Prediction of metabolites of epoxidation reaction in MetaToxFootnote^$

^$Presented at the 9th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, CMTPI-2017, 27–30 October 2017, Goa, India.

References

• M.S. Benedetti, R. Whomsley, I. Poggesi, W. Cawello, F.X. Mathy, M.L. Delporte, P. Papeleu, and J.B. Watelet, Drug metabolism and pharmacokinetics, Drug Metab. Rev. 41 (2009), pp. 344–390.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich, Cytochrome P450s and other enzymes in drug metabolism and toxicity, AAPS J. 8 (2006), pp. 101–111.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich, Intersection of roles of cytochrome P450 enzymes with xenobiotic and endogenous substrates. Relevance to toxicity and drug interactions, Chem. Res. Toxicol. 30 (2017), pp. 2–12.
   PubMed Web of Science ®Google Scholar
• W. Liu, J. Shi, L. Zhu, L. Dong, F. Luo, M. Zhao, Y. Wang, M. Hu, L. Lu, and Z. Liu, Reductive metabolism of oxymatrine is catalyzed by microsomal CYP3A4, Drug Des. Devel. Ther. 9 (2015), pp. 5771–5783.
   PubMedGoogle Scholar
• J. D’Agostino, H. Zhang, C. Kenaan, and P. Hollenberg, Mechanism-based inactivation of human cytochrome P450 2B6 by chlorpyrifos, Chem. Res. Toxicol. 28 (2015), pp. 1484–1495.
   PubMed Web of Science ®Google Scholar
• Li. Xiaohai, T.M. Kamenecka, and M.D. Cameron, Cytochrome P450-mediated bioactivation of the epidermal growth factor receptor inhibitor erlotinib to a reactive electrophile, Drug Metab. Dispos. 38 (2010), pp. 1238–1245.
   PubMed Web of Science ®Google Scholar
• S.M. Attia, Deleterious effects of reactive metabolites, Oxid. Med. Cell Longev. 3 (2010), pp. 238–253.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich, Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity, Chem. Res. Toxicol. 14 (2001), pp. 611–650.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich, Cytochrome P450 and chemical toxicology, Chem. Res. Toxicol. 21 (2008), pp. 70–83.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich, Metabolic-activation of carcinogens, Pharmacol. Ther. 54 (1992), pp. 17–61.
   PubMed Web of Science ®Google Scholar
• F.P. Guengerich and T. Shimada, Oxidation of toxic and carcinogenic chemicals by human cytochrome P-450 enzymes, Chem. Res. Toxicol. 4 (1991), pp. 391–407.
   PubMed Web of Science ®Google Scholar
• J. Uetrecht, Idiosyncratic drug reactions: Current understanding, Annu. Rev. Pharmacol. Toxicol. 47 (2007), pp. 513–539.
   PubMed Web of Science ®Google Scholar
• K. Ikehata, T.G. Duzhak, N.A. Galeva, T. Ji, Y.M. Koen, and R.P. Hanzlik, Protein targets of reactive metabolites of thiobenzamide in rat liver in vivo, Chem. Res. Toxicol. 21 (2008), pp. 1432–1442.
   PubMed Web of Science ®Google Scholar
• D.E. Amacher, Reactive intermediates and the pathogenesis of adverse drug reactions: The toxicology perspective, Curr Drug Metab. 7 (2006), pp. 219–229.
   PubMed Web of Science ®Google Scholar
• R. Vidyasagar and P.A. Guruprasad, Hepatotoxicity related to anti-tuberculosis drugs: Mechanisms and management, J. Clin. Exp. Hepatol. 3 (2013), pp. 37–49.
   PubMedGoogle Scholar
• R.M. Irving and A.A. Elfarra, Role of reactive metabolites in the circulation in extrahepatic toxicity, Expert Opin. Drug Metab. Toxicol. 8 (2012), pp. 1157–1172.
   PubMed Web of Science ®Google Scholar
• P.E. Levi and E. Hodgson, Reactive metabolites and toxicity, in Introduction to Biochemical Toxicology, 3rd ed., E. Hodgson and R.C. Smart, eds., Wiley, New York, 2001, pp. 199–220.
   Google Scholar
• T.B. Hughes, G.P. Miller, and S.J. Swamidass, Modeling epoxidation of drug-like molecules with a deep machine learning network, ACS Cent. Sci. 1 (2015), pp. 168–180.
   PubMed Web of Science ®Google Scholar
• P. Rydberg, R. Lonsdale, J. Harvey, A. Mulholland, and L. Olsen, Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions, J. Mol. Graph Model. 52 (2014), pp. 30–35.
   PubMed Web of Science ®Google Scholar
• J. Zhang, L. Ji, and W. Liu, In silico prediction of cytochrome P450-mediated biotransformations of xenobiotics: A case study of epoxidation, Chem. Res. Toxicol. 28 (2015), pp. 1522–1531.
   PubMed Web of Science ®Google Scholar
• K. Kim and K.D. Jordan, Comparison of density functional and MP2 calculations on the water monomer and dimer, J. Phys. Chem. 98 (1994), pp. 10089–10094.
   Web of Science ®Google Scholar
• P.J. Stephens, F.J. Devlin, C.F. Chabalowski, and M.J. Frisch, Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields, J. Phys. Chem. 98 (1994), pp. 11623–11627.
   Web of Science ®Google Scholar
• J. Zaretzki, M. Matlock, and S.J. Swamidass, XenoSite: Accurately predicting CYP-mediated sites of metabolism with neural networks, J. Chem. Inf. Model. 53 (2013), pp. 3373–3383.
   PubMed Web of Science ®Google Scholar
• A. Rudik, A. Dmitriev, A. Lagunin, D. Filimonov, and V. Poroikov, Metabolism site prediction based on xenobiotic structural formulas and PASS prediction algorithm, J. Chem. Inf. Model. 54 (2014), pp. 498–507.
   PubMed Web of Science ®Google Scholar
• P. Pogodin, A. Lagunin, D. Filimonov, and V. Poroikov, PASS targets: Ligand-based multi-target computational system based on a public data and naïve Bayes approach, SAR QSAR Environ. Res. 26 (2015), pp. 783–793.
   PubMed Web of Science ®Google Scholar
• V. Konova, A. Lagunin, P. Pogodin, E. Kolotova, A. Shtil, and V. Poroikov, Virtual screening of chemical compounds active against breast cancer cell lines based on cell cycle modelling, prediction of cytotoxicity and interaction with targets, SAR QSAR Environ. Res. 26 (2015), pp. 595–604.
   PubMed Web of Science ®Google Scholar
• M. Stasevych, V. Zvarych, V. Lunin, N. Deniz, Z. Gokmen, O. Akgun, E. Ulukaya, V. Poroikov, T. Gloriozova, and V. Novikov, Computer-aided prediction and cytotoxicity evaluation of dithiocarbamates of 9,10-anthracenedione as new anticancer agents, SAR QSAR Environ. Res. 28 (2017), pp. 355–366.
   PubMed Web of Science ®Google Scholar
• A.V. Rudik, V.M. Bezhentsev, A.V. Dmitriev, D.S. Druzhilovskiy, A.A. Lagunin, D.A. Filimonov, and V.V. Poroikov, MetaTox: Web application for predicting structure and toxicity of xenobiotics' metabolites, J. Chem. Inf. Model. 57 (2017), pp. 638–642.
   PubMed Web of Science ®Google Scholar
• D. Filimonov, V. Poroikov, Y. Borodina, and T. Gloriozova, Chemical similarity assessment through multilevel neighborhoods of atoms: Definition and comparison with the other descriptors, J. Chem. Inf. Comput. Sci. 39 (1999), pp. 666–670.
   Google Scholar
• A. Rudik, A. Dmitriev, A. Lagunin, D. Filimonov, and V. Poroikov, SOMP: Web server for in silico prediction of sites of metabolism for drug-like compounds, Bioinformatics 31 (2015), pp. 2046–2048.
   PubMed Web of Science ®Google Scholar
• A. Rudik, A. Dmitriev, A. Lagunin, D. Filimonov, and V. Poroikov, Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics, J. Cheminform. 26 (2016), pp. 595–604.
   Google Scholar
• Biovia Metabolite database, BIOVIA, San Diego, 2017; available at: http://accelrys.com/products/collaborative-science/databases/bioactivity-databases/biovia-metabolite.html
   Google Scholar
• L. Hovander, T. Malmberg, M. Athanasiadou, I. Athanassiadis, S. Rahm, A. Bergman, and E. Wehler, Identification of hydroxylated PCB metabolites and other phenolic halogenated pollutants in human blood plasma, Arch. Environ. Contam. Toxicol. 42 (2002), pp. 105–117.
   PubMed Web of Science ®Google Scholar
• J. Park, L. Linderholm, M. Charles, M. Athanasiadou, J. Petrik, A. Kocan, B. Drobna, T. Trnovec, A. Bergman, and I. Hertz-Picciotto, Polychlorinated biphenyls and their hydroxylated metabolites (OH-PCBs) in pregnant women from eastern Slovakia, Environ. Health Perspect. 115 (2007), pp. 20–27.
   PubMed Web of Science ®Google Scholar
• J. Zaretzki, C. Bergeron, P. Rydberg, T. Huang, K. Bennett, and C. Breneman, RS-Predictor: A new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4, J. Chem. Inf. Model. 51 (2011), pp. 1667–1689.
   PubMed Web of Science ®Google Scholar
• J. Swets, Measuring the accuracy of diagnostic systems, Rev. Sci. 240 (1988), pp. 1285–1293.
   Google Scholar
• J. Manier, W. Chang, J. Kirchner, and E. Beltaos, Hepatotoxicity associated with ticrynafen – a uricosuric diuretic, Am. J. Gastroenterol. 77 (1982), pp. 401–404.
   PubMed Web of Science ®Google Scholar
• P. Valadon, P. Dansette, J. Girault, C. Amar, and D. Mansuy, Thiophene sulfoxides as reactive metabolites: Formation upon microsomal oxidation of a 3-aroylthiophene and fate in the presence of nucleophiles in vitro and in vivo, Chem. Res. Toxicol. 9 (1996), pp. 1403–1413.
   PubMed Web of Science ®Google Scholar
• P. Dansette, G. Bertho, and D. Mansuy, First evidence that cytochrome P450 may catalyze both S-oxidation and epoxidation of thiophene derivatives, Biochem. Biophys. Res. Commun. 338 (2005), pp. 450–455.
   PubMed Web of Science ®Google Scholar
• C. Jaladanki, N. Taxak, R. Varikoti, and P. Bharatam, Toxicity originating from thiophene containing drugs: Exploring the mechanism using quantum chemical methods, Chem. Res. Toxicol. 28 (2015), pp. 2364–2376.
   PubMed Web of Science ®Google Scholar
• D. Gramec, M. Peterlin, and M. Sollner, Dolenc, Bioactivation potential of thiophene-containing drugs, Chem. Res. Toxicol. 27 (2014), pp. 1344–1358.
   PubMed Web of Science ®Google Scholar
• Marvin JS, ChemAxon, Budapest, Hungary, 2017; available at: https://www.chemaxon.com/products/marvin/marvin-js/
   Google Scholar
• P. Rademacher, C. Woods, Q. Huang, G. Szklarz, and S. Nelson, Differential oxidation of two thiophene-containing regioisomers to reactive metabolites by cytochrome P450 2C9, Chem. Res. Toxicol. 25 (2012), pp. 895–903.
   PubMed Web of Science ®Google Scholar
• M. López-García, P. Dansette, and J. Coloma, Kinetics of tienilic acid bioactivation and functional generation of drug-protein adducts in intact rat hepatocytes, Biochem. Pharmacol. 70 (2005), pp. 1870–1882.
   PubMed Web of Science ®Google Scholar
• M. Darnell, K. Breitholtz, E. Isin, U. Jurva, and L. Weidolf, Significantly different covalent binding of oxidative metabolites, acyl glucuronides, and S-acyl CoA conjugates formed from xenobiotic carboxylic acids in human liver microsomes, Chem. Res. Toxicol. 28 (2015), pp. 886–896.
   PubMed Web of Science ®Google Scholar
• M. Shipkova, V. Armstrong, M. Oellerich, and E. Wieland, Acyl glucuronide drug metabolites: Toxicological and analytical implications, Ther. Drug Monit. 25 (2003), pp. 1–16.
   PubMed Web of Science ®Google Scholar
• Y. Koen, D. Sarma, T. Williams, N. Galeva, R. Obach, and R. Hanzlik, Identification of protein targets of reactive metabolites of tienilic acid in human hepatocytes, Chem. Res. Toxicol. 5 (2012), pp. 1145–1154.
   Google Scholar