In silico site of metabolism prediction of cytochrome P450-mediated biotransformations

Bibliography

• Ortiz de Montellano P. Cytochrome P450 structure, mechanism, and biochemistry. 3rd edition. Kluwer Academic, New York; 2005
   Google Scholar
• Guengerich FP. Reactions and significance of cytochrome P-450 enzymes. J Biol Chem 1991;266:10019-22
   PubMed Web of Science ®Google Scholar
• Porter TD, Coon MJ. Cytochrome P-450. Multiplicity of isoforms, substrates, and catalytic and regulatory mechanisms. J Biol Chem 1991;266:13469
   PubMed Web of Science ®Google Scholar
• Kubota M, Sogawa K, Kaizu Y, Xenobiotic responsive element in the 5?-upstream region of the human P-450c gene. J Biochem 1991;110:232
   PubMed Web of Science ®Google Scholar
• Ioannides C. Cytochromes P450: metabolic and toxicological aspects. CRC Press, Boca Raton, FL; 1996
   Google Scholar
• de Groot MJ. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today 2006;11:601-6
   PubMed Web of Science ®Google Scholar
• Smith DA, Jones BC. Speculations on the substrate structure–activity relationship (SSAR) of cytochrome P450 enzymes. Biochem Pharmacol 1992;44:2089-98
   PubMed Web of Science ®Google Scholar
• Schlichting I, Berendzen J, Chu K, The catalytic pathway of cytochrome p450cam at atomic resolution. Science 2000;287:1615-22
   PubMed Web of Science ®Google Scholar
• Guengerich FP, Krauser JA, Johnson WW. Rate-limiting steps in oxidations catalyzed by rabbit cytochrome P450 1A2. Biochemistry 2004;43:10775-88
   PubMed Web of Science ®Google Scholar
• Bach RD. The rate-limiting step in P450 hydroxylation of hydrocarbons a direct comparison of the “somersault” versus the “consensus” mechanism involving compound I. J Phys Chem A 2010;114:9319-32
   PubMed Web of Science ®Google Scholar
• Keseru GM, Kolossvary I, Bertok B. Cytochrome P-450 catalyzed insecticide metabolism. Prediction of Regio- and Stereoselectivity in the Primer Metabolism of Carbofuran: A Theoretical Study. J Am Chem Soc 1997;119:5126-31
   Web of Science ®Google Scholar
• Williams PA, Cosme J, Ward A, Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 2003;424:464-8
   PubMed Web of Science ®Google Scholar
• Available from: www.pdb.org; 2010
   Google Scholar
• de Graaf C, Vermeulen NP, Feenstra KA. Cytochrome p450 in silico: an integrative modeling approach. J Med Chem 2005;48:2725-55
   PubMed Web of Science ®Google Scholar
• Otyepka M, Skopalik J, Anzenbacherova E, Anzenbacher P. What common structural features and variations of mammalian P450s are known to date? Biochim Biophys Acta 2007;1770:376-89
   PubMed Web of Science ®Google Scholar
• Wester MR, Yano JK, Schoch GA, The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. J Biol Chem 2004;279:35630-7
   PubMed Web of Science ®Google Scholar
• Yano JK, Wester MR, Schoch GA, The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution. J Biol Chem 2004;279:38091-4
   PubMed Web of Science ®Google Scholar
• Williams PA, Cosme J, Vinkovic DM, Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science 2004;305:683-6
   PubMed Web of Science ®Google Scholar
• Ekroos M, Sjogren T. Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci USA 2006;103:13682-7
   PubMed Web of Science ®Google Scholar
• Lee YT, Wilson RF, Rupniewski I, Goodin DB. P450cam visits an open conformation in the absence of substrate. Biochemistry 2010;49:3412-19
   PubMed Web of Science ®Google Scholar
• Unwalla RJ, Cross JB, Salaniwal S, Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism. J Comput Aided Mol Des 2010;24:237-56
   PubMed Web of Science ®Google Scholar
• Tarcsay A, Kiss R, Keseru GM. Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. J Comput Aided Mol Des 2010;24:399-408
   PubMed Web of Science ®Google Scholar
• Morris GM, Goodsell DS, Halliday RS, Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 1998;19:1639-62
   Web of Science ®Google Scholar
• Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001;15:411-28
   PubMed Web of Science ®Google Scholar
• Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-89
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739-49
   PubMed Web of Science ®Google Scholar
• Jones G, Willett P, Glen RC, Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-48
   PubMed Web of Science ®Google Scholar
• de Graaf C, Oostenbrink C, Keizers PH, Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem 2006;49:2417-30
   PubMed Web of Science ®Google Scholar
• Santos R, Hritz J, Oostenbrink C. Role of water in molecular docking simulations of cytochrome P450 2D6. J Chem Inf Model 2010;50:146-54
   PubMed Web of Science ®Google Scholar
• Vasanthanathan P, Hritz J, Taboureau O, Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands. J Chem Inf Model 2009;49:43-52
   PubMed Web of Science ®Google Scholar
• Afzelius L, Arnby CH, Broo A, State-of-the-art tools for computational site of metabolism predictions: comparative analysis, mechanistical insights, and future applications. Drug Metab Rev 2007;39:61-86
   PubMed Web of Science ®Google Scholar
• FRED, version v.1.2; Openeye Scientific Software: Santa Fe, NM; 2005
   Google Scholar
• Sykes MJ, McKinnon RA, Miners JO. Prediction of metabolism by cytochrome P450 2C9: alignment and docking studies of a validated database of substrates. J Med Chem 2008;51:780-91
   PubMed Web of Science ®Google Scholar
• Hritz J, de Ruiter A, Oostenbrink C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. J Med Chem 2008;51:7469-77
   PubMed Web of Science ®Google Scholar
• Boyer S, Zamora I. New methods in predictive metabolism. J Comput Aided Mol Des 2002;16:403-13
   PubMed Web of Science ®Google Scholar
• 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;46:2313-24
   PubMed Web of Science ®Google Scholar
• Cruciani G, Carosati E, De Boeck B, MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J Med Chem 2005;48:6970-9
   PubMed Web of Science ®Google Scholar
• Molecular Discovery Ld; 2010. Available from: www.moldiscovery.com
   Google Scholar
• Trunzer M, Faller B, Zimmerlin A. Metabolic soft spot identification and compound optimization in early discovery phases using MetaSite and LC-MS/MS validation. J Med Chem 2009;52:329-35
   PubMed Web of Science ®Google Scholar
• Zhou D, Afzelius L, Grimm SW, Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions. Drug Metab Dispos 2006;6:976-83
   Google Scholar
• de Groot MJ, Kirton SB, Sutcliffe MJ. In silico methods for predicting ligand binding determinants of cytochromes P450. Curr Top Med Chem 2004;4:1803-24
   PubMed Web of Science ®Google Scholar
• ROCS, version 2.2; Openeye Scientific Software: Santa Fe, NM; 2006
   Google Scholar
• Shaik S, Cohen S, Wang Y, P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. Chem Rev 2010;110:949-1017
   PubMed Web of Science ®Google Scholar
• Yin H, Anders MW, Korzekwa KR, Designing safer chemicals: predicting the rates of metabolism of halogenated alkanes. Proc Natl Acad Sci USA 1995;92:11076-80
   PubMed Web of Science ®Google Scholar
• Jones JP, Mysinger M, Korzekwa KR. Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction. Drug Metab Dispos 2002;30:7-12
   PubMed Web of Science ®Google Scholar
• Singh SB, Shen LQ, Walker MJ, Sheridan RP. A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules. J Med Chem 2003;46:1330-6
   PubMed Web of Science ®Google Scholar
• Park JY, 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;46:1645-60
   PubMed Web of Science ®Google Scholar
• Olsen L, Rydberg P, Rod TH, Ryde U. Prediction of activation energies for hydrogen abstraction by cytochrome p450. J Med Chem 2006;49:6489-99
   PubMed Web of Science ®Google Scholar
• Rydberg P, Vasanthanathan P, Oostenbrink C, Olsen L. Fast prediction of cytochrome P450 mediated drug metabolism. ChemMedChem 2009;4:2070-9
   PubMed Web of Science ®Google Scholar
• Rydberg P, Gloriam DE, Zaretzki J, SMARTCyp: a 2D method for prediction of cytochrome P450-mediated drug metabolism. ACS Med Chem Lett 2010;1:96-100
   PubMed Web of Science ®Google Scholar
• Mayeno AN, Robinson JL, Yang RS, Reisfeld B. Predicting activation enthalpies of cytochrome-P450-mediated hydrogen abstractions. 2. Comparison of semiempirical PM3, SAM1, and AM1 with a density functional theory method. J Chem Inf Model 2009;49:1692-703
   PubMed Web of Science ®Google Scholar
• Kim DN, Cho KH, Oh WS, EaMEAD: activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors. J Chem Inf Model 2009;49:1643-54
   PubMed Web of Science ®Google Scholar
• de Visser SP, Kumar D, Cohen S, A predictive pattern of computed barriers for C-h hydroxylation by compound I of cytochrome p450. J Am Chem Soc 2004;126:8362-3
   PubMed Web of Science ®Google Scholar
• Shaik S, Kumar D, de Visser SP. A valence bond modeling of trends in hydrogen abstraction barriers and transition states of hydroxylation reactions catalyzed by cytochrome P450 enzymes. J Am Chem Soc 2008;130:10128-40
   PubMed Web of Science ®Google Scholar
• Kumar D, Karamzadeh B, Sastry GN, de Visser SP. What factors influence the rate constant of substrate epoxidation by compound I of cytochrome P450 and analogous iron(IV)-oxo oxidants? J Am Chem Soc 2010;32:7656-67
   Google Scholar
• Shaik S, Lai W, Chen H, Wang Y. The valence bond way: reactivity patterns of cytochrome P450 enzymes and synthetic analogs. Acc Chem Res 2010;43:1154-65
   PubMed Web of Science ®Google Scholar
• Phase, version 3.2, Schrodinger, LLC, New York, NY; 2010
   Google Scholar
• Darvas F, Marokhazi S, Kormos P, MetabolExpert: its use in metabolism research and in combinatorial chemistry. In: Erhardt PW, editor, Drug metabolism: databases and high-throughput testing during drug design and development. International Union of Pure and Applied Chemistry and Blackwell Science, London; 1999
   Google Scholar
• Klopman G, Dimayuga M, Talafous J. META. 1. A program for the evaluation of metabolic transformation of chemicals. J Chem Inf Comput Sci 1994;34:1320-5
   PubMedGoogle Scholar
• Talafous J, Sayre LM, Mieyal JJ, Klopman G. META. 2. A dictionary model of mammalian xenobiotic metabolism. J Chem Inf Comput Sci 1994;34:1326-33
   PubMedGoogle Scholar
• Klopman G, Tu M, Talafous J. META. 3. A genetic algorithm for metabolic transform priorities optimization. J Chem Inf Comput Sci 1997;37:329-34
   PubMedGoogle Scholar
• Darvas F, Keseru G, Papp A, In silico and ex silico ADME approaches for drug discovery. Curr Top Med Chem 2002;2:1287-304
   PubMedGoogle Scholar
• CompuDrug; 2010. Available from: www.compudrug.com
   Google Scholar
• Button WG, Judson PN, Long A, Vessey JD. Using absolute and relative reasoning in the prediction of the potential metabolism of xenobiotics. J Chem Inf Comput Sci 2003;43:1371-7
   PubMedGoogle Scholar
• Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol 2007;152:9-20
   PubMed Web of Science ®Google Scholar
• Symyx (and Accelrys); 2010. Available from: www.symyx.com
   Google Scholar
• Carlsson L, Spjuth O, Adams S, Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. BMC Bioinformatics 2010;11:362
   PubMedGoogle Scholar
• Smith J, Stein V. SPORCalc: a development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design. Comput Biol Chem 2009;33:149-59
   PubMed Web of Science ®Google Scholar
• Boyer S, Arnby CH, Carlsson L, Reaction site mapping of xenobiotic biotransformations. J Chem Inf Model 2007;47:583-90
   PubMed Web of Science ®Google Scholar
• Sheridan RP, Korzekwa KR, Torres RA, Walker MJ. Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9. J Med Chem 2007;50:3173-84
   PubMed Web of Science ®Google Scholar
• Borodina Y, Rudik A, Filimonov D, A new statistical approach to predicting aromatic hydroxylation sites. Comparison with model-based approaches. J Chem Inf Comput Sci 2004;44:1998-2009
   PubMedGoogle Scholar
• de Groot MJ, Ackland MJ, Horne VA, 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;42:4062-70
   PubMed Web of Science ®Google Scholar
• Vaz RJ, Zamora I, Li Y, The challenges of in silico contributions to drug metabolism in lead optimization. Expert Opin Drug Metab Toxicol 2010;6:851-61
   PubMed Web of Science ®Google Scholar
• Molecular Discovery; 2010. Available from: www.moldiscovery.com/docs/metasite/
   Google Scholar
• Oh WS, Kim DN, Jung J, New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism. J Chem Inf Model 2008;48:591-601
   PubMed Web of Science ®Google Scholar
• Korzekwa KR, Jones JP, Gillette JR. Theoretical studies on cytochrome P-450 mediated hydroxylation: a predictive model for hydrogen atom abstractions. J Am Chem Soc 1990;112:7042-6
   Web of Science ®Google Scholar
• Jung J, Kim ND, Kim SY, Regioselectivity prediction of CYP1A2-mediated phase I metabolism. J Chem Inf Model 2008;48:1074-80
   PubMed Web of Science ®Google Scholar
• Bathelt CM, Mulholland AJ, Harvey JN. QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9. J Phys Chem A 2008;112:13149-56
   PubMed Web of Science ®Google Scholar
• Fishelovitch D, Hazan C, Hirao H, QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. J Phys Chem B 2007;111:13822-32
   PubMed Web of Science ®Google Scholar