Versatile applicability of a grid-based CYP3A4 Template to understand the interacting mechanisms with the small-size ligands; part 3 of CYP3A4 Template study

Yamazoe, 2011, Construction of a CYP2E1-template system for prediction of the metabolism on both site and preference order, Drug Metab Rev, 43, 409, 10.3109/03602532.2011.624103 Koyama, 2011, Development of two-dimensional template system for the prediction of CYP2B6-mediated reaction sites, Drug Metabol Pharmacokinet, 26, 309, 10.2133/dmpk.DMPK-10-RG-097 Yamaura, 2011, Predicting oxidation sites with order of occurrence among multiple sites for CYP4A-mediated reactions, Drug Metabol Pharmacokinet, 26, 351, 10.2133/dmpk.DMPK-11-RG-004 Sato, 2012, Unimolecular and bimolecular binding system for the prediction of CYP2D6-mediated metabolism, Drug Metab Dispos, 40, 486, 10.1124/dmd.111.043125 Yamazoe, 2016, Prediction of regioselectivity and preferred order of metabolisms on CYP1A2-mediated reactions. Part 1. Focusing on polycyclic arenes and the related chemicals, Drug Metabol Pharmacokinet, 31, 363, 10.1016/j.dmpk.2016.07.005 Yamazoe, 2017, Prediction of regioselectivity and preferred order of metabolisms on CYP1A2-mediated reactions. Part 2: solving substrate interactions of CYP1A2 with non-PAH substrates on the template system, Drug Metabol Pharmacokinet, 32, 229, 10.1016/j.dmpk.2017.05.004 Yamazoe, 2019, Prediction of regioselectivity and preferred order of metabolisms on CYP1A2-mediated reactions Part 3: difference in substrate specificity of human and rodent CYP1A2 and the refinement of predicting system, Drug Metabol Pharmacokinet, 34, 217, 10.1016/j.dmpk.2019.02.001 Yamazoe, 2020, Prediction of regioselectivity and preferred order of CYP1A1-mediated metabolism: solving the interaction of human and rat CYP1A1 forms with ligands on the template system, Drug Metabol Pharmacokinet, 10.1016/j.dmpk.2019.10.008 Yamazoe, 2019, Reconstitution of CYP3A4 active site through assembly of ligand interactions as a grid-template: solving the modes of the metabolism and inhibition, Drug Metabol Pharmacokinet, 34, 113, 10.1016/j.dmpk.2018.10.001 Goto, 2019, Solving the interactions of steroidal ligands with CYP3A4 using a grid-base template system, Drug Metabol Pharmacokinet, 34, 351, 10.1016/j.dmpk.2019.05.003 Williams, 2004, Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone, Science, 305, 683, 10.1126/science.1099736 Yano, 2004, The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution, J Biol Chem, 279, 38091, 10.1074/jbc.C400293200 Shou, 1994, The role of 12 cDNA-expressed human, rodent, and rabbit cytochromes P450 in the metabolism of benzo[a]pyrene and benzo[a]pyrene trans-7,8-dihydrodiol, Mol Carcinog, 10, 159, 10.1002/mc.2940100307 Bauer, 1995, Oxidation of benzo[a]pyrene by recombinant human cytochrome P450 enzymes, Chem Res Toxicol, 8, 136, 10.1021/tx00043a018 Seidel, 1998, Regio- and stereoselectivity in the metabolism of benzo[c]phenanthrene mediated by genetically engineered V79 Chinese hamster cells expressing rat and human cytochromes P450, Environ Toxicol Pharmacol, 5, 179, 10.1016/S1382-6689(97)10073-4 Shou, 1996, Metabolic activation of the potent carcinogen dibenzo[a,h]anthracene by cDNA-expressed human cytochromes P450, Arch Biochem Biophys, 328, 201, 10.1006/abbi.1996.0161 Kim, 2004, Identification of cytochrome P450 isoforms involved in 1-hydroxylation of pyrene, Environ Res, 94, 262, 10.1016/S0013-9351(03)00134-8 Jushchyshyn, 2005, Catalytic turnover of pyrene by CYP3A4: evidence that cytochrome b5 directly induces positive cooperativity, Arch Biochem Biophys, 438, 21, 10.1016/j.abb.2005.02.027 Shou, 1994, Activation of CYP3A4: evidence for the simultaneous binding of two substrates in a cytochrome P450 active site, Biochemistry, 33, 6450, 10.1021/bi00187a009 Cho, 2006, In vitro metabolism of naphthalene by human liver microsomal cytochrome P450 enzymes, Drug Metab Dispos, 34, 176, 10.1124/dmd.105.005785 Roberts-Thomson, 1995, Metabolism of polycyclic aza-aromatic carcinogens catalyzed by four expressed human cytochromes P450, Canc Res, 55, 1052 Koehl, 1996, Metabolism of 5-methylchrysene and 6-methylchrysene by human hepatic and pulmonary cytochrome P450 enzymes, Canc Res, 56, 316 Wojcikowski, 2010, Main contribution of the cytochrome P450 isoenzyme 1A2 (CYP1A2) to N-demethylation and 5-sulfoxidation of the phenothiazine neuroleptic chlorpromazine in human liver-A comparison with other phenothiazines, Biochem Pharmacol, 80, 1252, 10.1016/j.bcp.2010.06.045 Wojcikowski, 2003, Contribution of human cytochrome P-450 isoforms to the metabolism of the simplest phenothiazine neuroleptic promazine, Br J Pharmacol, 138, 1465, 10.1038/sj.bjp.0705195 Yoshii, 2000, Identification of human cytochrome P450 isoforms involved in the 7-hydroxylation of chlorpromazine by human liver microsomes, Life Sci, 67, 175, 10.1016/S0024-3205(00)00613-5 Kerr, 1994, Human liver carbamazepine metabolism Role of CYP3A4 and CYP2C8 in 10,11-epoxide formation, Biochem Pharmacol, 47, 1969, 10.1016/0006-2952(94)90071-X Pearce, 2002, Pathways of carbamazepine bioactivation in vitro I. Characterization of human cytochromes P450 responsible for the formation of 2- and 3-hydroxylated metabolites, Drug Metab Dispos, 30, 1170, 10.1124/dmd.30.11.1170 Egnell, 2003, In vivo CYP3A4 heteroactivation is a possible mechanism for the drug interaction between felbamate and carbamazepine, J Pharmacol Exp Therapeut, 305, 1251, 10.1124/jpet.102.047530 Ueng, 1997, Cooperativity in oxidations catalyzed by cytochrome P450 3A4, Biochemistry, 36, 370, 10.1021/bi962359z Pearce, 2008, Pathways of carbamazepine bioactivation in vitro. III. The role of human cytochrome P450 enzymes in the formation of 2,3-dihydroxycarbamazepine, Drug Metab Dispos, 36, 1637, 10.1124/dmd.107.019562 Yue, 1997, Different effects of inhibitors on the O- and N-demethylation of codeine in human liver microsomes, Eur J Clin Pharmacol, 52, 41, 10.1007/s002280050247 Bocker, 1986, Oxidation of 4-aryl- and 4-alkyl-substituted 2,6-dimethyl-3,5-bis(alkoxycarbonyl)-1,4-dihydropyridines by human liver microsomes and immunochemical evidence for the involvement of a form of cytochrome P-450, J Med Chem, 29, 1596, 10.1021/jm00159a007 Niwa, 1988, Stereoselective oxidation and plasma-protein binding of nilvadipine, a new dihydropyridine calcium-antagonist, Res Commun Chem Pathol Pharmacol, 60, 161 Ishiguro, 2000, Identification of CYP3A4 as the predominant isoform responsible for the metabolism of ambroxol in human liver microsomes, Xenobiotica, 30, 71, 10.1080/004982500237839 Komatsu, 2000, Formation of a dihydroxy metabolite of phenytoin in human liver microsomes/cytosol: roles of cytochromes P450 2C9, 2C19, and 3A4, Drug Metab Dispos, 28, 1361 Jacobsen, 1999, Comparison of cytochrome P-450-dependent metabolism and drug interactions of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors lovastatin and pravastatin in the liver, Drug Metab Dispos, 27, 173 Isin, 2007, Multiple sequential steps involved in the binding of inhibitors to cytochrome P450 3A4, J Biol Chem, 282, 6863, 10.1074/jbc.M610346200 Kim, 2003, alpha-Hydroxylation of tamoxifen and toremifene by human and rat cytochrome P450 3A subfamily enzymes, Chem Res Toxicol, 16, 1138, 10.1021/tx0300131 Dehal, 1999, Cytochrome P-450 3A and 2D6 catalyze ortho hydroxylation of 4-hydroxytamoxifen and 3-hydroxytamoxifen (droloxifene) yielding tamoxifen catechol: involvement of catechols in covalent binding to hepatic proteins, Drug Metab Dispos, 27, 681 Stresser, 1997, Catalytic characteristics of CYP3A4: requirement for a phenolic function in ortho hydroxylation of estradiol and mono-O-demethylated methoxychlor, Biochemistry, 36, 2203, 10.1021/bi962129k Foster, 1999, Methadone N-demethylation in human liver microsomes: lack of stereoselectivity and involvement of CYP3A4, Br J Clin Pharmacol, 47, 403, 10.1046/j.1365-2125.1999.00921.x Sullivan, 1973, Urinary metabolites of dl-methadone in maintenance subjects, J Med Chem, 16, 909, 10.1021/jm00266a009 Dilmaghanian, 2004, Enantioselectivity of inhibition of cytochrome P450 3A4 (CYP3A4) by ketoconazole: testosterone and methadone as substrates, Chirality, 16, 79, 10.1002/chir.10294 Giraud, 2004, In vitro characterization of clobazam metabolism by recombinant cytochrome P450 enzymes: importance of CYP2C19, Drug Metab Dispos, 32, 1279, 10.1124/dmd.32.11.1279 Kobayashi, 2004, Pharmacogenetic roles of CYP2C19 and CYP2B6 in the metabolism of R- and S-mephobarbital in humans, Pharmacogenetics, 14, 549, 10.1097/01.fpc.0000114764.78957.22 Yasumori, 1993, Species differences in stereoselective metabolism of mephenytoin by cytochrome P450s (CYP2C and CYP3A), J Pharmacol Exp Therapeut, 264, 89 Akutsu, 2007, Identification of human cytochrome P450 isozymes involved in diphenhydramine N-demethylation, Drug Metab Dispos, 35, 72, 10.1124/dmd.106.012088 He, 2001, Metabolism of sulfinpyrazone sulfide and sulfinpyrazone by human liver microsomes and cDNA-expressed cytochrome P450s, Drug Metab Dispos, 29, 701 Ramirez, 2004, CYP2B6, CYP3A4, and CYP2C19 are responsible for the in vitro N-demethylation of meperidine in human liver microsomes, Drug Metab Dispos, 32, 930 Laurenzana, 1997, Metabolism of phencyclidine by human liver microsomes, Drug Metab Dispos, 25, 557 Benetton, 2007, P450 phenotyping of the metabolism of selegiline to desmethylselegiline and methamphetamine, Drug Metabol Pharmacokinet, 22, 78, 10.2133/dmpk.22.78 Yun, 1993, Oxidation of the antihistaminic drug terfenadine in human liver microsomes. Role of cytochrome P-450 3A(4) in N-dealkylation and C-hydroxylation, Drug Metab Dispos, 21, 403 Czerwinski, 1991, Metabolic activation of 4-ipomeanol by complementary DNA-expressed human cytochromes P-450: evidence for species-specific metabolism, Canc Res, 51, 4636 Perini, 2005, Influence of CYP2C9 genotypes on the pharmacokinetics and pharmacodynamics of piroxicam, Clin Pharmacol Ther, 78, 362, 10.1016/j.clpt.2005.06.014 Riley, 2001, Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery, Pharm Res, 18, 652, 10.1023/A:1011085411050 Kalgutkar, 2005, Bioactivation of the nontricyclic antidepressant nefazodone to a reactive quinone-imine species in human liver microsomes and recombinant cytochrome P450 3A4, Drug Metab Dispos, 33, 243, 10.1124/dmd.104.001735 Chesne, 1998, Metabolism of meloxicam in human liver involves cytochromes P4502C9 and 3A4, Xenobiotica, 28, 1, 10.1080/004982598239704 Ludwig, 1999, Activation of human cytochrome P-450 3A4-catalyzed meloxicam 5'-methylhydroxylation by quinidine and hydroquinidine in vitro, J Pharmacol Exp Therapeut, 290, 1 Taavitsainen, 2001, In vitro inhibition of cytochrome P450 enzymes in human liver microsomes by a potent CYP2A6 inhibitor, trans-2-phenylcyclopropylamine (tranylcypromine), and its nonamine analog, cyclopropylbenzene, Drug Metab Dispos, 29, 217 Rotstein, 1992, Stereoisomers of ketoconazole: preparation and biological activity, J Med Chem, 35, 2818, 10.1021/jm00093a015 Nakamura, 2005, Inhibitory effects of nicardipine to cytochrome P450 (CYP) in human liver microsomes, Biol Pharm Bull, 28, 882, 10.1248/bpb.28.882 Katoh, 2000, Inhibition of human cytochrome P450 enzymes by 1,4-dihydropyridine calcium antagonists: prediction of in vivo drug-drug interactionse, Eur J Clin Pharmacol, 55, 843, 10.1007/s002280050706 Katoh, 2000, Inhibitory potencies of 1,4-dihydropyridine calcium antagonists to P- glycoprotein-mediated transport: comparison with the effects on CYP3A4, Pharm Res, 17, 1189, 10.1023/A:1007568811691 Foti, 2011, Mechanism-based inactivation of cytochrome P450 3A4 by mibefradil through heme destruction, Drug Metab Dispos, 39, 1188, 10.1124/dmd.111.038505 Fukuda, 1997, Specific CYP3A4 inhibitors in grapefruit juice: furocoumarin dimers as components of drug interaction, Pharmacogenetics, 7, 391, 10.1097/00008571-199710000-00008 Guo, 2000, Role of furanocoumarin derivatives on grapefruit juice-mediated inhibition of human CYP3A activity, Drug Metab Dispos, 28, 766 Tassaneeyakul, 2000, Inhibition selectivity of grapefruit juice components on human cytochromes P450, Arch Biochem Biophys, 378, 356, 10.1006/abbi.2000.1835