WO2005016000A1 - Derivatives of cyclic quinone and uses thereof - Google Patents
Derivatives of cyclic quinone and uses thereof Download PDFInfo
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- WO2005016000A1 WO2005016000A1 PCT/US2004/025038 US2004025038W WO2005016000A1 WO 2005016000 A1 WO2005016000 A1 WO 2005016000A1 US 2004025038 W US2004025038 W US 2004025038W WO 2005016000 A1 WO2005016000 A1 WO 2005016000A1
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- Prior art keywords
- compound
- substituted
- unsubstituted
- alkyl
- independently
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- 125000004122 cyclic group Chemical group 0.000 title claims description 16
- AZQWKYJCGOJGHM-UHFFFAOYSA-N 1,4-benzoquinone Chemical compound O=C1C=CC(=O)C=C1 AZQWKYJCGOJGHM-UHFFFAOYSA-N 0.000 title description 4
- 230000014509 gene expression Effects 0.000 claims abstract description 52
- 238000000034 method Methods 0.000 claims abstract description 52
- 150000003839 salts Chemical class 0.000 claims abstract description 28
- 206010028980 Neoplasm Diseases 0.000 claims abstract description 27
- 201000011510 cancer Diseases 0.000 claims abstract description 24
- 239000003795 chemical substances by application Substances 0.000 claims abstract description 16
- 108090000623 proteins and genes Proteins 0.000 claims description 143
- 150000001875 compounds Chemical class 0.000 claims description 139
- 125000000217 alkyl group Chemical group 0.000 claims description 68
- 125000005842 heteroatom Chemical group 0.000 claims description 35
- 229910052760 oxygen Inorganic materials 0.000 claims description 35
- 125000004432 carbon atom Chemical group C* 0.000 claims description 31
- 108091033319 polynucleotide Proteins 0.000 claims description 31
- 102000040430 polynucleotide Human genes 0.000 claims description 31
- 239000002157 polynucleotide Substances 0.000 claims description 31
- 229910052717 sulfur Inorganic materials 0.000 claims description 30
- 125000003118 aryl group Chemical group 0.000 claims description 28
- 125000000753 cycloalkyl group Chemical group 0.000 claims description 28
- 125000002950 monocyclic group Chemical group 0.000 claims description 23
- 229910052739 hydrogen Inorganic materials 0.000 claims description 22
- 239000001257 hydrogen Substances 0.000 claims description 22
- 125000001072 heteroaryl group Chemical group 0.000 claims description 21
- 230000008859 change Effects 0.000 claims description 20
- 125000004404 heteroalkyl group Chemical group 0.000 claims description 20
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 claims description 18
- 125000002619 bicyclic group Chemical group 0.000 claims description 17
- 125000000592 heterocycloalkyl group Chemical group 0.000 claims description 16
- 239000000203 mixture Substances 0.000 claims description 16
- 125000003545 alkoxy group Chemical group 0.000 claims description 14
- 125000001997 phenyl group Chemical group [H]C1=C([H])C([H])=C(*)C([H])=C1[H] 0.000 claims description 14
- 238000012360 testing method Methods 0.000 claims description 14
- 206010009944 Colon cancer Diseases 0.000 claims description 13
- 208000029742 colonic neoplasm Diseases 0.000 claims description 13
- 229910052757 nitrogen Inorganic materials 0.000 claims description 12
- 201000010099 disease Diseases 0.000 claims description 11
- 230000000694 effects Effects 0.000 claims description 11
- 125000002887 hydroxy group Chemical group [H]O* 0.000 claims description 11
- 229910052736 halogen Inorganic materials 0.000 claims description 10
- 150000002367 halogens Chemical class 0.000 claims description 10
- 229920001184 polypeptide Polymers 0.000 claims description 10
- 108090000765 processed proteins & peptides Proteins 0.000 claims description 10
- 102000004196 processed proteins & peptides Human genes 0.000 claims description 10
- IJGRMHOSHXDMSA-UHFFFAOYSA-N Atomic nitrogen Chemical compound N#N IJGRMHOSHXDMSA-UHFFFAOYSA-N 0.000 claims description 8
- 125000002877 alkyl aryl group Chemical group 0.000 claims description 8
- 125000003710 aryl alkyl group Chemical group 0.000 claims description 8
- 125000005309 thioalkoxy group Chemical group 0.000 claims description 8
- 125000003396 thiol group Chemical group [H]S* 0.000 claims description 8
- 241000124008 Mammalia Species 0.000 claims description 7
- 208000035475 disorder Diseases 0.000 claims description 7
- 230000001965 increasing effect Effects 0.000 claims description 7
- 208000009956 adenocarcinoma Diseases 0.000 claims description 6
- 230000003247 decreasing effect Effects 0.000 claims description 6
- 239000001301 oxygen Substances 0.000 claims description 6
- 239000004215 Carbon black (E152) Substances 0.000 claims description 5
- 229930195733 hydrocarbon Natural products 0.000 claims description 5
- 150000002430 hydrocarbons Chemical class 0.000 claims description 5
- 238000006467 substitution reaction Methods 0.000 claims description 5
- VQKFNUFAXTZWDK-UHFFFAOYSA-N 2-Methylfuran Chemical compound CC1=CC=CO1 VQKFNUFAXTZWDK-UHFFFAOYSA-N 0.000 claims description 4
- NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical compound [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 claims description 4
- 239000003937 drug carrier Substances 0.000 claims description 4
- 125000004446 heteroarylalkyl group Chemical group 0.000 claims description 4
- 125000003367 polycyclic group Chemical group 0.000 claims description 4
- 125000006413 ring segment Chemical group 0.000 claims description 4
- 239000011593 sulfur Substances 0.000 claims description 4
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 claims description 3
- OXHNLMTVIGZXSG-UHFFFAOYSA-N 1-Methylpyrrole Chemical compound CN1C=CC=C1 OXHNLMTVIGZXSG-UHFFFAOYSA-N 0.000 claims description 2
- VPUAYOJTHRDUTK-UHFFFAOYSA-N 1-ethylpyrrole Chemical compound CCN1C=CC=C1 VPUAYOJTHRDUTK-UHFFFAOYSA-N 0.000 claims description 2
- HLPIHRDZBHXTFJ-UHFFFAOYSA-N 2-ethylfuran Chemical compound CCC1=CC=CO1 HLPIHRDZBHXTFJ-UHFFFAOYSA-N 0.000 claims description 2
- GAWIXWVDTYZWAW-UHFFFAOYSA-N C[CH]O Chemical group C[CH]O GAWIXWVDTYZWAW-UHFFFAOYSA-N 0.000 claims description 2
- 208000024172 Cardiovascular disease Diseases 0.000 claims description 2
- 206010061218 Inflammation Diseases 0.000 claims description 2
- 206010027476 Metastases Diseases 0.000 claims description 2
- 208000001132 Osteoporosis Diseases 0.000 claims description 2
- 125000004848 alkoxyethyl group Chemical group 0.000 claims description 2
- 206010003246 arthritis Diseases 0.000 claims description 2
- 125000001797 benzyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C([H])([H])* 0.000 claims description 2
- 230000004054 inflammatory process Effects 0.000 claims description 2
- 230000009401 metastasis Effects 0.000 claims description 2
- 208000028169 periodontal disease Diseases 0.000 claims description 2
- 230000002265 prevention Effects 0.000 claims description 2
- 208000017520 skin disease Diseases 0.000 claims description 2
- 238000013518 transcription Methods 0.000 claims description 2
- 230000035897 transcription Effects 0.000 claims description 2
- 230000004614 tumor growth Effects 0.000 claims description 2
- 150000002431 hydrogen Chemical class 0.000 claims 10
- 239000003814 drug Substances 0.000 abstract description 7
- 239000004480 active ingredient Substances 0.000 abstract description 4
- 229940124597 therapeutic agent Drugs 0.000 abstract description 4
- 239000008194 pharmaceutical composition Substances 0.000 abstract description 3
- 230000001413 cellular effect Effects 0.000 abstract description 2
- 239000013043 chemical agent Substances 0.000 abstract description 2
- 150000004053 quinones Chemical class 0.000 abstract description 2
- 210000004027 cell Anatomy 0.000 description 54
- -1 small molecule compounds Chemical class 0.000 description 33
- WYURNTSHIVDZCO-UHFFFAOYSA-N Tetrahydrofuran Chemical compound C1CCOC1 WYURNTSHIVDZCO-UHFFFAOYSA-N 0.000 description 18
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 13
- 125000004429 atom Chemical group 0.000 description 13
- XEKOWRVHYACXOJ-UHFFFAOYSA-N Ethyl acetate Chemical compound CCOC(C)=O XEKOWRVHYACXOJ-UHFFFAOYSA-N 0.000 description 12
- 125000001188 haloalkyl group Chemical group 0.000 description 11
- 230000008569 process Effects 0.000 description 11
- 229910052799 carbon Inorganic materials 0.000 description 10
- 238000006243 chemical reaction Methods 0.000 description 10
- 125000004435 hydrogen atom Chemical class [H]* 0.000 description 10
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 description 9
- YMWUJEATGCHHMB-UHFFFAOYSA-N Dichloromethane Chemical compound ClCCl YMWUJEATGCHHMB-UHFFFAOYSA-N 0.000 description 9
- 125000005843 halogen group Chemical group 0.000 description 9
- RTZKZFJDLAIYFH-UHFFFAOYSA-N Diethyl ether Chemical compound CCOCC RTZKZFJDLAIYFH-UHFFFAOYSA-N 0.000 description 8
- 125000004104 aryloxy group Chemical group 0.000 description 8
- VLKZOEOYAKHREP-UHFFFAOYSA-N n-Hexane Chemical class CCCCCC VLKZOEOYAKHREP-UHFFFAOYSA-N 0.000 description 8
- 239000000047 product Substances 0.000 description 8
- 239000007787 solid Substances 0.000 description 8
- 125000001424 substituent group Chemical group 0.000 description 8
- 150000001336 alkenes Chemical class 0.000 description 7
- 125000003368 amide group Chemical group 0.000 description 7
- 125000005553 heteroaryloxy group Chemical group 0.000 description 7
- 230000001105 regulatory effect Effects 0.000 description 7
- 239000002904 solvent Substances 0.000 description 7
- IAZDPXIOMUYVGZ-UHFFFAOYSA-N Dimethylsulphoxide Chemical compound CS(C)=O IAZDPXIOMUYVGZ-UHFFFAOYSA-N 0.000 description 6
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 6
- 125000004442 acylamino group Chemical group 0.000 description 6
- 229940125904 compound 1 Drugs 0.000 description 6
- 125000001183 hydrocarbyl group Chemical group 0.000 description 6
- 239000007858 starting material Substances 0.000 description 6
- 150000001345 alkine derivatives Chemical class 0.000 description 5
- 125000001153 fluoro group Chemical group F* 0.000 description 5
- 230000001225 therapeutic effect Effects 0.000 description 5
- 125000002023 trifluoromethyl group Chemical group FC(F)(F)* 0.000 description 5
- 0 *C(C(*1*)=O)N(*)C(C(C2=C3*=*I=*2)=O)=C1C3=O Chemical compound *C(C(*1*)=O)N(*)C(C(C2=C3*=*I=*2)=O)=C1C3=O 0.000 description 4
- 229930194542 Keto Natural products 0.000 description 4
- 239000002246 antineoplastic agent Substances 0.000 description 4
- 125000006580 bicyclic heterocycloalkyl group Chemical group 0.000 description 4
- 239000011203 carbon fibre reinforced carbon Substances 0.000 description 4
- 125000001309 chloro group Chemical group Cl* 0.000 description 4
- 230000000295 complement effect Effects 0.000 description 4
- 239000002299 complementary DNA Substances 0.000 description 4
- JNGZXGGOCLZBFB-IVCQMTBJSA-N compound E Chemical compound N([C@@H](C)C(=O)N[C@@H]1C(N(C)C2=CC=CC=C2C(C=2C=CC=CC=2)=N1)=O)C(=O)CC1=CC(F)=CC(F)=C1 JNGZXGGOCLZBFB-IVCQMTBJSA-N 0.000 description 4
- 125000000468 ketone group Chemical group 0.000 description 4
- 238000002360 preparation method Methods 0.000 description 4
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 4
- 229920006395 saturated elastomer Polymers 0.000 description 4
- 238000012216 screening Methods 0.000 description 4
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 4
- 102000040650 (ribonucleotides)n+m Human genes 0.000 description 3
- RYHBNJHYFVUHQT-UHFFFAOYSA-N 1,4-Dioxane Chemical compound C1COCCO1 RYHBNJHYFVUHQT-UHFFFAOYSA-N 0.000 description 3
- QTBSBXVTEAMEQO-UHFFFAOYSA-N Acetic acid Chemical compound CC(O)=O QTBSBXVTEAMEQO-UHFFFAOYSA-N 0.000 description 3
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 3
- PEDCQBHIVMGVHV-UHFFFAOYSA-N Glycerine Chemical compound OCC(O)CO PEDCQBHIVMGVHV-UHFFFAOYSA-N 0.000 description 3
- OKKJLVBELUTLKV-UHFFFAOYSA-N Methanol Chemical compound OC OKKJLVBELUTLKV-UHFFFAOYSA-N 0.000 description 3
- ZMXDDKWLCZADIW-UHFFFAOYSA-N N,N-Dimethylformamide Chemical compound CN(C)C=O ZMXDDKWLCZADIW-UHFFFAOYSA-N 0.000 description 3
- 125000002252 acyl group Chemical group 0.000 description 3
- 150000001412 amines Chemical class 0.000 description 3
- 125000004093 cyano group Chemical group *C#N 0.000 description 3
- 238000010353 genetic engineering Methods 0.000 description 3
- 108020004999 messenger RNA Proteins 0.000 description 3
- 125000006239 protecting group Chemical group 0.000 description 3
- 102000004169 proteins and genes Human genes 0.000 description 3
- 239000000126 substance Substances 0.000 description 3
- 125000005323 thioketone group Chemical group 0.000 description 3
- FRASJONUBLZVQX-UHFFFAOYSA-N 1,4-dioxonaphthalene Natural products C1=CC=C2C(=O)C=CC(=O)C2=C1 FRASJONUBLZVQX-UHFFFAOYSA-N 0.000 description 2
- 238000001644 13C nuclear magnetic resonance spectroscopy Methods 0.000 description 2
- 238000005160 1H NMR spectroscopy Methods 0.000 description 2
- IUVCFHHAEHNCFT-INIZCTEOSA-N 2-[(1s)-1-[4-amino-3-(3-fluoro-4-propan-2-yloxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-6-fluoro-3-(3-fluorophenyl)chromen-4-one Chemical compound C1=C(F)C(OC(C)C)=CC=C1C(C1=C(N)N=CN=C11)=NN1[C@@H](C)C1=C(C=2C=C(F)C=CC=2)C(=O)C2=CC(F)=CC=C2O1 IUVCFHHAEHNCFT-INIZCTEOSA-N 0.000 description 2
- VOILDFZXZBSUTR-UHFFFAOYSA-N 2-chloro-3-(methylamino)naphthalene-1,4-dione Chemical compound C1=CC=C2C(=O)C(NC)=C(Cl)C(=O)C2=C1 VOILDFZXZBSUTR-UHFFFAOYSA-N 0.000 description 2
- LSBDFXRDZJMBSC-UHFFFAOYSA-N 2-phenylacetamide Chemical compound NC(=O)CC1=CC=CC=C1 LSBDFXRDZJMBSC-UHFFFAOYSA-N 0.000 description 2
- 108700028369 Alleles Proteins 0.000 description 2
- 229940126062 Compound A Drugs 0.000 description 2
- NLDMNSXOCDLTTB-UHFFFAOYSA-N Heterophylliin A Natural products O1C2COC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC2C(OC(=O)C=2C=C(O)C(O)=C(O)C=2)C(O)C1OC(=O)C1=CC(O)=C(O)C(O)=C1 NLDMNSXOCDLTTB-UHFFFAOYSA-N 0.000 description 2
- BAVYZALUXZFZLV-UHFFFAOYSA-N Methylamine Chemical compound NC BAVYZALUXZFZLV-UHFFFAOYSA-N 0.000 description 2
- JGFZNNIVVJXRND-UHFFFAOYSA-N N,N-Diisopropylethylamine (DIPEA) Chemical compound CCN(C(C)C)C(C)C JGFZNNIVVJXRND-UHFFFAOYSA-N 0.000 description 2
- 108700026244 Open Reading Frames Proteins 0.000 description 2
- GLUUGHFHXGJENI-UHFFFAOYSA-N Piperazine Chemical compound C1CNCCN1 GLUUGHFHXGJENI-UHFFFAOYSA-N 0.000 description 2
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 description 2
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- 125000004423 acyloxy group Chemical group 0.000 description 2
- 125000003275 alpha amino acid group Chemical group 0.000 description 2
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- 230000004071 biological effect Effects 0.000 description 2
- 125000001246 bromo group Chemical group Br* 0.000 description 2
- 125000003178 carboxy group Chemical group [H]OC(*)=O 0.000 description 2
- 150000001732 carboxylic acid derivatives Chemical class 0.000 description 2
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- HTFFABIIOAKIBH-UHFFFAOYSA-N diazinane Chemical compound C1CCNNC1 HTFFABIIOAKIBH-UHFFFAOYSA-N 0.000 description 2
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- BDAGIHXWWSANSR-UHFFFAOYSA-N methanoic acid Natural products OC=O BDAGIHXWWSANSR-UHFFFAOYSA-N 0.000 description 2
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- 125000000951 phenoxy group Chemical group [H]C1=C([H])C([H])=C(O*)C([H])=C1[H] 0.000 description 2
- BWHMMNNQKKPAPP-UHFFFAOYSA-L potassium carbonate Chemical compound [K+].[K+].[O-]C([O-])=O BWHMMNNQKKPAPP-UHFFFAOYSA-L 0.000 description 2
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- LVTJOONKWUXEFR-FZRMHRINSA-N protoneodioscin Natural products O(C[C@@H](CC[C@]1(O)[C@H](C)[C@@H]2[C@]3(C)[C@H]([C@H]4[C@@H]([C@]5(C)C(=CC4)C[C@@H](O[C@@H]4[C@H](O[C@H]6[C@@H](O)[C@@H](O)[C@@H](O)[C@H](C)O6)[C@@H](O)[C@H](O[C@H]6[C@@H](O)[C@@H](O)[C@@H](O)[C@H](C)O6)[C@H](CO)O4)CC5)CC3)C[C@@H]2O1)C)[C@H]1[C@H](O)[C@H](O)[C@H](O)[C@@H](CO)O1 LVTJOONKWUXEFR-FZRMHRINSA-N 0.000 description 2
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- CSNIZNHTOVFARY-UHFFFAOYSA-N 1,2-benzothiazole Chemical compound C1=CC=C2C=NSC2=C1 CSNIZNHTOVFARY-UHFFFAOYSA-N 0.000 description 1
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- VEPOHXYIFQMVHW-XOZOLZJESA-N 2,3-dihydroxybutanedioic acid (2S,3S)-3,4-dimethyl-2-phenylmorpholine Chemical compound OC(C(O)C(O)=O)C(O)=O.C[C@H]1[C@@H](OCCN1C)c1ccccc1 VEPOHXYIFQMVHW-XOZOLZJESA-N 0.000 description 1
- NGNBDVOYPDDBFK-UHFFFAOYSA-N 2-[2,4-di(pentan-2-yl)phenoxy]acetyl chloride Chemical compound CCCC(C)C1=CC=C(OCC(Cl)=O)C(C(C)CCC)=C1 NGNBDVOYPDDBFK-UHFFFAOYSA-N 0.000 description 1
- QXHJDVTUOFNBDR-UHFFFAOYSA-N 2-bromo-n-(3-chloro-1,4-dioxonaphthalen-2-yl)-n-methylpropanamide Chemical compound C1=CC=C2C(=O)C(N(C)C(=O)C(Br)C)=C(Cl)C(=O)C2=C1 QXHJDVTUOFNBDR-UHFFFAOYSA-N 0.000 description 1
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- DIQZCOIKLUEXFY-UHFFFAOYSA-N 4-[2-(dimethylamino)ethyl]-1-methyl-2-phenyl-2h-benzo[g]quinoxaline-3,5,10-trione Chemical compound CN1C(C(C2=CC=CC=C2C2=O)=O)=C2N(CCN(C)C)C(=O)C1C1=CC=CC=C1 DIQZCOIKLUEXFY-UHFFFAOYSA-N 0.000 description 1
- MERYDEMFYWCABH-UHFFFAOYSA-N 4-[2-(dimethylamino)ethyl]-1-methyl-3-phenyl-3H-benzo[g]quinoxaline-2,5,10-trione Chemical compound CN(C)CCN1C(C(=O)N(C)C2=C1C(=O)c1ccccc1C2=O)c1ccccc1 MERYDEMFYWCABH-UHFFFAOYSA-N 0.000 description 1
- UFTHEDBYLPFRDP-UHFFFAOYSA-N 5,6-dihydro-2h-oxazine Chemical compound C1CC=CNO1 UFTHEDBYLPFRDP-UHFFFAOYSA-N 0.000 description 1
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- XJPQCGZMDOXKRK-UHFFFAOYSA-N 7h-purine;quinoline Chemical compound C1=NC=C2NC=NC2=N1.N1=CC=CC2=CC=CC=C21 XJPQCGZMDOXKRK-UHFFFAOYSA-N 0.000 description 1
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- GWVMLCQWXVFZCN-UHFFFAOYSA-N C1NCc2ccccc12 Chemical compound C1NCc2ccccc12 GWVMLCQWXVFZCN-UHFFFAOYSA-N 0.000 description 1
- JBYHSSAVUBIJMK-UHFFFAOYSA-N C1OCCSC1 Chemical compound C1OCCSC1 JBYHSSAVUBIJMK-UHFFFAOYSA-N 0.000 description 1
- LOZWAPSEEHRYPG-UHFFFAOYSA-N C1SCCSC1 Chemical compound C1SCCSC1 LOZWAPSEEHRYPG-UHFFFAOYSA-N 0.000 description 1
- OYPRJOBELJOOCE-UHFFFAOYSA-N Calcium Chemical compound [Ca] OYPRJOBELJOOCE-UHFFFAOYSA-N 0.000 description 1
- VGCXGMAHQTYDJK-UHFFFAOYSA-N Chloroacetyl chloride Chemical compound ClCC(Cl)=O VGCXGMAHQTYDJK-UHFFFAOYSA-N 0.000 description 1
- 108020004635 Complementary DNA Proteins 0.000 description 1
- 102000004127 Cytokines Human genes 0.000 description 1
- 108090000695 Cytokines Proteins 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- DGAQECJNVWCQMB-PUAWFVPOSA-M Ilexoside XXIX Chemical compound C[C@@H]1CC[C@@]2(CC[C@@]3(C(=CC[C@H]4[C@]3(CC[C@@H]5[C@@]4(CC[C@@H](C5(C)C)OS(=O)(=O)[O-])C)C)[C@@H]2[C@]1(C)O)C)C(=O)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O.[Na+] DGAQECJNVWCQMB-PUAWFVPOSA-M 0.000 description 1
- FYYHWMGAXLPEAU-UHFFFAOYSA-N Magnesium Chemical compound [Mg] FYYHWMGAXLPEAU-UHFFFAOYSA-N 0.000 description 1
- XVBNFGXVURAEFY-UHFFFAOYSA-N N1=CC=NC2=CC=CC=C12.N1=CN=CC2=CC=CC=C12.C1=NN=CC2=CC=CC=C12.N1=NC=CC2=CC=CC=C12.C1=NC=CC2=CC=CC=C12 Chemical compound N1=CC=NC2=CC=CC=C12.N1=CN=CC2=CC=CC=C12.C1=NN=CC2=CC=CC=C12.N1=NC=CC2=CC=CC=C12.C1=NC=CC2=CC=CC=C12 XVBNFGXVURAEFY-UHFFFAOYSA-N 0.000 description 1
- YOIXBGPEZCGDHL-UHFFFAOYSA-N N1N=NN=C1.N1N=CN=C1.N1N=NC2=C1C=CC=C2 Chemical compound N1N=NN=C1.N1N=CN=C1.N1N=NC2=C1C=CC=C2 YOIXBGPEZCGDHL-UHFFFAOYSA-N 0.000 description 1
- 108091028043 Nucleic acid sequence Proteins 0.000 description 1
- PLBJUYMKNCQQKL-UHFFFAOYSA-N O1NCC=C1.O1N=CCC1.S1CSCC1.S1SCCC1.O1COCC1 Chemical compound O1NCC=C1.O1N=CCC1.S1CSCC1.S1SCCC1.O1COCC1 PLBJUYMKNCQQKL-UHFFFAOYSA-N 0.000 description 1
- 102000043276 Oncogene Human genes 0.000 description 1
- 108700020796 Oncogene Proteins 0.000 description 1
- ZCQWOFVYLHDMMC-UHFFFAOYSA-N Oxazole Chemical compound C1=COC=N1 ZCQWOFVYLHDMMC-UHFFFAOYSA-N 0.000 description 1
- 229910019142 PO4 Inorganic materials 0.000 description 1
- PCNDJXKNXGMECE-UHFFFAOYSA-N Phenazine Natural products C1=CC=CC2=NC3=CC=CC=C3N=C21 PCNDJXKNXGMECE-UHFFFAOYSA-N 0.000 description 1
- ZLMJMSJWJFRBEC-UHFFFAOYSA-N Potassium Chemical compound [K] ZLMJMSJWJFRBEC-UHFFFAOYSA-N 0.000 description 1
- KAESVJOAVNADME-UHFFFAOYSA-N Pyrrole Chemical compound C=1C=CNC=1 KAESVJOAVNADME-UHFFFAOYSA-N 0.000 description 1
- OBLNWSCLAYSJJR-UHFFFAOYSA-N Quinoclamin Chemical compound C1=CC=C2C(=O)C(N)=C(Cl)C(=O)C2=C1 OBLNWSCLAYSJJR-UHFFFAOYSA-N 0.000 description 1
- XJGWYCOIFJZYFN-UHFFFAOYSA-N S1N=NN=C1.O1N=NN=C1.O1C=NN=C1.O1N=CN=C1 Chemical compound S1N=NN=C1.O1N=NN=C1.O1C=NN=C1.O1N=CN=C1 XJGWYCOIFJZYFN-UHFFFAOYSA-N 0.000 description 1
- FAPWRFPIFSIZLT-UHFFFAOYSA-M Sodium chloride Chemical compound [Na+].[Cl-] FAPWRFPIFSIZLT-UHFFFAOYSA-M 0.000 description 1
- 108020005038 Terminator Codon Proteins 0.000 description 1
- FZWLAAWBMGSTSO-UHFFFAOYSA-N Thiazole Chemical compound C1=CSC=N1 FZWLAAWBMGSTSO-UHFFFAOYSA-N 0.000 description 1
- 108020004566 Transfer RNA Proteins 0.000 description 1
- 125000002777 acetyl group Chemical group [H]C([H])([H])C(*)=O 0.000 description 1
- 125000003668 acetyloxy group Chemical group [H]C([H])([H])C(=O)O[*] 0.000 description 1
- 230000002378 acidificating effect Effects 0.000 description 1
- 230000004913 activation Effects 0.000 description 1
- 229910052783 alkali metal Inorganic materials 0.000 description 1
- 229910052784 alkaline earth metal Inorganic materials 0.000 description 1
- 125000003342 alkenyl group Chemical group 0.000 description 1
- 125000005336 allyloxy group Chemical group 0.000 description 1
- 150000001408 amides Chemical class 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 230000000118 anti-neoplastic effect Effects 0.000 description 1
- 125000002029 aromatic hydrocarbon group Chemical group 0.000 description 1
- 238000003556 assay Methods 0.000 description 1
- JXLPJCAIPGVFAA-UHFFFAOYSA-N azanium;acetonitrile;hydroxide Chemical compound [NH4+].[OH-].CC#N JXLPJCAIPGVFAA-UHFFFAOYSA-N 0.000 description 1
- OOZMOOPLAHIWOE-UHFFFAOYSA-N azetidine aziridine oxetane oxirane oxolane pyrrolidine Chemical compound N1CCCC1.O1CCCC1.N1CCC1.O1CCC1.N1CC1.O1CC1 OOZMOOPLAHIWOE-UHFFFAOYSA-N 0.000 description 1
- 230000008901 benefit Effects 0.000 description 1
- 125000004369 butenyl group Chemical group C(=CCC)* 0.000 description 1
- 125000000484 butyl group Chemical group [H]C([*])([H])C([H])([H])C([H])([H])C([H])([H])[H] 0.000 description 1
- YASFVAJZJPYUSK-UHFFFAOYSA-N c1cc2cc(ccc(-c(cc3)cc4c3nc(cccc3)c3n4)c3)c3nc2cc1 Chemical compound c1cc2cc(ccc(-c(cc3)cc4c3nc(cccc3)c3n4)c3)c3nc2cc1 YASFVAJZJPYUSK-UHFFFAOYSA-N 0.000 description 1
- 229910052791 calcium Inorganic materials 0.000 description 1
- 239000011575 calcium Substances 0.000 description 1
- 125000003917 carbamoyl group Chemical group [H]N([H])C(*)=O 0.000 description 1
- 150000001721 carbon Chemical group 0.000 description 1
- 125000002915 carbonyl group Chemical group [*:2]C([*:1])=O 0.000 description 1
- 150000007942 carboxylates Chemical class 0.000 description 1
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- 210000004671 cell-free system Anatomy 0.000 description 1
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- QHTOIDKCEPKVCM-ZCFIWIBFSA-N cepham Chemical compound S1CCCN2C(=O)C[C@H]21 QHTOIDKCEPKVCM-ZCFIWIBFSA-N 0.000 description 1
- 150000003841 chloride salts Chemical class 0.000 description 1
- VZWXIQHBIQLMPN-UHFFFAOYSA-N chromane Chemical compound C1=CC=C2CCCOC2=C1 VZWXIQHBIQLMPN-UHFFFAOYSA-N 0.000 description 1
- OTAFHZMPRISVEM-UHFFFAOYSA-N chromone Chemical compound C1=CC=C2C(=O)C=COC2=C1 OTAFHZMPRISVEM-UHFFFAOYSA-N 0.000 description 1
- 238000004440 column chromatography Methods 0.000 description 1
- 229940125782 compound 2 Drugs 0.000 description 1
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- 239000013078 crystal Substances 0.000 description 1
- 238000002425 crystallisation Methods 0.000 description 1
- 230000008025 crystallization Effects 0.000 description 1
- 125000000113 cyclohexyl group Chemical group [H]C1([H])C([H])([H])C([H])([H])C([H])(*)C([H])([H])C1([H])[H] 0.000 description 1
- 125000001511 cyclopentyl group Chemical group [H]C1([H])C([H])([H])C([H])([H])C([H])(*)C1([H])[H] 0.000 description 1
- 125000001559 cyclopropyl group Chemical group [H]C1([H])C([H])([H])C1([H])* 0.000 description 1
- 231100000135 cytotoxicity Toxicity 0.000 description 1
- 230000003013 cytotoxicity Effects 0.000 description 1
- 125000003963 dichloro group Chemical group Cl* 0.000 description 1
- 239000003085 diluting agent Substances 0.000 description 1
- 229940079593 drug Drugs 0.000 description 1
- 150000002085 enols Chemical class 0.000 description 1
- 125000001495 ethyl group Chemical group [H]C([H])([H])C([H])([H])* 0.000 description 1
- 230000002349 favourable effect Effects 0.000 description 1
- 230000004907 flux Effects 0.000 description 1
- 235000019253 formic acid Nutrition 0.000 description 1
- 238000009472 formulation Methods 0.000 description 1
- 125000002485 formyl group Chemical group [H]C(*)=O 0.000 description 1
- 150000004820 halides Chemical class 0.000 description 1
- 125000001475 halogen functional group Chemical group 0.000 description 1
- 238000013537 high throughput screening Methods 0.000 description 1
- 238000009396 hybridization Methods 0.000 description 1
- 238000000338 in vitro Methods 0.000 description 1
- 230000001939 inductive effect Effects 0.000 description 1
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- 125000002346 iodo group Chemical group I* 0.000 description 1
- 150000002500 ions Chemical class 0.000 description 1
- 238000002955 isolation Methods 0.000 description 1
- 125000001449 isopropyl group Chemical group [H]C([H])([H])C([H])(*)C([H])([H])[H] 0.000 description 1
- CTAPFRYPJLPFDF-UHFFFAOYSA-N isoxazole Chemical compound C=1C=NOC=1 CTAPFRYPJLPFDF-UHFFFAOYSA-N 0.000 description 1
- 239000007788 liquid Substances 0.000 description 1
- 229910052749 magnesium Inorganic materials 0.000 description 1
- 239000011777 magnesium Substances 0.000 description 1
- 238000004519 manufacturing process Methods 0.000 description 1
- 230000000873 masking effect Effects 0.000 description 1
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- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 125000006578 monocyclic heterocycloalkyl group Chemical group 0.000 description 1
- AHKJGIUKIBGOKH-UHFFFAOYSA-N morpholine;piperidine Chemical compound C1CCNCC1.C1COCCN1 AHKJGIUKIBGOKH-UHFFFAOYSA-N 0.000 description 1
- UDGSVBYJWHOHNN-UHFFFAOYSA-N n',n'-diethylethane-1,2-diamine Chemical compound CCN(CC)CCN UDGSVBYJWHOHNN-UHFFFAOYSA-N 0.000 description 1
- KFIGICHILYTCJF-UHFFFAOYSA-N n'-methylethane-1,2-diamine Chemical compound CNCCN KFIGICHILYTCJF-UHFFFAOYSA-N 0.000 description 1
- 125000001624 naphthyl group Chemical group 0.000 description 1
- 125000004433 nitrogen atom Chemical group N* 0.000 description 1
- 150000007523 nucleic acids Chemical group 0.000 description 1
- 238000005457 optimization Methods 0.000 description 1
- 210000000056 organ Anatomy 0.000 description 1
- 150000007530 organic bases Chemical class 0.000 description 1
- AICOOMRHRUFYCM-ZRRPKQBOSA-N oxazine, 1 Chemical compound C([C@@H]1[C@H](C(C[C@]2(C)[C@@H]([C@H](C)N(C)C)[C@H](O)C[C@]21C)=O)CC1=CC2)C[C@H]1[C@@]1(C)[C@H]2N=C(C(C)C)OC1 AICOOMRHRUFYCM-ZRRPKQBOSA-N 0.000 description 1
- 125000004430 oxygen atom Chemical group O* 0.000 description 1
- HHXMXAQDOUCLDN-RXMQYKEDSA-N penem Chemical compound S1C=CN2C(=O)C[C@H]21 HHXMXAQDOUCLDN-RXMQYKEDSA-N 0.000 description 1
- 239000008177 pharmaceutical agent Substances 0.000 description 1
- 235000021317 phosphate Nutrition 0.000 description 1
- 150000003013 phosphoric acid derivatives Chemical class 0.000 description 1
- 230000001766 physiological effect Effects 0.000 description 1
- 229910052700 potassium Inorganic materials 0.000 description 1
- 239000011591 potassium Substances 0.000 description 1
- 229910000027 potassium carbonate Inorganic materials 0.000 description 1
- 230000003389 potentiating effect Effects 0.000 description 1
- 229940080818 propionamide Drugs 0.000 description 1
- 125000001501 propionyl group Chemical group O=C([*])C([H])([H])C([H])([H])[H] 0.000 description 1
- 125000001436 propyl group Chemical group [H]C([*])([H])C([H])([H])C([H])([H])[H] 0.000 description 1
- 238000000746 purification Methods 0.000 description 1
- VUMMLGMLCRBQSR-UHFFFAOYSA-N pyrazine;pyridazine;pyridine;pyrimidine;1,3,5-triazine Chemical compound C1=CC=NC=C1.C1=CC=NN=C1.C1=CN=CN=C1.C1=CN=CC=N1.C1=NC=NC=N1 VUMMLGMLCRBQSR-UHFFFAOYSA-N 0.000 description 1
- 125000005554 pyridyloxy group Chemical group 0.000 description 1
- 125000003410 quininyl group Chemical group 0.000 description 1
- 125000004151 quinonyl group Chemical group 0.000 description 1
- 210000002345 respiratory system Anatomy 0.000 description 1
- 230000004044 response Effects 0.000 description 1
- 108020004418 ribosomal RNA Proteins 0.000 description 1
- 210000003705 ribosome Anatomy 0.000 description 1
- 238000007086 side reaction Methods 0.000 description 1
- 230000019491 signal transduction Effects 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 229910052708 sodium Inorganic materials 0.000 description 1
- 239000011734 sodium Substances 0.000 description 1
- 239000011780 sodium chloride Substances 0.000 description 1
- 239000012453 solvate Substances 0.000 description 1
- 239000007921 spray Substances 0.000 description 1
- 238000005556 structure-activity relationship Methods 0.000 description 1
- 125000005346 substituted cycloalkyl group Chemical group 0.000 description 1
- 150000003871 sulfonates Chemical class 0.000 description 1
- YLQBMQCUIZJEEH-UHFFFAOYSA-N tetrahydrofuran Natural products C=1C=COC=1 YLQBMQCUIZJEEH-UHFFFAOYSA-N 0.000 description 1
- 229930192474 thiophene Natural products 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 210000001519 tissue Anatomy 0.000 description 1
- 125000003944 tolyl group Chemical group 0.000 description 1
- 231100000331 toxic Toxicity 0.000 description 1
- 230000002588 toxic effect Effects 0.000 description 1
- 230000001988 toxicity Effects 0.000 description 1
- 231100000419 toxicity Toxicity 0.000 description 1
- 230000001131 transforming effect Effects 0.000 description 1
- 238000013519 translation Methods 0.000 description 1
- 210000004881 tumor cell Anatomy 0.000 description 1
- 229930195735 unsaturated hydrocarbon Natural products 0.000 description 1
- 239000003981 vehicle Substances 0.000 description 1
- 125000000391 vinyl group Chemical group [H]C([*])=C([H])[H] 0.000 description 1
- 229920002554 vinyl polymer Polymers 0.000 description 1
- 125000005023 xylyl group Chemical group 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D241/00—Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings
- C07D241/36—Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings condensed with carbocyclic rings or ring systems
- C07D241/38—Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings condensed with carbocyclic rings or ring systems with only hydrogen or carbon atoms directly attached to the ring nitrogen atoms
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
- C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
- C07D401/06—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
- C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
- C07D403/06—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
- C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
- C07D471/04—Ortho-condensed systems
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
- C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
- C07D487/04—Ortho-condensed systems
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D495/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms
- C07D495/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
- C07D495/04—Ortho-condensed systems
Definitions
- the present invention relates to chemical agents affecting levels of gene expression in cellular systems, including cancer cells.
- the present invention relates to derivatives of quinone moiety, processes for their preparation, their use as antitumor drugs and pharmaceutical compositions containing them as active ingredients.
- Screening assays for novel drugs are based on the response of model cell based systems in vitro to treatment with specific compounds.
- Various measures of cellular response have been utilized, including the release of cytokines, alterations in cell surface markers, activation of specific enzymes, as well as alterations in ion flux and/or pH.
- Some such screens rely on specific genes, such as oncogenes or tumor suppressors.
- the present invention utilizes screening of small molecule compounds as potential anticancer drugs by taking advantage of the concept that for each specific tumor type, a unique signature set of genes, that are differentially expressed in tumor cells if compared to corresponding normal cells, can be established.
- the relatively small signature set containing 10-30 genes, allows for easy, high throughput screening for compounds that can reverse the gene expression profile from patterns typical for cancer cells to patterns seen in normal cells.
- Gene expression screening and subsequent cytotoxicity screening revealed that some of the compounds possess biological activity. Consequently, detailed structure-activity relationship resulted in compounds of formula I as new small molecule agents having antineoplastic activity.
- the present invention relates to organic compounds, derivatives of quinone, that have the ability to function as gene expression modulators for genes found in cancer cells, especially genes involved in misregulated signal transduction pathways typical for colon cancer.
- the compounds disclosed herein are able to up regulate genes found to be up regulated in normal (i.e., non-cancerous) cells versus cancer cells, especially colon cancer cells, thereby producing an expression profile for said gene(s) that resembles the expression profile found in normal cells.
- the compounds disclosed herein are found to down regulate genes otherwise up- regulated in cancer cells, especially colon cancer cells, relative to normal (i.e., non-cancerous) cells thereby producing an expression profile for said gene(s) that more resembles the expression profile found in normal cells.
- the agents disclosed herein in addition to activity in modulating a particular gene that may or may not have a major role in inducing or sustaining a cancerous condition, the agents disclosed herein also find value in regulating a set of gene whose combined activity is related to a disease condition, such as cancer, especially colon cancer, including adenocarcinoma of the colon.
- the present invention relates to novel organic compounds that have the ability to function as gene modulators for genes found in normal (i.e., non-cancer) cells and which genes are found to be up regulated or down regulated in normal cells, especially colon cells.
- a disease condition such as cancer
- administration of one or more of the agents disclosed herein may succeed in preventing a cancerous condition from arising.
- the agents disclosed herein find use in combination with each other as well as with other agents, such as where a mixture of one or more of the agents of the present invention are given in combination or where one or more of the agents disclosed herein is given together with some other already known therapeutic agent, possibly as a means of potentiating the affects of such known therapeutic agent or vice versa.
- the present invention also relates to processes of preventing or treating disease conditions, especially cancer, most especially colon cancer, by administering to a subject, such as a mammal, especially a human, a therapeutically active amount of one or more of the agents disclosed herein, including where such agents are given in combination with one or more known therapeutic agents.
- Preferred acyl groups include (for example) acetyl, formyl, and propionyl.
- Alkyl is a saturated hydrocarbon chain having 1 to 15 carbon atoms, preferably 1 to 10, more preferably 1 to 4 carbon atoms.
- Alkene is a hydrocarbon chain having at least one (preferably only one) carbon-carbon double bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms.
- Alkyne is a hydrocarbon chain having at least one (preferably only one) carbon-carbon triple bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms.
- Alkyl, alkene and alkyne chains (referred to collectively as "hydrocarbon chains”) may be straight or branched and may be unsubstituted or substituted.
- Preferred branched alkyl, alkene and alkyne chains have one or two branches, preferably one branch.
- Preferred chains are alkyl.
- Alkyl, alkene and alkyne hydrocarbon chains each may be unsubstituted or substituted with from 1 to 4 substituents; when substituted, preferred chains are mono-, di-, or tri-substituted.
- Alkyl, alkene and alkyne hydrocarbon chains each may be substituted with halo, hydroxy, aryloxy (e.g., phenoxy), heteroaryloxy, acyloxy (e.g., acetoxy), carboxy, aryl (e.g., phenyl), heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, amido, acylamino, keto, thioketo, cyano, or any combination thereof.
- Preferred hydrocarbon groups include methyl, ethyl, propyl, isopropyl, butyl, vinyl, allyl, butenyl, and exomethylenyl.
- a “lower” alkyl, alkene or alkyne moiety is a chain comprised of 1 to 6, preferably from 1 to 4, carbon atoms in the case of alkyl and 2 to 6, preferably 2 to 4, carbon atoms in the case of alkene and alkyne.
- Alkoxy is an oxygen radical having a hydrocarbon chain substituent, where the hydrocarbon chain is an alkyl or alkenyl (i.e., -O-alkyl or -O- alkenyl).
- Preferred alkoxy groups include (for example) methoxy, ethoxy, propoxy and allyloxy.
- Aryl is an aromatic hydrocarbon ring.
- Aryl rings are monocyclic or fused bicyclic ring systems.
- Monocyclic aryl rings contain 6 carbon atoms in the ring.
- Monocyclic aryl rings are also referred to as phenyl rings.
- Bicyclic aryl rings contain from 8 to 17 carbon atoms, preferably 9 to 12 carbon atoms, in the ring.
- Bicyclic aryl rings include ring systems wherein one ring is aryl and the other ring is aryl, cycloalkyl, or heterocycloakyl.
- Preferred bicyclic aryl rings comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7- membered rings.
- Aryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring.
- Aryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, aryloxy, alkoxy, heteroalkyloxy, carbamyl, haloalkyl, methylenedioxy, heteroaryloxy, or any combination thereof.
- Preferred aryl rings include naphthyl, tolyl, xylyl, and phenyl. The most preferred aryl ring radical is phenyl.
- Aryloxy is an oxygen radical having an aryl substituent (i.e., -O-aryl).
- Preferred aryloxy groups include (for example) phenoxy, napthyloxy, methoxyphenoxy, and methylenedioxyphenoxy.
- Cycloalkyl is a saturated or unsaturated hydrocarbon ring. Cycloalkyl rings are not aromatic. Cycloalkyl rings are monocyclic, or are fused, spiro, or bridged bicyclic ring systems. Monocyclic cycloalkyl rings contain from about 3 to about 9 carbon atoms, preferably from 3 to 7 carbon atoms, in the ring. Bicyclic cycloalkyl rings contain from 7 to 17 carbon atoms, preferably from 7 to 12 carbon atoms, in the ring. Preferred bicyclic cycloalkyl rings comprise 4-, 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings.
- Cycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Cycloalkyl may be substituted with halo, cyano, alkyl, heteroalkyl, haloalkyl, phenyl, keto, hydroxy, carboxy, amino, acylamino, aryloxy, heteroaryloxy, or any combination thereof. Preferred cycloalkyl rings include cyclopropyl, cyclopentyl, and cyclohexyl.
- Halo or "halogen” is fluoro, chloro, bromo or iodo. Preferred halo are fluoro, chloro and bromo; more preferred typically are chloro and fluoro, especially fluoro.
- Haloalkyl is a straight, branched, or cyclic hydrocarbon substituted with one or more halo substituents. Preferred are C1-C12 haloalkyls; more preferred are C-i-C ⁇ haloalkyls; still more preferred still are C1-C3 haloalkyls.
- Preferred halo substituents are fluoro and chloro.
- the most preferred haloalkyl is trifluoromethyl.
- Heteroatom is a nitrogen, sulfur, or oxygen atom. Groups containing more than one heteroatom may contain different heteroatoms.
- Heteroalkyl is a saturated or unsaturated chain containing carbon and at least one heteroatom, wherein no two heteroatoms are adjacent. Heteroalkyl chains contain from 2 to 15 member atoms (carbon and heteroatoms) in the chain, preferably 2 to 10, more preferably 2 to 5. For example, alkoxy (i.e., -O-alkyl or -O-heteroalkyl) radicals are included in heteroalkyl. Heteroalkyl chains may be straight or branched. Preferred branched heteroalkyl have one or two branches, preferably one branch.
- Preferred heteroalkyl are saturated. Unsaturated heteroalkyl have one or more carbon-carbon double bonds and/or one or more carbon-carbon triple bonds. Preferred unsaturated heteroalkyls have one or two double bonds or one triple bond, more preferably one double bond. Heteroalkyl chains may be unsubstituted or substituted with from 1 to 4 substituents. Preferred substituted heteroalkyl are mono-, di-, or tri-substituted.
- Heteroalkyl may be substituted with lower alkyl, haloalkyl, halo, hydroxy, aryloxy, heteroaryloxy, acyloxy, carboxy, monocyclic aryl, heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, acylamino, amido, keto, thioketo, cyano, or any combination thereof.
- Heteroaryl is an aromatic ring containing carbon atoms and from 1 to about 6 heteroatoms in the ring. Heteroaryl rings are monocyclic or fused bicyclic ring systems. Monocyclic heteroaryl rings contain from about 5 to about 9 member atoms (carbon and heteroatoms), preferably 5 or 6 member atoms, in the ring. Bicyclic heteroaryl rings contain from 8 to 17 member atoms, preferably 8 to 12 member atoms, in the ring. Bicyclic heteroaryl rings include ring systems wherein one ring is heteroaryl and the other ring is aryl, heteroaryl, cycloalkyl, or heterocycloalkyl.
- Preferred bicyclic heteroaryl ring systems comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings.
- Heteroaryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring.
- Heteroaryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy, heteroaryloxy, or any combination thereof.
- Preferred heteroaryl rings include, but are not limited to, the following:
- Heteroaryloxy is an oxygen radical having a heteroaryl substituent
- heteroaryloxy groups include (for example) pyridyloxy, furanyloxy, (thiophene)oxy, (oxazole)oxy, (thiazole)oxy, (isoxazole)oxy, pyrmidinyloxy, pyrazinyloxy, and benzothiazolyloxy.
- Heterocycloalkyl is a saturated or unsaturated ring containing carbon atoms and from 1 to about 4 (preferably 1 to 3) heteroatoms in the ring. Heterocycloalkyl rings are not aromatic. Heterocycloalkyl rings are monocyclic, or are fused, bridged, or spiro bicyclic ring systems.
- Monocyclic heterocycloalkyl rings contain from about 3 to about 9 member atoms (carbon and heteroatoms), preferably from 5 to 7 member atoms, in the ring.
- Bicyclic heterocycloalkyl rings contain from 7 to 17 member atoms, preferably 7 to 12 member atoms, in the ring.
- Bicyclic heterocycloalkyl rings contain from about 7 to about 17 ring atoms, preferably from 7 to 12 ring atoms.
- Bicyclic heterocycloalkyl rings may be fused, spiro, or bridged ring systems.
- Preferred bicyclic heterocycloalkyl rings comprise 5-, 6- or 7- membered rings fused to 5-, 6-, or 7-membered rings.
- Heterocycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring.
- Heterocycloalkyl may be substituted with halo, cyano, hydroxy, carboxy, keto, thioketo, amino, acylamino, acyl, amido, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy or any combination thereof.
- Preferred substituents on heterocycloalkyl include halo and haloalkyl.
- Preferred heterocycloalkyl rings include, but are not limited to, the following: Oxirane Aziridine Oxetane Azetidine Tetrahydrofuran Pyrrolidine 3H-lndole 1 ,3-Dioxolane 1,2-Dithiolane 1,3-Dithiolane 4,5-Dihydroisoxazole 2,3-Dihydroisoxazole
- alkyl, heteroalkyl, cycloalkyl, and heterocycloalkyl groups may be substituted with hydroxy, amino, and amido groups as stated above, the following are not envisioned in the invention: Enols (OH attached to a carbon bearing a double bond).
- More than one hydroxy, amino, or amido attached to a single carbon except where two nitrogen atoms are attached to a single carbon atom and all three atoms are member atoms within a heterocycloalkyl ring).
- a "pharmaceutically-acceptable salt” is a cationic salt formed at any acidic (e.g., carboxylic acid) group, or an anionic salt formed at any basic (e.g., amino) group. Many such salts are known in the art, as described in World Patent Publication 87/05297, Johnston et al., published September 11, 1987 incorporated by reference herein.
- Preferred cationic salts include the alkali metal salts (such as sodium and potassium), and alkaline earth metal salts (such as magnesium and calcium) and organic salts.
- Preferred anionic salts include the halides (such as chloride salts), sulfonates, carboxylates, phosphates, and the like.
- Such salts are well understood by the skilled artisan, and the skilled artisan is able to prepare any number of salts given the knowledge in the art. Furthermore, it is recognized that the skilled artisan may prefer one salt over another for reasons of solubility, stability, formulation ease and the like. Determination and optimization of such salts is within the purview of the skilled artisan's practice.
- a “solvate” is a complex formed by the combination of a solute (e.g., a metalloprotease inhibitor) and a solvent (e.g., water).
- a solute e.g., a metalloprotease inhibitor
- a solvent e.g., water
- Pharmaceutically-acceptable solvents used according to this invention include those that do not interfere with the biological activity of the metalloprotease inhibitor (e.g., water, ethanol, acetic acid, N,N- dimethylformamide and others known or readily determined by the skilled artisan).
- optical isomer “optical isomer”, “stereoisomer”, and “diastereomer” have the accepted meanings (see, e.g., Hawlev's Condensed Chemical Dictionary. 11th Ed.).
- the illustration of specific protected forms and other derivatives of the compounds of the instant invention is not intended to be limiting.
- the application of other useful protecting groups, salt forms, etc. is within the ability of the skilled artisan.
- the present invention relates to a compound having the structure of Formula (I)
- W, X, Y and Z are each independently selected from a bond (meaning that said group or substituent is not present), C-R 4 , C-R 5 , C-R 6 C-R 7 , O (oxygen), N (nitrogen) or S (sulfur) and that no more than two W, X, Y and Z are O, N and S; wherein, R 4 , R 5 , R 6 , and R 7 each independently hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF 3 , NO 2 , COOR ⁇ , CONR 8 R 9 , NR 8 R 9 , NR 8 COR 9 , NR 8 SO 2 R 9 , NR 8 CONR 9 R ⁇ 0 ; wherein R 8 , R 9 and Rio are independently hydrogen, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl
- Ri and R 3 are also independently selected from:
- n 2, 3, 4 and Rn, R 12 , R 1 3 and R ⁇ 4 are independently selected from hydrogen, alkyl, cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted heteroaryl, unsubstituted or substituted alkylaryl;
- NR 1 3R 14 is also unsubstituted, or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R 1 3 can be connected together to form 4, 5,6 or 7-member cyclic ring system;
- R 2 is also selected from:
- n 0, 1, 2 and 3 and Rn, R12, R 1 3 and R14 are independently selected from hydrogen, alkyl, unsubstituted or substituted cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted alkaryl ;
- NR- 13 R 14 is also unsubstituted or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R 13 can be connected together to form 4, 5, 6 or 7 member ring system provided n is 1, 2, and 3; including salts thereof.
- the present invention includes compounds of Formula I wherein: W, X, Y and Z are each independently selected from a bond, C-R 4 , C- R 5 , C-R 6 C-R 7 , O (oxygen), N (nitrogen) or S (sulfur) and that no more than two of W, X, Y and Z are O, N and S; wherein, R 4 , R 5 , R 6 , and R 7 each independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF 3 , NO 2 , COOR 8 , CONR 8 R 9 , NR 8 R 9 , NR 8 COR 9 , NR 8 S0 2 R 9 , NR 8 CONR 9 R ⁇ o; wherein R 8 , R 9 and R10 are independently hydrogen, alkyl, H, alkyl, heteroalky
- Ri and R 3 are also independently selected from:
- n 2, 3, 4, 5, 6 and R 11 ( R 12 , R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, heteroaryl, alkylaryl from 7 to 10 carbon atoms; NR13R14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R13 can be connected together to form 4, 5,6 or 7-member cyclic ring system;
- R2 is also selected from:
- n 0, 1, 2 , 3, 4, 5 and Rn, R 1 2, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, alkaryl from 7 to 10 carbon atoms; NR 13 R 14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R 13 can be connected together to form 4, 5,6 or 7 member ring system provided n is 1 , 2, and 3; including salts thereof.
- W and Z are each independently C-R 4 , C-R 7 or N while X and Y are each independently C-R5 or C-R6.
- W is C-R 4 or N and X, Y and Z are each independently C-R5, C-R ⁇ or C-R .
- Z is C-R , C-R 5 , C-R or N and W and Y are each independently C-R 4 , C-R 6 or C-R 7 .
- the compounds of the present invention include compounds of Formula I wherein X and Y are each independently C-R 5 , C-R 6 or N and wherein W and Z are each independently C-R4 or C-R 5 .
- X is C-R 5 or N and W
- Y and Z are each independently C-R 4 , C-R 6 or C-R 7 .
- Y is C-R 4 , C-R 5 , C-R 6 , C-R 7 or N and X and Z are each independently C-R 4 , C-R 5 or C-R 7 .
- W X, Y and Z are each independently C-R 4 , C- R 5 , C-RQ or C-R 7.
- the compound has the general structure:
- Ri and R3 are selected from -hydrogen, -alkyl, cycloalkyl, unsubstituted or substituted phenyl, unsubstituted or substituted benzyl, -methylpyridine, -ethylpyridine, -mehtylindole, -ethylindole, alkoxyethyl-, hydroxyethyl, N,N-dialkyl-ehtyl, , N,N-dialkyl-propyl, methylpyrrole, ethylpyrrole, methylfuran, ethylfuran, -alkyimorpholine, - alkylpiperizine, -alkypiperidine, -alkylpyrrolidine, and R 2 is H or lower alkyl.
- the compounds of the invention have structures wherein R 1 is
- the compounds of the invention have structures wherein R is wherein n is 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have structures wherein Ri is
- n 2, 3 and 4 and R2 is H or lower alkyl.
- the compounds of the invention have structures wherein R 3 is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have structures wherein R 1 is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have structures wherein R 3 is
- n 2, 3 and 4 and R is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein Ri is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein R 3 is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein Ri is wherein n is 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein R 3 is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein Ri is
- n 2, 3 and 4 and R 2 is H or lower alkyl.
- the compounds of the invention have the structure of Formula I wherein R 3 is
- R12 wherein n is 2, 3 and 4 and R 2 is H or lower alkyl.
- the present invention encompasses compounds having a structure found in Table 1, 2, 3, 4, 5, 6. 7, 8, 9, 10, 11, 12, or 13 including salts of any of these, preferably pharmaceutically acceptable salts thereof.
- the present invention relates to compositions of any of the compounds of the invention, preferably wherein such compound is present in a pharmaceutically acceptable carrier and in a therapeutically effective amount.
- Such compositions will generally comprise an amount of such compound that is not toxic (i.e., an amount that is safe for therapeutic uses).
- the present invention is directed to use of the compounds of the invention as active ingredients for medicaments, in particular for medicaments useful for the treatment of tumors.
- the compounds of the invention will thus be present in pharmaceutical compositions containing compounds of formula I as active ingredients, in admixture with pharmaceutically acceptable vehicles and excipients, which includes any pharmaceutical agent that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity.
- Pharmaceutically acceptable carriers include, but are not limited to, liquids such as water, saline, glycerol and ethanol, and the like, including carriers useful in forming sprays for nasal and other respiratory tract delivery or for delivery to the ophthalmic system.
- the present invention relates to a method for preventing or treating a disease associated with a change in levels of expression of particular sets of genes in a mammal comprising administering to said mammal an effective amount of a compound of the invention.
- the present invention relates to a method for preventing or treating a disorder modulated by altered gene expression, wherein the disorder is selected from the group consisting of cancer, cardiovascular disorders, arthritis, osteoporosis, inflammation, periodontal disease and skin disorders, comprising administering to a mammal in need of such treatment or prevention a therapeutically effective amount of a compound of the invention.
- the disorder is cancer, more preferably colon cancer, most preferably adenocarcinoma, and the treatment prevents, arrests or reverts tumor growth, metastasis or both.
- the compounds of the invention will commonly exert a therapeutic effect by modulation of one or more genes found in a cell, especially a mammalian cell, such as a cancer cell, preferably colon cancer and most preferably adenocarcinoma.
- a compound, or compounds, of the invention can be used to determine or demarcate a set of genes by determining modulation of such set of genes by one or more compounds of the invention.
- a set of genes can be determined by their common property of being modulated (based on a change in expression of the genes, such as a change in rate or amount of RNA transcribed or the amount of polypeptide produced by said expression) by contacting such genes, or a cell containing such genes, with one or more of the compounds of the invention.
- modulation may, of course, be related to the amount of said compound, or compounds, used in the contacting.
- Such modulation may include the increased expression of all the determined genes (i.e., the genes of the set), the decreased expression of all genes of the set, or the increase in expression of some of the genes of the set and decreased expression of others.
- a gene not modulated by the test compound is not considered a member of the set.
- the present invention relates to a gene set wherein expression of each member of said gene set is modulated as a result of contacting said gene set with a compound of the invention.
- expression of each member of said gene set is increased as a result of said contacting or is decreased as a result of said contacting.
- the gene set is present in a cell.
- Such a gene set will commonly be related to a specific disease process, such as a set of genes all of which are modulated by a compound of the invention wherein such compound has a specific therapeutic effect, such as being an anti-neoplastic agent.
- the present invention relates to a method for identifying an agent that modulates the expression of a gene set of the invention, comprising: (a) contacting, or otherwise using, a compound, such as a test compound, a test system, such as a source of genes or polynucleotides, for example, those found to be related to a given disease or disorder, or a set that is modulated by a given compound, or group of compounds, especially where these are found in a cell, so that the cell represents the test system, containing one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said treatment; wherein said change in expression of step (b) indicates modulation of the members of said gene set by the test compound thereby identifying a test compound that modulates the expression of said gene set.
- a compound such as
- the cell is a naturally derived cell that contains genes of a gene set or may be a recombinant cell engineered to comprise the genes or polynucleotides of the gene set.
- the test system may comprise the genes or polynucleotides in a cell-free system.
- the present invention provides a method for identifying a test compound that modulates the expression of a gene set, such as a gene set of the invention, comprising: (a) contacting a test compound with one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said contacting; wherein said change in expression of step (b) indicates modulation of the members of said gene set thereby identifying a test compound that modulates the expression of said gene set.
- corresponding genes or “corresponding polynucleotides” or “polynucleotides corresponding to genes” refers to polynucleotides and/or genes that encode an RNA that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical, and especially identical, to an RNA encoded by one of the genes disclosed herein in Tables 8 and 9. Such genes will also encode the same polypeptide sequence, but may include differences in such amino acid sequences where such differences are limited to conservative amino acid substitutions, such as where the same overall three dimensional structure, is maintained.
- a "corresponding gene” includes splice variants thereof.
- RNA processed or unprocessed, including naturally occurring splice variants and alleles
- RNA processed or unprocessed, including naturally occurring splice variants and alleles
- polynucleotides encoding the same proteins as any of these genes are also specifically contemplated by any of the methods of the present invention.
- the polynucleotides used in the methods of the invention also include any open reading frames, as defined herein, present therein.
- the term "open reading frame” or ORF means a series of triplets coding for amino acids without any termination codons and is a sequence (potentially) translatable into protein.
- polynucleotides useful in the methods of the invention may be genomic in nature and thus represent the sequence of an actual gene, such as a human gene, or may be a cDNA sequence derived from a messenger
- RNA and thus represent contiguous exonic sequences derived from a corresponding genomic sequence, or they may be wholly synthetic in origin for purposes of practicing the processes of the invention. Because of the processing that may take place in transforming the initial RNA transcript into the final mRNA, the sequences disclosed herein may represent less than the full genomic sequence. They may also represent sequences derived from ribosomal and transfer RNAs. Consequently, the gene as present in the cell
- genes and cDNA sequences may be identical or may be such that the cDNAs contain less than the full genomic sequence.
- genes and cDNA sequences are still considered "corresponding sequences" (as defined elsewhere herein) because they both encode the same or related RNA sequences (i.e., related in the sense of being splice variants or RNAs at different stages of processing).
- a gene that encodes an RNA transcript which is then processed into a shorter mRNA, is deemed to encode both such RNAs and therefore encodes an RNA complementary to (using the usual Watson-Crick complementarity rules), or that would otherwise be encoded by, a cDNA (for example, a sequence as disclosed herein).
- a cDNA for example, a sequence as disclosed herein.
- the sequences disclosed herein correspond to genes contained in the cancerous cells (here, breast cancer) and are used to determine gene activity or expression because they represent the same sequence or are complementary to RNAs encoded by the gene.
- Such a gene also includes different alleles and splice variants that may occur in the cells used in the methods of the invention, such as where recombinant cells are used to assay for anti-neoplastic agents and such cells have been engineered to express a polynucleotide as disclosed herein, including cells that have been engineered to express such polynucleotides at a higher level than is found in non-engineered cancerous cells or where such recombinant cells express such polynucleotides only after having been engineered to do so.
- Such engineering includes genetic engineering, such as where one or more of the polynucleotides disclosed herein has been inserted into the genome of such cell or is present in a vector.
- Such cells may also be engineered to express on their surfaces one or more of the polypeptides of the invention for testing with antibodies or other agents capable of masking such polypeptides and thereby removing the cancerous nature of the cell.
- Such engineering includes both genetic engineering, where the genetic complement of the cells is engineered to express the polypeptide, as well as non-genetic engineering, whereby the cell has been physically manipulated to incorporate a polypeptide of the invention in its plasma membrane, such as by direct insertion using chemical and/or other agents to achieve this result.
- the determined change in expression is a decrease in expression of said one or more polynucleotides or a decrease in said expression.
- the determined change in expression is a change in transcription of said one or more polynucleotides or a change in activity of a polypeptide, or expression product, encoded by said polynucleotide, including a change in the amount of said polypeptide synthesized, such as by a cell.
- expression product means that polypeptide or protein that is the natural translation product of the gene and any nucleic acid sequence coding equivalents resulting from genetic code degeneracy and thus coding for the same amino acid(s).
- said one or more polynucleotides are present in a cell, preferably a cancer cell, more preferably a colon cancer cell, and most preferably where the colon cancer cell is an adenocarcinoma cancer cell.
- the cell is a recombinant cell engineered to contain said set of genes.
- Such methods serve to identify other compounds that have like activity, including expected therapeutic activity, as the compounds of the invention and thus serve as the basis for large scale screening assays for therapeutic compounds.
- one or more compounds of the invention can be utilized to determine the presents of gene sets and subsets within the genome of a cell.
- the set of all genes modulated by a group of structurally related compounds of the invention can form a gene set while the different sets of genes regulated by each compound of a group will form a subset.
- a structurally related group of 5 of the compounds of the invention (all having generally the structure of Formula I) modulate (by increasing or decreasing) expression of determined genes 1-20, this latter group of genes forms a gene set.
- genes 1-6 are modulated by compound A
- genes 7-10 are modulated by compound B
- genes 2-4 and 9-12 are modulated by compound C
- genes 10-20 are modulated by compound D
- the even numbered genes are modulated by compound E.
- Each of these groups of genes, such as the genes modulated by compound C is considered a subset of the gene set of genes 1-20.
- the genes modulated by compound E can be themselves further subdivided into at least 2 subsets wherein one subset is made up of the genes whose expression is increased by compound E while the other subset is made up of genes whose expression is decreased by compound E, thus yielding subsets of subsets.
- each so-called subset is, in its own right, a gene set as used in the invention.
- the identification of sets and subsets is thus a function of the extent that a user of the methods of the invention wishes to determine modulation of genes resulting from contacting of one or more compounds of the invention.
- the genes modulated by a single compound form a gene set and it is not necessary, in carrying out the methods of the invention, to compare different groups of genes for modulation by more than one compound but this may, of course, be done.
- the present invention relates to a set of genes comprising a plurality of subsets of genes wherein each subset of said plurality is a gene set identified by the methods of the invention.
- the present invention also relates to compounds identified as having activity using the methods of the invention, such as novel compounds not specifically described herein by structure but which have been identified by their ability to modulates one or more gene sets modulated by compounds of the invention.
- the present invention encompasses the gene sets and subsets of the genes identified in Table 14 and/or in Table 15.
- the present invention specifically contemplates use of a compound that modulates the expression of a set of, or subset of, genes of Table 15.
- the present invention also comprises methods for the preparation of compounds of formula I, and the relative key intermediates
- the compounds of the invention can be prepared using a variety of procedures known in the art.
- the starting materials used in preparing the compounds of the invention are known, made by known methods, or are commercially available. Particularly preferred syntheses are described in the following general reaction schemes.
- the dichloro compound 1 is either commercially available or can be synthesized using methods known in the literature. 1. Shaikh I. A. et al, J. Med. Chem, 29(8), 1329-1340, (1986) 2. Vlderrama el al, Syn. Comrn., 27(12), 2143-2157, (1997) 3. Chu, Kwong-Yung; et al. Journal of the Chemical Society, Perkin Transactions 1: Organic and Bio-Organic Chemistry (1972-1999) (1978) 4. Matsuhisa A. et al, Patent WO 01/60803 A1 The compound 1 can be reacted with an amine in an appropriate solvent to provide the corresponding derivative 2.
- the compound 2 then can be reacted with an apporopriate 2-halo, 2-substituted acetyl halide to obtain the corresponding 3 derivatives.
- a reaction of crude or purified compound 3 with an amine can give compound 4.
- Compound 4 with or without isolation can be treated with a organic or inorganic base in a suitable solvent at an appropriate temperature can provide desired compound 5 of formula I.
- Compounds for which no preparation is given can be made by methods known in the literature or are of common knowledge by skilled artisan.
- one optical isomer may have favorable properties over the other and thus the disclosure of a racemic mixture within the present invention may also include either optically active isomer if such isomer has advantageous physiological activity in accordance with the methods of the invention.
- [1 ,4]naphthoquinone in 350 ml of anhydrous THF was added 200ml of 2.0M methyl amine in THF (200mmol, 2 equivalents).
- To the mixture was added 34 ml of N, N-diisopropylethylamine (200mmol, 2 equivalents) and it was shaken at room temperature for overnight (16-20 hours).
- Example A In a process analogous to Example C1 using appropriate 2-chloro-3- substituted amino-[1,4 ]naphthoquinone (Example A) and corresponding acid chloride following compounds are prepared.
Abstract
Chemical agents, such as derivatives of quinone, and including salts thereof, that modulate levels of gene expression in cellular systems, including cancer cells, are disclosed, along with methods for preparing such agents, as well as pharmaceutical compositions containing such agents as active ingredients and methods of using these as therapeutic agents.
Description
DERIVATIVES OF CYCLIC QUINONE AND USES THEREOF
This application claims priority of U.S. Provisional Application Serial No. 60/492,653, filed 5 August 2003, the disclosure of which is hereby incorporated by reference in its entirety.
FIELD OF THE INVENTION
The present invention relates to chemical agents affecting levels of gene expression in cellular systems, including cancer cells. In particular, the present invention relates to derivatives of quinone moiety, processes for their preparation, their use as antitumor drugs and pharmaceutical compositions containing them as active ingredients.
BACKGROUND OF THE INVENTION
Screening assays for novel drugs are based on the response of model cell based systems in vitro to treatment with specific compounds. Various measures of cellular response have been utilized, including the release of cytokines, alterations in cell surface markers, activation of specific enzymes, as well as alterations in ion flux and/or pH. Some such screens rely on specific genes, such as oncogenes or tumor suppressors.
The present invention utilizes screening of small molecule compounds as potential anticancer drugs by taking advantage of the concept that for each specific tumor type, a unique signature set of genes, that are differentially expressed in tumor cells if compared to corresponding normal cells, can be established. The relatively small signature set, containing 10-30 genes, allows for easy, high throughput screening for compounds that can reverse the gene expression profile from patterns typical for cancer cells to patterns seen in normal cells. As a part of our efforts to provide new diversified compounds for high throughput gene expression screening, we designed and synthesized a number of novel derivatives of quinines. Gene expression screening and subsequent cytotoxicity screening revealed that some of the compounds possess biological activity. Consequently, detailed structure-activity relationship resulted in compounds of formula I as new small molecule agents having antineoplastic activity.
BRIEF SUMMARY OF THE INVENTION In one aspect, the present invention relates to organic compounds, derivatives of quinone, that have the ability to function as gene expression modulators for genes found in cancer cells, especially genes involved in misregulated signal transduction pathways typical for colon cancer. In one embodiment of the present invention, the compounds disclosed herein are able to up regulate genes found to be up regulated in normal (i.e., non-cancerous) cells versus cancer cells, especially colon cancer cells, thereby producing an expression profile for said gene(s) that resembles the expression profile found in normal cells. In another embodiment, the compounds disclosed herein are found to down regulate genes otherwise up- regulated in cancer cells, especially colon cancer cells, relative to normal (i.e., non-cancerous) cells thereby producing an expression profile for said gene(s)
that more resembles the expression profile found in normal cells. Thus, in addition to activity in modulating a particular gene that may or may not have a major role in inducing or sustaining a cancerous condition, the agents disclosed herein also find value in regulating a set of gene whose combined activity is related to a disease condition, such as cancer, especially colon cancer, including adenocarcinoma of the colon. Thus, while an overall set of genes is modulated, the effect of modulating any subset of these may be disproportionately large or small with respect to the effect in ameliorating the overall disease process. Consequently, different disease conditions may rely on different subsets of genes to be active or inactive as a basis for the overall disease process.
Thus, the present invention relates to novel organic compounds that have the ability to function as gene modulators for genes found in normal (i.e., non-cancer) cells and which genes are found to be up regulated or down regulated in normal cells, especially colon cells. Such an effect may prevent a disease condition, such as cancer, from arising in those otherwise more susceptible to such a condition. In one such embodiment, administration of one or more of the agents disclosed herein may succeed in preventing a cancerous condition from arising.
In other embodiments, the agents disclosed herein find use in combination with each other as well as with other agents, such as where a mixture of one or more of the agents of the present invention are given in combination or where one or more of the agents disclosed herein is given together with some other already known therapeutic agent, possibly as a means of potentiating the affects of such known therapeutic agent or vice versa. The present invention also relates to processes of preventing or treating disease conditions, especially cancer, most especially colon cancer, by administering to a subject, such as a mammal, especially a human, a
therapeutically active amount of one or more of the agents disclosed herein, including where such agents are given in combination with one or more known therapeutic agents.
DEFINITIONS
The following is a list of definitions for terms used herein. "Acyl" or "carbonyl" is a radical formed by removal of the hydroxy from a carboxylic acid (i.e., R-C(=O)-). Preferred acyl groups include (for example) acetyl, formyl, and propionyl.
"Alkyl" is a saturated hydrocarbon chain having 1 to 15 carbon atoms, preferably 1 to 10, more preferably 1 to 4 carbon atoms. "Alkene" is a hydrocarbon chain having at least one (preferably only one) carbon-carbon double bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms. "Alkyne" is a hydrocarbon chain having at least one (preferably only one) carbon-carbon triple bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms. Alkyl, alkene and alkyne chains (referred to collectively as "hydrocarbon chains") may be straight or branched and may be unsubstituted or substituted. Preferred branched alkyl, alkene and alkyne chains have one or two branches, preferably one branch. Preferred chains are alkyl. Alkyl, alkene and alkyne hydrocarbon chains each may be unsubstituted or substituted with from 1 to 4 substituents; when substituted, preferred chains are mono-, di-, or tri-substituted. Alkyl, alkene and alkyne hydrocarbon chains each may be substituted with halo, hydroxy, aryloxy (e.g., phenoxy), heteroaryloxy, acyloxy (e.g., acetoxy), carboxy, aryl (e.g., phenyl), heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, amido, acylamino, keto, thioketo, cyano, or any combination thereof. Preferred hydrocarbon groups include methyl, ethyl, propyl, isopropyl, butyl, vinyl, allyl, butenyl, and exomethylenyl.
Also, as referred to herein, a "lower" alkyl, alkene or alkyne moiety (e.g., "lower alkyl") is a chain comprised of 1 to 6, preferably from 1 to 4, carbon atoms in the case of alkyl and 2 to 6, preferably 2 to 4, carbon atoms in the case of alkene and alkyne.
"Alkoxy" is an oxygen radical having a hydrocarbon chain substituent, where the hydrocarbon chain is an alkyl or alkenyl (i.e., -O-alkyl or -O- alkenyl). Preferred alkoxy groups include (for example) methoxy, ethoxy, propoxy and allyloxy.
"Aryl" is an aromatic hydrocarbon ring. Aryl rings are monocyclic or fused bicyclic ring systems. Monocyclic aryl rings contain 6 carbon atoms in the ring. Monocyclic aryl rings are also referred to as phenyl rings. Bicyclic aryl rings contain from 8 to 17 carbon atoms, preferably 9 to 12 carbon atoms, in the ring. Bicyclic aryl rings include ring systems wherein one ring is aryl and the other ring is aryl, cycloalkyl, or heterocycloakyl. Preferred bicyclic aryl rings comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7- membered rings. Aryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Aryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, aryloxy, alkoxy, heteroalkyloxy, carbamyl, haloalkyl, methylenedioxy, heteroaryloxy, or any combination thereof. Preferred aryl rings include naphthyl, tolyl, xylyl, and phenyl. The most preferred aryl ring radical is phenyl.
"Aryloxy" is an oxygen radical having an aryl substituent (i.e., -O-aryl). Preferred aryloxy groups include (for example) phenoxy, napthyloxy, methoxyphenoxy, and methylenedioxyphenoxy.
"Cycloalkyl" is a saturated or unsaturated hydrocarbon ring. Cycloalkyl rings are not aromatic. Cycloalkyl rings are monocyclic, or are fused, spiro, or
bridged bicyclic ring systems. Monocyclic cycloalkyl rings contain from about 3 to about 9 carbon atoms, preferably from 3 to 7 carbon atoms, in the ring. Bicyclic cycloalkyl rings contain from 7 to 17 carbon atoms, preferably from 7 to 12 carbon atoms, in the ring. Preferred bicyclic cycloalkyl rings comprise 4-, 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings. Cycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Cycloalkyl may be substituted with halo, cyano, alkyl, heteroalkyl, haloalkyl, phenyl, keto, hydroxy, carboxy, amino, acylamino, aryloxy, heteroaryloxy, or any combination thereof. Preferred cycloalkyl rings include cyclopropyl, cyclopentyl, and cyclohexyl.
"Halo" or "halogen" is fluoro, chloro, bromo or iodo. Preferred halo are fluoro, chloro and bromo; more preferred typically are chloro and fluoro, especially fluoro.
"Haloalkyl" is a straight, branched, or cyclic hydrocarbon substituted with one or more halo substituents. Preferred are C1-C12 haloalkyls; more preferred are C-i-Cβ haloalkyls; still more preferred still are C1-C3 haloalkyls.
Preferred halo substituents are fluoro and chloro. The most preferred haloalkyl is trifluoromethyl.
"Heteroatom" is a nitrogen, sulfur, or oxygen atom. Groups containing more than one heteroatom may contain different heteroatoms. "Heteroalkyl" is a saturated or unsaturated chain containing carbon and at least one heteroatom, wherein no two heteroatoms are adjacent. Heteroalkyl chains contain from 2 to 15 member atoms (carbon and heteroatoms) in the chain, preferably 2 to 10, more preferably 2 to 5. For example, alkoxy (i.e., -O-alkyl or -O-heteroalkyl) radicals are included in heteroalkyl. Heteroalkyl chains may be straight or branched. Preferred branched heteroalkyl have one or two branches, preferably one branch. Preferred heteroalkyl are saturated. Unsaturated heteroalkyl have one or
more carbon-carbon double bonds and/or one or more carbon-carbon triple bonds. Preferred unsaturated heteroalkyls have one or two double bonds or one triple bond, more preferably one double bond. Heteroalkyl chains may be unsubstituted or substituted with from 1 to 4 substituents. Preferred substituted heteroalkyl are mono-, di-, or tri-substituted. Heteroalkyl may be substituted with lower alkyl, haloalkyl, halo, hydroxy, aryloxy, heteroaryloxy, acyloxy, carboxy, monocyclic aryl, heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, acylamino, amido, keto, thioketo, cyano, or any combination thereof.
"Heteroaryl" is an aromatic ring containing carbon atoms and from 1 to about 6 heteroatoms in the ring. Heteroaryl rings are monocyclic or fused bicyclic ring systems. Monocyclic heteroaryl rings contain from about 5 to about 9 member atoms (carbon and heteroatoms), preferably 5 or 6 member atoms, in the ring. Bicyclic heteroaryl rings contain from 8 to 17 member atoms, preferably 8 to 12 member atoms, in the ring. Bicyclic heteroaryl rings include ring systems wherein one ring is heteroaryl and the other ring is aryl, heteroaryl, cycloalkyl, or heterocycloalkyl. Preferred bicyclic heteroaryl ring systems comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings. Heteroaryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Heteroaryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy, heteroaryloxy, or any combination thereof. Preferred heteroaryl rings include, but are not limited to, the following:
Furan Thiophene Pyrrole Pyrazole Imidazole Oxazole Isoxazole
Isothiazole Thiazole 1 ,2,5-Thiadiazole 1 ,2,3-Triazole 1 ,3,4-Thiadiazole Furazan
1 ,2,3-T iadiazole 1 ,2,4-T iadiazole Benzotriazole 1 ,2,4-Triazole Tetrazole
1,2,4-Oxadiazole 1 ,3,4-Oxadiazole 1 ,2,3,4-Oxatriazole 1 ,2,3,4-Thiatriazole 1 ,2,3,5-T iatriazole
Isoquinoline Cinnoline Phthalazine Quinazoline Quinoxaline 1,8-Napthypyridine
(i.e., -O-heteroaryl). Preferred heteroaryloxy groups include (for example) pyridyloxy, furanyloxy, (thiophene)oxy, (oxazole)oxy, (thiazole)oxy, (isoxazole)oxy, pyrmidinyloxy, pyrazinyloxy, and benzothiazolyloxy.
"Heterocycloalkyl" is a saturated or unsaturated ring containing carbon atoms and from 1 to about 4 (preferably 1 to 3) heteroatoms in the ring. Heterocycloalkyl rings are not aromatic. Heterocycloalkyl rings are monocyclic, or are fused, bridged, or spiro bicyclic ring systems. Monocyclic heterocycloalkyl rings contain from about 3 to about 9 member atoms (carbon and heteroatoms), preferably from 5 to 7 member atoms, in the ring. Bicyclic heterocycloalkyl rings contain from 7 to 17 member atoms, preferably 7 to 12 member atoms, in the ring. Bicyclic heterocycloalkyl rings contain from about 7 to about 17 ring atoms, preferably from 7 to 12 ring atoms. Bicyclic heterocycloalkyl rings may be fused, spiro, or bridged ring systems. Preferred bicyclic heterocycloalkyl rings comprise 5-, 6- or 7- membered rings fused to 5-, 6-, or 7-membered rings. Heterocycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Heterocycloalkyl may be substituted with halo, cyano, hydroxy, carboxy, keto, thioketo, amino, acylamino, acyl, amido, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy or any combination thereof. Preferred substituents on heterocycloalkyl include halo and haloalkyl. Preferred heterocycloalkyl rings include, but are not limited to, the following:
Oxirane Aziridine Oxetane Azetidine Tetrahydrofuran Pyrrolidine 3H-lndole
1 ,3-Dioxolane 1,2-Dithiolane 1,3-Dithiolane 4,5-Dihydroisoxazole 2,3-Dihydroisoxazole
P ύyrazo-lidine 2H O-Pyran 3,4-Dih 0ydro-2H-pyran Tetra Ohydropyran 2 C/-/-COromene
5,6-dihydro 0-4W-1°,3-oxazine 4H c-3,1-be?nzoxazine 1,3-Dioxane
While alkyl, heteroalkyl, cycloalkyl, and heterocycloalkyl groups may be substituted with hydroxy, amino, and amido groups as stated above, the following are not envisioned in the invention: Enols (OH attached to a carbon bearing a double bond).
Amino groups attached to a carbon bearing a double bond (except for vinylogous amides).
More than one hydroxy, amino, or amido attached to a single carbon (except where two nitrogen atoms are attached to a single carbon atom and all three atoms are member atoms within a heterocycloalkyl ring).
Hydroxy, amino, or amido attached to a carbon that also has a heteroatom attached to it.
Hydroxy, amino, or amido attached to a carbon that also has a halogen attached to it.
A "pharmaceutically-acceptable salt" is a cationic salt formed at any acidic (e.g., carboxylic acid) group, or an anionic salt formed at any basic (e.g., amino) group. Many such salts are known in the art, as described in World Patent Publication 87/05297, Johnston et al., published September 11, 1987 incorporated by reference herein. Preferred cationic salts include the alkali metal salts (such as sodium and potassium), and alkaline earth metal salts (such as magnesium and calcium) and organic salts. Preferred anionic salts include the halides (such as chloride salts), sulfonates, carboxylates, phosphates, and the like.
Such salts are well understood by the skilled artisan, and the skilled artisan is able to prepare any number of salts given the knowledge in the art. Furthermore, it is recognized that the skilled artisan may prefer one salt over another for reasons of solubility, stability, formulation ease and the like. Determination and optimization of such salts is within the purview of the skilled artisan's practice.
A "solvate" is a complex formed by the combination of a solute (e.g., a metalloprotease inhibitor) and a solvent (e.g., water). See J. Honig et al., The Van Nostrand Chemist's Dictionary, p. 650 (1953). Pharmaceutically-acceptable solvents used according to this invention include those that do not interfere with the biological activity of the metalloprotease inhibitor (e.g., water, ethanol, acetic acid, N,N- dimethylformamide and others known or readily determined by the skilled artisan).
The terms "optical isomer", "stereoisomer", and "diastereomer" have the accepted meanings (see, e.g., Hawlev's Condensed Chemical Dictionary. 11th Ed.). The illustration of specific protected forms and other derivatives of the compounds of the instant invention is not intended to be
limiting. The application of other useful protecting groups, salt forms, etc. is within the ability of the skilled artisan.
DETAILED SUMMARY OF THE INVENTION
In one aspect, the present invention relates to a compound having the structure of Formula (I)
wherein W, X, Y and Z are each independently selected from a bond (meaning that said group or substituent is not present), C-R4, C-R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two W, X, Y and Z are O, N and S; wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COORβ, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NR8CONR9Rι0; wherein R8, R9 and Rio are independently hydrogen, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl; NR8Rg is also unsubstituted, monosubstituted or polysubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S;
H
alkyl, unsubstituted, mono or polysubstituted phenyl or polyaromatic, unsubstituted, mono or polysubstituted heteroaromatic, with hetero atom(s) as N, O, S, Unsubstituted, mono or polysubstituted aralkyl,
Unsubstituted, mono or polysubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle (3-8 atoms per ring) with one to four hetero atoms as N, O, or S ; and wherein substitutions are independently selected from hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8R9 is also unsubstituted, monosubstituted or polysubstituted mono or polycyclic ring with one to four heteroatoms such as N, O, S; Additionally, R8 and Rio can be connected together to form 4, 5,6 or 7-member cyclic ring system;
Ri and R3 are also independently selected from:
wherein n is 2, 3, 4 and Rn, R12, R13 and Rι4 are independently selected from hydrogen, alkyl, cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted heteroaryl, unsubstituted or substituted alkylaryl; NR13R14 is also unsubstituted, or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R13 can be connected together to form 4, 5,6 or 7-member cyclic ring system; R2 is also selected from:
-CONR13R.|,
wherein n is 0, 1, 2 and 3 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, unsubstituted or substituted cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted alkaryl ; NR-13R14 is also unsubstituted or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R13 can be connected together to form 4, 5, 6 or 7 member ring system provided n is 1, 2, and 3; including salts thereof. In a preferred embodiment of such compounds, the present invention includes compounds of Formula I wherein: W, X, Y and Z are each independently selected from a bond, C-R4, C- R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two of W, X, Y and Z are O, N and S; wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8S02R9, NR8CONR9Rιo; wherein R8, R9 and R10 are independently hydrogen, alkyl, H, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl;
NR8Rg is also mono or bicyclic ring, with one to four heteroatoms such as N, O, S; Rι, R2 and R3 are: H alkyl of 1 to 6 carbon atoms, unsubstituted, mono or polysubstituted phenyl or polyaromatic, unsubstituted, mono or polysubstituted heteroaromatic, with hetero atom(s) as N, O, S, Unsubstituted, mono or polysubstituted aralkyl, Unsubstituted, mono or polysubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle (3-8 atoms per ring) with one to four hetero atoms as N, O, or S ; and wherein substitutions are selected from independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8CORg, NR8SO2Rg, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8Rg is also mono or polycyclic ring with one to four heteroatoms such as N, O, S; additionally, R8 and Rio can be connected together to form 4, 5,6 or 7- member cyclic ring system;
Ri and R3 are also independently selected from:
wherein n is 2, 3, 4, 5, 6 and R11 ( R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, heteroaryl, alkylaryl from 7 to 10 carbon atoms; NR13R14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R13 can be connected together to form 4, 5,6 or 7-member cyclic ring system;
R2 is also selected from:
wherein n is 0, 1, 2 , 3, 4, 5 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, alkaryl from 7 to 10 carbon atoms; NR13R14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R13 can be connected together to form 4, 5,6 or 7 member ring system provided n is 1 , 2, and 3; including salts thereof.
In a preferred embodiment of the latter compounds, W and Z are each independently C-R4, C-R7 or N while X and Y are each independently C-R5 or C-R6. In a highly preferred embodiment of the latter, W is C-R4 or N and X, Y and Z are each independently C-R5, C-Rβ or C-R . In another such highly preferred embodiment, Z is C-R , C-R5, C-R or N and W and Y are each independently C-R4, C-R6 or C-R7.
In another preferred embodiment, the compounds of the present invention include compounds of Formula I wherein X and Y are each independently C-R5, C-R6 or N and wherein W and Z are each independently C-R4 or C-R5. In a most preferred embodiment of the latter compounds, X is
C-R5 or N and W, Y and Z are each independently C-R4, C-R6 or C-R7. In another such embodiment, Y is C-R4, C-R5, C-R6, C-R7 or N and X and Z are each independently C-R4, C-R5 or C-R7. Especially preferred in the latter group are compounds wherein W X, Y and Z are each independently C-R4, C- R5, C-RQ or C-R7. In a highly preferred embodiment of the latter, the compound has the general structure:
most preferably wherein Ri and R3 are selected from -hydrogen, -alkyl, cycloalkyl, unsubstituted or substituted phenyl, unsubstituted or substituted benzyl, -methylpyridine, -ethylpyridine, -mehtylindole, -ethylindole, alkoxyethyl-, hydroxyethyl, N,N-dialkyl-ehtyl, , N,N-dialkyl-propyl, methylpyrrole, ethylpyrrole, methylfuran, ethylfuran, -alkyimorpholine, - alkylpiperizine, -alkypiperidine, -alkylpyrrolidine, and R2 is H or lower alkyl.
In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R1 is
wherein n is 2, 3 and 4 and R2 is H or lower alkyl. In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R is
wherein n is 2, 3 and 4 and R2 is H or lower alkyl.
In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein Ri is
In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R3 is
In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R1 is
In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R3 is
R11
-NR13S02Rι4
R12 wherein n is 2, 3 and 4 and R is H or lower alkyl.
In additional highly preferred embodiments, the compounds of the invention have the structure of Formula I wherein Ri is
wherein n is 2, 3 and 4 and R2 is H or lower alkyl. In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is
In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein Ri is
wherein n is 2, 3 and 4 and R2 is H or lower alkyl.
In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is
In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein Ri is
In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is
R 11
-NR13S02Rι4
R12
wherein n is 2, 3 and 4 and R2 is H or lower alkyl.
In highly preferred embodiments, the present invention encompasses compounds having a structure found in Table 1, 2, 3, 4, 5, 6. 7, 8, 9, 10, 11, 12, or 13 including salts of any of these, preferably pharmaceutically acceptable salts thereof.
In another aspect, the present invention relates to compositions of any of the compounds of the invention, preferably wherein such compound is present in a pharmaceutically acceptable carrier and in a therapeutically effective amount. Such compositions will generally comprise an amount of such compound that is not toxic (i.e., an amount that is safe for therapeutic uses). In accordance with the foregoing, the present invention is directed to use of the compounds of the invention as active ingredients for medicaments, in particular for medicaments useful for the treatment of tumors. The compounds of the invention will thus be present in pharmaceutical compositions containing compounds of formula I as active ingredients, in admixture with pharmaceutically acceptable vehicles and excipients, which includes any pharmaceutical agent that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Pharmaceutically acceptable carriers include, but are not limited to, liquids such as water, saline, glycerol and ethanol, and the like, including carriers useful in forming sprays for nasal and other respiratory tract delivery or for delivery to the ophthalmic system. A thorough discussion of pharmaceutically acceptable carriers, diluents, and other excipients is presented in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. current edition). Use of such carriers is well known to those skilled in the art and will not be discussed further herein.
Also in accordance with the foregoing, the present invention relates to a method for preventing or treating a disease associated with a change in levels of expression of particular sets of genes in a mammal comprising administering to said mammal an effective amount of a compound of the invention.
In another aspect, the present invention relates to a method for preventing or treating a disorder modulated by altered gene expression, wherein the disorder is selected from the group consisting of cancer, cardiovascular disorders, arthritis, osteoporosis, inflammation, periodontal disease and skin disorders, comprising administering to a mammal in need of such treatment or prevention a therapeutically effective amount of a compound of the invention. In a preferred embodiment thereof, the disorder is cancer, more preferably colon cancer, most preferably adenocarcinoma, and the treatment prevents, arrests or reverts tumor growth, metastasis or both.
The compounds of the invention will commonly exert a therapeutic effect by modulation of one or more genes found in a cell, especially a mammalian cell, such as a cancer cell, preferably colon cancer and most preferably adenocarcinoma. Thus, a compound, or compounds, of the invention can be used to determine or demarcate a set of genes by determining modulation of such set of genes by one or more compounds of the invention. For example, where a set of genes is found to be up-regulated in cancer cells versus otherwise normal cells, especially normal cells of the same tissue or organ as the cancer cells, a set of genes can be determined by their common property of being modulated (based on a change in expression of the genes, such as a change in rate or amount of RNA transcribed or the amount of polypeptide produced by said expression) by contacting such genes, or a cell containing such genes, with one or more of the compounds of the invention. The extent of such modulation may, of
course, be related to the amount of said compound, or compounds, used in the contacting. Such modulation may include the increased expression of all the determined genes (i.e., the genes of the set), the decreased expression of all genes of the set, or the increase in expression of some of the genes of the set and decreased expression of others. Thus, a gene not modulated by the test compound (the compound used in contacting the genes or cell containing them) is not considered a member of the set.
Thus, the present invention relates to a gene set wherein expression of each member of said gene set is modulated as a result of contacting said gene set with a compound of the invention. In specific embodiments, expression of each member of said gene set is increased as a result of said contacting or is decreased as a result of said contacting. In another preferred embodiment, the gene set is present in a cell. Such a gene set will commonly be related to a specific disease process, such as a set of genes all of which are modulated by a compound of the invention wherein such compound has a specific therapeutic effect, such as being an anti-neoplastic agent.
In another aspect, the present invention relates to a method for identifying an agent that modulates the expression of a gene set of the invention, comprising: (a) contacting, or otherwise using, a compound, such as a test compound, a test system, such as a source of genes or polynucleotides, for example, those found to be related to a given disease or disorder, or a set that is modulated by a given compound, or group of compounds, especially where these are found in a cell, so that the cell represents the test system, containing one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said treatment;
wherein said change in expression of step (b) indicates modulation of the members of said gene set by the test compound thereby identifying a test compound that modulates the expression of said gene set. In one embodiment, the cell is a naturally derived cell that contains genes of a gene set or may be a recombinant cell engineered to comprise the genes or polynucleotides of the gene set. In an alternative embodiment, the test system may comprise the genes or polynucleotides in a cell-free system. In a related aspect, the present invention provides a method for identifying a test compound that modulates the expression of a gene set, such as a gene set of the invention, comprising: (a) contacting a test compound with one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said contacting; wherein said change in expression of step (b) indicates modulation of the members of said gene set thereby identifying a test compound that modulates the expression of said gene set.
As used herein, "corresponding genes" or "corresponding polynucleotides" or "polynucleotides corresponding to genes" refers to polynucleotides and/or genes that encode an RNA that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical, and especially identical, to an RNA encoded by one of the genes disclosed herein in Tables 8 and 9. Such genes will also encode the same polypeptide sequence, but may include differences in such amino acid sequences where such differences are limited to conservative amino acid substitutions, such as where the same overall three dimensional structure, is maintained. A "corresponding gene" includes splice variants thereof.
Because a polynucleotide or gene used in the methods of the invention "corresponds to" a gene present in one of the gene sets of the invention, such as genes identified in Tables 8 and 9, such polynucleotide or gene encodes an RNA (processed or unprocessed, including naturally occurring splice variants and alleles) that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical to, and especially identical to, an RNA that would be encoded by, or be complementary to, such as by hybridization with, a gene of Table 14 or 15, or genes of any gene set identified according to the invention. Polynucleotides encoding the same proteins as any of these genes, regardless of the percent identity of the sequences of such genes and/or polynucleotides, are also specifically contemplated by any of the methods of the present invention. The polynucleotides used in the methods of the invention also include any open reading frames, as defined herein, present therein. As used herein, the term "open reading frame" (or ORF) means a series of triplets coding for amino acids without any termination codons and is a sequence (potentially) translatable into protein.
The polynucleotides useful in the methods of the invention may be genomic in nature and thus represent the sequence of an actual gene, such as a human gene, or may be a cDNA sequence derived from a messenger
RNA (mRNA) and thus represent contiguous exonic sequences derived from a corresponding genomic sequence, or they may be wholly synthetic in origin for purposes of practicing the processes of the invention. Because of the processing that may take place in transforming the initial RNA transcript into the final mRNA, the sequences disclosed herein may represent less than the full genomic sequence. They may also represent sequences derived from ribosomal and transfer RNAs. Consequently, the gene as present in the cell
(and representing the genomic sequence) and the polynucleotide transcripts disclosed herein, including cDNA sequences, may be identical or may be such that the cDNAs contain less than the full genomic sequence. Such genes and cDNA sequences are still considered "corresponding sequences"
(as defined elsewhere herein) because they both encode the same or related RNA sequences (i.e., related in the sense of being splice variants or RNAs at different stages of processing). Thus, by way of non-limiting example only, a gene that encodes an RNA transcript, which is then processed into a shorter mRNA, is deemed to encode both such RNAs and therefore encodes an RNA complementary to (using the usual Watson-Crick complementarity rules), or that would otherwise be encoded by, a cDNA (for example, a sequence as disclosed herein). Thus, the sequences disclosed herein correspond to genes contained in the cancerous cells (here, breast cancer) and are used to determine gene activity or expression because they represent the same sequence or are complementary to RNAs encoded by the gene. Such a gene also includes different alleles and splice variants that may occur in the cells used in the methods of the invention, such as where recombinant cells are used to assay for anti-neoplastic agents and such cells have been engineered to express a polynucleotide as disclosed herein, including cells that have been engineered to express such polynucleotides at a higher level than is found in non-engineered cancerous cells or where such recombinant cells express such polynucleotides only after having been engineered to do so. Such engineering includes genetic engineering, such as where one or more of the polynucleotides disclosed herein has been inserted into the genome of such cell or is present in a vector.
Such cells, especially mammalian cells, may also be engineered to express on their surfaces one or more of the polypeptides of the invention for testing with antibodies or other agents capable of masking such polypeptides and thereby removing the cancerous nature of the cell. Such engineering includes both genetic engineering, where the genetic complement of the cells is engineered to express the polypeptide, as well as non-genetic engineering, whereby the cell has been physically manipulated to incorporate a polypeptide of the invention in its plasma membrane, such as by direct insertion using chemical and/or other agents to achieve this result.
In a preferred embodiment of such method, the determined change in expression is a decrease in expression of said one or more polynucleotides or a decrease in said expression. In other preferred embodiments, the determined change in expression is a change in transcription of said one or more polynucleotides or a change in activity of a polypeptide, or expression product, encoded by said polynucleotide, including a change in the amount of said polypeptide synthesized, such as by a cell. The term "expression product" means that polypeptide or protein that is the natural translation product of the gene and any nucleic acid sequence coding equivalents resulting from genetic code degeneracy and thus coding for the same amino acid(s).
In additional preferred embodiments, said one or more polynucleotides are present in a cell, preferably a cancer cell, more preferably a colon cancer cell, and most preferably where the colon cancer cell is an adenocarcinoma cancer cell. In another preferred embodiment of the invention, the cell is a recombinant cell engineered to contain said set of genes.
Such methods serve to identify other compounds that have like activity, including expected therapeutic activity, as the compounds of the invention and thus serve as the basis for large scale screening assays for therapeutic compounds. As a result, one or more compounds of the invention can be utilized to determine the presents of gene sets and subsets within the genome of a cell. Thus, the set of all genes modulated by a group of structurally related compounds of the invention can form a gene set while the different sets of genes regulated by each compound of a group will form a subset. By way of non-limiting example, where a structurally related group of 5 of the compounds of the invention (all having generally the structure of Formula I) modulate (by increasing or decreasing) expression of determined genes 1-20, this latter group of genes forms a gene set. Further examination then determines that genes 1-6 are modulated by compound A, genes 7-10 are modulated by compound B, genes 2-4 and 9-12 are modulated by compound
C, genes 10-20 are modulated by compound D and the even numbered genes are modulated by compound E. Each of these groups of genes, such as the genes modulated by compound C, is considered a subset of the gene set of genes 1-20. In an analogous manner, the genes modulated by compound E can be themselves further subdivided into at least 2 subsets wherein one subset is made up of the genes whose expression is increased by compound E while the other subset is made up of genes whose expression is decreased by compound E, thus yielding subsets of subsets. It should be noted that within the context of the present invention, it is not necessary to identify subsets and that each so-called subset is, in its own right, a gene set as used in the invention. The identification of sets and subsets is thus a function of the extent that a user of the methods of the invention wishes to determine modulation of genes resulting from contacting of one or more compounds of the invention. Thus, the genes modulated by a single compound form a gene set and it is not necessary, in carrying out the methods of the invention, to compare different groups of genes for modulation by more than one compound but this may, of course, be done.
In accordance with the foregoing, the present invention relates to a set of genes comprising a plurality of subsets of genes wherein each subset of said plurality is a gene set identified by the methods of the invention. The present invention also relates to compounds identified as having activity using the methods of the invention, such as novel compounds not specifically described herein by structure but which have been identified by their ability to modulates one or more gene sets modulated by compounds of the invention.
In a preferred embodiment, the present invention encompasses the gene sets and subsets of the genes identified in Table 14 and/or in Table 15.
In using the compounds of the invention for treatment of disease, especially cancer, the present invention specifically contemplates use of a compound that modulates the expression of a set of, or subset of, genes of Table 15.
The present invention also comprises methods for the preparation of compounds of formula I, and the relative key intermediates
Compound Preparation:
The compounds of the invention can be prepared using a variety of procedures known in the art. The starting materials used in preparing the compounds of the invention are known, made by known methods, or are commercially available. Particularly preferred syntheses are described in the following general reaction schemes.
Scheme 1 :
The dichloro compound 1 is either commercially available or can be synthesized using methods known in the literature. 1. Shaikh I. A. et al, J. Med. Chem, 29(8), 1329-1340, (1986) 2. Vlderrama el al, Syn. Comrn., 27(12), 2143-2157, (1997) 3. Chu, Kwong-Yung; et al. Journal of the Chemical Society, Perkin Transactions 1: Organic and Bio-Organic Chemistry (1972-1999) (1978) 4. Matsuhisa A. et al, Patent WO 01/60803 A1
The compound 1 can be reacted with an amine in an appropriate solvent to provide the corresponding derivative 2. The compound 2 then can be reacted with an apporopriate 2-halo, 2-substituted acetyl halide to obtain the corresponding 3 derivatives. A reaction of crude or purified compound 3 with an amine can give compound 4. Compound 4 with or without isolation can be treated with a organic or inorganic base in a suitable solvent at an appropriate temperature can provide desired compound 5 of formula I. Additionally, further independent modification each R1 ( R2 and R3 using methods known in literature to obtain additional compounds of formula I. Compounds for which no preparation is given can be made by methods known in the literature or are of common knowledge by skilled artisan.
The skilled artisan will recognize that some reactions are best carried out when another potentially reactive functionality on the molecule is masked or protected, thus avoiding any undesirable side reactions and/or increasing the yield of the reaction. Often protecting groups are used to accomplish such increased yields or to avoid the undesired reactions. Such reactions are well within the ability of the skilled artisan. Some examples are found in T. Greene, Protecting Groups in Organic Synthesis.
In addition, it is to be appreciated that one optical isomer may have favorable properties over the other and thus the disclosure of a racemic mixture within the present invention may also include either optically active isomer if such isomer has advantageous physiological activity in accordance with the methods of the invention.
Example-A1 2-Chloro-3-methylamino-f1,4lnaphthoguinone
To a solution of 22.7g (lOOmmol, 1 equivalent) of 2,3-dichloro-
[1 ,4]naphthoquinone in 350 ml of anhydrous THF was added 200ml of 2.0M methyl amine in THF (200mmol, 2 equivalents). To the mixture was added 34 ml of N, N-diisopropylethylamine (200mmol, 2 equivalents) and it was shaken at room temperature for overnight (16-20 hours).
The red precipitates formed were filtered and washed with ether. The residue was again washed with water and ether. The solid was dried under vacuum. The filtrate was checked for the desired product, and then THF was evaporated. The residue was recrystallized with DCM/ether. The titled compound was collected as a red solid (18g, Yield 74% ).
In a process analogous to Example A1 using appropriate starting materials, the corresponding compounds are prepared as follows:
Example-B1 2-Bromo-N-(3-chloro-1 ,4-dioxo-1.4-dihvdro-naphthalen-2-yl.- propionamide
To a solution of 2.08g of 2-amino-3-chloro-[1,4]naphthoquinone (10mmol, lequivalent) in 250 ml 1 ,4-dioxane was added 2.67g of K2CO3 (20mmol, 2equivalents). The mixture was heated until the starting material was completely dissolved. To the solution 4.2ml of 2-bromopropionylbromide (40mmol, 4 equivalents) was added and refluxed for 16 hours. Inorganic materials were filtered and washed thoroughly with DCM. The filtrate was evaporated and the residue recrystallized with DCM/ether or hexanes. The titled compound was collected as a light green solid (1.7g Yield, 50%).
In a process analogous to Example B1 using appropriate starting materials, the corresponding compounds are prepared as follows:
2-Bromo-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen-2-yl)-acetamide 2-Bromo-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro-naphthalen-2-yl)-N-methyl- acetamide
2-Bromo-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen-2-yl)-N-methyl- propionamide
Example-C1 2-Chloro-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro-naphthalen-2-yl)-N-methyl- acetamide
To a solution of 10g of 2-chloro-3-methylamino-[1,4]naphthoquinone (45 mmol) in 250 mL of dioxane was added 172 ml of chloroacetyl chloride (48 equivalents). The reaction was heated at 85° C for 16 hours. The solvent was evaporated and the material was purified on silica gel using dichloromethane and hexanes as solvents. The pure fractions were combined and the solvent was evaporated. The product was collected as a yellow/brown solid. (12.1g, Yield 90%).
In a process analogous to Example C1 using appropriate 2-chloro-3- substituted amino-[1,4 ]naphthoquinone (Example A) and corresponding acid chloride following compounds are prepared.
2-Chloro-N-(3-chloro-1 ,4-dioxo-1.4-dihvdro-naphthalen-2-vπ-N-methyl-
2- phenyl-acetamide
To a solution of 2 g of 2-chloro-3-methylamino-[1 ,4]naphthoquinone (9mmol, lequivalent) in 30 ml anhydrous 1 ,4-dioxane was added 20g(106mmol, 12equivalents) of 2-chloro-2-phenylacetyl chloride. The mixture was refluxed for 16 hours. The reaction mixture was concentrated and purified column chromatography on silica gel using gradient system from 100% hexanes to 100% ethyl acetate. Fractions containing the desired product peak were combined and evaporated. The residue was further purified by crystallization using ethyl acetate. The crystals were filtered and washed with ethyl acetate and then with hexanes. The titled compound was collected as a light yellow solid (2g, Yield 59%).
Example 1 (Compound 1, Table 1)
4-(2-Diethylamino-ethyl)-3-methyl-3,4-dihvdro-1 H-benzofglαuinoxaline-2,5.10- trione
To a solution of 100 mg of 2-bromo-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro- naphthalen-2-yl)-acetamide (0.28 mmol, 1 equivalent) in 10 ml of anhydrous THF was added 40 micro liters of N,N-diethylethylenediamine (0.28 mmol, 1 equivalent) in 1ml of THF. The amine solution was added in three portions over one hour. The mixture was heated at 60 °C for one hour. To the mixture, 20 mg of NaH (95%) (0.84mmol, 3 equivalents) was added in two portions waiting 15minutes after each addition. Then 0.5ml DMSO was added to the reaction and the mixture was stirred for one hour. Precipitates were filtered and washed with THF. The THF was evaporated and the residue was dissolved in DMSO. It was then purified on preparative LCMS using 0.1%NH4OH-CH3CN as a mobile phase. The pure fractions were collected and concentrated to obtain the desired compound as a purple solid (25mg, Yield 25%).
In a process analogous to Example 1 using appropriate starting materials, the corresponding compounds of Tables1-5 were prepared.
Example 2 (Compound 1, Table 6 and Compound 1. Table 71
4-(2-Dimethylamino-ethyl)-1 -methyl-3-phenyl-3,4-dihydro-1 H- benzo[g]quinoxaline- 2,5,10-trione (Compound 1 , Table 6) and 1-(2- Dimethylamino-ethyl)-4-methyl-3-phenyl-3,4-dihydro-1H-benzo[g]quinoxaline- 2,5,10-trione (Compound 1, Table 6)
To a solution of 1g of 2-chloro-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen- 2-yl)-N-methyl-2-phenyl-acetamide (2.7mmol, 1 equivalent) in 5 ml of anhydrous THF was added 1.2 ml of N, N-methylethylenediamine (10.7mmol, 4equivalents) in 1 ml of tetrahydrofuran. The mixture was stirred at room temperature for 10 minutes. To the mixture, approx. 100 mg of NaH (60%) was added until the color of the mixture turned to dark red. Reaction was monitored using TLC. After completion of the reaction, a quick purification of the reaction mixture was carried out by preparative LCMS using 0.1% Formic acid in acetonitrile as a mobile phase. The fractions with the desired mass were combined and evaporated. TLC showed that the residue contains two products. The residue was purified through a normal phase column using ethyl acetate and methanol as a mobile phase and both the products A and B were isolated as pure compounds. The titled compound A was collected as a red-purple solid (500mg, 48% yield). 1H NMR (CDCI3, 400MHz): δ 8.01 (dd, J=2.0Hz, 6.8Hz, 2H), 7.71 (m, 2H), 7.27 (m, 5H), 5.25 (s, 1H), 4.41 (m, 1H), 4.29 (m, 1H), 3.66 (m, 1H), 3.50 (s, 3H), 3.19 (m, 1H), 2.95 (brs, 3H), 2.87 (brs, 3H). 13C NMR (CDCI3, 400MHz): δ 181.9, 178.2, 163.2, 135.0, 134.4, 133.9, 133.4, 131.8, 130.9, 129.3, 128.8, 126.5, 126.3, 126.1 , 125.5, 66.9, 56.3, 49.1 , 44.3, 42.9, 33.7.
The titled compound B was collected as a purple solid (500mg, 48% yield). 1H NMR (CDCI3, 400MHz): .68.18 (d, J=7.2Hz, 1H), 7.98 (d, J=8.8Hz, 1H), 7.69 (m, 2H), 7.31 (m, 3H), 7.20 (m, 2H), 5.07 (s, 1H), 4.62 (m, 1H), 4.26
(m, 1H), 3.75 (m, 1H), 3.63 (s, 3H), 3.30 (m, 1H), 2.99 (brs, 3H), 2.92 (brs,
3H). 13C NMR (CDCI3, 400MHz): 6181.2, 177.3, 163.3, 136.6, 134.4, 134.2,
133.1, 131.8, 131.0, 129.4, 128.9, 126.3, 126.0, 125.5, 121.6, 68.9, 55.7, 44.1,43.1,42.2,41.0.
In a process analogous to Example 2 using appropriate starting materials, the corresponding compounds of Table 6 and Table 7 were prepared
Table 1
Table 2
Table 3
Table 4
Table 5
Table 6
Table 7
Table 8
Table 9
Table 10
Table 11
Table 12
Table 13
Table 14
Table 15
Claims
1. A compound having the structure of Formula (I)
Formula I wherein W, X, Y and Z are each independently selected from a CH, C-R4, C-R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two W, X, Y and Z are O, N and S; wherein, R4, Rs, Re, and R each independently hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8COR9, NR8SO2R9, NRi0CONR8R9; wherein R8, Rg and Rio are independently hydrogen, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl; NR8Rg is also substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; and wherein R8 and R-io can be connected together to form 4, 5,6 or 7-member cyclic ring system, R-i, R2 and R3 are independently H, alkyl, substituted and unsubstituted phenyl or polyaromatic, substituted and unsubstituted heteroaromatic, with hetero atom(s) as N, O, S, substituted and unsubstituted mono or polysubstituted aralkyl, substituted and unsubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle of 3 to 8 ring atoms having one to four hetero atoms selected from N, O, or S ; and wherein substitutions are independently selected from hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl,
halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8R9 is also selected from substituted and unsubstituted mono or polycyclic ring with one to four heteroatoms such as N, O, S; and wherein R8 and R10 may be connected to form a 4, 5, 6 or 7-member cyclic ring system. i and R3 are also independently selected from:
NR13CONR14Ri5 :
-OR1
CONR13R14
wherein n is 2, 3, or 4 and Rn, R12, R13 and R14 are each independently selected from hydrogen, alkyl, cycloalkyl, substituted and unsubstituted aryl, substituted and unsubstituted heteroaryl, substituted and unsubstituted alkylaryl; NR13R14 is also substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; and wherein Rn and R13 may be connected to form 4, 5,6 or 7- member cyclic ring system;
R2 is also selected from:
R11 R11 11 -C — -SR13 -C — -COOR13 -c — -CONR13R14 R12 R12 R12 wherein n is 0, 1, 2 and 3 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, substituted and unsubstituted cycloalkyl, substituted and unsubstituted aryl, substituted and unsubstituted alkaryl ; and wherein NR13R14 is also selected from substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms selected from N, O, and S; and wherein Rn and R13 may be connected to form a 4, 5, 6 or 7 member ring system wherein n is 1, 2 or 3; including salts thereof. 2. The compound of claim 1 wherein W, X, Y and Z are each independently selected from CH, C-R4, C-R5, C-R6 C-R7, O, N or S and wherein no more than two of W, X, Y and Z are O, N and S and wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8COR9, NR8SO2Rg, NR8CONR9Rιo and wherein R8, Rg and R10 are independently hydrogen, alkyl,
H, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl and wherein NR8Rg is also selected from substituted and unsubstituted mono or bicyclic ring, with one to four heteroatoms such as N, O, S; Ri, R and R3 are selected from H, alkyl of 1 to 6 carbon atoms, substituted and unsubstituted phenyl or polyaromatic, substituted and unsubstituted heteroaromatic, with hetero atoms selected from N, O, and S, substituted and unsubstituted aralkyl, substituted and unsubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle of 3 to 8 ring atoms having one to four hetero atoms selected from N, O and S, and wherein substitutions are selected from hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COORs, CONR8R9, NR8R9, NR8CORg, NR8SO2R9, NRιoCONR8R9 wherein NR8Rg is also selected from a mono or polycyclic ring with one to four heteroatoms selected from N, O and S; and wherein R8 and R10 may be connected to form 4, 5,6 or 7-member cyclic ring system;
Ri and R3 are also independently selected from:
R11 R11 R11 -C— -NR13R14 i -c — -NR13COR14 -C — - 13CONRi4Ri5 : R-I2 R12 R12
wherein n is 2, 3, 4, 5 or 6 and Rn, Rι2, R13 and Ru are independently selected from hydrogen, alkyl, cycloalkyl, aryl, heteroaryl, alkylaryl from 7 to 10 carbon atoms; wherein NRι3Rι is also selected from mono or bicyclic ring with one to four heteroatoms selected from N, O and S, and wherein Rn and R-ι3 may be connected to form a 4, 5, 6 or 7-member cyclic ring system;
R2 is also selected from:
-OR13
NRι3R14
wherein n is 0, 1, 2, 3, 4 or 5 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, alkaryl from 7 to 10 carbon atoms, and NR13R-14 is also selected from a mono or bicyclic ring of one to four heteroatoms selected from N, O and S, and wherein Rn and Rι3 may be connected to form a 4, 5, 6 or 7 member ring wherein n is 1 ,
2 or 3, including salts thereof.
3. The compound of claim 2 wherein W and Z are each independently CH, C-R , C-R7 or N and wherein X and Y are each independently C- R5 or C-R6.
4. The compound of claim 1 wherein X and Y are each independently C-R5, C-R6 or N and wherein W and Z are each independently C-R4 or C-R5.
5. The compound of claim 3 wherein W is C-R4 or N and wherein X, Y and Z are each independently C-R5, C-R6 or C-R7.
6. The compound of claim 3 wherein Z is C-R , C-R5, C-R7 or N and wherein W and Y are each independently C-R4, C-R6 or C-R7.
7. The compound of claim 4 wherein X is C-R5 or N and wherein W, Y and Z are each independently C-R4, C-Rβ or C-R .
8. The compound of claim 4 wherein Y is C-R4, C-R5, C-R6, C-R7 or N and wherein X and Z are each independently C-R , C-R5 or C-R7.
9. The compound of claim 8 wherein W X, Y and Z are each independently CH, C-R , C-R5, C-R6or C-R7.
10. The compound of claim 9 wherein each of W, X, Y and Z is CH.
11. The compound of claim 10 wherein Ri and R3 are selected from - hydrogen, -alkyl, cycloalkyl, unsubstituted or substituted phenyl, unsubstituted or substituted benzyl, -methylpyridine, -ethylpyridine, -mehtylindole, - ethylindole, alkoxyethyl-, hydroxyethyl, N,N-dialkyl-ehtyl, , N,N-dialkyl-propyl, methylpyrrole, ethylpyrrole, methylfuran, ethylfuran, -alkylmorpholine, - alkylpiperizine, -alkypiperidine, -alkylpyrrolidine, and R2 is H or lower alkyl.
12. Compounds of claim 1 wherein Ri is
14. The compounds of claim 1 wherein Ri is
15. The compounds of claim 1 wherein R3 is
16. The compounds of claim 1 wherein R^ is
18. The compounds of claim 10 wherein Ri is
19. The compounds of claim 10 wherein R3 is
20. The compounds of claim 10 wherein Ri is
21. The compounds of claim 10 wherein R3 is
22. The compound of claim 10 wherein Ri is
R 11
-NR13S02Rι4
R12 wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
23. The compound of claim 10 wherein R3 is
24. A compound of claim 1 having a structure of Table 1 including salts thereof.
25. A compound of claim 1 having a structure of Table 2 including salts thereof.
26. A compound of claim 1 having a structure of Table 3 including salts thereof.
27. A compound of claim 1 having a structure of Table 4 including salts thereof.
28. A compound of claim 1 having a structure of Table 5 including salts thereof.
29. A compound of claim 1 having a structure of Table 6 including salts thereof.
30. A compound of claim 1 haying a structure of Table 7 including salts thereof.
31. A compound of claim 1 having a structure of Table 8 including salts thereof.
32. A compound of claim 1 having a structure of Table 9 including salts thereof.
33. A compound of claim 1 having a structure of Table 10 including salts thereof.
34. A compound of claim 1 having a structure of Table 11 including salts thereof.
35. A compound of claim 1 having a structure of Table 12 including salts thereof.
36. A compound of claim 1 having a structure of Table 13 including salts thereof.
37. A composition comprising a therapeutically effective amount of a compound of Claim 1 in a pharmaceutically acceptable carrier.
38. A method for preventing or treating a disease associated with a change in levels of expression of particular sets of genes in a mammal comprising administering to said mammal an effective amount of a compound of Claim 1.
39. A method for preventing or treating a disorder modulated by altered gene expression, wherein the disorder is selected from the group consisting of cancer, cardiovascular disorders, arthritis, osteoporosis, inflammation, periodontal disease and skin disorders, comprising administering to a mammal in need of such treatment or prevention a therapeutically effective amount of a compound of Claim 1.
40. The method of Claim 39, wherein the disorder is cancer, and the treatment prevents, arrests or reverts tumor growth, metastasis or both.
41. The method of Claim 39 wherein the cancer is colon cancer.
42. The method of claim 41 wherein said colon cancer is adenocarcinoma.
43. A gene set wherein expression of each member of said gene set is modulated as a result of treatment with a compound of claim 1.
44. The gene set of claim 43 wherein expression of each member of said gene set is increased or each member of said gene set is decreased as a result of said contacting.
45. The gene set of claim 43 wherein the members of said gene set are selected from the genes identified in Table 8.
46. The gene set of claim 43 wherein said gene set is present in a cell.
47. A set of genes comprising a plurality of subsets of genes wherein each subset of said plurality is a gene set identified by the method of claim 43.
48. A method for identifying an agent that modulates the expression of a gene set of claim 43, comprising: (a) contacting a compound with a test system containing one or more polynucleotides corresponding to each of the members of the gene set of claim 40 under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said contacting; wherein said change in expression in step (b) indicates modulation of the members of said gene set thereby identifying said test compound as an agent that modulates the expression of said gene set.
49. The method of claim 48 wherein said change in expression is a decrease in expression of said one or more polynucleotides.
50. The method of claim 48 wherein said change in expression is a change in transcription of said one or more polynucleotides.
51. The method of claim 48 wherein said change in expression is determined by determining a change in activity of a polypeptide encoded by said polynucleotide.
52. The method of claim 48 wherein said test system is a cell containing said polynucleotides.
53. The method of claim 51 wherein said cell is a cancer cell.
54. The method of claim 53 wherein said cancer cell is a colon cancer cell.
55. The method of claim 54 wherein said colon cancer cell is an adenocarcinoma cancer cell.
56. The method of claim 55 wherein said cell is a recombinant cell engineered to contain said set of genes.
57. Compounds identified as having activity using the method of claim
45.
58. The gene set of claim 43 wherein said gene set comprises a subset of the genes of Table 14.
59. The gene set of claim 43 wherein said gene set comprises a subset of the genes of Table 15.
60. The method of claim 48 wherein said compound modulates the expression of a subset of genes of Table 15.
I ll
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