Insights into molecular basis of cytochrome P450 inhibitory promiscuity of compounds

Journal of Chemical Information and Modeling

Volumn 51, Issue 10, 2011, Pages 2482-2495

  Cheng, Feixiong ^a   Yu, Yue ^a   Zhou, Yadi ^a   Shen, Zhonghua ^a   Xiao, Wen ^a   Liu, Guixia ^a   Li, Weihua ^a   Lee, Philip W ^a,b   Tang, Yun ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ECONOMIC AND SOCIAL EFFECTS; HYDROGEN BONDS; SUPPORT VECTOR MACHINES;

CLASSIFICATION MODELS; CROSS VALIDATION; MOLECULAR BASIS; MOLECULAR COMPLEXITY; MOLECULAR PROPERTIES; POTENTIAL EFFECTS; RECEIVER OPERATING CHARACTERISTIC CURVES; SUPPORT VECTOR MACHINE ALGORITHM;

DRUG INTERACTIONS;

CYTOCHROME P450; ENZYME INHIBITOR; ISOENZYME;

ALGORITHM; ARTICLE; BIOCATALYSIS; CHEMICAL PHENOMENA; CHEMISTRY; DRUG ANTAGONISM; DRUG INTERACTION; DRUG SCREENING; ENTROPY; ENZYME SPECIFICITY; METABOLISM; METHODOLOGY; MOLECULAR LIBRARY; PHYSICAL CHEMISTRY; SUPPORT VECTOR MACHINE;

ALGORITHMS; BIOCATALYSIS; CYTOCHROME P-450 ENZYME SYSTEM; DRUG EVALUATION, PRECLINICAL; DRUG INTERACTIONS; ENTROPY; ENZYME INHIBITORS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; ISOENZYMES; PHYSICOCHEMICAL PROCESSES; SMALL MOLECULE LIBRARIES; SUBSTRATE SPECIFICITY; SUPPORT VECTOR MACHINES;

EID: 80054965570     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200317s     Document Type: Article

References (41)

1. Hopkins, A. L. Network pharmacology: the next paradigm in drug discovery Nat. Chem. Biol. 2008, 4, 682-690
2. Wishart, D. S.; Knox, C.; Guo, A. C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. DrugBank: a knowledgebase for drugs, drug actions and drug targets Nucleic Acids Res. 2008, 36, D901-D906
3. Wienkers, L. C.; Heath, T. G. Predicting in vivo drug interactions from in vitro drug discovery data Nat. Rev. Drug Discovery 2005, 4, 825-833 (Pubitemid 41553963)
4. Lasser, K. E.; Allen, P. D.; Woolhandler, S. J.; Himmelstein, D. U.; Wolfe, S. M.; Bor, D. H. Timing of new black box warnings and withdrawals for prescription medications JAMA 2002, 287, 2215-2220 (Pubitemid 34441937)
5. Williams, J. A.; Hyland, R.; Jones, B. C.; Smith, D. A.; Hurst, S.; Goosen, T. C.; Peterkin, V.; Koup, J. R.; Ball, S. E. 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)
6. van Loo, B.; Jonas, S.; Babtie, A. C.; Benjdia, A.; Berteau, O.; Hyvonen, M.; Hollfelder, F. An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily Proc. Natl. Acad. Sci. 2010, 107, 2740-2745
7. Khersonsky, O.; Tawfik, D. S. Enzyme promiscuity: a mechanistic and evolutionary perspective Annu. Rev. Biochem. 2010, 79, 471-505
8. Nath, A.; Atkins, W. M. A quantitative index of substrate promiscuity Biochemistry 2008, 47, 157-166
9. Nath, A.; Zientek, M. A.; Burke, B. J.; Jiang, Y.; Atkins, W. M. Quantifying and predicting the promiscuity and isoform specificity of small-molecule cytochrome P450 inhibitors Drug Metab. Dispos. 2010, 38, 2195-2203
10. Foti, R. S.; Honaker, M.; Nath, A.; Pearson, J. T.; Buttrick, B.; Isoherranen, N.; Atkins, W. M. Catalytic versus Inhibitory Promiscuity in Cytochrome P450s: Implications for Evolution of New Function Biochemistry 2011, 50, 2387-2393
11. Veith, H.; Southall, N.; Huang, R.; James, T.; Fayne, D.; Artemenko, N.; Shen, M.; Inglese, J.; Austin, C. P.; Lloyd, D. G.; Auld, D. S. Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries Nat. Biotechnol. 2009, 27, 1050-1055
12. Shannon, C. E. A mathematical theory of communication Bell. Syst. Tech. J. 1948, 27 (379-423) 623-656
13. John, M. B.; Geoffrey, M. D.; Willett, P. Chemical Similarity Searching J. Chem. Inf. Comput. Sci. 1998, 38, 983-996 (Pubitemid 128591261)
14. Wang, Y.; Xiao, J.; Suzek, T. O.; Zhang, J.; Wang, J.; Bryant, S. H. PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res. 2009, W623-W633
15. Lewis, D. F.; Jacobs, M. N.; Dickins, M. Compound lipophilicity for substrate binding to human P450s in drug metabolism Drug Discovery Today 2004, 9, 530-537 (Pubitemid 38739334)
16. Lewis, D. F.; Dickins, M. Substrate SARs in human P450s Drug Discovery Today 2002, 7, 918-925
17. Yap, C. W. PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints J. Comput. Chem. 2011, 32, 1466-1474
18. Klekota, J.; Roth, F. P. Chemical substructures that enrich for biological activity Bioinformatics 2008, 24, 2518-2525
19. Shen, J.; Cheng, F.; Xu, Y.; Li, W.; Tang, Y. Estimation of ADME properties with substructure pattern recognition J. Chem. Inf. Model. 2010, 50, 1034-1041
20. Jensen, B. F.; Vind, C.; Padkjaer, S. B.; Brockhoff, P. B.; Refsgaard, H. H. In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors J. Med. Chem. 2007, 50, 501-511 (Pubitemid 46239784)
21. Corinna, C.; Vladimir, V. Support-Vector Networks Mach. Learn. 1995, 20, 273-297
22. Cheng, F.; Yu, Y; Shen, J.; Yang, L.; Li, W.; Liu, G.; Lee, P. W.; Tang, Y. Classification of Cytochrome P450 Inhibitors and non-Inhibitors using Combined Classifiers J. Chem. Inf. Model. 2011, 51, 996-1011
23. Cheng, F.; Shen, J.; Yu, Y.; Li, W.; Liu, G.; Lee, P. W.; Tang, Y. In silico prediction of Tetrahymena pyriformis toxicity for diverse industrial chemicals with substructure pattern recognition and machine learning methods Chemosphere 2011, 82, 1636-1643
24. Vasanthanathan, P.; Taboureau, O.; Oostenbrink, C.; Vermeulen, N. P.; Olsen, L.; Jorgensen, F. S. Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques Drug Metab. Dispos. 2009, 37, 658-664
25. Eitrich, T.; Kless, A.; Druska, C.; Meyer, W.; Grotendorst, J. Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques J. Chem. Inf. Model. 2007, 47, 92-103 (Pubitemid 46225564)
26. Michielan, L.; Terfloth, L.; Gasteiger, J.; Moro, S. Comparison of multilabel and single-label classification applied to the prediction of the isoform specificity of cytochrome p450 substrates J. Chem. Inf. Model. 2009, 49, 2588-2605
27. Yap, C. W.; Chen, Y. Z. Prediction of cytochrome P450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines J. Chem. Inf. Model. 2005, 45, 982-992 (Pubitemid 41156697)
28. Chang, C. C.; Lin., C.-J. LIBSVM: a library for support vector machines. http://www.csie.ntu.edu.tw/∼cjlin/libsvm (accessed Jan. 18, 2010).
29. Baldi, P.; Brunak, S.; Chauvin, Y.; Andersen, C. A.; Nielsen, H. Assessing the accuracy of prediction algorithms for classification: an overview Bioinformatics 2000, 16, 412-424 (Pubitemid 30487963)
30. Leeson, P. D.; Springthorpe, B. The influence of drug-like concepts on decision-making in medicinal chemistry Nat. Rev. Drug Discovery 2007, 6, 881-890 (Pubitemid 350042396)
31. Hopkins, A. L.; Mason, J. S.; Overington, J. P. Can we rationally design promiscuous drugs? Curr. Opin. Struct. Biol. 2006, 16, 127-136 (Pubitemid 43221881)
32. Hann, M. M.; Leach, A. R.; Harper, G. Molecular complexity and its impact on the probability of finding leads for drug discovery J. Chem. Inf. Comput. Sci. 2001, 41, 856-864
33. Peters, J. U.; Schnider, P.; Mattei, P.; Kansy, M. Pharmacological promiscuity: dependence on compound properties and target specificity in a set of recent Roche compounds ChemMedChem 2009, 4, 680-686
34. Yang, Y.; Chen, H.; Nilsson, I.; Muresan, S.; Engkvist, O. Investigation of the relationship between topology and selectivity for druglike molecules J. Med. Chem. 2010, 53, 7709-7714
35. Lewis, D. F.; Eddershaw, P. J.; Dickins, M.; Tarbit, M. H.; Goldfarb, P. S. Structural determinants of cytochrome P450 substrate specificity, binding affinity and catalytic rate Chem. Biol. Interact. 1998, 115, 175-199 (Pubitemid 28487023)
36. Ekroos, M.; Sjogren, T. Structural basis for ligand promiscuity in cytochrome P450 3A4 Proc. Natl. Acad. Sci. 2006, 103, 13682-13687 (Pubitemid 44413967)
37. Karaman, M. W.; Herrgard, S.; Treiber, D. K.; Gallant, P.; Atteridge, C. E.; Campbell, B. T.; Chan, K. W.; Ciceri, P.; Davis, M. I.; Edeen, P. T.; Faraoni, R.; Floyd, M.; Hunt, J. P.; Lockhart, D. J.; Milanov, Z. V.; Morrison, M. J.; Pallares, G.; Patel, H. K.; Pritchard, S.; Wodicka, L. M.; Zarrinkar, P. P. A quantitative analysis of kinase inhibitor selectivity Nat. Biotechnol. 2008, 26, 127-132
38. Hanley, J. A.; McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 1982, 143, 29-36 (Pubitemid 12142173)
39. Graczyk, P. P. Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases J. Med. Chem. 2007, 50, 5773-5779 (Pubitemid 350106032)
40. Cheng, A. C.; Eksterowicz, J.; Geuns-Meyer, S.; Sun, Y. Analysis of kinase inhibitor selectivity using a thermodynamics-based partition index J. Med. Chem. 2010, 53, 4502-4510
41. Uitdehaag, J. C.; Zaman, G. J. A theoretical entropy score as a single value to express inhibitor selectivity BMC Bioinf. 2011, 12, 94