most preferably a human.
  • compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated.
  • the compounds of the invention may be administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
  • Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • the oral compositions can also include
  • Injectable preparations for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil can be employed including synthetic mono- or diglycerides.
  • fatty acids such as oleic acid are used in the preparation of injectables.
  • the injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • a compound of the present invention In order to prolong the effect of a compound of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide.
  • the rate of compound release can be controlled.
  • biodegradable polymers include poly(orthoesters) and poly(anhydrides).
  • Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.
  • compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl
  • Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
  • the active compounds can also be in microencapsulated form with one or more excipients as noted above.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art.
  • the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch.
  • Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose.
  • the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
  • buffering agents include polymeric substances and waxes.
  • Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
  • the active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required.
  • Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention.
  • the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body.
  • Such dosage forms are prepared by dissolving or dispensing the compound in the proper medium.
  • Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
  • the compounds of the invention are useful as modulators of ABC transporters.
  • the compounds and compositions are particularly useful for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of ABC transporters is implicated in the disease, condition, or disorder.
  • hyperactivity or inactivity of an ABC transporter is implicated in a particular disease, condition, or disorder
  • the disease, condition, or disorder may also be referred to as a "ABC transporter-mediated disease, condition or disorder”.
  • the present invention provides a method for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of an ABC transporter is implicated in the disease state.
  • the compounds and pharmaceutically acceptable compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutically acceptable compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures.
  • the particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved.
  • the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another agent used to treat the same disorder), or they may achieve different effects (e.g., control of any adverse effects).
  • additional therapeutic agents that are normally administered to treat or prevent a particular disease, or condition are known as "appropriate for the disease, or condition, being treated".
  • the amount of additional therapeutic agent present in the compositions of this invention will be no more than the amount that would normally be administered in a composition comprising that therapeutic agent as the only active agent.
  • the amount of additional therapeutic agent in the presently disclosed compositions will range from about 50% to 100% of the amount normally present in a composition comprising that agent as the only therapeutically active agent.
  • the present invention in another aspect, includes a composition for coating an implantable device comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device.
  • the present invention includes an implantable device coated with a composition comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device.
  • Suitable coatings and the general preparation of coated implantable devices are described in US Patents 6,099,562; 5,886,026; and 5,304,121.
  • the coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polymethyldisiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof.
  • the coatings may optionally be further covered by a suitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition.
  • Another aspect of the invention relates to modulating ABC transporter activity in a biological sample or a patient (e.g., in vitro or in vivo), which method comprises administering to the patient, or contacting said biological sample with a compound of formula I or a composition comprising said compound.
  • biological sample includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
  • Modulation of ABC transporter activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, the study of ABC transporters in biological and pathological phenomena; and the comparative evaluation of new modulators of ABC transporters.
  • a method of modulating activity of an anion channel in vitro or in vivo comprising the step of contacting said channel with a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd).
  • the anion channel is a chloride channel or a bicarbonate channel. In other preferred embodiments, the anion channel is a chloride channel.
  • the present invention provides a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd).
  • a compound of formulae I, Ic, Id, II, Ha, lib, Hc, and Hd.
  • functional ABC transporter as used herein means an ABC transporter that is capable of transport activity.
  • said functional ABC transporter is CFTR.
  • the activity of the ABC transporter is measured by measuring the transmembrane voltage potential.
  • Means for measuring the voltage potential across a membrane in the biological sample may employ any of the known methods in the art, such as optical membrane potential assay or other electrophysiological methods.
  • the optical membrane potential assay utilizes voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells” Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer” Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VIPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets” Drug Discov Today 4(9): 431-439).
  • VIP Voltage/Ion Probe Reader
  • the present invention provides a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof.
  • a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof.
  • the kit further comprises instructions for a.) contacting an additional composition with the biological sample; b.) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c.) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of a composition of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd).
  • the kit is used to measure the density of CFTR.
  • the basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate which began to form at pH 4 was filtered and washed with 1 M hydrochloric acid two times.
  • the solid material was dissolved in dichloromethane and extracted two times with 1 M hydrochloric acid and one time with a saturated aqueous solution of sodium chloride.
  • the organic solution was dried over sodium sulfate and evaporated to dryness to give the cycloalkylcarboxylic acid. Yields and purities were typically greater than 90%.
  • the dark brown reaction mixture was diluted with water (400 mL) and extracted once with an equal volume of ethyl acetate and once with an equal volume of dichloromethane.
  • the basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate filtered and washed with 1 M hydrochloric acid.
  • the solid material was dissolved in dichloromethane (400 mL) and extracted twice with equal volumes of 1 M hydrochloric acid and once with a saturated aqueous solution of sodium chloride.
  • the organic solution was dried over sodium sulfate and evaporated to dryness to give a white to slightly off-white solid (5.23 g, 80%) ESI-MS tn/z calc.
  • Example 2 l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid
  • Example 5 l-(2-Oxo-2,3-dihydrobenzo[d]oxazol-5-yl)cyclopropane- carboxylic acid.
  • a flask was charged with water (10 mL), followed by a rapid addition of NaOH (10 g, 0.25 mol) in three portions over a 5 min period. The mixture was allowed to cool to room temperature. Subsequently, the flask was charged with toluene (6 mL), tetrabutyl- ammonium bromide (50 mg, 0.12 mmol), (6-fluoro-benzo[l,3]dioxol-5-yl)-acetonitrile (600 mg, 3.4 mmol) and l-bromo-2-chloroethane (1.7 g, 12 mmol). The mixture stirred vigorously at 50 0 C overnight.
  • Example 8 l-(2,3-Dihydrobenzofuran-6-yl)cyclopropanecarboxylic acid
  • Example 9 l-(3,3-Dimethyl-2,3-dihydrobenzofuran-5- yl)cyclopropanecarboxylic acid.
  • Example 10 2-(7-Methoxybenzo[d][l,3]dioxol-5-yl)acetonitrile.
  • Example 11 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitrile.
  • Example 12 2-(3-(Benzyloxy)-4-chlorophenyl)acetonitrile.
  • BBr 3 (17 g, 66 mmol) was slowly added to a solution of 2-(4-chloro-3- methoxyphenyl)acetonitrile (12 g, 66 mmol) in dichloromethane (120 mL) at -78 0 C under N 2 .
  • the reaction temperature was slowly increased to room temperature.
  • the reaction mixture was stirred overnight and then poured into ice and water.
  • the organic layer was separated, and the aqueous layer was extracted with dichloromethane (40 mL x 3).
  • Example 13 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitrile.
  • Example 14 2-(3-Chloro-4-methoxyphenyl)acetonitrile.
  • Example 15 2-(3-Fluoro-4-methoxyphenyl)acetonitrile.
  • Example 16 2-(4-Chloro-3-methoxyphenyl)acetonitrile.
  • Example 17 l-(3-(Hydroxymethyl)-4- methoxyphenyl)cyclopropanecarboxylic acid.
  • Example 18 2-(7-Chlorobenzo[d][l,3]dioxol-5-yl)acetonitrile. [00393] 3-Chloro-4,5-dihydroxybenzaldehyde
  • Example 19 l-(Benzo[d]oxazol-5-yl)cyclopropanecarboxylic acid. trimethyl orthoformate AICU
  • Example 21 l-(lH-Indol-5-yl)cyclopropanecarboxylic acid
  • Example 22 l-(4-Oxochroman-6-yl)cyclopropanecarboxylic acid
  • Example 23 l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid
  • Example 24 l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid
  • Example 25 l-(3-Methylbenzo[d]isoxazol-5-yl)cyclopropanecarboxylic acid
  • Example 26 l-CSpirotbenzotdHl ⁇ dioxole ⁇ r-cyclobutaneJ-S- yl)cyclopropane carboxylic acid
  • Example 30 2-fert-Butyl-6-fluoro-lH-indol-5-amine and 6-tert-bntoxy-2-tert- butyl- lH-indol-5-amine

Abstract

Compounds of the present invention and pharmaceutically acceptable compositions thereof, are useful as modulators of ATP-Binding Cassette ("ABC") transporters or fragments thereof, including Cystic Fibrosis Transmembrane Conductance Regulator ("CFTR"). The present invention also relates to methods of treating ABC transporter mediated diseases using compounds of the present invention.

Description

MODULATORS OF ATP-BINDING CASSETTE TRANSPORTERS
CROSS REFERNCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional Application Serial No. 61/112,152, which was filed November 6, 2008. The entire contents of U.S. Provisional Application Serial No. 61/112,152 is incorporated herein by reference.
TECHNICAL FIELD OF THE INVENTION
[0002] The present invention relates to modulators of ATP-Binding Cassette ("ABC") transporters or fragments thereof, including Cystic Fibrosis Transmembrane Conductance Regulator ("CFTR"), compositions thereof and methods therewith. The present invention also relates to methods of treating ABC transporter mediated diseases using such modulators.
BACKGROUND OF THE INVENTION
[0003] ABC transporters are a family of membrane transporter proteins that regulate the transport of a wide variety of pharmacological agents, potentially toxic drugs, and xenobiotics, as well as anions. ABC transporters are homologous membrane proteins that bind and use cellular adenosine triphosphate (ATP) for their specific activities. Some of these transporters were discovered as multidrug resistance proteins (like the MDRl-P glycoprotein, or the multidrug resistance protein, MRPl), defending malignant cancer cells against chemotherapeutic agents. To date, 48 ABC Transporters have been identified and grouped into 7 families based on their sequence identity and function.
[0004] ABC transporters regulate a variety of important physiological roles within the body and provide defense against harmful environmental compounds. Because of this, they represent important potential drug targets for the treatment of diseases associated with defects in the transporter, prevention of drug transport out of the target cell, and intervention in other diseases in which modulation of ABC transporter activity may be beneficial.
[0005] One member of the ABC transporter family commonly associated with disease is the cAMP/ATP-mediated anion channel, CFTR. CFTR is expressed in a variety of cells types, including absorptive and secretory epithelia cells, where it regulates anion flux across the membrane, as well as the activity of other ion channels and proteins. In epithelia cells, normal functioning of CFTR is critical for the maintenance of electrolyte transport throughout the body, including respiratory and digestive tissue. CFTR is composed of approximately 1480 amino acids that encode a protein made up of a tandem repeat of transmembrane domains, each containing six transmembrane helices and a nucleotide binding domain. The two transmembrane domains are linked by a large, polar, regulatory (R)-domain with multiple phosphorylation sites that regulate channel activity and cellular trafficking.
[0006] The gene encoding CFTR has been identified and sequenced (See Gregory, R. J. et al. (1990) Nature 347:382-386; Rich, D. P. et al. (1990) Nature 347:358-362), (Riordan, J. R. et al. (1989) Science 245:1066-1073). A defect in this gene causes mutations in CFTR resulting in Cystic Fibrosis ("CF"), the most common fatal genetic disease in humans. Cystic Fibrosis affects approximately one in every 2,500 infants in the United States. Within the general United States population, up to 10 million people carry a single copy of the defective gene without apparent ill effects. In contrast, individuals with two copies of the CF associated gene suffer from the debilitating and fatal effects of CF, including chronic lung disease.
[0007] In patients with cystic fibrosis, mutations in CFTR endogenously expressed in respiratory epithelia leads to reduced apical anion secretion causing an imbalance in ion and fluid transport. The resulting decrease in anion transport contributes to enhanced mucus accumulation in the lung and the accompanying microbial infections that ultimately cause death in CF patients. In addition to respiratory disease, CF patients typically suffer from gastrointestinal problems and pancreatic insufficiency that, if left untreated, results in death. In addition, the majority of males with cystic fibrosis are infertile and fertility is decreased among females with cystic fibrosis. In contrast to the severe effects of two copies of the CF associated gene, individuals with a single copy of the CF associated gene exhibit increased resistance to cholera and to dehydration resulting from diarrhea - perhaps explaining the relatively high frequency of the CF gene within the population.
[0008] Sequence analysis of the CFTR gene of CF chromosomes has revealed a variety of disease causing mutations (Cutting, G. R. et al. (1990) Nature 346:366-369; Dean, M. et al. (1990) Cell 61:863:870; and Kerem, B-S. et al. (1989) Science 245:1073-1080; Kerem, B-S et al. (1990) Proc. Natl. Acad. Sci. USA 87:8447-8451). To date, > 1000 disease causing mutations in the CF gene have been identified (http://www.genet.sickkids.on.ca/cftr/). The most prevalent mutation is a deletion of phenylalanine at position 508 of the CFTR amino acid sequence, and is commonly referred to as ΔF508-CFTR. This mutation occurs in approximately 70% of the cases of cystic fibrosis and is associated with a severe disease.
[0009] The deletion of residue 508 in ΔF508-CFTR prevents the nascent protein from folding correctly. This results in the inability of the mutant protein to exit the ER, and traffic to the plasma membrane. As a result, the number of channels present in the membrane is far less than observed in cells expressing wild-type CFTR. In addition to impaired trafficking, the mutation results in defective channel gating. Together, the reduced number of channels in the membrane and the defective gating lead to reduced anion transport across epithelia leading to defective ion and fluid transport. (Quinton, P. M. (1990), FASEB J. 4: 2709- 2727). Studies have shown, however, that the reduced numbers of ΔF508-CFTR in the membrane are functional, albeit less than wild-type CFTR. (Dalemans et al. (1991), Nature Lond. 354: 526-528; Denning et al., supra; Pasyk and Foskett (1995), J. Cell. Biochem. 270: 12347-50). In addition to ΔF508-CFTR, other disease causing mutations in CFTR that result in defective trafficking, synthesis, and/or channel gating could be up- or down-regulated to alter anion secretion and modify disease progression and/or severity.
[0010] Although CFTR transports a variety of molecules in addition to anions, it is clear that this role (the transport of anions) represents one element in an important mechanism of transporting ions and water across the epithelium. The other elements include the epithelial Na+ channel, ENaC, Na+/2C17K+ co-transporter, Na+-K+-ATPaSe pump and the basolateral membrane K+ channels, that are responsible for the uptake of chloride into the cell.
[0011] These elements work together to achieve directional transport across the epithelium via their selective expression and localization within the cell. Chloride absorption takes place by the coordinated activity of ENaC and CFTR present on the apical membrane and the Na+- K+- ATPase pump and Cl- channels expressed on the basolateral surface of the cell. Secondary active transport of chloride from the luminal side leads to the accumulation of intracellular chloride, which can then passively leave the cell via Cl" channels, resulting in a vectorial transport. Arrangement of Na+/2Q7K+ co-transporter, Na+-K+- ATPase pump and the basolateral membrane K+ channels on the basolateral surface and CFTR on the luminal side coordinate the secretion of chloride via CFTR on the luminal side. Because water is probably never actively transported itself, its flow across epithelia depends on tiny transepithelial osmotic gradients generated by the bulk flow of sodium and chloride.
[0012] In addition to Cystic Fibrosis, modulation of CFTR activity may be beneficial for other diseases not directly caused by mutations in CFTR, such as secretory diseases and other protein folding diseases mediated by CFTR. These include, but are not limited to, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
[0013] COPD is characterized by airflow limitation that is progressive and not fully reversible. The airflow limitation is due to mucus hypersecretion, emphysema, and bronchiolitis. Activators of mutant or wild-type CFTR offer a potential treatment of mucus hypersecretion and impaired mucociliary clearance that is common in COPD. Specifically, increasing anion secretion across CFTR may facilitate fluid transport into the airway surface liquid to hydrate the mucus and optimized periciliary fluid viscosity. This would lead to enhanced mucociliary clearance and a reduction in the symptoms associated with COPD. Dry eye disease is characterized by a decrease in tear aqueous production and abnormal tear film lipid, protein and mucin profiles. There are many causes of dry eye, some of which include age, Lasik eye surgery, arthritis, medications, chemical/thermal burns, allergies, and diseases, such as Cystic Fibrosis and Sjόgrens's syndrome. Increasing anion secretion via CFTR would enhance fluid transport from the corneal endothelial cells and secretory glands surrounding the eye to increase corneal hydration. This would help to alleviate the symptoms associated with dry eye disease. Sjόgrens's syndrome is an autoimmune disease in which the immune system attacks moisture-producing glands throughout the body, including the eye, mouth, skin, respiratory tissue, liver, vagina, and gut. Symptoms, include, dry eye, mouth, and vagina, as well as lung disease. The disease is also associated with rheumatoid arthritis, systemic lupus, systemic sclerosis, and polymypositis/dermatomyositis. Defective protein trafficking is believed to cause the disease, for which treatment options are limited. Modulators of CFTR activity may hydrate the various organs afflicted by the disease and help to elevate the associated symptoms.
[0014] As discussed above, it is believed that the deletion of residue 508 in ΔF508-CFTR prevents the nascent protein from folding correctly, resulting in the inability of this mutant protein to exit the ER, and traffic to the plasma membrane. As a result, insufficient amounts of the mature protein are present at the plasma membrane and chloride transport within epithelial tissues is significantly reduced. In fact, this cellular phenomenon of defective ER processing of ABC transporters by the ER machinery has been shown to be the underlying basis not only for CF disease, but for a wide range of other isolated and inherited diseases. The two ways that the ER machinery can malfunction is either by loss of coupling to ER export of the proteins leading to degradation, or by the ER accumulation of these defective/misfolded proteins [Aridor M, et al., Nature Med., 5(7), pp 745- 751 (1999); Shastry, B. S., et al., Neurochem. International, 43, pp 1-7 (2003); Rutishauser, J., et al., Swiss Med WkIy, 132, pp 211-222 (2002); Morello, JP et al., TIPS, 21, pp. 466- 469 (2000); Brass P., et al., Human Mut., 14, pp. 186-198 (1999)]. The diseases associated with the first class of ER malfunction are Cystic fibrosis (due to misfolded ΔF508-CFTR as discussed above), Hereditary emphysema (due to al -antitrypsin; non Piz variants), Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses (due to Lysosomal processing enzymes), Sandhof/Tay-Sachs (due to β-Hexosaminidase), Crigler- Najjar type II (due to UDP-glucuronyl-sialyc-transferase), Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus (due to Insulin receptor), Laron dwarfism (due to Growth hormone receptor), Myleoperoxidase deficiency, Primary hypoparathyroidism (due to Preproparathyroid hormone), Melanoma (due to Tyrosinase). The diseases associated with the latter class of ER malfunction are Glycanosis CDG type 1, Hereditary emphysema (due to αl- Antitrypsin (PiZ variant), Congenital hyperthyroidism, Osteogenesis imperfecta (due to Type I, II, IV procollagen), Hereditary hypofibrinogenemia (due to Fibrinogen), ACT deficiency (due to αl-Antichymotrypsin), Diabetes insipidus (DI), Neurophyseal DI (due to Vasopvessin hormone/V2-receptor), Neprogenic DI (due to Aquaporin II), Charcot-Marie Tooth syndrome (due to Peripheral myelin protein 22), Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease ( due to βAPP and presenilins), Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease (due to Prion protein processing defect), Fabry disease (due to lysosomal α-galactosidase A) and Straussler-Scheinker syndrome (due to Prp processing defect).
[0015] In addition to up-regulation of CFTR activity, reducing anion secretion by CFTR modulators may be beneficial for the treatment of secretory diarrheas, in which epithelial water transport is dramatically increased as a result of secretagogue activated chloride transport. The mechanism involves elevation of cAMP and stimulation of CFTR.
[0016] Although there are numerous causes of diarrhea, the major consequences of diarrheal diseases, resulting from excessive chloride transport are common to all, and include dehydration, acidosis, impaired growth and death.
[0017] Acute and chronic diarrheas represent a major medical problem in many areas of the world. Diarrhea is both a significant factor in malnutrition and the leading cause of death (5,000,000 deaths/year) in children less than five years old.
[0018] Secretory diarrheas are also a dangerous condition in patients of acquired immunodeficiency syndrome (AIDS) and chronic inflammatory bowel disease (IBD). 16 million travelers to developing countries from industrialized nations every year develop diarrhea, with the severity and number of cases of diarrhea varying depending on the country and area of travel.
[0019] Diarrhea in barn animals and pets such as cows, pigs and horses, sheep, goats, cats and dogs, also known as scours, is a major cause of death in these animals. Diarrhea can result from any major transition, such as weaning or physical movement, as well as in response to a variety of bacterial or viral infections and generally occurs within the first few hours of the animal's life.
[0020] The most common diarrhea causing bacteria is enterotoxogenic E-coli (ETEC) having the K99 pilus antigen. Common viral causes of diarrhea include rotavirus and coronavirus. Other infectious agents include Cryptosporidium, giardia lamblia, and salmonella, among others.
[0021] Symptoms of rotaviral infection include excretion of watery feces, dehydration and weakness. Coronavirus causes a more severe illness in the newborn animals, and has a higher mortality rate than rotaviral infection. Often, however, a young animal may be infected with more than one virus or with a combination of viral and bacterial microorganisms at one time. This dramatically increases the severity of the disease.
[0022] Accordingly, there is a need for modulators of an ABC transporter activity, and compositions thereof, that can be used to modulate the activity of the ABC transporter in the cell membrane of a mammal.
[0023] There is a need for methods of treating ABC transporter mediated diseases using such modulators of ABC transporter activity.
[0024] There is a need for methods of modulating an ABC transporter activity in an ex vivo cell membrane of a mammal.
[0025] There is a need for modulators of CFTR activity that can be used to modulate the activity of CFTR in the cell membrane of a mammal.
[0026] There is a need for methods of treating CFTR-mediated diseases using such modulators of CFTR activity.
[0027] There is a need for methods of modulating CFTR activity in an ex vivo cell membrane of a mammal. [0028] SUMMARY OF THE INVENTION
[0029] It has now been found that compounds of this invention, and pharmaceutically acceptable compositions thereof, are useful as modulators of ABC transporter activity, particularly CTFR activity. These compounds have the general formula I:
Figure imgf000008_0001
I or a pharmaceutically acceptable salt thereof, wherein R1, R2, ring A, ring B, and n are defined below.
It has also now been found that compounds of this invention, and pharmaceutically acceptable compositions thereof, are useful as modulators of ABC transporter activity. These compounds have the general formula II:
Figure imgf000008_0002
II or a pharmaceutically acceptable salt thereof, wherein R, R1, R2, R3, R4, and R5 are defined below.
[0030] These compounds and pharmaceutically acceptable compositions are useful for treating or lessening the severity of a variety of diseases, disorders, or conditions, including, but not limited to, cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation-fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, diabetes mellitus, laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, hereditary emphysema, congenital hyperthyroidism, osteogenesis imperfecta, hereditary hypofibrinogenemia, ACT deficiency, diabetes insipidus, neurophysiol, nephrogenic, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, spinocerebullar ataxia type I, spinal and bulbar muscular atrophy, dentatorubal pallidoluysian, and myotonic dystrophy, as well as spongiform encephalopathies, such as hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease.
[0031] DETAILED DESCRIPTION OF THE INVENTION
[0032] I. DEFINITIONS
[0033] As used herein, the following definitions shall apply unless otherwise indicated.
[0034] The term "ABC-transporter" as used herein means an ABC-transporter protein or a fragment thereof comprising at least one binding domain, wherein said protein or fragment thereof is present in vivo or in vitro. The term "binding domain" as used herein means a domain on the ABC-transporter that can bind to a modulator. See, e.g., Hwang, T. C. et al., J. Gen. Physiol. (1998): 111(3), 477-90.
[0035] The term "CFTR" as used herein means cystic fibrosis transmembrane conductance regulator or a mutation thereof capable of regulator activity, including, but not limited to, ΔF508 CFTR and G551D CFTR (see, e.g., http://www.genet.sickkids.on.ca/cftr/, for CFTR mutations).
[0036] The term "modulating" as used herein means increasing or decreasing, e.g. activity, by a measurable amount. Compounds that modulate ABC Transporter activity, such as CFTR activity, by increasing the activity of the ABC Transporter, e.g., a CFTR anion channel, are called agonists. Compounds that modulate ABC Transporter activity, such as CFTR activity, by decreasing the activity of the ABC Transporter, e.g., CFTR anion channel, are called antagonists. An agonist interacts with an ABC Transporter, such as CFTR anion channel, to increase the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding. An antagonist interacts with an ABC Transporter, such as CFTR, and competes with the endogenous ligand(s) or substrate(s) for binding site(s) on the receptor to decrease the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding. [0037] The phrase "treating or reducing the severity of an ABC Transporter mediated disease" refers both to treatments for diseases that are directly caused by ABC Transporter and/or CFTR activities and alleviation of symptoms of diseases not directly caused by ABC Transporter and/or CFTR anion channel activities. Examples of diseases whose symptoms may be affected by ABC Transporter and/or CFTR activity include, but are not limited to, Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1 , Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophysiol DI, Nephrogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders such as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease.
[0038] For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistry", Thomas Sorrell, University Science Books, Sausolito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001, the entire contents of which are hereby incorporated by reference.
[0039] As described herein, compounds of the invention may optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention.
[0040] As used herein the term "aliphatic" encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
[0041] As used herein, an "alkyl" group refers to a saturated aliphatic hydrocarbon group containing 1-12 (e.g., 1-8, 1-6, or 1-4) carbon atoms. An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl, or 2-ethylhexyl. An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, phospho, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)carbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino alkylaminocarbonyl, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, arylaminocarbonyl, or heteroarylaminocarbonyl], amino [e.g., aliphaticamino, cycloaliphaticamino, or heterocycloaliphaticamino], sulfonyl [e.g., aliphatic-SO2-], sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroarylalkoxy, alkoxycarbonyl, alkylcarbonyloxy, or hydroxy. Without limitation, some examples of substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkyl-SC>2-amino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, or haloalkyl.
[0042] As used herein, an "alkenyl" group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-12, 2-6, or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to allyl, isoprenyl, 2-butenyl, and 2-hexenyl. An alkenyl group can be optionally substituted with one or more substituents such as halo, phospho, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)carbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino alkylaminocarbonyl, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, arylaminocarbonyl, or heteroarylaminocarbonyl], amino [e.g., aliphaticamino, cycloaliphaticamino, heterocycloaliphaticamino, or aliphaticsulfonylamino], sulfonyl [e.g., alkyl-SC>2-, cycloaliphatic-SO2-, or aryl-SO2-], sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkoxy, alkoxycarbonyl, alkylcarbonyloxy, or hydroxy. Without limitation, some examples of substituted alkenyls include cyanoalkenyl, alkoxyalkenyl, acylalkenyl, hydroxyalkenyl, aralkenyl, (alkoxyaryl)alkenyl, (sulfonylamino)alkenyl (such as (alkyl-SO2-amino)alkenyl), aminoalkenyl, amidoalkenyl, (cycloaliphatic)alkenyl, or haloalkenyl.
[0043] As used herein, an "alkynyl" group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-12, 2-6, or 2-4) carbon atoms and has at least one triple bond. An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl. An alkynyl group can be optionally substituted with one or more substituents such as aroyl, heteroaroyl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, nitro, carboxy, cyano, halo, hydroxy, sulfo, mercapto, sulfanyl [e.g., aliphatic sulfanyl or cycloaliphaticsulfanyl], sulfinyl [e.g., aliphaticsulfinyl or cycloaliphaticsulfinyl], sulfonyl [e.g., aliphatic-SCV, aliphaticamino-SCV, or cycloaliphatic- SO2-], amido [e.g., aminocarbonyl, alkylaminocarbonyl, alkylcarbonylamino, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, cycloalkylcarbonylamino, arylaminocarbonyl, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (cycloalkylalkyl)carbonylamino, heteroaralkylcarbonylamino, heteroarylcarbonylamino or heteroarylaminocarbonyl], urea, thiourea, sulfamoyl, sulfamide, alkoxycarbonyl, alkylcarbonyloxy, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, acyl [e.g., (cycloaliphatic)carbonyl or (heterocycloaliphatic)carbonyl], amino [e.g., aliphaticamino], sulfoxy, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, or (heteroaryl)alkoxy.
[0044] As used herein, an "amido" encompasses both "aminocarbonyl" and "carbonylamino". These terms when used alone or in connection with another group refer to an amido group such as -N(RX)-C(O)-RY or -C(O)-N(RX)2, when used terminally, and -C(O)- N(RX)- or -N(RX)-C(O)- when used internally, wherein Rx and Rγ are defined below. Examples of amido groups include alkylamido (such as alkylcarbonylamino or alkylaminocarbonyl), (heterocycloaliphatic)amido, (heteroaralkyl)amido, (heteroaryl) amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido, or cycloalkylamido.
[0045] As used herein, an "amino" group refers to -NRXRY wherein each of Rx and Rγ is independently hydrogen, aliphatic, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted. Examples of amino groups include alkylamino, dialkylamino, or arylamino. When the term "amino" is not the terminal group (e.g., alkylcarbonylamino), it is represented by -NRX-. Rx has the same meaning as defined above.
[0046] As used herein, an "aryl" group used alone or as part of a larger moiety as in "aralkyl", "aralkoxy", or "aryloxyalkyl" refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl) ring systems in which the monocyclic ring system is aromatic or at least one of the rings in a bicyclic or tricyclic ring system is aromatic. The bicyclic and tricyclic groups include benzofused 2-3 membered carbocyclic rings. For example, a benzofused group includes phenyl fused with two or more C4_8 carbocyclic moieties. An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro; carboxy; amido; acyl [e.g., (aliphatic)carbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)carbonyl; (heterocycloaliphatic)carbonyl; ((heterocycloaliphatic)aliphatic)carbonyl; or (heteroaraliphatic)carbonyl]; sulfonyl [e.g., aliphatic-SO2- or amino-SO2-]; sulfinyl [e.g., aliphatic-S(O)- or cycloaliphatic-S(O)-]; sulfanyl [e.g., aliphatic-S-]; cyano; halo; hydroxy; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; or carbamoyl. Alternatively, an aryl can be unsubstituted.
[0047] Non-limiting examples of substituted aryls include haloaryl [e.g., mono-, di (such as
/?,m-dihaloaryl), and (trihalo)aryl] ; (carboxy)aryl [e.g., (alkoxycarbonyl)aryl,
((aralkyl)carbonyloxy)aryl, and (alkoxycarbonyl)aryl]; (amido)aryl [e.g.,
(aminocarbonyl)aryl, (((alkylamino)alkyl)aminocarbonyl)aryl, (alkylcarbonyl)aminoaryl,
(arylaminocarbonyl)aryl, and (((heteroaryl)amino)carbonyl)aryl]; aminoaryl [e.g., ((alkylsulfonyl)amino)aryl or ((dialkyl)amino)aryl]; (cyanoalkyl)aryl; (alkoxy)aryl; (sulfamoyl)aryl [e.g., (aminosulfonyl)aryl]; (alkylsulfonyl)aryl; (cyano)aryl; (hydroxyalkyl)aryl; ((alkoxy)alkyl)aryl; (hydroxy)aryl, ((carboxy)alkyl)aryl; (((dialkyl)amino)alkyl)aryl; (nitroalkyl)aryl; (((alkylsulfonyl)amino)alkyl)aryl; ((heterocycloaliphatic)carbonyl)aryl; ((alkylsulfonyl)alkyl)aryl; (cyanoalkyl)aryl; (hydroxyalkyl)aryl; (alkylcarbonyl)aryl; alkylaryl; (trihaloalkyl)aryl; p-amino-m- alkoxycarbonylaryl; /?-amino-m-cyanoaryl; /?-halo-m-aminoaryl; or (m-(heterocycloaliphatic)- o-(alkyl))aryl.
[0048] As used herein, an "araliphatic" such as an "aralkyl" group refers to an aliphatic group (e.g., a C1^ alkyl group) that is substituted with an aryl group. "Aliphatic," "alkyl," and "aryl" are defined herein. An example of an araliphatic such as an aralkyl group is benzyl.
[0049] As used herein, an "aralkyl" group refers to an alkyl group (e.g., a Ci_4 alkyl group) that is substituted with an aryl group. Both "alkyl" and "aryl" have been defined above. An example of an aralkyl group is benzyl. An aralkyl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl, including carboxyalkyl, hydroxyalkyl, or haloalkyl such as trifluoromethyl] , cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, amido [e.g., aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, or heteroaralkylcarbonylamino], cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[0050] As used herein, a "bicyclic ring system" includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common). Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls.
[0051] As used herein, a "carbocycle" or "cycloaliphatic" group encompasses a "cycloalkyl" group and a "cycloalkenyl" group, each of which being optionally substituted as set forth below. [0052] As used herein, a "cycloalkyl" group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]decyl, bicyclo[2.2.2]octyl, adamantyl, or ((aminocarbonyl)cycloalkyl)cycloalkyl.
[0053] A "cycloalkenyl" group, as used herein, refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds. Examples of cycloalkenyl groups include cyclopentenyl, 1 ,4-cyclohexa-di-enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, or bicyclo[3.3.1]nonenyl.
[0054] A cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as phosphor, aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino,
((cycloaliphatic)aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic)aliphatic)carbonylamino, (heteroaryl)carbonylamino, or (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, or alkylcarbonyloxy], acyl [e.g., (cycloaliphatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, or (heteroaraliphatic)carbonyl], cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkyl-SO2- and aryl-SO2-], sulfinyl [e.g., alkyl-S(O)-], sulfanyl [e.g., alkyl-S-], sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[0055] As used herein, the term "heterocycle" or "heterocycloaliphatic" encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
[0056] As used herein, a "heterocycloalkyl" group refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof). Examples of a heterocycloalkyl group include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxolanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octahydrobenzofuryl, octahydrochromenyl, octahydrothiochromenyl, octahydroindolyl, octahydropyrindinyl, decahydroquinolinyl, octahydrobenzo[Z?]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03'7]nonyl. A monocyclic heterocycloalkyl group can be fused with a phenyl moiety to form structures, such as tetrahydroisoquinoline, which would be categorized as heteroaryls.
[0057] A "heterocycloalkenyl" group, as used herein, refers to a mono- or bicylic (e.g., 5- to 10-membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S). Monocyclic and bicyclic heterocycloaliphatics are numbered according to standard chemical nomenclature.
[0058] A heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as phosphor, aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic)aliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic) aliphatic)carbonylamino, (heteroaryl)carbonylamino, or (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, or alkylcarbonyloxy], acyl [e.g., (cycloaliphatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, or (heteroaraliphatic)carbonyl], nitro, cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkylsulfonyl or arylsulfonyl], sulfinyl [e.g., alkylsulfinyl], sulfanyl [e.g., alkylsulfanyl], sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[0059] A "heteroaryl" group, as used herein, refers to a monocyclic, bicyclic, or tricyclic ring system having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and in which the monocyclic ring system is aromatic or at least one of the rings in the bicyclic or tricyclic ring systems is aromatic. A heteroaryl group includes a benzofused ring system having 2 to 3 rings. For example, a benzofused group includes benzo fused with one or two 4 to 8 membered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[^]furyl, benzo[Z?]thiophenyl, quinolinyl, or isoquinolinyl). Some examples of heteroaryl are azetidinyl, pyridyl, IH- indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo-l,2,5-thiadiazolyl, or 1,8-naphthyridyl.
[0060] Without limitation, monocyclic heteroaryls include furyl, thiophenyl, 2H-pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4-thiadiazolyl, 2H-pyranyl, 4-H-pranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl. Monocyclic heteroaryls are numbered according to standard chemical nomenclature.
[0061] Without limitation, bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H- indolyl, indolinyl, benzo[^]furyl, benzo[Z?]thiophenyl, quinolinyl, isoquinolinyl, indolizinyl, isoindolyl, indolyl, benzo[^]furyl, bexo[^]thiophenyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl. Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
[0062] A heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)carbonyl; (heterocycloaliphatic)carbonyl;
((heterocycloaliphatic)aliphatic)carbonyl; or (heteroaraliphatic)carbonyl] ; sulfonyl [e.g., aliphaticsulfonyl or aminosulfonyl] ; sulfinyl [e.g., aliphatic sulfinyl]; sulfanyl [e.g., aliphaticsulfanyl]; nitro; cyano; halo; hydroxy; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; or carbamoyl. Alternatively, a heteroaryl can be unsubstituted.
[0063] Non- limiting examples of substituted heteroaryls include (halo)heteroaryl [e.g., mono- and di-(halo)heteroaryl]; (carboxy )heteroaryl [e.g., (alkoxycarbonyl)heteroaryl] ; cyanoheteroaryl; aminoheteroaryl [e.g., ((alkylsulfonyl)amino)heteroaryl and ((dialkyl)amino)heteroaryl] ; (amido)heteroaryl [e.g., aminocarbonylheteroaryl, ((alkylcarbonyl)amino)heteroaryl, ((((alkyl)amino)alkyl)aminocarbonyl)heteroaryl, (((heteroaryl)amino)carbonyl)heteroaryl, ((heterocycloaliphatic)carbonyl)heteroaryl, and ((alkylcarbonyl)amino)heteroaryl] ; (cyanoalkyl)heteroaryl; (alkoxy)heteroaryl; (sulfamoyl)heteroaryl [e.g., (aminosulfonyl)heteroaryl] ; (sulfonyl)heteroaryl [e.g., (alkylsulfonyl)heteroaryl] ; (hydroxyalkyl)heteroaryl; (alkoxyalkyl)heteroaryl; (hydroxy)heteroaryl; ((carboxy)alkyl)heteroaryl; (((dialkyl)amino)alkyl]heteroaryl; (heterocycloaliphatic)heteroaryl; (cycloaliphatic)heteroaryl; (nitroalkyl)heteroaryl; (((alkylsulfonyl)amino)alkyl)heteroaryl; ((alkylsulfonyl)alkyl)heteroaryl; (cyanoalkyl)heteroaryl; (acyl)heteroaryl [e.g., (alkylcarbonyl)heteroaryl]; (alkyl)heteroaryl, and (haloalkyl)heteroaryl [e.g., trihaloalkylheteroaryl].
[0064] A "heteroaraliphatic" (such as a heteroaralkyl group) as used herein, refers to an aliphatic group (e.g., a C1-4 alkyl group) that is substituted with a heteroaryl group. "Aliphatic," "alkyl," and "heteroaryl" have been defined above.
[0065] A "heteroaralkyl" group, as used herein, refers to an alkyl group (e.g., a Ci_4 alkyl group) that is substituted with a heteroaryl group. Both "alkyl" and "heteroaryl" have been defined above. A heteroaralkyl is optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino, cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[0066] As used herein, "cyclic moiety" and "cyclic group" refer to mono-, bi-, and tricyclic ring systems including cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been previously defined.
[0067] As used herein, a "bridged bicyclic ring system" refers to a bicyclic heterocyclicaliphatic ring system or bicyclic cycloaliphatic ring system in which the rings are bridged. Examples of bridged bicyclic ring systems include, but are not limited to, adamantanyl, norbornanyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.2.3]nonyl, 2-oxabicyclo[2.2.2]octyl, l-azabicyclo[2.2.2]octyl, 3- azabicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03'7]nonyl. A bridged bicyclic ring system can be optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino, cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[0068] As used herein, an "acyl" group refers to a formyl group or RX-C(O)- (such as alkyl-C(O)-, also referred to as "alkylcarbonyl") where Rx and "alkyl" have been defined previously. Acetyl and pivaloyl are examples of acyl groups.
[0069] As used herein, an "aroyl" or "heteroaroyl" refers to an aryl-C(O)- or a heteroaryl-C(O)-. The aryl and heteroaryl portion of the aroyl or heteroaroyl is optionally substituted as previously defined.
[0070] As used herein, an "alkoxy" group refers to an alkyl-O- group where "alkyl" has been defined previously.
[0071] As used herein, a "carbamoyl" group refers to a group having the structure -O-CO-NRXRY or -NRX-CO-O-RZ, wherein Rx and Rγ have been defined above and Rz can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
[0072] As used herein, a "carboxy" group refers to -COOH, -COORX, -OC(O)H, -OC(O)RX, when used as a terminal group; or -OC(O)- or -C(O)O- when used as an internal group.
[0073] As used herein, a "haloaliphatic" group refers to an aliphatic group substituted with 1-3 halogen. For instance, the term haloalkyl includes the group -CF3.
[0074] As used herein, a "mercapto" group refers to -SH.
[[00007755]] AAss uusseedd hheerreeiinn,, aa ""ssulfo" group refers to -SO3H or -Sθ3Rx when used terminally or -S(O)3- when used internally.
[0076] As used herein, a "sulfamide" group refers to the structure -NRX-S(O)2-NRYRZ when used terminally and -NRX-S(O)2-NRY- when used internally, wherein Rx, Rγ, and Rz have been defined above. [0077] As used herein, a "sulfonamide" group refers to the structure -S(O)2-NRXRY or -NRX-S(O)2-RZ when used terminally; or -S(O)2-NRX- or -NRX -S(O)2- when used internally, wherein Rx, Rγ, and Rz are defined above.
[0078] As used herein a "sulfanyl" group refers to -S-Rx when used terminally and -S- when used internally, wherein Rx has been defined above. Examples of sulfanyls include aliphatic-S-, cycloaliphatic-S-, aryl-S-, or the like.
[0079] As used herein a "sulfinyl" group refers to -S(O)-RX when used terminally and - S(O)- when used internally, wherein R has been defined above. Exemplary sulfinyl groups include aliphatic-S(O)-, aryl-S(O)-, (cycloaliphatic(aliphatic))-S(O)-, cycloalkyl-S(O)-, heterocycloaliphatic-S(O)-, heteroaryl-S(O)-, or the like.
[0080] As used herein, a "sulfonyl" group refers to-S(O)2-Rx when used terminally and -S(O)2- when used internally, wherein Rx has been defined above. Exemplary sulfonyl groups include aliphatic-S(O)2-, aryl-S(O)2-, (cycloaliphatic(aliphatic))-S(O)2-, cycloaliphatic-S(O)2-, heterocycloaliphatic-S(O)2-, heteroaryl-S(O)2-, (cycloaliphatic(amido(aliphatic)))-S(O)2-or the like.
[0081] As used herein, a "sulfoxy" group refers to -O-SO-RX or -SO-O-RX, when used terminally and -0-S(O)- or -S(O)-O- when used internally, where Rx has been defined above.
[0082] As used herein, a "halogen" or "halo" group refers to fluorine, chlorine, bromine or iodine.
[0083] As used herein, an "alkoxycarbonyl," which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-.
[0084] As used herein, an "alkoxyalkyl" refers to an alkyl group such as alkyl-O-alkyl-, wherein alkyl has been defined above.
[0085] As used herein, a "carbonyl" refer to -C(O)-. [0086] As used herein, an "oxo" refers to =0.
[0087] As used herein, the term "phospho" refers to phosphinates and phosphonates. Examples of phosphinates and phosphonates include -P(O)(RP)2, wherein Rp is aliphatic, alkoxy, aryloxy, heteroaryloxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy aryl, heteroaryl, cycloaliphatic or amino.
[0088] As used herein, an "aminoalkyl" refers to the structure (Rx)2N-alkyl-.
[0089] As used herein, a "cyanoalkyl" refers to the structure (NC)-alkyl-. [0090] As used herein, a "urea" group refers to the structure -NRX-CO-NRYRZ and a "thiourea" group refers to the structure -NRX-CS-NRYRZ when used terminally and -NRX- C0-NRY- or
-NR -CS-NR - when used internally, wherein R , R , and R have been defined above.
[0091] As used herein, a "guanidine" group refers to the structure - N=C(N(RXRY))N(RXRY) or -NRX-C(=NRX)NRXRY wherein Rx and Rγ have been defined above.
[0092] As used herein, the term "amidino" group refers to the structure - C=(NRX)N(RXRY) wherein Rx and Rγhave been defined above.
[0093] In general, the term "vicinal" refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to adjacent carbon atoms.
[0094] In general, the term "geminal" refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to the same carbon atom.
[0095] The terms "terminally" and "internally" refer to the location of a group within a substituent. A group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure. Carboxyalkyl, i.e., RxO(O)C-alkyl is an example of a carboxy group used terminally. A group is internal when the group is present in the middle of a substituent of the chemical structure. Alkylcarboxy (e.g., alkyl-C(O)O- or alkyl-OC(O)-) and alkylcarboxyaryl (e.g., alkyl-C(O)O-aryl- or alkyl-O(CO)-aryl-) are examples of carboxy groups used internally.
[0096] As used herein, an "aliphatic chain" refers to a branched or straight aliphatic group (e.g., alkyl groups, alkenyl groups, or alkynyl groups). A straight aliphatic chain has the structure
-[CH2]V-, where v is 1-12. A branched aliphatic chain is a straight aliphatic chain that is substituted with one or more aliphatic groups. A branched aliphatic chain has the structure -[CQQIv- where each Q is independently a hydrogen or an aliphatic group; however, Q shall be an aliphatic group in at least one instance. The term aliphatic chain includes alkyl chains, alkenyl chains, and alkynyl chains, where alkyl, alkenyl, and alkynyl are defined above.
[0097] The phrase "optionally substituted" is used interchangeably with the phrase "substituted or unsubstituted. " As described herein, compounds of the invention can optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention. As described herein, the variables R1, R2, and R3, and other variables contained in formulae described herein encompass specific groups, such as alkyl and aryl. Unless otherwise noted, each of the specific groups for the variables R1, R2, and R3, and other variables contained therein can be optionally substituted with one or more substituents described herein. Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxo, alkoxy, hydroxy, amino, nitro, aryl, cycloaliphatic, heterocycloaliphatic, heteroaryl, haloalkyl, and alkyl. For instance, an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxo, alkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl. As an additional example, the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxy, nitro, haloalkyl, and alkyl. When two alkoxy groups are bound to the same atom or adjacent atoms, the two alkxoy groups can form a ring together with the atom(s) to which they are bound.
[0098] In general, the term "substituted," whether preceded by the term "optionally" or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. Specific substituents are described above in the definitions and below in the description of compounds and examples thereof. Unless otherwise indicated, an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position. A ring substituent, such as a heterocycloalkyl, can be bound to another ring, such as a cycloalkyl, to form a spiro-bicyclic ring system, e.g., both rings share one common atom. As one of ordinary skill in the art will recognize, combinations of substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
[0099] The phrase "stable or chemically feasible," as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein. In some embodiments, a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40 0C or less, in the absence of moisture or other chemically reactive conditions, for at least a week. [00100] As used herein, an "effective amount" is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight, and condition of the patient. The interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep., 50: 219 (1966). Body surface area may be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970). As used herein, "patient" refers to a mammal, including a human.
[00101] Unless otherwise stated, structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. Additionally, unless otherwise stated, structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 13C- or 14C-enriched carbon are within the scope of this invention. Such compounds are useful, for example, as analytical tools or probes in biological assays, or as therapeutic agents.
[00102] Compounds of the present invention are useful modulators of ABC transporters and are useful in the treatment of ABC transporter mediated diseases.
[00103] II. COMPOUNDS
[00104] A. Generic Compounds
[00105] The present invention relates to compounds of formula I useful as modulators of ABC transporter activity:
Figure imgf000023_0001
99 I or a pharmaceutically acceptable salt thereof.
[00106] Ri is -ZAR4, wherein each ZA is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZA are optionally and independently replaced by -CO-, -CS-, -C0NRA-, -C0NRANRA-, -CO2-, -OCO-, - NRAC02-,
-O-, -NRAC0NRA-, -0C0NRA-, -NRANRA-, -NRAC0-, -S-, -SO-, -SO2-, -NRA-, -S02NRA-, -NRAS02-, or -NRAS02NRA-. Each R4 Is independently RA, halo, -OH, -NH2, -NO2, -CN, or -OCF3. Each RA is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00107] R2 is -ZBR5, wherein each ZB is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain wherein up to two carbon units of Z are optionally and independently replaced by -CO-, -CS-, -C0NRB-, -C0NRBNRB-, -CO2-, -OCO-, - NRBC02-,
-O-, -NRBC0NRB-, -0C0NRB-, -NRBNRB-, -NRBC0-, -S-, -SO-, -SO2-, -NRB-, -S02NRB-, -NRBS02-, or -NRBS02NRB-. Each R5 is independently RB, halo, -OH, -NH2, -NO2, -CN, - CF3, or -OCF3. Each R is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. Alternatively, any two adjacent R2 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle.
[00108] Ring A is an optionally substituted 3-7 membered monocyclic ring having 0-3 heteroatoms selected from N, O, and S.
[00109] Ring B is a group having formula Ia:
Figure imgf000024_0001
Ia or a pharmaceutically acceptable salt thereof, wherein p is 0-3 and each R3 and R'3 is independently -Z0R6, where each Zc is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain wherein up to two carbon units of Zc are optionally and independently replaced by -CO-, -CS-, -CONRC-, -CONRCNRC-, -CO2-, -OCO-, - NR0CO2-, -O-,
-NRcC0NRc-, -0C0NRc-, -NRCNRC-, -NRcC0-, -S-, -SO-, -SO2-, -NRC-, -SO2NRC-, -NR0SO2-, or -NRcS02NRc-. Each R6 is independently Rc, halo, -OH, -NH2, -NO2, -CN, or -OCF3. Each R is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. Alternatively, any two adjacent R3 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle. Furthermore, R'3 and an adjacent R3 group, together with the atoms to which they are attached, form an optionally substituted heterocycle.
[00110] n is 1-3.
[00111] However, in several embodiments, when ring A is unsubstituted cyclopentyl, n is 1, R2 is 4-chloro, and R] is hydrogen, then ring B is not 2-(tertbutyl)indol-5-yl, or (2,6- dichlorophenyl(carbonyl))-3-methyl-lH-indol-5-yl; and when ring A is unsubstituted cyclopentyl, n is 0, and R] is hydrogen, then ring B is not
Figure imgf000025_0001
[00112] B. Specific Compounds
[00113] 1. R1 Group
[00114] Ri is -ZAR4, wherein each ZA is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain wherein up to two carbon units of ZA are optionally and independently replaced by -CO-, -CS-, -C0NRA-, -C0NRANRA-, -CO2-, -OCO-, -
NRAC02-, -O-, -NRACONRA-, -OCONRA-, -NRANRA-, -NRACO-, -S-, -SO-, -SO2-, -NRA-, -SO2NRA-, -NRASO2-, or -NRAS02NRA-. Each R4 is independently RA, halo, -OH, -NH2, -NO2, -CN, or -OCF3. Each RA is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00115] In several embodiments, R] is -ZARt, wherein each ZA is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain and each R4 is hydrogen.
[00116] In other embodiments, R] is -ZARt, wherein each ZA is a bond and each R4 is hydrogen.
[00117] 2. R7 Group
[00118] Each R2 is independently -ZBRs, wherein each ZB is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -CO-, -CS-, -C0NRB-, -C0NRBNRB-, -
CO2-,
-OCO-, -NRBC02-, -O-, -NRBC0NRB-, -0C0NRB-, -NRBNRB-, -NRBC0-, -S-, -SO-, -SO2-,
-NRB-, -SO2NRB-, -NRBSO2-, or -NRBS02NRB-. Each R5 is independently RB, halo, -OH, -
NH2,
-NO2, -CN, -CF3, or -OCF3. Each RB is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
Alternatively, any two adjacent R2 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle.
[00119] In several embodiments, R2 is an optionally substituted aliphatic. For example, R2 is an optionally substituted branched or straight Ci_6 aliphatic chain. In other examples, R2 is an optionally substituted branched or straight Ci_6 alkyl chain, an optionally substituted branched or straight C2_6 alkenyl chain, or an optionally substituted branched or straight C2_6 alkynyl chain. In alternative embodiments, R2 is a branched or straight Ci_6 aliphatic chain that is optionally substituted with 1-3 of halo, hydroxy, cyano, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof. For example, R2 is a branched or straight Ci_6 alkyl that is optionally substituted with 1-3 of halo, hydroxy, cyano, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof. In still other examples, R2 is a methyl, ethyl, propyl, butyl, isopropyl, or tert-butyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, aryl, heteroaryl, cycloaliphatic, or heterocycloaliphatic. In still other examples, R2 is a methyl, ethyl, propyl, butyl, isopropyl, or tert-butyl, each of which is unsubstituted.
[00120] In several other embodiments, R2 is an optionally substituted branched or straight Ci_5 alkoxy. For example, R2 is a Ci_s alkoxy that is optionally substituted with 1-3 of hydroxy, aryl, heteroaryl, cycloaliphatic, heterocycloaliphatic, or combinations thereof. In other examples, R2 is a methoxy, ethoxy, propoxy, butoxy, or pentoxy, each of which is optionally substituted with 1-3 of hydroxy, aryl, heteroaryl, cycloaliphatic, heterocycloaliphatic, or combinations thereof.
[00121] In other embodiments, R2 is hydroxy, halo, or cyano.
[00122] In several embodiments, R2 is -ZBRs, and ZB is independently a bond or an optionally substituted branched or straight C1-4 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -C(O)-, -O-, -S-, -S(O)2-, or -NH-, and R5 is R , halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3, and RB is hydrogen or aryl.
[00123] In several embodiments, two adjacent R2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle. For example, two adjacent R2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle, either of which is fused to the phenyl of formula I, wherein the carbocycle or heterocycle has formula Ib:
Figure imgf000027_0001
Ib
[00124] Each of Z1, Z2, Z3, Z4, and Z5 is independently a bond, -CRvRV-, -NR7-, or -O-; each R7 is independently -Z0R8, wherein each ZD is independently an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -C0NRD-, -CO2-, -OCO-, -NR0CO2-, -O-, -NR0CONR0-, -OCONR0-, -NR0NR0-, -NR0CO-, -S-, -SO-, -SO2-, -NR°-, -SO2NR0-, -NR0SO2-, or -NR0SO2NR0-. Each R8 is independently R°, halo, -OH, -NH2, -NO2, -CN, - CF3, or -OCF3. Each R° is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. Each R'7 is independently hydrogen, optionally substituted C1-6 aliphatic, hydroxy, halo, cyano, nitro, or combinations thereof. Alternatively, any two adjacent R7 groups together with the atoms to which they are attached form an optionally substituted 3-7 membered carbocyclic ring, such as an optionally substituted cyclobutyl ring, or any two R7 and R'7 groups together with the atom or atoms to which they are attached form an optionally substituted 3-7 membered carbocyclic ring or a heterocarbocyclic ring.
[00125] In several other examples, two adjacent R2 groups form an optionally substituted carbocycle. For example, two adjacent R2 groups form an optionally substituted 5-7 membered carbocycle that is optionally substituted with 1-3 of halo, hydroxy, cyano, oxo, cyano, alkoxy, alkyl, or combinations thereof. In another example, two adjacent R2 groups form a 5-6 membered carbocycle that is optionally substituted with 1-3 of halo, hydroxy, cyano, oxo, cyano, alkoxy, alkyl, or combinations thereof. In still another example, two adjacent R2 groups form an unsubstituted 5-7 membered carbocycle.
[00126] In alternative examples, two adjacent R2 groups form an optionally substituted heterocycle. For instance, two adjacent R2 groups form an optionally substituted 5-7 membered heterocycle having 1-3 heteroatoms independently selected from N, O, and S. In several examples, two adjacent R2 groups form an optionally substituted 5-6 membered heterocycle having 1-2 oxygen atoms. In other examples, two adjacent R2 groups form an unsubstituted 5-7 membered heterocycle having 1-2 oxygen atoms. In other embodiments, two adjacent R2 groups form a heterocyclic ring selected from:
Figure imgf000028_0001
XA1 XA2 XA3 XA4 XA5 XA6
Figure imgf000028_0002
Figure imgf000029_0001
XA19 XA20 XA21
[00127] In alternative examples, two adjacent R2 groups form an optionally substituted carbocycle or an optionally substituted heterocycle, and a third R2 group is attached to any chemically feasible position on the phenyl of formula I. For instance, an optionally substituted carbocycle or an optionally substituted heterocycle, both of which is formed by two adjacent R2 groups; a third R2 group; and the phenyl of formula I form a group having formula Ic:
Figure imgf000029_0002
Ic
[00128] Z1, Z2, Z3, Z4, and Z5 has been defined above in formula Ib, and R2 has been defined above in formula I.
[00129] In several embodiments, each R2 group is independently selected from hydrogen, halo,
-OCH3, -OH, -CH2OH, -CH3, and -OCF3, and/or two adjacent R2 groups together with the atoms to which they are attached form
Figure imgf000029_0003
Figure imgf000030_0001
XA19 XA20 XA21
[00130] In other embodiments, R2 is at least one selected from hydrogen, halo, methoxy, phenylmethoxy, hydroxy, hydroxymethyl, trifluoromethoxy, and methyl.
[00131] In some embodiments, two adjacent R2 groups, together with the atoms to which they are attached, form
Figure imgf000030_0002
XA1 XA2
[00132] 3. Ring A
[00133] Ring A is an optionally substituted 3-7 membered monocyclic ring having 0-3 heteroatoms selected from N, O, and S.
[00134] In several embodiments, ring A is an optionally substituted 3-7 membered monocyclic cycloaliphatic. For example, ring A is a cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl, each of which is optionally substituted with 1-3 of halo, hydroxy, Ci_5 aliphatic, or combinations thereof.
[00135] In other embodiments, ring A is an optionally substituted 3-7 membered monocyclic heterocycloaliphatic. For example, ring A is an optionally substituted 3-7 membered monocyclic heterocycloaliphatic having 1-2 heteroatoms independently selected from N, O, and S. In other examples, ring A is tetrahydrofuran-yl, tetrahydro-2H-pyran-yl, pyrrolidone-yl, or piperidine-yl, each of which is optionally substituted.
[00136] In still other examples, ring A is selected from
Figure imgf000031_0001
[00137] Each Rg is independently -ZER9, wherein each ZE is independently a bond or an optionally substituted branched or straight C1-5 aliphatic chain wherein up to two carbon units of ZE are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -CO2-, -OCO-, -NREC02-, -O-, -NREC0NRE-, -0C0NRE-, -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, -NRE-, -SO2NR1S -NRES02-, or -NRES02NRE-, each R9 is independently RE, -OH, -NH2, -NO2, - CN,
-CF3, oxo, or -OCF3. Each RE is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00138] q is 0-5. [00139] In other embodiments, ring A is one selected from
Figure imgf000032_0001
[00140] In several embodiments, ring A is
Figure imgf000032_0002
[00141] 4. Ring B
[00142] Ring B is a group having formula Ia:
Figure imgf000032_0003
Ia or a pharmaceutically acceptable salt thereof, wherein p is 0-3.
[00143] Each R3 and R'3 is independently -Z0R6, where each Zc is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Zc are optionally and independently replaced by -CO-, -CS-, -CONRC-, - CONRCNRC-, -CO2-,
-OCO-, -NR0CO2-, -O-, -NRCCONRC-, -OCONRC-, -NRCNRC-, -NRCCO-, -S-, -SO-, -SO2-, -NRC-, -SO2NRC-, -NR0SO2-, or -NRCSO2NRC-. Each R6 is independently Rc, halo, -OH, - NH2, -NO2, -CN, or -OCF3. Each Rc is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. Alternatively, any two adjacent R3 groups together with the atoms to which they are attached form an optionally substituted carbocycle or an optionally substituted heterocycle, or R'3 and an adjacent R3, i.e., attached to the 2 position of the indole of formula Ia, together with the atoms to which they are attached form an optionally substituted heterocycle. [00144] In several embodiments, ring B is
Figure imgf000033_0001
[00145] wherein q is 0-3 and each R2o is -ZGR2i, where each Z° is independently a bond or an optionally substituted branched or straight Ci_s aliphatic chain wherein up to two carbon units of ZG are optionally and independently replaced by -CO-, -CS-, -C0NRG-, -CO2-, - OCO-,
-NR0CO2-, -O-, -OCONR0-, -NR0NR0-, -NR0CO-, -S-, -SO-, -SO2-, -NR0-, -SO2NR0-, -NR0SO2-, or -NR0SO2NR0-. Each R21 is independently R°, halo, -OH, -NH2, -NO2, -CN, or -OCF3. Each R° is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00146] For example, ring B is
Figure imgf000033_0002
[00147] In several embodiments, R'3 is hydrogen and R3 is attached to the 2, 3, 4, 6, or 7 position of the indole of formula Ia. In several other examples, R3 is attached to the 2 or 3 position of the indole of formula Ia, and R3 is independently an optionally substituted aliphatic. For instance, R3 is an optionally substituted acyl group. In several instances, R3 is an optionally substituted (alkoxy)carbonyl. In other instances, R3 is (methoxy)carbonyl, (ethoxy)carbonyl, (propoxy)carbonyl, or (butoxy)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof. In other instances, R3 is an optionally substituted (aliphatic)carbonyl. For example, R3 is an optionally substituted (alkyl)carbonyl that is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof . In other examples, R3 is (methyl)carbonyl, (ethyl)carbonyl, (propyl)carbonyl, or
(butyl)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof.
[00148] In several embodiments, R3 is an optionally substituted (cycloaliphatic)carbonyl or an optionally substituted (heterocycloaliphatic)carbonyl. In several examples, R3 is an optionally substituted (C3_7 cycloaliphatic)carbonyl. For example, R3 is a (cyclopropyl)carbonyl, (cyclobutyl)carbonyl, (cyclopentyl)carbonyl, (cyclohexyl)carbonyl, or (cycloheptyl)carbonyl, each of which is optionally substituted with aliphatic, halo, hydroxy, nitro, cyano, or combinations thereof. In several alternative examples, R3 is an optionally substituted (heterocycloaliphatic)carbonyl. For example, R3 is an optionally substituted (heterocycloaliphatic)carbonyl having 1-3 heteroatoms independently selected from N, O, and S. In other examples, R3 is an optionally substituted (heterocycloaliphatic)carbonyl having 1-3 heteroatoms independently selected from N and O. In still other examples, R3 is an optionally substituted 4-7 membered monocyclic (heterocycloaliphatic)carbonyl having 1- 3 heteroatoms independently selected from N and O. Alternatively, R3 is (piperidine-1- yl,)carbonyl, (pyrrolidine- l-yl)carbonyl, or (morpholine-4-yl)carbonyl, (piperazine-1- yl)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, nitro, or aliphatic.
[00149] In still other instances, R3 is optionally substituted (aliphatic)amido such as (aliphatic(amino(carbonyl)) that is attached to the 2 or 3 position on the indole ring of formula Ia. In some embodiments, R3 is an optionally substituted (alkyl(amino))carbonyl that is attached to the 2 or 3 position on the indole ring of formula Ia. In other embodiments, R3 is an optionally substituted straight or branched (aliphatic(amino))carbonyl that is attached to the 2 or 3 position on the indole ring of formula Ia. In several examples, R3 is (N,N- dimethyl(amino))carbonyl, (methyl(amino))carbonyl, (ethyl(amino))carbonyl, (propyl(amino))carbonyl, (prop-2-yl(amino))carbonyl, (dimethyl(but-2-yl(amino)))carbonyl, (tertbutyl(amino))carbonyl, (butyl(amino))carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, or combinations thereof.
[00150] In other embodiments, R3 is an optionally substituted (alkoxy)carbonyl. For example, R3 is (methoxy)carbonyl, (ethoxy)carbonyl, (propoxy)carbonyl, or (butoxy)carbonyl, each of which is optionally substituted with 1-3 of halo, hydroxy, or combinations thereof. In several instances, R3 is an optionally substituted straight or branched Ci_6 aliphatic. For example, R3 is an optionally substituted straight or branched Ci_6 alkyl. In other examples, R3 is independently an optionally substituted methyl, ethyl, propyl, butyl, isopropyl, or tertbutyl, each of which is optionally substituted with 1-3 of halo, hydroxy, cyano, nitro, or combination thereof. In other embodiments, R3 is an optionally substituted C3-6 cycloaliphatic. Exemplary embodiments include cyclopropyl, 1-methyl- cycloprop-1-yl, etc. In other examples, p is 2 and the two R3 substituents are attached to the indole of formula Ia at the 2,4- or 2,6- or 2,7- positions. Exemplary embodiments include 6- F, 3-(optionally substituted C]_6 aliphatic or C3_6 cycloaliphatic); 7-F-2-(-(optionally substituted Ci_6 aliphatic or C3_6 cycloaliphatic)), 4F-2-(optionally substituted Ci_6 aliphatic or C3-6 cycloaliphatic); 7-CN-2-(optionally substituted C1-6 aliphatic or C3-6 cycloaliphatic); 7- Me-2-(optionally substituted C]_6 aliphatic or C3_6 cycloaliphatic) and 7-OMe-2-(optionally substituted C1-6 aliphatic or C3-6 cycloaliphatic).
[00151] In several embodiments, R3 is hydrogen. [00152] In several embodiments, R3 is one selected from:
-H, -CH3, -CH2OH, -CH2CH3, -CH2CH2OH, -CH2CH2CH3, -NH2, halo, -OCH3, -CN, -CF3, -C(O)OCH2CH3, -S(O)2CH3, -CH2NH2, -C(O)NH2,
Figure imgf000035_0001
Figure imgf000035_0002
Figure imgf000035_0003
Figure imgf000036_0001
Figure imgf000036_0002
Figure imgf000036_0003
Figure imgf000036_0004
[00153] In another embodiment, two adjacent R3 groups form
Figure imgf000036_0005
[00154] In several embodiments, R'3 is independently -Z0R6, where each Zc is independently a bond or an optionally substituted branched or straight Ci_6 aliphatic chain wherein up to two carbon units of Zc are optionally and independently replaced by -CO-, - CS-, -C0NRc-,
-C0NRcNRc-, -CO2-, -OCO-, -NR0CO2-, -0-, -NRcC0NRc-, -0C0NRc-, -NRCNRC-, NRCCO-, -S-, -SO-, -SO2-, -NRC-, -SO2NRC-, -NR0SO2-, or -NRCSO2NRC-. Each R6 is independently Rc, halo, -OH, -NH2, -NO2, -CN, or -OCF3. Each Rc is independently hydrogen, an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, or an optionally substituted heteroaryl. In one embodiment, each Rc is hydrogen, Ci_6 aliphatic, or C3-O cycloaliphatic, wherein either of the aliphatic or cycloaliphatic is optionally substituted with up to 4 -OH substituents. In another embodiment, Rc is hydrogen, or Ci_6 alkyl optionally substituted with up to 4 -OH substituents.
[00155] For example, in many embodiments, R'3 is is independently -Z0R6, where each Zc is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Zc are optionally and independently replaced by -C(O)-, -C(O)NRC-, -C(O)O-, -NRcC(0)0-, -O-, -NR0S(O)2-, or -NRC-. Each R6 is independently
Rc,
-OH, or -NH2. Each Rc is independently hydrogen, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, or an optionally substituted heteroaryl. In one embodiment, each Rc is hydrogen, Ci_6 aliphatic, or C3_6 cycloaliphatic, wherein either of the aliphatic or cycloaliphatic is optionally substituted with up to 4 -OH substituents. In another embodiment, Rc is hydrogen, or C1-6 alkyl optionally substituted with up to 4 -OH substituents.
[00156] In other embodiments, R'3 is hydrogen or
Figure imgf000037_0001
[00157] wherein R3] is H or a C1-2 aliphatic that is optionally substituted with 1-3 of halo, -
OH, or combinations thereof. R32 is -L-R33, wherein L is a bond, -CH2-, -CH2O-, -
CH2NHS(O)2-,
-CH2C(O)-, -CH2NHC(O)-, or -CH2NH-; and R33 is hydrogen, or Ci-2 aliphatic, cycloaliphatic, heterocycloaliphatic, or heteroaryl, each of which is optionally subsitututed with 1 of -OH,
-NH2, or -CN. For example, in one embodiment, R3] is hydrogen and R32 is Ci_2 aliphatic optionally substituted with -OH, -NH2, or -CN.
[00158] In several embodiments, R'3 is independently selected from one of the following: -H, -CH3, -CH2CH3, -C(O)CH3, -CH2CH2OH, -C(O)OCH3,
Figure imgf000038_0003
Figure imgf000038_0001
[00159] In several embodiments, ring B is one selected from:
Figure imgf000038_0002
Figure imgf000039_0001
Figure imgf000039_0002
Figure imgf000040_0001
Figure imgf000041_0001
[00160] 5. n term
[00161] n is 1-3.
[00162] In several embodiments, n is 1. In other embodiments, n is 2. In still other embodiments, n is 3.
In one aspect, the present invention relates to compounds of formula II useful as modulators of ABC transporter activity:
Figure imgf000041_0002
or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -OCH2O- or -OCF2O-; Ri is H or alkyl; R2 is H or F; R3 is H or CN;
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N(CH3)3, or -CH2CH2OH;
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment, the present invention provides compounds of formula II, wherein the compounds set forth below are excluded:
Figure imgf000042_0001
Figure imgf000042_0002
Figure imgf000043_0001
42
Figure imgf000044_0001
In one embodiment of the compounds, two R taken together form -OCF2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCF2O-, R] is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 and R5 taken together form a five membered ring.
In one embodiment of the compounds, two R taken together form -OCH2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of the compounds, R is OH, Ri is H, R2 is H, R3 is H, and R4 is - CH2OCH2CH(OH)CH2OH.
In one embodiment of the compounds, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is H. In another embodiment, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of the compounds, two R taken together form -CH2CH2CH2-, Ri is H, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment, the compound is represented by formula Ha:
Figure imgf000045_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
[00163] In one embodiment of the compounds, R4 is -CH2OCH2CH(OH)CH2OH, - CH2CH2N+(CH3)3, or -CH2CH2OH. In another embodiment, R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH. In another embodiment, R4 is - CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
[00164] C. Exemplary compounds of the present invention
[00165] Exemplary compounds of the present invention include, but are not limited to, those illustrated in Table 1 below.
Table 1: Exemplary compounds of the present invention.
Figure imgf000046_0001
Figure imgf000047_0001
Figure imgf000048_0001
Figure imgf000049_0001
Figure imgf000050_0001
49
Figure imgf000051_0001
Figure imgf000052_0001
Figure imgf000053_0001
Figure imgf000054_0001
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
157
Figure imgf000059_0001
160
Figure imgf000059_0003
163
Figure imgf000059_0004
166
Figure imgf000059_0005
Figure imgf000059_0002
Figure imgf000060_0001
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
In another aspect, the present invention relates to a pharmaceutical composition comprising (i) a compound of the present invention; and (ii) a pharmaceutically acceptable carrier. In another embodiment, the composition further comprises an additional agent selected from a mucolytic agent, bronchodialator, an anti-biotic, an anti-infective agent, an anti-inflammatory agent, CFTR corrector, or a nutritional agent. In another embodiment, the composition further comprises an additional agent selected from compounds disclosed in U.S. Patent Application Serial No. 11/165,818, published as U.S. Published Patent Application No. 2006/0074075, filed June 24, 2005, and hereby incorporated by reference in its entirety. In another embodiment, the composition further comprises N-(5-hydroxy-2,4- ditert-butyl-phenyl)-4-oxo-lH-quinoline-3-carboxamide. These compositions are useful for treating the diseases described below including cystic fibrosis. These compositions are also useful in the kits described below.
In another aspect, the present invention relates to a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formula II:
Figure imgf000074_0001
II wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or - OCF2O-;
Ri is H or alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment of this method, the ABC transporter is CFTR.
In one embodiment of this method, two R taken together form -OCF2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 and R5 taken together form a five membered ring.
In one embodiment of this method, two R taken together form -OCH2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, R is OH, Ri is H, R2 is H, R3 is H, and R4 is - CH2OCH2CH(OH)CH2OH. In one embodiment of this method, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is H. In another embodiment, at least one R is OCH3, at least two R] are methyl, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, two R taken together form -CH2CH2CH2-, Ri is H, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, the compound is represented by formula Ha:
Figure imgf000075_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment of this method, R4 is -CH2OCH2CH(OH)CH2OH, - CH2CH2N+(CH3)3, or -CH2CH2OH. In another embodiment, R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH. In another embodiment, R4 is - CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
In one embodiment of this method, the compound is selected from Table 1.
In another aspect, the present invention relates to a method of treating a condition, disease, or disorder in a patient implicated by ABC transporter activity, comprising the step of administering to said patient a compound having formula II:
Figure imgf000075_0002
II or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or - OCF2O-;
Ri is H or alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment of this method, two R taken together form -OCF2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 and R5 taken together form a five membered ring.
In one embodiment of this method, two R taken together form -OCH2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, R is OH, Ri is H, R2 is H, R3 is H, and R4 is - CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is H. In another embodiment, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, two R taken together form -CH2CH2CH2-, Ri is H, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this method, the compound is represented by formula Ha:
Figure imgf000077_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment of this method, R4 is -CH2OCH2CH(OH)CH2OH, - CH2CH2N+(CH3)3, or -CH2CH2OH. In another embodiment, R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH. In another embodiment, R4 is - CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
In one embodiment of this method, the compound is selected from Table 1.
In one embodiment of this method, said condition, disease, or disorder is selected from cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation- fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, diabetes mellitus, laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, hereditary emphysema, congenital hyperthyroidism, osteogenesis imperfecta, hereditary hypofibrinogenemia, ACT deficiency, diabetes insipidus (di), neurophyseal di, neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, spinocerebullar ataxia type I, spinal and bulbar muscular atrophy, dentatorubal pallidoluysian, and myotonic dystrophy, as well as spongiform encephalopathies, such as hereditary Creutzfeldt- Jakob disease, Fabry disease, Straussler- Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease. In another aspect, the present invention relates to a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo, comprising:
(i) a first composition comprising a compound of formula II:
Figure imgf000078_0001
II wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or - OCF2O-;
Ri is H or alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring; and (ii) instructions for: a) contacting the composition with the biological sample; and b) measuring activity of said ABC transporter or a fragment thereof.
In one embodiment, the kit further comprises instructions for a) contacting an additional composition with the biological sample; b) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of said first composition.
In one embodiment, the kit is used to measure the density of CFTR.
In one embodiment of this kit, two R taken together form -OCF2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is H. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F,
R3 is H, and R4 is -CH2CH2N+(CH3)3. In another embodiment, two R taken together form - OCF2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, two R taken together form -OCF2O-, Ri is H, R2 is F, R3 is H, and R4 and R5 taken together form a five membered ring.
In one embodiment of this kit, two R taken together form -OCH2O-, Ri is H, and R2 is F. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, and R3 is H. In another embodiment, two R taken together form -OCH2O-, Ri is H, R2 is F, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, R is OH, Ri is H, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH. In another embodiment, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is H. In another embodiment, at least one R is OCH3, at least two Ri are methyl, R2 is H, R3 is H, and R4 is - CH2OCH2CH(OH)CH2OH. In another embodiment, two R taken together form - CH2CH2CH2-, Ri is H, R2 is H, R3 is H, and R4 is -CH2OCH2CH(OH)CH2OH.
In one embodiment of this kit, the compound is represented by formula Ha:
Figure imgf000079_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a five membered ring.
In one embodiment of this kit, R4 is -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH. In another embodiment, R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH. In another embodiment, R4 is -CH2OCH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or - CH2CH2OH; and R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH.
In one embodiment of this kit, the compound is selected from Table 1. [00166] III. SUBGENERIC COMPOUNDS OF THE PRESENT INVENTION
[00167] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula Id:
Figure imgf000080_0001
Ic or a pharmaceutically acceptable salt thereof.
[00168] R1, R2, and ring A are defined above in formula I, and ring B, R3 and p are defined in formula Ia. Furthermore, when ring A is unsubstituted cyclopentyl, n is 1, R2 is 4-chloro, and Ri is hydrogen, then ring B is not 2-(tertbutyl)indol-5-yl, or (2,6- dichlorophenyl(carbonyl))-3-methyl-lH-indol-5-yl; and when ring A is unsubstituted cyclopentyl, n is 0, and Ri is hydrogen, then ring B is not
Figure imgf000080_0002
[00169] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula Id:
Figure imgf000080_0003
Id or a pharmaceutically acceptable salt thereof.
[00170] R1, R2, and ring A are defined above in formula I, and ring B, R3 and p are defined in formula Ia.
[00171] However, when Ri is H, n is 0, ring A is an unsubstituted cyclopentyl, and ring B is an indole-5-yl substituted with 1-2 of R3, th heenn 1 each R3 is independently -ZGRi2, where each Z° is independently a bond or an unsubstituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Z° are optionally and independently replaced by -CS-, - C0NRGNRG-, -CO2-, -OCO-, -NR0CO2-, -O-, -NR0CONR0-, -OCONR0-, -NR0NR0-, -S-, - SO-, -SO2-, -NR0-,
-SO2NR0-, -NR0SO2-, or -NR°S02NRc-, each R12 is independently R°, halo, -OH, -NH2, - NO2, -CN, or -OCF3, and each R° is independently hydrogen, an unsubstituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an unsubstituted aryl, or an optionally substituted heteroaryl; or any two adjacent R3 groups together with the atoms to which they are attached form an optionally substituted heterocycle.
Figure imgf000081_0001
II or a pharmaceutically acceptable salt thereof.
[00173] R1, R2, and ring A are defined above in formula I; R3, R'3, and p are defined above in formula Ia; and Z1, Z2, Z3, Z4, and Z5 are defined above in formula Ib.
[00174] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula Ha:
Figure imgf000082_0001
Ha or a pharmaceutically acceptable salt thereof.
[00175] R1, R2, and ring A are defined above in formula I; R3, R'3, and p are defined above in formula Ia; and Z1, Z2, Z3, Z4, and Z5 are defined above in formula Ib.
[00176] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula lib:
Figure imgf000082_0002
lib or a pharmaceutically acceptable salt thereof.
[00177] R1, R2, and ring A, are defined above in formula I; R3, R'3, and p are defined above in formula Ia; and Z1, Z2, Z3, Z4, and Z5 are defined above in formula Ib.
[00178] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula Hc:
Figure imgf000082_0003
lie or a pharmaceutically acceptable salt thereof.
[00179] R1, R2 and n are defined above in formula I; and R3, R'3, and p are defined in formula Ia. [00180] Another aspect of the present invention provides a compound that is useful for modulating ABC transporter activity. The compound has formula Hd:
Figure imgf000083_0001
Hd or a pharmaceutically acceptable salt thereof.
[00181] Both R2 groups, together with the atoms to which they are attached form a group selected from:
Figure imgf000083_0002
XA1 XA2 XA3 XA4 XA5 XA6
Figure imgf000083_0003
XA19 XA20 XA21
[00182] R'3 is independently selected from one of the following: -H, -CH3, -CH2CH3, -C(O)CH3, -CH2CH2OH, -C(O)OCH3, γ^°-
Figure imgf000084_0001
NHOOOH, Λ COsH HM. CM.
Figure imgf000084_0002
Figure imgf000084_0003
Figure imgf000084_0004
Figure imgf000084_0005
; and each R3 is independently selected from -H, -CH3, -CH2OH, -CH2CH3, -CH2CH2OH, -CH2CH2CH3, -NH2, halo, - OCH3, -CN, -CF3, -C(O)OCH2CH3, -S(O)2CH3, -CH2NH2, -C(O)NH2,
Figure imgf000085_0001
Figure imgf000085_0002
Figure imgf000085_0003
Figure imgf000085_0004
Figure imgf000086_0001
Figure imgf000086_0002
[00183] IV. GENERIC SYNTHETIC SCHEMES
[00184] The compounds of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) may be readily synthesized from commercially available or known starting materials by known methods. Exemplary synthetic routes to produce compounds of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) are provided below in Schemes 1-22 below.
[00185] Preparation of the compounds of the invention is achieved by the coupling of a ring B amine with a ring A carboxylic acid as illustrated in Scheme 1.
[00186] Scheme 1:
Figure imgf000086_0003
Figure imgf000086_0005
Figure imgf000086_0004
a) SOCl2, DMF (cat.), DCM; b) R1-N-(T) , pyr.; c) R -N-TB) , HATU, TEA,
DCM/DMF. [00187] Referring to Scheme 1, the acid Ia may be converted to the corresponding acid chloride Ib using thionyl chloride in the presence of a catalystic amount of dimethylformamide. Reaction of the acid chloride with the amine
Figure imgf000087_0001
provides compounds of the invention I. Alternatively, the acid Ia may be directly coupled to the amine using known coupling reagents such as, for example, HATU in the presence of triethylamine.
[00188] Preparation of the acids Ia may be achieved as illustrated in Scheme 2. Scheme 2:
Figure imgf000087_0002
2a 2b 1a
a) NaOH, BTEAC; b) NaOH, Δ
[00189] Referring to Scheme 2, the nitrile 2a reacts with a suitable bromochloroalkane in the presence of sodium hydroxide and a phase tranfer catalyst such as butyltriethylammonium chloride to provide the intermediate 2b. Hydrolysis of the nitrile of 2b provides the acid Ia. In some instances, isolation of the intermediate 2b is unnecessary.
[00190] The phenylacetonitriles 2a are commercially available or may be prepared as illustrated in Scheme 3.
Scheme 3
Figure imgf000087_0003
3d 2a a) Pd(PPh3)4, CO, MeOH; b) LiAlH4, THF; c) SOCl2; d) NaCN
[00191] Referring to Scheme 3, reaction of an aryl bromide 3a with carbon monoxide in the presence of methanol and tetrakis(triphenylphosphine)palladium (0) provides the ester 3b. Reduction of 3b with lithium aluminum hydride provides the alcohol 3c which is converted to the halide 3d with thionyl chloride. Reaction of 3d with sodium cyanide provides the nitrile 2a.
[00192] Other methods of producing the nitrile 2a are illustrated in schemes 4 and 5 below. Scheme 4
Figure imgf000088_0001
Figure imgf000088_0002
a) TosMIC; b) NaBH4, THF; c) SOCl2; d) NaCN
Scheme 5
Figure imgf000088_0003
a) NBS, AIBN, CCl4; b) NaCN, EtOH
[00193] Preparation of
Figure imgf000088_0004
components is illustrated in the schemes that follow.
A number of methods for preparing ring B compounds wherein ring B is an indole have been reported. See for example Angew. Chem. 2005, 44, 606; J. Am. Chem. Soc. 2005, 127, 5342,); J. Comb. Chem. 2005, 7, 130; Tetrahedron 2006, 62, 3439; J. Chem. Soc. Perkin Trans. 1, 2000, 1045.
[00194] One method for preparing Ri -N-Q is illustrated in Scheme 6.
Scheme 6
Figure imgf000089_0001
a) NaNO2, HCl, SnCl2; b) NaOH, R3CH2C(O)R3, EtOH; c) H3PO4, toluene; d) H2, Pd-C,
EtOH
[00195] Referring to Scheme 6, a nitroaniline 6a is converted to the hydrazine 6b using nitrous acid in the presence of HCl and stannous chloride. Reaction of 6b with an aldehyde or ketone CH3C(O)R3 provides the hydrazone 6c which on treatment with phophoric acid in toluene leads to a mixture of nitro indoles 6d and 6e. Catalytic hydrogenation in the presence of palladium on carbon provides a mixture of the amino indoles 6f and 6g which may be separated using know methods such as, for example, chromatography.
[00196] An alternative method is illustrated in scheme 7. [00197] Scheme 7
H
Figure imgf000090_0001
7a 7b 7c
Figure imgf000090_0002
7f 7g 7h a) R33COCl, Et3N, CH2Cl2; b) n-BuLi, THF; c) NaBH4, AcOH; d) KNO3, H2SO4; e) DDQ, 1,4-dioxane; f) NaNO2, HCl, SnCl2.2H2O, H2O; g) MeCOR3, EtOH; h) PPA; i) Pd/C, EtOH or H2, Raney Ni, EtOH or MeOH
[00198]
[00199] Scheme 8
Figure imgf000090_0003
a) HNO3, H2SO4; b) Me2NCH(OMe)2, DMF; c) H2, Raney Ni, EtOH [00200] Scheme 9
Figure imgf000091_0001
a) NBS, DMF; b) KNO3, H2SO4; c) HC≡C-TMS, Pd(PPh3)2Cl2, CuI, Et3N, toluene, H2O; d)
CuI, DMF; e) H2, Raney Ni, MeOH
[00201] Scheme 10
Figure imgf000091_0002
a) HNO3, H2SO4; b) SOCl2; EtOH; c) DMA, DMF; d) Raney Ni, H2, MeOH
[00202] Scheme 11
Figure imgf000092_0001
a) DMA, DMF; b) Raney Ni, H2, MeOH
[00203] Scheme 12
Figure imgf000092_0002
a) R33CH2COR3I,, AcOH, EtOH; b) H3PO4, toluene; c) H2, Pd/C, EtOH [00204] Scheme 14
Figure imgf000092_0003
a) NaBH3CN; b) When PG= SO2Ph: PhSO2Cl, Et3N, DMAP, CH2Cl2; When PG= Ac: AcCl, NaHCO3, CH2Cl2; c) When Rv= RCO: (RCO)2O, AlCl3, CH2Cl2; When Rv=Br: Br2, AcOH; d) HBr or HCl; e) KNO3, H2SO4; f) MnO2, CH2Cl2 or DDQ, 1,4-dioxane; g) H2, Raney Ni, EtOH. [00205] Scheme 14
Figure imgf000093_0001
Figure imgf000093_0002
a) NaBH3CN; b) RSO2Cl, DMAP, Et3N, CH2Cl2; c) R0C(O)Cl, AlCl3, CH2Cl2; d) NaBH4, THF; e) HBr; f) KNO3, H2SO2; g) MnO2; g) Raney Ni, H2, EtOH
[00206] Scheme 15
Figure imgf000093_0003
a) R3X (X=Br, I), zinc triflate, TBAI, DIEA, toluene; b) H2, Raney Ni, EtOH or H2, Pd/C, EtOH or SnCl2.2H2O, EtOH; c) ClSO2NCO, DMF, CH3CN
[00207] Scheme 16
Figure imgf000093_0004
a) when X=Cl, Br, I, or OTs: R3X, K2CO3, DMF or CH3CN; b) H2, Pd/C, EtOH or SnCl2.2H2O, EtOH or SnCl2.2H2O, DIEA, EtOH. [00208] Scheme 17
Figure imgf000094_0001
a) Br2, AcOH; b) RC(O)Cl, Et3N, CH2Cl2; c) HC≡CR3a, Pd(PPh3) 2C12, CuI, Et3N; d) TBAF, THF or tBuOK, DMF or Pd(PPh3) 2C12, CuI, DMF; e) H2, Pd/C, EtOH or SnCl2, MeOH or
HCO2NH4, Pd/C, EtOH
[00209] Scheme 18
Figure imgf000094_0002
a) Br2, AcOH, CHCl3; b) R3aC≡CH, CuI, Et3N, Pd(PPh3) 2C12; c) RCOCl, Et3N, CH2Cl2; d) TBAF, DMF; e) Raney Ni, H2, MeOH; f) ROK, DMF [00210] Scheme 19
Figure imgf000095_0001
a) Br2, AcOH; b) HC≡CR3a, Pd(PPh3) 2C12, CuI, Et3N; c) Pd(PPh3)2Cl2, CuI, DMF; d) H2, Pd/C, EtOH or SnCl2, MeOH or HCO2NH4, Pd/C, EtOH
[00211] Scheme 20
Figure imgf000095_0002
a) H2NR'3; b) X=Br: Br2, HOAc; X=I: NIS; c) HC≡CR3, Pd(PPh3)2Cl2, CuI, Et3N; d) CuI, DMF or TBAF, THF; e) H2, Pd/C, EtOH or SnCl2, MeOH or HCO2NH4, Pd/C, EtOH
[00212] Scheme 21
Figure imgf000095_0003
a) R'3NH2, DMSO; b) Br2, AcOH; c) TMS-C≡CH, CuI, TEA, Pd(PPh3) 2C12; d) CuI, DMSO; e) Raney Ni, H2, MeOH [00213] Scheme 22
Figure imgf000096_0001
Figure imgf000096_0002
a) R3aC≡CH, CuI, TEA, Pd(PPh3) 2C12; b) TBAF, THF; c) Raney Ni, MeOH [00214] Scheme 23
Figure imgf000096_0003
a) NaBH4, NiCl2, MeOH; b) RC(O)Cl; c) Pd(PPh3)Cl2, HC≡C-R3, CuI, Et3N; d) tBuOK, DMF; e) KNO3, H2SO4; f) NaBH4, NiCl2, MeOH
[00215] Scheme 24
Figure imgf000096_0004
a) SnCl2, EtOH or Pd/C, HCO2NH4 or H2, Pd/C, EtOH or Raney Ni, H2, EtOH [00216] Scheme 25
(
Figure imgf000097_0001
a) PPh3, HBr; b) Cl(O)CCH2CO2Et; c) tBuOK; d) (Boc) 20, DMAP; e) KHMDS, R-X; KHMDS, R-X; f) TFA; g) NaNO3, H2SO4; h) LiAlH4, THF; i) SnCl2, EtOH
[00217] Scheme 26
Figure imgf000097_0002
a) LiOH; b) EDC, HOBt, Et3N, HNRyRz; c) BH3-THF; d) if Rz=H, RC(O)Cl (Z=RC(O)-) or RSO2Cl (Z=RSO2-) or RO(CO)Cl (Z=RO(CO)-) or (RO(CO)) 20 (Z= Z=RO(CO)-), Et3N, CH2Cl2
[00218] Scheme 27
Figure imgf000097_0003
a) R'3-X (X=Br, I, or OTs), base (K2CO3 or Cs2CO3), DMF or CH3CN; b) H2, Pd/C, EtOH or Pd/C, HCO2NH4
[00219] Scheme 28
Figure imgf000098_0001
a) R3aX (X=Cl, Br, I), AlCl3, CH2Cl2; b) Raney Ni, H2, MeOH [00220] Scheme 29
Figure imgf000098_0002
a) HCl/MeOH; PtO2, H2; b) (Boc) 2O, Et3N, THF [00221] Scheme 30
Figure imgf000098_0003
a) NaOH or LiOH; b) ROH, HCl; c) NaBH4 or LiAlH4 or DIBAL-H, THF; d) HNRyRz, HATU, Et3N, EtOH or DMF; e) LiAlH4, THF or BH3 THF; f) H2O2, H2O (Ry=Rz=H); g) H2, Pd/C [00222] Scheme 31
Figure imgf000099_0001
a) R3-X, NaH; Rb-X, NaH; b) PCl5, CH2Cl2; c) NaOH; d) NaNH2, DMSO; e) CH2N2; f) Pd(PPh3)4, CuI, Et3N; g) RC(O)Cl, pyr, CH2Cl2; h) Pd(CH3CN) 2C12, CH3CN; i) Raney Ni, H2, MeOH
[00223] Scheme 32
Figure imgf000099_0002
a) LiOH, THF/H20; b) HNRyRz, HATU, TEA, DMF/CH2C12
[00224] Scheme 33
Figure imgf000100_0001
a) LiBH4, THF/H2O or LiAlH4, THF; b) R3-Li, THF [00225] Scheme 34
Figure imgf000100_0002
a) NaNO2, AcOH/H2O; b) Zn, AcOH [00226] Scheme 35
Figure imgf000100_0003
a) NaBH3CN; b) R'3CHO, NaHB(OAc) 3, TFA, DCE; c) chloranil or CDCl3, light or DDQ [00227] Scheme 36
Figure imgf000101_0001
a) NaH, DMF-THF; R3-X (X=Cl, Br, I, or OTs) [00228] Scheme 37
Figure imgf000101_0002
a) NBS; b) Ar-B(OR)2, Pd-FibreCat 1007, K2CO3, EtOH [00229] Scheme 38
Figure imgf000102_0001
a) RSO2Cl, NaH, THF-DMF; b) R3-X (X=Br, I, or OTs), NaH, THF-DMF; c) ethylene dioxide, InCl3; d) POCl3, DMF; e) H2N-OH, CH2Cl2; Ac2O
[00230] Scheme 39
Figure imgf000103_0001
a) NaH, THF-DMF; epichlorohydrin; b) ROH; c) HNRyRz [00231] Scheme 40
Figure imgf000103_0002
a) TsCl, Et3N, CH2Cl2; b) NaCN, DMF; c) NaOH, MeOH; d) NaN3, NH4Cl; e) NaN3, DMF; f) Pd/C, H2, MeOH (R=H); h) RXC(O)C1 (Z=RXC(O)-) or RXSO2C1 (Z=RXSO2-) or RXO(CO)C1 (Z=Rx0(C0)-) or (Rx0(C0)) 2O ( Z=Rx0(C0)-), Et3N, CH2Cl2 [00232] Scheme 41
Figure imgf000104_0001
a) ClCH2CHO, NaHB(OAc)3, CH2Cl2; CDCl3, light; b) NaN3, NaI, DMF; c) H2, Pd/C, MeOH, AcOH; d) RC(O)Cl (Z=RC(O)-) or RSO2Cl (Z=RSO2-) or RO(CO)Cl (Z=RO(CO)-) or (RO(CO)) 20 (Z= RO(CO)-), Et3N, CH2Cl2.
Scheme 42
Figure imgf000104_0002
b) R3-X, NaH; Rb-X, NaH; b) PCl5, CH2Cl2; c) NaOH; d) NaNH2, DMSO; e) R-OH, DCC; f) Pd(PPh3)2Cl2, CuI, Et3N; g) PdCl2, CH3CN Scheme 43
Figure imgf000105_0001
n= O or 1 a) DIBAL-H; b) P-LG; P= protecting group like TBDMS and LG= leaving group like Cl; c) R4-LG, base likeCs2CC>3; R4 is alkyl and LG is tosylate, Rc=H or R4; d) reducing conditions like Pd/C, H2 or ammonium formate.
Figure imgf000105_0002
Figure imgf000105_0003
R4-LG, base likeCs2CC>3; R4 is alkyl and LG is tosylate; b) LiAlH4; c) reducing conditions like Pd/C, H2 or ammonium formate.
[00233] In the schemes above, the radical R employed therein is a substituent, e.g., RW as defined hereinabove. One of skill in the art will readily appreciate that synthetic routes suitable for various substituents of the present invention are such that the reaction conditions and steps employed do not modify the intended substituents.
[00234] V. FORMULATIONS, ADMINISTRATIONS, AND USES
[00235] Accordingly, in another aspect of the present invention, pharmaceutically acceptable compositions are provided, wherein these compositions comprise any of the compounds as described herein, and optionally comprise a pharmaceutically acceptable carrier, adjuvant or vehicle. In certain embodiments, these compositions optionally further comprise one or more additional therapeutic agents.
[00236] It will also be appreciated that certain of the compounds of present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative or a prodrug thereof. According to the present invention, a pharmaceutically acceptable derivative or a prodrug includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.
[00237] As used herein, the term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. A "pharmaceutically acceptable salt" means any non-toxic salt or salt of an ester of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
[00238] Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2- naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(Ci_4alkyl)4 salts. This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersible products may be obtained by such quaternization. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.
[00239] As described above, the pharmaceutically acceptable compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, adjuvant, or vehicle, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980) discloses various carriers used in formulating pharmaceutically acceptable compositions and known techniques for the preparation thereof. Except insofar as any conventional carrier medium is incompatible with the compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutically acceptable composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylene-polyoxypropylene- block polymers, wool fat, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols; such a propylene glycol or polyethylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.
[00240] In yet another aspect, the present invention provides a method of treating a condition, disease, or disorder implicated by ABC transporter activity. In certain embodiments, the present invention provides a method of treating a condition, disease, or disorder implicated by a deficiency of ABC transporter activity, the method comprising administering a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) to a subject, preferably a mammal, in need thereof.
[00241] In certain preferred embodiments, the present invention provides a method of treating Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1 , Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick' s disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease (due to Prion protein processing defect), Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome, comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd), or a preferred embodiment thereof as set forth above. [00242] According to an alternative preferred embodiment, the present invention provides a method of treating cystic fibrosis comprising the step of administering to said mammal a composition comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd), or a preferred embodiment thereof as set forth above.
[00243] According to the invention an "effective amount" of the compound or pharmaceutically acceptable composition is that amount effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler- Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
[00244] The compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay- Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis
CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
[00245] The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like. The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression "dosage unit form" as used herein refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts. The term "patient", as used herein, means an animal, preferably a mammal, and most preferably a human.
[00246] The pharmaceutically acceptable compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect. [00247] Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
[00248] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.
[00249] The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
[00250] In order to prolong the effect of a compound of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of compound to polymer and the nature of the particular polymer employed, the rate of compound release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.
[00251] Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
[00252] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.
[00253] Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
[00254] The active compounds can also be in microencapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.
[00255] Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms are prepared by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
[00256] As described generally above, the compounds of the invention are useful as modulators of ABC transporters. Thus, without wishing to be bound by any particular theory, the compounds and compositions are particularly useful for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of ABC transporters is implicated in the disease, condition, or disorder. When hyperactivity or inactivity of an ABC transporter is implicated in a particular disease, condition, or disorder, the disease, condition, or disorder may also be referred to as a "ABC transporter-mediated disease, condition or disorder". Accordingly, in another aspect, the present invention provides a method for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of an ABC transporter is implicated in the disease state.
[00257] The activity of a compound utilized in this invention as a modulator of an ABC transporter may be assayed according to methods described generally in the art and in the Examples herein.
[00258] It will also be appreciated that the compounds and pharmaceutically acceptable compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutically acceptable compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another agent used to treat the same disorder), or they may achieve different effects (e.g., control of any adverse effects). As used herein, additional therapeutic agents that are normally administered to treat or prevent a particular disease, or condition, are known as "appropriate for the disease, or condition, being treated".
[00259] The amount of additional therapeutic agent present in the compositions of this invention will be no more than the amount that would normally be administered in a composition comprising that therapeutic agent as the only active agent. Preferably the amount of additional therapeutic agent in the presently disclosed compositions will range from about 50% to 100% of the amount normally present in a composition comprising that agent as the only therapeutically active agent.
[00260] The compounds of this invention or pharmaceutically acceptable compositions thereof may also be incorporated into compositions for coating an implantable medical device, such as prostheses, artificial valves, vascular grafts, stents and catheters. Accordingly, the present invention, in another aspect, includes a composition for coating an implantable device comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device. In still another aspect, the present invention includes an implantable device coated with a composition comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device. Suitable coatings and the general preparation of coated implantable devices are described in US Patents 6,099,562; 5,886,026; and 5,304,121. The coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polymethyldisiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof. The coatings may optionally be further covered by a suitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition.
[00261] Another aspect of the invention relates to modulating ABC transporter activity in a biological sample or a patient (e.g., in vitro or in vivo), which method comprises administering to the patient, or contacting said biological sample with a compound of formula I or a composition comprising said compound. The term "biological sample", as used herein, includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
[00262] Modulation of ABC transporter activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, the study of ABC transporters in biological and pathological phenomena; and the comparative evaluation of new modulators of ABC transporters.
[00263] In yet another embodiment, a method of modulating activity of an anion channel in vitro or in vivo, is provided comprising the step of contacting said channel with a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd). In preferred embodiments, the anion channel is a chloride channel or a bicarbonate channel. In other preferred embodiments, the anion channel is a chloride channel.
[00264] According to an alternative embodiment, the present invention provides a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd). The term "functional ABC transporter" as used herein means an ABC transporter that is capable of transport activity. In preferred embodiments, said functional ABC transporter is CFTR.
[00265] According to another preferred embodiment, the activity of the ABC transporter is measured by measuring the transmembrane voltage potential. Means for measuring the voltage potential across a membrane in the biological sample may employ any of the known methods in the art, such as optical membrane potential assay or other electrophysiological methods.
[00266] The optical membrane potential assay utilizes voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells" Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer" Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VIPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets" Drug Discov Today 4(9): 431-439).
[00267] These voltage sensitive assays are based on the change in fluorescence resonant energy transfer (FRET) between the membrane-soluble, voltage-sensitive dye, DiSBAC2(S), and a fluorescent phospholipid, CC2-DMPE, which is attached to the outer leaflet of the plasma membrane and acts as a FRET donor. Changes in membrane potential (V1n) cause the negatively charged DiSBAC2(S) to redistribute across the plasma membrane and the amount of energy transfer from CC2-DMPE changes accordingly. The changes in fluorescence emission can be monitored using VIPR™ II, which is an integrated liquid handler and fluorescent detector designed to conduct cell-based screens in 96- or 384-well microtiter plates.
[00268] In another aspect the present invention provides a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof. In one embodiment, the kit further comprises instructions for a.) contacting an additional composition with the biological sample; b.) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c.) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of a composition of formulae (I, Ic, Id, II, Ha, lib, Hc, and Hd). In preferred embodiments, the kit is used to measure the density of CFTR. [00269] In order that the invention described herein may be more fully understood, the following examples are set forth. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting this invention in any manner.
[00270] VI. PREPARATIONS AND EXAMPLES
[00271] General Procedure I: Carboxylic Acid Building Block
Figure imgf000117_0001
Hal = Cl, Br, I
[00272] Benzyltriethylammonium chloride (0.025 equivalents) and the appropriate dihalo compound (2.5 equivalents) were added to a substituted phenyl acetonitrile. The mixture was heated at 70 0C and then 50 % sodium hydroxide (10 equivalents) was slowly added to the mixture. The reaction was stirred at 70 0C for 12-24 hours to ensure complete formation of the cycloalkyl moiety and then heated at 130 0C for 24-48 hours to ensure complete conversion from the nitrile to the carboxylic acid. The dark brown / black reaction mixture was diluted with water and extracted with dichloromethane three times to remove side products. The basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate which began to form at pH 4 was filtered and washed with 1 M hydrochloric acid two times. The solid material was dissolved in dichloromethane and extracted two times with 1 M hydrochloric acid and one time with a saturated aqueous solution of sodium chloride. The organic solution was dried over sodium sulfate and evaporated to dryness to give the cycloalkylcarboxylic acid. Yields and purities were typically greater than 90%.
[00273] Example 1: l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid
Figure imgf000117_0002
[00274] A mixture of 2-(benzo[d][l,3]dioxol-5-yl)acetonitrile (5.10 g 31.7 mmol), 1- bromo-2-chloro-ethane (9.00 mL 109 mmol), and benzyltriethylammonium chloride (0.181 g, 0.795 mmol) was heated at 70 0C and then 50% (wt./wt.) aqueous sodium hydroxide (26 mL) was slowly added to the mixture. The reaction was stirred at 70 0C for 24 hours and then heated at 1300C for 48 hours. The dark brown reaction mixture was diluted with water (400 mL) and extracted once with an equal volume of ethyl acetate and once with an equal volume of dichloromethane. The basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate filtered and washed with 1 M hydrochloric acid. The solid material was dissolved in dichloromethane (400 mL) and extracted twice with equal volumes of 1 M hydrochloric acid and once with a saturated aqueous solution of sodium chloride. The organic solution was dried over sodium sulfate and evaporated to dryness to give a white to slightly off-white solid (5.23 g, 80%) ESI-MS tn/z calc. 206.1, found 207.1 (M+l)+. Retention time 2.37 minutes. 1H NMR (400 MHz, DMSO- d6) δ 1.07-1.11 (m, 2H), 1.38-1.42 (m, 2H), 5.98 (s, 2H), 6.79 (m, 2H), 6.88 (m, IH), 12.26 (s, IH).
[00275] General Procedure II: Carboxylic Acid Building Block
Figure imgf000118_0001
Hal = Cl, Br, I, all other variables are as defined in the text.
[00276] Sodium hydroxide (50 % aqueous solution, 7.4 equivalents) was slowly added to a mixture of the appropriate phenyl acetonitrile, benzyltriethylammonium chloride (1.1 equivalents), and the appropriate dihalo compound (2.3 equivalents) at 70 0C. The mixture was stirred overnight at 70 0C and the reaction mixture was diluted with water (30 mL) and extracted with ethyl acetate. The combined organic layers were dried over sodium sulfate and evaporated to dryness to give the crude cyclopropanecarbonitrile, which was used directly in the next step.
[00277] The crude cyclopropanecarbonitrile was refluxed in 10% aqueous sodium hydroxide (7.4 equivalents) for 2.5 hours. The cooled reaction mixture was washed with ether (100 mL) and the aqueous phase was acidified to pH 2 with 2M hydrochloric acid. The precipitated solid was filtered to give the cyclopropanecarboxylic acid as a white solid.
[00278] General Procedure III: Carboxylic Acid Building Block
Figure imgf000119_0001
Figure imgf000119_0002
Figure imgf000119_0003
[00279] Example 2: l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid
Figure imgf000119_0004
[00280] 2,2-Difluoro-benzo[l,3]dioxole-5-carboxylic acid methyl ester
[00281] A solution of 5-bromo-2,2-difluoro-benzo[l,3]dioxole (11.8 g, 50.0 mmol) and tetrakis(triphenylphosphine)palladium (0) [Pd(PPh3)4, 5.78 g, 5.00 mmol] in methanol (20 mL) containing acetonitrile (30 mL) and triethylamine (10 mL) was stirred under a carbon monoxide atmosphere (55 PSI) at 75 0C (oil bath temperature) for 15 hours. The cooled reaction mixture was filtered and the filtrate was evaporated to dryness. The residue was purified by silica gel column chromatography to give crude 2,2-difluoro-benzo [1,3] dioxole- 5-carboxylic acid methyl ester (11.5 g), which was used directly in the next step.
LiAIH4
Figure imgf000119_0006
Figure imgf000119_0005
[00282] (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-methanol
[00283] Crude 2,2-difluoro-benzo[l,3]dioxole-5-carboxylic acid methyl ester (11.5 g) dissolved in 20 mL of anhydrous tetrahydrofuran (THF) was slowly added to a suspension of lithium aluminum hydride (4.10 g, 106 mmol) in anhydrous THF (100 mL) at 0 0C. The mixture was then warmed to room temperature. After being stirred at room temperature for 1 hour, the reaction mixture was cooled to 0 0C and treated with water (4.1 g), followed by sodium hydroxide (10% aqueous solution, 4.1 mL). The resulting slurry was filtered and washed with THF. The combined filtrate was evaporated to dryness and the residue was purified by silica gel column chromatography to give (2,2-difluoro-benzo[l,3]dioxol-5-yl)- methanol (7.2 g, 38 mmol, 76 % over two steps) as a colorless oil.
Figure imgf000120_0001
[00284] 5-Chloromethyl-2,2-difluoro-benzo[l,3]dioxole
[00285] Thionyl chloride (45 g, 38 mmol) was slowly added to a solution of (2,2-difluoro- benzo[l,3]dioxol-5-yl)-methanol (7.2 g, 38 mmol) in dichloromethane (200 mL) at 0 0C. The resulting mixture was stirred overnight at room temperature and then evaporated to dryness. The residue was partitioned between an aqueous solution of saturated sodium bicarbonate (100 mL) and dichloromethane (100 mL). The separated aqueous layer was extracted with dichloromethane (150 mL) and the organic layer was dried over sodium sulfate, filtrated, and evaporated to dryness to give crude 5-chloromethyl-2,2-difluoro-benzo[l,3]dioxole (4.4 g) which was used directly in the next step.
Figure imgf000120_0002
[00286] (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile
[00287] A mixture of crude 5-chloromethyl-2,2-difluoro-benzo[l,3]dioxole (4.4 g) and sodium cyanide (1.36 g, 27.8 mmol) in dimethylsulfoxide (50 mL) was stirred at room temperature overnight. The reaction mixture was poured into ice and extracted with ethyl acetate (300 mL). The organic layer was dried over sodium sulfate and evaporated to dryness to give crude (2,2-difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile (3.3 g) which was used directly in the next step.
Figure imgf000121_0001
[00288] l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile
[00289] Sodium hydroxide (50% aqueous solution, 10 mL) was slowly added to a mixture of crude (2,2-difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile, benzyltriethylammonium chloride (3.00 g, 15.3 mmol), and l-bromo-2-chloroethane (4.9 g, 38 mmol) at 70 0C.
[00290] The mixture was stirred overnight at 70 0C before the reaction mixture was diluted with water (30 mL) and extracted with ethyl acetate. The combined organic layers were dried over sodium sulfate and evaporated to dryness to give crude l-(2,2-difluoro- benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile, which was used directly in the next step.
Figure imgf000121_0002
[00291] l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid
[00292] l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile (crude from the last step) was refluxed in 10% aqueous sodium hydroxide (50 mL) for 2.5 hours. The cooled reaction mixture was washed with ether (100 mL) and the aqueous phase was acidified to pH 2 with 2M hydrochloric acid. The precipitated solid was filtered to give l-(2,2-difluoro- benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid as a white solid (0.15 g, 1.6% over four steps). ESI-MS m/z calc. 242.04, found 241.58 (M+l)+; 1H NMR (CDCl3) δ 7.14-7.04 (m, 2H), 6.98-6.96 (m, IH), 1.74-1.64 (m, 2H), 1.26-1.08 (m, 2H).
[00293] Example 3: 2-(2,2-Dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile
2-dιmethoxy-propane p-TsOH toluene
Figure imgf000121_0003
Figure imgf000121_0004
Figure imgf000121_0005
[00294] (3,4-Dihydroxy-phenyl)-acetonitrile
[00295] To a solution of benzo[l,3]dioxol-5-yl-acetonitrile (0.50 g, 3.1 mmol) in CH2Cl2 (15 mL) was added dropwise BBr3 (0.78 g, 3.1 mmol) at -78 0C under N2. The mixture was slowly warmed to room temperature and stirred overnight. H2O (10 mL) was added to quench the reaction and the CH2Cl2 layer was separated. The aqueous phase was extracted with CH2Cl2 (2 x 7 mL). The combined organics were washed with brine, dried over Na2SO4 and purified by column chromatography on silica gel (petroleum ether/ethyl acetate 5:1) to give (3,4-dihydroxy-phenyl)-acetonitrile (0.25 g, 54%) as a white solid. 1H NMR (DMSO-J6, 400 MHz) δ 9.07 (s, 1 H), 8.95 (s, 1 H), 6.68-6.70 (m, 2 H), 6.55 (dd, / = 8.0, 2.0 Hz, 1 H), 3.32 (s, 2 H). 2,2-dιmethoxy-propane p-TsOH, toluene
Figure imgf000122_0002
Figure imgf000122_0001
[00296] 2-(2,2-Dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile
[00297] To a solution of (3,4-dihydroxy-phenyl)-acetonitrile (0.20 g, 1.3 mmol) in toluene (4 mL) was added 2,2-dimethoxy-propane (0.28 g, 2.6 mmol) and TsOH (0.010 g, 0.065 mmol). The mixture was heated at reflux overnight. The reaction mixture was evaporated to remove the solvent and the residue was dissolved in ethyl acetate. The organic layer was washed with NaHCθ3 solution, H2O, brine, and dried over Na2SO4. The solvent was evaporated under reduced pressure to give a residue, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 10:1) to give 2-(2,2- dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile (40 mg, 20%). 1H NMR (CDCl3, 400 MHz) δ 6.68-6.71 (m, 3 H), 3.64 (s, 2 H), 1.67 (s, 6 H).
[00298] Example 4: l-(3,4-Dihydroxy-phenyl)-cyclopropanecarboxylic acid
Figure imgf000122_0003
[00299] l-(3,4-Bis-benzyloxy-phenyl)-cyclopropanecarbonitrile
[00300] To a mixture of (n-C4H9)4NBr (0.50 g, 1.5 mmol), toluene (7 mL) and (3,4-bis- benzyloxy-phenyl)-acetonitrile (14 g, 42 mmol) in NaOH (50 g) and H2O (50 mL) was added BrCH2CH2Cl (30 g, 0.21 mol). The reaction mixture was stirred at 50 0C for 5 h before being cooled to room temperature. Toluene (30 mL) was added and the organic layer was separated and washed with H2O, brine, dried over anhydrous MgSO4, and concentrated. The residue was purified by column on silica gel (petroleum ether/ethyl acetate 10:1) to give l-(3,4-bis- benzyloxy-phenyl)-cyclopropanecarbonitrile (10 g, 66%). 1H NMR (DMSO 300 MHz) δ 7.46-7.30 (m, 10 H), 7.03 (d, J = 8.4 Hz, 1 H), 6.94 (d, J = 2.4 Hz, 1 H), 6.89 (dd, J = 2.4, 8.4 Hz, I H), 5.12 (d, / = 7.5 Hz, 4H), 1.66-1.62 (m, 2 H), 1.42-1.37 (m, 2 H).
Figure imgf000123_0001
[00301] l-(3,4-Dihydroxy-phenyl)-cyclopropanecarbonitrile
[00302] To a solution of l-(3,4-bis-benzyloxy-phenyl)-cyclopropanecarbonitrile (10 g, 28 mmol) in MeOH (50 mL) was added Pd/C (0.5 g) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature for 4 h. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum to give 1- (3,4-dihydroxy-phenyl)-cyclopropanecarbonitrile (4.5 g, 92%). 1H NMR (DMSO 400 MHz) δ 9.06 (br s, 2 H), 6.67-6.71 (m, 2 H), 6.54 (dd, J = 2.4, 8.4 Hz, 1 H), 1.60-1.57 (m, 2 H), 1.30-1.27 (m, 2 H).
Figure imgf000123_0002
[00303] l-(3,4-Dihydroxy-phenyl)-cyclopropanecarboxylic acid
[00304] To a solution of NaOH (20 g, 0.50 mol) in H2O (20 mL) was added l-(3,4- dihydroxy-phenyl)-cyclopropanecarbonitrile (4.4 g, 25 mmol). The mixture was heated at reflux for 3 h before being cooled to room temperature. The mixture was neutralized with HCl (0.5 N) to pH 3-4 and extracted with ethyl acetate (20 mL x 3). The combined organic layers were washed with water, brine, dried over anhydrous MgSO4, and concentrated under vacuum to obtain l-(3,4-dihydroxy-phenyl)-cyclopropanecarboxylic acid (4.5 g crude). From 900 mg crude, 500 mg pure l-(3,4-dihydroxy-phenyl)-cyclopropanecarboxylic acid was obtained by preparatory HPLC. 1H NMR (DMSO, 300 MHz) δ 12.09 (br s, 1 H), 8.75 (br s, 2 H), 6.50-6.67 (m, 3 H), 1.35-1.31 (m, 2 H), 1.01-0.97 (m, 2 H).
[00305] Example 5: l-(2-Oxo-2,3-dihydrobenzo[d]oxazol-5-yl)cyclopropane- carboxylic acid.
Figure imgf000124_0001
Ni/H, triphosgene
Figure imgf000124_0003
Figure imgf000124_0004
Figure imgf000124_0002
Figure imgf000124_0005
[00306] l-(4-Methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00307] To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid (50 g, 0.26 mol) in MeOH (500 mL) was added toluene-4-sulfonic acid monohydrate (2.5 g, 13 mmol) at room temperature. The reaction mixture was heated at reflux for 20 hours. MeOH was removed by evaporation under vacuum and EtOAc (200 mL) was added. The organic layer was washed with sat. aq. NaHCO3 (100 mL) and brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (53 g, 99%). 1H NMR (CDCl3, 400 MHz) δ 7.25-7.27 (m, 2 H), 6.85 (d, J = 8.8 Hz, 2 H), 3.80 (s, 3 H), 3.62 (s, 3 H), 1.58 (q, / = 3.6 Hz, 2 H), 1.15 (q, / = 3.6 Hz, 2 H).
Figure imgf000124_0006
[00308] l-(4-Methoxy-3-nitro-phenyl)-cyclopropanecarboxylic acid methyl ester
[00309] To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (30.0 g, 146 mmol) in Ac2O (300 mL) was added a solution of HNO3 (14.1 g, 146 mmol, 65%) in AcOH (75 mL) at 0 0C. The reaction mixture was stirred at 0 ~ 5 0C for 3 h before aq. HCl (20%) was added dropwise at 0 0C. The resulting mixture was extracted with EtOAc (200 mL x 3). The organic layer was washed with sat. aq. NaHCO3 then brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(4-methoxy-3-nitro-phenyl)- cyclopropanecarboxylic acid methyl ester (36.0 g, 98%), which was directly used in the next step. 1H NMR (CDCl3, 300 MHz) δ 7.84 (d, / = 2.1 Hz, 1 H), 7.54 (dd, / = 2.1, 8.7 Hz, 1 H),
7.05 (d, J = 8.7 Hz, 1 H), 3.97 (s, 3 H), 3.65 (s, 3 H), 1.68-1.64 (m, 2 H), 1.22-1.18 (m, 2 H).
Figure imgf000125_0001
[00310] l-(4-Hydroxy-3-nitro-phenyl)-cyclopropanecarboxylic acid methyl ester
[00311] To a solution of l-(4-methoxy-3-nitro-phenyl)-cyclopropane-carboxylic acid methyl ester (10.0 g, 39.8 mmol) in CH2Cl2 (100 mL) was added BBr3 (12.0 g, 47.8 mmol) at -70 0C. The mixture was stirred at -70 0C for 1 hour, then allowed to warm to -30 0C and stirred at this temperature for 3 hours. Water (50 mL) was added dropwise at -20 0C, and the resulting mixture was allowed to warm room temperature before it was extracted with EtOAc (200 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 15:1) to afford l-(4-hydroxy-3- nitro-phenyl)-cyclopropanecarboxylic acid methyl ester (8.3 g, 78%). 1H NMR (CDCl3, 400 MHz) δ 10.5 (s, 1 H), 8.05 (d, / = 2.4 Hz, 1 H), 7.59 (dd, / = 2.0, 8.8 Hz, 1 H), 7.11 (d, / = 8.4 Hz, 1 H), 3.64 (s, 3 H), 1.68-1.64 (m, 2 H), 1.20-1.15 (m, 2 H).
Figure imgf000125_0002
[00312] l-(3-Amino-4-hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00313] To a solution of l-(4-hydroxy-3-nitro-phenyl)-cyclopropanecarboxylic acid methyl ester (8.3 g, 35 mmol) in MeOH (100 mL) was added Raney Nickel (0.8 g) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at 35 0C for 8 hours. The catalyst was filtered off through a Celite pad and the filtrate was evaporated under vacuum to give crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 1:1) to give l-(3-amino-4-hydroxy-phenyl)- cyclopropanecarboxylic acid methyl ester (5.3 g, 74%). 1H NMR (CDCl3, 400 MHz) δ 6.77 (s, 1 H), 6.64 (d, / = 2.0 Hz, 2 H), 3.64 (s, 3 H), 1.55-1.52 (m, 2 H), 1.15-1.12 (m, 2 H).
Figure imgf000125_0003
[00314] l-(2-Oxo-2,3-dihydro-benzooxazol-5-yl)-cyclopropanecarboxylic acid methyl ester
[00315] To a solution of l-(3-amino-4-hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester (2.0 g, 9.6 mmol) in THF (40 mL) was added triphosgene (4.2 g, 14 mmol) at room temperature. The mixture was stirred for 20 minutes at this temperature before water (20 mL) was added dropwise at 0 0C. The resulting mixture was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(2-oxo-2,3-dihydro-benzooxazol-5-yl)-cyclopropanecarboxylic acid methyl ester (2.0 g, 91%), which was directly used in the next step. 1H NMR (CDCl3, 300 MHz) δ 8.66 (s, 1 H), 7.13-7.12 (m, 2 H), 7.07 (s, 1 H), 3.66 (s, 3 H), 1.68-1.65 (m, 2 H), 1.24-1.20 (m, 2 H).
Figure imgf000126_0001
[00316] l-(2-Oxo-2,3-dihydrobenzo[d]oxazol-5-yl)cyclopropanecarboxylic acid
[00317] To a solution of l-(2-oxo-2,3-dihydro-benzooxazol-5-yl)-cyclopropanecarboxylic acid methyl ester (1.9 g, 8.1 mmol) in MeOH (20 mL) and water (2 mL) was added LiOH.H2O (1.7 g, 41 mmol) in portions at room temperature. The reaction mixture was stirred for 20 hours at 50 0C. MeOH was removed by evaporation under vacuum before water (100 mL) and EtOAc (50 mL) were added. The aqueous layer was separated, acidified with HCl (3 mol/L) and extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(2-oxo-2,3- dihydrobenzo[d]oxazol-5-yl)cyclopropanecarboxylic acid (1.5 g, 84%). 1H NMR (DMSO1 400 MHz) δ 12.32 (brs, 1 H), 11.59 (brs, 1 H), 7.16 (d, / = 8.4 Hz, 1 H), 7.00 (d, / = 8.0 Hz, 1 H), 1.44-1.41 (m, 2 H), 1.13-1.10 (m, 2 H). MS (ESI) m/e (M+H+) 218.1.
[00318] Example 6: l-(6-Fluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid
Figure imgf000126_0002
Figure imgf000127_0001
[00319] 2-Fluoro-4,5-dihydroxy-benzaldehyde
[00320] To a stirred suspension of 2-fluoro-4,5-dimethoxy-benzaldehyde (3.00 g, 16.3 mmol) in dichloromethane (100 mL) was added BBr3 (12.2 mL, 130 mmol) dropwise at -78 0C under nitrogen atmosphere. After addition, the mixture was warmed to -30 0C and stirred at this temperature for 5 h. The reaction mixture was poured into ice water and the precipitated solid was collected by filtration and washed with dichloromethane to afford 2- fluoro-4,5-dihydroxy-benzaldehyde (8.0 g), which was used directly in the next step.
Figure imgf000127_0002
[00321] 6-Fluoro-benzo[l,3]dioxole-5-carbaldehyde To a stirred solution of 2-fluoro- 4,5-dihydroxy-benzaldehyde (8.0 g) and BrClCH2 (24.8 g, 190 mmol) in dry DMF (50 mL) was added Cs2CO3 (62.0 g, 190 mmol) in portions. The resulting mixture was stirred at 60 0C overnight and then poured into water. The mixture was extracted with EtOAc (200 mL x 3). The combined organic layers were washed with brine (200 mL), dried over Na2SO4, and evaporated in vacuo to give crude product, which was purified by column chromatography on silica gel (5-20% ethyl acetate/petroleum ether) to afford 6-fluoro-benzo[l,3]dioxole-5- carbaldehyde (700 mg, two steps yield: 24%). 1H-NMR (400 MHz, CDCl3) δ 10.19 (s, 1 H), 7.23 (d, / = 5.6, 1 H), 6.63 (d, / = 9.6, 1 H), 6.08 (s, 2 H).
Figure imgf000127_0003
[00322] (6-Fluoro-benzo[l,3]dioxol-5-yl)-methanol
[00323] To a stirred solution of 6-fluoro-benzo[l,3]dioxole-5-carbaldehyde (700 mg, 4.2 mmol) in MeOH (50 mL) was added NaBH4 (320 mg, 8.4 mmol) in portions at 0 0C. The mixture was stirred at this temperature for 30 min and was then concentrated in vacuo to give a residue. The residue was dissolved in EtOAc and the organic layer was washed with water, dried over Na2SO4, and concentrated in vacuo to afford (6-fluoro-benzo[l,3]dioxol-5-yl)- methanol (650 mg, 92%), which was directly used in the next step.
Figure imgf000128_0001
[00324] 5-Chloromethyl-6-fluoro-benzo[l,3]dioxole
[00325] (6-Fluoro-benzo[l,3]dioxol-5-yl)-methanol (650 mg, 3.8 mmol) was added to SOCl2 (20 mL) in portions at 0 0C. The mixture was warmed to room temperature for 1 h and then heated at reflux for 1 h. The excess SOCl2 was evaporated under reduced pressure to give the crude product, which was basified with sat. NaHCC>3 solution to pH ~ 7. The aqueous phase was extracted with EtOAc (50 mL x 3). The combined organic layers were dried over Na2SO4 and evaporated under reduced pressure to give 5-chloromethyl-6-fluoro- benzo[l,3]dioxole (640 mg, 90%), which was directly used in the next step.
Figure imgf000128_0002
[00326] (6-Fluoro-benzo[l,3]dioxol-5-yl)-acetonitrile
[00327] A mixture of 5-chloromethyl-6-fluoro-benzo[l,3]dioxole (640 mg, 3.4 mmol) and NaCN (340 mg, 6.8 mmol) in DMSO (20 mL) was stirred at 30 0C for 1 h and then poured into water. The mixture was extracted with EtOAc (50 mL x 3). The combined organic layers were washed with water (50 mL) and brine (50 mL), dried over Na2SO4, and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (5-10% ethyl acetate/petroleum ether) to afford (6-fluoro- benzo[l,3]dioxol-5-yl)-acetonitrile (530 mg, 70%). 1H-NMR (300 MHz, CDCl3) δ 6.82 (J, J = 4.8, 1 Hj. 6.62 (d. / = 5.4, 1 H), 5 Ψ> (s, 2 Hj, 3.65 (s, 2 H),
Figure imgf000128_0003
[00328] l-(6-Fluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile
[00329] A flask was charged with water (10 mL), followed by a rapid addition of NaOH (10 g, 0.25 mol) in three portions over a 5 min period. The mixture was allowed to cool to room temperature. Subsequently, the flask was charged with toluene (6 mL), tetrabutyl- ammonium bromide (50 mg, 0.12 mmol), (6-fluoro-benzo[l,3]dioxol-5-yl)-acetonitrile (600 mg, 3.4 mmol) and l-bromo-2-chloroethane (1.7 g, 12 mmol). The mixture stirred vigorously at 50 0C overnight. The cooled flask was charged with additional toluene (20 mL). The organic layer was separated and washed with water (30 mL) and brine (30 mL). The organic layer was removed in vacuo to give the crude product, which was purified by column chromatography on silica gel (5-10% ethyl acetate/petroleum ether) to give l-(6- fluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile (400 mg, 60%). 1H NMR (300 MHz, CDCl3) δ 6.73 (d, / = 3.0 Hz, 1 H), 6.61 (d, / = 9.3 Hz, 1 H), 5.98 (s, 2 H), 1.67-1.62 (m, 2 H), 1.31-1.27 (m, 2 H).
Figure imgf000129_0001
[00330] l-(6-Fluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid
[00331] A mixture of l-^-fluoro-benzofl^ldioxol-S-y^-cyclopropanecarbonitrile (400 mg, 0.196 mmol) and 10% NaOH (10 mL) was stirred at 100 0C overnight. After the reaction was cooled, 5% HCl was added until the pH < 5 and then EtOAc (30 mL) was added to the reaction mixture. The layers were separated and combined organic layers were evaporated in vacuo to afford l-(6-fluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid (330 mg, 76%). 1H NMR (400 MHz, DMSO) δ 12.2 (s, 1 H), 6.87-6.85 (m, 2 H), 6.00 (s, 1 H), 1.42-1.40 (m, 2 H), 1.14-1.07 (m, 2 H).
[00332] Example 7: l-(Benzofuran-5-yl)cyclopropanecarboxylic acid
Figure imgf000129_0002
PPA, xylene
Figure imgf000129_0003
Figure imgf000129_0004
[00333] l-[4-(2,2-Diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid
[00334] To a stirred solution of l-(4-hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester (15.0 g, 84.3 mmol) in DMF (50 mL) was added sodium hydride (6.7 g, 170 mmol, 60% in mineral oil) at 0 0C. After hydrogen evolution ceased, 2-bromo-l,l-diethoxy-ethane (16.5 g, 84.3 mmol) was added dropwise to the reaction mixture. The reaction was stirred at 160 0C for 15 hours. The reaction mixture was poured onto ice (100 g) and was extracted with CH2Cl2. The combined organics were dried over Na2SO4. The solvent was evaporated under vacuum to give l-[4-(2,2-diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid (10 g), which was used directly in the next step without purification.
PPA, xylene
Figure imgf000130_0001
Figure imgf000130_0002
[00335] l-Benzofuran-5-yl-cyclopropanecarboxylic acid
[00336] To a suspension of l-[4-(2,2-diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid (20 g, -65 mmol) in xylene (100 mL) was added PPA (22.2 g, 64.9 mmol) at room temperature. The mixture was heated at reflux (140 0C) for 1 hour before it was cooled to room temperature and decanted from the PPA. The solvent was evaporated under vacuum to obtain the crude product, which was purified by preparative HPLC to provide l-(benzofuran- 5-yl)cyclopropanecarboxylic acid (1.5 g, 5%). 1H NMR (400 MHz, DMSO-J6) δ 12.25 (br s, 1 H), 7.95 (d, / = 2.8 Hz, 1 H), 7.56 (d, / = 2.0 Hz, 1 H), 7.47 (d, / = 11.6 Hz, 1 H), 7.25 (dd, / = 2.4, 11.2 Hz, I H), 6.89 (d, / = 1.6 Hz, I H), 1.47-1.44 (m, 2 H), 1.17-1.14 (m, 2 H).
[00337] Example 8: l-(2,3-Dihydrobenzofuran-6-yl)cyclopropanecarboxylic acid
Figure imgf000130_0003
[00338] To a solution of l-(benzofuran-6-yl)cyclopropanecarboxylic acid (370 mg, 1.8 mmol) in MeOH (50 mL) was added PtO2 (75 mg, 20%) at room temperature. The reaction mixture was stirred under hydrogen atmosphere (1 atm) at 20 0C for 3 d. The reaction mixture was filtered and the solvent was evaporated in vacuo to afford the crude product, which was purified by prepared HPLC to give l-(2,3-dihydrobenzofuran-6- yl)cyclopropanecarboxylic acid (155 mg, 42%). 1H NMR (300 MHz, MeOD) δ 7.13 (d, J = 7.5 Hz, 1 H), 6.83 (d, J = 7.8 Hz, 1 H), 6.74 (s, 1 H), 4.55 (t, J = 8.7 Hz, 2 H), 3.18 (t, / = 8.7 Hz, 2 H), 1.56-1.53 (m, 2 H), 1.19-1.15 (m, 2 H).
[00339] Example 9: l-(3,3-Dimethyl-2,3-dihydrobenzofuran-5- yl)cyclopropanecarboxylic acid.
Figure imgf000131_0001
[00340] l-(4-Hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00341] To a solution of methyl l-(4-methoxyphenyl)cyclopropanecarboxylate (10.0 g, 48.5 mmol) in dichloromethane (80 mL) was added EtSH (16 mL) under ice- water bath. The mixture was stirred at 0 0C for 20 min before AICI3 (19.5 g, 0.15 mmol) was added slowly at 0 0C. The mixture was stirred at 0 0C for 30 min. The reaction mixture was poured into ice- water, the organic layer was separated, and the aqueous phase was extracted with dichloromethane (50 mL x 3). The combined organic layers were washed with H2O, brine, dried over Na2SO4 and evaporated under vacuum to give l-(4-hydroxy-phenyl)- cyclopropanecarboxylic acid methyl ester (8.9 g, 95%). 1H NMR (400 MHz, CDCl3) δ 7.20- 7.17 (m, 2 H), 6.75-6.72 (m, 2 H), 5.56 (s, 1 H), 3.63 (s, 3 H), 1.60-1.57 (m, 2 H), 1.17-1.15 (m, 2 H).
Figure imgf000131_0002
[00342] l-(4-Hydroxy-3,5-diiodo-phenyl)-cyclopropanecarboxylic acid methyl ester
[00343] To a solution of l-(4-hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester (8.9 g, 46 mmol) in CH3CN (80 mL) was added NIS (15.6 g, 69 mmol). The mixture was stirred at room temperature for 1 hour. The reaction mixture was concentrated and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 10:1) to give l-(4-hydroxy-3,5-diiodo-phenyl)-cyclopropanecarboxylic acid methyl ester (3.5 g, 18%). 1H NMR (400 MHz, CDCl3) δ 7.65 (s, 2 H), 5.71 (s, 1 H), 3.63 (s, 3 H), 1.59-1.56 (m, 2 H), 1.15-1.12 (m, 2 H).
Figure imgf000132_0001
[00344] l-[3,5-Diiodo-4-(2-methyl-allyloxy)-phenyl]-cyclopropanecarboxylic acid methyl ester
[00345] A mixture of l-(4-hydroxy-3,5-diiodo-phenyl)-cyclopropanecarboxylic acid methyl ester (3.2 g, 7.2 mmol), 3-chloro-2-methyl-propene (1.0 g, 11 mmol), K2CO3 (1.2 g, 8.6 mmol), NaI (0.1 g, 0.7 mmol) in acetone (20 mL) was stirred at 20 0C overnight. The solid was filtered off and the filtrate was concentrated under vacuum to give l-[3,5-diiodo-4- (2-methyl-allyloxy)-phenyl]-cyclopropane-carboxylic acid methyl ester (3.5 g, 97%). 1H NMR (300 MHz, CDCl3) δ 7.75 (s, 2 H), 5.26 (s, 1 H), 5.06 (s, 1 H), 4.38 (s, 2 H), 3.65 (s, 3 H), 1.98 (s, 3H), 1.62-1.58 (m, 2 H), 1.18-1.15 (m, 2 H).
Figure imgf000132_0002
[00346] l-(3,3-Dimethyl-2,3-dihydro-benzofuran-5-yl)-cyclopropanecarboxylic acid methyl ester
[00347] To a solution of l-[3,5-diiodo-4-(2-methyl-allyloxy)-phenyl]-cyclopropane- carboxylic acid methyl ester (3.5 g, 7.0 mmol) in toluene (15 mL) was added Bu3SnH (2.4 g, 8.4 mmol) and AIBN (0.1 g, 0.7 mmol). The mixture was heated at reflux overnight. The reaction mixture was concentrated under vacuum and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1) to give l-(3,3-dimethyl- 2,3-dihydro-benzofuran-5-yl)-cyclopropanecarboxylic acid methyl ester (1.05 g, 62%). 1H NMR (400 MHz, CDCl3) δ 7.10-7.07 (m, 2 H), 6.71 (d, / = 8 Hz, 1 H), 4.23 (s, 2 H), 3.62 (s, 3 H), 1.58-1.54 (m, 2 H), 1.34 (s, 6 H), 1.17-1.12 (m, 2 H).
Figure imgf000132_0003
[00348] l-(3,3-Dimethyl-2,3-dihydrobenzofuran-5-yl)cyclopropanecarboxylic acid
[00349] To a solution of l-(3,3-dimethyl-2,3-dihydro-benzofuran-5-yl)- cyclopropanecarboxylic acid methyl ester (1.0 g, 4.0 mmol) in MeOH (10 mL) was added LiOH (0.40 g, 9.5 mmol). The mixture was stirred at 40 0C overnight. HCl (10%) was added slowly to adjust the pH to 5. The resulting mixture was extracted with ethyl acetate (10 mL x 3). The extracts were washed with brine and dried over Na2SO4. The solvent was removed under vaccum and the crude product was purified by preparative HPLC to give l-(3,3- dimethyl-2,3-dihydrobenzofuran-5-yl)cyclopropanecarboxylic acid (0.37 g, 41%). 1H NMR (400 MHz, CDCl3) δ 7.11-7.07 (m, 2 H), 6.71 (d, / = 8 Hz, 1 H), 4.23 (s, 2 H), 1.66-1.63 (m, 2 H), 1.32 (s, 6 H), 1.26-1.23 (m, 2 H).
[00350] Example 10: 2-(7-Methoxybenzo[d][l,3]dioxol-5-yl)acetonitrile.
LiAIH4
Figure imgf000133_0001
[00351] 3,4-Dihydroxy-5-methoxybenzoate
[00352] To a solution of 3,4,5-trihydroxy-benzoic acid methyl ester (50 g, 0.27 mol) and Na2B4O7 (50 g) in water (1000 niL) was added Me2SO4 (120 niL) and aqueous NaOH solution (25%, 200 mL) successively at room temperature. The mixture was stirred at room temperature for 6 h before it was cooled to 0 0C. The mixture was acidified to pH ~ 2 by adding cone. H2SO4 and then filtered. The filtrate was extracted with EtOAc (500 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give methyl 3,4-dihydroxy-5-methoxybenzoate (15.3 g 47%), which was used in the next step without further purification.
Figure imgf000133_0002
[00353] Methyl 7-methoxybenzo[d][l,3]dioxole-5-carboxylate
[00354] To a solution of methyl 3,4-dihydroxy-5-methoxybenzoate (15.3 g, 0.0780 mol) in acetone (500 mL) was added CH2BrCl (34.4 g, 0.270 mol) and K2CO3 (75.0 g, 0.540 mol) at 80 0C. The resulting mixture was heated at reflux for 4 h. The mixture was cooled to room temperature and solid K2CO3 was filtered off. The filtrate was concentrated under reduced pressure, and the residue was dissolved in EtOAc (100 mL). The organic layer was washed with water, dried over anhydrous Na2SO4, and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10:1) to afford methyl 7-methoxybenzo[d][l,3]dioxole-5-carboxylate (12.6 g, 80%). 1H NMR (400 MHz, CDCl3) δ 7.32 (s, 1 H), 7.21 (s, 1 H), 6.05 (s, 2 H), 3.93 (s, 3 H), 3.88 (s, 3 H).
Figure imgf000134_0001
[00355] (7-Methoxybenzo[d][l,3]dioxol-5-yl)methanol
[00356] To a solution of methyl 7-methoxybenzo[d][l,3]dioxole-5-carboxylate (14 g, 0.040 mol) in THF (100 mL) was added LiAlH4 (3.1 g, 0.080 mol) in portions at room temperature. The mixture was stirred for 3 h at room temperature. The reaction mixture was cooled to 0 0C and treated with water (3.1 g) and NaOH (10%, 3.1 mL) successively. The slurry was filtered off and washed with THF. The combined filtrates were evaporated under reduced pressure to give (7-methoxy-benzo[d][l,3]dioxol-5-yl)methanol (7.2 g, 52%). 1H NMR (400 MHz, CDCl3) δ 6.55 (s, IH), 6.54 (s, IH), 5.96 (s, 2 H), 4.57 (s, 2 H), 3.90 (s, 3 H).
Figure imgf000134_0002
[00357] 6-(Chloromethyl)-4-methoxybenzo[d][l,3]dioxole
[00358] To a solution of SOCl2 (150 mL) was added (7-methoxybenzo[d][l,3]dioxol-5- yl)methanol (9.0 g, 54 mmol) in portions at 0 0C. The mixture was stirred for 0.5 h. The excess SOCl2 was evaporated under reduced pressure to give the crude product, which was basified with sat. aq. NaHCO3 to pH ~ 7 The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated to give 6-(chloromethyl)-4-methoxybenzo[d][l,3]dioxole (10 g 94%), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 6.58 (s, 1 H), 6.57 (s, 1 H), 5.98 (s, 2 H), 4.51 (s, 2 H), 3.90 (s, 3 H).
Figure imgf000135_0001
[00359] 2-(7-Methoxybenzo[d][l,3]dioxol-5-yl)acetonitrile
[00360] To a solution of 6-(chloromethyl)-4-methoxybenzo[d][l,3]dioxole (10 g, 40 mmol) in DMSO (100 mL) was added NaCN (2.4 g, 50 mmol) at room temperature. The mixture was stirred for 3 h and poured into water (500 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated to give the crude product, which was washed with ether to afford 2-(J- methoxybenzo[d][l,3]dioxol-5-yl)acetonitrile (4.6 g, 45%). 1H NMR (400 MHz, CDCl3) δ 6.49 (s, 2 H), 5.98 (s, 2 H), 3.91 (s, 3 H), 3.65 (s, 2 H). 13C NMR (400 MHz, CDCl3) δ 148.9, 143.4, 134.6, 123.4, 117.3, 107.2, 101.8, 101.3, 56.3, 23.1.
[00361] Example 11: 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitrile.
Figure imgf000135_0002
[00362] To a suspension of t-BuOK (20.2 g, 0.165 mol) in THF (250 mL) was added a solution of TosMIC (16.1 g, 82.6 mmol) in THF (100 mL) at -78 0C. The mixture was stirred for 15 minutes, treated with a solution of 3-benzyloxy-4-methoxy-benzaldehyde (10.0 g, 51.9 mmol) in THF (50 mL) dropwise, and continued to stir for 1.5 hours at -78 °C. To the cooled reaction mixture was added methanol (50 mL). The mixture was heated at reflux for 30 minutes. Solvent was removed to give a crude product, which was dissolved in water (300 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (petroleum ether/ethyl acetate 10:1) to afford 2-(3-(benzyloxy)-4-methoxyphenyl)- acetonitrile (5.0 g, 48%). 1H NMR (300 MHz, CDCl3) δ 7.48-7.33 (m, 5 H), 6.89-6.86 (m, 3 H), 5.17 (s, 2 H), 3.90 (s, 3 H), 3.66 (s, 2 H). 13C NMR (75 MHz, CDCl3) δ 149.6, 148.6, 136.8, 128.8, 128.8, 128.2, 127.5, 127.5, 122.1, 120.9, 118.2, 113.8, 112.2, 71.2, 56.2, 23.3.
[00363] Example 12: 2-(3-(Benzyloxy)-4-chlorophenyl)acetonitrile.
Figure imgf000136_0001
Figure imgf000136_0002
[00364] (4-Chloro-3-hydroxy-phenyl)acetonitrile
[00365] BBr3 (17 g, 66 mmol) was slowly added to a solution of 2-(4-chloro-3- methoxyphenyl)acetonitrile (12 g, 66 mmol) in dichloromethane (120 mL) at -78 0C under N2. The reaction temperature was slowly increased to room temperature. The reaction mixture was stirred overnight and then poured into ice and water. The organic layer was separated, and the aqueous layer was extracted with dichloromethane (40 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4, and concentrated under vacuum to give (4-chloro-3-hydroxy-phenyl)-acetonitrile (9.3 g, 85%). 1H NMR (300 MHz, CDCl3) δ 7.34 (d, J = 8.4 Hz, 1 H), 7.02 (d, J = 2.1 Hz, 1 H), 6.87 (dd, J = 2.1, 8.4 Hz, 1 H), 5.15 (brs, IH), 3.72 (s, 2 H).
Figure imgf000136_0003
[00366] 2-(3-(Benzyloxy)-4-chlorophenyl)acetonitrile
[00367] To a solution of (4-chloro-3-hydroxy-phenyl)acetonitrile (6.2 g, 37 mmol) in CH3CN (80 mL) was added K2CO3 (10 g, 74 mmol) and BnBr (7.6 g, 44 mmol). The mixture was stirred at room temperature overnight. The solids were filtered off and the filtrate was evaporated under vacuum. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 50: 1) to give 2-(3-(benzyloxy)-4-chlorophenyl)- acetonitrile (5.6 g, 60%). 1H NMR (400 MHz, CDCl3) δ 7.48-7.32 (m, 6 H), 6.94 (d, J = 2 Hz, 2 H), 6.86 (dd, J = 2.0, 8.4 Hz, 1 H), 5.18 (s, 2 H), 3.71 (s, 2 H).
[00368] Example 13: 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitrile.
Figure imgf000136_0004
[00369] To a suspension of t-BuOK (20.2 g, 0.165 mol) in THF (250 mL) was added a solution of TosMIC (16.1 g, 82.6 mmol) in THF (100 mL) at -78 0C. The mixture was stirred for 15 minutes, treated with a solution of 3-benzyloxy-4-methoxy-benzaldehyde (10.0 g, 51.9 mmol ) in THF (50 mL) dropwise, and continued to stir for 1.5 hours at -78 °C. To the cooled reaction mixture was added methanol (50 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (300 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (petroleum ether/ethyl acetate 10:1) to afford 2-(3-(benzyloxy)-4-methoxyphenyl)acetonitril (5.0 g, 48%). 1H NMR (300 MHz, CDCl3) δ 7.48-7.33 (m, 5 H), 6.89-6.86 (m, 3 H), 5.17 (s, 2 H), 3.90 (s, 3 H), 3.66 (s, 2 H). 13C NMR (75 MHz, CDCl3) δ 149.6, 148.6, 136.8, 128.8, 128.8, 128.2, 127.5, 127.5, 122.1, 120.9, 118.2, 113.8, 112.2, 71.2, 56.2, 23.3.
[00370] Example 14: 2-(3-Chloro-4-methoxyphenyl)acetonitrile.
Figure imgf000137_0001
[00371] To a suspension of t-BuOK (4.8 g, 40 mmol) in THF (30 mL) was added a solution of TosMIC (3.9 g, 20 mmol) in THF (10 mL) at -78 0C. The mixture was stirred for 10 minutes, treated with a solution of 3-chloro-4-methoxy-benzaldehyde (1.7 g, 10 mmol ) in THF (10 mL) dropwise, and continued to stir for 1.5 hours at -78 0C. To the cooled reaction mixture was added methanol (10 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (20 mL). The aqueous phase was extracted with EtOAc (20 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (petroleum ether/ethyl acetate 10:1) to afford 2-(3-chloro-4-methoxyphenyl)acetonitrile (1.5 g, 83%). 1H NMR (400 MHz, CDCl3) δ 7.33 (d, / = 2.4 Hz, 1 H), 7.20 (dd, / = 2.4, 8.4 Hz, 1 H), 6.92 (d, / = 8.4 Hz, 1 H), 3.91 (s, 3 H), 3.68 (s, 2 H). 13C NMR (100 MHz, CDCl3) δ 154.8, 129.8, 127.3, 123.0, 122.7, 117.60, 112.4, 56.2, 22.4.
[00372] Example 15: 2-(3-Fluoro-4-methoxyphenyl)acetonitrile.
Figure imgf000138_0001
[00373] To a suspension of t-BuOK (25.3 g, 0.207 mol) in THF (150 niL) was added a solution of TosMIC (20.3 g, 0.104 mol) in THF (50 niL) at -78 0C. The mixture was stirred for 15 minutes, treated with a solution of 3-fluoro-4-methoxy-benzaldehyde (8.00 g, 51.9 mmol) in THF (50 mL) drop wise, and continued to stir for 1.5 hours at -78 0C. To the cooled reaction mixture was added methanol (50 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (200 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (petroleum ether/ethyl acetate 10: 1) to afford 2-(3-fluoro-4-methoxyphenyl)acetonitrile (5.0 g, 58%). 1H NMR (400 MHz, CDCl3) δ 7.02-7.05 (m, 2 H), 6.94 (t, / = 8.4 Hz, 1 H), 3.88 (s, 3 H), 3.67 (s, 2 H). 13C NMR (100 MHz, CDCl3) δ 152.3, 147.5, 123.7, 122.5, 117.7, 115.8, 113.8, 56.3, 22.6.
[00374] Example 16: 2-(4-Chloro-3-methoxyphenyl)acetonitrile.
Figure imgf000138_0002
[00375] Chloro-2-methoxy-4-methyl-benzene
[00376] To a solution of 2-chloro-5-methyl-phenol (93 g, 0.65 mol) in CH3CN (700 mL) was added CH3I (110 g, 0.78 mol) and K2CO3 (180 g, 1.3 mol). The mixture was stirred at 25 0C overnight. The solid was filtered off and the filtrate was evaporated under vacuum to give l-chloro-2-methoxy-4-methyl-benzene (90 g, 89%). 1H NMR (300 MHz, CDCl3) δ 7.22 (d, / = 7.8 Hz, 1 H), 6.74-6.69 (m, 2 H), 3.88 (s, 3 H), 2.33 (s, 3 H).
Figure imgf000138_0003
[00377] 4-Bromomethyl-l-chloro-2-methoxy-benzene
[00378] To a solution of l-chloro-2-methoxy-4-methyl-benzene (50 g, 0.32 mol) in CCl4 (350 niL) was added NBS (57 g, 0.32 mol) and AIBN (10 g, 60 mmol). The mixture was heated at reflux for 3 hours. The solvent was evaporated under vacuum and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 20: 1) to give 4-bromomethyl-l-chloro-2-methoxy-benzene (69 g, 92%). 1H NMR (400 MHz, CDCl3) δ 7.33-7.31 (m, 1 H), 6.95-6.91 (m, 2 H), 4.46 (s, 2 H), 3.92 (s, 3 H).
Figure imgf000139_0001
[00379] 2-(4-Chloro-3-methoxyphenyl)acetonitrile
[00380] To a solution of 4-bromomethyl-l-chloro-2-methoxy-benzene (68.5 g, 0.290 mol) in C2H5OH (90%, 500 niL) was added NaCN (28.5 g, 0.580 mol). The mixture was stirred at 60 0C overnight. Ethanol was evaporated and the residue was dissolved in H2O. The mixture was extracted with ethyl acetate (300 mL x 3). The combined organic layers were washed with brine, dried over Na2SO4 and purified by column chromatography on silica gel (petroleum ether/ethyl acetate 30:1) to give 2-(4-chloro-3-methoxyphenyl)acetonitrile (25 g, 48%). 1H NMR (400 MHz, CDCl3) δ 7.36 (d, / = 8 Hz, 1 H), 6.88-6.84 (m, 2 H), 3.92 (s, 3 H), 3.74 (s, 2 H). 13C NMR (100 MHz, CDCl3) δ 155.4, 130.8, 129.7, 122.4, 120.7, 117.5, 111.5, 56.2, 23.5.
[00381] Example 17: l-(3-(Hydroxymethyl)-4- methoxyphenyl)cyclopropanecarboxylic acid.
Na2CO3
Figure imgf000139_0002
Figure imgf000139_0003
[00382] l-(4-Methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00383] To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid (50 g, 0.26 mol) in MeOH (500 mL) was added toluene-4-sulfonic acid monohydrate (2.5 g, 13 mmol) at room temperature. The reaction mixture was heated at reflux for 20 hours. MeOH was removed by evaporation under vacuum and EtOAc (200 mL) was added. The organic layer was washed with sat. aq. NaHCθ3 (100 mL) and brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (53 g, 99%). 1H NMR (CDCl3, 400 MHz) δ 7.25-7.27 (m, 2 H), 6.85 (d, J = 8.8 Hz, 2 H), 3.80 (s, 3 H), 3.62 (s, 3 H), 1.58 (m, 2 H), 1.15 (m, 2 H).
Figure imgf000140_0001
[00384] l-(3-Chloromethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00385] To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (30.0 g, 146 mmol) and MOMCl (29.1 g, 364 mmol) in CS2 (300 mL) was added TiCl4 (8.30 g, 43.5 mmol) at 5 0C. The reaction mixture was heated at 30 0C for 1 d and poured into ice- water. The mixture was extracted with CH2Cl2 (150 mL x 3). The combined organic extracts were evaporated under vacuum to give l-(3-chloromethyl-4-methoxy-phenyl)- cyclopropanecarboxylic acid methyl ester (38.0 g), which was used in the next step without further purification.
Figure imgf000140_0002
[00386] l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
[00387] To a suspension of l-(3-chloromethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (20 g) in water (350 mL) was added Bu4NBr (4.0 g) and Na2CO3 (90 g, 0.85 mol) at room temperature. The reaction mixture was heated at 65 0C overnight. The resulting solution was acidified with aq. HCl (2 mol/L) and extracted with EtOAc (200 mL x 3). The organic layer was washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give crude product, which was purified by column (petroleum ether/ethyl acetate 15:1) to give l-(3-hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (8.0 g, 39%). 1H NMR (CDCl3, 400 MHz) δ 7.23-7.26 (m, 2 H), 6.83 (d, J = 8.0 Hz, 1 H), 4.67 (s, 2 H), 3.86 (s, 3 H), 3.62 (s, 3 H), 1.58 (q, / = 3.6 Hz, 2 H), 1.14-1.17 (m, 2 H).
Figure imgf000141_0001
[00388] l-fS-Cfer^Butyl-dimethyl-silanyloxymethyO-Φmethoxy-phenylJcyclopropane carboxylic acid methyl ester
[00389] To a solution of l-(3-hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (8.0 g, 34 mmol) in CH2Cl2 (100 mL) were added imidazole (5.8 g, 85 mmol) and TBSCl (7.6 g, 51 mmol) at room temperature. The mixture was stirred overnight at room temperature. The mixture was washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give crude product, which was purified by column (petroleum ether/ethyl acetate 30:1) to give l-[3-(^rf-butyl-dimethyl-silanyloxymethyl)-4-methoxy- phenylj-cyclopropanecarboxylic acid methyl ester (6.7 g, 56%). 1H NMR (CDC13> 400 MHz) δ 7.44-7.45 (m, 1 H), 7.19 (dd, / = 2.0, 8.4 Hz, 1 H), 6.76 (d, / = 8.4 Hz, 1 H), 4.75 (s, 2 H), 3.81 (s, 3 H), 3.62 (s, 3 H), 1.57-1.60 (m, 2 H), 1.15- 1.18 (m, 2 H), 0.96 (s, 9 H), 0.11 (s, 6 H).
Figure imgf000141_0002
[00390] l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid
[00391] To a solution of l-[3-(ter^butyl-dimethyl-silanyloxymethyl)-4-methoxy-phenyl]- cyclopropane carboxylic acid methyl ester (6.2 g, 18 mmol) in MeOH (75 mL) was added a solution of LiOH.H2O (1.5 g, 36 mmol) in water (10 mL) at 0 0C. The reaction mixture was stirred overnight at 40 0C. MeOH was removed by evaporation under vacuum. AcOH (1 mol/L, 40 mL) and EtOAc (200 mL) were added. The organic layer was separated, washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum to provide l-(3- hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid (5.3 g).
[00392] Example 18: 2-(7-Chlorobenzo[d][l,3]dioxol-5-yl)acetonitrile.
Figure imgf000142_0001
[00393] 3-Chloro-4,5-dihydroxybenzaldehyde
[00394] To a suspension of 3-chloro-4-hydroxy-5-methoxy-benzaldehyde (10 g, 54 mmol) in dichloromethane (300 mL) was added BBr3 (26.7 g, 107 mmol) dropwise at -40 °C under N2. After addition, the mixture was stirred at this temperature for 5 h and then was poured into ice water. The precipitated solid was filtered and washed with petroleum ether. The filtrate was evaporated under reduced pressure to afford 3-chloro-4,5-dihydroxybenzaldehyde (9.8 g, 89%), which was directly used in the next step.
Figure imgf000142_0002
[00395] 7-Chlorobenzo[d][l,3]dioxole-5-carbaldehyde
[00396] To a solution of 3-chloro-4,5-dihydroxybenzaldehyde (8.0 g, 46 mmol) and BrClCH2 (23.9 g, 185 mmol) in dry DMF (100 mL) was added Cs2CO3 (25 g, 190 mmol). The mixture was stirred at 60 0C overnight and was then poured into water. The resulting mixture was extracted with EtOAc (50 mL x 3). The combined extracts were washed with brine (100 mL), dried over Na2SO4 and concentrated under reduced pressure to afford 7- chlorobenzo[d][l,3]dioxole-5-carbaldehyde (6.0 g, 70%). 1H NMR (400 MHz, CDCl3) δ 9.74 (s, 1 H), 7.42 (d, / = 0.4 Hz, 1 H), 7.26 (d, / = 3.6 Hz, 1 H), 6.15 (s, 2 H).
Figure imgf000142_0003
[00397] (7-Chlorobenzo[d][l,3]dioxol-5-yl)methanol
[00398] To a solution of 7-chlorobenzo[d][l,3]dioxole-5-carbaldehyde (6.0 g, 33 mmol) in THF (50 niL) was added NaBH4 (2.5 g, 64 mmol) ) in portions at 0 0C. The mixture was stirred at this temperature for 30 min and then poured into aqueous NH4Cl solution. The organic layer was separated, and the aqueous phase was extracted with EtOAc (50 mL x 3). The combined extracts were dried over Na2SO4 and evaporated under reduced pressure to afford (7-chlorobenzo[d][l,3]dioxol-5-yl)methanol, which was directly used in the next step.
Figure imgf000143_0001
[00399] 4-Chloro-6-(chloromethyl)benzo[d][l,3]dioxole
[00400] A mixture of (7-chlorobenzo[d][l,3]-dioxol-5-yl)methanol (5.5 g, 30 mmol) and SOCl2 (5.0 mL, 67 mmol) in dichloromethane (20 mL) was stirred at room temperature for 1 h and was then poured into ice water. The organic layer was separated and the aqueous phase was extracted with dichloromethane (50 mL x 3). The combined extracts were washed with water and aqueous NaHCθ3 solution, dried over Na2SO4 and evaporated under reduced pressure to afford 4-chloro-6-(chloromethyl)benzo[d][l,3]dioxole, which was directly used in the next step.
Figure imgf000143_0002
[00401] 2-(7-Chlorobenzo[d][l,3]dioxol-5-yl)acetonitrile
[00402] A mixture of 4-chloro-6-(chloromethyl)benzo[d][l,3]dioxole (6.0 g, 29 mmol) and NaCN (1.6 g, 32 mmol) in DMSO (20 mL) was stirred at 40 0C for 1 h and was then poured into water. The mixture was extracted with EtOAc (30 mL x 3). The combined organic layers were washed with water and brine, dried over Na2SO4 and evaporated under reduced pressure to afford 2-(7-chlorobenzo[d][l,3]dioxol-5-yl)acetonitrile (3.4 g, 58%). 1H NMR δ 6.81 (s, 1 H), 6.71 (s, 1 H), 6.07 (s, 2 H), 3.64 (s, 2 H). 13 C-NMR 5149.2, 144.3, 124.4, 122.0, 117.4, 114.3, 107.0, 102.3, 23.1.
[00403] Example 19: l-(Benzo[d]oxazol-5-yl)cyclopropanecarboxylic acid. trimethyl orthoformate AICU
Figure imgf000144_0001
Figure imgf000144_0002
Figure imgf000144_0003
Figure imgf000144_0004
[00404] l-Benzooxazol-5-yl-cyclopropanecarboxylic acid methyl ester
[00405] To a solution of l-(3-amino-4-hydroxyphenyl)cyclopropanecarboxylic acid methyl ester (3.00 g, 14.5 mmol) in DMF were added trimethyl orthoformate (5.30 g, 14.5 mmol) and a catalytic amount of p-tolueneslufonic acid monohydrate (0.3 g) at room temperature. The mixture was stirred for 3 hours at room temperature. The mixture was diluted with water and extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give l-benzooxazol-5-yl- cyclopropanecarboxylic acid methyl ester (3.1 g), which was directly used in the next step. 1H NMR (CDCl3, 400 MHz) δ 8.09 (s, 1), 7.75 (d, / = 1.2 Hz, 1 H), 7.53-7.51 (m, 1 H), 7.42- 7.40 (m, 1 H), 3.66 (s, 3 H), 1.69-1.67 (m, 2 H), 1.27-1.24 (m, 2 H).
Figure imgf000144_0005
[00406] l-(Benzo[d]oxazol-5-yl)cyclopropanecarboxylic acid
[00407] To a solution of l-benzooxazol-5-yl-cyclopropanecarboxylic acid methyl ester (2.9 g) in EtSH (30 mL) was added AlCl3 (5.3 g, 40 mmol) in portions at 0 0C. The reaction mixture was stirred for 18 hours at room temperature. Water (20 mL) was added dropwise at 0 0C. The resulting mixture was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 1:2) to give l-(benzo[d]oxazol-5-yl)cyclopropanecarboxylic acid (280 mg, 11% over two steps). 1H NMR (DMSO, 400 MHz) δ 12.25 (brs, 1 H), 8.71 (s, 1 H), 7.70-7.64 (m, 2 H), 7.40 (dd, / = 1.6, 8.4 Hz, 1 H), 1.49-1.46 (m, 2 H), 1.21-1.18 (m, 2 H). MS (ESI) m/e (M+H+) 204.4.
[00408] Example 20: 2-(7-Fluorobenzo[d][l,3]dioxol-5-yl)acetonitrile
Figure imgf000145_0001
[00409] 3-Fluoro-4,5-dihydroxy-benzaldehyde
[00410] To a suspension of 3-fluoro-4-hydroxy-5-methoxy-benzaldehyde (1.35 g, 7.94 mmol) in dichloromethane (100 mL) was added BBr3 (1.5 mL, 16 mmol) dropwise at - 78 °C under N2. After addition, the mixture was warmed to - 30 0C and it was stirred at this temperature for 5 h. The reaction mixture was poured into ice water. The precipitated solid was collected by filtration and washed with dichloromethane to afford 3-fluoro-4,5- dihydroxy-benzaldehyde (1.1 g, 89%), which was directly used in the next step.
Figure imgf000145_0002
[00411] 7-Fluoro-benzo[l,3]dioxole-5-carbaldehyde
[00412] To a solution of 3-fluoro-4,5-dihydroxy-benzaldehyde (1.5 g, 9.6 mmol) and BrClCH2 (4.9 g, 38.5 mmol) in dry DMF (50 mL) was added Cs2CO3 (12.6 g, 39 mmol). The mixture was stirred at 60 0C overnight and was then poured into water. The resulting mixture was extracted with EtOAc (50 mL x 3). The combined organic layers were washed with brine (100 mL), dried over Na2SO4 and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to afford 7-fluoro-benzo[l,3]dioxole-5-carbaldehyde (0.80 g, 49%). 1H NMR (300 MHz, CDCl3) δ 9.78 (d, / = 0.9 Hz, 1 H), 7.26 (dd, / = 1.5, 9.3 Hz, IH), 7.19 (d, / = 1.2 Hz, I H), 6.16 (s, 2 H).
Figure imgf000146_0001
[00413] (7-Fluoro-benzo[l,3]dioxol-5-yl)-methanol
[00414] To a solution of 7-fluoro-benzo[l,3]dioxole-5-carbaldehyde (0.80 g, 4.7 mmol) in MeOH (50 mL) was added NaBH4 (0.36 g, 9.4 mmol) in portions at 0 0C. The mixture was stirred at this temperature for 30 min and was then concentrated to dryness. The residue was dissolved in EtOAc. The EtOAc layer was washed with water, dried over Na2SO4 and concentrated to dryness to afford (7-fluoro-benzo[l,3]dioxol-5-yl)-methanol (0.80 g, 98%), which was directly used in the next step.
SOCIp
Figure imgf000146_0002
Figure imgf000146_0003
[00415] 6-Chloromethyl-4-fluoro-benzo[l,3]dioxole
[00416] To SOCl2 (20 mL) was added (7-fluoro-benzo[l,3]dioxol-5-yl)-methanol (0.80 g, 4.7 mmol) in portions at 0 0C. The mixture was warmed to room temperature over 1 h and then was heated at reflux for 1 h. The excess SOCl2 was evaporated under reduced pressure to give the crude product, which was basified with saturated aqueous NaHCθ3 to pH ~ 7. The aqueous phase was extracted with EtOAc (50 mL x 3). The combined organic layers were dried over Na2SO4 and evaporated under reduced pressure to give 6-chloromethyl-4- fluoro-benzo[l,3]dioxole (0.80 g, 92%), which was directly used in the next step.
Figure imgf000146_0004
[00417] 2-(7-Fluorobenzo[d][l,3]dioxol-5-yl)acetonitrile
[00418] A mixture of 6-chloromethyl-4-fluoro-benzo[l,3]dioxole (0.80 g, 4.3 mmol) and NaCN (417 mg, 8.51 mmol) in DMSO (20 mL) was stirred at 30 0C for 1 h and was then poured into water. The mixture was extracted with EtOAc (50 mL x 3). The combined organic layers were washed with water (50 mL) and brine (50 mL), dried over Na2SO4 and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to afford 2- (7- fluoiobenzo[d][l,3]dioxol-5-yl)acetonitrile (530 mg, 70%). 1H NMR (300 MHz, CDCl3) δ 6.68-6.64 (m, 2 H), 6.05 (s, 2 H), 3.65 (s, 2 H). 13 C-NMR 5151.1, 146.2, 134.1, 124.2, 117.5, 110.4, 104.8, 102.8, 23.3.
[00419] Example 21: l-(lH-Indol-5-yl)cyclopropanecarboxylic acid
Figure imgf000147_0001
[00420] Methyl l-phenylcyclopropanecarboxylate
[00421] To a solution of 1-phenylcyclopropanecarboxylic acid (25 g, 0.15 mol) in CH3OH (200 mL) was added TsOH (3 g, 0.1 mol) at room temperature. The mixture was refluxed overnight. The solvent was evaporated under reduced pressure to give crude product, which was dissolved into EtOAc. The EtOAc layer was washed with aq. sat. NaHCO3. The organic layer was dried over anhydrous Na2SO4 and evaporated under reduced pressure to give methyl 1-phenylcyclopropanecarboxylate (26 g, 96%), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 7.37-7.26 (m, 5 H), 3.63 (s, 3 H), 1.63-1.60 (m, 2 H), 1.22-1.19 (m, 2 H).
Figure imgf000147_0002
[00422] Methyl l-(4-nitrophenyl)cyclopropanecarboxylate
[00423] To a solution of l-phenylcyclopropanecarboxylate (20.62 g, 0.14 mol) in H2SO4ZCH2Cl2 (40 mL/40 mL) was added KNO3 (12.8 g, 0.13 mol) in portion at 0 0C. The mixture was stirred for 0.5 hr at 0 0C. Ice water was added and the mixture was extracted with EtOAc (100 mL x 3). The organic layers were dried with anhydrous Na2SO4 and evaporated to give methyl l-(4-nitrophenyl)cyclopropanecarboxylate (21 g, 68%), which was used directly in the next step. 1H NMR (300 MHz, CDCl3) δ 8.18 (dd, / = 2.1, 6.9 Hz, 2 H), 7.51 (dd, / = 2.1, 6.9 Hz, 2 H), 3.64 (s, 3 H), 1.72-1.69 (m, 2 H), 1.25-1.22 (m, 2 H).
Figure imgf000148_0001
[00424] Methyl l-(4-aminophenyl)cyclopropanecarboxylate
[00425] To a solution of methyl l-(4-nitrophenyl)cyclopropanecarboxylate (20 g, 0.09 mol) in MeOH (400 mL) was added Ni (2 g) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The catalyst was filtered off through a pad of Celite and the filtrate was evaporated under vacuum to give crude product, which was purified by chromatography column on silica gel (petroleum ether/ethyl acetate =10: 1) to give methyl l-(4-aminophenyl)cyclopropanecarboxylate (11.38 g, 66%). 1H NMR (300 MHz, CDCl3) δ 7.16 (d, / = 8.1 Hz, 2 H), 6.86 (d, / = 7.8 Hz, 2 H), 4.31 (br, 2 H), 3.61 (s, 3 H), 1.55-1.50 (m, 2 H), 1.30-1.12 (m, 2 H).
Figure imgf000148_0002
[00426] Methyl l-(4-amino-3-bromophenyl)cyclopropanecarboxylate
[00427] To a solution of methyl l-(4-aminophenyl)cyclopropanecarboxylate (10.38 g, 0.05 mol) in acetonitrile (200 mL) was added NBS (9.3 g, 0.05 mol) at room temperature. The mixture was stirred overnight. Water (200 mL) was added. The organic layer was separated and the aqueous phase was extracted with EtOAc (80 mL x3). The organic layers were dried with anhydrous Na2SO4 and evaporated to give methyl l-(4-amino-3- bromophenyl)cyclopropanecarboxylate (10.6 g, 78%), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 7.38 (d, J = 2.0 Hz, 1 H), 7.08 (dd, J = 1.6, 8.4 Hz, 1 H), 6.70 (d, / = 8.4 Hz, 1 H), 3.62 (s, 3 H), 1.56-1.54 (m, 2 H), 1.14-l.l l(m, 2 H).
Figure imgf000148_0003
[00428] Methyl l-(4-amino-3-((trimethylsilyl)ethynyl)phenyl)cyclopropane carboxylate
[00429] To a degassed solution of methyl l-(4-amino-3-bromophenyl)cyclopropane carboxylate (8 g, 0.03 mol) in Et3N (100 mL) was added ethynyl-trimethyl-silane (30 g, 0.3 mol), DMAP (5% mol) and Pd(PPh3)2Cl2 (5% mol) under N2. The mixture was refluxed at 70 0C overnight. The insoluble solid was filtered off and washed with EtOAc (100 mL x 3). The filtrate was evaporated under reduced pressure to give a residue, which was purified by chromatography column on silica gel (petroleum ether/ethyl acetate =20:1) to give methyl 1- (4-amino-3-((trimethylsilyl)ethynyl)phenyl)cyclopropanecarboxylate (4.8 g, 56%). 1H NMR (300 MHz, CDCl3) 57.27 (s, 1 H), 7.10 (dd, / = 2.1, 8.4 Hz, 1 H), 6.64 (d, / = 8.4 Hz, 1 H), 3.60 (s, 3 H), 1.55-1.51 (m, 2 H), 1.12-1.09 (m, 2 H), 0.24 (s, 9 H).
Figure imgf000149_0001
[00430] Methyl l-(lH-indol-5-yl)cyclopropanecarboxylate
[00431] To a degassed solution of methyl l-(4-amino-3-((trimethylsilyl)ethynyl)phenyl) cyclopropanecarboxylate (4.69 g, 0.02 mol) in DMF (20 mL) was added CuI (1.5 g, 0.008 mol) under N2 at room temperature. The mixture was stirred for 3 hr at room temperature. The insoluble solid was filtered off and washed with EtOAc (50 mL x 3). The filtrate was evaporated under reduced pressure to give a residue, which was purified by chromatography column on silica gel (petroleum ether/ethyl acetate =20: 1) to give methyl l-(lH-indol-5- yl)cyclopropanecarboxylate (2.2 g, 51%). 1H NMR (400 MHz, CDCl3) δ 7.61 (s, 1 H), 7.33 (d, / = 8.4 Hz, I H), 7.23-7.18 (m, 2 H), 6.52-6.51 (m, 1 H) 3.62 (s, 3 H), 1.65-1.62 (m, 2 H), 1.29-1.23(m, 2 H).
Figure imgf000149_0002
[00432] l-(lH-Indol-5-yl)cyclopropanecarboxylic acid
[00433] To a solution of methyl l-(lH-indol-5-yl)cyclopropanecarboxylate (1.74 g, 8 mmol) in CH3OH (50 m L) and water (20 mL) was added LiOH (1.7 g, 0.04 mol). The mixture was heated at 45 0C for 3 hr. Water was added and the mixture was acidified with concentrated HCl to pH ~3 before being extracted with EtOAc (20 mL x 3). The organic layers were dried over anhydrous Na2SO4 and evaporated to give l-(lH-indol-5- yl)cyclopropanecarboxylic acid (1.4 g, 87%). 1H NMR (300 MHz, DMSO-J6) 7.43 (s, 1 H), 7.30-7.26 (m, 2 H), 7.04 (dd, / = 1.5, 8.4 Hz, 1 H), 6.35 (s, 1 H), 1.45-1.41 (m, 2 H), 1.14- 1.10 (m, 2 H).
[00434] Example 22: l-(4-Oxochroman-6-yl)cyclopropanecarboxylic acid
Figure imgf000150_0001
[00435] l-[4-(2-fert-Butoxycarbonyl-ethoxy)-phenyl]-cyclopropanecarboxylic methyl ester
[00436] To a solution of l-(4-hydroxy-phenyl)-cyclopropanecarboxylic methyl ester (7.0 g, 3.6 mmol) in acrylic tert-butyl ester (50 mL) was added Na (42 mg, 1.8 mmol) at room temperature. The mixture was heated at 110 0C for 1 h. After cooling to room temperature, the resulting mixture was quenched with water and extracted with EtOAc (100 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1) to give l-[4-(2-terZ-butoxycarbonyl-ethoxy)-phenyl]- cyclopropanecarboxylic methyl ester (6.3 g, 54%) and unreacted start material (3.0 g). 1H NMR (300 MHz, CDCl3) δ 7.24 (d, J = 8.7 Hz, 2 H), 6.84 (d, J = 8.7 Hz, 2 H), 4.20 (t, J = 6.6 Hz, 2 H), 3.62 (s, 3 H), 2.69 (t, / = 6.6 Hz, 2 H), 1.59-1.56 (m, 2 H), 1.47 (s, 9 H), 1.17- 1.42 (m, 2 H).
Figure imgf000150_0002
[00437] l-[4-(2-Carboxy-ethoxy)-phenyl]-cyclopropanecarboxylic methyl ester
[00438] A solution of l-[4-(2-terZ-butoxycarbonyl-ethoxy)-phenyl]-cyclopropanecarboxylic methyl ester (6.3 g, 20 mmol) in HCl (20%, 200 mL) was heated at 110 0C for 1 h. After cooling to room temperature, the resulting mixture was filtered. The solid was washed with water and dried under vacuum to give l-[4-(2-carboxy-ethoxy)-phenyl]- cyclopropanecarboxylic methyl ester (5.0 g, 96%). 1H NMR (300 MHz, DMSO) δ 7.23-7.19 (m, 2 H), 6.85-6.81 (m, 2 H), 4.13 (t, / = 6.0 Hz, 2 H), 3.51 (s, 3 H), 2.66 (t, / = 6.0 Hz, 2 H), 1.43-1.39 (m, 2 H), 1.14-1.10 (m, 2 H).
Figure imgf000151_0001
[00439] l-(4-Oxochroman-6-yl)cyclopropanecarboxylic acid
[00440] To a solution of l-[4-(2-carboxy-ethoxy)-phenyl]-cyclopropanecarboxylic methyl ester (5.0 g, 20 mmol) in CH2Cl2 (50 mL) were added oxalyl chloride (4.8 g, 38 mmol) and two drops of DMF at 0 0C. The mixture was stirred at 0-5 0C for 1 h and then evaporated under vacuum. To the resulting mixture was added CH2Cl2 (50 mL) at 0 0C and stirring was continued at 0-5 0C for 1 h. The reaction was slowly quenched with water and was extracted with EtOAc (50 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1-2: 1) to give l-(4- oxochroman-6-yl)cyclopropanecarboxylic acid (830 mg, 19%) and methyl l-(4-oxochroman- 6-yl)cyclopropanecarboxylate (1.8 g, 38%). l-(4-Oxochroman-6-yl)cyclopropane-carboxylic acid: 1H NMR (400 MHz, DMSO) δ 12.33 (br s, 1 H), 7.62 (d, J = 2.0 Hz, 1 H), 7.50 (dd, J = 2.4, 8.4 Hz, 1 H), 6.95 (d, / = 8.4 Hz, 1 H), 4.50 (t, / = 6.4 Hz, 2 H), 2.75 (t, / = 6.4 Hz, 2 H), 1.44-1.38 (m, 2 H), 1.10-1.07 (m, 2H). MS (ESI) m/z (M+H+) 231.4. l-(4-Oxochroman-6- yl)cyclopropanecarboxylate: 1H NMR (400 MHz, CDCl3) δ 7.83 (d, J = 2.4 Hz, 1 H), 7.48 (dd, J = 2.4, 8.4 Hz, 1 H), 6.93 (d, J = 8.4 Hz, 1 H), 4.55-4.52 (m, 2 H), 3.62 (s, 3 H), 2.80 (t, / = 6.4 Hz, 2 H), 1.62-1.56 (m, 2 H), 1.18-1.15 (m, 2H).
[00441] Example 23: l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid
Figure imgf000151_0002
[00442] l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid [00443] To a solution of methyl l-(4-oxochroman-6-yl)cyclopropanecarboxylate (1.0 g, 4.1 mmol) in MeOH (20 niL) and water (20 niL) was added LiOH-H2O (0.70 g, 16 mmol ) in portions at room temperature. The mixture was stirred overnight at room temperature before the MeOH was removed by evaporation under vacuum. Water and Et2O were added to the residue and the aqueous layer was separated, acidified with HCl and extracted with EtOAc (50 mL x 3). The combined organic extracts dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(4-hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid (480 mg, 44%). 1H NMR (400 MHz, CDCl3) δ 12.16 (s, 1 H), 7.73 (d, / = 2.0 Hz, 1 H), 7.47 (dd, / = 2.0, 8.4 Hz, 1 H), 6.93 (d, / = 8.8 Hz, 1 H), 3.83-3.80 (m, 2 H), 3.39 (s, 3 H), 3.28- 3.25 (m, 2 H), 1.71-1.68 (m, 2 H), 1.25-1.22 (m, 2H). MS (ESI) m/z (M+H+) 263.1.
[00444] Example 24: l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid
Figure imgf000152_0001
[00445] l-Chroman-6-yl-cyclopropanecarboxylic methyl ester
[00446] To trifluoroacetic acid (20 mL) was added NaBH4 (0.70 g, 130 mmol) in portions at 0 0C under N2 atmosphere. After stirring for 5 min, a solution of l-(4-oxo-chroman-6-yl)- cyclopropanecarboxylic methyl ester (1.6 g, 6.5 mmol) was added at 15 0C. The reaction mixture was stirred for 1 h at room temperature before being slowly quenched with water. The resulting mixture was extracted with EtOAc (50 mL x 3). The combined organic extracts dried over anhydrous Na2SO4 and evaporated under vacuum to give l-chroman-6-yl- cyclopropanecarboxylic methyl ester (1.4 g, 92%), which was used directly in the next step. 1H NMR (300 MHz, CDCl3) δ 7.07-7.00 (m, 2 H), 6.73 (d, / = 8.4 Hz, 1 H), 4.17 (t, / = 5.1 Hz, 2 H), 3.62 (s, 3 H), 2.79-2.75 (m, 2 H), 2.05-1.96 (m, 2 H), 1.57-1.54 (m, 2 H), 1.16-1.13 (m, 2H).
Figure imgf000152_0002
[00447] l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid [00448] To a solution of l-chroman-6-yl-cyclopropanecarboxylic methyl ester (1.4 g, 60 mmol) in MeOH (20 mL) and water (20 mL) was added LiOH-H2O (1.0 g, 240 mmol ) in portions at room temperature. The mixture was stirred overnight at room temperature before the MeOH was removed by evaporation under vacuum. Water and Et2O were added and the aqueous layer was separated, acidified with HCl and extracted with EtOAc (50 mL x 3). The combined organic extracts dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(4-Hydroxy-4-methoxychroman-6-yl)cyclopropanecarboxylic acid (1.0 g, 76%). 1H NMR (400 MHz, DMSO) δ 12.10 (br s, 1 H), 6.95 (d, / = 2.4 Hz, 2 H), 6.61-6.59 (m, 1 H), 4.09-4.06 (m, 2 H), 2.70-2.67 (m, 2 H), 1.88-1.86 (m, 2 H), 1.37-1.35 (m, 2 H), 1.04-1.01 (m, 2H). MS (ESI) m/z (M+H+) 217.4.
[00449] Example 25: l-(3-Methylbenzo[d]isoxazol-5-yl)cyclopropanecarboxylic acid
MeOH/TsOH AICI3/ AcCI NHoOH
Figure imgf000153_0003
Figure imgf000153_0002
Figure imgf000153_0001
Figure imgf000153_0004
Figure imgf000153_0005
[00450] l-(3-Acetyl-4-hydroxy-phenyl)-cyclopropanecarboxylic methyl ester
[00451] To a stirred suspension of AlCl3 (58 g, 440 mmol) in CS2 (500 mL) was added acetyl chloride (7.4 g, 95 mmol) at room temperature. After stirring for 5 min, methyl l-(4- methoxyphenyl)cyclopropanecarboxylate (15 g, 73 mmol) was added. The reaction mixture was heated at reflux for 2 h before ice water was added carefully to the mixture at room temperature. The resulting mixture was extracted with EtOAc (150 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give l-(3-acetyl-4-hydroxy-phenyl)-cyclopropanecarboxylic methyl ester (15 g, 81%), which was used in the next step without further purification. 1H NMR (CDCl3, 400 MHz) δ 12.28 (s, 1 H), 7.67 (d, J = 2.0 Hz, 1 H), 7.47 (dd, J = 2.0, 8.4 Hz, 1 H), 6.94 (d, J = 8.4 Hz, 1 H), 3.64 (s, 3 H), 2.64 (s, 3 H), 1.65-1.62 (m, 2 H), 1.18-1.16(m, 2 H).
NHoOH-HCI
Figure imgf000154_0002
Figure imgf000154_0001
[00452] l-[4-Hydroxy-3-(l-hydroxyimino-ethyl)-phenyl]-cyclopropanecarboxylic methyl ester
[00453] To a stirred solution of l-(3-acetyl-4-hydroxy-phenyl)-cyclopropanecarboxylic methyl ester (14.6 g, 58.8 mmol) in EtOH (500 mL) were added hydroxylamine hydrochloride (9.00 g, 129 mmol) and sodium acetate (11.6 g, 141 mmol) at room temperature. The resulting mixture was heated at reflux overnight. After removal of EtOH under vacuum, water (200 mL) and EtOAc (200 mL) were added. The organic layer was separated and the aqueous layer was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give l-[4- hydroxy-3-(l-hydroxyimino-ethyl)-phenyl]-cyclopropanecarboxylic methyl ester (14.5 g, 98%), which was used in the next step without further purification. 1H NMR (CDCl3, 400 MHz) δ 11.09 (s, I H), 7.39 (d, / = 2.0 Hz, 1 H), 7.23 (d, / = 2.0 Hz, I H), 7.14 (s, 1 H), 6.91 (d, / = 8.4 Hz, 1 H), 3.63 (s, 3 H), 2.36 (s, 3 H), 1.62-1.59 (m, 2 H), 1.18-1.15 (m, 2 H).
Figure imgf000154_0003
[00454] (ZTt-Methyl l-(3-(l-(acetoxyimino)ethyl)-4-hydroxyphenyl)cyclopropane carboxylate
[00455] The solution of l-[4-hydroxy-3-(l-hydroxyimino-ethyl)-phenyl]- cyclopropanecarboxylic methyl ester (10.0 g, 40.1 mmol) in Ac2O (250 mL) was heated at 45 0C for 4 h. The Ac2O was removed by evaporation under vacuum before water (100 mL) and EtOAc (100 mL) were added. The organic layer was separated and the aqueous layer was extracted with EtOAc (100 mL x T). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give (£)-methyl l-(3-(l- (acetoxyimino)ethyl)-4-hydroxyphenyl)cyclopropanecarboxylate (10.5 g, 99%), which was used in the next step without further purification.
Figure imgf000155_0001
[00456] Methyl l-(3-methylbenzo[d]isoxazol-5-yl)cyclopropanecarboxylate
[00457] A solution of (£)-methyl l-(3-(l-(acetoxyimino)ethyl)-4- hydroxyphenyl)cyclopropane carboxylate (10.5 g, 39.6 mmol) and pyridine (31.3 g, 396 mmol) in DMF (150 mL) was heated at 125 0C for 10 h. The cooled reaction mixture was poured into water (250 mL) and was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 50:1) to give methyl l-(3-methylbenzo[d]isoxazol-5- yl)cyclopropanecarboxylate (7.5 g, 82%). 1H NMR (CDCl3 300 MHz) δ 7.58-7.54 (m, 2 H), 7.48 (dd, / = 1.5, 8.1 Hz, 1 H), 3.63 (s, 3 H), 2.58 (s, 3 H), 1.71-1.68 (m, 2 H), 1.27-1.23 (m, 2 H).
Figure imgf000155_0002
[00458] l-(3-Methylbenzo[d]isoxazol-5-yl)cyclopropanecarboxylic acid
[00459] To a solution of methyl l-(3-methylbenzo[d]isoxazol-5- yl)cyclopropanecarboxylate (1.5 g, 6.5 mmol) in MeOH (20 mL) and water (2 mL) was added LiOH-H2O (0.80 g, 19 mmol ) in portions at room temperature. The reaction mixture was stirred at room temperature overnight before the MeOH was removed by evaporation under vacuum. Water and Et2O were added and the aqueous layer was separated, acidified with HCl and extracted with EtOAc (50 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give l-(3-methylbenzo[d]isoxazol- 5-yl)cyclopropanecarboxylic acid (455 mg, 32%). 1H NMR (400 MHz, DMSO) δ 12.40 (br s, 1 H), 7.76 (s, 1 H), 7.60-7.57 (m, 2 H), 2.63 (s, 3 H), 1.52-1.48 (m, 2 H), 1.23-1.19 (m, 2H) . MS (ESI) m/z (M+H+) 218.1.
[00460] Example 26: l-CSpirotbenzotdHl^dioxole^r-cyclobutaneJ-S- yl)cyclopropane carboxylic acid
Figure imgf000156_0001
[00461] l-(3,4-Dihydroxy-phenyl)-cyclopropanecarboxylic methyl ester
[00462] To a solution of l-(3,4-dihydroxyphenyl)cyclopropanecarboxylic acid (4.5 g) in MeOH (30 niL) was added TsOH (0.25 g, 1.3 mmol). The stirring was continued at 50 0C overnight before the mixture was cooled to room temperature. The mixture was concentrated under vacuum and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 3:1) to give l-(3,4-dihydroxy-phenyl)-cyclopropanecarboxylic methyl ester (2.1 g). 1H NMR (DMSO 300 MHz) δ 8.81 (brs, 2 H), 6.66 (d, / = 2.1 Hz, 1 H), 6.61 (d, / = 8.1 Hz, 1 H), 6.53 (dd, / = 2.1, 8.1 Hz, 1 H), 3.51 (s, 3 H), 1.38-1.35 (m, 2 H), 1.07-1.03 (m, 2 H).
Figure imgf000156_0002
[00463] Methyl l-(spiro[benzo[d][l,3]dioxole-2,l'-cyclobutane]-5-yl)cyclopropane carboxylate
[00464] To a solution of l-(3,4-dihydroxy-phenyl)-cyclopropanecarboxylic methyl ester (1.0 g, 4.8 mmol) in toluene (30 mL) was added TsOH (0.10 g, 0.50 mmol) and cyclobutanone (0.70 g, 10 mmol). The reaction mixture was heated at reflux for 2 h before being concentrated under vacuum. The residue was purified by chromatography on silica gel (petroleum ether/ethyl acetate 15:1) to give methyl l-(spiro[benzo[d][l,3]dioxole-2,l'- cyclobutane]-5-yl)cyclopropanecarboxylate (0.6 g, 50%). 1H NMR (CDCl3300 MHz) δ 6.78-6.65 (m, 3 H), 3.62 (s, 3 H), 2.64-2.58 (m, 4 H), 1.89-1.78 (m, 2 H), 1.56-1.54 (m, 2 H), 1.53-1.12(m, 2 H).
Figure imgf000157_0001
[00465] l-(Spiro[benzo[d][l,3]dioxole-2,l'-cyclobutane]-5-yl)cyclopropane carboxylic acid
[00466] To a mixture of methyl l-(spiro[benzo[d][l,3]dioxole-2,l'-cyclobutane]-5-yl)cycl- opropanecarboxylate (0.60 g, 2.3 mmol) in THF/H2O (4: 1, 10 mL) was added LiOH (0.30 g, 6.9 mmol). The mixture was stirred at 60 0C for 24 h. HCl (0.5 N) was added slowly to the mixture at 0 0C until pH 2-3. The mixture was extracted with EtOAc (10 mL x 3). The combined organic phases were washed with brine, dried over anhydrous MgSO4, and washed with petroleum ether to give l-(spiro[benzo[d][l,3]-dioxole-2,l'-cyclobutane]-5- yl)cyclopropane carboxylic acid (330 mg, 59%). 1HNMR (400 MHz, CDCl3) δ 6.78-6.65 (m, 3 H), 2.65-2.58 (m, 4 H), 1.86-1.78 (m, 2 H), 1.63-1.60 (m, 2 H), 1.26-1.19 (m, 2 H).
[00467] Example 27: 2-(2,3-Dihydrobenzo[b][l,4]dioxin-6-yl)acetonitrile BrHpCCHpBr
Figure imgf000157_0003
Figure imgf000157_0002
Figure imgf000157_0004
BrHpCCHpBr
Figure imgf000157_0006
Figure imgf000157_0005
[00468] 2,3-Dihydro-benzo[l,4]dioxine-6-carboxylic acid ethyl ester
[00469] To a suspension of Cs2CO3 (270 g, 1.49 mol) in DMF (1000 mL) were added 3,4- dihydroxybenzoic acid ethyl ester (54.6 g, 0.3 mol) and 1 ,2-dibromoethane (54.3 g, 0.29 mol) at room temperature. The resulting mixture was stirred at 80 0C overnight and then poured into ice-water. The mixture was extracted with EtOAc (200 mL x 3). The combined organic layers were washed with water (200 mL x 3) and brine (100 mL), dried over Na2SO4 and concentrated to dryness. The residue was purified by column (petroleum ether/ethyl acetate 50:1) on silica gel to obtain 2,3-dihydro-benzo[l,4]dioxine-6-carboxylic acid ethyl ester (18 g, 29%). 1H NMR (300 MHz, CDCl3) δ 7.53 (dd, J = 1.8, 7.2 Hz, 2 H), 6.84-6.87 (m, 1 H), 4.22-4.34 (m, 6 H), 1.35 (t, J = 7.2 Hz, 3 H).
Figure imgf000158_0001
[00470] (2,3-Dihydro-benzo[l,4]dioxin-6-yl)-methanol
[00471] To a suspension of LiAlH4 (2.8 g, 74 mmol) in THF (20 niL) was added dropwise a solution of 2,3-dihydro-benzo[l,4]dioxine-6-carboxylic acid ethyl ester (15 g, 72 mmol) in THF (10 mL) at 0 0C under N2. The mixture was stirred at room temperature for 1 h and then quenched carefully with addition of water (2.8 mL) and NaOH (10%, 28 mL) with cooling. The precipitated solid was filtered off and the filtrate was evaporated to dryness to obtain (2,3-dihydro-benzo[l,4]dioxin-6-yl)-methanol (10.6 g). 1H NMR (300 MHz, DMSOd6) δ 6.73-6.78 (m, 3 H), 5.02 (t, J = 5.7 Hz, 1 H), 4.34 (d, J = 6.0 Hz, 2 H), 4.17-4.20 (m, 4 H).
Figure imgf000158_0002
[00472] 6-Chloromethyl-2,3-dihydro-benzo[l,4]dioxine
[00473] A mixture of (2,3-dihydro-benzo[l,4]dioxin-6-yl)methanol (10.6 g) in SOCl2 (10 mL) was stirred at room temperature for 10 min and then poured into ice-water. The organic layer was separated and the aqueous phase was extracted with dichloromethane (50 mL x 3). The combined organic layers were washed with NaHCθ3 (sat solution), water and brine, dried over Na2SO4 and concentrated to dryness to obtain 6-chloromethyl-2,3-dihydro- benzo[l,4]dioxine (12 g, 88% over two steps), which was used directly in next step.
Figure imgf000158_0003
[00474] 2-(2,3-Dihydrobenzo[b][l,4]dioxin-6-yl)acetonitrile
[00475] A mixture of 6-chloromethyl-2,3-dihydro-benzo[l,4]dioxine (12.5 g, 67.7 mmol) and NaCN (4.30 g, 87.8 mmol) in DMSO (50 mL) was stirred at rt for 1 h. The mixture was poured into water (150 mL) and then extracted with dichloromethane (50 mL x 4). The combined organic layers were washed with water (50 mL x 2) and brine (50 mL), dried over Na2SO4 and concentrated to dryness. The residue was purified by column (petroleum ether/ethyl acetate 50:1) on silica gel to obtain 2-(2,3-dihydrobenzo[b][l,4]dioxin-6- yl)acetonitrile as a yellow oil (10.2 g, 86%). 1H-NMR (300 MHz, CDCl3) δ 6.78-6.86 (m, 3 H), 4.25 (s, 4 H), 3.63 (s, 2 H). [00476] The following Table 2 contains a list of carboxylic acid building blocks that were commercially available, or prepared by one of the three methods described above:
Table 2: Carboxylic acid building blocks.
Figure imgf000159_0001
Figure imgf000160_0001
Figure imgf000161_0001
Figure imgf000162_0001
Figure imgf000163_0001
Figure imgf000164_0003
[00477] Specific Procedures: Synthesis of aminoindole building blocks [00478] Example 28: 3-Methyl-lH-indol-6-amine
Figure imgf000164_0001
[00479] (3-Nitro-phenyl)-hydrazine hydrochloride salt
[00480] 3-Nitro-phenylamine (27.6 g, 0.2 mol) was dissolved in the mixture of H2O (40 mL) and 37% HCl (40 mL). A solution of NaNO2 (13.8 g, 0.2 mol) in H2O (60 mL) was added to the mixture at 0 0C, and then a solution Of SnCl2-H2O (135.5 g, 0.6 mol) in 37% HCl (100 mL) was added at that temperature. After stirring at 0 0C for 0.5 h, the insoluble material was isolated by filtration and was washed with water to give (3- nitrophenyl)hydrazine hydrochloride (27.6 g, 73%).
Figure imgf000164_0002
[00481] jV-(3-Nitro-phenyl)-jV'-propylidene-hydrazine
[00482] Sodium hydroxide solution (10%, 15 mL) was added slowly to a stirred suspension of (3-nitrophenyl)hydrazine hydrochloride (1.89 g, 10 mmol) in ethanol (20 mL) until pH 6. Acetic acid (5 mL) was added to the mixture followed by propionaldehyde (0.7 g, 12 mmol). After stirring for 3 h at room temperature, the mixture was poured into ice-water and the resulting precipitate was isolated by filtration, washed with water and dried in air to obtain (E)-l-(3-nitrophenyl)-2-propylidenehydrazine, which was used directly in the next step.
[00483] 3-Methyl-4-nitro-lH-indole 3 and 3-methyl-6-nitro-lH-indole
[00484] A mixture of (E)-l-(3-nitrophenyl)-2-propylidenehydrazine dissolved in 85 % H3PO4 (20 niL) and toluene (20 niL) was heated at 90-100 0C for 2 h. After cooling, toluene was removed under reduced pressure. The resultant oil was basified to pH 8 with 10 % NaOH. The aqueous layer was extracted with EtOAc (100 mL x 3). The combined organic layers were dried, filtered and concentrated under reduced pressure to afford the mixture of 3- methyl-4-nitro-lH-indole and 3-methyl-6-nitro-lH-indole [1.5 g in total, 86 %, two steps from (3-nitrophenyl)hydrazine hydrochloride] which was used to the next step without further purification.
Figure imgf000165_0002
[00485] 3-Methyl-lH-indol-6-amine
[00486] The crude mixture from previous steps (3 g, 17 mmol) and 10% Pd-C (0.5 g) in ethanol (30 mL) was stirred overnight under H2 (1 atm) at room temperature. Pd-C was filtered off and the filtrate was concentrated under reduced pressure. The solid residue was purified by column to give 3-methyl-lH-indol-6-amine (0.6 g, 24%). 1H NMR (CDCl3) δ 7.59 (br s. IH), 7.34 (d, / = 8.0 Hz, IH), 6.77 (s, IH), 6.64 (s, IH), 6.57 (m, IH), 3.57 (brs, 2H), 2.28 (s, 3H); MS (ESI) m/e (M+H+) 147.2.
[00487] Example 29: 3-fert-Butyl-lH-indol-5-amine
Figure imgf000165_0003
[00488] 3-fert-Butyl-5-nitro-lH-indole
[00489] To a mixture of 5-nitro-lH-indole (6.0 g, 37 mmol) and AlCl3 (24 g, 0.18 mol) in CH2Cl2 (100 mL) at 0 0C was added 2-bromo-2-methyl-propane (8.1 g, 37 mmol) dropwise. After being stirred at 15 0C overnight, the mixture was poured into ice (100 mL). The precipitated salts were removed by filtration and the aqueous layer was extracted with CH2CI2 (30 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4 and concentrated under vacuum to obtain the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 20:1) to give 3-tert- butyl-5-nitro-lH-indole (2.5 g, 31%). 1H NMR (CDCl3, 400 MHz) δ 8.49 (d, J = 1.6 Hz, 1 H), 8.31 (brs, 1 H), 8.05 (dd, / = 2.0, 8.8 Hz, 1 H), 7.33 (d, / = 8.8 Hz, 1 H), 6.42 (d, / = 1.6 Hz, I H), 1.42 (s, 9 H).
Figure imgf000166_0001
[00490] 3-fert-Butyl-lH-indol-5-amine
[00491] To a solution of 3-te?t-butyl-5-nitro- lH-indole (2.5 g, 12 mmol) in MeOH (30 mL) was added Raney Nickel (0.2 g) under N2 protection. The mixture was stirred under hydrogen atmosphere (1 atm) at 15 0C for 1 h. The catalyst was filtered off and the filtrate was concentrated to dryness under vacuum. The residue was purified by preparative HLPC to afford 3-te?t-butyl-lH-indol-5-amine (0.43 g, 19%). 1H NMR (CDCl3, 400 MHz) δ 7.72 (br.s, 1 H), 7.11 (d, / = 8.4 Hz, 1 H), 6.86 (d, / = 2.0 Hz, 1 H), 6.59 (dd, / = 2.0, 8.4 Hz, 1 H), 6.09 (d, / = 1.6 Hz, 1 H), 1.37 (s, 9 H); MS (ESI) m/e (M+H+) 189.1.
[00492] Example 30: 2-fert-Butyl-6-fluoro-lH-indol-5-amine and 6-tert-bntoxy-2-tert- butyl- lH-indol-5-amine
Figure imgf000167_0001
[00493] 2-Bromo-5-fluoro-4-nitroaniline
[00494] To a mixture of 3-fluoro-4-nitroaniline (6.5 g, 42.2 mmol) in AcOH (80 mL) and chloroform (25 mL) was added dropwise Br2 (2.15 mL, 42.2 mmol) at 0 °C. After addition, the resulting mixture was stirred at room temperature for 2 h and then poured into ice water. The mixture was basified with aqueous NaOH (10%) to pH ~ 8.0-9.0 under cooling and then extracted with EtOAc (50 mL x 3). The combined organic layers were washed with water (80 mL x 2) and brine (100 mL), dried over Na2SO4 and concentrated under reduced pressure to give 2-bromo-5-fluoro-4-nitroaniline (9 g, 90%). 1H-NMR (400 MHz, DMSO-J6) δ 8.26 (d, / = 8.0, Hz, IH), 7.07 (brs, 2H), 6.62 (d, / = 9.6 Hz, IH).
Figure imgf000167_0002
[00495] 2-(3,3-Dimethylbut- l-ynyl)-5-fluoro-4-nitroaniline
[00496] A mixture of 2-bromo-5-fluoro-4-nitroaniline (9.0 g, 38.4 mmol), 3,3-dimethyl- but-1-yne (9.95 g, 121 mmol), CuI (0.5 g 2.6 mmol), Pd(PPh3)2Cl2 (3.4 g, 4.86 mmol) and Et3N (14 mL, 6.9 mmol) in toluene (100 mL) and water (50 mL) was heated at 70 0C for 4 h. The aqueous layer was separated and the organic layer was washed with water (80 mL x 2) and brine (100 mL), dried over Na2SO4 and concentrated under reduced pressure to dryness. The residue was recrystallized with ether to afford 2-(3,3-dimethylbut-l-ynyl)-5-fluoro-4- nitroaniline (4.2 g, 46%). 1H-NMR (400 MHz, DMSO-J6) δ 7.84 (d, / = 8.4 Hz, IH), 6.84 (brs, 2H), 6.54 (d, / = 14.4 Hz, IH), 1.29 (s, 9H).
Figure imgf000168_0001
[00497] iV-(2-(3,3-Dimethylbut-l-ynyl)-5-fluoro-4-nitrophenyl)butyramide
[00498] To a solution of 2-(3,3-dimethylbut-l-ynyl)-5-fluoro-4-nitroaniline (4.2 g, 17.8 mmol) in dichloromethane (50 mL) and Et3N (10.3 mL, 71.2 mmol) was added butyryl chloride (1.9 g, 17.8 mmol) at 0 0C. The mixture was stirred at room temperature for 1 h and then poured into water. The aqueous phase was separated and the organic layer was washed with water (50 mL x 2) and brine (100 mL), dried over Na2SO4 and concentrated under reduced pressure to dryness. The residue was washed with ether to give N-(2-(3,3- dimethylbut-l-ynyl)-5-fluoro-4-nitrophenyl)butyramide (3.5 g, 67%), which was used in the next step without further purification.
Figure imgf000168_0002
[00499] 2-fert-Butyl-6-fluoro-5-nitro-lH-indole
[00500] A solution of N-(2-(3,3-dimethylbut-l-ynyl)-5-fluoro-4-nitrophenyl)butyramide (3.0 g, 9.8 mmol) and TBAF (4.5 g, 17.2 mmol) in DMF (25 mL) was heated at 100 0C overnight. The mixture was poured into water and then extracted with EtOAc (80 mL x 3). The combined extracts were washed with water (50 mL) and brine (50 mL), dried over Na2SO4 and concentrated under reduced pressure to dryness. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1) to give compound 2-tert-butyl-6-fluoro-5-nitro-lH-indole (1.5 g, 65%). 1H-NMR (400 MHz, CDCl3) δ 8.30 (d, / = 7.2 Hz, IH), 7.12 (d, / = 11.6 Hz, IH), 6.35 (d, / = 1.2 Hz, IH), 1.40 (s, 9H).
Figure imgf000168_0003
[00501] 2-fert-Butyl-6-fluoro-lH-indol-5-amine
[00502] A suspension of 2-tert-butyl-6-fluoro-5-nitro-lH-indole (1.5 g, 6.36 mmol) and Ni (0.5 g) in MeOH (20 mL) was stirred under H2 atmosphere (1 atm) at the room temperature for 3 h. The catalyst was filtered off and the filtrate was concentrated under reduced pressure to dryness. The residue was recrystallized in ether to give 2-tert-butyl-6-fluoro-lH-indol-5- amine (520 mg, 38%). 1H-NMR (300 MHz, DMSO-J6) δ 10.46 (brs, IH), 6.90 (d, J = 8.7 Hz, IH), 6.75 (d, / = 9.0 Hz, IH), 5.86 (s, IH), 4.37 (brs, 2H), 1.29 (s, 9H); MS (ESI) m/e 206.6.
Figure imgf000169_0001
[00503] 6-fert-Butoxy-2-tert-butyl-5-nitro-lH-indole
[00504] A solution of N-(2-(3,3-dimethylbut-l-ynyl)-5-fluoro-4-nitrophenyl)butyramide (500 mg, 1.63 mmol) and J-BuOK (0.37 g, 3.26 mmol) in DMF (10 mL) was heated at 70 0C for 2 h. The mixture was poured into water and then extracted with EtOAc (50 mL x 3). The combined extracts were washed with water (50 mL) and brine (50 mL), dried over Na2SO4 and concentrated under reduced pressure to give 6-tert-butoxy-2-tert-butyl-5-nitro-lH-indole (100 mg , 21%). 1H-NMR (300 MHz, DMSO-J6) δ 11.35 (brs, IH), 7.99 (s, IH), 7.08 (s, IH), 6.25 (s, IH), 1.34 (s, 9H), 1.30 (s, 9H).
Figure imgf000169_0002
[00505] 6-fert-Butoxy-2-fert-butyl-lH-indol-5-amine
[00506] A suspension of 6-terZ-butoxy-2-tert-butyl-5-nitro-lH-indole (100 mg, 0.36 mmol) and Raney Ni (0.5 g) in MeOH (15 mL) was stirred under H2 atmosphere (1 atm) at the room temperature for 2.5 h. The catalyst was filtered off and the filtrate was concentrated under reduced pressure to dryness. The residue was recrystallized in ether to give 6-terZ-butoxy-2- tert-butyl-lH-indol-5-amine (30 mg, 32%). 1H-NMR (300 MHz, MeOD) 6.98 (s, IH), 6.90 (s, IH), 5.94 (d, / = 0.6 Hz, IH), 1.42 (s, 9H), 1.36 (s, 9H); MS (ESI) m/e 205.0.
[00507] Example 31: l-fert-Butyl-lH-indol-5-amine
Figure imgf000170_0001
[00508] N-fert-Butyl-4-nitroaniline
[00509] A solution of l-fluoro-4-nitro-benzene (1 g, 7.1 mmol) and tert-butylamine (1.5 g, 21 mmol) in DMSO (5 mL) was stirred at 75 0C overnight. The mixture was poured into water (10 mL) and extracted with EtOAc (7 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4 and concentrated under vacuum to dryness. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 30:1) to afford N-terf-butyl-4-nitroaniline (1 g, 73%). 1H ΝMR (CDCl3, 400 MHz) δ 8.03- 8.00 (m, 2H), 6.61-6.57 (m, 2H), 4.67 (brs, IH), 1.42 (s, 9H).
Figure imgf000170_0002
[00510] (2-Bromo-4-nitro-phenyl)-fert-butyl-amine
[00511] To a solution of N-ferZ-butyl-4-nitroaniline (1 g, 5.1 mmol) in AcOH (5 mL) was added Br2 (0.86 g, 54 mmol) dropwise at 15 0C. After addition, the mixture was stirred at 30 0C for 30 min and then filtered. The filter cake was basified to pH 8-9 with aqueous NaHCO3. The aqueous layer was extracted with EtOAc (10 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4 and concentrated under vacuum to give (2-bromo-4-nitro-phenyl)-tert-butyl-amine (0.6 g, 43%). 1H-NMR (CDCl3, 400 MHz) δ 8.37 (dd, / = 2.4 Hz, IH), 8.07 (dd, / = 2.4, 9.2 Hz, IH), 6.86 (d, / = 9.2 Hz, IH), 5.19 (brs, IH), 1.48 (s, 9H).
Figure imgf000171_0001
[00512] ter/-Butyl-(4-nitro-2-trimethylsilanylethynyl-phenyl)-amine
[00513] To a solution of (2-bromo-4-nitro-phenyl)-tert-butyl-amine (0.6 g, 2.2 mmol) in Et3N (10 niL) was added Pd(PPh3)2Cl2 (70 mg, 0.1 mmol), CuI (20.9 mg, 0.1 mmol) and ethynyl-trimethyl-silane (0.32 g, 3.3 mmol) successively under N2 protection. The reaction mixture was heated at 70 0C overnight. The solvent was removed under vacuum and the residue was washed with EtOAc (10 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4 and concentrated under vacuum to dryness. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1) to afford tert-butyl-(4-nitro-2-trimethylsilanylethynyl-phenyl)-amine (100 mg, 16%). 1H-NMR (CDCl3, 400 MHz) δ 8.20 (d, / = 2.4, Hz, IH), 8.04 (dd, / = 2.4, 9.2 Hz, IH), 6.79 (d, / = 9.6 Hz, IH), 5.62 (brs, IH), 1.41 (s, 9H), 0.28 (s, 9H).
Figure imgf000171_0002
[00514] l-fert-Butyl-5-nitro-lH-indole
[00515] To a solution of tert-butyl-(4-nitro-2-trimethylsilanylethynyl-phenyl)-amine (10 mg, 0.035 mmol) in DMF (2 mL), was added CuI (13 mg, 0.07 mmol) under N2 protection. The reaction mixture was stirred at 100 0C overnight. At this time, EtOAc (4 mL) was added to the mixture. The mixture was filtered and the filtrate was washed with water, brine, dried over Na2SO4 and concentrated under vacuum to obtain l-tert-butyl-5-nitro-lH-indole (7 mg, 93%). 1H-NMR (CDCl3, 300 MHz) δ 8.57 (d, / = 2.1 Hz, IH), 8.06 (dd, / = 2.4, 9.3 Hz, IH), 7.65 (d, / = 9.3 Hz, IH), 7.43 (d, / = 3.3 Hz, IH), 6.63 (d, / = 3.3 Hz, IH), 1.76 (s, 9H).
Raney Ni/ H2
Figure imgf000171_0003
Figure imgf000171_0004
[00516] l-fert-Butyl-lH-indol-5-amine [00517] To a solution of l-terf-butyl-5-nitro-lH-indole (6.5 g, 0.030 mol) in MeOH (100 mL) was added Raney Nickel (0.65 g, 10%) under N2 protection. The mixture was stirred under hydrogen atmosphere (1 atm) at 30 0C for 1 h. The catalyst was filtered off and the filtrate was concentrated under vacuum to dryness. The residue was purified by column chromatography on silica gel (PE/EtOAc 1:2) to give l-terZ-butyl-lH-indol-5-amine (2.5 g, 45%). 1H-NMR (CDCl3, 400 MHz) δ 7.44 (d, / = 8.8 Hz, IH), 7.19 (dd, / = 3.2 Hz, IH), 6.96 (d, / = 2.0 Hz, IH), 6.66 (d, / = 2.0, 8.8 Hz, IH), 6.26 (d, / = 3.2 Hz, IH), 1.67 (s, 9H). MS (ESI) m/e (M+H+) 189.2.
[00518] Example 32: 2-fert-Butyl-l-methyl-lH-indol-5-amine
Figure imgf000172_0001
[00519] (2-Bromo-4-nitro-phenyl)-methyl-amine
[00520] To a solution of methyl-(4-nitro-phenyl)-amine (15.2 g, 0.1 mol) in AcOH (150 mL) and CHCl3 (50 mL) was added Br2 (16.0 g, 0.1 mol) dropwise at 5 0C. The mixture was stirred at 10 0C for Ih and then basified with sat. aq. NaHCO3. The resulting mixture was extracted with EtOAc (100 mL x 3), and the combined organics were dried over anhydrous Na2SO4 and evaporated under vacuum to give (2-bromo-4-nitro-phenyl)-methyl-amine (2- bromo-4-nitro-phenyl)-methyl-amine (23.0 g, 99%), which was used in the next step without further purification. 1H NMR (300 MHz, CDCl3) δ 8.37 (d, J = 2.4 Hz, 1 H), 8.13 (dd, J = 2.4, 9.0 Hz, 1 H), 6.58 (d, J = 9.0 Hz, 1 H), 5.17 (brs, 1 H), 3.01 (d, J = 5.4 Hz, 3 H).
Figure imgf000172_0002
[00521] [2-(3,3-Dimethyl-but-l-ynyl)-4-nitro-phenyl]-methyl-amine [00522] To a solution of (2-bromo-4-nitro-phenyl)-methyl-amine (22.5 g, 97.4 mmol) in toluene (200 niL) and water (100 niL) were added Et3N (19.7 g, 195 mmol), Pd(PPh3)2Cl2 (6.8 g, 9.7 mmol), CuI (0.7 g, 3.9 mmol) and 3,3-dimethyl-but-l-yne (16.0 g, 195 mmol) successively under N2 protection. The mixture was heated at 70 0C for 3 hours and then cooled down to room temperature. The resulting mixture was extracted with EtOAc (100 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give [2-(3,3-dimethyl-but-l-ynyl)-4-nitro-phenyl]-methyl-amine (20.1 g, 94%), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 8.15 (d, J = 2.4 Hz, IH), 8.08 (dd, J = 2.8, 9.2 Hz, IH), 6.50 (d, J = 9.2 Hz, IH), 5.30 (brs, IH), 3.00 (s, 3H), 1.35 (s, 9H).
Figure imgf000173_0001
[00523] 2-fert-Butyl-l-methyl-5-nitro-lH-indole
[00524] A solution of [2-(3,3-dimethyl-but-l-ynyl)-4-nitro-phenyl]-methyl-amine (5.0 g, 22.9 mmol) and TBAF (23.9 g, 91.6 mmol) in THF (50 mL) was heated at reflux overnight. The solvent was removed by evaporation under vacuum and the residue was dissolved in brine (100 mL) and EtOAc (100 mL). The organic phase was separated, dried over Na2SO4 and evaporated under vacuum to give 2-tert-butyl-l-methyl-5-nitro-lH-indole (5.0 g, 99%), which was used in the next step without further purification. 1H NMR (CDCl3, 400 MHz) δ 8.47 (d, J = 2.4 Hz, IH), 8.07 (dd, J = 2.4, 9.2 Hz, IH), 7.26-7.28 (m, IH), 6.47 (s, IH), 3.94 (s, 3H), 1.50 (s, 9H).
Raney Ni/H2
Figure imgf000173_0002
Figure imgf000173_0003
[00525] 2-fert-Butyl-l-methyl-lH-indol-5-amine
[00526] To a solution of 2-tert-butyl-l-methyl-5-nitro-lH-indole (3.00 g, 13.7 mmol) in MeOH (30 mL) was added Raney Ni (0.3 g) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The mixture was filtered through a Celite pad and the filtrate was evaporated under vacuum. The crude residue was purified by column chromatography on silica gel (P.E/EtOAc 20:1) to give 2-tert-butyl- l-methyl-lH-indol-5-amine (1.7 g, 66%). 1H NMR (300 MHz, CDCl3) δ 7.09 (d, J = 8.4 Hz, IH), 6.89-6.9 (m, IH), 6.66 (dd, J = 2.4, 8.7 Hz, IH), 6.14 (d, J = 0.6 Hz, IH), 3.83 (s, 3H), 3.40 (brs, 2H), 1.45 (s, 9H); MS (ESI) m/e (M+H+) 203.1.
[00527] Example 33: 2-Cyclopropyl-lH-indol-5-amine
Figure imgf000174_0001
Raney Ni
Figure imgf000174_0003
Figure imgf000174_0002
Figure imgf000174_0004
[00528] 2-Bromo-4-nitroaniline
[00529] To a solution of 4-nitro-aniline (25 g, 0.18 mol) in HOAc (150 niL) was added liquid Br2 (30 g, 0.19 mol) dropwise at room temperature. The mixture was stirred for 2 hours. The solid was collected by filtration and poured into water (100 mL), which was basified with sat. aq. NaHCO3 to pH 7 and extracted with EtOAc (300 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give 2-bromo-4-nitroaniline (30 g, 80%), which was directly used in the next step.
Figure imgf000174_0005
[00530] 2-(Cyclopropylethynyl)-4-nitroaniline
[00531] To a deoxygenated solution of 2-bromo-4-nitroaniline (2.17 g, 0.01 mmol), ethynyl-cyclopropane (1 g, 15 mmol) and CuI (10 mg, 0.05 mmol) in triethylamine (20 mL) was added Pd(PPh3)2Cl2 (210 mg, 0.3 mmol) under N2. The mixture was heated at 70 0C and stirred for 24 hours. The solid was filtered off and washed with EtOAc (50 mL x 3). The filtrate was evaporated under reduced pressure, and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give 2- (cyclopropylethynyl)-4-nitroaniline (470 mg, 23%). 1H NMR (300 MHz, CDCl3) δ 8.14 (d, J = 2.1 Hz, IH), 7.97 (dd, / = 2.7, 9.0 Hz, IH), 6.63 (d, / = 9.0 Hz, IH), 4.81 (brs, 2H), 1.55- 1.46 (m, IH), 0.98-0.90 (m, 2H), 0.89-0.84 (m, 2H).
Figure imgf000175_0001
[00532] iV-(2-(Cyclopropylethynyl)phenyl)-4-nitrobutyramide
[00533] To a solution of 2-(cyclopropylethynyl)-4-nitroaniline (3.2 g, 15.8 mmol) and pyridine (2.47 g, 31.7 mmol) in CH2Cl2 (60 mL) was added butyryl chloride (2.54 g, 23.8 mmol) at 0 0C. The mixture was warmed to room temperature and stirred for 3 hours. The resulting mixture was poured into ice-water. The organic layer was separated. The aqueous phase was extracted with CH2Cl2 (30 m L x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give N-(2-(cyclopropylethynyl)phenyl)-4-nitrobutyramide (3.3 g, 76%). 1H NMR (400 MHz, CDCl3) δ 8.61 (d, / = 9.2 Hz, IH), 8.22 (d, / = 2.8 Hz, IH), 8.18 (brs, IH), 8.13 (dd, J = 2.4, 9.2 Hz, IH), 2.46 (t, J = 7.2 Hz, 2H), 1.83-1.76 (m, 2H), 1.59-1.53 (m, IH), 1.06 (t, J = 7.2 Hz, 3H), 1.03-1.01 (m, 2H), 0.91-0.87 (m, 2H).
Figure imgf000175_0002
[00534] 2-Cyclopropyl-5-nitro- lH-indole
[00535] A mixture of N-(2-(cyclopropylethynyl)phenyl)-4-nitrobutyramide (3.3 g, 0.01 mol) and TBAF (9.5 g, 0.04 mol) in THF (100 mL) was heated at reflux for 24 hours. The mixture was cooled to the room temperature and poured into ice water. The mixture was extracted with CH2Cl2 (50 m L x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give 2- cyclopropyl-5-nitro-lH-indole (1.3 g, 64%). 1H NMR (400 MHz, CDCl3) δ 8.44 (d, J = 2.0 Hz, IH), 8.40 (brs, IH), 8.03 (dd, / = 2.0, 8.8 Hz, IH), 7.30 (d, / = 8.8 Hz, IH), 6.29 (d, / = 0.8 Hz, IH), 2.02-1.96 (m, IH) 1.07-1.02 (m, 2H), 0.85-0.81(m, 2H). Raney NI
Figure imgf000176_0002
Figure imgf000176_0001
[00536] 2-Cyclopropyl- lH-indol-5-amine
[00537] To a solution of 2-cyclopropyl-5-nitro-lH-indole (1.3 g, 6.4 mmol) in MeOH (30 mL) was added Raney Nickel (0.3 g) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The catalyst was filtered through a Celite pad and the filtrate was evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 5/1) to give 2-cyclopropyl-lH-indol-5-amine (510 mg, 56%). 1H NMR (400 MHz, CDCl3) δ 6.89 (d, / = 8.4 Hz, IH), 6.50 (d, / = 1.6 Hz, IH), 6.33 (dd, / = 2.0, 8.4 Hz, IH), 5.76 (s, IH), 4.33 (brs, 2H), 1.91-1.87 (m, IH), 0.90-0.85(m, 2H), 0.70-0.66 (m, 2H); MS (ESI) m/e (M+H+) 173.2.
[00538] Example 34: 3-fert-Butyl-lH-indol-5-amine
Figure imgf000176_0003
[00539] 3-fert-Butyl-5-nitro-lH-indole
[00540] To a mixture of 5-nitro-lH-indole (6 g, 36.8 mmol) and AlCl3 (24 g, 0.18 mol) in CH2Cl2 (100 mL) was added 2-bromo-2-methyl-propane (8.1 g, 36.8 mmol) dropwise at 0 0C. After being stirred at 15 0C overnight, the reaction mixture was poured into ice (100 mL). The precipitated salts were removed by filtration and the aqueous layer was extracted with CH2Cl2 (30 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4 and concentrated under vacuum to obtain the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 20:1) to give 3-tert-butyl- 5 -nitro-lH-indole (2.5 g, 31%). 1H NMR (CDCl3, 400 MHz) δ 8.49 (d, / = 1.6 Hz, IH), 8.31 (brs, IH), 8.05 (dd, / = 2.0, 8.8 Hz, IH), 7.33 (d, / = 8.8 Hz, IH), 6.42 (d, / = 1.6 Hz, IH), 1.42 (s, 9H).
Figure imgf000177_0001
[00541] 3-fert-Butyl-lH-indol-5-amine
[00542] To a solution of 3-tert-butyl-5-nitro-lH-indole (2.5 g, 11.6 mmol) in MeOH (30 mL) was added Raney Nickel (0.2 g) under N2 protection. The mixture was stirred under hydrogen atmosphere (1 atm) at 15 0C for 1 hr. The catalyst was filtered off and the filtrate was concentrated under vacuum to dryness. The residue was purified by preparative HLPC to afford 3-tert-butyl-lH-indol-5-amine (0.43 g, 19%). 1H NMR (CDCl3, 400 MHz) δ 7.72 (brs, IH), 7.11 (d, / = 8.4 Hz, IH), 6.86 (d, / = 2.0 Hz, IH), 6.59 (dd, / = 2.0, 8.4 Hz, IH), 6.09 (d, / = 1.6 Hz, IH), 1.37 (s, 9H); MS (ESI) m/e (M+H+) 189.1.
[00543] Example 35: 2-Phenyl-lH-indol-5-amine
Figure imgf000177_0002
Raney Ni
Figure imgf000177_0003
Figure imgf000177_0004
Figure imgf000177_0005
[00544] 2-Bromo-4-nitroaniline
[00545] To a solution of 4-nitroaniline (50 g, 0.36 mol) in AcOH (500 mL) was added liquid Br2 (60 g, 0.38 mol) dropwise at 5 0C. The mixture was stirred for 30 min at that temperature. The insoluble solid was collected by filtration and poured into EtOAc (200 mL). The mixture was basified with saturated aqueous NaHCO3 to pH 7. The organic layer was separated. The aqueous phase was extracted with EtOAc (300 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give 2-bromo-4- nitroaniline (56 g, 72%), which was directly used in the next step.
Figure imgf000178_0001
[00546] 4-Nitro-2-(phenylethynyl)aniline
[00547] To a deoxygenated solution of 2-bromo-4-nitroaniline (2.17 g, 0.01 mmol), ethynyl-benzene (1.53 g, 0.015 mol) and CuI (10 mg, 0.05 mmol) in triethylamine (20 mL) was added Pd(PPh3)2Cl2 (210 mg, 0.2 mmol) under N2. The mixture was heated at 70 0C and stirred for 24 hours. The solid was filtered off and washed with EtOAc (50 mL x 3). The filtrate was evaporated under reduced pressure and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give 4-nitro-2- (phenylethynyl)aniline (340 mg, 14%). 1H NMR (300 MHz, CDCl3) δ 8.37-8.29 (m, IH), 8.08-8.00 (m, IH), 7.56-7.51 (m, 2H), 7.41-7.37 (m, 3H), 6.72 (m, IH), 4.95 (brs, 2H).
Figure imgf000178_0002
[00548] N-(2-(Phenylethynyl)phenyl)-4-nitrobutyramide
[00549] To a solution of 4-nitro-2-(phenylethynyl)aniline (17 g, 0.07 mmol) and pyridine (11.1 g, 0.14 mol) in CH2Cl2 (100 mL) was added butyryl chloride (11.5 g, 0.1 mol) at 0 0C. The mixture was warmed to room temperature and stirred for 3 hours. The resulting mixture was poured into ice-water. The organic layer was separated. The aqueous phase was extracted with CH2Cl2 (30 m L x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give N- (2- (phenylethynyl)phenyl)-4-nitrobutyramide (12 g, 55%). 1H NMR (400 MHz, CDCl3) δ 8.69 (d, / =9.2 Hz, IH), 8.39 (d, / =2.8 Hz, IH), 8.25-8.20 (m, 2H), 7.58-7.55 (m, 2H), 7.45-7.42 (m, 3H), 2.49 (t, / =7.2 Hz, 2H), 1.85-1.79 (m, 2H), 1.06 (t, / = 7.2 Hz, 3H).
Figure imgf000178_0003
[00550] 5-Nitro-2-phenyl-lH-indole [00551] A mixture of N-(2-(phenylethynyl)phenyl)-4-nitrobutyramide (5.0 g, 0.020 mol) and TBAF (12.7 g, 0.050 mol) in THF (30 niL) was heated at reflux for 24 h. The mixture was cooled to room temperature and poured into ice water. The mixture was extracted with CH2Cl2 (50 m L x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give 5-nitro-2-phenyl-lH-indole (3.3 g, 69%). 1H NMR (400 MHz, CDCl3) δ 8.67 (s, IH), 8.06 (dd, / = 2.0, 8.8 Hz, IH), 7.75 (d, / =7.6 Hz, 2H), 7.54 (d, / =8.8 Hz, IH), 7.45 (t, / =7.6 Hz, 2H), 7.36 (t, / = 7.6 Hz, IH). 6.95 (s, IH).
Raney Ni
Figure imgf000179_0002
Figure imgf000179_0001
[00552] 2-Phenyl-lH-indol-5-amine
[00553] To a solution of 5-nitro-2-phenyl-lH-indole (2.83 g, 0.01 mol) in MeOH (30 mL) was added Raney Ni (510 mg) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The catalyst was filtered through a Celite pad and the filtrate was evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 5/1) to give 2-phenyl-lH-indol-5 -amine (1.6 g, 77%). 1H NMR (400 MHz, CDCl3) δ 7.76 (d, / =7.6 Hz, 2H), 7.39 (t, / = 7.6 Hz, 2H), 7.24 (t, / = 7.6 Hz, IH), 7.07 (d, / = 8.4 Hz, IH), 6.64 (d, / = 1.6 Hz, IH), 6.60 (d, / =1.2 Hz, IH), 6.48 (dd, / = 2.0, 8.4 Hz, IH), 4.48 (brs, 2H); MS (ESI) m/e (M+H+) 209.0.
[00554] Example 36: 2-fert-Butyl-4-fluoro-lH-indol-5-amine
Figure imgf000179_0003
Figure imgf000179_0004
[00555] 2-Bromo-3-fluoroaniline
[00556] To a solution of 2-bromo-l-fluoro-3 -nitrobenzene (1.0 g, 5.0 mmol) in CH3OH (50 mL) was added NiCl2 (2.2 g 10 mmol) and NaBH4 (0.50 g 14 mmol) at 00C. After the addition, the mixture was stirred for 5 min. Water (20 mL) was added and the mixture was extracted with EtOAc (20 mL x 3). The organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum to give 2-bromo-3-fluoroaniline (600 mg, 70%). 1H NMR (400 MHz, CDCl3) δ 7.07-7.02 (m, 1 H), 6.55-6.49(m, 1 H), 4.22 (br s, 2 H).
Figure imgf000180_0001
[00557] N-(2-Bromo-3-fluorophenyl)butyramide
[00558] To a solution of 2-bromo-3-fluoroaniline (2.0 g, 11 mmol) in CH2Cl2 (50 mL) was added butyryl chloride (1.3 g, 13 mmol) and pyridine (1.7 g, 21 mmol) at 00C. The mixture was stirred at room temperature for 24 h. Water (20 mL) was added and the mixture was extracted with CH2Cl2 (50 mL x 3). The organic layers were dried anhydrous over Na2SO4 and evaporated under vacuum to give N-(2-bromo-3-fluorophenyl)butyramide (2.0 g, 73%), which was directly used in the next step.
Figure imgf000180_0002
[00559] iV-(2-(3,3-Dimethylbut-l-ynyl)-3-fluorophenyl)butyramide
[00560] To a solution of N-(2-bromo-3-fluorophenyl)butyramide (2.0 g, 7.0 mmol) in Et3N (100 mL) was added 4,4-dimethylpent-2-yne (6.0 g, 60 mmol), CuI (70 mg, 3.8 mmol), and Pd(PPh3)2Cl2 (500 mg) successively at room temperature under N2. The mixture was heated at 800C overnight. The cooled mixture was filtered and the filtrate was extracted with EtOAc (40 mL x 3). The organic layers were washed with sat. NaCl, dried over anhydrous Na2SO4, and evaporated under vacuum. The crude compound was purified by column chromatography on silica gel (10% EtOAc in petroleum ether) to give N-(2-(3,3-dimethylbut- l-ynyl)-3-fluorophenyl)butyramide (1.1 g, 55%). 1H ΝMR (400 MHz, CDCl3) δ 8.20 (d, J = 7.6, 1 H), 7.95 (s, 1 H), 7.21 (m, 1 H), 6.77 (t, J = 7.6 Hz, 1 H), 2.39 (t, J = 7.6 Hz, 2 H), 1.82-1.75 (m, 2 H), 1.40 (s, 9 H), 1.12 (t, / = 7.2 Hz, 3 H).
Figure imgf000181_0001
[00561] 2-fert-Butyl-4-fluoro-lH-indole
[00562] To a solution of N-(2-(3,3-dimethylbut-l-ynyl)-3-fluorophenyl)butyramide (6.0 g, 20 mmol) in DMF (100 mL) was added Z-BuOK (5.0 g, 50 mmol) at room temperature. The mixture was heated at 90 0C overnight before it was poured into water and extracted with EtOAc (100 mL x 3). The organic layers were washed with sat. NaCl and water, dried over anhydrous Na2SO4, and evaporated under vacuum to give 2-terZ-butyl-4-fluoro-lH-indole (5.8 g, 97%). 1H NMR (400 MHz, CDCl3) δ 8.17 (br s, 1 H), 7.11 (d, /=7.2 Hz, 1 H), 7.05- 6.99 (m, 1 H), 6.76-6.71 (m, 1 H), 6.34 (m, 1 H), 1.41 (s, 9 H).
Figure imgf000181_0002
[00563] 2-fert-Butyl-4-fluoro-5-nitro-lH-indole
[00564] To a solution of 2-terZ-butyl-4-fluoro-lH-indole (2.5 g, 10 mmol) in H2SO4 (30 mL) was added KNO3 (1.3 g, 10 mmol) at 00C. The mixture was stirred for 0.5 h at -10 0C. The mixture was poured into water and extracted with EtOAc (100 mL x 3). The organic layers were washed with sat. NaCl and water, dried over anhydrous Na2SO4, and evaporated under vacuum. The crude compound was purified by column chromatography on silica gel (10% EtOAc in petroleum ether) to give 2-terZ-butyl-4-fluoro-5-nitro-lH-indole (900 mg, 73%). 1H NMR (400 MHz, CDCl3) δ 8.50 (br s, 1 H), 7.86 (dd, / = 7.6, 8.8 Hz, 1 H), 7.13 (d, J = 8.8 Hz, 1 H), 6.52 (dd, J = 0.4, 2.0 Hz, 1 H), 1.40 (s, 9 H).
Figure imgf000181_0003
[00565] 2-fert-Butyl-4-fluoro-lH-indol-5-amine
[00566] To a solution of 2-ferZ-butyl-4-fluoro-5-nitro- lH-indole (2.1 g, 9.0 mmol) in methanol (50 mL) was added NiCl2 (4.2 g, 18 mmol) and NaBH4 (1.0 g, 27 mmol) at 00C. After the addition, the mixture was stirred for 5 min. Water (20 mL) was added and the mixture was extracted with EtOAc (30 mL x 3). The organic layers were washed with sat. NaCl and water, dried over anhydrous Na2SO4, evaporated under vacuum to give 2-tert-butyl- 4-fluoro-lH-indol-5-amine (900 mg, 50%). 1H NMR (300 MHz, CDCl3) δ 7.80 (brs, 1 H), 6.91 (d, / = 8.4 Hz, 1 H), 6.64 (dd, / = 0.9, 2.4 Hz, 1 H), 6.23 (s, 1 H), 1.38 (s, 9 H).
[00567] Example 37: 2,3,4,9-Tetrahydro-lH-carbazol-6-amine
Figure imgf000182_0001
[00568] 2,3,4,9-Tetrahydro-lH-carbazol-6-amine
[00569] 6-Nitro-2,3,4,9-tetrahydro-lH-carbazole (0.100 g, 0.462 mmol) was dissolved in a 40 mL scintillation vial containing a magnetic stir bar and 2 mL of ethanol. Tin(II) chloride dihydrate (1.04 g, 4.62 mmol) was added to the reaction mixture and the resulting suspension was heated at 70 0C for 16 h. The crude reaction mixture was then diluted with 15 mL of a saturated aqueous solution of sodium bicarbonate and extracted three times with an equivalent volume of ethyl acetate. The ethyl acetate extracts were combined, dried over sodium sulfate, and evaporated to dryness to yield 2,3,4,9-tetrahydro-lΗ-carbazol-6-amine (82 mg, 95%) which was used without further purification.
[00570] Example 38: 2-fert-Butyl-7-fluoro-lH-indol-5-amine
Figure imgf000182_0002
Raney-Nι/H2
Figure imgf000182_0003
Figure imgf000182_0004
Figure imgf000182_0005
[00571] 2-Bromo-6-fluoro-4-nitro-phenylamine
[00572] To a solution of 2-fluoro-4-nitro-phenylamine (12 g, 77 mmol) in AcOH (50 mL) was added Br2 (3.9 mL, 77 mmol) dropwise at 0 0C. The mixture was stirred at 20 0C for 3 h. The reaction mixture was basified with sat. aq. NaHCO3, and extracted with EtOAc (100 mL x 3). The combined organics were dried over anhydrous Na2SO4 and evaporated under vacuum to give 2-bromo-6-fluoro-4-nitro-phenylamine (18 g, 97%). 1H NMR (400 MHz, CDCl3) δ 8.22 (m, 1 H), 7.90 (dd, / = 2.4, 10.8 Hz, 1 H), 4.88 (brs, 2 H).
Figure imgf000183_0001
[00573] 2-(3,3-Dimethyl-but-l-ynyl)-6-fluoro-4-nitro-phenylamine
[00574] To a solution of 2-bromo-6-fluoro-4-nitro-phenylamine (11 g, 47 mmol) in dry Et3N (100 mL) was added CuI (445 mg, 5% mol), Pd(PPh3)2Cl2 (550 mg, 5% mol) and 3,3- dimethyl-but-1-yne (9.6 g, 120 mmol) under N2 protection. The mixture was stirred at 80 0C for 10 h. The reaction mixture was filtered, poured into ice (100 g), and extracted with EtOAc (50 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 50:1) to give 2-(3,3-dimethyl- but-l-ynyl)-6-fluoro-4-nitro-phenylamine (4.0 g, 36%). 1H NMR (400 MHz, CDCl3) δ 8.02 (d, J = 1.2 Hz, 1 H), 7.84 (dd, J = 2.4, 10.8 Hz, 1 H), 4.85 (brs, 2 H), 1.36 (s, 9 H).
Figure imgf000183_0002
[00575] iV-[2-(3,3-Dimethyl-but-l-ynyl)-6-fluoro-4-nitro-phenyl]-butyramide
[00576] To a solution of 2-(3,3-dimethyl-but-l-ynyl)-6-fluoro-4-nitro-phenylamine (4.0 g, 17 mmol) and pyridine (2.7 g, 34 mmol) in anhydrous CH2Cl2 (30 mL) was added and butyryl chloride (1.8 g, 17 mmol) dropwise at 0 0C. After stirring for 5 h at 0 0C, the reaction mixture was poured into ice (50 g) and extracted with CH2Cl2 (30 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give N- [2-(3,3-dimethyl- but-l-ynyl)-6-fluoro-4-nitro-phenyl]-butyramide (3.2 g, 62%), which was used in the next step without further purification. 1H ΝMR (300 MHz, DMSO) δ 8.10 (dd, J = 1.5, 2.7 Hz, 1 H), 7.95 (dd, J = 2.4, 9.6 Hz, 1 H), 7.22 (brs, 1 H), 2.45 (t, J = 7.5 Hz, 2 H), 1.82 (m, 2 H), 1.36 (s, 9 H), 1.06 (t, / = 7.5 Hz, 3 H).
Figure imgf000184_0001
[00577] 2-fert-Butyl-7-fluoro-5-nitro-lH-indole
[00578] To a solution of N-[2-(3,3-dimethyl-but- 1-ynyl)- 6-fluoro-4-nitro-phenyl]- butyramide (3.2 g, 10 mmol) in DMF (20 niL) was added t-BuOK (2.3 g, 21 mmol) at room temperature. The mixture was heated at 120 0C for 2 g before being cooled down to room temperature. Water (50 mL) was added to the reaction mixture and the resulting mixture was extracted with CH2Cl2 (30 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give 2-terZ-butyl-7-fluoro- 5-nitro-lH- indole (2.0 g, 81%), which was used in the next step without further purification. 1H NMR (300 MHz, CDCl3) δ 9.95 (brs, 1 H), 8.30 (d, / = 2.1 Hz, 1 H), 7.74 (dd, / = 1.8, 11.1 Hz, 1 H), 6.43 (dd, / = 2.4, 3.3 Hz, 1 H), 1.43 (s, 9 H).
Raney Nι/H2
Figure imgf000184_0002
Figure imgf000184_0003
[00579] 2-fert-Butyl-7-fluoro-lH-indol-5-amine
[00580] To a solution of 2-tert-butyl-7-fluoro- 5-nitro-lH-indole (2.0 g, 8.5 mmol) in MeOH (20 mL) was added Ni (0.3 g) under nitrogen atmosphere. The reaction mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The catalyst was filtered off through the celite pad and the filtrate was evaporated under vacuum. The crude product was purified by column chromatography on silica gel (petroleum ether/ethyl acetate 100: 1) to give 2-te^butyl-7-fluoro-lH-indol-5-amine (550 mg, 24%). 1H NMR (300 MHz, CDCl3) δ 7.87 (brs, 1 H), 6.64 (d, / = 1.5 Hz, 1 H), 6.37 (dd, / = 1.8, 12.3 Hz, 1 H), 6.11 (dd, J = 2.4, 3.6 Hz, 1 H), 1.39 (s, 9 H). MS (ESI) m/z (M+H+) 207.
[00581] Example 39: 5-Amino-2-ter/-butyl-lH-indole-7-carbonitrile
Figure imgf000184_0004
Figure imgf000185_0001
[00582] 2-Amino-3-(3,3-dimethylbut-l-ynyl)- 5-nitrobenzonitrile
[00583] To a stirred solution of 2-amino-3-bromo-5-nitrobenzonitrile (2.4 g, 10 mmol) in dry Et3N (60 mL) was added CuI (380 mg, 5% mol) and Pd(PPh3)2Cl2 (470 mg, 5% mol) at room temperature. 3,3-dimethyl-but-l-yne (2.1 g, 25 mmol) was added dropwise to the mixture at room temperature. The reaction mixture was stirred at 80 0C for 1O h. The reaction mixture was filtered and the filtrate was poured into ice (60 g), extracted with ethyl acetate. The phases were separated and the organic phase was dried over Na2SO4. The solvent was removed under vacuum to obtain the crude product, which was purified by column chromatography (2-10% EtOAc in petroleum ether) to obtain 2-amino-3-(3,3- dimethylbut-1-ynyl)- 5-nitrobenzonitrile (1.7 g, 71%). 1H NMR (300 MHz, CDCl3) δ 8.28 (d, J = 2.7 Hz, 1 H), 8.27 (d, J = 2.7 Hz, 1 H), 5.56 (br s, 2 H), 1.37 (s, 9 H).
Figure imgf000185_0002
[00584] 2-ter/-Butyl-5-nitro-lH-indole-7-carbonitrile
[00585] To a solution of 2-amino-3-(3,3-dimethylbut-l-ynyl)- 5-nitrobenzonitrile (1.7 g, 7.0 mmol) in THF (35 mL) was added TBAF (9.5 g, 28 mmol) at room temperature. The mixture was heated at reflux overnight. The reaction mixture was cooled and the THF was removed under reduced pressure. Water (50ml) was added to the residue and the mixture was extracted with EtOAc. The organics were dried over Na2SO4 and the solvent was evaporated under vacuum to obtain 0.87 g of crude product 2-ferZ-butyl-5-nitro-lH-indole-7-carbonitrile which was used directly in the next step without purification.
Figure imgf000185_0003
[00586] 5-Amino-2-fert-butyl- lH-indol-7-carbonitrile [00587] To a solution of crude product 2-^rf-butyl-5-nitro-lH-indole-7-carbonitrile (0.87 g, 3.6 mmol) in MeOH (10 mL) was added NiCl2-OH2O (1.8 g, 7.2 mmol) at -5 0C. The reaction mixture was stirred for 30 min, then NaBH4 (0.48g, 14.32 mmol) was added to the reaction mixture at 0 0C. After 5 min, the reaction mixture was quenched with water, filtered and extracted with EtOAc. The combined organic layers were dried over Na2SO4 and concentrated under vacuum to obtain the crude product, which was purified by column chromatography (5-20% EtOAc in petroleum ether) to obtain 5-amino-2-terZ-butyl-lH-indol- 7-carbonitrile (470 mg, 32% over two steps). 1H NMR (400 MHz, CDCl3) δ 8.25 (s, 1 H), 7.06 (d, J =2.4 Hz, 1 H), 6.84 (d, J = 2.4 Hz, 1 H), 6.14 (d, J = 2.4 Hz, 1 H), 3.57 (br s, 2 H), 1.38 (s, 9 H). MS (ESI) m/z: 214 (M+H+).
[00588] Example 40: Methyl 5-amino-2-ferM)utyl-lH-indole-7-carboxylate
Figure imgf000186_0001
[00589] 2-fert-Butyl-5-nitro-lH-indole-7-carboxylic acid
[00590] 2-^rf-Butyl-5-nitro-lH-indole-7-carbonitrile (4.6 g, 19 mmol) was added to a solution of KOH in EtOH (10%, 100 mL) and the mixture was heated at reflux overnight. The solution was evaporated to remove alcohol, a small amount of water was added, and then the mixture was acidified with dilute hydrochloric acid. Upon standing in the refrigerator, an orange-yellow solid precipitated, which was purified by chromatography on silica gel (15% EtOAc in petroleum ether) to afford 2-terZ-butyl-5-nitro-lH-indole-7-carboxylic acid (4.0 g, 77%). 1H NMR (CDCl3, 300 MHz) δ 10.79 (brs, 1 H), 8.66 (s, 1 H), 8.45(s, 1 H), 6.57 (s, 1 H), 1.39 (s, 9 H).
Figure imgf000186_0002
[00591] Methyl 2-fert-butyl-5-nitro-lH-indole-7-carboxylate [00592] SOCl2 (3.6 g, 30mol) was added dropwise to a solution of 2-tørt-butyl-5-nitro-lH- indole-7-carboxylic acid (4.0 g, 15 mol) and methanol (30 mL) at 00C. The mixture was stirred at 80 0C for 12 h. The solvent was evaporated under vacuum and the residue was purified by column chromatography on silica gel (5% EtOAc in petroleum ether) to afford methyl 2-te?t-butyl-5-nitro-lH-indole-7-carboxylate (2.95 g, 70%). 1H NMR (CDCl3, 300 MHz) δ 9.99 (brs, 1 H), 8.70 (d, / = 2.1 Hz, 1 H), 8.65 (d, / = 2.1 Hz, 1 H), 6.50 (d, / = 2.4 Hz, 1 H), 4.04 (s, 3H), 1.44(s, 9H).
Figure imgf000187_0001
[00593] Methyl 5-amino-2-ferM)utyl-lH-indole-7-carboxylate
[00594] A solution of 2-ferf-butyl-5-nitro-lH-indole-7-carboxylate (2.0 g, 7.2 mmol) and Raney Nickel (200 mg) in CH3OH (50 mL) was stirred for 5 h at the room temperature under H2 atmosphere. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum to give methyl 5-amino-2-tert-butyl-lH-indole-7-carboxylate (1.2 g, 68%) 1H NMR (CDCl3, 400 MHz) δ 9.34 (brs, IH), 7.24 (d, / = 1.6 Hz, IH), 7.10 (s, IH), 6.12 (d, J = 1.6 Hz, IH), 3.88 (s, 3H), 1.45 (s, 9H).
[00595] Example 41: (5-Amino-2-fert-butyl-lH-indol-7-yl)methanol
Figure imgf000187_0002
[00596] (2-fert-Butyl-5-nitro-lH-indol-7-yl) methanol
[00597] To a solution of methyl 2-^rf-butyl-5-nitro-lH-indole-7-carboxylate (6.15 g, 22.3 mmol) and dichloromethane (30ml) was added DIBAL-H (1.0 M, 20 mL, 20 mmol) at 78 °C. The mixture was stirred for 1 h before water (10 mL) was added slowly. The resulting mixture was extracted with EtOAc (120 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give (2-terZ-butyl-5-nitro-lH-indol- 7-yl)methanol (4.0 g, 73%), which was used in the next step directly. Raney Nι/H2
Figure imgf000188_0002
Figure imgf000188_0001
[00598] (5-Amino-2-tert-butyl-lH-indol-7-yl)methanol
[00599] A mixture of (2-^rf-butyl-5-nitro-lH-indol-7-yl)methanol (4.0 g, 16 mmol) and Raney Nickel (400 mg) in CH3OH (100 mL) was stirred for 5 g at room temperature under H2. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum to give (5-amino-2-te?t-butyl-lH-indol-7-yl)methanol (3.4g, 80%). 1H NMR (CDCl3, 400 MHz) δ 8.53 (br s, IH), 6.80 (d, J = 2.0 Hz, 1 H), 6.38 (d, / = 1.6 Hz, 1 H), 4.89 (s, 2 H), 1.37 (s, 9H).
[00600] Example 42: 2-(l-Methylcyclopropyl)-lH-indol-5-amine
Figure imgf000188_0003
\ n-BuLi
\
^Si- 7 .Si-
Me2SO4
[00601] TrimethyHl-methyl-cyclopropylethynyO-silane
[00602] To a solution of cyclopropylethynyl-trimethyl-silane (3.0 g, 22 mmol) in ether (20 mL) was added dropwise n-BuLi (8.6 mL, 21.7 mol, 2.5 M solution in hexane) at 0 0C. The reaction mixture was stirred at ambient temperature for 24 h before dimethyl sulfate (6.85 g, 54.3 mmol) was added dropwise at -10 0C. The resulting solution was stirred at 10 0C and then at 20 0C for 30 min each. The reaction was quenched by adding a mixture of sat. aq. NH4Cl and 25% aq. ammonia (1:3, 100 mL). The mixture was then stirred at ambient temperature for 1 h. The aqueous phase was extracted with diethyl ether (3 x 50 mL) and the combined organic layers were washed successively with 5% aqueous hydrochloric acid (100 mL), 5% aq. NaHCθ3 solution (100 mL), and water (100 mL). The organics were dried over anhydrous NaSO4 and concentrated at ambient pressure. After fractional distillation under reduced pressure, trimethyl-(l-methyl-cyclopropylethynyl)-silane (1.7 g, 52%) was obtained as a colorless liquid. 1H NMR (400 MHz, CDCl3) δ 1.25 (s, 3 H), 0.92-0.86 (m, 2 H), 0.58- 0.56 (m, 2 H), 0.15 (s, 9 H).
Figure imgf000189_0001
[00603] l-Ethynyl-l-methyl-cyclopropane
[00604] To a solution of trimethyl-(l-methyl-cyclopropylethynyl)-silane (20 g, 0.13 mol) in THF (250 niL) was added TBAF (69 g, 0.26 mol). The mixture was stirred overnight at 20 0C. The mixture was poured into water and the organic layer was separated. The aqueous phase was extracted with THF (50 mL). The combined organic layers were dried over anhydrous Na2SO4 and distilled under atmospheric pressure to obtain 1-ethynyl-l -methyl- cyclopropane (7.0 g, contained 1/2 THF, 34%). 1H NMR (400 MHz, CDCl3) δ 1.82 (s, 1 H), 1.26 (s, 3 H), 0.90-0.88 (m, 2 H), 0.57-0.55 (m, 2 H).
Figure imgf000189_0002
[00605] 2-Bromo-4-nitroaniline
[00606] To a solution of 4-nitro-phenylamine (50 g, 0.36 mol) in AcOH (500 mL) was added Br2 (60 g, 0.38 mol) dropwise at 5 0C. The mixture was stirred for 30 min at that temperature. The insoluble solid was collected by filtration and basified with saturated aqueous NaHCO3 to pH 7. The aqueous phase was extracted with EtOAc (300 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to obtain compound 2-bromo-4-nitroaniline (56 g, 72%), which was directly used in the next step.
Figure imgf000189_0003
[00607] 2-((l-Methylcyclopropyl)ethynyl)-4-nitroaniline
[00608] To a deoxygenated solution of 2-bromo-4-nitroaniline (430 mg, 2.0 mmol) and 1- ethynyl-1 -methyl-cyclopropane (630 mg, 8.0 mmol) in triethylamine (20 mL) was added CuI (76 mg, 0.40 mmol) and Pd(PPh3)2Cl2 (140 mg, 0.20 mmol) under N2. The mixture was heated at 70 0C and stirred for 24 h. The solid was filtered off and washed with EtOAc (50 mL x 3). The filtrate was evaporated under reduced pressure and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to give 2-((l- methylcyclopropyl)ethynyl)-4-nitroaniline (340 mg, 79%). 1H NMR (300 MHz, CDCl3) δ 8.15-8.14 (m, 1 H), 7.98-7.95 (m, 1 H), 6.63 (d, / = 6.9 Hz, 1 H), 4.80 (brs, 2 H), 1.38 (s, 3 H), 1.04-1.01 (m, 2 H), 0.76-0.73 (m, 2 H).
Figure imgf000190_0001
[00609] iV-[2-(l-Methyl-cyclopropylethynyl)-4-nitro-phenyl]-butyramide
[00610] To a solution of 2-((l-methylcyclopropyl)ethynyl)-4-nitroaniline (220 mg, 1.0 mmol) and pyridine (160 mg, 2.0 mol) in CH2Cl2 (20 mL) was added butyryl chloride (140 mg, 1.3 mmol) at 0 0C. The mixture was warmed to room temperature and stirred for 3 h. The mixture was poured into ice-water. The organic layer was separated and the aqueous phase was extracted with CH2Cl2 (30 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to obtain N-[2-(l-methyl- cyclopropyl-ethynyl)-4-nitro-phenyl]-butyramide (230 mg, 82%), which was directly used in the next step.
Figure imgf000190_0002
[00611] 2-(l-Methylcyclopropyl)-5-nitro-lH-indole
[00612] A mixture of N-[2-(l-methyl-cyclopropylethynyl)-4-nitro-phenyl]-butyramide (1.3 g, 4.6 mmol) and TBAF (2.4 g, 9.2 mmol) in THF (20 mL) was heated at reflux for 24 h. The mixture was cooled to room temperature and poured into ice water. The mixture was extracted with CH2Cl2 (30 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to afford 2-(l- methylcyclopropyl)-5-nitro-lH-indole (0.70 g, 71%). 1H NMR (400 MHz, CDCl3) δ 8.56 (brs, 1 H), 8.44 (d, J = 2.0 Hz, 1 H), 8.01 (dd, J = 2.4, 8.8 Hz, 1 H), 7.30 (d, J = 8.8 Hz, 1 H), 6.34 (d, / = 1.6 Hz, 1 H), 1.52 (s, 3 H), 1.03-0.97 (m, 2 H), 0.89-0.83 (m, 2 H).
Figure imgf000191_0001
[00613] 2-(l-Methyl-cyclopropyl)-lH-indol-5-ylamine
[00614] To a solution of 2-(l-methylcyclopropyl)-5-nitro-lH-indole (0.70 g, 3.2 mmol) in EtOH (20 mL) was added Raney Nickel (100 mg) under nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature overnight. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 5/1) to afford 2-(l-methyl-cyclopropyl)-lH -indol-5-ylamine (170 mg, 28%). 1H NMR (400 MHz, CDCl3) δ 7.65 (brs, 1 H), 7.08 (d, / = 8.4 Hz, 1 H), 6.82 (s, 1 H), 6.57 (d, / = 8.4 Hz, 1 H), 6.14 (s, 1 H), 3.45 (brs, 2 H), 1.47 (s, 3 H), 0.82-0.78 (m, 2 H), 0.68-0.63 (m, 2 H).
[00615] Example 43: Methyl 2-(5-amino-lH-indol-2-yl)-2-methylpropanoate
Figure imgf000191_0002
Raney Ni
Figure imgf000191_0003
Figure imgf000191_0004
Figure imgf000191_0005
[00616] Methyl 2,2-dimethyl-3-oxobutanoate [00617] To a suspension of NaH (42 g, 1.1 mol, 60%) in THF (400 mL) was added dropwise a solution of methyl 3-oxobutanoate (116 g, 1.00 mol) in THF (100 mL) at 0 °C. The mixture was stirred for 0.5 h at that temperature before MeI (146 g, 1.1 mol) was added dropwise at 0 0C. The resultant mixture was warmed to room temperature and stirred for 1 h. NaH (42 g, 1.05 mol, 60%) was added in portions at 0 0C and the resulting mixture was continued to stir for 0.5 h at this temperature. MeI (146 g, 1.05 mol) was added dropwise at 0 0C. The reaction mixture was warmed to room temperature and stirred overnight. The mixture was poured into ice water and the organic layer was separated. The aqueous phase was extracted with EtOAc (500 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give methyl 2,2-dimethyl-3-oxobutanoate (85 g), which was used directly in the next step.
Figure imgf000192_0001
[00618] Methyl 3-chloro-2,2-dimethylbut-3-enoate
[00619] To a suspention of PCl5 (270 g, 1.3 mol) in CH2Cl2 (1000 mL) was added dropwise methyl 2,2-dimethyl-3-oxobutanoate (85 g) at 0 0C, following by addition of approximately 30 drops of dry DMF. The mixture was heated at reflux overnight. The reaction mixture was cooled to ambient temperature and slowly poured into ice water. The organic layer was separated and the aqueous phase was extracted with CH2Cl2 (500 mL x 3). The combined organic layers were washed with saturated aqueous NaHCO3 and dried over anhydrous Na2SO4. The solvent was evaporated and the residue was distilled under reduced pressure to give methyl 3-chloro-2,2-dimethylbut-3-enoate (37 g, 23%). 1H NMR (400 MHz, CDCl3) δ 5.33 (s, 1 H), 3.73 (s, 3 H), 1.44 (s, 6 H).
Figure imgf000192_0002
[00620] 3-Chloro-2,2-dimethylbut-3-enoic acid
[00621] A mixture of methyl 3-chloro-2,2-dimethylbut-3-enoate (33 g, 0.2 mol) and NaOH (9.6 g, 0.24 mol) in water (200 mL) was heated at reflux for 5 h. The mixture was cooled to ambient temperature and extracted with ether. The organic layer was discarded. The aqueous layer was acidified with cold 20% HCl solution and extracted ether (200 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give 3- chloro-2,2-dimethyl-but-3-enoic acid (21 g, 70%), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 7.90 (brs, 1 H), 5.37 (dd, J = 2.4, 6.8 Hz, 2 H), 1.47 (s, 6 H).
Figure imgf000193_0001
[00622] 2,2-Dimethyl-but-3-ynoic acid
[00623] Liquid NH3 was condensed in a 3-neck, 250 mL round bottom flask at -78 0C. Na (3.98 g, 0.173 mol) was added to the flask in portions. The mixture was stirred for 2 h at -78 0C before anhydrous DMSO (20 mL) was added dropwise at - 78 0C. The mixture was stirred at room temperature until no more NH3 was given off. A solution of 3-chloro-2,2- dimethyl-but-3-enoic acid (6.5 g, 43 mmol) in DMSO (10 mL) was added dropwise at -40 0C. The mixture was warmed and stirred at 50 0C for 5 h, then stirred at room temperature overnight. The cloudy, olive green solution was poured into cold 20% HCl solution and then extracted three times with ether. The ether extracts were dried over anhydrous Na2SO4 and concentrated to give crude 2,2-dimethyl-but-3-ynoic acid (2 g), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 2.30 (s, 1 H), 1.52 (s, 6 H).
Figure imgf000193_0002
[00624] Methyl 2,2-dimethylbut-3-ynoate
[00625] To a solution of diazomethane (-10 g) in ether (400 mL) was added dropwise 2,2- dimethyl-but-3-ynoic acid (10.5 g, 93.7 mmol) at 0 0C. The mixture was warmed to room temperature and stirred overnight. The mixture was distilled under atmospheric pressure to give crude methyl 2,2-dimethylbut-3-ynoate (14 g), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 3.76 (s, 3 H), 2.28 (s, 1 H), 1.50 (s, 6 H).
Figure imgf000193_0003
[00626] Methyl 4-(2-amino-5-nitrophenyl)-2,2-dimethylbut-3-ynoate [00627] To a deoxygenated solution of compound 2-bromo-4-nitroaniline (9.43 g, 43.7 mmol), methyl 2,2-dimethylbut-3-ynoate (5.00 g, 39.7 mmol), CuI (754 mg, 3.97 mmol) and triethylamine (8.03 g, 79.4 mmol) in toluene/H2O (100/30 mL) was added Pd(PPh3)4 (6.17 g, 3.97 mmol) under N2. The mixture was heated at 70 0C and stirred for 24 h. After cooling, the solid was filtered off and washed with EtOAc (50 mL x 3). The organic layer was separated and the aqueous phase was washed with EtOAc (50 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give a residue, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 10/1) to obtain methyl 4-(2-amino-5-nitrophenyl)-2,2-dimethylbut-3-ynoate (900 mg, 9%). 1H NMR (400 MHz, CDCl3) δ 8.17 (d, J = 2.8 Hz, 1 H), 8.01 (dd, J = 2.8, 9.2 Hz, 1 H), 6.65 (d, J = 9.2 Hz, 1 H), 5.10 (brs, 2 H), 3.80 (s, 3 H), 1.60 (s, 6 H).
Figure imgf000194_0001
[00628] Methyl 4-(2-butyramido-5-nitrophenyl)-2,2-dimethylbut-3-ynoate
[00629] To a solution of methyl 4-(2-amino-5-nitrophenyl)-2,2-dimethylbut-3-ynoate (260 mg, 1.0 mmol) and pyridine (160 mg, 2.0 mol) in CH2Cl2 (20 mL) was added butyryl chloride (140 mg, 1.3 mmol) at 0 0C. The reaction mixture was warmed to room temperature and stirred for 3 h before the mixture was poured into ice- water. The organic layer was separated and the aqueous phase was extracted with CH2Cl2 (30 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to obtain methyl 4-(2-butyramido-5-nitrophenyl)-2,2-dimethylbut-3-ynoate (150 mg, 45%), which was used directly in the next step. 1H NMR (400 MHz, CDCl3) δ 8.79 (brs, 1 H), 8.71 (d, / = 9.2 Hz, 1 H), 8.24 (d, / = 2.8 Hz, 1 H), 8.17 (dd, / = 2.8, 9.2 Hz, 1 H), 3.82 (s, 3 H), 2.55 (t, J = 7.2 Hz, 2 H), 1.85-1.75 (m, 2 H), 1.63 (s, 6 H), 1.06 (t, J = 6.8 Hz, 3 H).
Figure imgf000194_0002
[00630] Methyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate [00631] To a deoxygenated solution of methyl 4-(2-butyramido-5-nitrophenyl)-2,2- dimethylbut-3-ynoate (1.8 g, 5.4 mmol) in acetonitrile (30 mL) was added Pd(CH3CN)2Cl2 (0.42 g, 1.6= mmol) under N2. The mixture was heated at reflux for 24 h. After cooling the mixture to ambient temperature, the solid was filtered off and washed with EtOAc (50 mL x 3). The filtrate was evaporated under reduced pressure to give a residue, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 30/1) to give methyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate (320 mg, 23%). 1H NMR (400 MHz, CDCl3) δ 9.05 (brs, 1 H), 8.52 (d, J = 2.0 Hz, 1 H), 8.09 (dd, J = 2.0, 8.8 Hz, 1 H), 7.37 (d, J = 8.8 Hz, 1 H), 6.54 (d, / = 1.6 Hz, 1 H), 3.78 (d, / = 9.6 Hz, 3 H), 1.70 (s, 6 H).
Raney Ni
Figure imgf000195_0001
Figure imgf000195_0002
[00632] Methyl 2-(5-amino-lH-indol-2-yl)-2-methylpropanoate
[00633] A suspension of methyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate (60 mg, 0.23 mmol) and Raney Nickel (10 mg) in MeOH (5 mL) was hydrogenated under hydrogen (1 atm) at room temperature overnight. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum to give a residue, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 5/1) to give methyl 2-(5-amino- lH-indol-2-yl)-2-methylpropanoate (20 mg, 38%). 1H NMR (400 MHz, CDCl3) δ 8.37 (br s, 1 H), 7.13 (d, J = 8.4 Hz, 1 H), 6.87 (d, J = 2.0 Hz, 1 H), 6.63 (dd, J = 2.0, 8.4 Hz, 1 H), 6.20 (d, / = 1.2 Hz, 1 H), 3.72 (d, / = 7.6 Hz, 3 H), 3.43 (br s, 1 H), 1.65 (s, 6 H); MS (ESI) m/e (M+H+) 233.2.
[00634] Example 44: 2-Isopropyl-lH-indol-5-amine
Figure imgf000195_0003
[00635] 2-Isopropyl-5-nitro-lH-indole [00636] A mixture of methyl 4-(2-butyramido-5-nitrophenyl)-2,2-dimethylbut-3-ynoate (0.50 g, 1.5 mmol) and TBAF (790 mg, 3.0 mmol) in DMF (20 niL) was heated at 70 °C for 24 h. The reaction mixture was cooled to room temperature and poured into ice water. The mixture was extracted with ether (30 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give a residue, which was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 20/1) to give 2-isopropyl-5-nitro-lH-indole (100 mg, 33%). 1H NMR (400 MHz, CDCl3) δ 8.68 (s, 1 H), 8.25 (br s, 1 H), 8.21 (dd, J = 2.4, 10.0 Hz, 1 H), 7.32 (d, J = 8.8 Hz, 1 H), 6.41 (s, 1 H), 3.07-3.14 (m, 1 H), 1.39 (d, / = 6.8 Hz, 6 H).
Raney Ni
Figure imgf000196_0001
Figure imgf000196_0002
[00637] 2-Isopropyl- lH-indol-5-amine
[00638] A suspension of 2-isopropyl-5-nitro-lH-indole (100 mg, 0.49 mmol) and Raney Nickel (10 mg) in MeOH (10 mL) was hydrogenated under hydrogen (1 atm) at the room temperature overnight. The catalyst was filtered off through a celite pad and the filtrate was evaporated under vacuum to give a residue, which was purified by column (petroleum ether/ethyl acetate = 5/1) to give 2-isopropyl-lH-indol-5 -amine (35 mg, 41%). 1H NMR (400 MHz, CDCl3) δ 7.69 (br s, 1 H), 7.10 (d, / = 8.4 Hz, 1 H), 6.86 (d, / = 2.4Hz, 1 H), 6.58 (dd, J = 2.4, 8.8 Hz, 1 H), 6.07 (t, / = 1.2 Hz, 1 H), 3.55 (br s, 2 H), 3.06-2.99 (m, 1 H), 1.33 (d, / = 7.2 Hz, 6 H); MS (ESI) m/e (M+H+) 175.4.
[00639] Example 45: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-(l-hydroxy-2-methylpropan-2- yl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000197_0001
Figure imgf000197_0002
[00640] Triphenyl(2-aminobenzyl)phosphonium bromide
[00641] 2-Aminobenzyl alcohol (60.0 g, 0.487 mol) was dissolved in acetonitrile (2.5 L) and brought to reflux. Triphenylphosphine hydrobromide (167 g, 0.487 mol) was added and the mixture was heated at reflux for 3 h. The reaction mixture was concentrated to approximately 500 mL and left at room temperature for 1 h. The precipitate was filtered and washed with cold acetonitrile followed by hexane. The solid was dried overnight at 40 0C under vacuum to give triphenyl(2-aminobenzyl)phosphonium bromide (193 g, 88%).
Figure imgf000197_0003
[00642] Triphenyl((ethyl(2-carbamoyl)acetate)-2-benzyl)phosphonium bromide
[00643] To a suspension of triphenyl(2-aminobenzyl)phosphonium bromide (190 g, 0.43 mol) in anhydrous dichloromethane (1 L) was added ethyl malonyl chloride (55 ml, 0.43 mol). The reaction was stirred for 3 h at room temperature. The mixture was evaporated to dryness before ethanol (400 mL) was added. The mixture was heated at reflux until a clear solution was obtained. The solution was left at room temperature for 3 h. The precipitate was filtered, washed with cold ethanol followed by hexane and dried. A second crop was obtained from the mother liquor in the same way. In order to remove residual ethanol both crops were combined and dissolved in dichloromethane (approximately 700 mL) under heating and evaporated. The solid was dried overnight at 50 0C under vacuum to give triphenyl((ethyl(2-carbamoyl)acetate)-2-benzyl)-phosphonium bromide (139 g, 58%).
Figure imgf000198_0001
[00644] Ethyl 2-(lH-indol-2-yl)acetate
[00645] Triphenyl((ethyl(2-carbamoyl)acetate)-2-benzyl)phosphonium bromide (32.2 g, 57.3 mmol) was added to anhydrous toluene (150 mL) and the mixture was heated at reflux. Fresh potassium terz-butoxide (7.08 g, 63.1 mmol) was added in portions over 15 minutes. Reflux was continued for another 30 minutes. The mixture was filtered hot through a plug of celite and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (0-30% ethyl acetate in hexane over 45 min) to give ethyl 2- (lH-indol-2-yl)acetate (9.12 g, 78%).
Figure imgf000198_0002
[00646] ter/-Butyl 2-((ethoxycarbonyl)methyl)-lH-indole-l-carboxylate
[00647] To a solution of ethyl 2-(lH-indol-2-yl)acetate (14.7 g, 72.2 mmol) in dichloromethane (150 mL) was added 4-dimethylaminopyridine (8.83 g, 72.2 mmol) and di- tert-butyl carbonate (23.7 g, 108 mmol) in portions. After stirring for 2 h at room temperature, the mixture was diluted with dichloromethane, washed with water, dried over magnesium sulfate and purified by silica gel chromatography (0 to 20% EtOAc in hexane) to give tert-buty\ 2-((ethoxycarbonyl)methyl)-lH-indole-l-carboxylate (20.0 g, 91%).
Figure imgf000198_0003
[00648] ter/-Butyl 2-(2-(ethoxycarbonyl)propan-2-yl)-lH-indole-l-carboxylate
[00649] tert-Butyl 2-((ethoxycarbonyl)methyl)-lH-indole-l-carboxylate (16.7 g, 54.9 mmol) was added to anhydrous THF (100 mL) and cooled to -78 0C. A 0.5M solution of potassium hexamethyldisilazane (165 mL, 82 mmol) was added slowly such that the internal temperature stayed below -60 0C. Stirring was continued for 30 minutes at -78 0C. To this mixture, methyl iodide (5.64 mL, 91 mmol) was added. The mixture was stirred for 30 min at room temperature and then cooled to -78 0C. A 0.5M solution of potassium hexamethyldisilazane (210 mL, 104 mmol) was added slowly and the mixture was stirred for another 30 minutes at -78 0C. More methyl iodide (8.6 mL, 137 mmol) was added and the mixture was stirred for 1.5 h at room temperature. The reaction was quenched with sat. aq. ammonium chloride and partitioned between water and dichloromethane. The aqueous phase was extracted with dichloromethane and the combined organic phases were dried over magnesium sulfate and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (0 to 20% ethylacetate in hexane) to give tert-buty\ 2-(2-(ethoxycarbonyl)propan-2-yl)-lH-indole-l-carboxylate (17.1 g, 94%).
Figure imgf000199_0001
[00650] Ethyl 2-(lH-indol-2-yl)-2-methylpropanoate
[00651] tert-Butyl 2-(2-(ethoxycarbonyl)propan-2-yl)- lH-indole- 1-carboxylate (22.9 g, 69.1 mmol) was dissolved in dichloromethane (200 mL) before TFA (70 mL) was added. The mixture was stirred for 5 h at room temperature. The mixture was evaporated to dryness, taken up in dichloromethane and washed with saturated sodium bicarbonate solution, water, and brine. The product was purified by column chromatography on silica gel (0-20% EtOAc in hexane) to give ethyl 2-(lH-indol-2-yl)-2-methylpropanoate (12.5 g, 78%).
Figure imgf000199_0002
[00652] Ethyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate
[00653] Ethyl 2-(lH-indol-2-yl)-2-methylpropanoate (1.0 g, 4.3 mmol) was dissolved in concentrated sulfuric acid (6 mL) and cooled to -10 0C (salt/ice-mixture). A solution of sodium nitrate (370 mg, 4.33 mmol) in concentrated sulfuric acid (3 mL) was added dropwise over 30 min. Stirring was continued for another 30 min at -10 0C. The mixture was poured into ice and the product was extracted with dichloromethane. The combined organic phases were washed with a small amount of sat. aq. sodium bicarbonate. The product was purified by column chromatography on silica gel (5-30% EtOAc in hexane) to give ethyl 2-methyl-2- (5-nitro-lH-indol-2-yl)propanoate (0.68 g, 57%).
Figure imgf000200_0001
[00654] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propan-l-ol
[00655] To a cooled solution of LiAlH4 (1.0 M in THF, U mL1 Ll mmol) in THF (5 mL) at 0 0C was added a solution of ethyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate (0.20 g, 0.72 mmol) in THF (3.4 mL) dropwise. After addition, the mixture was allowed to warm up to room temperature and was stirred for 3 h. The mixture was cooled to 0 0C before water (2 mL) was slowly added followed by careful addition of 15% NaOH (2 mL) and water (4 mL). The mixture was stirred at room temperature for 0.5 h and was filtered through a short plug of celite using ethyl acetate. The organic layer was separated from the aqueous layer, dried over Na2SO4, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (ethyl acetate/hexane = 1/1) to give 2-methyl-2-(5-nitro-lH- indol-2-yl)propan-l-ol (0.098 g, 58%).
Figure imgf000200_0002
[00656] 2-(5-Amino-lH-indol-2-yl)-2-methylpropan-l-ol
[00657] To a solution of 2-methyl-2-(5-nitro-lH-indol-2-yl)propan-l-ol (0.094 g, 0.40 mmol) in ethanol (4 mL) was added tin chloride dihydrate (0.451 g, 2.0 mmol). The mixture was heated in the microwave at 120 0C for 1 h. The mixture was diluted with ethyl acetate and water before being quenched with saturated aqueous NaHCO3. The reaction mixture was filtered through a plug of celite using ethyl acetate. The organic layer was separated from the aqueous layer, dried over Na2SO4, filtered and evaporated under reduced pressure to give 2- (5-amino-lH-indol-2-yl)-2-methylpropan-l-ol (0.080 g, 98%).
[00658] Example 46: 2-(Pyridin-2-yl)-lH-indol-5-amine
Figure imgf000201_0001
Figure imgf000201_0002
[00659] 4-Nitro-2-(pyridin-2-ylethynyl)aniline
[00660] To the solution of 2-iodo-4-nitroaniline (3.0 g, 11 mmol) in DMF (6OmL) and Et3N (60 niL) was added 2-ethynylpyridine (3.0 g, 45 mmol), Pd(PPh3)2Cl2 (600 mg) and CuI (200 mg) under N2. The reaction mixture was stirred at 60 0C for 12 h. The mixture was diluted with water and extracted with dichloromethane (3 x 100 mL). The combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was purified by chromatography on silica gel (5-10% ethyl acetate/petroleum ether) to afford 4-nitro-2-(pyridin-2-ylethynyl)aniline (1.5 g, 60%). 1H NMR (300 MHz, CDCl3) δ 8.60 (s, 1 H), 8.13 (d, / = 2.1 Hz, 1 H), 7.98 (d, / = 1.8, 6.9 Hz, 1 H), 7.87-7.80 (m, 2 H), 7.42-7.39 (m, 1 H), 7.05 (brs, 2 H), 6.80 (d, / = 6.9 Hz, 1 H).
Figure imgf000201_0003
[00661] 5-Nitro-2-(pyridin-2-yl)-lH-indole
[00662] To the solution of 4-nitro-2-(pyridin- 2-ylethynyl) aniline (1.5 g, 6.3 mmol) in DMF (50 mL) was added t-BuOK (1.5 g, 13 mmol). The reaction mixture was stirred at 90 0C for 2 h. The mixture was diluted with water and extracted with dichloromethane (3 x 50 mL). The combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was purified by chromatography on silica gel (5-10% ethyl acetate/petroleum ether) to afford 5-nitro-2-(pyridin-2-yl)-lH-indole (1.0 g, 67%yield). 1H NMR (300 MHz, d-DMSO) δ 12.40 (s, IH), 8.66 (d, / = 2.1 Hz, 1 H), 8.58 (d, / = 1.8 Hz, 1 H), 8.07-7.91 (m, 3 H), 7.59 (d, / = 6.6 Hz, 1 H), 7.42-7.37 (m, 2 H).
Figure imgf000202_0001
[00663] 2-(Pyridin-2-yl)-lH-indol-5-amine
[00664] To a solution of 5-nitro-2-(pyridin-2-yl)-lH-indole (700 mg, 2.9 mmol) in EtOH (20 mL) was added SnCl2 (2.6 g, 12 mmol). The mixture was heated at reflux for 1O h. Water was added and the mixture was extracted with EtOAc (50 mL x 3). The combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was purified by chromatography on silica gel (5-10% ethyl acetate/petroleum ether) to afford 2-(pyridin-2-yl)-lH-indol-5-amine (120 mg, 20%). 1H NMR (400 MHz, CDCl3) δ 9.33 (brs, 1 H), 8.55 (dd, / = 1.2, 3.6 Hz, 1 H), 7.76-7.67 (m, 2 H), 7.23 (d, J = 6.4 Hz, 1 H), 7.16-7.12 (m, 1 H), 6.94 (d, J = 2.0 Hz, 1 H), 6.84 (d, J = 2.4 Hz, 1 H), 6.71-6.69 (dd, / = 2.0, 8.4 Hz, 1 H).
[00665] Example 47: 2-(Pyridin-2-yl)-lH-indol-5-amine
Figure imgf000202_0002
[00666] [2-(ter/-Butyl-dimethyl-silanyloxy)-ethyl]-(2-iodo-4-nitro-phenyl)-amine
[00667] To a solution of 2-iodo-4-nitroaniline (2.0 g, 7.6 mmol) and 2-(tert- butyldimethylsilyloxy)-acetaldehyde (3.5 g, 75% purity, 15 mmol) in methanol (30 mL) was added TFA (1.5 mL) at 0 0C. The reaction mixture was stirred at this temperature for 30 min before NaCNBH3 (900 mg, 15 mmol) was added in portions. The mixture was stirred for 2 h and was then quenched with water. The resulting mixture was extracted with EtOAc (30 mL x 3), the combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum, and the residue was purified by chromatography on silica gel (5 % ethyl acetate/petroleum) to afford [2-(terf-butyl-dimethyl-silanyloxy)-ethyl]-(2-iodo-4-nitro- phenyl)-amine (800 mg, 25 %). 1H NMR (300 MHz, CDCl3) δ 8.57 (d, J = 2.7 Hz, 1 H), 8.12 (dd, / = 2.4 ,9.0 Hz, 1 H), 6.49 (d, / = 9.3 Hz, 1 H), 5.46 (br s, 1 H), 3.89 (t, / = 5.4 Hz, 2 H), 3.35 (q, J = 5.4 Hz, 2 H), 0.93 (s, 9 H), 0.10 (s, 6 H).
Figure imgf000203_0001
[00668] 5-{2-[2-(ter/-Butyl-dimethyl-silanyloxy)-ethylamino]-5-nitro-phenyl}-3,3- dimethyl-pent-4-ynoic acid ethyl ester
[00669] To a solution of [2-(terf-butyl-dimethyl-silanyloxy)-ethyl]-(2-iodo-4-nitro-phenyl)- amine (800 mg, 1.9 mmol) in Et3N (20 mL) was added Pd(PPh3)2Cl2 (300 mg, 0.040 mmol), CuI (76 mg, 0.040 mmol) and 3,3-dimethyl-but-l-yne (880 mg, 5.7 mmol) successively under N2 protection. The reaction mixture was heated at 800C for 6 h and allowed to cool down to room temperature. The resulting mixture was extracted with EtOAc (30 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give 5-{2-[2-(^rf-butyl-dimethyl-silanyloxy)-ethylamino]-5-nitro-phenyl}-3,3- dimethyl-pent-4- ynoic acid ethyl ester (700 mg, 82 %), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 8.09 (s, 1 H), 8.00 (d, J = 9.2 Hz, 1 H), 6.54 (d, / = 9.2 Hz, 1 H), 6.45 (brs, 1 H), 4.17-4.10 (m, 4 H), 3.82 (t, / = 5.6 Hz, 2 H), 3.43 (q, J = 5.6 Hz, 2 H), 2.49 (s, 2 H), 1.38 (s, 6 H), 1.28 (t, J = 7.2 Hz, 3 H), 0.84 (s, 9 H), 0.00 (s, 6 H).
Figure imgf000203_0002
[00670] 3-[l-(2-Hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3-methyl-butyric acid ethyl ester [00671] A solution of 5-{2-[2-(^rf-butyl-dimethyl-silanyloxy)-ethylamino]-5-nitro- phenyl}-3,3- dimethyl-pent-4- ynoic acid ethyl ester (600 mg, 1.34 mmol) and PdCl2(650 mg) in CH3CN (30 mL) was heated at reflux overnight. The resulting mixture was extracted with EtOAc (30 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum. The residue was dissolved in THF (20 mL) and TBAF (780 mg, 3.0 mmol) was added. The mixture was stirred at room temperature for 1 h, the solvent was removed under vaccum, and the residue was purified by chromatography on silica gel (10% ethyl acetate/petroleum) to afford 3-[l-(2-hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3- methyl-butyric acid ethyl ester (270 mg, 60 %). 1H NMR (300 MHz, CDCl3) δ 8.45 (d, J = 2.1 Hz, 1 H), 8.05 (dd, / = 2.1, 9.0 Hz, 1 H), 6.36 (d, / = 9.0 Hz, 1 H), 6.48 (s, 1 H), 4.46 (t, J = 6.6 Hz, 2 H), 4.00-3.91 (m, 4 H), 2.76 (s, 2 H), 1.61 (s, 6 H), 0.99 (t, J = 7.2 Hz, 1 H), 0.85 (s, 9 H), 0.03 (s, 6 H).
DIBAL-H
Figure imgf000204_0002
Figure imgf000204_0001
[00672] 3-[l-(2-Hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3-methyl-butan-l-ol
[00673] To a solution of 3-[l-(2-hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3-methyl-butyric acid ethyl ester (700 mg, 2.1 mmol) in THF (25 mL) was added DIBAL-H (1.0 M, 4.2 mL, 4.2 mmol) at -78 0C. The mixture was stirred at room temperature for 1 h. Water (2 mL) was added and the resulting mixture was extracted with EtOAc (15 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under vacuum. The residue was purified by chromatography on silica gel (15 % ethyl acetate/petroleum) to afford 3-[l- (2-hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3-methyl-butan-l-ol (300 mg, 49%). 1H NMR (300 MHz, d-DMSO) δ 8.42 (d, / = 1.5 Hz, 1 H), 7.95 (dd, / = 1.2, 8.7 Hz, 1 H), 6.36 (d, / = 9.3 Hz, 1 H), 6.50 (s, 1 H), 5.25 (br s, 1 H), 4.46-4.42 (m, 4 H), 3.69-3.66 (m ,2 H), 3.24-3.21 (m, 2 H), 1.42 (s, 6 H).
Hg/Raney-Ni
Figure imgf000204_0004
Figure imgf000204_0003
[00674] 3-[5-Amino-l-(2-hydroxy-ethyl)-lH-indol-2-yl]-3-methyl-butan-l-ol [00675] A solution of 3-[l-(2-hydroxy-ethyl)-5-nitro-lH-indol-2-yl]-3-methyl-butan-l-ol (300 mg, 1.03 mmol) and Raney Nickel (200 mg,) in CH3OH (30 mL) was stirred for 5 h at room temperature under a H2 atmosphere. The catalyst was filtered through a celite pad and the filtrate was evaporated under vacuum to give a residue, which was purified by preparative TLC to afford 3-[5-amino-l-(2-hydroxy-ethyl)-lH-indol-2-yl]-3-methyl-butan-l-ol (70 mg, 26%). 1H NMR (300 MHz, CDCl3) δ 7.07 (d, J = 8.7 Hz, 1 H), 6.83 (d, J = 2.1 Hz, 1 H), 6.62 (dd, J = 2.1, 8.4 Hz, 1 H), 6.15 (s, 1 H), 4.47 (t, J = 5.4 Hz, 2 H), 4.07 (t, J = 5.4 Hz, 2 H), 3.68 (t, J = 5.7 Hz, 2 H), 2.16 (t, J = 5.7 Hz, 2 H), 4.00-3.91 (m, 4 H), 2.76 (s, 2 H), 1.61 (s, 6 H), 1.42 (s, 6 H).
[00676] Example 48: tert-Butyi 2-(5-amino-lH-indol-2-yl)piperidine-l-carboxylate
Figure imgf000205_0001
[00677] 2-(Piperidin-2-yl)-lH-indol-5-amine
[00678] 5-Nitro-2-(pyridin-2-yl)- lH-indole (1.0 g, 4.2 mmol) was added to HCl/MeOH (2 M, 50 mL). The reaction mixture was stirred at room temperature for 1 h and the solvent was evaporated under vacuum. PtO2 (200 mg) was added to a solution of the residue in MeOH (50 mL) and the reaction mixture was stirred under hydrogen atmosphere (1 atm) at room temperature for 2 h. The catalyst was filtered through a celite pad and the solvent was evaporated under vacuum to afford 2-(piperidin-2-yl)-lH-indol-5-amine (1.0 g), which was directly used in the next step.
Figure imgf000205_0002
[00679] ter/-Butyl 2-(5-amino-lH-indol-2-yl)piperidine-l-carboxylate
[00680] To a solution of 2-(piperidin-2-yl)-lH-indol-5-amine (1.0 g) in Et3N (25 mL) and THF (25mL) was added BoC2O (640 mg, 2.9 mmol). The reaction mixture was stirred at room temperature overnight. The mixture was diluted with water and extracted with dichloromethane (3 x 25 mL). The combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated in vacuum. The residue was purified by chromatography on silica gel (5-10% ethyl acetate/petroleum ether) followed by preparative HPLC to afford tert-buty\ 2-(5-amino-lH-indol-2-yl)piperidine-l-carboxylate (15 mg, 1% over 2 steps). 1H NMR (400 MHz, CDCl3) δ 8.82 (s, 1 H), 7.58 (s, 1 H), 7.22 (d, J = 8.8 Hz, 1 H), 7.02 (d, / = 1.6, 8.0 Hz, 1 H), 6.42 (s, IH), 6.25 (s, 1 H), 3.91-3.88 (m, 1 H), 3.12-3.10 (m, 1 H), 2.81-2.76 (m, 1 H), 2.06-1.97 (m, 4 H), 1.70-1.58 (m, 2H), 1.53 (s, 9 H).
[00681] Example 49: ό-amino-lH-indole^-carbonitrile
Figure imgf000206_0001
(CF3O)2O Raney Ni/H2
Figure imgf000206_0003
Figure imgf000206_0002
Figure imgf000206_0004
[00682] (3-Nitrophenyl)hydrazine hydrochloride
[00683] 3-Nitroaniline (28 g, 0.20 mol) was dissolved in a mixture of H2O (40 mL) and 37% HCl (40 mL). A solution of NaNO2 (14 g, 0.20 mol) in H2O (60 mL) was added to the mixture at 0 0C, and then a solution of SnCl2-H2O (140 g, 0.60 mol) in 37% HCl (100 mL) was added. After stirring at 0 0C for 0.5 h, the insoluble material was isolated by filtration and was washed with water to give (3-nitrophenyl)hydrazine hydrochloride (28 g, 73%).
Figure imgf000206_0005
[00684] (£>Ethyl 2-(2-(3-nitrophenyl)hydrazono)propanoate
[00685] (3-Nitrophenyl)hydrazine hydrochloride (30 g, 0.16 mol) and 2-oxo-propionic acid ethyl ester (22 g, 0.19 mol) were dissolved in ethanol (300 mL). The mixture was stirred at room temperature for 4 h before the solvent was evaporated under reduced pressure to give (£)-ethyl 2-(2-(3-nitrophenyl)hydrazono)propanoate, which was used directly in the next step.
Figure imgf000207_0001
[00686] Ethyl 4-nitro-lH-indole-2-carboxylate and ethyl 6-nitro-lH-indole-2- carboxylate
[00687] (£)-Ethyl 2-(2-(3-nitrophenyl)hydrazono)propanoate was dissolved in toluene (300 mL) and PPA (30 g) was added. The mixture was heated at reflux overnight and then was cooled to room temperature. The solvent was decanted and evaporated to obtain a crude mixture that was taken on to the next step without purification (15 g, 40%).
Figure imgf000207_0002
[00688] 4-Nitro-lH-indole-2-carboxylic acid and 6-nitro-lH-indole-2-carboxylic acid
[00689] A mixture of ethyl 6-nitro-lH-indole-2-carboxylate (0.5 g) and 10 % NaOH (20 mL) was heated at reflux overnight and then was cooled to room temperature. The mixture was extracted with ether and the aqueous phase was acidified with HCl to pH 1-2. The insoluble solid was isolated by filtration to give a crude mixture that was taken on to the next step without purification (0.3 g, 68%).
Figure imgf000207_0003
[00690] 4-Nitro-lH-indole-2-carboxamide and 6-nitro-lH-indole-2-carboxamide
[00691] A mixture of 6-nitro-lH-indole-2-carboxylic acid (12 g, 58 mmol) and SOCl2 (50 mL, 64 mmol) in benzene (150 mL) was heated at reflux for 2 h. The benzene and excess SOCl2 was removed under reduced pressure. The residue was dissolved in anhydrous CH2Cl2 (250 mL) and NH3-H2O (22 g, 0.32 mol) was added dropwise at 0 0C. The mixture was stirred at room temperature for 1 h. The insoluble solid was isolated by filtration to obtain crude mixture (9.0 g, 68%), which was used directly in the next step.
Figure imgf000207_0004
[00692] 4-Nitro-lH-indole-2-carbonitrile and 6-nitro-lH-indole-2-carbonitrile
[00693] 6-Nitro-lH-indole-2-carboxamide (5.0 g, 24 mmol) was dissolved in CH2Cl2 (200 niL). Et3N (24 g, 0.24 mol) and (CF3CO)2O (51 g, 0.24 mol) were added dropwise to the mixture at room temperature. The mixture was continued to stir for 1 h and was then poured into water (100 mL). The organic layer was separated and the aqueous layer was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over Na2SO4, filtered and concentrated under reduced pressure to obtain crude product which was purified by column chromatography on silica gel to give a impure sample of 4-nitro-lH-indole-2- carbonitrile (2.5 g, 55%).
Raney IWH2
Figure imgf000208_0002
Figure imgf000208_0001
[00694] 6-Amino-lH-indole-2-carbonitrile
[00695] A mixture of 6-nitro-lH-indole-2-carbonitrile (2.5 g, 13 mmol) and Raney Nickel (500 mg) in EtOH (50 mL) was stirred at room temperature under H2 (1 atm) for 1 h. Raney Nickel was removed via filtration and the filtrate was evaporated under reduced pressure to give a residue, which was purified by column chromatograpy on silica get to give 6-amino- lH-indole-2-carbonitrile (1.0 g, 49 %). 1H NMR (DMSO-J6) δ 12.75 (br s, 1 H), 7.82 (d, / = 8 Hz, 1 H), 7.57 (s, IH), 7.42 (s, 1 H), 7.15 (d, / = 8 Hz, 1 H); MS (ESI) m/e (M+H+) 158.2.
[00696] Example 50: δ-Amino-lH-indole-S-carbonitrile
Figure imgf000208_0003
[00697] δ-Nitro-lH-indole-S-carbonitrile
[00698] To a solution of 6-nitroindole (4.9 g 30 mmol) in DMF (24 mL) and CH3CN (240 mL) was added dropwise a solution of ClSO2NCO (5.0 mL) in CH3CN (39 mL) at 0 0C. After addition, the reaction was allowed to warm to room temperature and was stirred for 2 h. The mixture was then poured into ice-water and basified with sat. NaHCO3 solution to pH 7-8. The mixture was extracted with ethyl acetate. The organics were washed with brine, dried over Na2SO4 and concentrated to give 6-nitro-lH-indole-3-carbonitrile (4.6 g, 82%).
Figure imgf000209_0001
[00699] ό-Amino-lH-indole-S-carbonitrile
[00700] A suspention of ό-nitro-lH-indole-S-carbonitrile (4.6 g, 25 mmol) and 10% Pd-C (0.46 g) in EtOH (50 mL) was stirred under H2 (1 atm) at room temperature overnight. After filtration, the filtrate was concentrated and the residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 3/1) to give 6-amino-lH- indole-3-carbonitrile (1.0 g, 98%) as a pink solid. 1H NMR (DMSO-J6) δ 11.51 (s, 1 H), 7.84 (d, / = 2.4 Hz, 1 H), 7.22 (d, / = 8.4 Hz, 1 H), 6.62 (s, IH), 6.56 (d, / = 8.4 Hz, 1 H), 5.0 (s, 2H); MS (ESI) m/e (M+H+) 157.1.
[00701] Example 51: 2-fert-Butyl-lH-indol-6-amine
Figure imgf000209_0002
Raney Nι/H2
Figure imgf000209_0004
Figure imgf000209_0003
[00702] N-o-Tolylpivalamide
[00703] To a solution of o-tolylamine (21 g, 0.20 mol) and Et3N (22 g, 0.22 mol) in CH2Cl2 was added 2,2-dimethyl-propionyl chloride (25 g, 0.21 mol) at 10 0C. After addition, the mixture was stirred overnight at room temperature. The mixture was washed with aq. HCl (5%, 80 mL), saturated aq. NaHCO3 and brine. The organic layer was dried over Na2SO4 and concentrated under vacuum to give N-o-tolylpivalamide (35 g, 91%). 1H ΝMR (300 MHz, CDCl3) δ 7.88 (d, / = 7.2 Hz, 1 H), 7.15-7.25 (m, 2 H), 7.05 (t, / = 7.2 Hz, 1 H), 2.26 (s, 3 H), 1.34 (s, 9 H).
Figure imgf000209_0005
[00704] 2-fert-Butyl-lH-indole
[00705] To a solution of N-o-tolylpivalamide (30.0 g, 159 mmol ) in dry THF (100 mL) was added dropwise n-BuLi (2.5 M in hexane, 190 mL) at 15 °C. After addition, the mixture was stirred overnight at 15 0C. The mixture was cooled in an ice- water bath and treated with saturated NH4Cl. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organic layers were dried over anhydrous Na2SO4, filtered, and concentrated in vacuum. The residue was purified by column chromatography on silica gel to give 2-terf-butyl-lH-indole (24 g, 88%). 1H NMR (300 MHz, CDCl3) δ 7.99 (br. s, 1 H), 7.54 (d, / = 7.2 Hz, 1 H), 7.05 (d, / = 7.8 Hz, 1 H), 7.06 -7.13 (m, 2 H), 6.26 (s, 1 H), 1.39 (s, 9 H).
Figure imgf000210_0001
[00706] 2-fert-Butylindoline
[00707] To a solution of 2-tert-butyl-lH-indole (10 g, 48 mmol) in AcOH (40 mL) was added NaBH4 at 10 0C. The mixture was stirred for 20 minutes at 10 0C before being treated dropwise with H2O under ice cooling. The mixture was extracted with ethyl acetate. The combined organic layers were dried over anhydrous Na2SO4, filtered, and concentrated under vacuum to give 2-ferZ-butylindoline (9.8 g), which was used directly in the next step.
Figure imgf000210_0002
[00708] 2-fert-butyl-6-nitroindoline and 2-fert-butyl-5-nitro-lH-indole
[00709] To a solution of 2-ført-butylindoline (9.7 g) in H2SO4 (98%, 80 mL) was slowly added KNO3 (5.6 g, 56 mmol) at 0 0C. After addition, the reaction mixture was stirred at room temperature for 1 h. The mixture was carefully poured into cracked ice, basified with Na2CO3 to pH 8 and extracted with ethyl acetate. The combined extracts were washed with brine, dried over anhydrous Na2SO4 and concentrated under vacuum. The residue was purified by column chromatography to give 2-terZ-butyl-6-nitroindoline (4.0 g, 31% over two steps). 1H NMR (300 MHz, CDCl3) δ 7.52 (dd, / = 1.8, 8.1 Hz, 1 H), 7.30 (s, 1 H), 7.08 (d, J = 7.8 Hz, 1 H), 3.76 (t, J = 9.6 Hz, 1 H), 2.98 - 3.07 (m, 1 H), 2.82 - 2.91 (m, 1 H), 0.91 (s, 9 H).
Figure imgf000211_0001
[00710] 2-fert-Butyl-6-nitro-lH-indole
[00711] To a solution of 2-fe?t-butyl-6-nitroindoline (2.0 g, 9.1 mmol) in 1,4-dioxane (20 mL) was added DDQ (6.9 g, 30 mmol) at room temperature. The mixture was heated at reflux for 2.5 h before being filtered and concentrated under vacuum. The residue was purified by column chromatography to give 2-terZ-butyl-6-nitro-lH-indole (1.6 g, 80%). 1H NMR (300 MHz, CDCl3) δ 8.30 (br. s, 1 H), 8.29 (s, 1 H), 8.00 (dd, / = 2.1, 8.7 Hz, 1 H), 7.53 (d, / = 9.3 Hz, 1 H), 6.38 (s, 1 H), 1.43 (s, 9 H).
Raney IWH2
Figure imgf000211_0002
Figure imgf000211_0003
[00712] 2-fert-Butyl-lH-indol-6-amine
[00713] To a solution of 2-te?t-butyl-6-nitro-lH-indole (1.3 g, 6.0 mmol) in MeOH (10 mL) was added Raney Nickel (0.2 g). The mixture was hydrogenated under 1 atm of hydrogen at room temperature for 3 h. The reaction mixture was filtered and the filtrate was concentrated. The residue was washed with petroleum ether to give 2-terZ-butyl-lH-indol-6- amine (1.0 g, 89%). 1H NMR (300 MHz, DMSO-J6) δ 10.19 (s, 1 H), 6.99 (d, / = 8.1 Hz, 1 H), 6.46 (s, I H), 6.25 (dd, / = 1.8, 8.1 Hz, 1 H), 5.79 (d, / = 1.8 Hz, 1 H), 4.52 (s, 2 H), 1.24 (s, 9 H); MS (ESI) m/e (M+H+) 189.1.
[00714] Example 52: 3-fert-Butyl-lH-indol-6-amine
Figure imgf000211_0004
[00715] 3-fert-Butyl-6-nitro-lH-indole
[00716] To a mixture of 6-nitroindole (1.0 g, 6.2 mmol), zinc triflate (2.1 g, 5.7 mmol), and TBAI (1.7 g, 5.2 mmol) in anhydrous toluene (11 mL) was added DIEA (1.5 g, 11 mmol) at room temperature under nitrogen. The reaction mixture was stirred for 10 min at 120 0C, followed by the addition of z-butyl bromide (0.71 g, 5.2 mmol). The resulting mixture was stirred for 45 min at 120 0C. The solid was filtered off and the filtrate was concentrated to dryness. The residue was purified by column chromatography on silica gel (petroleum ether/ethyl acetate = 20:1) to give 3-terZ-butyl-6-nitro-lH-indole (0.25 g, 19%) as a yellow solid. 1H-NMR (CDCl3) δ 8.32 (d, / = 2.1 Hz, IH), 8.00 (dd, / = 2.1, 14.4 Hz, IH), 7.85 (d, J = 8.7 Hz, IH), 7.25 (s, IH), 1.46 (s, 9H).
Raney Ni-H2
Figure imgf000212_0001
Figure imgf000212_0002
[00717] 3-fert-Butyl-lH-indol-6-amine
[00718] A suspension of 3-terZ-butyl-6-nitro-lH-indole (3.0 g, 14 mmol) and Raney Nickel (0.5 g) was hydrogenated under H2 (1 atm) at room temperature for 3 h. The catalyst was filtered off and the filtrate was concentrated to dryness. The residue was purified by column on silica gel (petroleum ether/ethyl acetate = 4:1) to give 3-terZ-butyl-lH-indol-6-amine (2.0 g, 77%) as a gray solid. 1HNMR (CDCl3) δ 7.58 (m, 2H), 6.73 (d, J = 1.2 Hz, IH), 6.66 (s, IH), 6.57(dd, / = 0.8, 8.6 Hz, IH), 3.60 (br, 2H), 1.42 (s, 9H).
[00719] Example 53: 5-(Trifluoromethyl)-lH-indol-6-amine
Figure imgf000212_0003
[00720] l-Methyl-2,4-dinitro-5-(trifluoromethyl)benzene
[00721] To a mixture of HNO3 (98%, 30 mL) and H2SO4 (98%, 30 mL) was added dropwise l-methyl-3-trifluoromethyl-benzene (10 g, 63 mmol) at 0 0C. After addition, the mixture was stirred at rt for 30 min and was then poured into ice-water. The precipitate was filtered and washed with water to give l-methyl-2,4-dinitro-5-trifluoromethyl-benzene (2.0 g, 13%).
Figure imgf000212_0004
[00722] (£)-2-(2,4-Dinitro-5-(trifluoromethyl)phenyl)-N,N-dimethylethenamine
[00723] A mixture of l-methyl-2,4-dinitro-5-trifluoromethyl-benzene (2.0 g, 8.0 mmol) and DMA (1.0 g, 8.2 mmol) in DMF (20 niL) was stirred at 100 0C for 30 min. The mixture was poured into ice-water and stirred for 1 h. The precipitate was filtered and washed with water to give (£)-2-(2,4-dinitro-5-(trifluoromethyl)phenyl)-N,N-dimethylethenamine (2.1 g, 86%).
Figure imgf000213_0001
[00724] 5-(Trifluoromethyl)-lH-indol-6-amine
[00725] A suspension of (£>2-(2,4-dinitro-5-(trifluoromethyl)phenyl)-N,N- dimethylethenamine (2.1 g, 6.9 mmol) and Raney Nickel (1 g) in ethanol (80 mL) was stirred under H2 (1 atm) at room temperature for 5 h. The catalyst was filtered off and the filtrate was concentrated to dryness. The residue was purified by column on silica gel to give 5- (trifluoromethyl)-lH-indol-6-amine (200 mg, 14%). 1H NMR (DMSO-J6) δ 10.79 (br s, 1 H), 7.55 (s, 1 H), 7.12 (s, 1 H), 6.78 (s, 1 H), 6.27(s, 1 H), 4.92 (s, 2 H); MS (ESI) vale, (M+H+): 200.8.
[00726] Example 54: 5-Ethyl-lH-indol-6-amine
Figure imgf000213_0002
[00727] l-(Phenylsulfonyl)indoline
[00728] To a mixture of DMAP (1.5 g), benzenesulfonyl chloride (24.0 g, 136 mmol) and indoline (14.7 g, 124 mmol) in CH2Cl2 (200 mL) was added dropwise Et3N (19.0 g, 186 mmol) at O 0C. The mixture was stirred at room temperature overnight. The organic layer was washed with water (2x), dried over Na2SO4 and concentrated to dryness under reduced pressure to obtain l-(phenylsulfonyl)indoline (30.9 g, 96%).
Figure imgf000214_0001
[00729] l-(l-(Phenylsulfonyl)indolin-5-yl)ethanone
[00730] To a suspension of AlCl3 (144 g, 1.08 mol) in CH2Cl2 (1070 niL) was added acetic anhydride (54 mL). The mixture was stirred for 15 minutes before a solution of 1- (phenylsulfonyl)indoline (46.9 g, 0.180 mol) in CH2Cl2 (1070 mL) was added drop wise. The mixture was stirred for 5 h and was quenched by the slow addition of crushed ice. The organic layer was separated and the aqueous layer was extracted with CH2Cl2. The combined organics were washed with saturated aqueous NaHCO3 and brine, dried over Na2SO4, and concentrated under vacuum to obtain l-(l-(phenylsulfonyl)indolin-5-yl)ethanone (42.6 g).
Figure imgf000214_0002
[00731] 5-Ethyl-l-(phenylsulfonyl)indoline
[00732] To TFA (1600 mL) at 0 0C was added sodium borohydride (64.0 g, 1.69 mol) over 1 h. To this mixture was added dropwise a solution of l-(l-(phenylsulfonyl)indolin-5- yl)ethanone (40.0 g, 0.133 mol) in TFA (700 mL) over 1 h. The mixture was then stirred overnight at 25 0C. After dilution with H2O (1600 mL), the mixture was made basic by the addition of sodium hydroxide pellets at 0 0C. The organic layer was separated and the aqueous layer was extracted with CH2Cl2. The combined organic layers were washed with brine, dried over Na2SO4 and concentrated under reduced pressure. The residue was purified by silica column to give 5-ethyl-l-(phenylsulfonyl)indoline (16.2 g, 47% over two steps).
Figure imgf000215_0001
[00733] 5-Ethylindoline
[00734] A mixture of 5-ethyl-l-(phenylsulfonyl)indoline (15 g, 0.050 mol) in HBr (48%, 162 mL) was heated at reflux for 6 h. The mixture was basified with sat. NaOH to pH 9 and then it was extracted with ethyl acetate. The organic layer was washed with brine, dried over Na2SO4, and concentrated under reduced pressure. The residue was purified by silica column to give 5-ethylindoline (2.5 g, 32%).
Figure imgf000215_0002
[00735] 5-Ethyl-6-nitroindoline
[00736] To a solution of 5-ethylindoline (2.5 g, 17 mmol) in H2SO4 (98%, 20 mL) was slowly added KNO3 (1.7 g, 17 mmol) at 0 0C. The mixture was stirred at 0 - 10 0C for 10 minutes. The mixture was then carefully poured into ice, basified with NaOH solution to pH 9, and extracted with ethyl acetate. The combined extracts were washed with brine, dried over Na2SO4 and concentrated to dryness. The residue was purified by silica column to give 5-ethyl-6-nitroindoline (1.9 g, 58%).
Figure imgf000215_0003
[00737] 5-Ethyl-6-nitro-lH-indole
[00738] To a solution of 5-ethyl-6-nitroindoline (1.9 g, 9.9 mmol) in CH2Cl2 (30 mL) was added MnO2 (4.0 g, 46 mmol). The mixture was stirred at ambient temperature for 8 h. The solid was filtered off and the filtrate was concentrated to dryness to give 5-ethyl-6-nitro-lH- indole (1.9 g).
Raney IWH2
Figure imgf000215_0004
Figure imgf000215_0005
[00739] 5-Ethyl-lH-indol-6-amine [00740] A suspension of 5-ethyl-6-nitro-lH-indole (1.9 g, 10 mmol) and Raney Nickel (1 g) was hydrogenated under H2 (1 atm) at room temperature for 2 h. The catalyst was filtered off and the filtrate was concentrated to dryness. The residue was purified by silica gel column to give 5-ethyl-lH-indol-6-amine (760 mg, 48% over two steps). 1H NMR (CDCl3) δ 7.90 (br s, IH), 7.41 (s, IH), 7.00 (s, IH), 6.78 (s, 2H), 6.39 (s, IH), 3.39 (br s, 2H), 2.63 (q, J = 7.2 Hz, 2H), 1.29 (t, / = 6.9 Hz, 3H); MS (ESI) m/e (M+H+) 161.1.
[00741] Example 55: Ethyl ό-amino-lH-indole^-carboxylate
Figure imgf000216_0001
DIWVDMF SnCIp
Figure imgf000216_0002
Figure imgf000216_0003
Figure imgf000216_0004
[00742] 2-Methyl-3,5-dinitrobenzoic acid
[00743] To a mixture of HNO3 (95%, 80 niL) and H2SO4 (98%, 80 niL) was slowly added 2-methylbenzic acid (50 g, 0.37 mol) at 0 0C. After addition, the reaction mixture was stirred below 30 0C for 1.5 h. The mixture then was poured into ice-water and stirred for 15 min. The precipitate was filtered and washed with water to give 2-methyl-3,5-dinitrobenzoic acid
(70 g, 84%).
Figure imgf000216_0005
[00744] Ethyl 2-methyl-3,5-dinitrobenzoate
[00745] A mixture of 2-methyl-3,5-dinitrobenzoic acid (50 g, 0.22 mol) in SOCl2 (80 mL) was heated at reflux for 4 h and then was concentrated to dryness. The residue was dissolved in CH2Cl2 (50 mL), to which EtOH (80 mL) was added and the mixture was stirred at room temperature for 1 h. The mixture was poured into ice-water and extracted with EtOAc (3 x
100 mL). The combined extracts were washed sat. Na2CO3 (80 mL), water (2 x 100 mL) and brine (100 mL), dried over Na2SO4 and concentrated to dryness to give ethyl 2-methyl-3,5- dinitrobenzoate (50 g, 88%)
Figure imgf000217_0001
[00746] (£)-Ethyl 2-(2-(dimethylamino)vinyl)-3,5-dinitrobenzoate
[00747] A mixture of ethyl 2-methyl-3,5-dinitrobenzoate (35 g, 0.14 mol) and DMA (32 g, 0.27 mol) in DMF (200 mL) was heated at 100 0C for 5 h. The mixture was poured into ice- water and the precipitated solid was filtered and washed with water to give (£)-ethyl 2-(2- (dimethylamino)vinyl)-3,5-dinitrobenzoate (11 g, 48%)
Figure imgf000217_0002
[00748] Ethyl 6-amino-lH-indole-4-carboxylate
[00749] A mixture of (£>ethyl 2-(2-(dimethylamino)vinyl)-3,5-dinitrobenzoate (11 g, 0.037 mol) and SnCl2 (83 g, 0.37 mol) in ethanol was heated at reflux for 4 h. The mixture was concentrated to dryness and the residue was poured into water and basified using sat. aq. Na2CC^ to pH 8. The precipitated solid was filtered and the filtrate was extracted with ethyl acetate (3 x 100 mL). The combined extracts were washed with water (2 x 100 mL) and brine (150 mL), dried over Na2SO4, and concentrated to dryness. The residue was purified by column on silica gel to give ethyl 6-amino-lH-indole-4-carboxylate (3.0 g, 40%). 1HNMR (DMSO-J6) δ 10.76 (br s, 1 H), 7.11-7.14 (m, 2 H), 6.81-6.82 (m, 1 H), 6.67-6.68 (m, 1 H), 4.94 (br s, 2 H), 4.32-4.25 (q, J = 7.2 Hz, 2 H), 1.35-1.31 (t, J = 7.2, 3 H); MS (ESI) m/e (M+H+) 205.0.
[00750] Example 56: 5-Fluoro-lH-indol-6-amine
Figure imgf000217_0003
H2/Raney-Ni
Figure imgf000217_0005
Figure imgf000217_0004
Figure imgf000218_0001
[00751] l-Fluoro-5-methyl-2,4-dinitrobenzene
[00752] To a stirred solution of HNO3 (60 niL) and H2SO4 (80 niL) was added dropwise 1- fluoro-3-methylbenzene (28 g, 25 mmol) under ice-cooling at such a rate that the temperature did not rise above 35 0C. The mixture was allowed to stir for 30 min at rt and was then poured into ice water (500 mL). The resulting precipitate (a mixture of l-fluoro-5-methyl- 2,4-dinitrobenzene and l-fluoro-3-methyl-2,4-dinitrobenzene, 32 g, ca. 7:3 ratio) was collected by filtration and purified by recrystallization from 50 mL isopropyl ether to give pure l-fluoro-5-methyl-2,4-dinitro-benzene as a white solid (18 g, 36%).
Figure imgf000218_0002
[00753] (£>2-(5-Fluoro-2,4-dinitrophenyl)-N,N-dimethylethenamine
[00754] A mixture of l-fluoro-5-methyl-2,4-dinitro-benzene (10 g, 50 mmol), DMA (12 g, 100 mmol) and DMF (50 mL) was heated at 100 0C for 4h. The solution was cooled and poured into water. The precipitated red solid was collected, washed with water, and dried to give (£)-2-(5-fluoro-2,4-dinitrophenyl)-N,N-dimethylethenamine (8.0 g, 63%).
Figure imgf000218_0003
[00755] 5-Fluoro-lH-indol-6-amine
[00756] A suspension of (£")-2-(5-fluoro-2,4-dinitrophenyl)-N,N-dimethylethenamine (8.0 g, 31 mmol) and Raney Nickel (8 g) in EtOH (80 mL) was stirred under H2 (40 psi) at room temperature for 1 h. After filtration, the filtrate was concentrated and the residue was purified by column chromatography (petroleum ether/ethyl acetate = 5/1) to give 5-fluoro- lH-indol-6-amine (1.0 g, 16%) as a brown solid. 1HNMR (DMSO-J6) δ 10.56 (br s, 1 H), 7.07 (d, / = 12 Hz, 1 H), 7.02 (m, IH), 6.71 (d, / = 8 Hz, IH), 6.17 (s, IH), 3.91 (br s , 2H); MS (ESI) m/e (M+H+) 150.1.
[00757] Example 57: 5-Chloro-lH-indol-6-amine
Figure imgf000219_0001
[00758] l-Chloro-5-methyl-2,4-dinitrobenzene
[00759] To a stirred solution of HNO3 (55 niL) and H2SO4 (79 niL) was added dropwise 1- chloro-3-methylbenzene (25.3 g, 200 mmol) under ice-cooling at such a rate that the temperature did not rise above 35 0C. The mixture was allowed to stir for 30 min at ambient temperature and was then poured into ice water (500 mL). The resulting precipitate was collected by filtration and purified by recrystallization to give l-chloro-5-methyl-2,4- dinitrobenzene (26 g, 60%).
Figure imgf000219_0002
[00760] (£>2-(5-Chloro-2,4-dinitrophenyl)-N,N-dimethylethenamine
[00761] A mixture of l-chloro-5-methyl-2,4-dinitro-benzene (11.6 g, 50.0 mmol), DMA (11.9 g, 100 mmol) in DMF (50 mL) was heated at 100 0C for 4 h. The solution was cooled and poured into water. The precipitated red solid was collected by filtration, washed with water, and dried to give (£")-2-(5-chloro-2,4-dinitrophenyl)-N,N-dimethylethenamine (9.84 g,
72%).
H2/Raney-Νι
Figure imgf000219_0003
Figure imgf000219_0004
[00762] 5-Chloro-lH-indol-6-amine
[00763] A suspension of (£")-2-(5-chloro-2,4-dinitrophenyl)-N,N-dimethylethenamine (9.8 g, 36 mmol) and Raney Nickel (9.8 g) in EtOH (140 mL) was stirred under H2 (1 atm) at room temperature for 4 h. After filtration, the filtrate was concentrated and the residue was purified by column chromatograph (petroleum ether/ethyl acetate = 10:1) to give 5-chloro- lH-indol-6-amine (0.97 g, 16%) as a gray powder. 1HNMR (CDCl3) δ 7.85 (br s, 1 H), 7.52 (s, 1 H), 7.03 (s, IH), 6.79 (s, IH), 6.34 (s, IH), 3.91 (br s, IH); MS (ESI) m/e (M+H+) 166.0.
[00764] Example 58: Ethyl ό-amino-lH-indole-T-carboxylate
Figure imgf000220_0001
[00765] 3-Methyl-2,6-dinitrobenzoic acid
[00766] To a mixture of HNO3 (95%, 80 mL) and H2SO4 (98%, 80 mL) was slowly added 3-methylbenzic acid (50 g, 0.37 mol) at 0 0C. After addition, the mixture was stirred below 30 0C for 1.5 hours. The mixture was then poured into ice-water and stirred for 15 min. The precipitate solid was filtered and washed with water to give a mixture of 3-methyl-2,6- dinitro-benzoic acid and 5-methyl-2,4-dinitrobenzoic acid (70 g, 84%). To a solution of this mixture (70 g, 0.31 mol) in EtOH (150 mL) was added dropwise SOCl2 (54 g, 0.45 mol). The mixture was heated at reflux for 2 h before being concentrated to dryness under reduced pressure. The residue was partitioned between EtOAc (100 mL) and aq. Na2CO3 (10%, 120 mL). The organic layer was washed with brine (50 mL), dried over Na2SO4, and concentrated to dryness to obtain ethyl 5-methyl-2,4-dinitrobenzoate (20 g), which was placed aside. The aqueous layer was acidified by HCl to pH 2 ~ 3 and the precipitated solid was filtered, washed with water, and dried in air to give 3-methyl-2,6-dinitrobenzoic acid (39 g, 47%).
Figure imgf000220_0002
[00767] Ethyl 3-methyl-2,6-dinitrobenzoate [00768] A mixture of 3-methyl-2,6-dinitrobenzoic acid (39 g, 0.15 mol) and SOCl2 (80 mL) was heated at reflux 4 h. The excess SOCl2 was evaporated off under reduced pressure and the residue was added dropwise to a solution of EtOH (100 mL) and Et3N (50 mL). The mixture was stirred at 20 0C for 1 h and then concentrated to dryness. The residue was dissolved in EtOAc (100 mL), washed with Na2CO3 (10 %, 40 mL x 2), water (50 mL x 2) and brine (50 mL), dried over Na2SO4 and concentrated to give ethyl 3-methyl-2,6- dinitrobenzoate (20 g, 53%).
Figure imgf000221_0001
[00769] (£)-Ethyl 3-(2-(dimethylamino)vinyl)-2,6-dinitrobenzoate
[00770] A mixture of ethyl 3-methyl-2,6-dinitrobenzoate (35 g, 0.14 mol) and DMA (32 g, 0.27 mol) in DMF (200 mL) was heated at 100 0C for 5 h. The mixture was poured into ice water. The precipitated solid was filtered and washed with water to give (£)-ethyl 3-(2- (dimethylamino)vinyl)-2,6-dinitrobenzoate (25 g, 58%).
Figure imgf000221_0002
[00771] Ethyl 6-amino-lH-indole-7-carboxylate
[00772] A mixture of (£>ethyl 3-(2-(dimethylamino)vinyl)-2,6-dinitrobenzoate (30 g, 0.097 mol) and Raney Nickel (10 g) in EtOH (1000 mL) was hydrogenated at room temperature under 50 psi for 2 h. The catalyst was filtered off and the filtrate was concentrated to dryness. The residue was purified by column on silica gel to give ethyl 6- amino-lH-indole-7-carboxylate as an off-white solid (3.2 g, 16%). 1H NMR (DMSO-J6) δ 10.38 (s, 1 H), 7.42 (d, J = 8.7 Hz, 1 H), 6.98 (t, J = 3.0 Hz, 1 H), 6.65 (s, 2 H), 6.48 (d, J = 8.7 Hz, 1 H), 6.27-6.26 (m, 1 H), 4.38 (q, /= 7.2 Hz, 2 H), 1.35 (t, /= 7.2 Hz, 3 H).
[00773] Example 59: Ethyl ό-amino-lH-indole-S-carboxylate
Figure imgf000221_0003
Figure imgf000222_0001
[00774] (£)-Ethyl 5-(2-(dimethylamino)vinyl)-2,4-dinitrobenzoate
[00775] A mixture of ethyl 5-methyl-2,4-dinitrobenzoate (39 g, 0.15 mol) and DMA (32 g, 0.27 mol) in DMF (200 mL) was heated at 100 0C for 5 h. The mixture was poured into ice water and the precipitated solid was filtered and washed with water to afford (£)-ethyl 5-(2- (dimethylamino)vinyl)-2,4-dinitrobenzoate (15 g, 28%).
Figure imgf000222_0002
[00776] Ethyl 6-amino-lH-indole-5-carboxylate
[00777] A mixture of (£>ethyl 5-(2-(dimethylamino)vinyl)-2,4-dinitrobenzoate (15 g, 0.050 mol) and Raney Nickel (5 g) in EtOH (500 mL) was hydrogenated at room temperature under 50 psi of hydrogen for 2 h. The catalyst was filtered off and the filtrate was concentrated to dryness. The residue was purified by column on silica gel to give ethyl 6- amino-lH-indole-5-carboxylate (3.0 g, 30%). 1H NMR (DMSO-J6) δ 10.68 (s, 1 H), 7.99 (s, 1 H), 7.01-7.06 (m, 1 H), 6.62 (s, 1 H), 6.27-6.28 (m, 1 H), 6.16 (s, 2 H), 4.22 (q, / = 7.2 Hz, 2 H), 1.32-1.27 (t, / = 7.2 Hz, 3 H).
[00778] Example 60: 5-fert-Butyl-lH-indol-6-amine
Figure imgf000222_0003
[00779] 2-fert-Butyl-4-methylphenyl diethyl phosphate
[00780] To a suspension of NaH (60% in mineral oil, 8.4 g, 0.21 mol) in THF (200 mL) was added dropwise a solution of 2-ferZ-butyl-4-methylphenol (33 g, 0.20 mol) in THF (100 mL) at 0 0C. The mixture was stirred at 0 0C for 15 min and then phosphorochloridic acid diethyl ester (37 g, 0.21 mol) was added dropwise at 0 °C. After addition, the mixture was stirred at ambient temperature for 30 min. The reaction was quenched with sat. NH4Cl (300 mL) and then extracted with Et2O (350 mL x T). The combined organic layers were washed with brine, dried over anhydrous Na2SO4, and then evaporated under vacuum to give 2-tert- butyl-4-methylphenyl diethyl phosphate (contaminated with mineral oil) as a colorless oil (60 g, -100%), which was used directly in the next step.
Figure imgf000223_0001
[00781] l-fert-Butyl-3-methylbenzene
[00782] To NH3 (liquid, 1000 mL) was added a solution of 2-te?t-butyl-4-methylphenyl diethyl phosphate (60 g, crude from last step, about 0.2 mol) in Et2O (anhydrous, 500 mL) at -78 0C under N2 atmosphere. Lithium metal was added to the solution in small pieces until the blue color persisted. The reaction mixture was stirred at -78 0C for 15 min and then was quenched with sat. NH4Cl until the mixture turned colorless. Liquid NH3 was evaporated and the residue was dissolved in water. The mixture was extracted with Et2O (400 mL x 2). The combined organics were dried over Na2SO4 and evaporated to give l-terZ-butyl-3- methylbenzene (contaminated with mineral oil) as a colorless oil (27 g, 91%), which was used directly in next step.
Figure imgf000223_0002
[00783] l-fert-Butyl-5-methyl-2,4-dinitrobenzene and l-tert-butyl-3-methyl-2,4- dinitro-benzene
[00784] To HNO3 (95%, 14 mL) was added H2SO4 (98 %, 20 mL) at 0 0C and then l-tert- butyl-3-methylbenzene (7.4 g, -50 mmol, crude from last step) dropwise to the with the temperature being kept below 30 0C. The mixture was stirred at ambient temperature for 30 min, poured onto crushed ice (100 g), and extracted with EtOAc (50 mL x 3). The combined organic layers were washed with water and brine, before being evaporated to give a brown oil, which was purified by column chromatography to give a mixture of l-terZ-butyl-5- methyl-2,4-dinitrobenzene and l-ferZ-butyl-3-methyl-2,4-dinitrobenzene (2:1 by NMR) as a yellow oil (9.0 g, 61%).
Figure imgf000224_0001
[00785] (£)-2-(5-te^Butyl-2,4-dinitrophenyl)-N,N-dimethylethenamine
[00786] A mixture of l-terZ-butyl-5-methyl-2,4-dinitrobenzene and l-terZ-butyl-3-methyl- 2,4-dinitrobenzene (9.0 g, 38 mmol, 2: 1 by NMR) and DMA (5.4 g, 45 mmol) in DMF (50 mL) was heated at reflux for 2 h before being cooled to room temperature. The reaction mixture was poured into water-ice and extracted with EtOAc (50 mL x 3). The combined organic layers were washed with water and brine, before being evaporated to give a brown oil, which was purified by column to give (£)-2-(5-terZ-butyl-2,4-dinitrophenyl)-N,N- dimethylethen-amine (5.0 g, 68%).
SnCIc
Figure imgf000224_0002
Figure imgf000224_0003
[00787] 5-fert-Butyl-lH-indol-6-amine
[00788] A solution of (£)-2-(5-te^butyl-2,4-dinitrophenyl)-N,N-dimethylethen-amine (5.3 g, 18 mmol) and tin (II) chloride dihydrate (37 g, 0.18 mol) in ethanol (200 mL) was heated at reflux overnight. The mixture was cooled to room temperature and the solvent was removed under vacuum. The residual slurry was diluted with water (500 mL) and was basifed with 10 % aq. Na2CC^ to pH 8. The resulting suspension was extracted with ethyl acetate (3 x 100 mL). The ethyl acetate extract was washed with water and brine, dried over Na2SO4, and concentrated. The residual solid was washed with CH2Cl2 to afford a yellow powder, which was purified by column chromatography to give 5-terZ-butyl-lH-indol-6- amine (0.40 g, 12%). 1H NMR (DMSO-rfe) δ 10.34 (br s, 1 H), 7.23 (s, 1 H), 6.92 (s, 1 H), 6.65 (s, IH), 6.14 (s, 1 H), 4.43 (br s, 2 H), 2.48 (s, 9 H); MS (ESI) m/e (M+H+) 189.1.
[00789] General Procedure IV: Synthesis of acylaminoindoles
Figure imgf000224_0004
[00790] One equivalent of the appropriate carboxylic acid and one equivalent of the appropriate amine were dissolved in N,N-dimethylformamide (DMF) containing triethylamine (3 equivalents). O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU) was added and the solution was allowed to stir. The crude product was purified by reverse-phase preparative liquid chromatography to yield the pure product.
[00791] Example 61: N-(2-fert-Butyl-lH-indol-5-yl)-l-(4-methoxyphenyl)- cyclopropanecarboxamide
Figure imgf000225_0001
[00792] 2-te?t-Butyl-lH-indol-5-amine (19 mg, 0.10 mmol) and l-(4-methoxyphenyl)- cyclopropanecarboxylic acid (19 mg, 0.10 mmol) were dissolved in N,N-dimethylformamide (1.00 mL) containing triethylamine (28 μL, 0.20 mmol). O-(7-Azabenzotriazol-l-yl)- N,N,N',N'-tetramethyluronium hexafluorophosphate (42 mg, 0.11 mmol) was added to the mixture and the resulting solution was allowed to stir for 3 hours. The crude reaction mixture was filtered and purified by reverse phase HPLC. ESI-MS tn/z calc. 362.2, found 363.3 (M+l)+; Retention time 3.48 minutes.
[00793] General Procedure V: Synthesis of acylaminoindoles
Figure imgf000225_0002
[00794] One equivalent of the appropriate carboxylic acid was placed in an oven-dried flask under nitrogen. A minimum (3 equivalents) of thionyl chloride and a catalytic amount of and N,N-dimethylformamide were added and the solution was allowed to stir for 20 minutes at 60 0C. The excess thionyl chloride was removed under vacuum and the resulting solid was suspended in a minimum of anhydrous pyridine. This solution was slowly added to a stirred solution of one equivalent the appropriate amine dissolved in a minimum of anhydrous pyridine. The resulting mixture was allowed to stir for 15 hours at 110 0C. The mixture was evaporated to dryness, suspended in dichloromethane, and then extracted three times with IN HCl. The organic layer was then dried over sodium sulfate, evaporated to dryness, and then purified by column chromatography. [00795] Example 62: Ethyl 5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)- lH-indole-2-carboxylate (Compd. 28) ane
Figure imgf000226_0002
Figure imgf000226_0001
H2N OEt
[00796] l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (2.07 g, 10.0 mmol) was dissolved in thionyl chloride (2.2 mL) under N2. N,N-dimethylformamide (0.3 mL) was added and the solution was allowed to stir for 30 minutes. The excess thionyl chloride was removed under vacuum and the resulting solid was dissolved in anhydrous dichloromethane (15 mL) containing triethylamine (2.8 mL, 20.0 mmol). Ethyl 5-amino-lH-indole-2- carboxylate (2.04 g, 10.0 mmol) in 15 mL of anhydrous dichloromethane was slowly added to the reaction. The resulting solution was allowed to stir for 1 hour. The reaction mixture was diluted to 50 mL with dichloromethane and washed three times with 50 mL of IN HCl, saturated aqueous sodium bicarbonate, and saturated aqueous sodium chloride. The organic layer was dried over sodium sulfate and evaporated to dryness to yield ethyl 5-(l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indole-2-carboxylate as a gray solid (3.44 g, 88 %). ESI-MS m/z calc. 392.4; found 393.1 (M+l)+ Retention time 3.17 minutes. 1H ΝMR (400 MHz, DMSO-d6) δ 11.80 (s, IH), 8.64 (s, IH), 7.83 (m, IH), 7.33- 7.26 (m, 2H), 7.07 (m, IH), 7.02 (m, IH), 6.96-6.89 (m, 2H), 6.02 (s, 2H), 4.33 (q, / = 7.1 Hz, 2H), 1.42-1.39 (m, 2H), 1.33 (t, / = 7.1 Hz, 3H), 1.06-1.03 (m, 2H).
[00797] Example 63: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-tert-butyl-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000226_0003
[00798] l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (1.09 g, 5.30 mmol) was dissolved in 2 mL of thionyl chloride under nitrogen. A catalytic amount (0.3 mL) of NN- dimethylformamide (DMF) was added and the reaction mixture was stirred for 30 minutes. The excess thionyl chloride was evaporated and the resulting residue was dissolved in 15 mL of dichloromethane. This solution was slowly added to a solution of 2-ferZ-butyl-lH-indol-5- amine (1.0 g, 5.3 mmol) in 10 mL of dichloromethane containing triethylamine (1.69 mL, 12.1 mmol). The resulting solution was allowed to stir for 10 minutes. The solvent was evaporated to dryness and the crude reaction mixture was purified by silica gel column chromatography using a gradient of 5-50 % ethyl acetate in hexanes. The pure fractions were combined and evaporated to dryness to yield a pale pink powder (1.24 g 62%). ESI-MS mJz calc. 376.18, found 377.3 (M+l)+. Retention time of 3.47 minutes. 1H NMR (400 MHz, DMSO) δ 10.77 (s, IH), 8.39 (s, IH), 7.56 (d, / = 1.4 Hz, IH), 7.15 (d, / = 8.6 Hz, IH), 7.05 - 6.87 (m, 4H), 6.03 (s, 3H), 1.44 - 1.37 (m, 2H), 1.33 (s, 9H), 1.05-1.00 (m, 2H).
[00799] Example 64: l-(Benzo[rf][l,3]dioxol-5-yl)-N-(l-methyl-2-(l- methylcyclopropyl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000227_0001
[00800] l-Methyl-2-(l-methylcyclopropyl)-lH-indol-5-amine (20.0 mg, 0.100 mmol) and l-(benzo[J][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (20.6 mg, 0.100 mmol) were dissolved in N,N-dimethylformamide (1 mL) containing triethylamine (42.1 μL, 0.300 mmol) and a magnetic stir bar. O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (42 mg, 0.11 mmol) was added to the mixture and the resulting solution was allowed to stir for 6 h at 80 0C. The crude product was then purified by preparative ΗPLC utilizing a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(l-methyl-2-(l-methylcyclopropyl)-lH-indol-5- yl)cyclopropanecarboxamide. ESI-MS m/z calc. 388.2, found 389.2 (M+l)+. Retention time of 3.05 minutes.
[00801] Example 65: ΗBenzo[rf][l,3]dioxol-5-yl)-ΛMU-dimethyl-2,3-dihydro-lH- pyrrolofl^-aJindol-T-yOcyclopropanecarboxamide
Figure imgf000227_0002
[00802] l,l-Dimethyl-2,3-dihydro-lH-pyrrolo[l,2-α]indol-7-amine (40.0 mg, 0.200 mmol) and l-(benzo[<i][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (41.2 mg, 0.200 mmol) were dissolved in N,N-dimethylformamide (1 mL) containing triethylamine (84.2 μL, 0.600 mmol) and a magnetic stir bar. O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (84 mg, 0.22 mmol) was added to the mixture and the resulting solution was allowed to stir for 5 minutes at room temperature. The crude product was then purified by preparative HPLC utilizing a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(l,l-dimethyl-2,3-dihydro-lH- pyrrolo[l,2-a]-indol-7-yl)cyclopropanecarboxamide. ESI-MS m/z calc. 388.2, found 389.2 (M+l)+. Retention time of 2.02 minutes. 1H ΝMR (400 MHz, DMSO-J6) δ 8.41 (s, IH), 7.59 (d, / = 1.8 Hz, IH), 7.15 (d, / = 8.6 Hz, IH), 7.06 - 7.02 (m, 2H), 6.96 - 6.90 (m, 2H), 6.03 (s, 2H), 5.98 (d, / = 0.7 Hz, IH), 4.06 (t, / = 6.8 Hz, 2H), 2.35 (t, / = 6.8 Hz, 2H), 1.42- 1.38 (m, 2H), 1.34 (s, 6H), 1.05-1.01 (m, 2H).
[00803] Example 66: Methyl 5-(l-(benzo[rf][l,3]dioxol-5- yl)cyclopropanecarboxamido)-2-fert-butyl-lH-indole-7-carboxylate
Figure imgf000228_0001
[00804] l-(Benzo[J][l,3]dioxol-5-yl)cyclopropanecarbonyl chloride (45 mg, 0.20 mmol) and methyl 5-amino-2-terZ-butyl-lH-indole-7-carboxylate (49.3 mg, 0.200 mmol) were dissolved in N,N-dimethylformamide (2 mL) containing a magnetic stir bar and triethylamine (0.084 mL, 0.60 mmol). The resulting solution was allowed to stir for 10 minutes at room temperature. The crude product was then purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield methyl 5-(l- (benzo[<i][l,3]dioxol-5-yl)cyclopropanecarbox-amido)-2-^rf-butyl-lH-indole-7-carboxylate. ESI-MS m/z calc. 434.2, found 435.5. (M+l)+. Retention time of 2.12 minutes.
[00805] Example 67: l-(Benzo[d][l,3]dioxol-5-yl)-Λ42-(l-hydroxy-2-methylpropan-2- yl)-lΗ-indol-5-yl)cyclopropanecarboxamide
Figure imgf000228_0002
[00806] To a solution of l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (0.075 g, 0.36 mmol) in acetonitrile (1.5 mL) were added HBTU (0.138 g, 0.36 mmol) and Et3Ν (152 μL, 1.09 mmol) at room temperature. The mixture was stirred at room temperature for 10 minutes before a solution of 2-(5-amino-lH-indol-2-yl)-2-methylpropan-l-ol (0.074 g, 0.36 mmol) in acetonitrile (1.94 mL) was added. After addition, the reaction mixture was stirred at room temperature for 3 h. The solvent was evaporated under reduced pressure and the residue was dissolved in dichlorome thane. The organic layer was washed with 1 N HCl (1 x 3 mL) and saturated aqueous NaHCC>3 (1 x 3 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The crude material was purified by column chromatography on silica gel (ethyl acetate/hexane = 1/1) to give 1- (benzo[d][l,3]dioxol-5-yl)-N-(2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide (0.11 g, 75%). 1H ΝMR (400 MHz, DMSO-d6) δ 10.64 (s, IH), 8.38 (s, IH), 7.55 (s, IH), 7.15 (d, J = 8.6 Hz, IH), 7.04-6.90 (m, 4H), 6.06 (s, IH), 6.03 (s, 2H), 4.79 (t, J = 2.7 Hz, IH), 3.46 (d, J = 0.0 Hz, 2H), 1.41-1.39 (m, 2H), 1.26 (s, 6H), 1.05-1.02 (m, 2H).
[00807] Example 67: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2,3,4,9-tetrahydro-lH-carbazol- 6-yl)cyclopropanecarboxamide
Figure imgf000229_0001
[00808] 2,3,4,9-Tetrahydro-lH-carbazol-6-amine (81.8 mg, 0.439 mmol) and 1- (benzo[J][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (90.4 mg, 0.439 mmol) were dissolved in acetonitrile (3 mL) containing diisopropylethylamine (0.230 mL, 1.32 mmol) and a magnetic stir bar. O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (183 mg, 0.482 mmol) was added to the mixture and the resulting solution was allowed to stir for 16 h at 70 0C. The solvent was evaporated and the crude product was then purified on 40 g of silica gel utilizing a gradient of 5-50% ethyl acetate in hexanes to yield l-(benzo[<i][l,3]dioxol-5-yl)-N-(2,3,4,9-tetrahydro-lH-carbazol-6- yl)cyclopropanecarboxamide as a beige powder (0.115 g, 70%) after drying. ESI-MS m/z calc. 374.2, found 375.3 (M+l)+. Retention time of 3.43 minutes. 1H ΝMR (400 MHz, DMSO-J6) δ 10.52 (s, IH), 8.39 (s, IH), 7.46 (d, / = 1.8 Hz, IH), 7.10 - 6.89 (m, 5H), 6.03 (s, 2H), 2.68 - 2.65 (m, 2H), 2.56 - 2.54 (m, 2H), 1.82 - 1.77 (m, 4H), 1.41 - 1.34 (m, 2H), 1.04 - 0.97 (m, 2H).
[00809] Example 69: tert-Buty\ 4-(5-(l-(benzo[rf][l,3]dioxol-5-yl)cyclopropanecarbox- amido)-lH-indol-2-yl)piperidine-l-carboxylate
Figure imgf000229_0002
[00810] l-(Benzo[<i][l,3]dioxol-5-yl)cyclopropanecarbonyl chloride (43 mg, 0.19 mmol) and tert-buty\ 4-(5-amino-lH-indol-2-yl)piperidine-l-carboxylate (60 mg, 0.19 mmol) were dissolved in dichloromethane (1 mL) containing a magnetic stir bar and triethylamine (0.056 mL, 0.40 mmol). The resulting solution was allowed to stir for two days at room temperature. The crude product was then evaporated to dryness, dissolved in a minimum of N,N-dimethylformamide, and then purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield tert-buty\ 4-(5-(l- (benzo[rf][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2-yl)piperidine-l- carboxylate. ESI-MS m/z calc. 503.2, found 504.5. (M+l)+. Retention time of 1.99 minutes.
[00811] Example 70: Ethyl 2-(5-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-lΗ-indol-2-yl)propanoate
Figure imgf000230_0001
Figure imgf000230_0002
[00812] ter/-Butyl 2-(l-ethoxy-l-oxopropan-2-yl)-lH-indole-l-carboxylate
[00813] te?t-Butyl 2-(2-ethoxy-2-oxoethyl)-lH-indole-l-carboxylate (3.0 g, 9.9 mmol) was added to anhydrous THF (29 mL) and cooled to -78 0C. A 0.5M solution of potassium hexamethyldisilazane (20 mL, 9.9 mmol) was added slowly such that the internal temperature stayed below -60 0C. Stirring was continued for 1 h at -78 0C. Methyl iodide (727 μL, 11.7 mmol) was added to the mixture. The mixture was stirred for 30 minutes at room temperature. The mixture was quenched with sat. aq. ammonium chloride and partitioned between water and dichloromethane. The aqueous phase was extracted with dichloromethane and the combined organic phases were dried over Na2SO4 and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (ethylacetate/hexane = 1/9) to give
Figure imgf000230_0003
2-(l-ethoxy-l-oxopropan-2-yl)-lH-indole-l- carboxylate (2.8 g, 88%).
Figure imgf000231_0001
[00814] Ethyl 2-(lH-indol-2-yl)propanoate
[00815] tert-Butyl 2-(l-ethoxy-l-oxopropan-2-yl)-lH-indole-l-carboxylate (2.77 g, 8.74 mmol) was dissolved in dichloromethane (25 mL) before TFA (9.8 mL) was added. The mixture was stirred for 1.5 h at room temperature. The mixture was evaporated to dryness, taken up in dichloromethane and washed with sat. aq. sodium bicarbonate, water, and brine. The product was purified by column chromatography on silica gel (0-20% EtOAc in hexane) to give ethyl 2-(lH-indol-2-yl)propanoate (0.92 g, 50%).
Figure imgf000231_0002
[00816] Ethyl 2-(5-nitro-lH-indol-2-yl)propanoate
[00817] Ethyl 2-(lH-indol-2-yl)propanoate (0.91 g, 4.2 mmol) was dissolved in concentrated sulfuric acid (3.9 mL) and cooled to -10 0C (salt/ice-mixture). A solution of sodium nitrate (0.36 g, 4.2 mmol) in concentrated sulfuric acid (7.8 mL) was added dropwise over 35 min. Stirring was continued for another 30 min at -10 0C. The mixture was poured into ice and the product was extracted with ethyl acetate. The combined organic phases were washed with a small amount of sat. aq. sodium bicarbonate. The product was purified by column chromatography on silica gel (5-30% EtOAc in hexane) to give ethyl 2-(5-nitro-lH- indol-2-yl)propanoate (0.34 g, 31%).
Figure imgf000231_0003
[00818] Ethyl 2-(5-amino-lH-indol-2-yl)propanoate
[00819] To a solution of ethyl 2-(5-nitro-lH-indol-2-yl)propanoate (0.10 g, 0.38 mmol) in ethanol (4 mL) was added tin chloride dihydrate (0.431 g, 1.91 mmol). The mixture was heated in the microwave at 120 0C for 1 h. The mixture was diluted with ethyl acetate before water and saturated aqueous NaHCθ3 were added. The reaction mixture was filtered through a plug of celite using ethyl acetate. The organic layer was separated from the aqueous layer. The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure to give ethyl 2-(5-amino-lH-indol-2-yl)propanoate (0.088 g, 99%).
Figure imgf000232_0001
[00820] Ethyl 2-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol- 2-yl)propanoate
[00821] To a solution of l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (0.079 g, 0.384 mmol) in acetonitrile (1.5 niL) were added HBTU (0.146 g, 0.384 mmol) and Et3N (160 μL, 1.15 mmol) at room temperature. The mixture was allowed to stir at room temperature for 10 min before a solution of ethyl 2-(5-amino-lH-indol-2-yl)propanoate (0.089 g, 0.384 mmol) in acetonitrile (2.16 mL) was added. After addition, the reaction mixture was stirred at room temperature for 2 h. The solvent was evaporated under reduced pressure and the residue was dissolved in dichloromethane. The organic layer was washed with 1 N HCl (1 x 3 mL) and then saturated aqueous NaHCO3 (1 x 3 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The crude material was purified by column chromatography on silica gel (ethyl acetate/hexane = 1/1) to give ethyl 2-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2- yl)propanoate (0.081 g, 50%). 1H NMR (400 MHz, CDCl3) δ 8.51 (s, IH), 7.67 (s, IH), 7.23-7.19 (m, 2H), 7.04-7.01 (m, 3H), 6.89 (d, J = 0.0 Hz, IH), 6.28 (s, IH), 6.06 (s, 2H), 4.25-4.17 (m, 2H), 3.91 (q, J = 7.2 Hz, IH), 1.72-1.70 (m, 2H), 1.61 (s, 2H), 1.29 (t, J = 7.1 Hz, 4H), 1.13-1.11 (m, 2H).
[00822] Example 71: tert-Butyi 2-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarbox- amido)-lH-indol-2-yl)-2-methylpropylcarbamate
Figure imgf000232_0002
Figure imgf000233_0001
[00823] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propanoic acid
[00824] Ethyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propanoate (4.60 g, 16.7 mmol) was dissolved in THF/water (2:1, 30 niL). LiOH H2O (1.40 g, 33.3 mmol) was added and the mixture was stirred at 50 0C for 3 h. The mixture was made acidic by the careful addition of 3N HCl. The product was extracted with ethylacetate and the combined organic phases were washed with brine and dried over magnesium sulfate to give 2-methyl-2-(5-nitro-lH-indol-2- yl)propanoic acid (4.15 g, 99%).
Figure imgf000233_0002
[00825] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propanamide
[00826] 2-Methyl-2-(5-nitro-lH-indol-2-yl)-propanoic acid (4.12 g, 16.6 mmol) was dissolved in acetonitrile (80 mL). EDC (3.80 g, 0.020 mmol), HOBt (2.70 g, 0.020 mmol), Et3N (6.9 mL, 0.050 mmol) and ammonium chloride (1.34 g, 0.025 mmol) were added and the mixture was stirred overnight at room temperature. Water was added and the mixture was extracted with ethylacetate. Combined organic phases were washed with brine, dried over magnesium sulfate and dried to give 2-methyl-2-(5-nitro-lH-indol-2-yl)propanamide (4.3 g, 99%).
Figure imgf000233_0003
[00827] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propan-l-amine
[00828] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propanamide (200 mg, 0.81 mmol) was suspended in THF (5 ml) and cooled to 0 0C. Borane-THF complex solution (1.0 M, 2.4 mL, 2.4 mmol) was added slowly and the mixture was allowed to stir overnight at room temperature. The mixture was cooled to 0 0C and carefully acidified with 3 N HCl. THF was evaporated off, water was added and the mixture was washed with ethylacetate. The aqueous layer was made alkaline with 50% NaOH and the mixture was extracted with ethylacetate. The combined organic layers were dried over magnesium sulfate, filtered and evaporated to give 2-methyl-2-(5-nitro-lH-indol-2-yl)propan-l-amine (82 mg, 43%).
Figure imgf000234_0001
[00829] ter/-Butyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propylcarbamate
[00830] 2-Methyl-2-(5-nitro-lH-indol-2-yl)propan-l-amine (137 mg, 0.587 mmol) was dissolved in THF (5 niL) and cooled to 0 0C. Et3N (82 μL, 0.59 mmol) and di-ført-butyl dicarbonate (129 mg, 0.587 mmol) were added and the mixture was stirred at room temperature overnight. Water was added and the mixture was extracted with ethylacetate. The residue was purified by silica gel chromatography (10-40% ethylacetate in hexane) to give tert-buty\ 2-methyl-2-(5-nitro-lH-indol-2-yl)propylcarbamate (131 mg, 67%).
Figure imgf000234_0002
[00831] ter/-Butyl 2-(5-amino-lH-indol-2-yl)-2-methylpropylcarbamate
[00832] To a solution of fe?t-butyl 2-methyl-2-(5-nitro-lH-indol-2-yl)propylcarbamate (80 mg, 0.24 mmol) in THF (9 mL) and water (2 mL) was added ammonium formate (60 mg, 0.96 mmol) followed by 10% Pd/C (50 mg). The mixture was stirred at room temperature for 45 minutes. Pd/C was filtered off and the organic solvent was removed by evaporation. The remaining aqueous phase was extracted with dichloromethane. The combined organic phases were dried over magnesium sulfate and evaporated to give tert-buty\ 2-(5-amino-lH-indol-2- yl)-2-methylpropylcarbamate (58 mg, 80%).
Figure imgf000234_0003
[00833] ter/-Butyl 2-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH- indol-2-yl)-2-methylpropylcarbamate
[00834] tert-Butyl 2-(5-amino-lH-indol-2-yl)-2-methylpropylcarbamate (58 mg, 0.19 mmol), l-(benzo[d][l,3]dioxol-6-yl)cyclopropanecarboxylic acid (47 mg , 0.23 mmol), EDC (45 mg, 0.23 mmol), HOBt (31 mg, 0.23 mmol) and Et3N (80 μL, 0.57 mmol) were dissolved in DMF (4 mL) and stirred overnight at room temperature. The mixture was diluted with water and extracted with ethylacetate. The combined organic phases were dried over magnesium sulfate and evaporated to dryness. The residue was purified by silica gel chromatography (10-30% ethylacetate in hexane) to give tert-buty\ 2-(5-(l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2-yl)-2-methylpropyl- carbamate (88 mg, 94%). 1H NMR (400 MHz, CDCl3) δ 8.32 (s, IH), 7.62 (d, J = 1.5 Hz, IH), 7.18 - 7.16 (m, 2H), 7.02 - 6.94 (m, 3H), 6.85 (d, J = 7.8 Hz, IH), 6.19 (d, J = 1.5 Hz, IH), 6.02 (s, 2H), 4.54 (m, IH), 3.33 (d, J = 6.2 Hz, 2H), 1.68 (dd, J = 3.7, 6.8 Hz, 2H), 1.36 (s, 9H), 1.35 (s, 6H), 1.09 (dd, J = 3.7, 6.8 Hz, 2H).
[00835] Example 72: (Λ)-iV-(2-tert-Butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000235_0001
[00836] (Λ)-2-tert-Butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-5-nitro-lH-indole
[00837] To a stirred solution of (S)-(2,2-dimethyl-l,3-dioxolan-4-yl)methyl 4- methylbenzenesulfonate (1.58 g, 5.50 mmol) in anhydrous DMF (10 mL) under nitrogen gas was added 2-te?t-butyl-5-nitro-lH-indole (1.00 g, 4.58 mmol) followed by Cs2CO3 (2.99 g, 9.16 mol). The mixture was stirred and heated at 80 0C under nitrogen gas. After 20 hours, 50% conversion was observed by LCMS. The reaction mixture was re-treated with Cs2CO3 (2.99 g, 9.16 mol) and (5')-(2,2-dimethyl-l,3-dioxolan-4-yl)methyl 4-methylbenzenesulfonate (1.58 g, 5.50 mmol) and heated at 80 0C for 24 hours. The reaction mixture was cooled to room temperature. The solids were filtered and washed with ethyl acetate and hexane (1:1). The layers were separated and the organic layer was washed with water (2 x 10 mL) and brine (2 x 10 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (dichloromethane /hexane = 1.5/1) to give (K)-2-terZ-butyl-l-((2,2-dimethyl-l,3-dioxolan-4- yl)methyl)-5-nitro-lH-indole (1.0 g, 66%). 1H NMR (400 MHz, CDCl3) δ 8.48 (d, J = 2.2 Hz, IH), 8.08 (dd, J = 2.2, 9.1 Hz, IH), 7.49 (d, J = 9.1 Hz, IH), 6.00 (s, IH), 4.52-4.45 (m, 3H), 4.12 (dd, J = 6.0, 8.6 Hz, IH), 3.78 (dd, J = 6.0, 8.6 Hz, IH), 1.53 (s, 3H), 1.51 (s, 9H), 1.33 (s, 3H).
Figure imgf000236_0001
[00838] (Λ)-2-tert-Butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl-lH-indol-5-amine
[00839] To a stirred solution of («)-2-^rf-butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-5- nitro-lΗ-indole (1.0 g, 3.0 mmol) in ethanol (20 mL) and water (5 mL) was added ammonium formate (0.76 g, 12 mmol) followed by slow addition of 10 % palladium on carbon (0.4 g). The mixture was stirred at room temperature for 1 h. The reaction mixture was filtered through a plug of celite and rinsed with ethyl acetate. The filtrate was evaporated under reduced pressure and the crude product was dissolved in ethyl acetate. The organic layer was washed with water (2 x 5 mL) and brine (2 x 5 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure to give (/?)-2-terZ-butyl-l-((2,2-dimethyl-l,3-dioxolan-4- yl)methyl-lH-indol-5-amine (0.89 g, 98%). 1H NMR (400 MHz, CDCl3) δ 7.04 (d, J = 4 Hz, IH), 6.70 (d, J = 2.2 Hz, IH), 6.48 (dd, / = 2.2, 8.6 Hz, IH), 6.05 (s, IH,), 4.38-4.1 (m, 2H), 4.21 (dd, J = 7.5, 16.5 Hz, IH), 3.87 (dd, J = 6.0, 8.6 Hz, IH), 3.66 (dd, J = 6.0, 8.6 Hz, IH), 3.33 (br s, 2H), 1.40 (s, 3H), 1.34 (s, 9H), 1.25 (s, 3H).
Figure imgf000236_0002
[00840] iV-((Λ)-2-tert-Butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-lH-indol-5-yl)-l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide [00841] To l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (0.73 g, 3.0 mmol) was added thionyl chloride (660 μL, 9.0 mmol) and DMF (20 μL) at room temperature. The mixture was stirred for 30 minutes before the excess thionyl chloride was evaporated under reduced pressure. To the resulting acid chloride, dichloromethane (6.0 mL) and Et3N (2.1 mL, 15 mmol) were added. A solution of (R)-2-ter^butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl-lH-indol- 5-amine (3.0 mmol) in dichloromethane (3.0 mL) was added to the cooled acid chloride solution. After addition, the reaction mixture was stirred at room temperature for 45 minutes. The reaction mixture was filtered and the filtrate was evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (ethyl acetate/hexane = 3/7) to give N-((R)-2- ^rt-butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide (1.33 g, 84%). 1H NMR (400 MHz, CDCl3) δ 7.48 (d, J = 2 Hz, IH,), 7.31 (dd, J = 2, 8 Hz, IH), 7.27 (dd, J = 2, 8 Hz, IH), 7.23 (d, J = 8 Hz, IH), 7.14 (d, J = 8 Hz, IH), 7.02 (dd, J = 2, 8 Hz, IH), 6.92 (br s, IH), 6.22 (s, IH), 4.38-4.05 (m, 3H), 3.91 (dd, J = 5, 8 Hz, IH), 3.75 (dd, J = 5, 8 Hz, IH), 2.33 (q, J = 8 Hz, 2H), 1.42 (s, 3H), 1.37 (s, 9H), 1.22 (s, 3H), 1.10 (q, J = 8 Hz, 2H).
Figure imgf000237_0001
[00842] iV-((Λ)-2-tert-Butyl-l-((2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,2-difluorobenzo- [d][l,3]dioxol-5-yl)cyclopropanecarboxamide
[00843] To a stirred solution of N-(2-ferf-butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)- lΗ-indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (1.28 g, 2.43 mmol) in methanol (34 mL) and water (3.7 mL) was added para-toluenesulfonic acid-hydrate (1.87 g, 9.83 mmol). The reaction mixture was stirred and heated at 80 0C for 25 minutes. The solvent was evaporated under reduced pressure. The crude product was dissolved in ethyl acetate. The organic layer was washed with saturated aqueous NaHCO3 (2 x 10 mL) and brine (2 x 10 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (ethyl acetate/hexane = 13/7) to give N-((«)-2-^rf-butyl-l-((2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide (0.96 g, 81%). 1H ΝMR (400 MHz, CDCl3) δ 7.50 (d, J = 2 Hz, IH), 7.31 (dd, J = 2, 8 Hz, IH), 7.27 (dd, J = 2, 8 Hz, IH), 7.23 (d, J = 8 Hz, IH), 7.14 (d, J = 8 Hz, IH), 7.02 (br s, IH,), 6.96 (dd, J = 2, 8 Hz, IH), 6.23 (s, IH), 4.35 (dd, J = 8, 15 Hz, IH), 4.26 (dd, J = 4, 15 Hz, IH,), 4.02-3.95 (m, IH), 3.60 (dd, J = 4, 11 Hz, IH), 3.50 (dd, J = 5, 11 Hz, IH), 1.75 (q, J = 8 Hz, 3H), 1.43 (s, 9H), 1.14 (q, J = 8 Hz, 3H).
[00844] Example 73: 3-(2-fert-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2-hydroxypropanoic acid
Figure imgf000238_0001
[00845] 3-(2-ter/-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarbox- amido)-lH-indol-l-yl)-2-oxopropanoic acid
[00846] To a solution of N-(2-te^butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdltl^ldioxol-S-y^cyclopropane-carboxamide (97 mg, 0.20 mmol) in DMSO (1 mL) was added Dess-Martin periodinane (130 mg, 0.30 mmol). The mixture was stirred at room temperature for 3 h. The solid was filtered off and washed with EtOAc. The filtrate was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with brine and dried over MgSO4. After the removal of solvent, the residue was purified by preparative TLC to yield 3-(2-terZ-butyl- 5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2- oxopropanoic acid that was used without further purification.
Figure imgf000238_0002
[00847] 3-(2-ter/-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarbox- amido)-lH-indol-l-yl)-2-hydroxypropanoic acid
[00848] To a solution of 3-(2-terf-butyl-5-(l-(2,2-difluoiobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2-oxopropanoic acid (50 mg, 0.10 mmol) in MeOH (1 mL) was added NaBH4 (19 mg, 0.50 mmol) at 0 0C. The mixture was stirred at room temperature for 15 min. The resulting mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with brine and dried over anhydrous MgSO4. After the removal of the solvent, the residue was taken up in DMSO and purified by preparative LC/MS to give 3-(2-tert- butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-l-yl)- 2-hydroxypropanoic acid. 1H NMR (400 MHz, CDCl3) δ 7.36 (s), 7.27-7.23 (m, 2H), 7.15- 7.11 (m, 2H), 6.94 (d, J = 8.5 Hz, IH), 6.23 (s, IH), 4.71 (s, 3H), 4.59 (q, J = 10.3 Hz, IH), 4.40-4.33 (m, 2H), 1.70 (d, J = 1.9 Hz, 2H), 1.15 (q, J = 4.0 Hz, 2H). 13C NMR (400 MHz, CDCl3) δ 173.6, 173.1, 150.7, 144.1, 143.6, 136.2, 135.4, 134.3, 131.7, 129.2, 129.0, 127.6, 126.7, 116.6, 114.2, 112.4, 110.4, 110.1, 99.7, 70.3, 48.5, 32.6, 30.9, 30.7, 16.8. MS (ESI) m/e (M+H+) 501.2.
[00849] Example 74: (Λ)-iV-(2-tert-Butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l- (2,2-dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000239_0001
Figure imgf000239_0002
[00850] Methyl l-(3,4-dihydroxyphenyl)cyclopropanecarboxylate
[00851] To a solution of l-(3,4-dihydroxyphenyl)cyclopropanecarboxylic acid (190 mg, 1.0 mmol) in MeOH (3 mL) was added 4-methylbenzenesulfonic acid (19 mg, 0.10 mmol). The mixture was heated at 800C overnight. The reaction mixture was concentrated in vacuo and partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with sat. NaHCθ3 and brine and dried over MgSO4. After the removal of solvent, the residue was dried in vacuo to yield methyl l-(3,4- dihydroxyphenyl)cyclopropanecarboxylate (190 mg, 91%) that was used without further purification. 1H NMR (400 MHz, DMSO-d6) δ 6.76-6.71 (m, 2H), 6.66 (d, J = 7.9 Hz, IH), 3.56 (s, 3H), 1.50 (q, J = 3.6 Hz, 2H), 1.08 (q, J = 3.6 Hz, 2H).
Figure imgf000240_0001
[00852] Methyl l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylate
[00853] To a solution of methyl l-(3,4-dihydroxyphenyl)cyclopropanecarboxylate (21 mg, 0.10 mmol) and CD2Br2 (35 mg, 0.20 mmol) in DMF (0.5 mL) was added Cs2CO3 (19 mg, 0.10 mmol). The mixture was heated at 1200C for 30 min. The reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with IN NaOH and brine before being dried over MgSO4. After the removal of solvent, the residue was dried in vacuo to yield methyl 1- (2,2-dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylate (22 mg) that was used without further purification. 1H NMR (400 MHz, CDCl3) δ 6.76-6.71 (m, 2H), 6.66 (d, J = 7.9 Hz, IH), 3.56 (s, 3H), 1.50 (q, J = 3.6 Hz, 2H), 1.08 (q, J = 3.6 Hz, 2H).
Figure imgf000240_0002
[00854] l-(2,2-Dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid
[00855] To a solution of methyl l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxylate (22 mg, 0.10 mmol) in THF (0.5 mL) was added NaOH (IN, 0.25 mL, 0.25 mmol). The mixture was heated at 800C for 2 h. The reaction mixture was partitioned between EtOAc and IN NaOH. The aqueous layer was extracted with EtOAc twice, neutralized with IN HCl and extracted with EtOAc twice. The combined organic layers were washed with brine and dried over MgSO4. After the removal of solvent, the residue was dried in vacuo to yield l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxylic acid (21 mg) that was used without further purification.
Figure imgf000241_0001
[00856] (Λ)-iV-(2-tert-Butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-lH-indol-5-yl)- l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
[00857] To a solution of l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxylic acid (21 mg, 0.10 mmol), (/?)-2-terZ-butyl-l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-lH-indol-5-amine (30 mg, 0.10 mmol), HATU (42 mg, 0.11 mol) in DMF (1 mL) was added triethylamine (0.030 mL, 0.22 mmol). The mixture was heated at room temperature for 5 min. The reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with IN NaOH, IN HCl, and brine before being dried over MgSO4. After the removal of solvent, the residue was purified by column chromatography (20-40% ethyl acetate/hexane) to yield (Λ)-N-(2-^rf-butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-lH- indol-5-yl)-l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (24 mg, 49% from methyl l-(3,4-dihydroxyphenyl)cyclopropanecarboxylate). MS (ESI) m/e (M+H+) 493.5.
Figure imgf000241_0002
[00858] (Λ)-iV-(2-tert-Butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,2- dideuterium-benzofdHl^Jdioxol-S-yOcyclopropanecarboxamide
[00859] To a solution of («)-N-(2-^rf-butyl-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)- lH-indol-5-yl)-l-(2,2-dideuterium-benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (24 mg, 0.050 mmol), in methanol (0.5 mL) and water (0.05 mL) was added 4- methylbenzenesulfonic acid (2.0 mg, 0.010 mmol). The mixture was heated at 800C for 30 min. The reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc twice and the combined organic layers were washed with sat. ΝaHCθ3 and brine before being dried over MgSO4. After the removal of solvent, the residue was purified by preparative HPLC to yield (/?)-N-(2-^rf-butyl-l-((2,2-dimethyl-l,3-dioxolan-4- yl)methyl)-lH-indol-5-yl)-l-(2,2-dideuteriumbenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide (12 mg, 52%). 1H ΝMR (400 MHz, CDCl3) δ 7.44 (d, J = 2.0 Hz, IH), 7.14 (dd, J = 22.8, 14.0 Hz, 2H), 6.95-6.89 (m, 2H), 6.78 (d, J = 7.8 Hz, IH), 6.14 (s, IH), 4.28 (dd, J = 15.1, 8.3 Hz, IH), 4.19 (dd, J = 15.1, 4.5 Hz, IH), 4.05 (q, J = 7.1 Hz, IH), 3.55 (dd, J = 11.3, 4.0 Hz, IH), 3.45 (dd, J = 11.3, 5.4 Hz, IH), 1.60 (q, J = 3.5 Hz, 2H), 1.35 (s, 9H), 1.02 (q, J = 3.5 Hz, 2H). 13C ΝMR (400 MHz, CDCl3) δ 171.4, 149.3, 147.1, 146.5, 134.8, 132.3, 129.2, 126.5, 123.6, 114.3, 111.4, 110.4, 109.0, 107.8, 98.5, 70.4, 63.1, 46.6, 31.6, 30.0, 29.8, 15.3. MS (ESI) m/e (M+H+) 453.5.
[00860] It is further noted that the mono-deuterated analogue for this compound can be synthesized by substitution the reagent CHDBR2 for CD2BR2 and following the procedures described in example 74. Furthermore, mono-deuterated analogues of other compounds of the present invention can be synthesized by substituting the reagent CHDBR2 for CD2BR2 and following the steps described herein.
[00861] Example 75: 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH- indol-2-yl)-4-methylpentanoic acid
Figure imgf000242_0001
[00862] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-(4-cyano-2-methylbutan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[00863] To l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (0.068 g, 0.33 mmol) was added thionyl chloride (72 μL, 0.99 mmol) and DMF (20 μL) at room temperature. The mixture was stirred for 30 minutes before the excess thionyl chloride was evaporated under reduced pressure. To the resulting acid chloride, dichloromethane (0.5 mL) and Et3N (230 μL, 1.7 mmol) were added. A solution of 4-(5-amino-lH-indol-2-yl)-4-methylpentanenitrile (0.33 mmol) in dichloromethane (0.5 mL) was added to the acid chloride solution and the mixture was stirred at room temperature for 1.5 h. The resulting mixture was diluted with dichloromethane and washed with 1 N HCl (2 x 2 mL), saturated aqueous NaHCθ3 (2 x 2 mL) and brine (2 x 2 mL). The organic layer was dried over anhydrous Na2SO4 and evaporated under reduced pressure to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-(4-cyano-2- methylbutan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide.
Figure imgf000243_0001
[00864] 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2-yl)-4- methylpentanoic acid
[00865] A mixture of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-(4-cyano-2-methylbutan-2-yl)-lH- indol-5-yl)cyclopropanecarboxamide (0.060 g, 0.15 mmol) and KOH (0.081 g, 1.5 mmol) in 50% EtOH/water (2 mL) was heated in the microwave at 100 0C for 1 h. The solvent was evaporated under reduced pressure. The crude product was dissolved in DMSO (1 mL), filtered, and purified by reverse phase preparative HPLC to give 4-(5-(l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2-yl)-4-methylpentanoic acid. 1H ΝMR (400 MHz, DMSO-d6) δ 11.98 (s, IH), 10.79 (s, IH), 8.44 (s, IH), 7.56 (s, IH), 7.15 (d, J = 8.6 Hz, IH), 7.03-6.90 (m, 4H), 6.05 (s, IH), 6.02 (s, 2H), 1.97-1.87 (m, 4H), 1.41-1.38 (m, 2H), 1.30 (s, 6H), 1.04-1.02 (m, 2H).
[00866] Example 76: l-(Benzo[d][l,3]dioxol-5-yl)-Ν-(2-(l-hydroxypropan-2-yl)-lH- indol-5-yl)cyclopropanecarboxamide
Figure imgf000243_0002
[00867] 2-(5-Nitro-lH-indol-2-yl)propan-l-ol [00868] To a cooled solution of LiAlH4 (1.0 M in THF, 1.2 mL, 1.2 mmol) in THF (5.3 mL) at 0 0C was added a solution of ethyl 2-(5-nitro-lH-indol-2-yl)propanoate (0.20 g, 0.76 mmol) in THF (3.66 mL) dropwise. After addition, the mixture was allowed to warm up to room temperature and was stirred at room temperature for 3 h. The mixture was cooled to 0 0C. Water (2 mL) was slowly added followed by careful addition of 15% NaOH (2 mL) and water (4 mL). The mixture was stirred at room temperature for 0.5 h and was then filtered through a short plug of celite using ethyl acetate. The organic layer was separated from the aqueous layer, dried over Na2SO4, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (ethyl acetate/hexane = 1/1) to give 2-(5-nitro-lH-indol-2-yl)propan-l-ol (0.14 g, 81%).
Figure imgf000244_0001
[00869] 2-(5-Amino-lH-indol-2-yl)propan-l-ol
[00870] To a solution of 2-(5-nitro-lH-indol-2-yl)propan-l-ol (0.13 g, 0.60 mmol) in ethanol (5 mL) was added tin chloride dihydrate (0.67 g, 3.0 mmol). The mixture was heated in the microwave at 120 0C for 1 h. The mixture was diluted with ethyl acetate before water and saturated aqueous NaHCθ3 were added. The reaction mixture was filtered through a plug of celite using ethyl acetate. The organic layer was separated from the aqueous layer, dried over Na2SO4, filtered and evaporated under reduced pressure to give 2-(5-amino-lH- indol-2-yl)propan-l-ol (0.093 g, 82%).
Figure imgf000244_0002
[00871] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-(l-hydroxypropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[00872] To a solution of l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (0.10 g, 0.49 mmol) in acetonitrile (2.0 mL) were added HBTU (0.185 g, 0.49 mmol) and Et3N (205 μL, 1.47 mmol) at room temperature. The mixture was allowed to stir at room temperature for 10 minutes before a slurry of 2-(5 -amino- IH- indol-2-yl)propan-l-ol (0.093 g, 0.49 mmol) in acetonitrile (2.7 mL) was added. After addition, the reaction mixture was stirred at room temperature for 5.5 h. The solvent was evaporated under reduced pressure and the residue was dissolved in dichloromethane. The organic layer was washed with 1 N HCl (1 x 3 mL) and saturated aqueous NaHCO3 (1 x 3 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The crude material was purified by column chromatography on silica gel (ethyl acetate/hexane = 13/7) to give l-(benzo[d][l,3]dioxol-5- yl)-N-(2-(l-hydroxypropan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide (0.095 g, 51%). 1H ΝMR (400 MHz, DMSO-d6) δ 10.74 (s, IH), 8.38 (s, IH), 7.55 (s, IH), 7.14 (d, J = 8.6 Hz, IH), 7.02-6.90 (m, 4H), 6.06 (s, IH), , 6.02 (s, 2H), 4.76 (t, J = 5.3 Hz, IH), 3.68-3.63 (m, IH), 3.50-3.44 (m, IH), 2.99-2.90 (m, IH), 1.41-1.38 (m, 2H), 1.26 (d, J = 7.0 Hz, 3H), 1.05-1.02 (m, 2H).
[00873] Example 77: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-tert-butyl-lH-indol-5-yl)-iV- methylcyclopropanecarboxamide
Figure imgf000245_0001
[00874] l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-tert-butyl-lH-indol-5-yl)-iV- methylcyclopropanecarboxamide
[00875] 2-te?t-Butyl-N-methyl- lH-indol-5-amine (20.2 mg, 0.100 mmol) and 1- (benzo[J][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (20.6 mg, 0.100 mmol) were dissolved in N,N-dimethylformamide (1 mL) containing triethylamine (42.1 μL, 0.300 mmol) and a magnetic stir bar. O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (42 mg, 0.11 mmol) was added to the mixture and the resulting solution was allowed to stir for 16 h at 80 0C. The crude product was then purified by preparative ΗPLC utilizing a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(2-^rf-butyl-lH-indol-5-yl)-N- methylcyclopropanecarboxamide. ESI-MS tn/z calc. 390.2, found 391.3 (M+l)+. Retention time of 3.41 minutes.
[00876] Example 78: iV-(2-tert-Butyl-l-methyl-lΗ-indol-5-yl)-l-(benzo[d][l,3]dioxol- 6-yl)-Ν-methylcyclopropanecarboxamide
Figure imgf000245_0002
[00877] Sodium hydride (0.028 g, 0.70 mmol, 60% by weight dispersion in oil) was slowly added to a stirred solution of N-(2-tert-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]dioxol-6- yl)cyclopropanecarboxamide (0.250 g, 0.664 mmol) in a mixture of 4.5 mL of anhydrous tetrahydrofuran (THF) and 0.5 mL of anhydrous N,N-dimethylformamide (DMF). The resulting suspension was allowed to stir for 2 minutes and then iodomethane (0.062 mL, 1.0 mmol) was added to the reaction mixture. Two additional aliquots of sodium hydride and iodomethane were required to consume all of the starting material which was monitored by LC / MS. The crude reaction product was evaporated to dryness, redissolved in a minimum of DMF and purified by preparative LC / MS chromatography to yield the pure product (0.0343 g, 13%) ESI-MS m/z calc. 404.2, found 405.3 (M+l)+. Retention time of 3.65 minutes.
[00878] Example 79: l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-(hydroxymethyl)-lH-indol-5- yl)cyclopropanecarboxamide
hrs
Figure imgf000246_0001
Figure imgf000246_0002
[00879] Ethyl 5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indole-2- carboxylate (1.18 g, 3.0 mmol) was added to a solution of LiBH4 (132 mg, 6.0 mmol) in THF (10 mL) and water (0.1 mL). The mixture was allowed to stir for 16h at 25 0C before it was quenched with water (10 mL) and slowly made acidic by addition of 1 N HCl. The mixture was extracted with three 50-mL portions of ethyl acetate. The organic extracts were dried over Na2SO4 and evaporated to yield l-(benzo[d][l,3]dioxol-5-yl)-N-(2-(hydroxymethyl)- lH-indol-5-yl)cyclopropanecarboxamide (770 mg, 73%). A small amount was further purified by reverse phase HPLC. ESI-MS m/z calc. 350.4, found 351.3 (M+l)+; retention time 2.59 minutes.
[00880] Example 80: 5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-jV- fert-butyl-lH-indole-2-carboxamide
Figure imgf000246_0003
[00881] 5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indole-2- carboxylic acid
[00882] Ethyl 5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indole-2- carboxylate (392 mg, 1.0 mmol) and LiOH (126 mg, 3 mmol) were dissolved in H2O (5 mL) and 1,4-dioxane (3 mL). The mixture was heated in an oil bath at 100 0C for 24 hours before it was cooled to room temperature. The mixture was acidified with IN HCl and it was extracted with three 20 mL portions of dichloromethane. The organic extracts were dried over Na2SO4 and evaporated to yield 5-(l-(benzo[d][l,3]-dioxol-5- yl)cyclopropanecarboxamido)-lH-indole-2-carboxylic acid (302 mg, 83%). A small amount was further purified by reverse phase HPLC. ESI-MS m/z calc. 364.1, found 365.1 (M+l)+; retention time 2.70 minutes.
DMF
Figure imgf000247_0001
Figure imgf000247_0002
[00883] 5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-N-fert-butyl-lH- indole-2-carboxamide
[00884] 5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropane-carboxamido)-lH-indole-2- carboxylic acid (36 mg, 0.10 mmol) and 2-methylpropan-2-amine (8.8 mg, 0.12 mmol) were dissolved in N,N-dimethylformamide (1.0 mL) containing triethylamine (28 μL, 0.20 mmol). O-(7-Azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (46 mg, 0.12 mmol) was added to the mixture and the resulting solution was allowed to stir for 3 hours. The mixture was filtered and purified by reverse phase HPLC to yield 5-(l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-N-^rf-butyl-lH-indole-2- carboxamide. ESI-MS m/z calc. 419.2, found 420.3 (M+l)+; retention time 3.12 minutes.
[00885] Example 81: iV-(3-Amino-2-tert-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide
Figure imgf000247_0003
[00886] A solution of l-(benzo[d][l,3]dioxol-5-yl)-Ν-(2-tert-butyl-lH-indol-5- yl)cyclopropane carboxamide (50 mg, 0.13 mmol) was dissolved in AcOH (2 mL) and warmed to 45 0C. To the mixture was added a solution of NaNO2 (9 mg) in H2O (0.03 mL). The mixture was allowed to stir for 30 min at 45 °C before the precipitate was collected and washed with Et2O. This material was used in the next step without further purification. To the crude material, l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-3-m'troso-lH-indol-5- yl)cyclopropanecarboxamide, was added AcOH (2 mL) and Zn dust (5 mg). The mixture was allowed to stir for Ih at ambient temperature. EtOAc and H2O were added to the mixture. The layers were separated and the organic layer was washed with sat. aq. NaHCθ3, dried over MgSO4, and concentrated in vacuo. The residue was taken up in DMF (1 mL) and was purified using prep-HPLC. LCMS: m/z 392.3; retention time of 2.18 min.
[00887] Example 82: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-(methylsulfonyl)- lH-indol-5-yl)cyclopropanecarboxamide
[00888] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-(methylsulfonyl)-lH-indol-5- yl)cyclopropanecarboxamide
[00889] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (120 mg, 0.31 mmol) in anhydrous DMF-THF (3.3 mL, 1:9) was added NaH (60% in mineral oil, 49 mg, 1.2 mmol) at room temperature. After 30 min under N2, the suspension was cooled down to -15 0C and a solution of methanesulfonyl chloride (1.1 eq.) in DMF (0.5 mL) was added dropwise. The reaction mixture was stirred for 30 min at -15 0C then for 6 h at room temperature. Water (0.5 mL) was added at 0 0C, solvent was removed, and the residue was diluted with MeOH, filtrated and purified by preparative HPLC to give l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-3-(methylsulfonyl)-lH-indol-5- yl)cyclopropanecarboxamide. 1H ΝMR (400 MHz, DMSO) δ 11.6 (s, IH), 8.7 (s, IH), 7.94 (d, / =1.7 Hz, IH), 7.38 (d, 7 =8.7 Hz, IH), 7.33 (dd, Jl =1.9 Hz, 72 =8.7 Hz, IH), 7.03 (d, 7 =1.7 Hz, IH), 6.95 (dd, Jl =1.7 Hz, 72 =8.0 Hz, IH), 6.90 (d, 7 =8.0 Hz, IH), 6.02 (s, 2H), 3.07 (s, 3H), 1.56-1.40 (m, 9H), 1.41 (dd, Jl =4.0 Hz, 72 =6.7 Hz, 2H), 1.03 (dd, Jl =4.0 Hz, 72 =6.7 Hz, 2H). MS (ESI) m/e (M+H+) 455.5.
[00890] Example 83: l-(Benzo[rf][l,3]dioxol-5-yl)-Λ43-phenyl-lH-indol-5- yl)cyclopropane carboxamide
Figure imgf000248_0002
Figure imgf000249_0001
[00891] l-(Benzo[rf][l,3]dioxol-5-yl)-Λ43-bromo-lH-indol-5- yl)cyclopropanecarboxamide
[00892] Freshly recrystallized N-bromosuccinimde (0.278 g, 1.56 mmol) was added portionwise to a solution of l-(benzo[<i][l,3]dioxol-5-yl)-N-(lH-indol-5- yl)cyclopropanecarboxamide (0.500 g, 1.56 mmol) in N,N-dimethylformamide (2 mL) over 2 minutes. The reaction mixture was protected from light and was stirred bar for 5 minutes. The resulting green solution was poured into 40 mL of water. The grey precipitate which formed was filtered and washed with water to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(3- bromo-lH-indol-5-yl)cyclopropanecarboxamide (0.564 g, 91%). ESI-MS m/z calc. 398.0, found 399.3 (M+l)+. Retention time of 3.38 minutes. 1H ΝMR (400 MHz, DMSO-J6) 11.37 (s, IH), 8.71 (s, IH), 7.67 (d, / = 1.8 Hz, IH), 7.50 (d, / = 2.6 Hz, IH), 7.29 (d, / = 8.8 Hz, IH), 7.22 (dd, / = 2.0, 8.8 Hz, IH), 7.02 (d, / = 1.6 Hz, IH), 6.96 - 6.88 (m, 2H), 6.03 (s, 2H), 1.43 - 1.40 (m, 2H), 1.09 - 1.04 (m, 2H).
Figure imgf000249_0002
[00893] l-(Benzo[rf][l,3]dioxol-5-yl)-Λ^3-phenyl-lH-indol-5- yl)cyclopropanecarboxamide
[00894] Phenyl boronic acid (24.6 mg, 0.204 mmol) was added to a solution of 1- (benzo[J][l,3]-dioxol-5-yl)-N-(3-bromo-lH-indol-5-yl)cyclopropanecarboxamide (39.9 mg, 0.100 mmol) in ethanol (1 mL) containing FibreCat 1001 (6 mg) and IM aqueous potassium carbonate (0.260 mL). The reaction mixture was then heated at 130 0C in a microwave reactor for 20 minutes. The crude product was then purified by preparative ΗPLC utilizing a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield 1- (benzo[J][l,3]dioxol-5-yl)-N-(3-phenyl-lH-indol-5-yl)cyclopropane carboxamide. ESI-MS m/z calc. 396.2, found 397.3 (M+l)+. Retention time of 3.52 minutes. 1H ΝMR (400 MHz, DMSO-J6) δ 11.27 (d, / = 1.9 Hz, IH), 8.66 (s, IH), 8.08 (d, / = 1.6 Hz, IH), 7.65-7.61 (m, 3H), 7.46-7.40 (m, 2H), 7.31 (d, / = 8.7 Hz, IH), 7.25-7.17 (m, 2H), 7.03 (d, / = 1.6 Hz, IH), 6.98-6.87 (m, 2H), 6.02 (s, 2H), 1.43-1.39 (m, 2H), 1.06-1.02 (m, 2H).
[00895] Example 84: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-cyano-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000250_0001
[00896] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-formyl-lH-indol-5- yl)cyclopropane-carboxamide
[00897] POCl3 (12 g, 80 mmol) was added dropwise to DMF (40 mL) held at -20 °C. After the addition was complete, the reaction mixture was allowed to warm to 0 0C and was stirred for 1 h. l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (3.0 g, 8.0 mmol) was added and the mixture was warmed to 25 0C. After stirring for 30 minutes the reaction mixture was poured over ice and stirred for 2 h. The mixture was then heated at 100 0C for 30 min. The mixture was cooled and the solid precipitate was collected and washed with water. The solid was then dissolved in 200 mL dichloromethane and washed with 200 mL of a saturated aq. NaHCO3. The organics were dried over Na2SO4 and evaporated to yield l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ-butyl-3- formyl-lH-indol-5-yl)cyclopropane-carboxamide (2.0 g, 61%). ESI-MS m/z calc. 404.5, found 405.5 (M+l)+; retention time 3.30 minutes. 1H ΝMR (400 MHz, DMSO-d6) δ 11.48 (s, IH), 10.39 (s, IH), 8.72 (s, IH), 8.21 (s, IH), 7.35-7.31 (m, 2H), 7.04-7.03 (m, IH), 6.97- 6.90 (m, 2H), 6.03 (s, 2H), 1.53 (s, 9H), 1.42-1.39 (m, 2H), 1.05-1.03 (m, 2H).
Figure imgf000250_0002
[00898] (Z)-l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-((hydroxyimino)methyl)-lH- indol-5-yl)cyclopropanecarboxamide
[00899] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-fe^butyl-3-formyl-lH-indol-5- yl)cyclopropanecarboxamide (100 mg, 0.25 mmol) in dichloromethane (5 mL) was added hydroxylamine hydrochloride (21 mg, 0.30 mmol). After stirring for 48 h, the mixture was evaporated to dryness and purified by column chromatography (0-100% ethyl acetate/hexanes) to yield (Z)-l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ-butyl-3- ((hydroxyimino)methyl)-lH-indol-5-yl)cyclopropanecarboxamide (81 mg, 77%). ESI-MS m/z calc. 419.5, found 420.5 (M+l)+; retention time 3.42 minutes. 1H ΝMR (400 MHz, DMSO-d6) δ 10.86 (s, 0.5H), 10.55 (s, 0.5H), 8.56-8.50 (m, 2H), 8.02 (m, IH), 7.24-7.22 (m, IH), 7.12-7.10 (m, IH), 7.03 (m, IH), 6.96-6.90 (m, 2H), 6.03 (s, 2H), 1.43 (s, 9H), 1.40- 1.38 (m, 2H), 1.04-1.01 (m, 2H).
Figure imgf000251_0001
[00900] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-cyano-lH-indol-5- yl)cyclopropane-carboxamide
[00901] (Z)-l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-3-((hydroxyimino)-methyl)-lH- indol-5-yl)cyclopropanecarboxamide (39 mg, 0.090 mmol) was dissolved in acetic anhydride (1 mL) and heated at reflux for 3 h. The mixture was cooled in an ice bath and the precipitate was collected and washed with water. The solid was further dried under high vacuum to yield l-(benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-3-cyano-lH-indol-5- yl)cyclopropanecarboxamide. ESI-MS m/z calc. 401.5, found 402.5 (M+l)+; retention time 3.70 minutes. 1H ΝMR (400 MHz, DMSO-d6) δ 11.72 (s, IH), 8.79 (s, IH), 7.79 (s, IH), 7.32 (m, 2H), 7.03-7.02 (m, IH), 6.95-6.89 (m, 2H), 6.03 (s, 2H), 1.47 (s, 9H), 1.43-1.41 (m, 2H), 1.06-1.04 (m, 2H).
[00902] Example 85: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-methyl-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000251_0002
[00903] A solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (75 mg, 0.20 mmol) and iodomethane (125 μL, 2.0 mmol) in N,N-dimethylformamide (1 mL) was heated at 120 0C in a sealed tube for 24 h. The reaction was filtered and purified by reverse phase HPLC. ESI-MS tn/z calc. 390.5, found 391.3 (M+l)+; retention time 2.04 minutes. 1H ΝMR (400 MHz, DMSO-d6) δ 10.30 (s, IH), 8.39 (s, IH), 7.51 (m, IH), 7.13-7.11 (m, IH), 7.03-6.90 (m, 4H), 6.03 (s, 2H), 2.25 (s, 3H), 1.40- 1.38 (m, HH), 1.03-1.01 (m, 2H).
[00904] Example 86: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-3-(2-hydroxyethyl)- lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000252_0001
[00905] Approximately 100 μL of ethylene dioxide was condensed in a reaction tube at -78 0C. A solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-lH-indol-5- yl)cyclopropanecarboxamide (200 mg, 0.50 mmol) and indium trichloride (20 mg, 0.10 mmol) in dichloromethane (2 mL) was added and the reaction mixture was irradiated in the microwave for 20 min at 100 0C. The volatiles were removed and the residue was purified by column chromatography (0-100 % ethyl acetate/hexanes) to give l-(benzo[d][l,3]dioxol-5- yl)-N-(2-^rf-butyl-3-(2-hydroxyethyl)-lH-indol-5-yl)cyclopropanecarboxamide (5 mg, 3%). ESI-MS m/z calc. 420.5, found 421.3 (M+l)+; retention time 1.67 minutes. 1H ΝMR (400 MHz, CD3CN) δ 8.78 (s, IH), 7.40 (m, IH), 7.33 (s, IH), 7.08 (m, IH), 6.95 - 6.87 (m, 3H), 6.79 (m, IH), 5.91 (s, 2H), 3.51 (dd, J = 5.9, 7.8 Hz, 2H), 2.92 - 2.88 (m, 2H), 2.64 (t, J = 5.8 Hz, IH), 1.50 (m, 2H), 1.41 (s, 9H), 1.06 (m, 2H).
[00906] Example 87: 2-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH- indol-2-yl)acetic acid
Figure imgf000252_0002
[00907] To a solution of ethyl 2-(5-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-lH-indol-2-yl)acetate (0.010 g, 0.025 mmol) in THF (0.3 mL) were added LiOKH2O (0.002 g, 0.05 mmol) and water (0.15 mL) were added. The mixture was stirred at room temperature for 2 h. dichloromethane (3 mL) was added to the reaction mixture and the organic layer was washed with 1 N HCl (2 x 1.5 mL) and water (2 x 1.5 mL). The organic layer was dried over Na2SO4 and filtered. The filtrate was evaporated under reduced pressure to give 2-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH- indol-2-yl)-acetic acid. 1H NMR (400 MHz, DMS0-d6) δ 12.53 (s, IH), 10.90 (s, IH), 8.42 (s, IH), 7.57 (s, IH), 7.17 (d, J = 8.6 Hz, IH), 7.05-6.90 (m, 4H), 6.17 (s, IH), 6.02 (s, 2H), 3.69 (s, 2H), 1.41-1.39 (m, 2H), 1.04-1.02 (m, 2H).
[00908] Example 88: 5-(l-(Benzo[rf][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-tert- butyl- lH-indole-7-carboxylic acid
Figure imgf000253_0001
[00909] Methyl 5-(l-(benzo[<i][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-ferf-butyl- lH-indole-7-carboxylate (30 mg, 0.069 mmol) was dissolved in a mixture of 1,4-dioxane (1.5 mL) and water (2 mL) containing a magnetic star bar and lithium hydroxide (30 mg, 0.71 mmol). The resulting solution was stirred at 70 0C for 45 minutes. The crude product was then acidified with 2.6 M hydrochloric acid and extracted three times with an equivalent volume of dichloromethane. The dichloromethane extracts were combined, dried over sodium sulfate, filtered, and evaporated to dryness. The residue was dissolved in a minimum of N,N-dimethylformamide and then purified by preparative ΗPLC using a gradient of 0- 99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield 5-(l- (benzo[<i][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-^rf-butyl-lH-indole-7-carboxylic acid. ESI-MS m/z calc. 434.2, found 435.5. Retention time of 1.85 minutes. 1H NMR (400 MHz, DMSO-J6) δ 13.05 (s, IH), 9.96 (d, / = 1.6 Hz, IH), 7.89 (d, / = 1.9 Hz, IH), 7.74 (d, / = 2.0 Hz, IH), 7.02 (d, / = 1.6 Hz, IH), 6.96-6.88 (m, 2H), 6.22 (d, / = 2.3 Hz, IH), 6.02 (s, 2H), 1.43 - 1.40 (m, 2H), 1.37 (s, 9H), 1.06-1.02 (m, 2H).
[00910] Example 89: l-(Benzo[rf][l,3]dioxol-5-yl)-N-(2-fert-butyl-l-(l,3- dihydroxypropan^-yO-lH-indol-S-yOcyclopropanecarboxamide
Figure imgf000253_0002
Figure imgf000254_0001
[00911] l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-tert-butyl-l-(l,3-dihydroxypropan-2- yl)indolin-5-yl)cyclopropanecarboxamide
[00912] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te^butylindolin-5- yl)cyclopropanecarboxamide (50 mg, 0.13 mmol) was dissolved in dichloroethane (0.20 mL) and 2,2-dimethyl-l,3-dioxan-5-one (0.20 mL). Trifluoroacetic acid was added (0.039 mL) and the resulting solution was allowed to stir for 20 minutes. Sodium triacetoxyborohydride was added (55 mg, 0.26 mmol) and the reaction mixture was stirred for 30 minutes. The crude reaction mixture was then evaporated to dryness, dissolved in N,N-dimethylformamide and purified by preparative HPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid.
Chloranil
Figure imgf000254_0003
Figure imgf000254_0002
[00913] l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-tert-butyl-l-(l,3-dihydroxypropan-2-yl)-lH- indol-5-yl)cyclopropanecarboxamide
[00914] l-(Benzo[J][l,3]dioxol-5-yl)-N-(2-^rf-butyl-l-(l,3-dihydroxypropan-2-yl)indolin- 5-yl)cyclopropanecarboxamide (40.3 mg, 0.0711 mmol as the trifluoracetic acid salt) was dissolved in toluene (1 mL). To the resulting solution was added 2,3,5,6- tetrachlorocyclohexa-2,5-diene-l,4-dione (35 mg, 0.14 mmol). The resulting suspension was heated at 100 0C in an oil bath for 10 minutes. The crude product was then evaporated to dryness, dissolved in a 1 mL of N,N-dimethylformamide and purified by purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[<i][l,3]dioxol-5-yl)-N-(2-terz-butyl-l-(l,3- dihydroxypropan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide. ESI-MS m/z calc. 450.2, found 451.5 (M+l)+. Retention time of 1.59 minutes.
[00915] Example 90: iV-(7-(Aminomethyl)-2-tert-butyl-lH-indol-5-yl)-l- (benzofrfJfl^J-dioxol-S-yOcyclopropanecarboxamide
Figure imgf000255_0001
[00916] iV-CT-CAminomethyO^-tert-butyl-lH-indol-S-yO-l-Cbenzorøtl^ldioxol-S- yl)cyclopropanecarboxamide
[00917] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-7-cyano-lH-indol-5- yl)cyclopropanecarboxamide (375 mg, 0.934 mmol) was dissolved in 35 mL of ethyl acetate. The solution was recirculated through a continuous flow hydrogenation reactor containing 10% palladium on carbon at 100 0C under 100 bar of hydrogen for 8 h. The crude product was then evaporated to dryness and purified on 12 g of silica gel utilizing a gradient of 0- 100% ethyl acetate (containing 0.5% triethylamine) in hexanes to yield N-(7-(aminomethyl)- 2-^rf-butyl-lH-indol-5-yl)-l-(benzo[(i][l,3]-dioxol-5-yl)-cyclopropanecarboxamide (121 mg, 32%). ESI-MS m/z calc. 405.2, found 406.5 (M+l)+. Retention time of 1.48 minutes.
[00918] Example 91: 5-(l-(Benzo[rf][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-tørt- butyl- lH-indole-7-carboxamide
Figure imgf000255_0002
[00919] 5-(l-(Benzo[rf][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-tert-butyl-lH- indole-7-carboxamide
[00920] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te^butyl-7-cyano-lH-indol-5-yl)- cyclopropanecarboxamide (45 mg, 0.11 mmol) was suspended in a mixture of methanol (1.8 mL), 30% aqueous hydrogen peroxide (0.14 mL, 4.4 mmol) and 10% aqueous sodium hydroxide (0.150 mL). The resulting suspension was stirred for 72 h at room temperature. The hydrogen peroxide was then quenched with sodium sulfite. The reaction mixture was diluted with 0.5 mL of N,N-dimethylformamide, filtered, and purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield 5-(l-(benzo[J][l,3]dioxol-5-yl)cyclopropane-carboxamido)-2-^rf-butyl-lH-indole-7- carboxamide. ESI-MS m/z calc. 419.2, found 420.3 (M+l)+. Retention time of 1.74 minutes.
[00921] Example 92: l-(Benzo[rf][l,3]dioxol-5-yl)-W-(2-fert-butyl-7-
(methylsulfonamido-methyO-lH-indol-S-yOcyclopropanecarboxamide
Figure imgf000256_0001
[00922] l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-ter/-butyl-7-(methylsulfonamidomethyl)-lH- indol-5-yl)cyclopropanecarboxamide
[00923] N-(7-(Aminomethyl)-2-^rf-butyl-lH-indol-5-yl)-l-(benzo[J][l,3]dioxol-5- yl)cyclopropanecarboxamide (20 mg, 0.049 mmol) was dissolved in DMF (0.5 mL) containing triethylamine (20.6 μL, 0.147 mmol) and a magnetic stir bar. Methanesulfonyl chloride (4.2 μL, 0.054 mmol) was then added to the reaction mixture. The reaction mixture was allowed to stir for 12 h at room temperature. The crude product was purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(2-terZ-butyl-7- (methylsulfonamidomethyl)-lH-indol-5-yl)cyclopropanecarboxamide. ESI-MS tn/z calc. 483.2, found 484.3 (M+l)+. Retention time of 1.84 minutes.
[00924] Example 93: Λ47-(Acetamidomethyl)-2-fert-butyl-lH-indol-5-yl)-l- (benzofrfΗl^J-dioxol-S-yOcyclopropanecarboxamide
Figure imgf000256_0002
[00925] N-(7-(Aminomethyl)-2-^rf-butyl-lH-indol-5-yl)-l-(benzo[J][l,3]dioxol-5- yl)cyclopropanecarboxamide (20 mg, 0.049 mmol) was dissolved in DMF (0.5 mL) containing triethylamine (20.6 μL, 0.147 mmol) and a magnetic stir bar. Acetyl chloride (4.2 μL, 0.054 mmol) was then added to the reaction mixture. The reaction mixture was allowed to stir for 16 h at room temperature. The crude product was purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield N-(7-(acetamidomethyl)-2-^rf-butyl-lH-indol-5-yl)-l-(benzo[J][l,3]dioxol-5- yl)cyclopropanecarboxamide. ESI-MS m/z calc. 447.2, found 448.3 (M+l)+. Retention time of 1.76 minutes.
[00926] Example 94: ΛΗl-Acetyl^-fe^butyl-lΗ-indol-S-ylΗ-CbenzotdΗl^Jdioxol-S- yl)-cyclopropanecarboxamide
Figure imgf000257_0001
[00927] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-fe?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (120 mg, 0.31 mmol) in anhydrous DMF-THF (3.3 mL, 1:9) was added NaH (60% in mineral oil, 49 mg, 1.2 mmol) at room temperature. After 30 min under N2, the suspension was cooled down to -15 0C and a solution of acetyl chloride (1.1 eq.) in DMF (0.5 mL) was added dropwise. The reaction mixture was stirred for 30 min at - 15 0C then for 6 h at room temperature. Water (0.5 mL) was added at 0 0C, solvent was removed, and the residue was diluted with MeOH, filtrated and purified by preparative HPLC to give N-(l-acetyl-2-^rf-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]dioxol-5-yl)cyclo- propanecarboxamide. 1H ΝMR (400 MHz, DMSO) δ 8.9 (s, IH), 7.74 (d, / =2.1 Hz, IH), 7.54 (d, 7 =9.0 Hz, IH), 7.28 (dd, Jl =2.1 Hz, 72 =9.0 Hz, IH), 7.01 (d, 7 =1.5 Hz, IH), 6.93 (dd, Jl =1.7 Hz, 72 =8.0 Hz, IH), 6.89 (d, 7 =8.0 Hz, IH), 6.54 (bs, IH), 6.02 (s, 2H), 2.80 (s, 3H), 1.42-1.40 (m, HH), 1.06-1.05 (m, 2H). MS (ESI) m/e (M+H+) 419.3.
[00928] Example 95: iV-(l-(2-Acetamidoethyl)-2-tert-butyl-6-fluoro-lH-indol-5-yl)-l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000257_0002
[00929] iV-(l-(2-Aminoethyl)-2-tert-butyl-6-fluoro-lH-indol-5-yl)-l-(2,2-difluorobenzo- [dHl^Jdioxol-S-yOcyclopropanecarboxamide [00930] To a solution of tert-butyl 2-(2-te^butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-6-fluoro-lH-indol-l-yl)ethylcarbamate (620 mg, 1.08 mmol) in CH2Cl2 (8 mL) was added TFA (2 mL). The reaction was stirred at room temperature for 1.5 h before being neutralized with solid NaHCO3. The solution was partitioned between H2O and CH2Cl2. The organic layer was dried over MgSO4, filtered and concentrated to yield the product as a cream colored solid (365 mg, 71%). 1H NMR (400 MHz, DMSO-d6) δ 8.38 (s, IH), 7.87 (br s, 3H, NH3 +), 7.52 (s, IH), 7.45-7.38 (m, 3H), 7.32 (dd, J = 8.3, 1.5 Hz, IH), 6.21 (s, IH), 4.46 (m, 2H), 3.02 (m, 2H), 1.46 (m, 2H), 1.41 (s, 9H), 1.14 (m, 2H). HPLC ret. time 1.66 min, 10-99 % CH3CN, 3 min run; ESI-MS 474.4 m/z (M+H+).
Figure imgf000258_0001
[00931] iV-(l-(2-Acetamidoethyl)-2-tert-butyl-6-fluoro-lH-indol-5-yl)-l-(2,2- difluorobenzo [dHl^Jdioxol-S-yOcyclopropanecarboxamide
[00932] To a solution of N-(l-(2-aminoethyl)-2-te^butyl-6-fluoro-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropane-carboxamide (47 mg, 0.10 mmol) and Et3N (28 μL, 0.20 mmol) in DMF (1 mL) was added acetyl chloride (7.1 μL, 0.10 mmol). The mixture was stirred at room temperature for 1 h before being filtered and purified by reverse phase HPLC (10 - 99 % CH3CN/ H2O) to yield N-(l-(2-acetamidoethyl)-2-te?t-butyl-6- fluoro-lH-indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide. 1H NMR (400 MHz, DMSO-d6) δ 8.35 (s, IH), 8.15 (t, J = 5.9 Hz, IH), 7.53 (s, IH), 7.43- 7.31 (m, 4H), 6.17 (s, IH), 4.22 (m, 2H), 3.30 (m, 2H), 1.85 (s, 3H), 1.47 (m, 2H), 1.41 (s, 9H), 1.13 (m, 2H). HPLC ret. time 2.06 min, 10-99 % CH3CN, 3 min run; ESI-MS 516.4 m/z (M+H+).
[00933] Example 96: l-(Benzo[d][l,3]dioxol-5-yl)-Λ42-fert-butyl-l-(2-hydroxy-3- methoxy-propyl)-lH-indol-5-yl)cyclopropenecarboxamide
1. NaH1 DMF-THF
Figure imgf000258_0002
[00934] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (320 mg, 0.84 mmol) was dissolved in a mixture composed of anhydrous DMF (0.5 mL) and anhydrous THF (5 mL) under N2. NaH (60% in mineral oil, 120 mg, 3.0 mmol) was added at room temperature. After 30 min of stirring, the reaction mixture was cooled to -15 0C before a solution of epichlorohydrin (79 μL, 1.0 mmol) in anhydrous DMF (1 mL) was added dropwise. The reaction mixture was stirred for 15 min at -15 0C, then for 8 h at room temperature. MeOH (1 mL) was added and the mixture was heated for 10 min at 105 0C in the microwave oven. The mixture was cooled, filtered and purified by preparative HPLC to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ-butyl-l-(2- hydroxy-S-methoxy-propy^-lH-indol-S-yOcyclopropanecarboxamide. 1H ΝMR (400 MHz, DMSO-d6) δ 8.44 (s, IH), 7.59 (d, / = 1.9 Hz, IH), 7.31 (d, J = 8.9 Hz, IH), 7.03 (dd, / = 8.7, 1.9 Hz, 2H), 6.95 (dd, 7 = 8.0, 1.7 Hz, IH), 6.90 (d, / = 8.0 Hz, IH), 6.16 (s, IH), 6.03 (s, 2H), 4.33 (dd, / = 15.0, 4.0 Hz, IH), 4.19 (dd, / = 15.0, 8.1 Hz, IH), 4.02 (ddd, / = 8.7, 4.8 Hz, IH), 3.41-3.32 (m, 2H), 3.30 (s, 3H), 1.41 (s, 9H), 1.41-1.38 (m, 2H), 1.03 (dd, / = 6.7, 4.0 Hz, 2H). MS (ESI) m/e (M+H+) 465.0.
[00935] Example 97: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-l-(2-hydroxy-3- (methyl-amino)propyl)-lH-indol-5-yl)cyclopropanecarboxamide
1. NaH1 DMF-THF
Figure imgf000259_0001
[00936] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-lH-indol-5- yl)cyclopropanecarboxamide (320 mg, 0.84 mmol) was dissolved in a mixture composed of anhydrous DMF (0.5 mL) and anhydrous THF (5 mL) under N2. NaH (60% in mineral oil, 120 mg, 3.0 mmol) was added at room temperature. After 30 min of stirring, the reaction mixture was cooled to -15 0C before a solution of epichlorohydrin (79 μL, 1.0 mmol) in anhydrous DMF (1 mL) was added dropwise. The reaction mixture was stirred for 15 min at -15 0C, then for 8 h at room temperature. MeNH2 (2.0 M in MeOH, 1.0 mL) was added and the mixture was heated for 10 min at 105 0C in the microwave oven. The mixture was cooled, filtered and purified by preparative HPLC to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2- ^rt-butyl-l-(2-hydroxy-3-(methylamino)propyl)-lH-indol-5-yl)cyclopropanecarboxamide. 1H ΝMR (400 MHz, DMSO-d6) δ 8.50 (s, IH), 7.60-7.59 (m, IH), 7.35 (dd, J = 14.3, 8.9 Hz, IH), 7.10 (d, J = 8.8 Hz, IH), IH), 6.94 (dd, J = 8.0, 1.6 Hz, IH), 6.91 (d, J = 7.9 Hz, IH), 6.20 (d, J = 2.3 Hz, IH), 6.03 (s, 2H), 2.82 (d, J = 4.7 Hz, IH), 2.72 (d, J = 4.7 Hz, IH), 2.55 (dd, J = 5.2, 5.2 Hz, IH), 2.50 (s, 3H), 1.43 (s, 9H), 1.39 (dd, J = 6.4, 3.7 Hz, 2H), 1.04 (dd, J = 6.5, 3.9 Hz, 2H). MS (ESI) m/e (M+H+) 464.0.
[00937] Example 98: (5)-iV-(l-(3-Amino-2-hydroxypropyl)-2-tert-butyl-lH-indol-5-yl)- l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000260_0001
[00938] (Λ)-3-(2-tert-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarbox-amido)-lH-indol-l-yl)-2-hydroxypropyl-4- methylbenzenesulfonate
[00939] To a stirred solution of (#)-N-(2-te^butyl-l-(2,3-dihydroxypropyl)-lH-indol-5- yl)-l-(2,2-difluoro-benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (3.0 g, 6.1 mmol) in dichloromethane (20 mL) was added triethylamine (2 mL) and para-toluenesulfonylchloride (1.3 g, 7.0 mmol). After 18 hours, the reaction mixture was partitioned between 10 mL of water and 10 mL of ethyl acetate. The organic layer was dried over magnesium sulfate, filtered and evaporated. The residue was purified using column chromatography on silica gel (0-60% ethyl acetate/hexane) providing (Λ)-3-(2-^rf-butyl-5-(l-(2,2-difluorobenzo[d][l,3]- dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2-hydroxypropyl-4-methyl- benzenesulfonate (3.21 g, 86%). LC/MS (M + 1) = 641.2. 1H ΝMR (400 MHz, CDCl3) δ 7.77 (d, 2H, / = 16 Hz), 7.55 (d, IH, / = 2 Hz), 7.35 (d, 2H, J = 16 Hz), 7.31 (m, 3H), 6.96 (s, IH), 6.94 (dd, IH, J = 2, 8 Hz), 6.22 (s, IH), 4.33 (m, IH), 4.31 (dd, IH, / = 6, 15 Hz), 4.28 (dd, IH, / = 11, 15 Hz), 4.18 (m, IH), 3.40 (dd, IH, / = 3, 6 Hz), 3.36 (dd, IH, / = 3, 6 Hz),
2.46 (s, 3H), 2.40 (br s, IH), 1.74 (m, 2H), 1.40 (s, 9H), 1.11 (m, 2 H).
Figure imgf000261_0001
[00940] (Λ)-iV-(l-(3-Azido-2-hydroxypropyl)-2-tert-butyl-lH-indol-5-yl)-l-(2,2- difluorobenzo [dHl^Jdioxol-S-yOcyclopropanecarboxamide
[00941] To a stirred solution (/?)-3-(2-terf-butyl-5-(l-(2,2-difluoiobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)- lH-indol- 1 -yl)-2-hydroxypropyl-4-methylbenzenesulfonate (3.2 g, 5.0 mmol) in DMF (6 mL) was added sodium azide (2.0 g, 30 mmol). The reaction was heated at 80 0C for 2 h. The mixture was partitioned between 20 mL ethyl acetate and 20 mL water. The layers were separated and the organic layer was evaporated. The residue was purified using column chromatography (0-85% ethyl acetate/hexane) to give (R)-N-(l-(3- azido-2-hydroxypropyl)-2-^rf-butyl-lH-indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)-cyclopropanecarboxamide (2.48 g). LC/MS (M + 1) = 512.5. 1H NMR (400 MHz, CDCl3) δ 7.55 (d, IH, / = 2 Hz), 7.31 (m, 3H), 6.96 (s, IH), 6.94 (dd, IH, / = 2, 8 Hz), 6.22 (s, IH), 4.33 (m, IH), 4.31 (dd, IH, / = 6, 15 Hz), 4.28 (dd, IH, / = 11, 15 Hz), 4.18 (m, IH), 3.40 (dd, IH, / = 3, 6 Hz), 3.36 (dd, IH, / = 3, 6 Hz), 2.40 (br s, IH), 1.74 (m, 2H), 1.40 (s, 9H), 1.11 (m, 2 H).
Figure imgf000261_0002
[00942] (5)-iV-(l-(3-Amino-2-hydroxypropyl)-2-tert-butyl-lH-indol-5-yl)-l-(2,2- difluoro-benzofdHl^Jdioxol-S-yOcyclopropanecarboxamide
[00943] To a stirred solution (#)-N-(l-(3-azido-2-hydroxypropyl)-2-te?t-butyl-lH-indol-5- yl)-l-(2,2-difluorobenzo [d][l,3]dioxol-5-yl)cyclopropanecarboxamide (2.4 g, 4.0 mmol) in MeOH (25 mL ) was added 5 % Pd/C (2.4 g) under a Hydrogen gas filled balloon. After 18 h, the reaction mixture was filtered through celite and rinsed with 300 mL ethyl acetate. The organic layer was washed with 1 Ν HCl and evaporated to give (5)-N-(l-(3-amino-2- hydroxypropyl)-2-^rf-butyl-lH-indol-5-yl)-l-(2,2-difluoro-benzo[d][l,3]-dioxol-5- yl)cyclopropane-carboxamide (1.37 g). MS (M + 1) = 486.5. [00944] Example 99: (S)-Methyl 3-(2-fert-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol- 5-yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2-hydroxypropylcarbamate
Figure imgf000262_0001
[00945] To a stirred solution (#)-N<H3-amino-2-hydroxypropyl)-2-te?t-butyl-lH-indol-5- yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (0.10 g, 0.20 mmol) in methanol (1 mL) was added 2 drops of triethylamine and methylchloroformyl chloride (0.020 mL, 0.25 mmol). After 30 min, the reaction mixture was filtered and purified using reverse phase HPLC providing (5)-methyl 3-(2-^rt-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclo-propanecarboxamido)- lH-indol- 1 -yl)-2-hydroxypropylcarbamate. The retention time on a three minute run is 1.40 min. LC/MS (M + 1) = 544.3. 1H ΝMR (400 MHz, CDCl3) δ 7.52 (d, IH, / = 2Hz), 7.30 (dd, IH, / = 2, 8 Hz), 7.28(m, IH), 7.22 (d, IH, / = 8 Hz), 7.14 (d, IH, / = 8 Hz), 7.04 (br s, IH), 6.97 (dd, IH, / = 2, 8 Hz), 6.24 (s, IH), 5.19 (1H, br s), 4.31 (dd, IH, J = 6, 15 Hz), 4.28 (dd, IH, / = 11, 15 Hz), 4.18 (m, IH), 3.70 (s, 3H), 3.40 (dd, IH, / = 3, 6 Hz), 3.36 (dd, IH, / = 3, 6 Hz), 3.26 (m, IH), 1.74 (m, 2H), 1.40 (s, 9 H), 1.11 (m, 2 H).
[00946] Example 100: 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2- fert-butyl-lH-indol-l-yl)butanoic acid
Figure imgf000262_0002
AcOH
Figure imgf000262_0003
Figure imgf000262_0004
[00947] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butylindolin-5- yl)cyclopropanecarboxamide
[00948] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terf-butyl-lH-indol-5-yl)cyclo- propanecarboxamide (851 mg, 2.26 mmol) in acetic acid (60 mL) was added NaBH3CN (309 mg, 4.91 mmol) at 0 0C. The reaction mixture was stirred for 5 min at room temperature after which no starting material could be detected by LCMS. The solvent was evaporated under reduced pressure and the residue was purified by column chromatography on silica gel (5- 40% ethyl acetate/hexanes) to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terf-butylindolin-5- yl)cyclopropanecarboxamide (760 mg, 89%).
Figure imgf000263_0001
[00949] 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-tørt- butylindolin-l-yl)butanoic acid
[00950] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-ferf-butylindolin-5- yl)cyclopropanecarboxamide (350 mg, 0.93 mmol, 1 eq) in anhydrous methanol (6.5 mL) and AcOH (65 μL) was added 4-oxobutanoic acid (15% in water, 710 mg, 1.0 mmol) at room temperature. After 20 min of stirring, NaBH3CN (130 mg, 2.0 mmol) was added in one portion and the reaction mixture was stirred for another 4 h at room temperature. The reaction mixture was quenched by addition of AcOH (0.5 mL) at 0 0C and the solvent was removed under reduced pressure. The residue was purified by column chromatography on silica gel (5-75% ethyl acetate/hexanes) to give 4-(5-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-2-terZ-butylindolin-l-yl)butanoic acid (130 mg, 30%).
Figure imgf000263_0002
[00951] 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-tørt-butyl-lH- indol-l-yl)butanoic acid [00952] 4-(5-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2-^rf-butylindolin- l-yl)butanoic acid (130 mg, 0.28 mmol) was taken up in a mixture of acetonitrile-H2θ-TFA. The solvent was removed under reduced pressure and the residue obtained was dissolved in CDCI3. After a brief exposition to daylight (5-10 min), the solution turned purple. The mixture was stirred open to the atmosphere at room temperature until complete disappearance of the starting material (8 h). Solvent was removed under reduced pressure and the residue was purified by reverse pharse HPLC to give 4-(5-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-2-tert-butyl-lH-indol-l-yl)butanoic acid. 1H NMR (400 MHz, CDCl3) δ 7.52 (d, J = 1.9 Hz, IH), 7.18 (d, J = 2.1 Hz, IH), 7.16 (s, IH), 7.03 (dd, J = 9.4, 1.9 Hz, IH), 7.00-6.98 (m, 2H), 6.85 (d, J = 7.9 Hz, IH), 6.16 (s, IH), 6.02 (s, 2H), 4.29-4.24 (m, 2H), 2.48 (dd, J = 6.9, 6.9 Hz, 2H), 2.12-2.04 (m, 2H), 1.69 (dd, J = 6.8, 3.7 Hz, 2H), 1.43 (s, 9H), 1.09 (dd, J = 6.8, 3.7 Hz, 2H). MS (ESI) m/e (M+H+) 463.0.
[00953] Example 101: l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-fert-butyl-l-(4-(2- hydroxyethyl-amino)-4-oxobutyl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000264_0001
[00954] To a solution of 4-(5-(l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-2- tert-butyl-lH-indol-l-yl)butanoic acid (10 mg) in anhydrous DMF (0.25 mL) were successively added Et3N (9.5 mL, 0.069 mmol) and HBTU (8.2 mg, 0.022 mmol). After stirring for 10 min at 60 0C, ethanolamine (1.3 μL, 0.022 mmol) was added, and the mixture was stirred for another 4 h at 60 0C. l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-l-(4-(2- hydroxyethyl-amino)-4-oxobutyl)-lH-indol-5-yl)cyclopropanecarboxamide (5.8 mg, 64%) was obtained after purification by preparative HPLC. MS (ESI) m/e (M+H+) 506.0.
[00955] Example 102: l-(Benzo[d][l,3]dioxol-5-yl)-Ν-(2-fert-butyl-l-(2- (dimethylamino)-2-oxoethyl)-lH-indol-5-yl)cyclopropanecarboxamide 1. NaH, DMF-THF
Figure imgf000265_0001
[00956] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te^butylindolin-5- yl)cyclopropanecarboxamide (62 mg, 0.16 mmol) in anhydrous DMF (0.11 mL) and THF (1 mL) was added NaH (60% in mineral oil, 21 mg, 0.51 mmol) at room temperature under N2. After 30 min of stirring, the reaction mixture was cooled to 0 0C and 2-chloro-N,N- dimethylacetamide (11 mL, 0.14 mmol,) was added. The reaction mixture was stirred for 5 min at 0 0C and then for 10 h at room temperature. The mixture was purified by preparative HPLC and the resultant solid was dissolved in DMF (0.6 mL) in the presence of Pd-C (10 mg). The mixture was stirred open to the atmosphere overnight at room temperature. The reaction mixture was filtrated and purified by preparative HPLC providing 1- (benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-l-(2-(dimethylamino)-2-oxoethyl)-lH-indol-5- yl)cyclopropanecarboxamide. MS (ESI) m/e (M+H+) 462.0.
[00957] Example 103: 3-(2-tert-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclo- propanecarboxamido) - lH-indol- 1 -yl)pr opanoic acid
Figure imgf000265_0002
air
Figure imgf000265_0003
Figure imgf000265_0005
Figure imgf000265_0004
[00958] iV-(2-tert-Butyl-l-(2-chloroethyl)indolin-5-yl)-l-(2,2- difluorobenzofdHl^dioxol-S-yOcyclopropanecarboxamide [00959] To a solution of N-(2-tert-buty\- l-(2-cyanoethyl)indolin-5-yl)- l-(2,2- difluorobenzofdltl^ldioxol-S-y^cyclopropanecarboxamide (71 mg, 0.17 mmol) in anhydrous dichloromethane (1 mL) was added chloroacetaldehyde (53 μL, 0.41 mmol) at room temperature under N2. After 20 min of stirring, NaBH(O Ac)3 (90 mg, 0.42 mmol) was added in two portions. The reaction mixture was stirred overnight at room temperature. The product was purified by column chromatography on silica gel (2-15% ethyl acetate/hexanes) providing N-(2-^rf-butyl-l-(2-chloroethyl)indolin-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol- 5-yl)cyclopropanecarboxamide (51 mg, 63%).
Figure imgf000266_0001
[00960] iV-(2-tert-Butyl-l-(2-cyanoethyl)indolin-5-yl)-l-(2,2- difluorobenzofdHl^Jdioxol-S-yOcyclopropanecarboxamide
[00961] N-(2-^rf-butyl-l-(2-chloroethyl)indolin-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol- 5-yl)cyclopropanecarboxamide (51 mg), ΝaCΝ (16 mg, 0.32 mmol) and KI (cat) in EtOH (0.6 mL) and water (0.3 mL) were combined and heated at 110 0C for 30 min in the microwave. The solvent was removed under reduced pressure and the residue was purified by column chromatography on silica gel (2-15% ethyl acetate/hexanes) providing N-(2-tert- butyl-l-(2-cyanoethyl)indolin-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide (24 mg, 48%).
air
Figure imgf000266_0003
Figure imgf000266_0002
[00962] 3-(2-tert-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclo- propanecarbox-amido) - lH-indol- 1 -yl)pr opanoic acid
[00963] N-(2-^rf-butyl-l-(2-cyanoethyl)indolin-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol- 5-yl)cyclopropane-carboxamide (24 mg, 0.050 mmol) was taken up in 50% aq. KOH (0.5 mL) and 1,4-dioxane (1 mL). The mixture was heated at 125 0C for 2 h. The solvent was removed and the residue was purified by preparative HPLC. The residue was dissolved in CDCI3 (1 mL) then briefly exposed to daylight. The purple solution that formed was stirred until complete disappearance of the starting material (1 h). The solvent was removed under reduced pressure and the residue was purified by preparative HPLC providing 3-(2-tert-buty\- 5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclo-propanecarboxamido)-lH-indol-l- yl)propanoic acid. MS (ESI) m/e (M+H+) 485.0.
[00964] Example 104: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-6-fluoro-l-(2- hydroxy-ethyl)-lH-indol-5-yl)cyclopropenecarboxamide
Figure imgf000267_0001
[00965] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te^butyl-6-fluoroindolin-5- yl)cyclopropanecarboxamide (340 mg, 0.86 mmol) in anhydrous MeOH (5.7 mL) containing 1% of acetic acid was added glyoxal 40% in water (0.60 mL, 5.2 mmol) at room temperature under N2. After 20 min of stirring, NaBH3CN (120 mg, 1.9 mmol) was added in one portion and the reaction mixture was stirred overnight at room temperature. The solvent was removed under reduced pressure and the residue obtained was purified by column chromatography on silica gel (10-40% ethyl acetate/hexanes) providing a pale yellow oil which was treated with 50/50 CH3CN-H2O containing 0.05% TFA and CDCl3. Solvent was removed under reduced pressure and the residue was purified by column chromatography on silica gel (20-35% ethyl acetate/hexanes) to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-ferZ- butyl-6-fluoro-l-(2-hydroxyethyl)-lH-indol-5-yl)cyclopropanecarboxamide. 1H ΝMR (400 MHz, CDCl3) δ 8.02 (d, J = 7.7 Hz, IH), 7.30 (d, J = 2.1 Hz, IH), 6.93 (dd, J = 1.6, 7.9 Hz, IH), 6.90 (d, J = 1.6 Hz, IH), 6.90 (d, J = 1.6 Hz, IH), 6.78 (d, J = 7.9 Hz, IH), 6.08 (s, IH), 5.92 (s, 2H), 4.21 (dd, J = 6.9, 6.9 Hz, 2H), 3.68 (m, 2H), 2.28 (s, IH), 1.60 (dd, J = 3.7, 6.7 Hz, 2H), 1.35 - 1.32 (m, 9H), 1.04 (dd, J = 3.7, 6.8 Hz, 2H). MS (ESI) m/e (M+H+) 439.0.
[00966] Example 105: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-6-fluoro-l-(3- hydroxy-propyl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000267_0002
OH PCC, DCM °
"OBn ^ OBn
[00967] 3-(Benzyloxy)propanal
[00968] To a suspension of PCC (606 mg, 2.82 mmol) in anhydrous dichloromethane (8 mL) at room temperature under N2 was added a solution of 3-benzyloxy-l-propanol (310 mg, 1.88 mmol) in anhydrous dichloromethane. The reaction mixture was stirred overnight at room temperature, filtrated through Celite, and concentrated. The residue was purified by column chromatography on silica gel (1-10% ethyl acetate/hexanes) to give 3- (benzyloxy)propanal (243 mg, 79%).
Figure imgf000268_0001
[00969] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-6-fluoro-l-(3-hydroxypropyl)-lH- indol-5-yl)cyclopropanecarboxamide
[00970] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te^butyl-6-fluoroindolin-5- yl)cyclopropanecarboxamide (160 mg, 0.50 mmol) in anhydrous dichloromethane (3.4 mL) was added 3-(benzyloxy)propanal (160 mg, 0.98 mmol) at room temperature. After 10 min of stirring, ΝaBH(OAc)3 (140 mg, 0.65 mmol) was added in one portion and the reaction mixture was stirred for 4 h at room temperature. The solvent was removed under reduced pressure and the residue was taken-up in a mixture of 50/50 CH3CN-H2O containing 0.05% TFA. The mixture was concentrated to dryness and the residue was dissolved in CDCl3 (5 mL) and briefly exposed to daylight. The purple solution was stirred open to the atmosphere at room temperature for 2 h. The solvent was removed under reduced pressure and the residue was treated with Pd-C (10 mg) in MeOH (2 mL) under 1 atm of H2 for 2 h. The catalyst was filtered through Celite and the solvent was removed under reduced pressure. The residue was purified by preparative TLC 30% ethyl acetate/hexanes to provide 1- (benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-6-fluoro-l-(3-hydroxypropyl)-lH-indol-5- yl)cyclopropanecarboxamide (18 mg, 8% from l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ-butyl- 6-fluoroindolin-5-yl)cyclopropane-carboxamide). 1H ΝMR (400 MHz, CDCl3) δ 8.11 (d, J = 7.8 Hz, IH), 7.31 (d, J = 2.2 Hz, IH), 6.94 (dd, J = 7.9, 1.7 Hz, IH), 6.91 (d, J = 1.6 Hz, IH), 6.85 (d, J = 11.7 Hz, IH), 6.79 (d, J = 7.9 Hz, IH), 6.10 (s, IH), 5.94 (s, 2H), 4.25-4.21 (m, 2H), 3.70 (dd, J = 5.7, 5.7 Hz, 2H), 1.93-1.86 (m, 2H), 1.61 (dd, J = 6.8, 3.7 Hz, 2H), 1.35 (s, 9H), 1.04 (dd, J = 6.8, 3.7 Hz, 2H). MS (ESI) m/e (M+H+) 453.0.
[00971] Example 106: Λ41-(2-Acetamidoethyl)-2-fert-butyl-lH-indol-5-yl)-l- (benzo[d][l,3]-dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000269_0001
[00972] iV-(l-(2-azidoethyl)-2-tert-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]dioxol-5-yl)- cyclopropanecarboxamide
[00973] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te^butylindolin-5- yl)cyclopropane-carboxamide (73 mg, 0.19 mmol) in anhydrous dichloromethane (1.2 mL) was added chloroacetaldehyde (60 μL, 0.24 mmol) at room temperature. After 10 min of stirring, ΝaBH(OAc)3 (52 mg, 0.24 mmol) was added in one portion and the reaction mixture was stirred for another 30 min at room temperature. The solvent was removed under reduced pressure and the residue was purified by preparative HPLC to give the indoline, which oxidized to the corresponding indole when taken-up in CDCI3. The resulting indole was treated with NaN3 (58 mg, 0.89 mmol) and NaI (cat) in anhydrous DMF (0.8 mL) for 2 h at 85 0C. The reaction mixture was purified by preparative HPLC providing N-(l-(2- azidoethyl)-2-^rf-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide (15 mg, 18% from l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ- butylindolin-5-yl)cyclopropane-carboxamide).
Figure imgf000269_0002
[00974] iV-(l-(2-Acetamidoethyl)-2-tert-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]-dioxol-5- yl)cyclopropanecarboxamide
[00975] A solution of N-(l-(2-azidoethyl)-2-te?t-butyl-lH-indol-5-yl)-l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (13 mg, 0.029 mmol) in MeOH-AcOH (0.2 mL, 99:1) in the presence of Pd-C (2 mg) was stirred at room temperature under 1 atm of H2 for 2 h, filtered through Celite, and concentrated under reduced pressure. The crude product was treated with AcCl (0.05 mL) and Et3N (0.05 mL) in anhydrous THF (0.2 mL) at 0 0C for 30 min and then 1 h at room temperature. The mixture was purified by preparative HPLC providing N-(l-(2-acetamidoethyl)-2-ferf-butyl-lH-indol-5-yl)-l-(benzo[d][l,3]- dioxol-5-yl)cyclopropanecarboxamide. MS (ESI) m/e (M+H+) 462.0.
[00976] Example 107: iV-(2-ter/-Butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000270_0001
[00977] 3-(2-ter/-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarbox- amido)-lH-indol-l-yl)-2-hydroxypropyl-4-methylbenzenesulfonate
[00978] To a solution of N-(2-te^butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^l-dioxol-S-yOcyclopropanecarboxamide (172 mg, 0.35 mmol) in anhydrous dichloromethane (1.4 mL) at 0 0C in the presence Of Et3N (56 μL, 0.40 mmol) was added TsCl (71 mg, 0.37 mmol). The reaction mixture was stirred for 2 h at room temperature before being cooled to 0 0C and another portion of TsCl (71 mg, 0.37 mmol) was added. After 1 h of stirring at room temperature, the mixture was purified by column chromatography on silica gel (10-30% ethyl acetate/hexanes) providing 3-(2-terZ-butyl-5-(l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-l-yl)-2- hydroxypropyl-4-methylbenzene-sulfonate (146 mg, 64%).
Figure imgf000271_0001
[00979] iV-(2-tert-Butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdHl^Jdioxol-S-yOcyclopropanecarboxamide
[00980] N-(2-^rf-Butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdltl^ldioxol-S-y^-cyclopropanecarboxamide (145 mg, 0.226 mmol) was treated with powdered ΝaCΝ (34 mg, 0.69 mmol) in anhydrous DMF (1.5 mL) at 85 0C for 2 h. The reaction mixture was cooled down to room temperature before it was diluted with dichloromethane (10 mL) and aq. sat. ΝaHCC>3 (10 mL). The organic phase was separated and the aqueous phase was extracted with dichloromethane (2 x 10 mL). The organic phases were combined, washed with brine, dried with sodium sulfate, filtered then concentrated. The residue was purified by column chromatography on silica gel (25-55% ethyl acetate/hexanes) providing N-(2-terZ-butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide (89 mg, 79%). 1H ΝMR (400 MHz, CDCl3) δ 7.43 (d, J = 1.9 Hz, IH), 7.20-7.16 (m, 2H), 7.08 (d, J = 8.8 Hz, IH), 7.04 (d, J = 8.2 Hz, IH), 6.94 (s, IH), 6.88 (dd, J = 8.7, 2.0 Hz, IH), 6.16 (s, IH), 4.32-4.19 (m, 3H), 2.83 (s, IH), 2.40 (dd, J = 5.2, 5.2 Hz, 2H), 1.62 (dd, J = 6.6, 3.6 Hz, 2H), 1.35 (s, 9H), 1.04 (dd, J = 6.9, 3.9 Hz, 2H). MS (ESI) m/e (M+H+) 496.0.
[00981] Example 108: iV-(2-tert-Butyl-l-(2-hydroxy-3-(2H-tetrazol-5-yl)propyl)-lH- indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
Figure imgf000271_0002
[00982] To a solution of N-(2-^rf-butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l- (2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (27 mg, 0.054 mmol) in anhydrous DMF (1.2 mL) were successively added NH4Cl (35 mg, 0.65 mmol) and NaN3 (43 mg, 0.65 mmol) at room temperature. The reaction mixture was stirred for 4 h at 110 0C in the microwave, at which stage 50% of the starting material was converted to the desired product. The reaction mixture was purified by preparative HPLC to provide N-(2-terZ-butyl- l-(2-hydroxy-3-(2H-tetrazol-5-yl)propyl)-lH-indol-5-yl)-l-(2,2-difluorobenzo- [d][l,3]dioxol-5-yl)cyclopropanecarboxamide. MS (ESI) m/e (M+H+) 539.0.
[00983] Example 109: 4-(2-tert-Butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclo- propanecarboxamido)-lH-indol-l-yl)-3-hydroxybutanoic acid
Figure imgf000272_0001
[00984] A solution of N-(2-te?t-butyl-l-(3-cyano-2-hydroxypropyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdltl^ldioxol-S-y^cyclopropanecarboxamide (14 mg, 0.028 mmol) in methanol (0.8 mL) and 4 M NaOH (0.8 mL) was stirred at 60 0C for 4 h. The reaction mixture was neutralized with 4 M HCl and concentrated. The residue was purified by preparative HPLC to provide 4-(2-^rf-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-lH-indol-l-yl)-3-hydroxybutanoic acid. MS (ESI) m/e (M+H+) 515.0.
[00985] Example 110: iV-(l-(2-(2H-Tetrazol-5-yl)ethyl)-2-tert-butyl-lH-indol-5-yl)-l- (benzofdHl^Jdioxol-S-yOcyclopropanecarboxamide
Figure imgf000272_0002
[00986] l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-l-(2-cyanoethyl)indolin-5-yl)- cyclopropanecarboxamide
[00987] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-l-(2- chloroethyl)indolin-5-yl)cyclopropanecarboxamide (66 mg, 0.15 mmol) in ethanol (0.8 mL) and water (0.4 mL) were added ΝaCΝ (22 mg, 0.45 mmol) and KI (cat) at room temperature. The reaction mixture was stirred for 30 min at 110 0C in the microwave before being purified by column chromatography on silica gel (5-15% ethyl acetate/hexanes) to provide 1- (benzo[d][l,3]dioxol-5-yl)-N-(2-^rf-butyl-l-(2-cyano-ethyl)indolin-5- yl)cyclopropanecarboxamide (50 mg, 77%).
Figure imgf000273_0001
[00988] iV-(l-(2-(2H-Tetrazol-5-yl)ethyl)-2-tert-butyl-lH-indol-5-yl)-l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
[00989] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-te?t-butyl-l-(2-cyano- ethyl)indolin-5-yl)cyclopropanecarboxamide (50 mg, 0.12 mmol) in anhydrous DMF (2.6 mL) was added NH4Cl (230 mg, 4.3 mmol) and NaN3 (280 mg, 4.3 mmol). The reaction mixture was stirred for 30 min at 110 0C in the microwave, filtrated, and purified by preparative HPLC. The solid residue was dissolved in CDCl3 (3 mL) and briefly (2 to 4 min) exposed to daylight, which initiated a color change (purple). After 2 h of stirring open to the atmosphere at room temperature, the solvent was removed and the residue was purified by preparative HPLC to give N-(l-(2-(2H-tetrazol-5-yl)ethyl)-2-^rf-butyl-lH-indol-5-yl)-l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide. MS (ESI) m/e (M+H+) 473.0.
[00990] Example 111: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-tert-butyl-6-fluoro-l- ((tetrahydro^H-pyran-S-yOmethyO-lH-indol-S-yOcyclopropanecarboxamide
Figure imgf000273_0002
2. CDCl3
[00991] To a solution of l-(benzo[d][l,3]dioxol-5-yl)-N-(2-ferf-butyl-6-fluoroindolin-5- yl)cyclopropane-carboxamide (150 mg, 0.38 mmol) in anhydrous dichloromethane (2.3 mL) at room temperature under Ν2 was added tetrahydropyran-3-carbaldehyde (54 mg, 0.47 mmol). After 20 min of stirring, NaBH(OAc)3 (110 mg, 0.51 mmol) was added in one portion at room temperature. The reaction mixture was stirred for 6 h at room temperature before being purified by column chromatography on silica gel (5-20% ethyl acetate/hexanes) to provide l-(benzo[d][l,3]dioxol-5-yl)-N-(2-ter^butyl-6-fluoro-l-((tetrahydro-2H-pyran-3- yl)methyl)indolin-5-yl)cyclopropanecarboxamide (95 mg, 50%). CDCl3 was added to the indoline and the solution was allowed to stir overnight at ambient temperature. The solution was concentrated to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-terZ-butyl-6-fluoro-l- ((tetrahydro^H-pyran-S-yOmethy^-lH-indol-S-y^cyclopropanecarboxamide. MS (ESI) m/e (M+H+) 493.0.
[00992] Example 112: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-(2-hydroxypropan-2-yl)-lH- indol-5-yl)cyclopropanecarboxamide
Figure imgf000274_0001
[00993] Methyl 5-(l-(benzo[<i][l,3]dioxol-5-yl)cyclopropane-carboxamido)-lH-indole-2- carboxylate (100 mg, 0.255 mmol) was dissolved in anhydrous tetrahydrofuran (2 mL) under an argon atmosphere. The solution was cooled to 0 0C in an ice water bath before methyllithium (0.85 mL, 1.6 M in diethyl ether) was added by syringe. The mixture was allowed to warm to room temperature. The crude product was then partitioned between a saturated aqueous solution of sodium chloride (5 mL) and dichloromethane (5 mL). The organic layers were combined, dried over sodium sulfate, filtered, evaporated to dryness, and purified on 12 g of silica gel utilizing a gradient of 20-80% ethyl acetate in hexanes to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(2-(2-hydroxypropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide (35 mg, 36%) as a white solid. ESI-MS tn/z calc. 378.2, found 379.1 (M+l)+. Retention time of 2.18 minutes. 1H ΝMR (400 MHz, DMSO- dβ) δ 10.78 (s, IH), 8.39 (s, IH), 7.57 (d, / = 1.7 Hz, IH), 7.17 (d, / = 8.6 Hz, IH), 7.03 - 6.90 (m, 4H), 6.12 (d, / = 1.5 Hz, IH), 6.03 (s, 2H), 5.18 (s, IH), 1.50 (s, 6H), 1.41 - 1.38 (m, 2H), 1.05-0.97 (m, 2H).
[00994] Example 113: iV-(2-(l-Amino-2-methylpropan-2-yl)-lH-indol-5-yl)-l- (benzofdHl^J-dioxol-S-yrtcyclopropanecarboxamide
[00995] Trifluoroacetic acid (0.75 mL) was added to a solution of terz-butyl 2-(5-(l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-lH-indol-2-yl)-2- methylpropylcarbamate (77 mg, 0.16 mmol) in dichloromethane (3 mL) and the mixture was stirred at room temperature for 1.5 h. The mixture was evaporated, dissolved in dichloromethane, washed with saturated sodium bicarbonate solution, dried over magnesium sulfate and evaporated to dryness to give N-(2-(l-amino-2-methylpropan-2-yl)-lH-indol-5- yl)-l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (53 mg, 86%). 1H NMR (^O MHz, CDCl3) δ 9.58 (s, IH), 7.60 (d, J = 1.6 Hz, IH), 7.18 - 7.15 (m, 2H), 7.02 - 6.94 (m, 3H), 6.85 (d, J = 7.8 Hz, IH), 6.14 (d, J = 1.2 Hz, IH), 6.02 (s, 2H), 2.84 (s, 2H), 1.68 (dd, J = 3.6, 6.7 Hz, 2H), 1.32 (s, 6H), 1.08 (dd, J = 3.7, 6.8 Hz, 2H).
[00996] Example 114: l-(Benzo[d][l,3]dioxol-5-yl)-iV-(2-(l-(dimethylamino)-2-methyl- propan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000275_0001
[00997] To a solution of N-(2-(l-amino-2-methylpropan-2-yl)-lH-indol-5-yl)-l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (20 mg, 0.051 mmol) in DMF (1 mL) was added potassium carbonate (35 mg, 0.26 mmol) and iodomethane (7.0 μL, 0.11 mmol). The mixture was stirred for 2 h. Water was added and the mixture was extracted with dichloromethane. Combined organic phases were dried over magnesium sulfate, evaporated, coevaporated with toluene (3x) and purified by silica gel chromatography (0-30% EtOAc in hexane) to give l-(benzo[d][l,3]dioxol-5-yl)-N-(2-(l-(dimethylamino)-2-methylpropan-2-yl)- lH-indol-5-yl)cyclopropanecarboxamide (7 mg, 33%). 1H ΝMR (400 MHz, CDCl3) δ 9.74 (s, IH), 7.58 (d, J = 1.9 Hz, IH), 7.20 (d, J = 8.6 Hz, IH), 7.15 (s, IH), 7.01 - 6.95 (m, 3H), 6.85 (d, J = 7.9 Hz, IH), 6.10 (d, J = 0.9 Hz, IH), 6.02 (s, 2H), 2.43 (s, 2H), 2.24 (s, 6H), 1.68 (dd, J = 3.7, 6.7 Hz, 2H), 1.33 (s, 6H), 1.08 (dd, J = 3.7, 6.8 Hz, 2H).
[00998] Example 115: iV-(2-(l-Acetamido-2-methylpropan-2-yl)-lH-indol-5-yl)-l- (benzofdHl^J-dioxol-S-yOcyclopropanecarboxamide
Figure imgf000275_0002
[00999] To a solution of N-(2-(l-amino-2-methylpropan-2-yl)-lH-indol-5-yl)-l- (benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (21 mg, 0.054 mmol) in dichloromethane (1 mL) was added pyridine (14 μL, 0.16 mmol) followed by acetic anhydride (6.0 μL, 0.059 mmol). The mixture was stirred for 2 h. Water was added and the mixture was extracted with dichloromethane, evaporated, coevaporated with toluene (3x) and purified by silica gel chromatography (60-100% ethylacetate in hexane) to give N-(2-(l- acetamido-2-methylpropan-2-yl)-lH-indol-5-yl)-l-(benzo[d][l,3]-dioxol-5- yl)cyclopropanecarboxamide (17 mg, 73%). 1H ΝMR (400 MHz, DMSO) δ 10.79 (s, IH),
8.39 (s, IH), 7.66 (t, J = 6.2 Hz, IH), 7.56 (d, J = 1.7 Hz, IH), 7.18 - 7.14 (m, IH), 7.02 - 6.89 (m, 4H), 6.08 (d, J = 1.5 Hz, IH), 6.03 (s, 2H), 3.31 (d, J = 6.2 Hz, 2H), 1.80 (s, 3H), 1.41 - 1.38 (m, 2H), 1.26 (s, 6H), 1.04 - 1.01 (m, 2H).
[001000] Example 116: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-(2-methyl-4-(lH-tetrazol-5- yl)butan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000276_0001
[001001] l-(Benzo[d][l,3]dioxol-5-yl)-N-(2-(4-cyano-2-methylbutan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide (83 mg, 0.20 mmol) was dissolved in N,N-dimethylformamide (1 mL) containing ammonium chloride (128 mg, 2.41 mmol), sodium azide (156 mg, 2.40 mmol), and a magnetic stir bar. The reaction mixture was heated at 110 0C for 40 minutes in a microwave reactor. The crude product was filtered and then purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield l-(benzo[J][l,3]dioxol-5-yl)-N-(2-(2-methyl-4-(lH-tetrazol-5-yl)butan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide. ESI-MS m/z calc. 458.2, found 459.2 (M+l)+. Retention time of 1.53 minutes. 1H ΝMR (400 MHz, CD3CN) 9.23 (s, IH), 7.51 - 7.48 (m, 2H), 7.19 (d, / = 8.6 Hz, IH), 7.06 - 7.03 (m, 2H), 6.95 - 6.89 (m, 2H), 6.17 (dd, / = 0.7, 2.2 Hz, IH), 6.02 (s, 2H), 2.61 - 2.57 (m, 2H), 2.07 - 2.03 (m, 2H), 1.55-1.51 (m, 2H), 1.39 (s, 6H), 1.12-1.09 (m, 2H).
[001002] Example 117: l-(Benzo[rf][l,3]dioxol-5-yl)-iV-(2-(piperidin-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000276_0002
[001003] ^rf-Butyl 2-(5-(l-(benzo[J][l,3]dioxol-5-yl)cyclo-propanecarboxamido)-lH- indol-2-yl)piperidine-l-carboxylate (55 mg, 0.11 mmol) was dissolved in dichloromethane (2.5 mL) containing trifluoroacetic acid (1 mL). The reaction mixture was stirred for 6 h at room temperature. The crude product was purified by preparative ΗPLC using a gradient of 0-99% acetonitrile in water containing 0.05% trifluoroacetic acid to yield 1- (benzo[J][l,3]dioxol-5-yl)-N-(2-(piperidin-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide. ESI-MS m/z calc. 403.2, found 404.4 (M+l)+. Retention time of 0.95 minutes.
[001004] Example 118: 5-fert-Butyl-lΗ-indol-6-ylamine
Figure imgf000277_0001
[001005] 2-Bromo-4-ter/-butyl-phenylamine
[001006] To a solution of 4-ført-Butyl-phenylamine (447 g, 3.00 mol) in DMF (500 niL) was added dropwise NBS (531 g, 3.00 mol) in DMF (500 mL) at room temperature. Upon completion, the reaction mixture was diluted with water and extracted with EtOAc. The organic layer was washed with water, brine, dried over Na2SO4 and concentrated. The crude product was directly used in the next step without further purification.
Figure imgf000277_0002
[001007] 2-Bromo-4-ter/-butyl-5-nitro-phenylamine
[001008] 2-Bromo-4-terZ-butyl-phenylamine (160 g, 0.71 mol) was added dropwise to H2SO4 (410 mL) at room temperature to yield a clear solution. This clear solution was then cooled down to -5 to -10 0C. A solution of KNO3 (83 g, 0.82 mol) in H2SO4 (410 mL) was added dropwise while the temperature was maintained between -5 to -10 0C. Upon completion, the reaction mixture was poured into ice / water and extracted with EtOAc. The combined organic layers were washed with 5% Na2CO3 and brine, dried over Na2SO4 and concentrated. The residue was purified by a column chromatography (ethyl acetate/petroleum ether 1:10) to give 2-bromo-4-terZ-butyl-5-nitro-phenylamine as a yellow solid (150 g, 78%).
Figure imgf000277_0003
[001009] 4-ter/-Butyl-5-nitro-2-trimethylsilanylethynyl-phenylamine
[001010] To a mixture of 2-bromo-4-^rf-butyl-5-nitro-phenylamine (27.3 g, 100 mmol) in toluene (200 mL) and water (100 mL) was added Et3N (27.9 mL, 200 mmol), Pd(PPh3)2Cl2 (2.11 g, 3.00 mmol), CuI (950 mg, 0.500 mmol) and trimethylsilyl acetylene (21.2 mL, 150 mmol) under a nitrogen atmosphere. The reaction mixture was heated at 70 0C in a sealed pressure flask for 2.5 h., cooled down to room temperature and filtered through a short plug of Celite. The filter cake was washed with EtOAc. The combined filtrate was washed with 5% NH4OH solution and water, dried over Na2SO4 and concentrated. The crude product was purified by column chromatography (0 - 10 % ethyl acetate/petroleum ether) to provide 4- ^rf-butyl-5-nitro-2-trimethylsilanylethynyl-phenylamine as a brown viscous liquid (25 g, 81 %).
Figure imgf000278_0001
[001011] 5-fert-Butyl-6-nitro-lH-indole
[001012] To a solution of 4-ferf-butyl-5-nitro-2-trimethylsilanylethynyl-phenylamine (25 g, 86 mmol) in DMF (100 mL) was added CuI (8.2 g, 43 mmol) under a nitrogen atmosphere. The mixture was heated at 135 0C in a sealed pressure flask overnight, cooled down to room temperature and filtered through a short plug of Celite. The filter cake was washed with EtOAc. The combined filtrate was washed with water, dried over Na2SO4 and concentrated. The crude product was purified by column chromatography (10 - 20 % ethyl aetate/hexane) to provide 5-terZ-butyl-6-nitro-lH-indole as a yellow solid (13 g, 69 %).
H2, Raney Ni
Figure imgf000278_0003
Figure imgf000278_0002
[001013] 5-fert-Butyl-lH-indol-6-ylamine
[001014] Raney Nickel (3 g) was added to 5-terZ-butyl-6-nitro-lH-indole (15 g, 67 mmol) in methanol (100 mL). The mixture was stirred under hydrogen (1 atm) at 30 0C for 3 h. The catalyst was filtered off. The filtrate was dried over Na2SO4 and concentrated. The crude dark brown viscous oil was purified by column chromatography (10 - 20 % ethyl acetate/petroleum ether) to give 5-terZ-butyl-lH-indol-6-ylamine as a gray solid (11 g, 87 %). 1H NMR (300 MHz, DMSO-d6) δ 10.3 (br s, IH), 7.2 (s, IH), 6.9 (m, IH), 6.6 (s, IH), 6.1 (m, IH), 4.4 (br s, 2H), 1.3 (s, 9H). l-(2,3-Dihydro-lH-inden-5-yl)cyclopropanecarboxylic acid
Figure imgf000279_0001
a) Ac2O, AlCl3, CH2Cl2; b) NaClO; c) LiAlH4, THF, -78°C; d) SOCl2, CHCl3; e) NaCN, DMSO; f) BrCH2CH2Cl, NaOH, Bu4NBr, toluene; g) NaOH
[001] Step a: l-(2,3-Dihydro-lH-inden-6-yl)ethanone
[002] A mixture of 2,3-dihydro-lH-indene (100.0 g, 0.85 mol) and acetic anhydride (104.2 g, 1.35 mol) was added drop-wise to a slurry of AlCl3 (272.0 g, 2.04 mol) in CH2Cl2 (1000 ml) at 0 0C over a period of 3h. The reaction mixture was stirred at room temperature under a nitrogen atmosphere for 15 h. Then the reaction mixture was poured into ice water (500 mL) and extracted with ethyl acetate (500 mL x 3). The combined organic layers were washed with brine (500 mL), dried over Na2SO4 and evaporated in vacuo. The residue that was purified by column chromatography (petroleum ether : ethyl acetate = 20 : 1) to give the product (120.0 g, 88%). 1H NMR (400 MHz, CDCl3) δ 2.08-2.15 (m, 2H), 2.58 (s, 3H), 2.95 (t, / = 7.2, 4 H), 7.28 (d, / = 8.0, IH), 7.75 (d, / = 8.0, IH) 7.82 (s,lH).
[003] Step b: 2,3-dihydro-lH-indene-5-carboxylic acid
[004] To a stirred aqueous sodium hypochlorite solution (2230 ml, 1.80 mmol, 6%) at 55°C was added l-(2,3-dihydro-lH-inden-6-yl) ethanone (120.0 g,0.75 mol)
and the mixture was stirred at 550C for 2 h. After cooling to room temperature, saturated
NaHCO3 solution was added until the solution became clear. The produced precipitate was filtered, washed several times with water and dried to afford the desired product (120.0 g, 99%). 1H NMR (CDCl3, 300MHz) δ 2.07-2.17 (m, 2H), 2.96 (t, / = 7.5Hz, 4H), 7.30 (d, J =7.8, IH,), 7.91 (d, / = 7.8, IH), 7.96 (s, IH).
[005] Step c: (2,3-dihydro-lH-inden-5-yl)methanol
[006] To a stirred solution of LAH (72.8 g, 1.92 mol) in THF (2.5 L) at 00C was slowly added 2,3-dihydro-lH-indene-5-carboxylic acid (100.0 g, 0.62 mol). The reaction mixture was stirred at 00C for Ih. Then the reaction was quenched with H2O (72 ml) and
NaOH (68 ml, 20%). The mixture was filtered and the organic layer was dried over Na2SO4, evaporated in vacuo and the residue was purified by column chromatography (petroleum ether : ethyl acetate = 10 : 1) to give the desired product (82.0 g, 90%). 1H NMR (CDCl3, 300MHz); δ 2.03-2.13 (m, 2H), 2.91 (t, / = 7.5Hz, 4H), 4.64 (s, 2H), 7.13 (d, / = 7.5, IH), 7.18-7.24 (m, 2H).
[007] Step d: 5-(chloromethyl)-2,3-dihydro-lH-indene
[008] Thionyl chloride (120 ml, 1.65 mol) was added drop- wise to a rapidly stirred mixture of (2,3-dihydro-lH-inden-5-yl)methanol (81.4 g, 0.55 mol) in chloroform (500 ml) at O0C. After the addition was complete, the resulting mixture was allowed to warm to room temperature and the stirring was continued for an additional 12 h. The chloroform was evaporated under reduced pressure to give a residue, that was purified by column chromatography (petroleum ether : ethyl acetate = 15 : 1) to afford 5-(chloromethyl)-2,3- dihydro-lH-indene (90.5 g, 99%). 1H NMR (300 MHz, CDC13) δ 2.06-2.19 (m, 4H), 2.93 (t, J = 7.5, 4H), 4.54 (s, 2H), 7.15-7.31 (m, 3H).
[009] Step e: 2-(2,3-dihydro-lH-inden-5-yl)acetonitrile
[010] To a stirred solution of 5-(chloromethyl)-2,3-dihydro- lH-indene (90.0 g, 0.54 mol) in DMSO (500 ml) was added sodium cyanide (54.0 g, 1.08mol) at O0C portion wise. The reaction mixture was then stirred at room temperature for 3 hours. The reaction was quenched with water (1000 ml), extracted with ethyl acetate (3 x 250 mL). The combined organic layers were washed with brine, dried over Na2SO4 and evaporated in vacuo to afford 2-(2,3-dihydro-lH-inden-5-yl)acetonitrile (82.2 g, 97%), that was used in the next step without further purification.
[011] Step f: l-(2,3-dihydro-lH-inden-6-yl)cyclopropanecarbonitrile
[012] To a stirred solution of 2-(2,3-dihydro- lH-inden-5-yl)acetonitrile (50.0 g, 0.32 mol) in toluene (150 mL) was added sodium hydroxide (300 mL, 50 percent in water WAV), l-bromo-2-chloroethane (92.6 ml,1.12 mol) and (n-Bu)4NBr (5 g, 15.51 mmol). The mixture was heated at 60 0C overnight. After cooling to room temperature, the reaction mixture was diluted with water (400 mL) and extracted with EtOAc (3 x 200 mL). The combined organic extracts were washed with brine, dried over Na2SO4, filtered and concentrated under vacuum and purified by column chromatography (petroleum ether : ethyl acetate = 10 : 1) to yield l-(2,3-dihydro-lH-inden-6-yl)cyclopropanecarbonitrile (9.3 g,16%). 1H NMR (CDCl3,300MHz) δ 1.35-1.38 (m, 2H), 1.66-1.69 (m, 2H), 2.05-2.13 (m, 2H), 2.87- 294 (m, 4H), 7.07-7.22 (m,3H).
[013] Step g: l-(2,3-dihydro-lH-inden-6-yl)cyclopropanecarboxylic acid
[014] To a stirred l-(2,3-dihydro-lH-inden-6-yl)cyclopropanecarbonitrile (9.3 g,50.8 mmol) in methanol (40 mL) was added a solution of 150 mL of sodium hydroxide (25% NaOH w/w in water). The mixture was heated at 100 0C for 8 hours. After cooling to room temperature, the reaction mixture was poured over ice-water (0 0C), the pH was adjusted to pH=4 with hydrogen chloride (1 N) and the mixture was extracted with dichloromethane (3 x 100 mL). The combined organic layers were dried over Na2SO4 and evaporated under vacuum. The residue that was purified by column chromatography (petroleum ether : ethyl acetate = 5 : 1) to give l-(2,3-dihydro-lH-inden-6- yl)cyclopropanecarboxylic acid (4.8 g,47%). 1H NMR (CDCl3, 400 MHz) δ 1.23-1.26 (m, 2H), 1.62-1.65 (m, 2H), 2.03-210 (m, 2H), 2.81-2.91 (m, 4H), 7.11-7.21 (m, 3H).
5-Amino-2-tert-butyl-lH-indole-4-carbonitrile
Figure imgf000281_0001
a) KCN, DMSO; b) Pd/C, EtOAc
[015] Step a: 2-tert-butyl-5-nitro-lH-indole-4-carbonitrile
[016] To a solution of 2-tert-butyl-4-fluoro-5-nitro-lH-indole (4.0 g, 17 mmol) in DMSO (30 mL) was added KCN (3.4 g, 51 mmol). The mixture was stirred at 700C for 3 hours, and poured into water (80 mL) and extracted with ethyl acetate (50 mL x 3). The combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated under vacuum. The residue was purified by column chromatography on silica gel (7% EtOAc in petroleum ether) to afford 2-tert-butyl-5-nitro-lH-indole-4-carbonitrile (2.2 g, 53%). 1H NMR (DMSO, 300 MHz) δ 12.23 (br s, 1 H), 8.09 (d, J = 9.0 Hz, 1 H), 7.75 (d, / = 9.0 Hz, 1 H), 6.50 (s, 1 H), 1.38 (s, 9 H). MS (ESI) m/z: 244.2 [M+H+].
[017] Step b: 5-amino-2-tert-butyl-lH-indole-4-carbonitrile
[018] To a solution of 2-tert-butyl-5-nitro-lH-indole-4-carbonitrile (550 mg, 2.3 mmol) in EtOAc (10 mL) was added Raney Ni (0.1 g) under a nitrogen atmosphere. The mixture was stirred under hydrogen atmosphere (1 atm) at room temperature for 1 h. The catalyst was filtered over Celite and the filtrate was evaporated in vacuo to afford 5-amino-2- tert-butyl-lH-indole-4-carbonitrile (250 mg, 51%). 1H NMR (DMSO, 300 MHz) δ 10.93 (br s, 1 H), 7.25 (d, / = 8.7 Hz, 1 H), 6.49 (d, / = 8.7 Hz, 1 H), 5.94 (d, / = 2.1 Hz, 1 H), 5.40 (br s, 2 H), 1.30 (s, 9 H). MS (ESI) m/z: 214.0 [M+H+].
N-(2-tert-butyl-4-cyano-lH-indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide
Figure imgf000282_0001
[019] Step a: N-(2-tert-butyl-4-cyano-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide
[020] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarbonyl chloride (26 mg, 0.1 mmol) was added to a solution of 5-amino-2-tert-butyl-lH-indole-4- carbonitrile (21 mg, 0.1 mmol) and triethylamine (41.7 μL, 0.3 mmol) in DMF (1 mL). The reaction was stirred at room temperature overnight, then filtered and purified by reverse- phase HPLC to yield the product, N-(2-tert-butyl-4-cyano-lH-indol-5-yl)-l-(2,2- difluorobenzofdltl^ldioxol-S-y^cyclopropanecarboxamide. ESI-MS m/z calc. 437.2, found 438.7 (M+l)+. Retention time 2.10 minutes. 1H NMR (400 MHz, DMSO- dβ) δ 11.48 (s, IH), 8.88 (s, IH), 7.52 (d, J = 8.5 Hz, 2H), 7.41 (d, J = 8.3 Hz, IH), 7.32 (dd, J = 1.5, 8.3 Hz, IH), 7.03 (d, J = 8.6 Hz, IH), 6.21 (d, J = 1.8 Hz, IH), 1.51 - 1.49 (m, 2H), 1.36 (s, 9H), 1.18 - 1.16 (m, 2H).
N-(2-tert-butyl-4-cyano-l-(2-hydroxyethyl)-lH-indol-5-yl)-l-(2,2- difluorobenzotdHl^Jdioxol-S-yOcyclopropanecarboxamide
Figure imgf000282_0002
[021] Step a: 2-tert-butyl-l-(2-hydroxyethyl)-5-nitro-lH-indole-4-carbonitrile
[022] A mixture of 2-tert-butyl-5-nitro-lH-indole-4-carbonitrile (200 mg, 0.82 mmol), 2-iodoethanol (77 μL, 0.98 mmol), cesium carbonate (534 mg, 1.64 mmol) and DMF (1.3 mL) was heated to 90 0C overnight. Then more 2-iodoethanol (77 μL, 0.98 mmol) was added and the reaction was stirred at 90 0C for 3 days. The reaction mixture was partitioned between ethyl acetate and water. The aqueous layer was washed with ethyl acetate and then the combined ethyl acetate layers were washed with water (x3) and brine, dried over MgSO4 and concentrated. The residue was purified by column chromatography (50 - 100% CH2Cl2 - Hexanes) to yield the product as a yellow solid (180 mg, -25% purity by NMR, product co-elutes with the indole starting material). ESI-MS m/z calc. 287.1, found 288.5 (M+l)+. Retention time 1.59 minutes. 1H NMR (400 MHz, DMSO-J6) δ 12.23 (s, IH), 8.14 (d, J = 9.1 Hz, IH), 8.02 (d, J = 9.1 Hz, IH), 6.60 (s, IH), 5.10 (t, J = 5.5 Hz, IH), 4.55 (t, J = 6.3 Hz, 2H), 3.78 - 3.73 (m, 2H) and 1.49 (s, 9H) ppm.
[023] Step b: 5-amino-2-tert-butyl-l-(2-hydroxyethyl)-lH-indole-4-carbonitrile
[024] To a solution of 2-tert-butyl-l-(2-hydroxyethyl)-5-nitro-lH-indole-4- carbonitrile (180 mg, 0.63 mmol) in ethanol (6 mL) under N2 atmosphere was added Pd-C (5% wt, 18 mg). The reaction was flushed with N2 (g) and then with H2 (g) and stirred under H2 (atm) at room temperature for 1.5 hours. The reaction was filtered over Celite and concentrated to yield the product (150 mg, 93 %). ESI-MS m/z calc. 257.2, found 258.5 (M+l)+. Retention time 1.26 minutes.
[025] Step c: N-(2-tert-butyl-4-cyano-l-(2-hydroxyethyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide
[026] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarbonyl chloride (196 mg, 0.75 mmol) was added to a solution of 5-amino-2-tert-butyl-l-(2- hydroxyethyl)-lH-indole-4-carbonitrile (150 mg, 0.58 mmol) and triethylamine (242 μL, 1.74 mmol) in dichloromethane (2 mL). The reaction was stirred at room temperature overnight. The reaction mixture was diluted with dichloromethane and extracted with IN HCl solution (x2), saturated NaHCθ3 solution (x2), brine, dried over MgSO4, filtered and concentrated. The residue was dissolved in DMSO and purified by reverse-phase HPLC to yield the product, N-(2-tert-butyl-4-cyano-l-(2-hydroxyethyl)-lH-indol-5-yl)-l-(2,2- difluorobenzofdlfl^ldioxol-S-yOcyclopropanecarboxamide. ESI-MS m/z calc. 481.2, found 482.5 (M+l)+. Retention time 1.99 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.93 (s, IH), 7.71 (d, J = 8.8 Hz, IH), 7.51 (s, IH), 7.42 (d, J = 8.3 Hz, IH), 7.33 (d, J = 1.6 Hz, IH), 7.08 (d, J = 8.8 Hz, IH), 6.28 (s, IH), 5.05 (t, J = 5.6 Hz, IH), 4.42 (t, J = 6.8 Hz, 2H), 3.70 - 3.65 (m, 2H), 1.51 - 1.48 (m, 2H), 1.44 (s, 9H), 1.19 - 1.16 (m, 2H). 2-(2-tert-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-6-fluoro-lH-indol-l-yl)-N,N,N- trimethylethanaminium chloride
Figure imgf000284_0001
DMF
Figure imgf000284_0002
Figure imgf000284_0003
[027] Step a: tert-Butyl 2-(2-te^butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-6-fluoro- lH-indol- 1 -yl)ethylcarbamate
[028] To l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (90.14 mg, 0.3722 mmol) in thionyl chloride (81.28 μL, 1.117 mmol) was added N1N - dimethyl formamide (8.204 μL, 0.1064 mmol). The reaction mixture was stirred at room temperature for 30 minutes before excess thionyl chloride and NN -dimethyl formamide were removed in vacuo to yield the acid chloride. The acid chloride was then dissolved in dichloromethane (1.5 mL) and added slowly to a solution of tert-buty\ 2-(5-amino-2-terZ- butyl-6-fluoro-lH-indol-l-yl)ethylcarbamate (156.1 mg, 0.4467 mmol) and triethylamine (155.6 μL, 1.117 mmol) in dichloromethane (1.5 mL). The resulting reaction mixture was stirred at room temperature for 21 hours. The reaction mixture was diluted with dichloromethane (5 mL) and washed with IN aqueous HCl (5 mL) and a saturated aqueous ΝaHCC>3 solution (5 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The crude product was purified by column chromatography on silica gel (0-30% ethyl acetate in hexane) to yield tert-butyl 2-(2-te?t-butyl-5-(l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-6-fluoro-lH-indol-l- yl)ethylcarbamate as a white solid (140 mg, 66%). ESI-MS m/z calc. 573.2, found 574.7 (M+l)+. Retention time 2.41 minutes. IH NMR (400.0 MHz, DMSO) d 8.35 (s, IH), 7.53 (s, IH), 7.44 - 7.41 (m, 2H), 7.34 - 7.29 (m, 2H), 7.13 - 7.10 (m, IH), 6.17 (s, IH), 4.24 - 4.20 (m, 2H), 3.20 - 3.17 (m, 2H), 1.48-1.45 (m, 2H), 1.41 (s, 18H) and 1.15-1.12 (m, 2H) ppm.
[029] Step b: N-(l-(2-aminoethyl)-2-^rf-butyl-6-fluoro-lH-indol-5-yl)-l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide
[030] To a solution of tert-buty\ 2-(2-tert-buty\-5-(l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)-6-fluoro-lH-indol-l- yl)ethylcarbamate (137.5 mg, 0.24 mmol) in dichloromethane (1.8 mL) was added trifluoroacetic acid (444 μL, 5.8 mmol) and the mixture was stirred at room temperature for 1 hour. The reaction was diluted with dichloromethane and washed with saturated aqueous NaHCO3 solution (3 mL) and brine (3 mL). The organic layer was dried over Na2SO4, filtered and evaporated under reduced pressure. The crude product was purified by column chromatography on silica gel (0-10% methanol in dichloromethane) to yield N-(l-(2- aminoethyl)-2-^rf-butyl-6-fluoro-lH-indol-5-yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamide as a white solid (93.7 mg, 82%). ESI-MS m/z calc. 473.19, found 474.5 (M+l)+. Retention time 1.61 minutes.
[031] Step c: 2-(2-^rf-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-6-fluoro- lH-indol- 1 -yl)-N,N,N-trimethylethanaminium chloride
[032] To a clear solution of N-(l-(2-aminoethyl)-2-^rf-butyl-6-fluoro-lH-indol-5- yl)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamide (50 mg, 0.1056 mmol) in N1N -dimethyl formamide (1 mL), methyl iodide (336.8 mg, 147.7 μL, 2.37 mmol) and triethylamine (106.9 mg, 147.2 μL, 1.05 mmol) were added and the mixture was heated at 80 0C for 2 hours. The crude product was purified by reverse phase preparative HPLC. 22 mg of this product were dissolved in 1.25 M HCl in methanol (112 μL, 0.14 mmol) and heated at 60 0C for 1 hour. The reaction was cooled to room temperature. The product was first dried and then dissolved in dichloromethane and dried again. This procedure was repeated four times to yield 2-(2-^rf-butyl-5-(l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)-6-fluoro- lH-indol- 1 -yl)-Ν,Ν,Ν-trimethylethanaminium chloride. ESI-MS m/z calc. 516.25, found 516.7 (M+l)+. Retention time 1.69 minutes. IH NMR (400.0 MHz, DMSO) d 8.43 (s, IH), 7.53 (s, IH), 7.45 - 7.41 (m, 2H), 7.36 - 7.31 (m, 2H), 6.27 (s, IH), 4.74 - 4.70 (m, 2H), 3.57 - 3.53 (m, 2H), 3.29 (s, 9H), 1.48 - 1.42 (m, HH), and 1.15 (dd, J = 3.9, 6.8 Hz, 2H) ppm.
2-(4-(Tert-butyldimethylsilyloxy)-2-methylbutan-2-yl)-6-fluoro-5-nitro-lH- indole
Figure imgf000286_0001
PdCI2/CH3CN
[033] Step a: 3-fluoro-4-nitroaniline
[034] A mixture of N-(3-fluoro-4-nitro-phenyl)-2, 2-dimethyl-propionamide (87.0 g, 0.36 mol) in CH2Cl2 (400 niL) and 6N hydrochloric acid (800 niL) was heated to reflux for 2 hours. The reaction mixture was cooled to room temperature. The reaction mixture was diluted with 1000 mL of ethyl acetate and potassium carbonate (500.0 g) was added portion wise. The aqueous solution was separated and the organic layer was washed with brine and dried over anhydrous Na2SO4. The solvent was removed by evaporation under reduced pressure; the residue was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 30: 1) to afford 3-fluoro-4-nitroaniline (56.0 g, 99 %). 1H NMR (300 MHz, CDCl3) δ 8.07 (t, J = 8.7 Hz, 1 H), 7.86 (dd, J= 2.1, 13.2 Hz 1 H), 7.59 (brs, 2 H), 7.22 (s, 1 H).
[035] Step b: 2-bromo-5-fluoro-4-nitroaniline
To a solution of 3-fluoro-4-nitroaniline (56 g, 0.36 mol) in acetic acid (500 mL) was added drop-wise bromine (17.7 mL, 0.36 mol) over 1 hour. The reaction mixture was stirred for 1 hour at 0-5 °C in an ice bath. The reaction mixture was basified with saturated Na2CO3 and extracted with ethyl acetate (200 mL x 3). The combined organic layers were washed with brine, dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to yield a residue that was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 10 : 1) to give the 2-bromo-5-fluoro-4-nitroaniline ( 45.6 g, 84 % ) as a yellow solid. 1H NMR (400 MHz, CDCl3) δ 8.29 (d, / = 7.6 Hz, 1 H), 653 (d, / = 12.4 Hz, 1 H), 4.94 (br s, 2 H).
[036] Step c: ethyl 5-(2-amino-4-fluoro-5-nitrophenyl)-3,3-dimethylpent-4-ynoate
[037] To a solution of 2-bromo-5-fluoro-4-nitroaniline (45.7 g, 0.19 mol) and ethyl 3,3-dimethylpent-4-ynoate (88.3 g, 0.57 mol) in Et3N (700 mL) was added Pd(PPh3)2Cl2 (13.8 g, 0.02 mol) and CuI (3.6 g, 0.02 mol) under N2. The reaction mixture was stirred at 70°C for 8 hours. The reaction mixture was diluted with 500 mL of ethyl acetate and 1500 mL of water. The organic layer was separated and the aqueous phase was extracted with ethyl acetate (500 mLx3), the combined organic layers were washed with brine and dried over anhydrous Na2SO4, filtered and evaporated under reduced pressure and the residue was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 10: 1) to give ethyl-5-(2-amino-4-fluoro-5- nitrophenyl)-3,3-dimethylpent-4-ynoate (34.5 g, 57 %). 1H NMR (300 MHz, CDCl3) δ 8.05 (d, / = 8.1Hz, 1 H), 6.36 (d, / = 13.2 Hz, 1 H), 5.60 (brs, 2 H), 4.16 (q, / = 7.2 Hz, 2 H), 2.51 (s, 2 H), 1.40 (s, 6 H), 1.28 (t, / = 7.2 Hz, 3 H).
[038] Step d: ethyl 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3-methylbutanoate
[039] To a mixture of ethyl 5-(2-amino-4-fluoro-5-nitrophenyl)-3, 3- dimethylpent-4-ynoate (34.5 g, 0.11 mol) and PdCl2 (10.4 g, 58.6 nmol) in CH3CN (350 mL) was heated to reflux for 1.5 hours. The reaction mixture was cooled down to room temperature. Ethyl acetate (300 mL) was added, the precipitate was filtered off and washed with methanol. The filtrate was concentrated under reduced pressure and the residue was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 40: 1) to give ethyl 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3-methylbutanoate (34.0 g, 98 %) as a deep yellow solid. 1H NMR (300 MHz, CDCl3) δ 10.11 (brs, 1 H), 8.30 (d, / = 7.2 Hz, 1 H), 7.14 (d, J = 11.7 Hz, 1 H), 6.35 (d, J = 1.5 Hz, 1 H), 4.17 (q, J = 7.2 Hz, 2 H), 2.69 (s, 2 H), 1.51 (s, 6 H), 1.25 (t, J = 7.2 Hz, 3 H).
[040] Step e: 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3-methylbutan-l-ol
[041] To a solution of ethyl 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutanoate (34 g, 0.11 mol) in dry CH2Cl2 (400 mL) was added drop- wise DIBAL-H (283.4 mL, 0.27 mol) over 2 hours at -78°C. The reaction mixture was stirred for 10 hours at -78°C and then quenched by adding water (200 mL). The precipitate was filtered off and washed with methanol. The filtrate was extracted with CH2Cl2 (200 mLx3), the combined organic layers were washed with brine, dried over anhydrous Na2SO4 and concentrated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 50: 1) to give 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutan-1-ol (6.6 g, 22 %). 1H NMR (400 MHz, CDCl3) δ 9.35 (brs, 1 H), 8.30 (d, J = 7.6 Hz, 1 H), 7.11 (d, / = 12.0 Hz, 1 H), 6.35 (d, J = 1.2 Hz, 1 H), 3.74 (t, J = 6.4 Hz, 2 H), 1.9 (t, J = 6.4 Hz, 2 H), 1.4 (s, 6 H).
[042] Step f: 2-(4-(tert-butyldimethylsilyloxy)-2-methylbutan-2-yl)-6-fluoro-5-nitro-lH- indole
[043] To a solution of 3-(6-fluoro-5-nitro- lH-indol-2-yl)-3-methylbutan- l-ol (6.6 g, 25 mmol) in CH2Cl2 (80 mL) was added TBSCl (3.7 g, 25 nmol) and imidazole (4.2 g, 62 nmol) at 00C. The reaction mixture was stirred at room temperature for 12 hours. The precipitate was filtered off and washed with the methanol. The filtrate was concentrated under reduced pressure. The residue was purified by column chromatography on silica gel (petroleum ether / ethyl acetate 10: 1) to give the desired product as a brown solid (5.0 g, 53 %). 1H NMR (300 MHz, CDCl3) δ 9.80 (brs, 1 H), 8.30 (d, 7 = 7.2 Hz, 1 H), 7.05 (d, 7 = 11.7 Hz, 1 H), 6.33 (t, 7 = 1.2 Hz, 1 H), 3.7 (t, J = 6.0 Hz, 2 H), 1.91 (t, J = 6.0 Hz, 2 H), 1.42 (s , 6 H), 0.94 (s , 9 H), 0.12 (s , 6 H). MS (ESI) m/z (M+H+): 381.1.
Benzyl 2,2-dimethylbut-3-ynoate NaOH1 H2O reflux **
Figure imgf000288_0001
Figure imgf000288_0002
[044] Step a: methyl 2,2-dimethyl-3-oxobutanoate
[045] To a suspension of NaH (28.5 g, 0.718 mol, 60%) in THF (270 niL) was added dropwise a solution of 3-oxo-butyric acid methyl ester (78.6 g, 0.677 mol) in THF (70 niL) at 0 0C. The mixture was stirred for 0.5 hours at 0 0C. MeI (99.0 g, 0.698 mol) was added dropwise at 0 0C. The resultant mixture was warmed to room temperature and stirred for 1 hour. NaH (28.5 g, 0.718 mol, 60%) was added in portions at 0 0C and the resulting mixture was continued to stir for 0.5 h at 0 0C. MeI (99.0 g, 0.698 mol) was then added dropwise at 0 0C. The reaction mixture was warmed to room temperature and stirred overnight. The mixture was poured into ice water. The organic layer was separated. The aqueous phase was extracted with EtOAc (300 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give methyl 2,2-dimethyl-3-oxobutanoate (52 g, 53%), which was used directly in the next step.
[046] Step b: methyl 3-chloro-2,2-dimethylbut-3-enoate
[047] To a suspention of PCl5 (161 g, 0.772 mol) in dichloromethane (600 mL) was added dropwise methyl 2,2-dimethyl-3-oxobutanoate (52 g, 0.361 mol, crude from last step) at 0 0C, followed by the addition of approximately 20 drops of dry DMF. The mixture was heated at reflux overnight. After cooling, the reaction mixture was slowly poured into ice water. The organic layer was separated and the aqueous phase was extracted with dichloromethane (300 mL x 3). The combined organic layers were washed with saturated aqueous NaHCO3 solution and dried over anhydrous Na2SO4. The solvent was evaporated to give the product, methyl 3-chloro-2,2-dimethylbut-3-enoate which was used without further purification (47 g, 82%).
[048] Step c: 3-chloro-2,2-dimethylbut-3-enoic acid
[049] A mixture of methyl 3-chloro-2,2-dimethylbut-3-enoate (42.0 g, 0.26 mol) and NaOH (12.4 g, 0.31 mol) in water (300 mL) was heated at reflux overnight. After cooling, the reaction mixture was extracted with ether. The organic layer contained 2Og of methyl 3- chloro-2,2-dimethylbut-3-enoate (48 % recovered). The aqueous layer was acidified with cold 20% HCl solution and was extracted with ether (250 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give 3-chloro-2,2-dimethylbut-3- enoic acid (17 g, 44 %), which was used directly in the next step.
[050] Step d: 2,2-dimethylbut-3-ynoic acid
[051] To a three-neck flask (500 mL) was added NaNH2 (17.8 g, 0.458 mmol, pellets) and DMSO (50 mL). The mixture was stirred at room temperature until no more NH3 (g) was given off. A solution of 3-chloro-2,2-dimethylbut-3-enoic acid (17.0 g, 114 mmol) in DMSO (50 mL) was added dropwise at 0 0C. The mixture was warmed and stirred at 50 0C for 5 hours, then stirred at room temperature overnight. The mixture was poured into cold 20% HCl solution, and then extracted three times with ether. The ether extracts were dried over anhydrous Na2SO4 and concentrated to give a 6:1 ratio of starting material and alkyne product. The residue was re-dried using ether and Na2SO4 and re-subjected to the reaction conditions above. The reaction mixture was worked up in the same manner to provide 2,2-dimethylbut-3-ynoic acid (12.0 g, 94 %).
[052] benzyl 2,2-dimethylbut-3-ynoate
[053] To a stirred solution of 2,2-dimethylbut-3-ynoic acid (87.7 g, 0.782 mmol) and benzyl alcohol (114.6 g, 0.938 mol) in dichloromethane (800 mL) was added DCC (193.5 g, 0.938 mmol) at -20 0C. The reaction mixture was stirred at room temperature overnight and then the solvent was evaporated in vacuo. The residue was purified by chromatography on silica gel (2% ethyl acetate in petroleum ether as eluant) to afford benzyl 2,2-dimethylbut-3- ynoate (100 g, 59 % yield). 1H NMR (CDCl3, 400 MHz) δ 7.37-7.36 (m, 5 H), 5.19 (s, 2 H), 2.28 (s, 1 H), 1.52 (s, 6 H).
2-(l-(Tert-butyldimethylsilyloxy)-2-methylpropan-2-yl)-6-fluoro-5-nitro-lH- indole
Figure imgf000290_0001
Figure imgf000290_0002
[054] Step a: benzyl 4-(2-amino-4-fluoro-5-nitrophenyl)-2,2-dimethylbut-3-ynoate
[055] To a solution of 2-bromo-5-fluoro-4-nitroaniline (23.0 g, 0.1 mol) in Et3N (250 mL) was added benzoic 2,2-dimethylbut-3-ynoic anhydride (59.0 g, 0.29 mol), CuI
(1.85 g) and Pd(PPh3)2Cl2 (2.3 g) at room temperature. The mixture was stirred at 800C overnight. After cooling to room temperature, the reaction was quenched with water and the aqueous layer was extracted with ethyl acetate (100 mL x 3). The combined organic layer was dried over anhydrous Na2SO4, the solvent was evaporated in vacuo. The residue was purified by chromatography on silica gel (10% ethyl acetate in petroleum ether) to give benzyl 4-(2-amino-4-fluoro-5-nitrophenyl)-2,2-dimethylbut-3-ynoate (20.0 g, 56%). 1H NMR (400 MHz, CDCl3) 8.05 (d, / = 8.4 Hz, 1 H), 7.39-7.38 (m, 5 H), 6.33 (d, / = 13.2 Hz, 1 H), 5.20 (s, 2 H), 4.89 (br s, 2 H), 1.61 (s, 6 H).
[056] Step b: benzyl 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate
[057] To a solution of benzyl 4-(2-amino-4-fluoro-5-nitrophenyl)-2,2-dimethylbut- 3-ynoate (20.0 g, 56 mmol) in acetonitrile (100 mL) was added PdCl2 (5.0 g, 28 mmol) at room temperature. The mixture was stirred at 800C overnight. The mixture was filtered off and the solvent was evaporated in vacuo, the residue was purified by chromatography on silica gel (10% EtOAc in petroleum ether) to give benzyl 2-(6-fluoro-5-nitro-lH-indol-2-yl)- 2-methylpropanoate (18.0 g, 90%). 1H NMR (300 MHz, CDCl3) 8.96 (br s, 1 H), 8.33 (d, J = 7.2 Hz, 1 H) 7.35-7.28 (m, 5 H) 7.08 (d, / = 11.7 Hz, 1 H), 6.47 (s, 1 H), 5.18 (s, 2 H) 1.69 (s, 6 H).
[058] Step c: 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropan-l-ol
To a solution of benzyl 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate (18.0 g, 0.05 mol) in CH2Cl2 (IOO mL) was added DIBAL-H (12 mL) at -78°C. The mixture was stirred for 1 h at that temperature and was warmed to room temperature. The reaction was quenched with water and the aqueous layer was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4, the solvent was evaporated in vacuo. The residue was purified by chromatography on silica gel (10% EtOAc in petroleum ether) to give 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropan-l-ol (10.0 g, 77%). 1H NMR (300 MHz, CDCl3) 9.37 (s, I H), 8.32 (d, 7 = 7.2 Hz, 1 H), 7.11 (d, 7 = 11.7 Hz, 1 H), 6.36 (s, 1 H), 3.73 (d, 7 = 5.1 Hz 2 H), 1.97 (t, J = 5.1 Hz, I H), 1.39 (s, 6 H).
[059] Step d: 2-(l-(tert-butyldimethylsilyloxy)-2-methylpropan-2-yl)-6-fluoro-5-nitro- lH-indole
[060] To a stirred solution of 2-(6-fluoro-5-nitro- lH-indol-2-yl)-2-methylpropan- 1- ol (10.Og) in CH2Cl2 was added TBSCl (8.9 g), imidazole (8.1g, 0.12 mol) at room temperature. The mixture was stirred overnight. The solvent was evaporated in vacuo and the residue was purified by chromatography on silica gel (10% EtOAc in petroleum ether) to give 2-(l-(tert-butyldimethylsilyloxy)-2-methylpropan-2-yl)-6-fluoro-5-nitro-lH-indole (5.3 g, 38 %). 1H NMR (300 MHz, CDCl3) 9.51 (s, 1 H), 8.31 (d, J = 7.5 Hz, 1 H), 7.02 (d, J = 11.7 Hz, 1 H), 6.32 (s, 1 H), 3.63 (s, 2 H), 1.35 (s, 6 H), 0.99 (s, 9 H), 0.11 (s, 6 H).
6-fluoro-l,l-dimethyl-7-nitro-2,3-dihydro-lH-pyrrolo[l,2-a]indole, (R)-3- (l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2- yl)-3-methylbutan-l-ol, 2-(4-(((R)-2,2-dimethyl-l,3-dioxolan-4- yl)methoxy)-2-methylbutan-2-yl)-l-(((R)-2,2-dimethyl-l,3-dioxolan-4- yl)methyl)-6-fluoro-5-nitro-lH-indole, 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutan-1-ol and (R)-2-(4-((2,2-dimethyl-l,3-dioxolan-4-yl)methoxy)- 2-methylbutan-2-yl)-6-fluoro-5-nitro-lH-indole
Figure imgf000291_0001
[061] Step a: 6-fluoro-l,l-dimethyl-7-nitro-2,3-dihydro-lH-pyrrolo[l,2-a]indole, (R)-3-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutan-1-ol, 2-(4-(((R)-2,2-dimethyl-l,3-dioxolan-4-yl)methoxy)-2-methylbutan-2-yl)- l-(((R)-2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indole, 3-(6-fluoro-5- nitro-lH-indol-2-yl)-3-methylbutan-l-ol and (R)-2-(4-((2,2-dimethyl-l,3-dioxolan-4- yl)methoxy)-2-methylbutan-2-yl)-6-fluoro-5-nitro-lH-indole
[062] To a solution of 2-(4-(tert-butyldimethylsilyloxy)-2-methylbutan-2-yl)-6- fluoro-5-nitro-lH-indole (1.9 g, 5.0 mmol) and (S)-(2,2-dimethyl-l,3-dioxolan-4-yl)methyl 4-methylbenzenesulfonate (2.86 g, 10.0 mmol) in DMF (10 niL) was added Cs2CO3 (4.88 g, 15.0 mmol). The mixture was heated at 90 0C for 24 hours. The reaction was partitioned between ethyl acetate and water. The aqueous layer was extracted with ethyl acetate and the combined organic layers were washed with brine and dried over MgSO4. After the removal of solvent, the residue was purified by column chromatography (10-50% ethyl acetate - hexane) to afford 6-fluoro-l,l-dimethyl-7-nitro-2,3-dihydro-lH-pyrrolo[l,2-a]indole (600 mg, 48%). ESI-MS m/z calc. 248.1, found 249.2 (M+ 1)+. Retention time 2.00 minutes; 2- (4-(((R)-2,2-dimethyl-l,3-dioxolan-4-yl)methoxy)-2-methylbutan-2-yl)-l-(((R)-2,2-dimethyl- l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indole (270 mg, containing some (R)-2-(4- ((2,2-dimethyl-l,3-dioxolan-4-yl)methoxy)-2-methylbutan-2-yl)-6-fluoro-5-nitro-lH-indole). ESI-MS m/z calc. 494.2 and 380.2, found 495.4 and 381.4 (M+l)+. Retention time 2.12 and 1.92 minutes; (R)-3-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol- 2-yl)-3-methylbutan-l-ol (1.0 g, containing some 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutan-1-ol). ESI-MS m/z calc. 380.2 and 266.1, found 381.2 and 267.2 (M+l)+. Retention time 1.74 and 1.48 minutes.
(R)-2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol- 2-yl)-2-methylpropan-l-ol and 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methy lbutan- 1 -ol
Figure imgf000292_0001
DMF
Figure imgf000292_0002
[063] A mixture containing (R)- 3-dioxolan-4-yl)methyl)-6- fluoro-5-nitro-lH-indol-2-yl)-2-methylpropan-l-ol and 3-(6-fluoro-5-nitro-lH-indol-2-yl)-3- methylbutan-1-ol was obtained following the procedure shown above starting from 2-(l-(tert- butyldimethylsilyloxy)-2-methylpropan-2-yl)-6-fluoro-5-nitro-lH-indole. (R)-2-(l-((2,2- dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropan-l-ol, ESI-MS m/z calc. 366.2, found 367.2 (M+l)+. Retention time 1.71 minutes; 3-(6-fluoro-5- nitro-lH-indol-2-yl)-3-methylbutan-l-ol, ESI-MS m/z calc. 252.1, found 253.4 (M+l)+. Retention time 1.42 minutes. l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-l,l-dimethyl-2,3-dihydro- lH-pyrrolo[l,2-a]indol-7-yl)cyclopropanecarboxamide
Figure imgf000292_0003
DMF
Figure imgf000292_0004
[064] Step a: 6-fluoro-l,l-dimethyl-2,3-dihydro-lH-pyrrolo[l,2-a]indol-7-amine
[065] To a solution of 6-fluoro-l,l-dimethyl-7-nitro-2,3-dihydro-lH- pyrrolo[l,2-a]indole (600 mg, 2.4 mmol) in ethanol (15 mL) was added ammonium formate (600 mg, 9.5 mmol) and Pd/C (10%, 129 mg, 0.12 mmol). The mixture was refluxed for 10 min. The Pd catalyst was removed via filtration through Celite and washed with ethanol. The filtrate was concentrated and purified by column chromatography (20-40% ethyl acetate- hexanes) to provide 6-fluoro-l,l-dimethyl-2,3-dihydro-lH-pyrrolo[l,2-a]indol-7-amine (260 mg, 49 %). ESI-MS m/z calc. 218.1, found 219.2 (M+l)+. Retention time 1.01 minutes.
[066] Step b: l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-l,l-dimethyl- 2,3-dihydro-lH-pyrrolo[l,2-a]indol-7-yl)cyclopropanecarboxamide
[067] To a mixture of l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxylic acid (346 mg,1.4 mmol), 6-fluoro-l,l-dimethyl-2,3-dihydro-lH- pyrrolo[l,2-a]indol-7-amine (260 mg, 1.2 mmol) and HATU (543 mg, 1.4 mmol) in DMF (5 mL) was added triethylamine (0.40 mL, 2.9 mmol). The reaction was stirred at room temperature overnight and then partitioned between ethyl acetate and water. The aqueous layer was extracted with ethyl acetate and the combined organic layers were washed with brine and dried over MgSO4. After the removal of solvent, the residue was purified by column chromatography (10-20% ethyl acetate - hexanes) to afford l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-l,l-dimethyl-2,3-dihydro-lH-pyrrolo[l,2- a]indol-7-yl)cyclopropanecarboxamide (342 mg, 65 %). ESI-MS m/z calc. 442.2, found 443.5 (M+l)+. Retention time 2.30 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.20 (d, J = 7.6 Hz, IH), 7.30 - 7.25 (m, 3H), 7.20 (m, IH), 7.12 (d, J = 8.2 Hz, IH), 6.84 (d, J = 11.1 Hz, IH), 6.01 (d, J = 0.5 Hz, IH), 3.98 (t, J = 6.8 Hz, 2H), 2.37 (t, J = 6.8 Hz, 2H), 1.75 (dd, J = 3.8, 6.9 Hz, 2H), 1.37 (s, 6H) and 1.14 (dd, J = 3.9, 6.9 Hz, 2H) ppm.
(R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3-dihydroxypropyl)-6- fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
DMF
Figure imgf000293_0001
Figure imgf000293_0002
Figure imgf000293_0003
[068] Step a: (R)-3-(5-amino-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro- 1 H-indol-2-yl)-3 -methylbutan- 1 -ol
[069] To a solution of (R)-3-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6- fluoro-5-nitro-lH-indol-2-yl)-3-methylbutan-l-ol containing some 3-(6-fluoro-5-nitro-lH- indol-2-yl)-3-methylbutan-l-ol (500 mg, 1.3 mmol) in ethanol (10 mL) was added ammonium formate (500 mg, 7.9 mmol) and Pd/C (10%, 139 mg, 0.13 mmol). The mixture was refluxed for 5 min. The Pd catalyst was removed via filtration through Celite and washed with ethanol. The filtrate was evaporated to dryness and purified by column chromatography (30-50% ethyl acetate-hexanes) to provide (R)-3-(5-amino-l-((2,2-dimethyl- l,3-dioxolan-4-yl)methyl)-6-fluoro-lH-indol-2-yl)-3-methylbutan-l-ol (220 mg, 48 %, contains some 3-(5-amino-6-fluoro-lH-indol-2-yl)-3-methylbutan-l-ol). ESI-MS m/z calc. 350.2 found 351.4 (M+l)+. Retention time 0.94 minutes.
[070] Step b: (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[071] To a mixture of l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)cyclopropanecarboxylic acid (183 mg, 0.75 mmol), (R)-3-(5-amino-l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-lH-indol-2-yl)-3-methylbutan-l-ol containing some 3-(5- amino-6-fluoro-lH-indol-2-yl)-3-methylbutan-l-ol (220 mg, 0.63 mmol) and HATU (287 mg, 0.75 mmol) in DMF (3.0 mL) was added triethylamine (0.21 mL, 1.5 mmol). The reaction was stirred at room temperature overnight and then partitioned between ethyl acetate and water. The aqueous layer was extracted with ethyl acetate and the combined organic layers were washed with brine and dried over MgSO4. After the removal of solvent, the residue was purified by column chromatography (20-40% ethyl acetate - hexanes) to afford (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)- 6-fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide (315 mg, 87 %, contains some l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-2-(4-hydroxy- 2-methylbutan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide). ESI-MS m/z calc. 574.2 found 575.7 (M+l)+. Retention time 2.08 minutes.
[072] Step c: (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3- dihydroxypropyl)-6-fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[073] To a solution of (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l- ((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH- indol-S-y^cyclopropanecarboxamide containing some l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)-N-(6-fluoro-2-(4-hydroxy-2-methylbutan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide (315 mg, 0.55 mmol) in methanol (3 mL) and water (0.3 mL) was added P-TsOH-H2O (21 mg, 0.11 mmol). The mixture was heated at 80 0C for 30 minutes. The reaction was partitioned between ethyl acetate and water and the aqueous layer was extracted with ethyl acetate twice. The combined organic layers were washed with saturated. NaHCθ3 solution and brine and dried over MgSO4. After the removal of solvent, the residue was purified by column chromatography (20-80% ethyl acetate - hexanes) to provide (R)-l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3-dihydroxypropyl)-6-fluoro-2-(4-hydroxy-2- methylbutan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide (92 mg, 31%). ESI-MS tn/z calc. 534.2, found 535.5 (M+l)+. Retention time 1.72 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.32 (s, IH), 7.53 (d, J = 1.0 Hz, IH), 7.43 - 7.31 (m, 4H), 6.17 (s, IH), 4.97 - 4.92 (m, 2H), 4.41 (dd, J = 2.4, 15.0 Hz, IH), 4.23 (t, J = 5.0 Hz, IH), 4.08 (dd, J = 8.6, 15.1 Hz, IH), 3.87 (s, IH), 3.48 - 3.44 (m, IH), 3.41 - 3.33 (m, IH), 3.20 (dd, J = 7.4, 12.7 Hz, 2H), 1.94 - 1.90 (m, 2H), 1.48 - 1.45 (m, 2H), 1.42 (s, 3H), 1.41 (s, 3H) and 1.15 - 1.12 (m, 2H) ppm. l-(2,2-diπuorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-((S)-2,3-dihydroxypropoxy)- 2-methylbutan-2-yl)-l-((R)-2,3-dihydroxypropyl)-6-fluoro-lH-indol-5- yl)cyclopropanecarboxamide and (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5- yl)-N-(2-(4-(2,3-dihydroxypropoxy)-2-methylbutan-2-yl)-6-fluoro-lH- indol-5-yl)cyclopropanecarboxamide
Figure imgf000295_0001
[074] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-((S)-2,3-dihydroxypropoxy)- 2-methylbutan-2-yl)-l-((R)-2,3-dihydroxypropyl)-6-fluoro-lH-indol-5- yl)cyclopropanecarboxamide and (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-(2,3- dihydroxypropoxy)-2-methylbutan-2-yl)-6-fluoro-lH-indol-5-yl)cyclopropanecarboxamide
[075] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-((S)-2,3-dihydroxypropoxy)- 2-methylbutan-2-yl)-l-((R)-2,3-dihydroxypropyl)-6-fluoro-lH-indol-5- yl)cyclopropanecarboxamide and (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-(2,3- dihydroxypropoxy)-2-methylbutan-2-yl)-6-fluoro-lH-indol-5-yl)cyclopropanecarboxamide were made following a scheme similar as shown above starting from 2-(4-(((R)-2,2-dimethyl- l,3-dioxolan-4-yl)methoxy)-2-methylbutan-2-yl)-l-(((R)-2,2-dimethyl-l,3-dioxolan-4- yl)methyl)-6-fluoro-5-nitro-lH-indole containing some (R)-2-(4-((2,2-dimethyl-l,3-dioxolan- 4-yl)methoxy)-2-methylbutan-2-yl)-6-fluoro-5-nitro-lH-indole). l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4-((S)-2,3-dihydroxypropoxy)-2-methylbutan-2-yl)- l-((R)-2,3-dihydroxypropyl)-6-fluoro-lH-indol-5-yl)cyclopropanecarboxamide, ESI-MS m/z calc. 608.2, found 609.5 (M+l)+. Retention time 1.67 minutes. 1H NMR (400 MHz, DMSO- dβ) δ 8.32 (s, IH), 7.53 (s, IH), 7.43 - 7.31 (m, 4H), 6.19 (s, IH), 4.95 - 4.93 (m, 2H), 4.51 (d, J = 5.0 Hz, IH), 4.42 - 4.39 (m, 2H), 4.10 - 4.04 (m, IH), 3.86 (s, IH), 3.49 - 3.43 (m, 2H), 3.41 - 3.33 (m, IH), 3.30 - 3.10 (m, 6H), 2.02 - 1.97 (m, 2H), 1.48 - 1.42 (m, 8H) and 1.13 (dd, J = 4.0, 6.7 Hz, 2H) ppm ; (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(2-(4- (2,3-dihydroxypropoxy)-2-methylbutan-2-yl)-6-fluoro-lH-indol-5- yl)cyclopropanecarboxamide, ESI-MS m/z calc. 534.2, found 535.5 (M+l)+. Retention time 1.81 minutes. 1H NMR (400 MHz, DMSO-J6) δ 10.91 (d, J = 1.5 Hz, IH), 8.30 (s, IH), 7.53 (s, IH), 7.42 - 7.33 (m, 3H), 7.03 (d, J = 10.9 Hz, IH), 6.07 (d, J = 1.6 Hz, IH), 4.56 (d, J = 5.0 Hz, IH), 4.43 (t, J = 5.7 Hz, IH), 3.51 - 3.46 (m, IH), 3.31 - 3.13 (m, 6H), 1.88 (t, J = 7.3 Hz, 2H), 1.48 - 1.45 (m, 2H), 1.31 (s, 6H) and 1.15 - 1.12 (m, 2H) ppm. l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-2-(l-hydroxy-2- methylpropan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000296_0001
[076] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-2-(l-hydroxy-2- methylpropan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide
[077] l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(6-fluoro-2-(l-hydroxy-2- methylpropan-2-yl)-lH-indol-5-yl)cyclopropanecarboxamide was made following the scheme shown above starting from a mixture containing (R)-2-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropan-l-ol and 3-(6-fluoro- 5-nitro-lH-indol-2-yl)-3-methylbutan-l-ol. ESI-MS m/z calc. 446.2, found 447.5 (M+l)+. Retention time 1.88 minutes. 1H NMR (400 MHz, CDCl3) δ 8.68 (s, IH), 8.20 (d, J = 7.7 Hz, IH), 7.30 - 7.21 (m, 3H), 7.12 (d, J = 8.2 Hz, IH), 6.94 (d, J = 11.2 Hz, IH), 6.18 (s, IH), 3.64 (s, 2H), 1.75 (dd, J = 3.8, 6.8 Hz, 2H), 1.34 (s, 6H) and 1.14 (dd, J = 3.9, 6.9 Hz, 2H) ppm. (R)-l-(2,2-Difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3-dihydroxypropyl)-6- fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000297_0001
[078] Step a: (R)-Benzyl 2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5- nitro-lH-indol-2-yl)-2-methylpropanoate and ((S)-2,2-Dimethyl-l,3-dioxolan-4-yl)methyl 2- (l-CCC^^^-dimethyl-l^-dioxolan^-y^methyO-ό-fluoro-S-nitro-lH-indol^-yl)^- methylpropanoate
[079] Cesium carbonate (8.23 g, 25.3 mmol) was added to a mixture of benzyl 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate (3.0 g, 8.4 mmol) and (S)- (2,2-dimethyl-l,3-dioxolan-4-yl)methyl 4-methylbenzenesulfonate (7.23 g, 25.3 mmol) in DMF (17 mL). The reaction was stirred at 80 0C for 46 hours under nitrogen atmosphere. The mixture was then partitioned between ethyl acetate and water. The aqueous layer was extracted with ethyl acetate. The combined ethyl acetate layers were washed with brine, dried over MgSO4, filtered and concentrated. The crude product, a viscous brown oil which contains both of the products shown above, was taken directly to the next step without further purification. (R)-Benzyl 2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH- indol-2-yl)-2-methylpropanoate, ESI-MS m/z calc. 470.2, found 471.5 (M+l)+. Retention time 2.20 minutes. ((S)-2,2-Dimethyl-l,3-dioxolan-4-yl)methyl 2-(l-(((R)-2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate, ESI-MS m/z calc. 494.5, found 495.7 (M+l)+. Retention time 2.01 minutes.
[080] Step b: (R)-2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro- lH-indol-2-yl)-2-methylpropan-l-ol
[081] To the crude reaction mixture obtained in step (a) was dissolved in THF (42 mL) and cooled in an ice-water bath. LiAlH4 (16.8 mL of 1 M solution, 16.8 mmol) was added drop- wise. After the addition was complete, the reaction was stirred for an additional 5 minutes. The reaction was quenched by adding water (1 mL), 15% NaOH solution (1 mL) and then water (3 mL). The mixture was filtered over Celite, and the solids were washed with THF and ethyl acetate. The filtrate was concentrated and purified by column chromatography (30-60% ethyl acetate- hexanes) to obtain the product as a brown oil (2.68g, 87 % over 2 steps). ESI-MS m/z calc. 366.4, found 367.3 (M+l)+. Retention time 1.68 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.34 (d, J = 7.6 Hz, IH), 7.65 (d, J = 13.4 Hz, IH), 6.57 (s, IH), 4.94 (t, J = 5.4 Hz, IH), 4.64 - 4.60 (m, IH), 4.52 - 4.42(m, 2H), 4.16 - 4.14 (m, IH), 3.76 - 3.74 (m, IH), 3.63 - 3.53 (m, 2H), 1.42 (s, 3H), 1.38 - 1.36 (m, 6H) and 1.19 (s, 3H) ppm
[082] Step c: (R)-2-(5-amino-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro- lH-indol-2-yl)-2-methylpropan-l-ol
[083] (R)-2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro- lH-indol-2-yl)-2-methylpropan-l-ol (2.5 g, 6.82 mmol) was dissolved ethanol (70 mL) and the reaction was flushed with N2. Then Pd-C (250 mg, 5% wt) was added. The reaction was flushed with nitrogen again and then stirred under H2 (atm). After 2.5 hours only partial conversion to the product was observed by LCMS. The reaction was filtered through Celite and concentrated. The residue was re-subjected to the conditions above. After 2 hours LCMS indicated complete conversion to product. The reaction mixture was filtered through Celite. The filtrate was concentrated to yield the product as a black solid (1.82 g, 79 %). ESI-MS m/z calc. 336.2, found 337.5 (M+l)+. Retention time 0.86 minutes. 1H NMR (400 MHz, DMSO- dβ) δ 7.17 (d, J = 12.6 Hz, IH), 6.76 (d, J = 9.0 Hz, IH), 6.03 (s, IH), 4.79 - 4.76 (m, IH), 4.46 (s, 2H), 4.37 - 4.31 (m, 3H),4.06 (dd, J = 6.1, 8.3 Hz, IH), 3.70 - 3.67 (m, IH), 3.55 - 3.52 (m, 2H), 1.41 (s, 3H), 1.32 (s, 6H) and 1.21 (s, 3H) ppm.
[084] Step d: (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[085] DMF (3 drops) was added to a stirring mixture of l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (1.87 g, 7.7 mmol) and thionyl chloride (1.30 mL, 17.9 mmol). After 1 hour a clear solution had formed. The solution was concentrated under vacuum and then toluene (3 mL) was added and the mixture was concentrated again. The toluene step was repeated once more and the residue was placed on high vacuum for 10 minutes. The acid chloride was then dissolved in dichloromethane (10 mL) and added to a mixture of (R)-2-(5-amino-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6- fluoro-lH-indol-2-yl)-2-methylpropan-l-ol (1.8 g, 5.4 mmol) and triethylamine (2.24 mL, 16.1 mmol) in dichloromethane (45 mL). The reaction was stirred at room temperature for 1 hour. The reaction was washed with IN HCl solution, saturated NaHCC>3 solution and brine, dried over MgSO4 and concentrated to yield the product as a black foamy solid (3g, 100%). ESI-MS m/z calc. 560.6, found 561.7 (M+l)+. Retention time 2.05 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.31 (s, IH), 7.53 (s, IH), 7.42 - 7.40 (m, 2H), 7.34 - 7.30 (m, 3H), 6.24 (s, IH), 4.51 - 4.48 (m, IH), 4.39 - 4.34 (m,2H), 4.08 (dd, J = 6.0, 8.3 Hz, IH), 3.69 (t, J = 7.6 Hz, IH), 3.58 - 3.51 (m, 2H), 1.48 - 1.45 (m, 2H), 1.39 (s, 3H), 1.34 - 1.33 (m, 6H), 1.18 (s, 3H) and 1.14 - 1.12 (m, 2H) ppm
[086] Step e: (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3- dihydroxypropyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[087] (R)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide (3.0 g, 5.4 mmol) was dissolved in methanol (52 mL). Water (5.2 mL) was added followed by p-TsOH.H2O (204 mg, 1.1 mmol). The reaction was heated at 80 0C for 45 minutes. The solution was concentrated and then partitioned between ethyl acetate and saturated NaHCθ3 solution. The ethyl acetate layer was dried over MgSO4 and concentrated. The residue was purified by column chromatography (50-100 % ethyl acetate - hexanes) to yield the product as a cream colored foamy solid. (1.3 g, 47 %, ee >98% by SFC). ESI-MS m/z calc. 520.5, found 521.7 (M+l)+. Retention time 1.69 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.31 (s, IH), 7.53 (s, IH), 7.42 - 7.38 (m, 2H), 7.33 - 7.30 (m, 2H), 6.22 (s, IH), 5.01 (d, J = 5.2 Hz, IH), 4.90 (t, J = 5.5 Hz, IH), 4.75 (t, J = 5.8 Hz, IH), 4.40 (dd, J = 2.6, 15.1 Hz, IH), 4.10 (dd, J = 8.7, 15.1 Hz, IH), 3.90 (s, IH), 3.65 - 3.54 (m, 2H), 3.48 - 3.33 (m, 2H), 1.48 - 1.45 (m, 2H), 1.35 (s, 3H), 1.32 (s, 3H) and 1.14 - 1.11 (m, 2H) ppm.
(S)-l-(2,2-Difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3-dihydroxypropyl)-6- fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
Figure imgf000299_0001
[088] Step a: (S)-Benzyl 2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5- nitro-lH-indol-2-yl)-2-methylpropanoate and ((R)-2,2-Dimethyl-l,3-dioxolan-4-yl)methyl 2- (l-(((S)-2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2- methylpropanoate
[089] Cesium carbonate (2.74 g, 8.4 mmol) was added to a mixture of benzyl 2-(6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate (1.0 g, 2.8 mmol) and (S)-(2,2- dimethyl-l,3-dioxolan-4-yl)methyl 4-methylbenzenesulfonate (3.21 g, 11.2 mmol) in DMF (5.6 mL). The reaction was stirred at 80 0C for 64 hours under nitrogen atmosphere. The mixture was then partitioned between ethyl acetate and water. The aqueous layer was extracted with ethyl acetate. The combined ethyl acetate layers were washed with brine, dried over MgSO4, filtered and concentrated. The crude product, a viscous brown oil which contains both of the products shown above, was taken directly to the next step without further purification. (S)-Benzyl 2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH- indol-2-yl)-2-methylpropanoate, ESI-MS m/z calc. 470.2, found 471.5 (M+l)+. Retention time 2.22 minutes. ((R)-2,2-Dimethyl-l,3-dioxolan-4-yl)methyl 2-(l-(((S)-2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate, ESI-MS m/z calc. 494.5, found 495.5 (M+l)+. Retention time 2.03 minutes.
[090] Step b: (S)-2-(l-((2,2-Dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro- lH-indol-2-yl)-2-methylpropan-l-ol
[091] The mixture of crude reaction mixture of (S)-benzyl 2-(l-((2,2- dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate and ((R)-2,2-dimethyl-l,3-dioxolan-4-yl)methyl 2-(l-(((S)-2,2-dimethyl-l,3-dioxolan-4- yl)methyl)-6-fluoro-5-nitro-lH-indol-2-yl)-2-methylpropanoate was dissolved in THF (15 mL) and cooled in an ice- water bath. LiAlH4 (2.8 mL of 1 M solution, 2.8 mmol) was added drop wise. After addition was complete the reaction was stirred for 5 minutes. The reaction was quenched by adding water (0.5 mL), 15% NaOH solution (0.5 mL) and then water (1.5 mL). The mixture was filtered over Celite, and the solids were washed with THF and ethyl acetate. The filtrate was concentrated and purified by column chromatography (30-60% ethyl acetate- hexanes) to obtain the product as a brown oil (505 mg, 49 % over 2 steps). ESI-MS m/z calc. 366.4, found 367.3 (M+l)+. Retention time 1.68 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.34 (d, J = 7.6 Hz, IH), 7.65(d, J = 13.5 Hz, IH), 6.57 (s, IH), 4.94 (t, J = 5.4 Hz, IH), 4.64 - 4.60 (m, IH), 4.52 - 4.42 (m, 2H), 4.14 (dd, J = 6.2, 8.4 Hz, IH), 3.74 (dd, J = 7.0, 8.3 Hz, IH), 3.63 - 3.53 (m,2H), 1.42 (s, 3H), 1.37 (m, 6H) and 1.19 (s, 3H) ppm. [092] Step c: (S)-2-(5-amino-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro- lH-indol-2-yl)-2-methylpropan-l-ol
[093] (S)-2-(l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6-fluoro-5-nitro- lH-indol-2-yl)-2-methylpropan-l-ol (500 mg, 1.4 mmol) was dissolved ethanol (15 mL) and the reaction was flushed with N2. Then Pd-C (50 mg, 5% wt) was added. The reaction was flushed with nitrogen again and then stirred under H2 (atm). After 1 hour only partial conversion to the product was observed by LCMS. The reaction was filtered through Celite and concentrated. The residue was resubjected to the conditions above. After 1 hour LCMS indicated complete conversion to product. The reaction mixture was filtered through Celite. The filtrate was concentrated to yield the product as a black solid (420 mg, 91 %). ESI-MS m/z calc. 336.2, found 337.5 (M+l)+. Retention time 0.90 minutes. 1H NMR (400 MHz, DMSO- dβ) δ 7.17 (d, J = 12.6 Hz, IH), 6.76 (d, J = 9.0 Hz, IH), 6.03 (s, IH), 4.78 (br s, IH), 4.46 (s, 2H), 4.41 - 4.27 (m, 3H), 4.06(dd, J = 6.1, 8.3 Hz, IH), 3.70 - 3.67 (m, IH), 3.53 (dd, J = 10.7, 17.2 Hz, 2H), 1.40 (s, 3H), 1.32 (s, 6H) and 1.21 (s, 3H) ppm.
[094] Step d: (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[095] DMF (3 drops) was added to a stirring mixture of l-(2,2- difluorobenzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid (187 mg, 0.8 mmol) and thionyl chloride (0.13 mL, 1.8 mmol). After 30 minutes a clear solution had formed. A small amount was mixed piperidine to test that the acid chloride had been formed. The solution was concentrated on the rotovap and then toluene (1 mL) was added and the mixture was concentrated again. The toluene step was repeated once more and the residue was placed on high vacuum for 10 minutes. The acid chloride was then dissolved in dichloromethane (2 mL) and added to a mixture of (S)-2-(5-amino-l-((2,2-dimethyl-l,3-dioxolan-4-yl)methyl)-6- fluoro-lH-indol-2-yl)-2-methylpropan-l-ol (200 mg, 0.6 mmol) and triethylamine (0.25 mL, 1.8 mmol) in dichloromethane (4 mL). The reaction was stirred at room temperature for 45 minutes. The reaction was washed with IN HCl solution, saturated NaHCθ3 solution and brine, dried over MgSO4 and concentrated to yield the product as a black foamy solid (320 mg, 96 %). ESI-MS m/z calc. 560.6, found 561.5 (M+l)+. Retention time 2.05 minutes. 1H NMR (400 MHz, DMSO- dβ) δ 8.31 (s, IH), 7.53 (s, IH), 7.42 - 7.40 (m, 2H), 7.34 - 7.30 (m, 3H), 6.24 (s, IH), 4.84 (t, J = 5.5 Hz, IH), 4.51 - 4.46 (m, IH), 4.41 - 4.32 (m, 2H), 4.08 (dd, J = 6.0, 8.3 Hz, IH), 3.71 - 3.67 (m, IH), 3.58 - 3.50 (m, 2H), 1.48 - 1.45 (m, 2H), 1.40 (s, 3H), 1.34 - 1.33 (m, 6H), 1.18 (s, 3H) and 1.14 - 1.12 (m, 2H) ppm.
[096] Step e: (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-(2,3- dihydroxypropyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide
[097] (S)-l-(2,2-difluorobenzo[d][l,3]dioxol-5-yl)-N-(l-((2,2-dimethyl-l,3- dioxolan-4-yl)methyl)-6-fluoro-2-(l-hydroxy-2-methylpropan-2-yl)-lH-indol-5- yl)cyclopropanecarboxamide (290 g, 0.5 mmol) was dissolved in methanol (5 mL). Water (0.5 mL) was added followed by P-TsOH-H2O (20 mg, 0.1 mmol). The reaction was heated at 80 0C for 45 minutes. The solution was then partitioned between ethyl acetate and saturated NaHCO3 solution. The ethyl acetate layer was dried over MgSO4 and concentrated. The residue was purified by column chromatography (50-100 % ethyl acetate - hexanes) to yield the product as a cream colored foamy solid. (146 mg, 54 %, ee >97% by SFC). ESI-MS m/z calc. 520.5, found 521.5 (M+l)+. Retention time 1.67 minutes. 1H NMR (400 MHz, DMSO-J6) δ 8.31 (s, IH), 7.53 (d, J = Ll Hz, IH), 7.42 - 7.37 (m, 2H), 7.33 - 7.30 (m, 2H), 6.22 (s, IH), 5.01 (d, J = 5.0 Hz, IH), 4.91 (t, J = 5.5 Hz, IH), 4.75 (t, J = 5.8 Hz, IH), 4.42 - 4.38 (m, IH), 4.10 (dd, J = 8.8, 15.1 Hz, IH), 3.90 (s, IH), 3.64 - 3.54 (m, 2H), 3.48 - 3.33 (m, 2H), 1.48 - 1.45 (m, 2H), 1.35 (s, 3H), 1.32 (s, 3H) and 1.14 - 1.11 (m, 2H) ppm.
(R)-l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-6- fluoro-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000302_0001
[098] (R)-l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-6- fluoro-lH-indol-5-yl)cyclopropanecarboxamide was prepared using an experimental procedure similar to example 72 from l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid and 2-tert-butyl-6-fluoro-5-nitro-lH-indole.
(S)-l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-6- fluoro-lH-indol-5-yl)cyclopropanecarboxamide
Figure imgf000303_0001
[099] (S)-l-(benzo[d][l,3]dioxol-5-yl)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-6- fluoro-lH-indol-5-yl)cyclopropanecarboxamide was prepared using an experimental procedure similar to Example 72 from l-(benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxylic acid and 2-tert-butyl-6-fluoro-5-nitro-lH-indole.
(R)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(3,4- dihydroxyphenyl)cyclopropanecarboxamide
Figure imgf000303_0002
[0100] (R)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(3,4- dihydroxyphenyl)cyclopropanecarboxamide was prepared using an experimental procedure similar to Example 72 from l-(3,4-dihydroxyphenyl)cyclopropanecarboxylic acid and 2-tert- butyl-5-nitro-lH-indole.
(R)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,3-dihydro- lH-inden-5-yl)cydopropanecarboxamide
Figure imgf000303_0003
[001015] (R)-N-(2-tert-butyl-l-(2,3-dihydroxypropyl)-lH-indol-5-yl)-l-(2,3-dihydro-lH- inden-5-yl)cyclopropanecarboxamide was prepared using an experimental procedure similar to Example 72 from l-(2,3-dihydro-lH-inden-5-yl)cyclopropanecarboxylic acid and 2-tert- butyl-5-nitro-lH-indole.
[001016] A person skilled in the chemical arts can use the examples and schemes along with known synthetic methodologies to synthesize compounds of the present invention, including the compounds in Table 3, below. Table 3: Physical data of exemplary compounds.
Figure imgf000305_0002
Figure imgf000305_0001
Figure imgf000306_0001
Figure imgf000306_0002
Figure imgf000307_0002
Figure imgf000307_0001
Figure imgf000308_0001
Figure imgf000308_0002
Figure imgf000309_0002
Figure imgf000309_0001
Figure imgf000310_0002
Figure imgf000310_0001
Figure imgf000311_0001
Figure imgf000311_0002
Figure imgf000312_0002
Figure imgf000312_0001
Figure imgf000313_0001
Figure imgf000313_0002
Figure imgf000314_0001
Figure imgf000314_0002
Figure imgf000315_0001
Figure imgf000315_0002
Figure imgf000316_0001
Figure imgf000316_0002
Figure imgf000317_0002
Figure imgf000317_0001
Figure imgf000318_0001
Figure imgf000319_0001
Figure imgf000319_0002
Figure imgf000320_0001
Figure imgf000320_0002
Figure imgf000320_0003
Figure imgf000321_0001
Figure imgf000322_0001
Assays for Detecting and Measuring ΔF508-CFTR Correction Properties of Compounds
Membrane potential optical methods for assaying ΔF508-CFTR modulation properties of compounds.
The assay utilizes fluorescent voltage sensing dyes to measure changes in membrane potential using a fluorescent plate reader (e.g., FLIPR III, Molecular Devices, Inc.) as a readout for increase in functional ΔF508-CFTR in NIH 3T3 cells. The driving force for the response is the creation of a chloride ion gradient in conjunction with channel activation by a single liquid addition step after the cells have previously been treated with compounds and subsequently loaded with a voltage sensing dye.
Identification of Correction Compounds
To identify small molecules that correct the trafficking defect associated with ΔF508- CFTR; a single-addition HTS assay format was developed. Assay Plates containing cells are incubated for -2-4 hours in tissue culture incubator at 37oC, 5%CO2, 90% humidity. Cells are then ready for compound exposure after adhering to the bottom of the assay plates.
The cells were incubated in serum-free medium for 16-24 hrs in tissue culture incubator at 37oC, 5%CO2, 90% humidity in the presence or absence (negative control) of test compound. The cells were subsequently rinsed 3X with Krebs Ringers solution and loaded with a voltage sensing redistribution dye. To activate ΔF508-CFTR, 10 μM forskolin and the CFTR potentiator, genistein (20 μM), were added along with Cl"-free medium to each well. The addition of Cl"-free medium promoted Cl" efflux in response to ΔF508-CFTR activation and the resulting membrane depolarization was optically monitored using voltage sensor dyes.
Identification of Potentiator Compounds
To identify potentiators of ΔF508-CFTR, a double-addition HTS assay format was developed. This HTS assay utilizes fluorescent voltage sensing dyes to measure changes in membrane potential on the FLIPR III as a measurement for increase in gating (conductance) of ΔF508 CFTR in temperature-corrected ΔF508 CFTR NIH 3T3 cells. The driving force for the response is a Cl" ion gradient in conjunction with channel activation with forskolin in a single liquid addition step using a fluoresecent plate reader such as FLIPR III after the cells have previously been treated with potentiator compounds (or DMSO vehicle control) and subsequently loaded with a redistribution dye.
Solutions:
Bath Solution #1: (in mM) NaCl 160, KCl 4.5, CaCl2 2, MgCl2 1, HEPES 10, pH 7.4 with NaOH.
Chloride-free bath solution: Chloride salts in Bath Solution #1 are substituted with g &luconate salts.
Cell Culture
NIH3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for optical measurements of membrane potential. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For all optical assays, the cells were seeded at -20,000/well in 384-well matrigel-coated plates and cultured for 2 hrs at 37 °C before culturing at 27 °C for 24 hrs. for the potentiator assay. For the correction assays, the cells are cultured at 27 °C or 37 °C with and without compounds for 16 - 24 hours.
Electrophysiological Assays for assaying ΔF508-CFTR modulation properties of compounds.
l.Ussing Chamber Assay
Ussing chamber experiments were performed on polarized airway epithelial cells expressing ΔF508-CFTR to further characterize the ΔF508-CFTR modulators identified in the optical assays. Non-CF and CF airway epithelia were isolated from bronchial tissue, cultured as previously described (Galietta, L.J.V., Lantero, S., Gazzolo, A., Sacco, O., Romano, L., Rossi, G.A., & Zegarra-Moran, O. (1998) In Vitro Cell. Dev. Biol. 34, 478-481), and plated onto Costar® Snapwell™ filters that were precoated with NIH3T3-conditioned media. After four days the apical media was removed and the cells were grown at an air liquid interface for >14 days prior to use. This resulted in a monolayer of fully differentiated columnar cells that were ciliated, features that are characteristic of airway epithelia. Non-CF HBE were isolated from non-smokers that did not have any known lung disease. CF-HBE were isolated from patients homozygous for ΔF508- CFTR.
HBE grown on Costar® Snapwell™ cell culture inserts were mounted in an Ussing chamber (Physiologic Instruments, Inc., San Diego, CA), and the transepithelial resistance and short-circuit current in the presence of a basolateral to apical Cl" gradient (Isc) were measured using a voltage-clamp system (Department of Bioengineering, University of Iowa, IA). Briefly, HBE were examined under voltage-clamp recording conditions (Vhoid = 0 mV) at 37 0C. The basolateral solution contained (in mM) 145 NaCl, 0.83 K2HPO4, 3.3 KH2PO4, 1.2 MgCl2, 1.2 CaCl2, 10 Glucose, 10 HEPES (pH adjusted to 7.35 with NaOH) and the apical solution contained (in mM) 145 NaGluconate, 1.2 MgCl2, 1.2 CaCl2, 10 glucose, 10 HEPES (pH adjusted to 7.35 with NaOH).
Identification of Correction Compounds Typical protocol utilized a basolateral to apical membrane Cl" concentration gradient. To set up this gradient, normal ringer was used on the basolateral membrane, whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl" concentration gradient across the epithelium. All experiments were performed with intact monolayers. To fully activate ΔF508-CFTR, forskolin (10 μM), PDE inhibitor, IBMX (100 μM) and CFTR potentiator, genistein (50 μM) were added to the apical side.
As observed in other cell types, incubation at low temperatures of FRT cells and human bronchial epithelial cells isolated from diseased CF patients (CF-HBE)expressing ΔF508-CFTR increases the functional density of CFTR in the plasma membrane. To determine the activity of correction compounds, the cells were incubated with test compound for 24-48 hours at 37°C and were subsequently washed 3X prior to recording. The cAMP- and genistein-mediated Isc in compound-treated cells was normalized to 37°C controls and expressed as percentage activity of CFTR activity in wt-HBE. Preincubation of the cells with the correction compound significantly increased the cAMP- and genistein-mediated Isc compared to the 37 °C controls.
Identification of Potentiator Compounds
Typical protocol utilized a basolateral to apical membrane Cl" concentration gradient. To set up this gradient, normal ringers was used on the basolateral membrane, whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl" concentration gradient across the epithelium. Forskolin (10 μM) and all test compounds were added to the apical side of the cell culture inserts. The efficacy of the putative ΔF508-CFTR potentiators was compared to that of the known potentiator, genistein.
2. Patch-clamp Recordings
Total Cl" current in ΔF508-NIH3T3 cells was monitored using the perforated-patch recording configuration as previously described (Rae, J., Cooper, K., Gates, P., & Watsky, M. (1991) /. Neurosci. Methods 37, 15-26). Voltage-clamp recordings were performed at 22 0C using an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc., Foster City, CA). The pipette solution contained (in mM) 150 iV-methyl-D-glucamine (NMDG)-Cl, 2 MgCl2, 2 CaCl2, 10 EGTA, 10 HEPES, and 240 μg/ml amphotericin-B (pH adjusted to 7.35 with HCl). The extracellular medium contained (in mM) 150 NMDG-Cl, 2 MgCl2, 2 CaCl2, 10 HEPES (pH adjusted to 7.35 with HCl). Pulse generation, data acquisition, and analysis were performed using a PC equipped with a Digidata 1320 A/D interface in conjunction with Clampex 8 (Axon Instruments Inc.). To activate ΔF508-CFTR, 10 μM forskolin and 20 μM genistein were added to the bath and the current-voltage relation was monitored every 30 sec.
Identification of Correction Compounds
To determine the activity of correction compounds for increasing the density of functional ΔF508-CFTR in the plasma membrane, we used the above-described perforated- patch-recording techniques to measure the current density following 24-hr treatment with the correction compounds. To fully activate ΔF508-CFTR, 10 μM forskolin and 20μM genistein were added to the cells. Under our recording conditions, the current density following 24-hr incubation at 27°C was higher than that observed following 24-hr incubation at 37 °C. These results are consistent with the known effects of low-temperature incubation on the density of ΔF508-CFTR in the plasma membrane. To determine the effects of correction compounds on CFTR current density, the cells were incubated with 10 μM of the test compound for 24 hours at 37°C and the current density was compared to the 27°C and 37°C controls (% activity). Prior to recording, the cells were washed 3X with extracellular recording medium to remove any remaining test compound. Preincubation with 10 μM of correction compounds significantly increased the cAMP- and genistein-dependent current compared to the 37 °C controls.
Identification of Potentiator Compounds
The ability of ΔF508-CFTR potentiators to increase the macroscopic ΔF508-CFTR Cl" current (IΔFSOS) in NIH3T3 cells stably expressing ΔF508-CFTR was also investigated using perforated-patch-recording techniques. The potentiators identified from the optical assays evoked a dose-dependent increase in IΔFSO8 with similar potency and efficacy observed in the optical assays. In all cells examined, the reversal potential before and during potentiator application was around -30 mV, which is the calculated ECi (-28 mV).
Cell Culture
NIH3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for whole-cell recordings. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For whole-cell recordings, 2,500 - 5,000 cells were seeded on poly-L-lysine-coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use to test the activity of potentiators; and incubated with or without the correction compound at 37 °C for measuring the activity of correctors.
3. Single-channel recordings
Gating activity of wt-CFTR and temperature-corrected ΔF508-CFTR expressed in NIH3T3 cells was observed using excised inside-out membrane patch recordings as previously described (Dalemans, W., Barbry, P., Champigny, G., Jallat, S., Dott, K., Dreyer, D., Crystal, R.G., Pavirani, A., Lecocq, J-P., Lazdunski, M. (1991) Nature 354, 526 - 528) using an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc.). The pipette contained (in mM): 150 NMDG, 150 aspartic acid, 5 CaCl2, 2 MgCl2, and 10 HEPES (pH adjusted to 7.35 with Tris base). The bath contained (in mM): 150 NMDG-Cl, 2 MgCl2, 5 EGTA, 10 TES, and 14 Tris base (pH adjusted to 7.35 with HCl). After excision, both wt- and ΔF508-CFTR were activated by adding 1 mM Mg-ATP, 75 nM of the catalytic subunit of cAMP-dependent protein kinase (PKA; Promega Corp. Madison, WI), and 10 mM NaF to inhibit protein phosphatases, which prevented current rundown. The pipette potential was maintained at 80 mV. Channel activity was analyzed from membrane patches containing < 2 active channels. The maximum number of simultaneous openings determined the number of active channels during the course of an experiment. To determine the single-channel current amplitude, the data recorded from 120 sec of ΔF508-CFTR activity was filtered "off-line" at 100 Hz and then used to construct all-point amplitude histograms that were fitted with multigaussian functions using Bio-Patch Analysis software (Bio-Logic Comp. France). The total microscopic current and open probability (P0) were determined from 120 sec of channel activity. The P0 was determined using the Bio-Patch software or from the relationship P0 = IZi(N), where I = mean current, i = single-channel current amplitude, and N = number of active channels in patch.
Cell Culture
NIH3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for excised- membrane patch-clamp recordings. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For single channel recordings, 2,500 - 5,000 cells were seeded on poly-L-lysine-coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use.
[001017] The compounds of Table 1 were found to exhibit Correction activity as measured in the assay described above.
[001018] Compounds of the invention are useful as modulators of ATP binding cassette transporters. Using the procedures described above, the activities, i.e., EC50s, of compounds of the present invention have been measured to be from about 3.8 nM to about 13.5 μM. Furthermore, using those methods described above, the efficacies of compounds of the present invention have been measured to be from about 35 % to about 110 %.
In Table 4, the following meanings apply:
EC50: "+++" means <2 uM; "++" means between 2 uM to 5 uM; "+" means between 5 uM to 25 uM.
% Efficacy: "+" means < 25%; "++" means between 25% and 100%; "+++" means > 100%.
Table 4.
Figure imgf000329_0001
[001019] OTHER EMBODIMENTS
[001020] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

We claim:
1. A compound of formula II:
Figure imgf000330_0001
II or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or -OCF2O-;
R1 is H or up to two C1-C6 alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, and R2 is F.
The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, and R3 is H.
The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is H.
The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3.
The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
7. The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
8. The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH
9. The compound of claim 1, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 and R5 taken together form a fused pyrrolidine ring.
10. The compound of claim 1, wherein two R taken together form -OCH2O-, R1 is H, and R2 is F.
11. The compound of claim 1, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, and R3 is H.
12. The compound of claim 1, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
13. The compound of claim 1, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
14. The compound of claim 1, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
15. The compound of claim 1, having formula Ha:
Figure imgf000331_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
16. The compound of claim 15, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH.
17. The compound of claim 15, wherein R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH.
18. The compound of claim 15, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
19. A compound is selected from Table 1.
20. A pharmaceutical composition comprising (i) a compound according to claim 1; and (ii) a pharmaceutically acceptable carrier.
21. The composition of claim 20, further comprising an additional agent selected from a mucolytic agent, bronchodialator, an anti-biotic, an anti-infective agent, an antiinflammatory agent, CFTR corrector, CFTR potentiator, or a nutritional agent.
22. A method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formula II:
Figure imgf000332_0001
II wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or -OCF2O-;
R1 is H or up to two C1-C6 alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
23. The method of claim 22, wherein the ABC transporter is CFTR.
24. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, and R2 is F.
25. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, and R3 is H.
26. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is H.
27. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3.
28. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
29. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
30. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
31. The method of claim 22, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 and R5 taken together form a fused pyrrolidine ring.
32. The method of claim 22, wherein two R taken together form -OCH2O-, R1 is H, and R2 is F.
33. The method of claim 22, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, and R3 is H.
34. The method of claim 22, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
35. The method of claim 22, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
36. The method of claim 22, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
37. The method of claim 22, wherein the compound is represented by formula Ha:
Figure imgf000334_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
38. The method of claim 37, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH.
39. The method of claim 37, wherein R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH. 40. The method of claim 37, wherein R4 is R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
41. The method of claim 22, wherein the compound is selected from Table 1. 42. A method of treating a condition, disease, or disorder in a patient implicated by ABC transporter activity, comprising the step of administering to said patient a compound having formula II:
Figure imgf000334_0002
II or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or -OCF2O-;
R1 is H or up to two C1-C6 alkyl;
R2 is H or F;
R3 is H or CN;
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
43. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, and R2 is F.
44. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, and R3 is H.
45. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is H.
46. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3.
47. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
48. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
49. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
50. The method of claim 42, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 and R5 taken together form a fused pyrrolidine ring.
51. The method of claim 42, wherein two R taken together form -OCH2O-, R1 is H, and R2 is F.
52. The method of claim 42, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, and R3 is H.
53. The method of claim 42, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
54. The method of claim 42, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
55. The method of claim 42, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
56. The method of claim 42, wherein the compound is represented by formula Ha:
Figure imgf000336_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
57. The method of claim 56, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH.
58. The method of claim 56, wherein R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH. 59. The method of claim 56, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)- CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, - CH2OCH2CH(OH)CH2OH, or -CH2OH.
60. The method of claim 42, wherein the compound is selected from Table 1. 61. The method according to claim 42, wherein said condition, disease, or disorder is selected from cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation- fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, diabetes mellitus, laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, hereditary emphysema, congenital hyperthyroidism, osteogenesis imperfecta, hereditary hypofibrinogenemia, ACT deficiency, diabetes insipidus (di), neurophyseal di, neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, spinocerebullar ataxia type I, spinal and bulbar muscular atrophy, dentatorubal pallidoluysian, and myotonic dystrophy, as well as spongiform encephalopathies, such as hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease.
62. A kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo, comprising:
(i) a first composition comprising a compound of formula II:
Figure imgf000337_0001
II wherein independently for each occurrence:
R is H, OH, OCH3 or two R taken together form -CH2CH2CH2-, -OCH2O- or -OCF2O-;
R1 is H or up to two C1-C6 alkyl;
R2 is H or F; R3 is H or CN;
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring; and
(ii) instructions for: a) contacting the composition with the biological sample; b) measuring activity of said ABC transporter or a fragment thereof.
63. The kit according to claim 62, further comprising instructions for a) contacting an additional composition with the biological sample; b) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of said first composition.
64. The kit of claim 62, wherein the kit is used to measure the density of CFTR.
65. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, and R2 is F.
66. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, and R3 is H.
67. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is H.
68. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH2N+(CH3)3.
69. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
70. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
71. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
72. The kit of claim 62, wherein two R taken together form -OCF2O-, R1 is H, R2 is F, R3 is H, and R4 and R5 taken together form a fused pyrrolidine ring.
73. The kit of claim 62, wherein two R taken together form -OCH2O-, R1 is H, and R2 is F.
74. The kit of claim 62, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, and R3 is H.
75. The kit of claim 62, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is -CH2CH(OH)CH2OH.
76. The kit of claim 62, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (R)-CH2CH(OH)CH2OH.
77. The kit of claim 62, wherein two R taken together form -OCH2O-, R1 is H, R2 is F, R3 is H, and R4 is (S)-CH2CH(OH)CH2OH.
78. The kit of claim 62, wherein the compound is represented by formula Ua:
Figure imgf000339_0001
Ha or a pharmaceutically acceptable salt thereof, wherein:
R4 is H, -CH2CH(OH)CH2OH, -CH2CH2N+(CH3)3, or -CH2CH2OH; and
R5 is H, OH, -CH2OCH2CH(OH)CH2OH, -CH2OH, or R4 and R5 taken together form a fused pyrrolidine ring.
79. The kit of claim 78, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)-CH2CH(OH)CH2OH, - CH2CH2N+(CH3)3, or -CH2CH2OH.
80. The kit of claim 78, wherein R5 is OH, -CH2OCH2CH(OH)CH2OH, or -CH2OH.
81. The kit of claim 78, wherein R4 is (R)-CH2CH(OH)CH2OH, (S)-CH2CH(OH)CH2OH, CH2CH2N+(CH3)3, or -CH2CH2OH; and R5 is OH, -CH2OCH2CH(OH)CH2OH, or - CH2OH.
82. The kit of claim 62, wherein the compound is selected from Table 1.
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