Molecular dynamics simulations of CYP2E1

Medicinal Chemistry

Volumn 8, Issue 2, 2012, Pages 208-221

  Li, Jue ^a   Wei, Dong Qing ^a,d   Wang, Jing Fang ^b,d   Yu, Zheng Tian ^c   Chou, Kuo Chen ^d  

^a Shanghai Jiao Tong University   (China)

^b Shanghai Jiao Tong University   (China)

^c Novartis Institutes for Biomedical Research   (China)

^d GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

Aromatic substrates; CYP2E1; Diversity; Drug metabolism; Molecular dynamics simulations

Indexed keywords

ANILINE; BENZENE; CHLORZOXAZONE; CYTOCHROME P450 2E1; PARACETAMOL; PHENYLALANINE; THEOPHYLLINE;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG INTERACTION; DRUG METABOLISM; HUMAN; HYDROGEN BOND; HYDROPHOBICITY; HYDROXYLATION; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; X RAY;

EID: 84861940931     PISSN: 15734064     EISSN: 18756638     Source Type: Journal    
DOI: 10.2174/157340612800493692     Document Type: Article

References (125)

1. Hines, R. Ontogeny of human hepatic cytochromes P450. J. Biochem. Mol. Toxicol., 2007, 21, 169-175 (Pubitemid 350194376)
2. Danielson, P. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr. Drug Metab., 2002, 3, 561-597 (Pubitemid 35331660)
3. Wang, J.; Zhang, C.; Chou, K.; Wei, D. Structure of cytochrome P450s and personalized drug. Curr. Med. Chem., 2009, 16, 232-244
4. Meunier, B.; De Visser, S.; Shaik, S. Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes. Chem. Rev., 2004, 104, 3947-3980
5. Makino, M.; Sugimoto, H.; Shiro, Y.; Asamizu, S.; Onaka, H.; Nagano, S. Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton. Proc. Natl. Acad. Sci. USA, 2007, 104, 11591-11596 (Pubitemid 47175057)
6. Li, D.; Huang, X.; Han, K.; Zhan, C.G. Catalytic mechanism of cytochrome P450 for 5'-hydroxylation of nicotine: fundamental reaction pathways and stereoselectivity. J. Am. Chem. Soc., 2011, 133, 7416-7427
7. de Visser, S.P.; Shaik, S. A proton-shuttle mechanism mediated by the porphyrin in benzene hydroxylation by cytochrome p450 enzymes. J. Am. Chem. Soc., 2003, 125, 7413-7424 (Pubitemid 36798988)
8. Sharma, P.K.; de Visser, S.P.; Ogliaro, F.; Shaik, S. Is the rethenium analogue of compound I of cytochrome p450 an efficient oxidant? A theoretical investigation of the methane hydroxylation reactions. J. Am. Chem. Soc., 2003, 125, 2291-2300 (Pubitemid 36245722)
9. Wang, Y.; Hirao, H.; Chen, H.; Onaka, H.; Nagano, S.; Shaik, S. Electron transfer activation of chromopyrrolic acid by cytochrome P450 en route to the formation of an antitumor indolocarbazole derivative: theory supports experiment. J. Am. Chem. Sco., 2008, 130, 7170-7171 (Pubitemid 351813178)
10. Seliskar, M.; Rozman, D. Mammalian cytochromes P450-importance of tissue specificity. Biochim. Biophys. Acta., 2007, 1770, 458-466 (Pubitemid 46136750)
11. Chen, Q.; Zhang, T.; Wang, J.F.; Wei, D.Q. Advances in human cytochrome P450 and personalized medicine. Curr. Drug Metab., 2011, 12, 436-444
12. Guengerich, P. Catalytic selectivity of human cytochrome P450 enzymes: relevance to drug metabolism and toxicity. Toxicol. Lett., 1994, 70, 133-138
13. Wang, J.F.; Chou, K. Molecular modeling of cytochrome P450 and drug metabolism. Curr. Drug Metab., 2010, 11, 342-346
14. Miller, G. Advances in the interpretation and prediction of CYP2E1 metabolism from a biochemical perspective. Expert. Opin. Drug Metab. Toxicol, 2008, 4, 1053-1064
15. Trafalis, D.; Panteli, E.; Grivas, A.; Tsigris, C.; Karamanakos, P. CYP2E1 and risk of chemically mediated cancers. Expert. Opin. Drug Metab. Toxicol., 2010, 6, 307-319
16. Ioannides, C.; Lewis, V.; David, F. Cytochromes P450 in the bioactivation of chemicals. Curr. Topics Med. Chem., 2004, 4, 1767-1788 (Pubitemid 39662666)
17. Nanji, A.; Zhao, S.; Sadrzadeh, S.; Dannenberg, A.; Tahan, S.; Waxman, D. Markedly enhanced cytochrome P450 2E1 induction and lipid peroxidation is associated with severe liver injury in fish Oil-ethanol-fed rats. Alcohol. Clin. Exp. Res., 1994, 18, 1280-1285 (Pubitemid 24345545)
18. Wang, M.; Wade, D.; Chen, L.; White, S.; Yang, C. Probing the Active Sites of Rat and Human Cytochrome-P450 2E1 with Alcohols and Carboxylic Acids. Arch. Biochem. Biophys., 1995, 317, 299-304
19. Robertson, G.; Leclercq, I.; Farrell, G. Nonalcoholic steatosis and steatohepatitis: II. Cytochrome P-450 enzymes and oxidative stress. Am. J. Physiol. Gastrointest. Liver Physiol., 2001, 281, G1135
20. Salazar, D.; Sorge, C.; Corcoran, G. Obesity as a risk factor for drug-induced organ injury. VI. Increased hepatic P450 concentration and microsomal ethanol oxidizing activity in the obese overfed rat1. Biochem. Biophys. Res. Commun., 1988, 157, 315-320
21. Song, B.; Matsunaga, T.; Hardwick, J.; Park, S.; Veech, R.; Yang, C.; Gelboin, H.; Gonzalez, F. Stabilization of cytochrome P450j messenger ribonucleic acid in the diabetic rat. Mol. Endocrinol., 1987, 1, 542
22. Johansson, I.; Ekstrom, G.; Scholte, B.; Puzycki, D.; Jornvall, H.; Ingelman-Sundberg, M. Ethanol-, fasting, and aceton-inducible cytochromes P450 in rat liver: regulation and characteristics of enzymes belonging to the 2B and 2E gene subfamilies. Biochemistry, 1988, 27, 1925-1934
23. Barnett, C.; Rudd, S.; Flatt, P.; Ioannides, C. Sex differences in the diabetes-induced modulation of rat hepatic cytochrome P450 proteins. Biochem. Pharmacol., 1993, 45, 313-319 (Pubitemid 23042629)
24. Guengerich, F.; Kim, D.; Iwasaki, M. Role of human cytochrome P-450 IIE1 in the oxidation of many low molecular weight cancer suspects. Chem. Res. Toxicol., 1991, 4, 168-179
25. Koop, D. Hydroxylation of p-nitrophenol by rabbit ethanolinducible cytochrome P-450 isozyme 3a. Mol. Pharmacol., 1986, 29, 399
26. Peter, R.; Boecker, R.; Beaune, P.; Iwasaki, M.; Guengerich, F.; Yang, C. Hydroxylation of chlorzoxazone as a specific probe for human liver cytochrome P-450IIE1. Chem. Res. Toxicol., 1990, 3, 566-573
27. Laethem, R.; Halpert, J.; Koop, D. Epoxidation of arachidonic acid as an active-site probe of cytochrome P-450 2B isoforms. Biochim. Biophys. Acta, 1994, 1206, 42-48 (Pubitemid 24153284)
28. Roy, U.; Joshua, R.; Stark, R.; Balazy, M. Cytochrome P450/ NADPH-dependent biosynthesis of 5, 6-trans-epoxyeicosatrienoic acid from 5, 6-trans-arachidonic acid. Biochem. J., 2005, 390, 719
29. Doty, S.; Shang, T.; Wilson, A.; Tangen, J.; Westergreen, A.; Newman, L.; Strand, S.; Gordon, M. Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1. Proc. Natl. Acad. Sci. USA, 2000, 97, 6287
30. Banerjee, S.; Shang, T.; Wilson, A.; Moore, A.; Strand, S.; Gordon, M.; Lafferty Doty, S. Expression of functional mammalian P450 2E1 in hairy root cultures. Biotechnol. Bioeng., 2002, 77, 462-466 (Pubitemid 34121539)
31. Yamazaki, H.; Nakano, M.; Gillam, E.; Bell, L.; Guengerich, F.; Shimada, T. Requirements for cytochrome b5 in the oxidation of 7-ethoxycoumarin, chlorzoxazone, aniline, and N-nitrosodimethylamine by recombinant cytochrome P450 2E1 and by human liver microsomes* 1. Biochem. Pharmacol., 1996, 52, 301-309 (Pubitemid 26233759)
32. Patten, C.; Thomas, P.; Guy, R.; Lee, M.; Gonzalez, F.; Guengerich, F.; Yang, C. Cytochrome P450 enzymes involved in acetaminophen activation by rat and human liver microsomes and their kinetics. Chem. Res. Toxicol., 1993, 6, 511-518 (Pubitemid 23212521)
33. Raucy, J.; Lasker, J.; Lieber, C.; Black, M. Acetaminophen activation by human liver cytochromes P450IIE1 and P450IA2* 1. Arch. Biochem. Biophys., 1989, 271, 270-283 (Pubitemid 19145373)
34. Bronstein, A.; Spyker, D.; Cantilena Jr, L.; Green, J.; Rumack, B.; Heard, S. annual report of the American association of poison control centers' National Poison Data System (NPDS). Clin. Toxicol. (Phila), 2007, 45, 815-917
35. Porubsky, P.; Meneely, K.; Scott, E. 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
36. Chou, K.C.; Wei, D.Q.; Zhong, W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun., 2003, 308, 148-151
37. Xu, H. Inhibition Kinetics of Flavonoids on Yeast alpha-Glucosidase Merged with Docking Simulations. Protein Pept. Lett., 2010, 17, 1270-1279
38. Zhou, G.P.; Troy, F.A., 2nd. NMR study of the preferred membrane orientation of polyisoprenols (dolichol) and the impact of their complex with polyisoprenyl recognition sequence peptides on membrane structure. Glycobiology, 2005, 15, 347-359
39. Cheng, F.; Shen, J.; Xu, X.; Luo, X.; Chen, K.; Shen, X.; Jiang, H. Interaction models of a series of oxadiazole-substituted alphaisopropoxy phenylpropanoic acids against PPARalpha and PPARgamma: molecular modeling and comparative molecular similarity indices analysis studies. Protein Pept. Lett., 2009, 16, 150-162
40. Cai, L.; Wang, Y.; Wang, J.F.; Chou, K.C. Identification of proteins interacting with human SP110 during the process of viral infections. Med. Chem., 2011, 7, 121-126
41. Liao, Q.H.; Gao, Q.Z.; Wei, J.; Chou, K.C. Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR). Med. Chem., 2011, 7, 24-31
42. Wang, S.Q.; Cheng, X.C.; Dong, W.L.; Wang, R.L.; Chou, K.C. Three new powerful Oseltamivir derivatives for inhibiting the neuraminidase of influenza virus. Biochem. Biophys. Res. Commun., 2010, 401, 188-191
43. Wang, J.F.; Wei, D.Q.; Chou, K.C. Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem. Biophys. Res. Commun., 2009, 388, 413-417
44. Wang, J.F.; Wei, D.Q.; Li, L.; Zheng, S.Y.; Li, Y.X.; Chou, K.C. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem. Biophys. Res. Commun., 2007, 355, 513-519 (Pubitemid 46282658)
45. Chou, K.C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134
46. Chou, K.C. The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition . Biophys. Chem., 1984, 20, 61-71
47. Chou, K.C. Low-frequency vibration of DNA molecules. Biochem. J., 1984, 221, 27-31
48. Chou, K.C. The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophys. J., 1984, 45, 881-890
49. Chou, K.C. The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers, 1987, 26, 285-295
50. Chou, K.C. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem. Sci., 1989, 14, 212
51. Chou, K.C.; Zhang, C.T.; Maggiora, G.M. Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers, 1994, 34, 143-153
52. Wang, J.F.; Chou, K.C. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem. Biophys. Res. Commun., 2009, 390, 608-612
53. Gordon, G. Extrinsic electromagnetic fields, low frequency (phonon) vibrations, and control of cell function: a non-linear resonance system. J. Biomed. Sci. Eng., 2008, 1, 152-156. (open accessible at http://www. srpublishing.org/journal/jbise/)
54. Madkan, A.; Blank, M.; Elson, E.; Chou, K.C.; Geddis, M.S.; Goodman, R. Steps to the clinic with ELF EMF. Nat. Sci., 2009, 1, 157-165. (Openly accessible at http://www.scirp.org/journal/NS/)
55. Martel, P. Biophysical aspects of neutron scattering from vibrational modes of proteins. Prog. Biophys. Mol. Biol., 1992, 57, 129-179
56. Huang, Z.; Zhu, L.; Cao, Y.; Wu, G.; Liu, X.; Chen, Y.; Wang, Q.; Shi, T.; Zhao, Y.; Wang, Y.; Li, W.; Li, Y.; Chen, H.F.; Chen, Q.; Zhang, J. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res., 2011, 39, D663-D669
57. Qin, F.; Jiang, Y.; Chen, Y.; Wu, M.; Yan, G.; Ye, W.; Li, Y.X.; Zhang, J.; Chen, H.F. Conformational selection or induced fit for brinker and DNA recognition. Phys. Chem. Chem. Phys., 2011, 13, 1407-1412
58. Qin, F.; Chen, Y.; Wu, M.; Li, Y.X.; Zhang, J.; Chen, H.F. Induced fit or conformational selection for RNA/U1A folding. RNA, 2010, 16, 1053-1061
59. Chen, Y.; He, Y.J.; Wu, M.; Yan, G.; Li, Y.X.; Zhang, J.; Chen, H.F. Insight into the stability of cross- amyloid fibril from molecular dynamics simulation. Biopolymers, 2010, 93, 578-586
60. Chen, Y.; Li, Z.; Chen, H.F. Computational study of CCR5 antagonist with support vector machines and three dimensional quantitative structure activity relationship methods. Chem. Biol. Drug Des., 2010, 75, 295-309
61. Li, Z.; Zhang, H.; Li, Y.; Zhang, J.; Chen, H.F. Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. Chem. Biol. Drug Des., 2010, 77, 64-74
62. Chen, H.F. Post-translational modification of phosphorylated KID from molecular dynamics simulation. PLoS One, 2009, 4, e6516
63. Xiong, J.; Wang, H.; Guo, G.; Wang, S.; He, L.; Chen, H.F.; Wu, J. Male germ cell apoptosis and epigenetic histone modification induced by tripterygium wilfordii Hook F. PLoS One, 2011, 6, e20751
64. Qin, F.; Chen, Y.; Li, Y.X.; Chen, H.F. Induced fit of mRNA/TIS11d complex. J. Chem. Phys., 2009, 131, 115103
65. Chen, H.F. Aggregation mechanism investigation of the GIFQINS cross- Amyloid Fibril. Comput. Biol. Chem., 2009, 33, 41-45
66. Chen, H.F. In silico logp prediction for a large data set with support vector machines, radial basis neural networks and multiple linear regression. Chem. Biol. Drug Des., 2009, 74, 142-147
67. Chen, H.F. Mechanism of coupled folding and binding in the siRNA-PAZ complex. J. Chem. Theor. Comput., 2008, 4, 1360-1368
68. Chen, H.F. Quantitative predictions of gas chromatography retention indexes with support vector machines, radial basis neural networks and multiple linear regression. Anal. Chim. Acta, 2008, 609, 24-36
69. Chen, H.F. Computational study of histamine H3-receptor antagonist with support vector machines and three dimension quantitative structure activity relationship methods. Anal. Chim. Acta, 2008, 624, 203-209
70. Chen, H.F. Computational Study of the Binding Mode of Epidermal Growth Factor Receptor Kinase Inhibitors. Chem. Biol. Drug Des., 2008, 71, 434-446
71. Li, Z.; Han, J.; Chen, H.F. Revealing Interaction Mode between HIV-1 Reverse Transcriptase and Diaryltriazine Analog Inhibitor. Chem. Biol. Drug Des., 2008, 72, 350-359
72. Chen, H.F.; Luo, R. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc., 2007, 129, 2930-2937 (Pubitemid 46417970)
73. Chen, H.F.; Wu, M.Y.; Wang, Z.; Wei, D.Q. Insight into the metabolism rate of quinone analogues from molecular dynamics simulation and 3D-QSMR methods. Chem. Biol. Drug Des., 2007, 70, 290-301 (Pubitemid 47537686)
74. Sun, J.; Chen, H.F.; Yao, J.H.; Fan, B.T. Comparative study of factor Xa inhibitors using molecular docking/SVM/HQSAR/3DQSAR methods. QSAR Comb. Sci., 2006, 25, 25-45 (Pubitemid 43189606)
75. Chou, K.C. Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophys. Chem., 1988, 30, 3-48
76. He, Z.; Zhang, J.; Shi, X.H.; Hu, L.L.; Kong, X.; Cai, Y.D.; Chou, K.C. Predicting drug-target interaction networks based on functional groups and biological features. PLoS One, 2010, 5, e9603
77. He, J.; Wei, D.Q.; Wang, J.F.; Chou, K.C. Predicting protein-ligand binding sites based on an improved geometric algorithm. Protein Pept. Lett., 2011, 18, 997-1001
78. Huang, T.; Niu, S.; Xu, Z.; Huang, Y.; Kong, X.; Cai, Y.D.; Chou, K.C. Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties. PLoS One, 2011, 6, e22940
79. Chou, K.C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948
80. Chou, K.C. Review: Prediction of HIV protease cleavage sites in proteins Anal. Biochem., 1996, 233, 1-14
81. Hu, L.L.; Huang, T.; Cai, Y.D.; Chou, K.C. Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS One, 2011, 6, e22989
82. Huang, T.; Shi, X.H.; Wang, P.; He, Z.; Feng, K.Y.; Hu, L.; Kong, X.; Li, Y.X.; Cai, Y.D.; Chou, K.C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One, 2010, 5, e10972
83. Chou, K.C.; Shen, H.B. Signal-CF: a subsite-coupled and windowfusing approach for predicting signal peptides. Biochem. Biophys. Res. Commun., 2007, 357, 633-640
84. Chen, L.; Feng, K.Y.; Cai, Y.D.; Chou, K.C.; Li, H.P. Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics, 2010, 11, 293
85. Wang, P.; Xiao, X.; Chou, K.C. NR-2L: A Two-Level predictor for identifying nuclear receptor subfamilies based on sequence-derived features. PLoS One, 2011, 6, e23505
86. Chou, K.C.; Shen, H.B. Cell-PLoc: A package of web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3, 153-162
87. Chou, K.C.; Wu, Z.C.; Xiao, X. iLoc-Euk: A multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One, 2011, 6, e18258
88. Chen, L.; Huang, T.; Shi, X.H.; Cai, Y.D.; Chou, K.C. Analysis of protein pathway networks using hybrid properties. Molecules, 2010, 15, 8177-8192
89. Lin, W.Z.; Fang, J.A.; Xiao, X.; Chou, K.C. iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model. PLoS One, 2011, 6, e24756
90. Huang, T.; Chen, L.; Cai, Y.D.; Chou, K.C. Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS One, 2011, 6, e25297
91. Chou, K.C.; Shen, H.B. ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem. Biophys. Res. Commun., 2008, 376, 321-325
92. Wang, P.; Hu, L.; Liu, G.; Jiang, N.; Chen, X.; Xu, J.; Zheng, W.; Li, L.; Tan, M.; Chen, Z.; Song, H.; Cai, Y.D.; Chou, K.C. Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS One, 2011, 6, e18476
93. Chou, K.C.; Shen, H.B. MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Commun., 2007, 360, 339-345
94. Xiao, X.; Wang, P.; Chou, K.C. GPCR-2L: Predicting G proteincoupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions. Mol. Biosyst., 2011, 7, 911-919
95. Chou, K.C.; Shen, H.B. Review: recent advances in developing web-servers for predicting protein attributes. Nat. Sci., 2009, 2, 63-92. (openly accessible at http://www.scirp.org/journal/NS/)
96. Bernstein, F.; Koetzle, T.; Williams, G.; Meyer, E. The Protein Data Bank: a computer-based archival file for macromolecular structures. Arch. Biochem. Biophys., 1978, 185, 584-591 (Pubitemid 8291122)
97. Guex, N.; Peitsch, M. SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis, 1997, 18, 2714-2723 (Pubitemid 28059943)
98. Georgescu, R.; Alexov, E.; Gunner, M. Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins. Biophys. J., 2002, 83, 1731-1748
99. Rocchia, W.; Alexov, E.; Honig, B. Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions. J. Phys. Chem. B, 2001, 105, 6507-6514 (Pubitemid 35339019)
100. Case, D.; Cheatham III, T.; Darden, T.; Gohlke, H.; Luo, R.; Merz Jr, K.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. The Amber biomolecular simulation programs. J. Comput. Chem., 2005, 26, 1668-1688 (Pubitemid 43076180)
101. Ponder, J.; Case, D. Force fields for protein simulations. Adv. protein chem., 2003, 66, 27-85 (Pubitemid 37392314)
102. Sch neboom, J.; 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 (Pubitemid 34755533)
103. Wang, J.F.; Wei, D.Q.; Lin, Y.; Wang, Y.H.; Du, H.L.; Li, Y.X.; Chou, K.C. Insights from modeling the 3D structure of NAD(P)Hdependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun., 2007, 359, 323-329 (Pubitemid 46887686)
104. Zeng, Q.K.; Du, H.L.; Wang, J.F.; Wei, D.Q.; Wang, X.N.; Li, Y.X.; Lin, Y. Reversal of coenzyme specificity and improvement of catalytic efficiency of Pichia stipitis xylose reductase by rational site-directed mutagenesis. Biotechnol. Lett., 2009, 31, 1025-1029
105. Gong, K.; Li, L.; Wang, J.F.; Chen, H.F.; Wei, D.Q.; Chou, K.C. Binding mechanism of H5N1 influenza virus neuraminidase with ligands and its implication for drug design. Med. Chem., 2009, 5, 242-249
106. Gu, R.X.; Gu, H.; Xie, Z.Y.; Wang, J.F.; Arias, H.R.; Wei, D.Q.; Chou, K.C. Possible drug candidates for Alzheimer's disease deduced from studying their binding interactions with alpha7 nicotinic acetylcholine receptor. Med. Chem., 2009, 5, 250-262
107. Wang, J.F.; Yan, J.Y.; Wei, D.Q.; Chou, K.C. Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism. Med. Chem., 2009, 5, 263-270
108. Wang, J.F.; Zhang, C.C.; Wei, D.Q.; Li, Y.X. Docking and molecular dynamics studies on CYP2D6. Chinese Sci. Bull., 2010, 55, 1877-1880
109. Wang, J.F.; Chou, K.C. Insights from modeling the 3D structure of New Delhi metallo-lactamse and its binding interactions with antibiotic drugs. PLoS One, 2011, 6, e18414
110. Wang, J.F.; Wei, D.Q.; Wang, C.Y.; Ye, Y.; Li, Y.X.; Luo, Y.; Wang, W.W.; Liu, L.Z.; Zhao, Y.F. A theoretical study on the mechanism of 2:1 1,3 dipolar cycloaddition reactions. J. Theor. Comput. Chem., 2007, 6, 861-867
111. Morris, G.; Huey, R.; Lindstrom, W.; Sanner, M.; Belew, R.; Goodsell, D.; Olson, A. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30, 2785-2791
112. Wang, J.F.; Gong, K.; Wei, D.Q.; Li, Y.X.; Chou, K.C. Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. Protein Eng. Des. Sel., 2009, 22, 349-355
113. Tang, B.; Gong, K.; Wang, J.F.; Li, Y.X.; Wei, D.Q. The structure of phospholamban and its MD simulations. Chinese Sci. Bull., 2010, 55, 1619-1624
114. Gu, H.; Chen, H.F.; Wei, D.Q.; Wang, J.F. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. Chinese Sci. Bull., 2010, 55, 2677-2683
115. Wang, Y.; Wei, D.Q.; Wang, J.F. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J. Chem. Inf. Model., 2010, 50, 875-878
116. Wang, J.F.; Chou, K.C. Insights from studying the mutationinduced allostery in the M2 proton channel by molecular dynamics. Protein Eng. Des. Sel., 2010, 23, 663-666
117. Lian, P.; Wei, D.Q.; Wang, J.F.; Chou, K.C. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One, 2011, 6, e18587
118. Blobaum, A.; Kent, U.; Alworth, W.; Hollenberg, P. Novel reversible inactivation of cytochrome P450 2E1 T303A by tertbutyl acetylene: the role of threonine 303 in proton delivery to the active site of cytochrome P450 2E1. J. Pharmaco. Exp. Ther., 2004, 310, 281
119. 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
120. Vaz, A.; Pernecky, S.; Raner, G.; Coon, M. 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
121. Vaz, A.; McGinnity, D.; Coon, M. Epoxidation of olefins by cytochrome P450: evidence from site-specific mutagenesis for hydroperoxo-iron as an electrophilic oxidant. Proc. Natl. Acad. Sci. USA, 1998, 95, 3555
122. Fukuda, T.; Imai, Y.; Komori, M.; Nakamura, M.; Kusunose, E.; Kusunose, M. Replacement of thr-303 of P450 2E11 with serine modifies the regioselectivity of its fatty acid hydroxylase activity. J. Biochem., 1993, 113, 7
123. 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
124. Moreno, R.; Goosen, T.; Kent, U.; Chung, F.; Hollenberg, P. Differential effects of naturally occurring isothiocyanates on the activities of cytochrome P450 2E1 and the mutant P450 2E1 T303A. Arch. Biochem. Biophys., 2001, 391, 99-110 (Pubitemid 32612577)
125. Spatzenegger, M.; Liu, H.; Wang, Q.; Debarber, A.; Koop, D.; Halpert, J. Analysis of differential substrate selectivities of CYP2B6 and CYP2E1 by site-directed mutagenesis and molecular modeling. J. Pharmacol. Exp. Ther., 2003, 304, 477.