In silico techniques for the study and prediction of xenobiotic metabolism: A review

Xenobiotica

Volumn 35, Issue 10-11, 2005, Pages 955-973

  Kulkarni, S A ^a   Zhu, J ^a   Blechinger, S ^a  

^a HEALTH CANADA   (Canada)

Author keywords

In silico; META ; MetabolExpert ; Metabolism; METEOR ; TIMES (Tissue Metabolism Simulator)

Indexed keywords

ALGORITHM; CHEMISTRY; COMPUTER MODEL; COMPUTER PROGRAM; HEALTH HAZARD; PHYSICAL CHEMISTRY; PREDICTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; XENOBIOTIC METABOLISM;

ALGORITHMS; ANIMALS; CELL PHYSIOLOGY; COMPUTER SIMULATION; HUMANS; METABOLISM; MODELS, BIOLOGICAL; SOFTWARE; XENOBIOTICS;

ANIMALIA;

EID: 30344455919     PISSN: 00498254     EISSN: 13665928     Source Type: Journal    
DOI: 10.1080/00498250500354402     Document Type: Review

References (37)

1. Anders MW, Dekant W. 1998. Glutathione-dependent bioactivation of haloalkanes. Annual Reviews in Pharmacology and Toxicology 38:501-537.
2. Baker A, Granger J, Castro-Perez J, Kirby J, McCullagh M, McSweeney N. 2004. Advances in automated metabolite identification software tools couple with in-silico metabolite prediction using LC-TOF-MS-MS. Drug Metabolism Reviews 36:1-247.
3. 2u-globulin nephropathy. Annual Reviews in Pharmacology and Toxicology 30:349-367.
4. Cronin MTD, Schultz WT. 1996. Structure-toxicity relationships for phenols to Tetrahymena pyriformis. Chemosphere 32:1453-1468.
5. Darvas F. 1987. MetabolExpert, an expert system for predicting metabolism of substances. In: Kaiser K, editor. QSAR in environmental toxicology. Dordrecht: Riedel. pp 71-81.
6. Darvas F. 1988. Predicting metabolic pathways by logic programming. Journal of Molecular Graphics 6:80-86.
7. Darvas F, Marakhazi S, Kormos P, Kulkarni G, Kalasz H, Papp A. 1999. In: Erhard PE, editor. Drug metabolism, databases and high throughput testing during drug design and development. 1st ed. IUPAC Chemical Data Series. Oxford: Blackwell. pp 237-270.
8. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. 1984. AM1: A new general purpose quantum mechanical molecular model. Journal of the American Chemistry Society 107, 13:3902-3909.
9. Greene N. 1999. Knowledge based expert systems for toxicity and metabolism prediction. In: Erhardt PW, editor. Drug metabolism, databases in high-throughput testing during drug design and development. Oxford: Blackwell. pp 289-296.
10. Greene N, Judson PN, Langowski JJ, Marchant CA. 1999. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR, and METEOR. SAR and QSAR in Environmental Research 10:299-313.
11. Guengerich FP. 2000. Metabolism of chemical carcinogens. Carcinogenesis 21:345-351.
12. Guengerich FP, Shimada T. 1998. Activation of procarcinogens by human cytochrome P450 enzymes. Mutation Research 400:201-203.
13. Ioannides C. 2000. Xenobiotic metabolism and bioactivation by cytochromes P-450. In: Wiseman H, Goldfarb P, Ridgway T, Wiseman A, editors. Biomolecular free radical toxicity: causes and prevention. Chichester: Wiley. pp 103-144.
14. Judson PN, Fox J, Krause PJ. 1996. Using new reasoning technology in chemical information systems. Journal of Chemical Information and Computer Science 37:621-624.
15. Klopman G. 1984. Artificial intelligence approach to structure-activity studies. Computer automated structure evaluation of biological activity of organic molecules. Journal of the American Chemistry Society 106:7315-7320.
16. Klopman G. 1992. MULTICASE 1. A hierarchical computer automated structure evaluation program. Quantitative Structure-Activity Relationships 11:176-184.
17. Klopman G, Dimayuga M, Talafous J. 1994. META 1. A program for evaluation of metabolic transformation of chemicals. Journal of Chemical Information and Computer Science 34:1320-1325.
18. Könemann WH. 1981. Quantitative structure-activity relationships in fish toxicity studies. Part 1: Relationships for 50 industrial pollutants. Toxicology 19:209-221.
19. Kriek E, Rojas M, Alexandrov K, Bartsch H. 1998. Polycyclic aromatic hydrocarbon-DNA adducts in humans: relevance as biomarkers for exposure and cancer risk. Mutation Research 400:215-231.
20. Kulkarni SA, Raje DV, Chakrabarti T. 2001. Quantitative structure-activity relationships based on functional and structural characteristics of organic compounds. SAR and QSAR in Environmental Research 12:565-591.
21. Mekenyan OG, Dimitrov SD, Pavlov TS, Veith GD. 2004. A systematic approach to simulating metabolism in computational toxicology. I. The TIMES heuristic modelling framework. Current Pharmacology Design 10:1273-1293.
22. Mekenyan OG, Nikolova N. Karabunarliev S, Bradbury S, Ankley G, Hansen B. 1999. New developments in a hazard identification algorithm for hormone receptor ligands. Quantitative Structure-Activity Relationships 18:139-153.
23. Meylan WM, Howard PH. 1995. Atom/fragment contribution method for estimating octanol-water partition coefficients. Journal of Pharmacology Science 84:84-92.
24. Mollerup S, Ryberg D, Hewer A, Phillips D, Haugen A. 1999. Sex differences in lung CYP1A1 expression and DNA adduct levels among lung cancer patients. Cancer Research 59:3317-3320.
25. Monks TJ, Anders MW, Dekant W, Stevens JL, Lau SS, Van Bladeren PJ. 1990. Glutathione conjugate mediated toxicities. Toxicology and Applied Pharmacology 106:1-19.
26. Ozawa N, Guengerich FP. 1983. Evidence for formation of an S-[2-(N7-guanyl)ethyl]glutathione adduct in glutathione-mediated binding of 1,2-dibromoethane to DNA. Proceedings of the National Academy of Sciences, USA 80:5266-5270.
27. Pfeiffer S, Borchert H. 1963. Biotransformation von Arzneimitteln. Berlin: VEB.
28. Rannug U, Sundvall A, Ramel C. 1978. The mutagenic effect of 1,2-dichloroethane on Salmonella typhimurium. I. Activation through conjugation with glutathione in vitro. Chemico-Biological Interactions 20:1-16.
29. Russell WMS, Birch RL. 1959. Principles of humane experimental technique. London: Methuen.
30. Spann ML, Chu KC, Wipke WT, Ouchi G. 1978. Use of computerised methods to predict metabolic pathways and metabolites. Journal of Environmental Pathology and Toxicology 2:123.
31. Stewart JJP. 1990. MOPAC: a semiempirical molecular orbital program. Journal of Computer-Aided Molecular Design 4:1-105.
32. Tang D, Phillips DH, Stampfer M, Mooney LA, Hsu Y, Cho S, Tsai W-Y, Jing Ma, Cole KJ, She MN, Perera FP. 2001. Association between carcinogen-DNA adducts in white blood cells and lung cancer risk in the physicians' health study. Cancer Research 61:6708-6712.
33. Testa B. 1995. The metabolism of drugs and other xenobiotics - biochemistry of redox reactions. London: Academic Press.
34. Testa B, Jenner P. 1976. Drug metabolism: chemical and biochemical aspects. New York, NY: Marcel Dekker.
35. Testa B, Jenner P, editors. 1980. Concepts in drug metabolism. New York, NY: Marcel Dekker.
36. Tonnelier CAG, Fox J, Judson PN, Krause PJ, Pappas N, Patel M. 1997. Representation of chemical structures in knowledge-based systems: the StAR system. Journal of Chemical Information and Computer Science 37:117-123.
37. Weinenger D. 1981. SMILES, a chemical language and information systems. Journal of Chemical Information and Computer Science 21:48.