Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening

MedChemComm

Volumn 2, Issue 9, 2011, Pages 853-859

  Vasanthanathan, Poongavanam ^a   Lastdrager, Jeroen ^b   Oostenbrink, Chris ^b,c   Commandeur, Jan N M ^b   Vermeulen, Nico P E ^b   Jørgensen, Flemming S ^a   Olsen, Lars ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 1A2; ENZYME INHIBITOR; LIGAND;

ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG BINDING; DRUG SCREENING; DRUG STRUCTURE; ENZYME ACTIVE SITE; ENZYME INHIBITION; IC 50; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL;

EID: 80052378180     PISSN: 20402503     EISSN: 20402511     Source Type: Journal    
DOI: 10.1039/c1md00087j     Document Type: Article

References (43)

1. F. P. Guengerich A malleable catalyst dominates the metabolism of drugs Proc. Natl. Acad. Sci. U. S. A. 2006 103 13565 13566 (Pubitemid 44413947)
2. F. P. Guengerich Cytochrome P450 and chemical toxicology Chem. Res. Toxicol. 2008 21 70 83 (Pubitemid 351219709)
3. D. W. Nebert D. W. Russell Clinical importance of the cytochromes P450 Lancet 2002 360 1155 1162 (Pubitemid 35246494)
4. R. Ortiz de Montellano, Cytochrome P450: Structure, Mechanism, and Biochemistry, Kluwer Academic/Plenum Publishers, New York, 2005
5. L. C. Wienkers T. G. Heath Predicting in vivo drug interactions from in vitro drug discovery data Nat. Rev. Drug Discovery 2005 4 825 833 (Pubitemid 41553963)
6. J. A. Williams R. Hyland B. C. Jones D. A. Smith S. Hurst T. C. Goosen V. Peterkin J. R. Koup S. E. Ball Drug-drug interactions for UDP- glucuronosyltransferase substrates: a pharmacokinetic explanation for typically observed low exposure (AUCi/AUC) ratios Drug Metab. Dispos. 2004 32 1201 1208 (Pubitemid 39410902)
7. M. Pirmohamed B. K. Park Cytochrome P450 enzyme polymorphisms and adverse drug reactions Toxicology 2003 192 23 32 (Pubitemid 37153341)
8. D. Kim F. P. Guengerich Cytochrome P450 activation of arylamines and heterocyclic amines Annu. Rev. Pharmacol. 2005 45 27 49 (Pubitemid 40261797)
9. T. Shimada H. Yamazaki M. Mimura Y. Inui F. P. Guengerich Interindividual variations in human liver cytochrome P-450 enzymes involved in the oxidation of drugs, carcinogens and toxic chemicals: studies with liver microsomes of 30 Japanese and 30 Caucasians J. Pharmacol. Exp. Ther. 1994 270 414 423 (Pubitemid 24229655)
10. L. H. Patterson G. I. Murray Tumour cytochrome P450 and drug activation Curr. Pharm. Des. 2002 8 1335 1347 (Pubitemid 34591350)
11. C. C. Hong B. K. Tang G. Hammond D. Tritchler M. Yaffe N. Boyd Cytochrome P450 1A2 (CYP1A2) activity and risk factors for breast cancer: a cross-sectional study Breast Cancer Res. 2004 6 R352 R365
12. A. Seow B. Zhao E. J. Lee W. T. Poh M. Teh P. Eng Y. T. Wang W. C. Tan H. P. Lee Cytochrome P4501A2 (CYP1A2) activity and lung cancer risk: a preliminary study among Chinese women in Singapore Carcinogenesis 2001 22 673 677 (Pubitemid 32293531)
13. I. Kola J. Landis Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discovery 2004 3 711 715 (Pubitemid 39173511)
14. L. Afzelius C. H. Arnby A. Broo L. Carlsson C. Isaksson U. Jurva B. Kjellander K. Kolmodin K. Nilsson F. Raubacher L. Weidolf State-of-the-art tools for computational site of metabolism predictions: comparative analysis, mechanistical insights, and future applications Drug Metab. Rev. 2007 39 61 86
15. G. Cruciani E. Carosati B. B. De K. Ethirajulu C. Mackie T. Howe R. Vianello MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist J. Med. Chem. 2005 48 6970 6979 (Pubitemid 41533118)
16. E. Stjernschantz N. P. Vermeulen C. Oostenbrink Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450 Expert Opin. Drug Metab. Toxicol. 2008 4 513 527 (Pubitemid 351890736)
17. P. Czodrowski J. M. Kriegl S. Scheuerer T. Fox Computational approaches to predict drug metabolism Expert Opin. Drug Metab. Toxicol. 2009 5 15 27
18. M. Hennemann A. Friedl M. Lobell J. Keldenich A. Hillisch T. Clark A. H. Goller CypScore: quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory ChemMedChem 2009 4 657 669
19. P. Rydberg D. E. Gloriam J. Zaretzki C. Breneman L. Olsen SMARTCyp: a 2D method for prediction of cytochrome P450-mediated drug metabolism ACS Med. Chem. Lett. 2010 1 96 100
20. R. P. Sheridan K. R. Korzekwa R. A. Torres M. J. Walker Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9 J. Med. Chem. 2007 50 3173 3184 (Pubitemid 47065966)
21. S. B. Singh L. Q. Shen M. J. Walker R. P. A. Sheridan Model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules J. Med. Chem. 2003 46 1330 1336 (Pubitemid 36512698)
22. P. Rydberg D. E. Gloriam L. Olsen The SMARTCyp cytochrome P450 metabolism prediction server Bioinformatics 2010 26 2988 2989
23. J. M. Kriegl L. Eriksson T. Arnhold B. Beck E. Johansson T. Fox Multivariate modeling of cytochrome P450 3A4 inhibition Eur. J. Pharm. Sci. 2005 24 451 463 (Pubitemid 40387259)
24. J. M. Kriegl T. Arnhold B. Beck T. Fox Prediction of human cytochrome P450 inhibition using support vector machines QSAR Comb. Sci. 2005 24 491 502 (Pubitemid 40839677)
25. L. Afzelius I. Zamora M. Ridderström T. B. Andersson A. Karlén C. M. Masimirembwa Competitive CYP2C9 inhibitors: enzyme inhibition studies, protein homology modeling, and three-dimensional quantitative structure-activity relationship analysis Mol. Pharmacol. 2001 59 909 919 (Pubitemid 32274021)
26. L. Terfloth B. Bienfait J. Gasteiger Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates J. Chem. Inf. Model. 2007 47 1688 1701 (Pubitemid 47210071)
27. P. Vasanthanathan O. Taboureau C. Oostenbrink N. P. Vermeulen L. Olsen F. S. Jørgensen Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques Drug Metab. Dispos. 2009 37 658 664
28. D. Zhou R. Liu S. A. Otmani S. W. Grimm R. J. Zauhar I. Zamora Rapid classification of CYP3A4 inhibition potential using support vector machine approach Lett. Drug Des. Discovery 2007 4 192 200 (Pubitemid 46474159)
29. PubChem bioassay website, http://pubchem. ncbi. nlm. nih. gov, accessed August 2009
30. M. Ekroos T. Sjogren Structural basis for ligand promiscuity in cytochrome P450 3A4 Proc. Natl. Acad. Sci. U. S. A. 2006 103 13682 13687 (Pubitemid 44413967)
31. P. R. Porubsky K. M. Meneely E. E. Scott Structures of human cytochrome P-450 2E1. Insights into the binding of inhibitors and both small molecular weight and fatty acid substrates J. Biol. Chem. 2008 283 33698 33707
32. P. R. Porubsky K. P. Battaile E. E. Scott Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode J. Biol. Chem. 2010 285 22282 22290
33. P. Rowland F. E. Blaney M. G. Smyth J. J. Jones V. R. Leydon A. K. Oxbrow C. J. Lewis M. G. Tennant S. Modi D. S. Eggleston R. J. Chenery A. M. Bridges Crystal structure of human cytochrome P450 2D6 J. Biol. Chem. 2006 281 7614 7622 (Pubitemid 43847532)
34. S. Sansen J. K. Yano R. L. Reynald G. A. Schoch K. J. Griffin C. D. Stout E. F. Johnson Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2 J. Biol. Chem. 2007 282 14348 14355 (Pubitemid 47100434)
35. M. R. Wester J. K. Yano G. A. Schoch C. Yang K. J. Griffin C. D. Stout E. F. Johnson The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution J. Biol. Chem. 2004 279 35630 35637 (Pubitemid 39100565)
36. P. A. Williams J. Cosme A. Ward H. C. Angove V. D. Matak H. Jhoti Crystal structure of human cytochrome P450 2C9 with bound warfarin Nature 2003 424 464 468 (Pubitemid 36917499)
37. P. A. Williams J. Cosme D. M. Vinkovic A. Ward H. C. Angove P. J. Day C. Vonrhein I. J. Tickle H. Jhoti Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone Science 2004 305 683 686 (Pubitemid 39006760)
38. J. K. Yano M. R. Wester G. A. Schoch K. J. Griffin C. D. Stout E. F. Johnson The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution J. Biol. Chem. 2004 279 38091 38094 (Pubitemid 39295952)
39. J. K. Yano M. H. Hsu K. J. Griffin C. D. Stout E. F. Johnson Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen Nat. Struct. Mol. Biol. 2005 12 822 823 (Pubitemid 43086258)
40. P. Vasanthanathan J. Hritz O. Taboureau L. Olsen F. S. Jørgensen N. P. Vermeulen C. Oostenbrink Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands J. Chem. Inf. Model. 2009 49 43 52
41. C. A. Baxter C. W. Murray D. E. Clark D. R. Westhead M. D. Eldridge Flexible docking using Tabu search and an empirical estimate of binding affinity Proteins: Struct., Funct., Genet. 1998 33 367 382 (Pubitemid 28516342)
42. M. D. Eldridge C. W. Murray T. R. Auton G. V. Paolini R. P. Mee Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes J. Comput.-Aided Mol. Des. 1997 11 425 445 (Pubitemid 127505895)
43. J. K. Yano T. T. Denton M. A. Cerny X. Zhang E. F. Johnson J. R. Cashman Synthetic inhibitors of cytochrome P-450 2A6: inhibitory activity, difference spectra, mechanism of inhibition, and protein cocrystallization J. Med. Chem. 2006 49 6987 7001 (Pubitemid 44885987)