Comparative QSAR analyses of competitive CYP2C9 inhibitors using three-dimensional molecular descriptors

Chemical Biology and Drug Design

Volumn 78, Issue 1, 2011, Pages 112-123

  Lather, Viney ^a,b   Fernandes, Miguel X ^a  

^a UNIVERSITY OF MADEIRA   (Portugal)

^b Jan Nayak Ch Devi Lal Memorial College of Pharmacy   (India)

Author keywords

3D MoRSE; ADMET; CYP2C9; GETAWAY; QSAR; RDF; WHIM

Indexed keywords

A 4438; CYTOCHROME P450 2C9 INHIBITOR; D 62126; DICOUMAROL; ENZYME INHIBITOR; FLUINDOSTATIN; FLUVOXAMINE; KAEMPFEROL; MICONAZOLE; NICARDIPINE; OMEPRAZOLE; OMEPRAZOLE SULFONE; PANTOPRAZOLE; PHENYLBUTAZONE; PHENYTOIN; PROGESTERONE; PYRANOCOUMARIN DERIVATIVE; PYRIMETHAMINE; QUERCETIN; QUININE; QUINOLINE 4 CARBOXAMIDE DERIVATIVE; RABEPRAZOLE; SULFAPHENAZOLE; TIABENDAZOLE; UNCLASSIFIED DRUG; WARFARIN; ZAFIRLUKAST;

ARTICLE; COMPARATIVE STUDY; CONFORMATION; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME INHIBITION; MATHEMATICAL MODEL; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ARYL HYDROCARBON HYDROXYLASES; ENZYME INHIBITORS; HUMANS; LEAST-SQUARES ANALYSIS; MODELS, MOLECULAR; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79958865966     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2011.01106.x     Document Type: Article

References (35)

1. Nelson D.R., Koymans L., Kamataki T., Steqeman J.J., Feyereisen R., Waxman D.J., Waterman M.R., Gotoh O., Coon M.J., Estabrook R.W., Gunsalus I.C., Nebert D.W. (1996) P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics;6:1-42.
2. Wrighton S.A., Stevens J.C. (1992) The human hepatic cytochromes P450 involved in drug metabolism. Crit Rev Toxicol;22:1-21.
3. Gonzalez F.J. (1992) Human cytochromes P450: problems and prospects. Trends Pharmacol Sci;13:346-352.
4. Nelson D.R., Zeldin D.C., Hoffman S M.G., Maltais L.J., Wain H.M., Nebert D.W. (2004) Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics;14:1-18.
5. Cholerton S., Daly A.K., Idle J.R. (1992) The role of individual human cytochromes P450 in drug metabolism and clinical response. Trends Pharmcol Sci;13:434-439.
6. Miners J.O., Birkett D.J. (1998) Cytochrome P4502C9: an enzyme of major importance in human drug metabolism. Br J Clin Pharmacol;45:525-538.
7. Hall S.D., Hamman M.A., Rettie A.E., Wienkers L.C., Trager W.F., VandenBranden M., Wrighton S.A. (1994) Relationships between the levels of cytochrome P4502C9 and its prototypic catalytic activities in human liver microsomes. Drug Metab Dispos;22:975-977.
8. Rettie A.E., Jones J.P. (2005) Clinical and toxicological relevance of CYP2C9: drug-drug interactions and pharmacogenetics. Ann Rev Pharmacol Toxicol;45:477-494.
9. Williams P.A., Cosme J., Ward A., Angove H.C., Matak Vinkovic D., Jhoti H. (2003) Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature;424:464-468.
10. Wester M.R., Yano J.K., Schoch G.A., Yang C., Griffin K.J., Stout C.D., Johnson E.F. (2004) The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0 A resolution. J Biol Chem;279:35630-35637.
11. Mancy A., Broto P., Dijols S., Dansette P.M., Mansuy D. (1995) The substrate binding site of human liver cytochrome P4502C9: an approach using designed tienilic acid derivatives and molecular modeling. Biochemistry;34:10365-10375.
12. Morsman J.M., Smith D.A., Jones B.C., Hawksworth G.M. (1995) Role of hydrogen-bonding in substrate structure-activity relationships for CYP2C9. ISSX Proc;8:259.
13. Klose T.S., Ibeanu G.C., Ghanayem B.I., Pedersen L.G., Li L., Hall S.D., Goldstein J.A. (1998) Identification of residues 286 and 289 as critical for conferring substrate specificity of human CYP2C9 for diclofenac and ibuprofen. Arch Biochem Biophys;357:240-248.
14. Poli-Scaife S., Attias R., Dansette P.M., Mansuy D. (1997) The substrate binding site of human liver cytochrome P4502C9: an NMR study. Biochemistry;36:12672-12682.
15. Jones J.P., He M., Trager W.F., Rettie A.E. (1996b) Three-dimensional quantitative structure activity relationship for inhibitors of cytochrome P4502C9. Drug Metab Dispos;24:1-6.
16. Ekins S., Bravi G., Binkley S., Gillespie J.S., Ring B.J., Wikel J.H., Wrighton S.A. (2000) Three- and four-dimensional quantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2C9 inhibitors. Drug Metab Dispos;28:994-1002.
17. Afzelius L., Masimirembwa C.M., Karlen A., Andersson T.B., Zamora I. (2002) Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors. J Comp Aid Mol Des;16:443-458.
18. Afzelius L., Zamora I., Masimirembwa C.M., Karlen A., Andersson T.B., Mecucci S., Baroni M., Cruciani G. (2004) Conformer- and alignment-independent model for predicting structurally diverse competitive CYP2C9 inhibitors. J Med Chem;47:907-914.
19. Weininger D. (1998) SMILES 1. Introduction and encoding rules. J Chem Inf Comput Sci;28:31.
20. Bostrom J., Greenwood J.R., Gottfries J. (2003) Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model;21:449-462.
21. Tetko I.V., Gasteiger J., Todeschini R., Mauri A., Livingstone D., Ertl P., Palyulin V.A., Rodchenko E.V., Zefirov N.S., Makarenko A.S., Tanchuk V.Y., Prokopenko V.V. (2005) Virtual computational chemistry laboratory-design and description. J Comput Aid Mol Des;19:453-463.
22. Schuur J.H., Seizer P., Gasteiger J. (1996) The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. J Chem Inf Comput Sci;36:334-344.
23. Saiz-Urra L., Gonzalez M.P., Teijeira M. (2006) QSAR studies about cytotoxicity of benzophenazines with dual inhibition toward both topoisomerases I and II: 3D-MoRSE descriptors and statistical considerations about variable selection. Bioorg Med Chem;14:7347-7358.
24. Consonni V., Todeschini R., Pavan M. (2002) Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 1. Theory of the novel 3D molecular descriptors. J Chem Inf Comput Sci;42:682-692.
25. 2A adenosine receptor agonists. Eur J Med Chem;40:1080-1086.
26. Todeschini R., Consonni V. (2000) Handbook of Molecular Descriptors. Weinheim, Germany: Wiley-VCH.
27. Gonzalez M.P., Teran C., Teijeira M., Helguera A.M. (2006) Radial distribution function descriptors: an alternative for predicting A2A adenosine receptor agonists. Eur J Med Chem;41:56-62.
28. Bravi G., Gancia E., Mascani P., Pegna M., Todeschini R., Zaliani A. (1997) MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: a comparative 3D-QSAR study in a series of steroids. J Comput Aid Mol Des;11:79-92.
29. Bravi G., Wikel J.H. (2000a) Application of MS-WHIM descriptors 1. Introduction of new molecular surface properties and 2. Prediction of binding affinity data. Quant Struct Act Rel;19:29-38.
30. Golbraikh A., Trophsa A. (2000) Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. Mol Div;5:231-234.
31. Wold S., Eriksson L. (1995) Validation tools. In: van de Waterbeemd H., editor. Chemometric Methods in Molecular Design. Weinheim: VCH; p. 312-317.
32. Darlington R.B. (1990) Regression and Linear Models. New York: McGraw-Hill.
33. Golbraikh A., Trophsa A. (2002) Beware of q2! J Mol Graph Model;20:269-276.
34. Roy P., Roy K. (2008) On some aspects of variable selection for partial least squares regression models. QSAR Comb Sci;27:302-313.
35. Peng C., Cape J.L., Rushmore T., Crouch G.J., Jones J.P. (2008) Cytochrome P450 2C9 Type II binding studies on Quinoline-4-carboxamide analogs. J Med Chem;51:8000-8011.