WO2005056814A3 - Methods and systems for analyzing and determining ligand-residue interaction - Google Patents

Methods and systems for analyzing and determining ligand-residue interaction Download PDF

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Publication number
WO2005056814A3
WO2005056814A3 PCT/US2004/041016 US2004041016W WO2005056814A3 WO 2005056814 A3 WO2005056814 A3 WO 2005056814A3 US 2004041016 W US2004041016 W US 2004041016W WO 2005056814 A3 WO2005056814 A3 WO 2005056814A3
Authority
WO
WIPO (PCT)
Prior art keywords
binding
protein
basis
residue
fragment
Prior art date
Application number
PCT/US2004/041016
Other languages
French (fr)
Other versions
WO2005056814A2 (en
Inventor
Stephan Brunner
David Mosenkis
Frank Hollinger
William Chiang
Original Assignee
Locus Pharmaceuticals Inc
Stephan Brunner
David Mosenkis
Frank Hollinger
William Chiang
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US10/730,267 external-priority patent/US20050123993A1/en
Application filed by Locus Pharmaceuticals Inc, Stephan Brunner, David Mosenkis, Frank Hollinger, William Chiang filed Critical Locus Pharmaceuticals Inc
Priority to EP04813345A priority Critical patent/EP1704493A4/en
Priority to CA002548882A priority patent/CA2548882A1/en
Publication of WO2005056814A2 publication Critical patent/WO2005056814A2/en
Publication of WO2005056814A3 publication Critical patent/WO2005056814A3/en

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—Bacteria
    • G01N33/5695—Mycobacteria
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/50—Molecular design, e.g. of drugs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like

Abstract

A method implemented in the form of a computer simulation code for evaluating the free energy of binding between polypeptide amino acid residues and one or more molecular fragment types is presented. The basis of the method is a novel weighted Metropolis Monte Carlo approach for sampling the grand canonical ensemble. By making use of the properties of the grand canonical ensemble, the affinity of fragments for binding in the vicinity of each protein residue can be efficiently computed. The binding volume associated to each fragment-residue pair is estimated on the basis of a simple proximity criteria, and a useful affinity mapping of the protein surface can be obtained in this way. The analysis of such data for various fragment types provides valuable information to help identify protein binding sites, as well as to identify key fragments used for building potential drug leads
PCT/US2004/041016 2003-12-09 2004-12-08 Methods and systems for analyzing and determining ligand-residue interaction WO2005056814A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP04813345A EP1704493A4 (en) 2003-12-09 2004-12-08 Methods and systems for analyzing and determining ligand-residue interaction
CA002548882A CA2548882A1 (en) 2003-12-09 2004-12-08 Methods and systems for analyzing and determining ligand-residue interaction

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US10/730,267 2003-12-09
US10/730,267 US20050123993A1 (en) 2003-12-09 2003-12-09 Methods of determining ligand residue binding affinity
US10/920,234 US7415361B2 (en) 2003-12-09 2004-08-18 Methods and systems for analyzing and determining ligand-residue interaction
US10/920,234 2004-08-18

Publications (2)

Publication Number Publication Date
WO2005056814A2 WO2005056814A2 (en) 2005-06-23
WO2005056814A3 true WO2005056814A3 (en) 2005-10-06

Family

ID=34681738

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/041016 WO2005056814A2 (en) 2003-12-09 2004-12-08 Methods and systems for analyzing and determining ligand-residue interaction

Country Status (4)

Country Link
US (1) US7415361B2 (en)
EP (1) EP1704493A4 (en)
CA (1) CA2548882A1 (en)
WO (1) WO2005056814A2 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040267456A1 (en) * 2003-06-27 2004-12-30 Stephan Brunner Method and computer program product for drug discovery using weighted grand canonical metropolis Monte Carlo sampling
US20050222776A1 (en) * 2004-03-31 2005-10-06 Locus Pharmaceuticals, Inc. Method for fragment preparation
US20070005258A1 (en) * 2004-06-07 2007-01-04 Frank Guarnieri Identification of ligands for macromolecules
US20110130968A1 (en) * 2009-11-29 2011-06-02 Matthew Clark Method for computing ligand - host binding free energies
CN105593861A (en) * 2013-10-23 2016-05-18 陶氏环球技术有限责任公司 Methods, systems, and devices for designing molecules

Citations (3)

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US20020055536A1 (en) * 1996-09-26 2002-05-09 Dewitte Robert S. System and method for structure-based drug design that includes accurate prediction of binding free energy
US20020099506A1 (en) * 2000-03-23 2002-07-25 Floriano Wely B. Methods and apparatus for predicting ligand binding interactions
US6735530B1 (en) * 1998-09-23 2004-05-11 Sarnoff Corporation Computational protein probing to identify binding sites

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US5453937A (en) 1993-04-28 1995-09-26 Immunex Corporation Method and system for protein modeling
US5884230A (en) 1993-04-28 1999-03-16 Immunex Corporation Method and system for protein modeling
US5600571A (en) 1994-01-18 1997-02-04 The Trustees Of Columbia University In The City Of New York Method for determining protein tertiary structure
US6341256B1 (en) 1995-03-31 2002-01-22 Curagen Corporation Consensus configurational bias Monte Carlo method and system for pharmacophore structure determination
AU5721596A (en) 1995-04-27 1996-11-18 Mount Sinai School Of Medicine Of The City University Of New York, The Method for identifying structurally active compounds using c onformational memories
US6251620B1 (en) 1995-08-30 2001-06-26 Ariad Pharmaceuticals, Inc. Three dimensional structure of a ZAP tyrosine protein kinase fragment and modeling methods
SK88997A3 (en) 1995-10-30 1998-05-06 Smithkline Beecham Corp Method of inhibiting cathepsin k
US6622094B2 (en) 1996-02-15 2003-09-16 The Trustees Of Columbia University In The City Of New York Method for determining relative energies of two or more different molecules
US6083711A (en) 1996-05-15 2000-07-04 Smithkline Beecham Corporation Proteases compositions capable of binding to said site, and methods of use thereof
GB9616105D0 (en) 1996-07-31 1996-09-11 Univ Kingston TrkA binding site of NGF
US5854992A (en) 1996-09-26 1998-12-29 President And Fellows Of Harvard College System and method for structure-based drug design that includes accurate prediction of binding free energy
US6178384B1 (en) 1997-09-29 2001-01-23 The Trustees Of Columbia University In The City Of New York Method and apparatus for selecting a molecule based on conformational free energy
US6426205B1 (en) 1997-10-24 2002-07-30 Mount Sinai Hospital Corporation Methods and compositions for modulating ubiquitin dependent proteolysis
EP1047107B1 (en) 1999-04-06 2006-10-04 Micromass UK Limited Method of identifying peptides and protein by mass spectrometry
US6716614B1 (en) 1999-09-02 2004-04-06 Lexicon Genetics Incorporated Human calcium dependent proteases, polynucleotides encoding the same, and uses thereof
US6640191B1 (en) 1999-12-30 2003-10-28 The Regents Of The University Of California Library design in combinatorial chemistry by Monte Carlo methods
WO2004078932A2 (en) 2003-03-03 2004-09-16 Locus Pharmaceuticals, Inc. Methods and systems for preparing virtual representations of molecules
US20040267456A1 (en) 2003-06-27 2004-12-30 Stephan Brunner Method and computer program product for drug discovery using weighted grand canonical metropolis Monte Carlo sampling
EP1644860A4 (en) * 2003-06-27 2008-08-06 Locus Pharmaceuticals Inc Method and computer program product for drug discovery using weighted grand canonical metropolis monte carlo sampling

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020055536A1 (en) * 1996-09-26 2002-05-09 Dewitte Robert S. System and method for structure-based drug design that includes accurate prediction of binding free energy
US6735530B1 (en) * 1998-09-23 2004-05-11 Sarnoff Corporation Computational protein probing to identify binding sites
US20020099506A1 (en) * 2000-03-23 2002-07-25 Floriano Wely B. Methods and apparatus for predicting ligand binding interactions

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
APOSTOLAKIS J. ET AL: "Docking Small Ligands in Flexible Binding Sites", JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 19, no. 1, 1998, pages 21 - 37, XP002988645 *
FAHMY A. AND WAGNER G.: "TreeDock: A tool for protein docking based on minimizing van der Waals energies", JOURNAL OF AMERICAN CHEMICAL SOCIETY, vol. 124, no. 7, 2002, pages 1241 - 1250, XP002988646 *

Also Published As

Publication number Publication date
US20050123995A1 (en) 2005-06-09
EP1704493A4 (en) 2008-09-10
WO2005056814A2 (en) 2005-06-23
EP1704493A2 (en) 2006-09-27
US7415361B2 (en) 2008-08-19
CA2548882A1 (en) 2005-06-23

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