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WO2003040994A3 - Cyp2c9 binding models - Google Patents

Cyp2c9 binding models Download PDF

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Publication number
WO2003040994A3
WO2003040994A3 PCT/US2002/034982 US0234982W WO03040994A3 WO 2003040994 A3 WO2003040994 A3 WO 2003040994A3 US 0234982 W US0234982 W US 0234982W WO 03040994 A3 WO03040994 A3 WO 03040994A3
Authority
WO
WIPO (PCT)
Prior art keywords
measure
descriptors
cyp2c9
compound
binding affinity
Prior art date
Application number
PCT/US2002/034982
Other languages
French (fr)
Other versions
WO2003040994A2 (en
Inventor
Jean-Pierre Kocher
Todd J A Ewing
Kenneth R Korzekwa
Original Assignee
Arqule Inc
Jean-Pierre Kocher
Todd J A Ewing
Kenneth R Korzekwa
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
Application filed by Arqule Inc, Jean-Pierre Kocher, Todd J A Ewing, Kenneth R Korzekwa filed Critical Arqule Inc
Priority to AU2002357683A priority Critical patent/AU2002357683A1/en
Publication of WO2003040994A2 publication Critical patent/WO2003040994A2/en
Publication of WO2003040994A3 publication Critical patent/WO2003040994A3/en

Links

Classifications

    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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
    • G16C20/60—In silico combinatorial chemistry
    • 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
    • G16C20/60—In silico combinatorial chemistry
    • G16C20/64—Screening of libraries
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Landscapes

  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Library & Information Science (AREA)
  • Computing Systems (AREA)
  • Molecular Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Artificial Intelligence (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Computer models described herein predict the binding affinity of compounds with the 2C9 isoform of the Cytochrome p450 family of enzymes. The models predict Ki or pKi for arbitrary compounds. They accomplish this by using selected molecular properties of the compound in question. Numeric values of these properties (also called descriptors) are received by the model. Execution of the model performs a calculation based on these descriptors and returns a value of binding affinity. The descriptors may include a measure of lipophilicity, a measure of aromaticity, and a measure of partial negative charge on the compound.
PCT/US2002/034982 2001-11-02 2002-11-01 Cyp2c9 binding models WO2003040994A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002357683A AU2002357683A1 (en) 2001-11-02 2002-11-01 Cyp2c9 binding models

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US35011701P 2001-11-02 2001-11-02
US60/350,117 2001-11-02

Publications (2)

Publication Number Publication Date
WO2003040994A2 WO2003040994A2 (en) 2003-05-15
WO2003040994A3 true WO2003040994A3 (en) 2005-01-13

Family

ID=23375311

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/034982 WO2003040994A2 (en) 2001-11-02 2002-11-01 Cyp2c9 binding models

Country Status (2)

Country Link
AU (1) AU2002357683A1 (en)
WO (1) WO2003040994A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7194359B2 (en) 2004-06-29 2007-03-20 Pharmix Corporation Estimating the accuracy of molecular property models and predictions

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7148046B2 (en) 2001-04-02 2006-12-12 Astex Therapeutics Limited Crystal structure of cytochrome P450
US20040053383A1 (en) * 2001-10-25 2004-03-18 Astex Technology Ltd. Crystals of cytochrome P450 2C9, structures thereof and their use

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998038208A2 (en) * 1997-02-28 1998-09-03 Bearsden Bio, Inc. Method of determining protein-ligand interactions via computer modeling
WO2001036980A2 (en) * 1999-11-18 2001-05-25 Melacure Therapeutics Ab A process for identifying the active site in a biological target

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998038208A2 (en) * 1997-02-28 1998-09-03 Bearsden Bio, Inc. Method of determining protein-ligand interactions via computer modeling
WO2001036980A2 (en) * 1999-11-18 2001-05-25 Melacure Therapeutics Ab A process for identifying the active site in a biological target

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
EKINS S ET AL: "PHARMACOPHORE AND THREE-DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP METHODS FOR MODELING CYTOCHROME P450 ACTIVE SITES", DRUG METABOLISM AND DISPOSITION, WILLIAMS AND WILKINS., BALTIMORE, MD, US, vol. 29, no. 7, July 2001 (2001-07-01), pages 936 - 944, XP001122105, ISSN: 0090-9556 *
JONES J P: "ACCELERATED COMMUNICATION THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP FOR INHIBITORS OF CYTOCHROME P4502C9", DRUG METABOLISM AND DISPOSITION, WILLIAMS AND WILKINS., BALTIMORE, MD, US, vol. 24, no. 1, January 1996 (1996-01-01), pages 1 - 6, XP000997854, ISSN: 0090-9556 *
KREPETS V V ET AL: "Prediction of binding affinities for protein-ligand complexes with neural network models", DISCOVERY SCIENCE. THIRD INTERNATIONAL CONFERENCE, DS 2000. PROCEEDINGS (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE VOL.1967) SPRINGER-VERLAG BERLIN, GERMANY, 2000, pages 240 - 241, XP008039020, ISBN: 3-540-41352-9 *
RAO SREEDHARA ET AL: "A refined 3-dimensional QSAR of cytochrome P450 2C9: Computational predictions of drug interactions", JOURNAL OF MEDICINAL CHEMISTRY, vol. 43, no. 15, 27 July 2000 (2000-07-27), pages 2789 - 2796, XP002306303, ISSN: 0022-2623 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7194359B2 (en) 2004-06-29 2007-03-20 Pharmix Corporation Estimating the accuracy of molecular property models and predictions

Also Published As

Publication number Publication date
AU2002357683A1 (en) 2003-05-19
WO2003040994A2 (en) 2003-05-15

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