Advances in human cytochrome P450 and personalized medicine

Current Drug Metabolism

Volumn 12, Issue 5, 2011, Pages 436-444

  Chen, Qi ^a   Zhang, Tao ^a   Wang, Jing Fang ^b   Wei, Dong Qing ^a  

^a Shanghai Jiao Tong University   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Cytochrome P450; Drug metabolism; Personalized medicine; SNP

Indexed keywords

CYTOCHROME P450; CYTOCHROME P450 1A1; CYTOCHROME P450 1B1; CYTOCHROME P450 2C19; CYTOCHROME P450 2D6; CYTOCHROME P450 3A5; DRUG METABOLIZING ENZYME; MULTIDRUG RESISTANCE PROTEIN 1;

ALGORITHM; ALLELE; ARTICLE; BIOINFORMATICS; COMPUTER AIDED DESIGN; DATA BASE; ENZYME ACTIVITY; GENE; HUMAN; NATURAL LANGUAGE PROCESSING; PERSONALIZED MEDICINE; PHARMACOGENOMICS; PHENOTYPE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTATIONAL BIOLOGY; CYTOCHROME P-450 ENZYME SYSTEM; DATABASES, FACTUAL; DRUG DESIGN; HUMANS; INDIVIDUALIZED MEDICINE; PHARMACEUTICAL PREPARATIONS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79955685155     PISSN: 13892002     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920011795495259     Document Type: Article

References (116)

1. Vogel, F. Moderne probleme der humangenetik. Ergebn. Inn. Med. Kinderheilk, 1959, 12, 52-60.
2. Wang, J.F.; Wei, D.Q.; Chou, K.C. Pharmacogemonics and personalized use of drugs. Curr. Top. Med. Chem., 2008, 8(18), 1573-1579.
3. Wang, J.F.; Wei, D.Q. Role of structural bioinformatics and traditional Chinese medicine databases in pharmacogenomics. Pharmacogenomics, 2009, 10(8), 1213-1215.
4. Tanmay, S.P.; Shaun, F.N.; Sanish, D.; Vishal, M.S.; Nilima, A.K.; Nithya, J.G. Evaluation of the activity of CYP2C19 in Gujrati and Marwadi subjects living in Mumbasi (Bombay). BMC Clin. Pharm., 2006, 6(8), 1-5.
5. Lewis, D.F.V. The CYP2 family: models, mutants and interactions. Xenobiotica, 1998, 28(77), 617-661. (Pubitemid 28352417)
6. Sheweita, S.A. Drug-metabolizing enzymes: mechanisms and functions. Curr. Drug. Metab. 2000, 1(2), 107-132.
7. Nebert, D.W.; Russell, D.W. Clinical importance of the cytochrome P450. Lancet, 2002, 360(9340), 1155-1162.
8. Wang, J.F.; Wei, D.Q.; Chen, C.; Li, Y.; Chou, K.C. Molecular Modeling of Two CYP2C19 SNPs and Its Implications for Personalized Drug Design. Protein Pept. Lett., 2008, 15(1), 27-32. (Pubitemid 351206472)
9. Fischer, M.; Knoll, M.; Sirim, D.; Wagner, F.; Funke, S.; Pleiss, J. The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. BIOINFORMATICS APPLICATIONS NOTE, 2007, 23(15), 2015-2017. (Pubitemid 47299844)
10. Lynch, T.; Price, A. The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects. Am. Fam. Physician, 2007, 76(3), 391-396. (Pubitemid 47219454)
11. Hodgson, J. ADMET-turning chemicals into drugs. Nat. Biotechnol., 2001, 19(8), 722-726.
12. Robertson, G.R.; Field, J.; Goodwin, B.; Bierach, S.; Tran, M.; Lehnert, A.; Liddle, C. Transgenic mouse models of human CYP3A4 gene regulation. Mol. Pharmacol., 2003, 64 (1), 42-50. (Pubitemid 36759816)
13. Arimoto, R. Computational models for predicting interactions with cytochrome p450 enzyme. Curr. Top. Med. Chem., 2006, 6 (15), 1609-1618. (Pubitemid 44313416)
14. Hu, S.X.; Foster, T.; Kieffaber, A. Pharmacogenomics and personalized medicine: mapping of future value creation. BioTechniques, 2005, 39(4), 1-6.
15. Rettie, A.E.; Tai, G. The Pharmocogenomics of Warfarin Closing in on Personalized Medicine. Mol. Interv., 2006, 6 (4), 223-227. (Pubitemid 44455204)
16. Yang, S.; Xu, L.; Wu, H.M. Rapid Genotyping of SNPs Influencing Warfarin Drug Response by SELDI-TOF Mass Spectrometry. J. Mol. Diagn., 2010, 12(2), 162-168.
17. Daly, A.K. Pharmacogenetics of the cytochromes P450. Curr. Top. Med. Chem., 2004, 4(16), 1733-1744. (Pubitemid 39654459)
18. Teng, S.; Michonova-Alexova, E.; Alexov, E. Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr. Pharm. Biotechnol., 2008, 9(2), 123-133. (Pubitemid 351513490)
19. Sadée, W.; Dai, Z. Pharmacogenetics/genomics and personalized medicine. Hum. Mol. Genet., 2005, 14(2), R207-R214. (Pubitemid 41631889)
20. Larsen L.A.; Christiansen M.; Vuust J.; Andersen P.S. Recent developments in high-throughput mutation screening. Pharmacogenomics, 2001, 2(4), 387-399. (Pubitemid 33115061)
21. Yu B.; Sawyer N.A.; Chiu C.; Oefner P.J.; Underhill P.A. DNA mutation detection using denaturing high-performance liquid chromatography (DHPLC). Curr. Protoc. Hum. Genet., 2006, Chapter 7, Unit7.10.
22. Kim S.; Misra A. SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng., 2007, 9, 289-320. (Pubitemid 350246659)
23. Ding C.; Jin S. High-throughput methods for SNP genotyping. Methods Mol Biol, 2009, 578, 245-254.
24. Matukumalli L.K.; Grefenstette J.J.; Hyten D.L.; Choi I.Y.; Cregan P.B.; Van Tassell C.P. Application of machine learning in SNP discovery. BMC Bioinform., 2006, 7, 4.
25. Panitz F.; Stengaard H.; Hornshøj H.; Gorodkin J.; Hedegaard J.; Cirera S.; Thomsen B.; Madsen L.B.; Høj A.; Vingborg R.K.; Zahn B.; Wang X.; Wang X.; Wernersson R.; Jørgensen C.B.; Scheibye- Knudsen K.; Arvin T.; Lumholdt S.; Sawera M.; Green T.; Nielsen B.J.; Havgaard J.H.; Brunak S.; Fredholm M.; Bendixen C. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics, 2007, 23(13), i387-i391 (Pubitemid 47244424)
26. Chorley B.N.; Wang X.; Campbell M.R.; Pittman G.S.; Noureddine M.A.; Bell D.A. Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat. Res., 2008, 659(1-2), 147-57.
27. Kelemen A.; Vasilakos A.V.; Liang Y. Computational intelligence in bioinformatics: SNP/haplotype data in genetic association study for common diseases. IEEE Trans. Inf. Technol. Biomed., 2009, 13(5), 841-847.
28. Mooney S.D.; Krishnan V.G.; Evani U.S. Bioinformatic tools for identifying disease gene and SNP candidates. Methods Mol. Biol., 2010, 628, 307-319.
29. Wang J.; Zou Q.; Guo M.Z. Mining SNPs from EST sequences using filters and ensemble classifiers. Genet. Mol. Res., 2010, 9(2), 820-834.
30. Kjellander, B.; Masimirembwa, C.M.; Zamora, I. Exploration of Enzyme-Ligand Interactions in CYP2D6 & 3A4 Homology Models and Crystal Structures Using a Novel Computational Approach. J. Chem. Inf. Model., 2007, 47(3), 1234-1247. (Pubitemid 46973737)
31. Arranz, M.J.; de Leon, J. Pharmacogenetics and pharmacogenomics of schizophrenia: a review of last decade of research. Mol. Psychiatry, 2007, 12(8), 707-747. (Pubitemid 47172693)
32. Arranz, M.J.; Kapur, S. Pharmacogenetics in psychiatry: Are we ready for widespread clinical use? Schizophr. Bull., 2008, 34(6), 1130-1144.
33. Mooney, S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform., 2005, 6(1), 44-56. (Pubitemid 40528579)
34. Bairoch, A.; Apweiler,R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res., 1999, 27(1), 49-54. (Pubitemid 29209398)
35. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov ,I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res., 2000, 28(1), 235-242. (Pubitemid 30047768)
36. Nelson, D.R. Cytochrome P450 nomenclature, 2004. Methods Mol. Biol., 2006, 320, 1-10.
37. Geer, L.Y.; Marchler-Bauer, A.; Geer, R.C.; Han, L.; He, J.; He, S.; Liu, C.; Shi, W.; Bryant, S.H. The NCBI BioSystems database. Nucleic Acids Res., 2010, 38, D492-496.
38. Sim, S.C.; Ingelman-Sundberg, M. The human cytochrome P450 Allele Nomenclature Committee Web site: submission criteria, procedures, and objectives. Methods Mol. Biol., 2006, 320, 183-191.
39. Sirim, D.; Wagner, F.; Lisitsa, A.; Pleiss, J. The Cytochrome P450 Engineering Database: integration of biochemical properties. BMC Biochem., 2009, 10, 27.
40. Radhakrishnan, M.L.; Tidor, B. Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems. J. Chem. Inf. Model., 2008, 48(5), 1055-1073.
41. Preissner, S.; Kroll, K.; Dunkel, M.; Senger, C.; Goldsobel, G.; Kuzman, D.; Guenther, S.; Winnenburg, R.; Schroeder, M.; Preissner, R. SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010, 38, D237-243.
42. Thomas, J.; Milward, D.; Ouzounis, C.; Pulman, S.; Carroll, M. Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput., 2000, 5, 541-552.
43. Horn, F.; Lau, A.L.; Cohen, F.E. Automated extraction of mutation data from the literature: application of MuteXt to G proteincoupled receptors and nuclear hormone receptors. Bioinformatics, 2004, 20(4), 557-568. (Pubitemid 38344336)
44. Hu, Z.Z.; Narayanaswamy, M.; Ravikumar, K. E.; Vijay-Shanker, K.; Wu, C. H. Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics, 2005, 21(11), 2759-2765. (Pubitemid 40852324)
45. Feng, C.; Yamashita, F.; Hashida, M. Automated Extraction of Information from the Literature on Chemical-CYP3A4 Interactions. J. Chem. Inf. Model., 2007, 47(6), 2449-2455. (Pubitemid 350275109)
46. Yang, X.; Zhang, B.; Molony, C.; Chudin, E.; Hao, K.; Zhu, J.; Gaedigk, A.; Suver, C.; Zhong, H.; Leeder, J.S.; Guengerich, F.P.; Strom, S.C.; Schuetz, E.; Rushmore, T.H.; Ulrich, R.G.; Slatter, J.G.; Schadt, E.E.; Kasarskis, A.; Lum, P.Y. Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res., 2010, 20(8), 1020-1036.
47. Ramensky, V.; Bork, P.; Sunyaev, S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res., 2002, 30(17), 3894-3900. (Pubitemid 35012462)
48. Wang, L.L.; Li, Y.; Zhou, S.F. A Bioinformatics Approach for the Phenotype Prediction of Nonsynonymous Single Nucleotide Polymorphisms in Human Cytochromes P450. Drug Metab. Dispos., 2009, 37(5), 977-991.
49. Varela-Lema, L.; Taioli, E.; Ruano-Ravina, A.; Barros-Dios, J.M.; Anantharaman, D.; Benhamou, S.; Boccia, S.; Bhisey, R.A.; Cadoni, G.; Capoluongo, E.; Chen, C.J.; Foulkes, W.; Goloni- Bertollo, E.M.; Hatagima, A.; Hayes, R.B.; Katoh, T.; Koifman, S.; Lazarus, P.; Manni, J.J.; Mahimkar, M.; Morita, S.; Park, J.; Park, K.K.; Pavarino Bertelli, E.C.; de Souza Fonseca Ribeiro, E.M.; Roy, B.; Spitz, M.R.; Strange, R.C.; Wei, Q.; Ragin, C.C. Metaanalysis and pooled analysis of GSTM1 and CYP1A1 polymorphisms and oral and pharyngeal cancers: a HuGE-GSEC review. Genet. Med., 2008, 10(6), 369-384.
50. Shi, X.; Zhou, S.; Wang, Z.; Zhou, Z. CYP1A1 and GSTM1 polymorphisms and lung cancer risk in Chinese populations: a metaanalysis. Lung Cancer, 2008, 59(2), 155-163. (Pubitemid 351173406)
51. Shaik, A.P.; Jamil, K.; Das, P. CYP1A1 polymorphisms and risk of prostate cancer: a meta-analysis. Urol. J., 2009, 6(2), 78-86.
52. Zhuo, W.L.; Zhang, Y.S.; Wang, Y.; Zhuo, X.L.; Zhu, B.; Cai, L.; Chen, Z.T. Association studies of CYP1A1 and GSTM1 polymorphisms with esophageal cancer risk: evidence-based meta-analyses. Arch. Med. Res., 2009, 40(3), 169-179.
53. Sergentanis, T.N.; Economopoulos, K.P. Four polymorphisms in cytochrome P450 1A1 (CYP1A1) gene and breast cancer risk: a meta-analysis. Breast Cancer Res. Treat., 2010, 122(2), 459-469.
54. Economopoulos, K.P.; Sergentanis, T.N. Three polymorphisms in cytochrome P450 1B1 (CYP1B1) gene and breast cancer risk: a meta-analysis. Breast Cancer Res. Treat., 2010, 122(2), 545-551.
55. Neafsey, P.; Ginsberg, G.; Hattis, D.; Johns, D.O.; Guyton, K.Z.; Sonawane, B. Genetic polymorphism in CYP2E1: Population distribution of CYP2E1 activity. J. Toxicol. Environ. Health B Crit. Rev., 2009, 12(5-6), 362-388.
56. White, P.C.; Speiser, P.W. Congenital adrenal hyperplasia due to 21-hydroxylase deficiency. Endocr. Rev., 2000, 21, 245-291. (Pubitemid 32275589)
57. Concolino, P.; Mello, E.; Zuppi, C.; Capoluongo, E. Molecular diagnosis of Congenital adrenal hyperplasia due to 21-hydroxylase deficiency: an update of new CYP21A2 mutations. Clin. Chem. Lab. Med., 2010, 48(8), 1057-1062.
58. Anderson, J.L.; Carlquist, J.F.; Horne, B.D.; Muhlestein, J.B. Cardiovascular pharmacogenomics: Current status, future prospects. J. Cardiovasc. Pharmacol. Ther., 2003, 8(1), 71-83. (Pubitemid 36363213)
59. Simon, T.; Verstuyft, C.; Mary-Krause, M.; Quteineh, L.; Drouet, E.; Meneveau, N.; Steg, P.G.; Ferrieres, J.; Danchin, N.; Becquemont, L. Genetic determinants of response to clopidogrel and cardiovascular events. N. Engl. J. Med., 2009, 360(4), 363-375.
60. Mega, J.L.; Close, S.L.; Wiviott, S.D.; Shen, L.; Hockett, R.D.; Brandt, J.T.; Walker, J.R.; Antman, E.M.; Macias, W.; Braunwald, E. Cytochrome p-450 polymorphisms and response to clopidogrel. N. Engl. J. Med., 2009, 360(4), 354-362.
61. Wang, J.F.; Wei, D.Q.; Chou, K.C. Drug candidates from traditional Chinese medicine. Curr. Top. Med. Chem., 2008, 8(18), 1656-1665.
62. Vandel, P.; Talon, J.M.; Haffen, E.; Sechter, D. Pharmacogenetics and drug therapy in psychiatry: The role of the CYP2D6 polymorphism. Curr. Pharm. Des., 2007, 13(2), 241-250. (Pubitemid 46085296)
63. van Schaik R.H. Cancer treatment and pharmacogenetics of cytochrome P450 enzymes. Invest. New Drugs, 2005, 23(6), 513-522. (Pubitemid 43162470)
64. Bradford, L.D. CYP2D6 allele frequency in European Caucasians, Asians, Africans and their descendants. Pharmacogenomics, 2002, 3(2), 229-243. (Pubitemid 34223859)
65. Blonk, M.I.; van der Velde, N.; van den Bemt, P.M.; van Schaik, R.H.; van der Cammen, T.J. CYP2D6*4, CYP3A5*3 and ABCB1 3435T polymorphisms and drug-related falls in elderly people. Pharm. World Sci., 2010, 32(1), 26-29.
66. Sofi, F.; Giusti, B.; Marcucci, R.; Gori, A.M.; Abbate, R.; Gensini, G.F. Cytochrome P450 2C19(*)2 polymorphism and cardiovascular recurrences in patients taking clopidogrel: a meta-analysis. Pharmacogenomics J., 2010, [Epub ahead of print].
67. Fleeman, N.; McLeod, C.; Bagust, A.; Beale, S.; Boland, A.; Dundar, Y.; Jorgensen, A.; Payne, K.; Pirmohamed, M.; Pushpakom, S.; Walley, T.; de Warren-Penny, P.; Dickson, R. The clinical effectiveness and cost-effectiveness of testing for cytochrome P450 polymorphisms in patients with schizophrenia treated with antipsychotics: a systematic review and economic evaluation. Health Technol. Assess., 2010, 14(3), 1-157.
68. Jorgensen, W. L. The many roles of computation in drug discovery. Science, 2004, 303 (5665), 1813-1818. (Pubitemid 38374866)
69. Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat. Rev. Drug Discov., 2004, 3 (11), 935-949. (Pubitemid 39529931)
70. Schlichting, I.; Berendze, J.; Chu, K.; Stoch, A.M.; Maves, S.A.; Benson, D.E.; Sweet, R.M.; Ringe, D.; Petsko, G.A.; Sligar, S.G. The catalytic pathway of cytochrome P450cam at atomic resolution. Science, 2000, 287, 1615-1622. (Pubitemid 30127756)
71. Wang, J.F.; Chou, K.C. Molecular modeling of cytochrome P450 and drug metabolism. Curr. Drug Metab., 2010, 11(4), 342-346.
72. Wang, J.F.; Zhang, C.C.; Chou K.C.; Wei, D.Q. Structure of cytochrome P450s and personalized drug. Curr. Med. Chem., 2009, 16(2), 232-244.
73. de Graaf, C.; Vermeulen, N.P.E.; Feenstra, A. Cytochrome P450 in Silico: An Integrative Modeling Approach. J. Med. Chem., 2005, 48(8), 2725-2755. (Pubitemid 40548088)
74. Crivori, P.; Poggesi, I. Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs. Eur. J. Med. Chem., 2006, 41(7), 795-808. (Pubitemid 44015977)
75. Lill, M.A. Multi-dimensional QSAR in drug discovery. Drug Discov. Today, 2007, 12(23-24), 1013-1017. (Pubitemid 350180557)
76. Kubinyi, H. QSAR and 3D QSAR in drug design 0.1. methodology. Drug Discov. Today, 1997, 2 (11), 457-467. (Pubitemid 27450428)
77. Marshall, G.R.; Cramer, R.D. 3rd. Three-dimensional structureactivity relationships. Trends Pharmacol. Sci., 1988, 9(8), 285-289.
78. Khan, M.T. Predictions of the ADMET Properties of Candidate Drug Molecules Utilizing Different QSAR/QSPR Modelling Approaches. Curr. Drug Metab., 2010, 11(4), 285-295.
79. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors. Methods and Principles in Medicinal Chemistry Series. Volume 11. Edited by Mannold, R.; Kubinyi, H.; Timmerman, H. Wiley-VCH: Weinheim and New York. 2000.
80. Gibbs, A.C.; Agrafiotis, D.K. In Exploiting Chemical Diversity for Drug Discovery, Barlett, P.A.; Entzeroth, M.; Eds.; RSC Publishing: Cambridge, 2006, pp. 137-159.
81. Liu, P.; Long, W. Current Mathematical Methods used in QSAR/QSPR Studies. Int. J. Mol. Sci., 2009, 10(5), 1978-1998.
82. Michielan, L.; Moro, S. Pharmaceutical Perspectives of Nonlinear QSAR Strategies. J. Chem. Inf. Model., 2010, 50(6), 961-978.
83. Kontijevskis, A.; Komorowski, J.; Wikberg, J.E.S. Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors. J. Chem. Inf. Model., 2008, 48 (9), 1840-1850.
84. Dagliyan, O.; Kavakli, I.H.; Turkay, M. Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC50 Using Common Molecular Descriptors. J. Chem. Inf. Model., 2009, 49(10), 2403-2411.
85. 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 (4), 982-992. (Pubitemid 41156697)
86. Arimoto, R.; Prasad, M.; Gifford, E. Development of CYP3A4 inhibition models: comparisons of machine-learning techniques and molecular descriptors. J. Biomol. Screen, 2005, 10(3), 197-205. (Pubitemid 40617157)
87. Terfloth, L.; Bienfait, B.; Gasteiger, J. Ligand-based models for the isoform specificity of cytochrome P4503A4, 2D6, and 2C9 substrates. J. Chem. Inf. Model., 2007, 47 (4), 1688-1701. (Pubitemid 47210071)
88. Leong, M.; Chen, T. Prediction of cytochrome P450 2B6-substrate interactions using pharmacophore ensemble/support vector machine (PhE/SVM) approach. Med. Chem., 2008, 4(4), 396-406.
89. Leong, M.; Chen, Y.; Chen, H.; Chen, P. Development of a new predictive model for interactions with human cytochrome P450 2A6 using Pharmacophore Ensemble/Support Vector Machine( PhE/SVM) approach. Pharm. Res., 2009, 26(4), 987-1000.
90. Vasanthanathan, P.; Taboureau, O.; Oostenbrink, C.; Vermeulen, N.; Olsen, L.; Jorgensen, F. Classification of cytochrome P450 1A2 inhibitors and non-inhibitors by machine learning techniques. Drug Metab. Dispos., 2009, 37 (3),658-664.
91. Xie, Z.Y.; Zhang, T.; Wang, J.F.; Chou, K.C.; Wei, D.Q. The computational model to predict accurately inhibitory activity for inhibitors towards CYP3A4. Comput. Biol. Med., 2010, (in press), doi:10.1016/j.compbiomed.2010.09.004.
92. Raha, K.; Peters, M.B.; Wang, B.; Yu, N.; Wollacott, A.M.; Westerhoff, L.M.; Merz, K.M. Jr. The role of quantum mechanics in structure-based drug design. Drug Discov. Today, 2007, 12(17- 18), 725-31. (Pubitemid 47364833)
93. Hensen, C.; Hermann, J.C.; Nam, K.; Ma, S.; Gao, J.; Höltje, H.D. A combined QM/MM approach to protein-ligand interaction: polarization effects of HIV-1 protease on selected high affinity inhibitors. J. Med. Chem., 2004, 47(27), 6673-6680. (Pubitemid 40053756)
94. Gowthaman, U.; Jayakanthan, M.; Sundar, D. Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry, BMC Bioinform., 2008, 9 (Suppl 12): S14.
95. Jayakanthan, M.; Wadhwa, G.; Madhan Mohan, T.; Arul, L.; Balasubramanian, P.; Sundar, D. Computer aided drug design for cancer- causing H-Ras P21 mutant protein. Lett. Drug Des. Discov., 2009, 6(1), 14-20.
96. Jayakanthan, M.; Chandrasekar, S.; Muthukumaran, J.; Mathur, P.P. Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for Highly Active Antiretroviral Therapy in HIV/AIDS. J. Mol. Graph. Model., 2010, 28(5), 455-463.
97. 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(2), 513-519. (Pubitemid 46282658)
98. Erratum in: Biochem. Biophys. Res. Commun., 2007, 357(1), 330.
99. Biochem. Biophys. Res. Commun., 2009, 384(3), 399.
100. 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(3), 263-267.
101. Wang, J.F.; Zhang, C.C.; Wei, D.Q. Docking and molecular dynamics studies on CYP2D6. Chin. Sci. Bull., 2010, 55(18), 1877- 1880.
102. Wei, D.Q.; Sirois, S.; Du, Q.S.; Arias, H.R.; Chou, K.C. Theoretical studies of Alzheimer's disease drug candidate 3-[(2,4- dimethoxy)benzylidene]- anabaseine (GTS-21) and its derivatives. Biochem. Biophys. Res. Commun., 2005, 338(2), 1059-1064. (Pubitemid 41597746)
103. Chou, K.C.; Wei, D.Q.; Du, Q.S.; Sirois, S.; Zhong, W.Z. Progress in computational approach to drug development against SARS. Curr. Med. Chem., 2006, 13(27), 3263-3270. (Pubitemid 44669774)
104. Wei, D.Q.; Zhang, R.; Du, Q.S.; Gao, W.N.; Li, Y.;Gao, H.; Wang, S.Q.; Zhang, X.; Li, A.X.; Sirois, S.; Chou, K.C. Anti-SARS Drug Screening by Molecular Docking. Amino Acids, 2006, 31(1), 73-80. (Pubitemid 44086400)
105. Gu, H.; Chen, H.F.; Wei, D.Q.; Wang, J.F. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. Chin. Sci. Bull., 2010, 55(24), 2677-2683.
106. Wang, J.F.; Wei, D.Q.; Wang, C.F.; 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(4), 861-867.
107. 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(2), 323-329. (Pubitemid 46887686)
108. Wang, J.F.; Wei, D.Q.; Du, H.L; Li, Y.X.; Chou, K.C. Molecular modeling studies on NADP-dependence of Candida tropicalis strains xylose reductase. Open Bioinformatics J., 2008, 2, 72-79.
109. Wang, J.F.; Gong, K.; Wei, D.Q.; Li, Y.X. Structural flexibility and interactions of PTP1B's S-loop. Interdiscip. Sci., 2009, 1(3), 214-219.
110. 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(6), 349-355.
111. Wang, J.F.; Wei, D.Q.; Chou, K.C. Insights from investigating the interactions of adamantine-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem. Biophys. Res. Commun., 2009, 388(2), 413-417.
112. 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(3), 608-612.
113. Wang, Y.; Wei, D.Q.; Wang, J.F. Molecular dynamics studies on T1 lipase: Insights into a double-flap mechanism. J. Chem. Inf. Model., 2010, 50(5), 875-878.
114. Wang, J.F.; Chou, K.C. Insight from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics. Protein Eng. Des. Sel., 2010, 23(8), 663-666.
115. Rosales-Hernandez, M.C.; Bermúdez-Lugo, J.; Garcia, J.; Trujillo- Ferrara, J.; Correa-Basurto, J. Molecular Modeling Applied to Anti-Cancer Drug Development. Anticancer Agents Med. Chem., 2009, 9(2), 230-238.
116. Sano, E.; Li, W.; Yuki, H.; Liu, X.; Furihata, T.; Kobayashi, K.; Chiba, K.; Neya, S.; Hoshino, T. Mechanism of the Decrease in Catalytic Activity of Human Cytochrome P450 2C9 Polymorphic Variants Investigated by Computational Analysis. J. Comput. Chem., 2009, 31(15), 2746-2758.