π-π Stacking mediated drug-drug interactions in human CYP2E1

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 6, 2013, Pages 945-954

  Liu, Yue ^a   Liu, Bing Ya ^b   Hao, Pei ^c,d   Li, Xuan ^d,e   Li, Yi Xue ^d,f   Wang, Jing Fang ^a,d  

^a Shanghai Jiao Tong University   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^d SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^e INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^f Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

Cytochrome P450 enzymes; Drug metabolism; Drug drug interactions; GPU accelerated molecular dynamics simulation; Multiple substrate binding

Indexed keywords

AROMATIC COMPOUND; CYTOCHROME P450 2E1;

ARTICLE; BINDING SITE; CATALYSIS; DRUG PROTEIN BINDING; ENZYME SUBSTRATE COMPLEX; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION;

BINDING SITES; CYTOCHROME P-450 CYP2E1; DRUG INTERACTIONS; HUMANS; MOLECULAR DYNAMICS SIMULATION; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; SUBSTRATE SPECIFICITY;

EID: 84878117701     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24260     Document Type: Article

References (54)

1. Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab 2002; 3: 561-597.
2. Wang JF, Chou KC. Molecular modeling of cytochrome P450 and drug metabolism. Curr Drug Metab 2010; 11: 342-346.
3. Nelson DR. Cytochrome P450 and the individuality of species. Arch Biochem Biophys 1999; 369: 1-10.
4. Wang JF, Zhang CC, Chou KC, Wei DQ. Structure of cytochrome p450s and personalized drug. Curr Med Chem 2009; 16: 232-244.
5. Gonzalez FJ, Skoda RC, Kimura S, Umeno M, Zanger UM, Nebert DW, Gelboin HV, Hardwick JP, Meyer UA. Characterization of the common genetic defect in humans deficient in debrisoquine metabolism. Nature 1988; 331: 442-446.
6. Isin EM, Guengerich FP. Complex reactions catalyzed by cytochrome P450 enzymes. Biochim Biophys Acta 2007; 1770: 314-329.
7. Nebert DW, Russell DW. Clinical importance of the cytochromes P450. Lancet 2002; 360: 1155-1162.
8. Omdahl JL, Bobrovnikova EA, Choe S, Dwivedi PP, May BK. Overview of regulatory cytochrome P450 enzymes of the vitamin D pathway. Steroids 2001; 66: 381-389.
9. Sanga M, Younis IR, Tirumalai PS, Bland TM, Banaszewska M, Konat GW, Tracy TS, Gannett PM, Callery PS. Epoxidation of the methamphetamine pyrolysis product, trans-phenylpropene, to trans-phenylpropylene oxide by CYP enzymes and stereoselective glutathione adduct formation. Toxicol Appl Pharmacol 2006; 211: 148-156.
10. Chen Q, Zhang T, Wang JF, Wei DQ. Advances in human cytochrome p450 and personalized medicine. Curr Drug Metab 2011; 12: 436-444.
11. Ingelman-Sundberg M. The human genome project and novel aspects of cytochrome P450 research. Toxicol Appl Pharmacol 2005; 207( 2 Suppl): 52-56.
12. Meunier B, de Visser SP, Shaik S. Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes. Chem Rev 2004; 104: 3947-3980.
13. Davydov DR, Halpert JR. Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both? Expert Opin Drug Metab Toxicol 2008; 4: 1523-1535.
14. Denisov IG, Frank DJ, Sligar SG. Cooperative properties of cytochromes P450. Pharmacol Ther 2009; 124: 151-167.
15. Korzekwa KR, Krishnamachary N, Shou M, Ogai A, Parise RA, Rettie AE, Gonzalez FJ, Tracy TS. Evaluation of atypical cytochrome P450 kinetics with two-substrate models: evidence that multiple substrates can simultaneously bind to cytochrome P450 active sites. Biochemistry 1998; 37: 4137-4147.
16. Cameron MD, Wen B, Roberts AG, Atkins WM, Campbell AP, Nelson SD. Cooperative binding of acetaminophen and caffeine within the P450 3A4 active site. Chem Res Toxicol 2007; 20: 1434-1441.
17. Isin EM, Guengerich FP. Kinetics and thermodynamics of ligand binding by cytochrome P450 3A4. J Biol Chem 2006; 281: 9127-9136.
18. Isin EM, Guengerich FP. Multiple sequential steps involved in the binding of inhibitors to cytochrome P450 3A4. J Biol Chem 2007; 282: 6863-6874.
19. Collom SL, Laddusaw RM, Burch AM, Kuzmic P, Perry MD, Jr, Miller GP. CYP2E1 substrate inhibition. Mechanistic interpretation through an effector site for monocyclic compounds. J Biol Chem 2008; 283: 3487-3496.
20. Harrelson JP, Atkins WM, Nelson SD. Multiple-ligand binding in CYP2A6: probing mechanisms of cytochrome P450 cooperativity by assessing substrate dynamics. Biochemistry 2008; 47: 2978-2988.
21. Koop DR. Hydroxylation of p-nitrophenol by rabbit ethanol-inducible cytochrome P-450 isozyme 3a. Mol Pharmacol 1986; 29: 399-404.
22. Porubsky PR, Meneely KM, Scott EE. 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.
23. DeVore NM, Meneely KM, Bart AG, Stephens ES, Battaile KP, Scott EE. Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine. FEBS J 2012; 279: 1621-1631.
24. Kaplan W, Littlejohn TG. Swiss-PDB Viewer (Deep View). Brief Bioinform 2001; 2: 195-197.
25. Williams PA, Cosme J, Sridhar V, Johnson EF, McRee DE. Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol Cell 2000; 5: 121-131.
26. Wang JF, Wei DQ, Chen C, Li Y, Chou KC. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Prot Pept Lett 2008; 15: 27-32.
27. Wang JF, Wei DQ, Li L, Zheng SY, Li YX, Chou KC. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem Biophys Res Commun 2007; 355: 513-519.
28. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010; 31: 455-461.
29. Wang JF, Chou KC. Insights into the mutation-induced HHH syndrome from modeling human mitochondrial ornithine transporter-1. PLoS One 2012; 7: e31048.
30. Wang JF, Chou KC. Insights from modeling the 3D structure of New Delhi metallo-beta-lactamse and its binding interactions with antibiotic drugs. PLoS One 2011; 6: e18414.
31. Wang YJ, Wang JF, Ping J, Yu Y, Wang Y, Lian P, Li X, Li YX, Hao P. Computational studies on the substrate interactions of influenza A virus PB2 subunit. PLoS One 2012; 7: e44079.
32. Lian P, Wei DQ, Wang JF, Chou KC. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 2011; 6: e18587.
33. Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem 2003; 66: 27-85.
34. Schoneboom JC, Lin H, Reuter N, Thiel W, Cohen S, Ogliaro F, Shaik S. The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. J Am Chem Soc 2002; 124: 8142-8151.
35. Wang JF, Hao P, Li YX, Dai JL, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2012; 18: 2717-2725.
36. Wang Y, Wei DQ, Wang JF. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J Chem Inf Model 2010; 50: 875-878.
37. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684-3690.
38. Wang Y, Wu XL, Wei DQ, Li YX, Wang JF. Autoinhibitory mechanism for the mutation-induced impaired FGF9 signaling. J Chem Inf Model 2012; 52: 2422-2429.
39. Gu H, Chen HF, Wei DQ, Wang JF. Molecular dynamics simulations exploring drug resistance in HIV-1 protease. Chinese Sci Bull 2010; 55: 2677-2683.
40. Ekroos M, Sjogren T. Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci U S A 2006; 103: 13682-13687.
41. Ping J, Wang YJ, Wang JF, Li X, Li YX, Hao P. Negatively cooperative binding properties of human cytochrome P450 2E1 with monocyclic substrates. Curr Drug Metab 2012; 13: 1024-1031.
42. Laurie AT, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005; 21: 1908-1916.
43. Guengerich FP, Shimada T. Oxidation of toxic and carcinogenic chemicals by human cytochrome P-450 enzymes. Chem Res Toxicol 1991; 4: 391-407.
44. Spatzenegger M, Liu H, Wang Q, Debarber A, Koop DR, Halpert JR. Analysis of differential substrate selectivities of CYP2B6 and CYP2E1 by site-directed mutagenesis and molecular modeling. J Pharmacol Exp Ther 2003; 304: 477-487.
45. Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4. J Am Chem Soc 2007; 129: 1602-1611.
46. Blobaum AL, Kent UM, Alworth WL, Hollenberg PF. Novel reversible inactivation of cytochrome P450 2E1 T303A by tert-butyl acetylene: the role of threonine 303 in proton delivery to the active site of cytochrome P450 2E1. J Pharmacol Exp Ther 2004; 310: 281-290.
47. Vaz AD, Pernecky SJ, Raner GM, Coon MJ. Peroxo-iron and oxenoid-iron species as alternative oxygenating agents in cytochrome P450-catalyzed reactions: switching by threonine-302 to alanine mutagenesis of cytochrome P450 2B4. Proc Natl Acad Sci USA 1996; 93: 4644-4648.
48. Imai M, Shimada H, Watanabe Y, Matsushima-Hibiya Y, Makino R, Koga H, Horiuchi T, Ishimura Y. Uncoupling of the cytochrome P-450cam monooxygenase reaction by a single mutation, threonine-252 to alanine or valine: possible role of the hydroxy amino acid in oxygen activation. Proc Natl Acad Sci USA 1989; 86: 7823-7827.
49. Fukuda T, Imai Y, Komori M, Nakamura M, Kusunose E, Satouchi K, Kusunose M. Different mechanisms of regioselection of fatty acid hydroxylation by laurate (omega-1)-hydroxylating P450s, P450 2C2 and P450 2E1. J Biochem 1994; 115: 338-344.
50. Fukuda T, Imai Y, Komori M, Nakamura M, Kusunose E, Satouchi K, Kusunose M. Replacement of Thr-303 of P450 2E1 with serine modifies the regioselectivity of its fatty acid hydroxylase activity. JBiochem 1993; 113: 7-12.
51. Li J, Wei DQ, Wang JF, Yu ZT, Chou KC. Molecular dynamics simulations of CYP2E1. Med Chem 2011; 8: 208-221.
52. Burley SK, Petsko GA. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 1985; 229: 23-28.
53. McGaughey GB, Gagne M, Rappe AK. pi-Stacking interactions. Alive and well in proteins. J Biol Chem 1998; 273: 15458-15463.
54. Tauer TP, Sherrill CD. Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions. J Phys Chem A 2005; 109: 10475-10478.