Regioselectivity prediction of CYP1A2-mediated phase I metabolism

Journal of Chemical Information and Modeling

Volumn 48, Issue 5, 2008, Pages 1074-1080

  Jung, Jihoon ^a   Kim, Nam Doo ^a,b   Kim, Su Yeon ^a   Choi, Inhee ^a   Cho, Kwang Hwi ^c   Oh, Won Seok ^a   Kim, Doo Nam ^d   No, Kyoung Tai ^a,d  

^a Yonsei University   (South Korea)

^b Equispharm Co Ltd   (South Korea)

^c Soongsil University   (South Korea)

^d Bioinformatics and Molecular Design Research Center (BMDRC)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; BINDING ENERGY; CRYSTAL STRUCTURE; ENZYMES; FORECASTING; METABOLISM; MOLECULAR ORBITALS; REGIOSELECTIVITY;

AUTOMATED DOCKING; BINDING MODELS; BINDING MODES; DOCKING SIMULATIONS; DRUG METABOLISMS; PHASE I; QUALITATIVE PREDICTIONS; SEMIEMPIRICAL MOLECULAR ORBITAL CALCULATIONS;

ORBITAL CALCULATIONS;

CYTOCHROME P450 1A2; DRUG;

ARTICLE; BINDING SITE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; ENZYME SPECIFICITY; KINETICS; METABOLISM; OXIDATION REDUCTION REACTION; PROTEIN BINDING; PROTEIN CONFORMATION; STEREOISOMERISM; THERMODYNAMICS;

BINDING SITES; CYTOCHROME P-450 CYP1A2; DRUG DESIGN; KINETICS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; OXIDATION-REDUCTION; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; PROTEIN CONFORMATION; STEREOISOMERISM; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 45749087429     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800001m     Document Type: Article

References (40)

1. Crivori, P.; Poggesi, I. Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs. Eur. J. Med. Chem. 2006, 41, 795-808.
2. Korzekwa, K. R.; Jones, J. P.; Gillette, J. R. Theoretical studies on cytochrome P-450 mediated hydroxylation: a predictive model for hydrogen atom abstractions. J. Am. Chem. Soc. 1990, 112, 7042-7046.
3. Korzekwa, K. R.; Grogan, J.; DeVito, S.; Jones, J. P. Electronic models for cytochrome P450 oxidations. Adv. Exp. Med. Biol. 1996, 387, 361-369.
4. Jones, J. P.; Mysinger, M.; Korzekwa, K. R. Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction. Drug Metab. Dispos. 2002, 30, 7-12.
5. Singh, S. B.; Shen, L. Q.; Walker, M. J.; Sheridan, R. P. A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules. J. Med. Chem. 2003, 46, 1330-1336.
6. Sheridan, R. P.; Korzekwa, K. R.; Torres, R. A.; Walker, M. J. Empirical Regioselectivity Models for Human Cytochromes P450 3A4, 2D6, and 2C9. J. Med. Chem. 2007, 50, 3173-3184.
7. Borodina, Y.; Rudik, A.; Filimonov, D.; Kharchevnikova, N.; Dmitriev, A.; Blinova, V.; Poroikov, V. A new statistical approach to predicting aromatic hydroxylation sites. Comparison with model-based approaches. J. Chem. Inf. Comput Sci. 2004, 44, 1998-2009.
8. Manga, N.; Duffy, J. C.; Rowe, P. H.; Cronin, M. T. Structure-based methods for the prediction of the dominant P450 enzyme in human drug biotransformation: consideration of CYP3A4, CYP2C9, CYP2D6. SAR QSAR Environ. Res. 2005, 16, 43-61.
9. 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.
10. Terfloth, L.; Bienfait, B.; Gasteiger, J. Ligand-Based Models for the Isoform Specificity of Cytochrome P450 3A4, 2D6, and 2C9 Substrates. J. Chem. Inf. Model. 2007, 47, 1688-1701.
11. Koymans, L.; Vermeulen, N. P.; van Acker, S. A.; te Koppele, J. M.; Heykants, J. J.; Lavrijsen, K.; Meuldermans, W.; Donne-Op, den; Kelder, G. M. A predictive model for substrates of cytochrome P450-debrisoquine (2D6). Chem. Res. Toxicol. 1992, 5, 211-219.
12. Lewis, D. F.; Eddershaw, P. J.; Goldfarb, P. S.; Tarbit, M. H. Molecular modelling of CYP3A4 from an alignment with CYP102: identification of key interactions between putative active site residues and CYP3A-specific chemicals. Xenobiotica 1996, 26, 1067-1086.
13. Lewis, D. F.; Lake, B. G. Molecular modelling of CYP1A subfamily members based on an alignment with CYP102: rationalization of CYP1A substrate specificity in terms of active site amino acid residues. Xenobiotica 1996, 26, 723-753.
14. de Groot, M. J.; Vermeulen, N. P.; Kramer, J. D.; van Acker, F. A.; Donne-Op, den; Kelder, G. M. A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108. Chem. Res. Toxicol. 1996, 9. 1079-1091.
15. Modi, S.; Paine, M. J.; Sutcliffe, M. J.; Lian, L. Y.; Primrose, W. U.; Wolf, C. R.; Roberts, G. C. A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry 1996, 35, 4540-4550.
16. Lewis, D. F.; Eddershaw, P. J.; Goldfarb, P. S.; Tarbit, M. H. Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: structural studies on specific CYP2D6 substrate metabolism. Xenobiotica 1997, 27, 319-339.
17. Lozano, J. J.; Lopez-de-Brinas, E.; Centeno, N. B.; Guigo, R.; Sanz, F. Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ. J. Comput.-Aided Mol. Des. 1997, 11, 395-408.
18. Payne, V. A.; Chang, Y. T.; Loew, G. H. Homology modeling and substrate binding study of human CYP2C9 enzyme. Proteins 1999, 37, 176-190.
19. Lewis, D. F.; Bird, M. G.; Dickins, M.; Lake, B. G.; Eddershaw, P. J.; Tarbit, M. H.; Goldfarb, P. S. Molecular modelling of human CYP2E1 by homology with the CYP102 haemoprotein domain: investigation of the interactions of substrates and inhibitors within the putative active site of the human CYP2E1 isoform. Xenobiotica 2000, 30, 1-25.
20. Lewis, D. F. Molecular modeling of human cytochrome P450-substrate interactions. Drug Metab. Rev. 2002, 34, 55-67.
21. Lewis, D. F.; Lake, B. G.; Dickins, M.; Goldfarb, P. S. Homology modelling of CYP3A4 from the CYP2C5 crystallographic template: analysis of typical CYP3A4 substrate interactions. Xenobiotica 2004, 34, 549-569.
22. de Groot, M. J.; Ackland, M. J.; Home, V. A.; Alex, A. A.; Jones, B. C. A novel approach to predicting P450 mediated drug metabolism. CYP2D6 catalyzed N-dealkylation reactions and qualitative metabolite predictions using a combined protein and pharmacophore model for CYP2D6, J. Med. Chem. 1999, 42, 4062-4070.
23. de Groot, M. J.; Ackland, M. J.; Home, V. A.; Alex, A. A.; Jones, B. C. Novel approach to predicting P450-mediated drug metabolism: development of a combined protein and pharmacophore model for CYP2D6. J. Med. Chem. 1999, 42, 1515-1524.
24. de Groot, M. J.; Alex, A. A.; Jones, B. C. Development of a combined protein and pharmacophore model for cytochrome P450 2C9. J. Med. Chem. 2002, 45, 1983-1993.
25. Park, J. Y.; Harris, D. Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations, J. Med. Chem. 2003, 46, 1645-1660.
26. Zamora, I.; Afzelius, L.; Cruciani, G. Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9. J. Med. Chem. 2003, 46, 2313-2324.
27. Cruciani, G.; Carosati, E.; De Boeck, B.; Ethirajulu, K.; Mackie, C.; Howe, T.; Vianello, R. MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J. Med. Chem. 2005, 48, 6970-6979.
28. Zhou, D.; Afzelius, L.; Grimm, S. W.; Andersson, T. B.; Zauhar, R. J.; Zamora, I. Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions. Drug Metab. Dispos. 2006, 34, 976-983.
29. Anzenbacher, P.; Anzenbacherova, E. Cytochromes P450 and metabolism of xenobiotics. Cell. Mol. Life Sci. 2001, 58, 737-747.
30. Danielson, P. B. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr. Drug Metab. 2002, 3, 561-597.
31. Sansen, S.; Yano, J. K.; Reynald, R. L.; Schoch, G. A.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. Adaptations for the Oxidation of Polycyclic Aromatic Hydrocarbons Exhibited by the Structure of Human P450 1A2. J. Biol. Chem. 2007, 282, 14348-14355.
32. de Graaf, C.; Vermeulen, N. P.; Feenstra, K. A. Cytochrome p450 in silico: an integrative modeling approach. J. Med. Chem. 2005, 48, 2725-2755.
33. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
34. Rendic, S. Fujitsu Kyushu System Engineering Ltd. ADME Database. http://jp.fujitsu.com/group/fqs/services/lifescience/english/asp/admedb/ index.html(accessed Feb 8, 2007).
35. Rendic, S.; Di Carlo, F. J. Human cytochrome P450 enzymes: a status report summarizing their reactions, substrates, inducers, and inhibitors. Drug Metab. Rev. 1997, 29, 413-580.
36. Rendic, S. Summary of information on human CYP enzymes: human P450 metabolism data. Drug Metab. Rev. 2002, 34, 83-448.
37. Cerius2, version 4.10; Accelrys Software Inc.: San Diego, CA, 2005.
38. Insight II, version 2000; Accelrys Software Inc.: San Diego, CA, 2000.
39. Oda, A.; Yamaotsu, N.; Hirono, S. New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models. J. Comput. Chem. 2005, 26, 818-826.
40. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Reith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.