Identification of the structural requirements for mutagencitiy, by incorporating molecular flexibility and metabolic activation of chemicals. II. General ames mutagenicity model

Chemical Research in Toxicology

Volumn 20, Issue 4, 2007, Pages 662-676

  Serafimova, R ^a   Todorov, M ^a   Pavlov, T ^a   Kotov, S ^a   Jacob, E ^b   Aptula, A ^c   Mekenyan, O ^a  

^a ASSEN ZLATAROV UNIVERSITY   (Bulgaria)

^b BASF SE   (Germany)

^c UNILEVER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMES TEST; ARTICLE; CORRELATION ANALYSIS; INTERACTIONS WITH DNA; METABOLIC ACTIVATION; MODEL; MUTAGENICITY; SALMONELLA TYPHIMURIUM; SIMULATION; STRUCTURE ACTIVITY RELATION; TISSUE METABOLIC SIMULATOR MODELING; TISSUE METABOLISM;

COMPUTER SIMULATION; DATABASES, GENETIC; DNA; MODELS, BIOLOGICAL; MOLECULAR STRUCTURE; MUTAGENS; PHARMACEUTICAL PREPARATIONS;

BACTERIA (MICROORGANISMS); SALMONELLA TYPHIMURIUM;

EID: 34248597840     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx6003369     Document Type: Article

References (81)

1. Mekenyan, O., Dimitrov, S., Serafimova, R., Thompson, E., Kotov, S., Dimitrova, N., and Walker, J. (2004) Identification of the structural requirements for mutagenicity by incorporating molecular flexibility and metabolic activation of chemicals I: TA100 model. Chem. Res. Toxicol. 17 (6), 753-766.
2. OECD (2003) Final Report of the Sixth Meeting of the Task Force on Endocrine Disrupters Testing and Assessment (EDTA 6), ENV/JM/TG/EDTA/M, (2003) 4, OECD.
3. Schultz, T., Cronin, M., Walker, J., and Aptula, A. (2003) Quantitative structure - activity relationships (QSARs) in toxicology: A historical perspective. J. Mol. Struct. (THEOCHEM) 622, 1-22.
4. Ariens, E. J. (1984) Domestication of chemistry by design of safer chemicals: Structure-activity relationships. Drug Metab. Rev. 15 (3), 425-504.
5. Benigni, R., and Bossa, C. (2006) Structural alerts of mutagens and carcinogens. Curr. Comput.-Aided Drug Des. 2, 1-19.
6. Ashby, J. (1985) Fundamental structural alerts to potencial carcinogenicity and noncarcinogenicity. Environ. Mutagen. 7, 919-921.
7. Ashby, J., and Tennant, R. (1988) Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents by the U.S. NCI/NTP. Mutat. Res. 204 (1), 17-115.
8. Tennant, R., and Ashby, J. (1991) Classification according to chemical structure, mutagenicity to Salmonella and level of carcinogenicity of a further 39 chemicals tested for carcinogenicity by the U.S. national toxicology program. Mutat. Res. - Rev. Mutat. Res. 257 (3), 209-227.
9. Ashby, J., and Tennant, R. (1991) Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP. Mutat. Res. - Rev. Mutat. Res. 257 (3), 229-306.
10. Kazius, J., McGuire, R., and Bursi, R. (2005) Derivation and validation of toxicophores for mutagenicity prediction. J. Med. Chem. 48 (1), 312-320.
11. Sanderson, D., and Earnshaw, C. (1991) Computer prediction of possible toxic action from chemical structure; The DEREK system. Hum. Exp. Toxicol. 10 (4), 261-273.
12. Ridings, J. E., Barratt, M. D., Cary, R., Earnshaw, C. G., Eggington, C. E., Ellis, M. K., and Judson, P. N., et al. (1996) Computer prediction of possible toxic action from chemical structure: An update on the DEREK system. Toxicology 106 (1-3), 267-279.
13. Woo, Y.-T., Lai, D. Y., Argus, M. F., and Arcos, J. C. (1995) Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals. Toxicol. Lett. 79 (1-3), 219-228.
14. Singer, B., and Kusmierek, J. (1982) Chemical mutagenesis. Annu. Rev. Biochem. 51, 655-693.
15. Klopman, G., Frierson, M., and Rosenkranz, H. (1990) The structural basis of the mutagenicity of chemicals in Salmonella typhimurium: The Gene-Tox Data Base. Mutat. Res. 228, 1-50.
16. Rozenkranz, H., and Klopman, G. (1990) The structural basis of the mutagenicity of chemicals in Salmonella typhimirium: The National Toxicological Program Data Base. Mutat. Res. 228, 51-80.
17. Deadren, J., Barrat, M., Benigni, R., Bristol, D., and Combes, R., et al. (1997) The development and Validation of expert Systems for Predicting Toxicity. ATLA, 223-252; available at http://altweb.jh-sph.edu/ publications/ECVAM/ecvam24.htm.
18. Greene, N. (2002) Computer systems for the prediction of toxicity: An update. Adv. Drug Delivery Rev. 54, 417-431.
19. Pearl, G., Livingston-Carr, S., and Durham, S. (2001) Integration of computational analysis as a sentinel tool in toxicological assessments. Curr. Top. Med. Chem. 1, 247-255.
20. Johnson, D., and Wolfgang, G. (2000) Predicting human safety: Screening and computational approaches. Drug Discovery Today 5, 445-454.
21. Benfenati, E., and Gini, G. (1997) Computational predictive programs (expert systems) in toxicology. Toxicology 119, 213-225.
22. Cronin, M., Jaworska, J., Walker, J., Comber, M., and Watts, C., et al. (2003) Use of QSARs in international decision-making frameworks to predict health effects of chemicals substances. Environ. Health Perspect. 111, 1391-1401.
23. Benigni, R., and Richard, A. (1998) Quantitative structural-based modeling applied to characterization and prediction of chemical toxicity. Methods 14, 264-276.
24. Benigni, R., and Guliani, A. (1992) QSAR studies in genetic toxicology: Congeneric and non-congeneric chemicals. Arch. Toxicol. Suppl. 15, 228-237.
25. Richard, A. (1994) Application of SAR methods to non-congeneric data bases associated with carcinogenicity and muatgenicity: Issues and approaches. Mutat. Res. 305, 73-97.
26. Enslein, K., Borgstedt, H., Tomb, M., Blake, B., and Hart, H. (1987) A structure-activity prediction model of carcinogenicity based on NCI/ NTP assays and food additives. Toxicol. Ind. Health 3, 267-287.
27. Enslein, K. (1988) An overview of structure-activity relationships as an alternative to testing in animals for carcinogenicity, mutagenicity, dermal and eye irritation, and acute oral toxicity. Toxicity and Industrial Health (4), 479-498.
28. Klopman, G. (1992) MULTICASE. 1. A hierarchical computer automated structure evaluation program. Quant. Struct.-Act. Relat. 11 (2), 176-184.
29. Schultz, T. W., Cronin, M. T. D., and Netzeva, T. I. (2003) The present status of QSAR in toxicology. J. Mol. Struct. (THEOCHEM) 622, 23-38.
30. Purdy, R. (1996) A mechanism-mediated model for carcinogenicity: Model content and prediction of the outcome of rodent carcinogenicity bioassays currently being conducted on 25 organic chemicals. Environ. Health Perspect. 104, 1085-1094.
31. Lewis, D. F. V., Ioannides, C., and Parke, D. V. (1993) Validation of a nuvel molecular orbital approach (COMPACT) for the prospective safety evaluation of chemicals, by comparison with rodent carcinogenicity and Salmonella mutagenicity data evaluated by the US NCI/ NTP. Mutat. Res. 291, 61-77.
32. Mekenyan, O. G., Ivanov, J. M., Karabunarliev, S. H., Bradbary, S. P., Ankley, G. T., and Karcher, W. (1997) COREPA: A new approach for the evaluation of coman reactivity pattern of chemicals. I. Stereoelectronic requiermants for androgen receptor binding. Environ. Sci. Technol. 31, 3702-3711.
33. Mekenyan, O., Nikolova, N., Schmieder, P., and Veith, G. (2004) COREPA-M: A multi-dimensional formulation of COREPA. QSAR Comb. Sci. 23 (1), 5-18.
34. Mekenyan, O., Dimitrov, S., Pavlov, T., and Veith, G. (2004) A systematic approach to stimulating metabolism in computational toxicology. I. The TIMES heuristic modelling framework. Curr. Pharm. Des. 10 (11), 1273-1293.
35. Jaworska, J., Dimitrov, S., Nikolova, N., and Mekenyan, O. (2001) Probabilistic assessment of biodegradability based on metabolic pathways: CATABOL system. SAR QSAR Environ. Res. 13, 307-323.
36. Dimitrov, S., Breton, R., MacDonald, D., Walker, J., and Mekenyan, O. (2001) Quantitative prediction of biodegradability, metabolite distribution and toxicity of stable metabolites. SAR QSAR Environ. Res. 13, 445-455.
37. Dimitrov, S., Dimitrova, N., Walker, J., Veith, G., and Mekenyan, O. (2003) Bioconcentration potential predictions based on molecular attributes- an early warning approach for chemicals found in humans, birds, fish and wildlife. QSAR Comb. Sci. 22, 58-68.
38. Kroger-Koepke, M. B., Koepke, S. R., McClusky, G. A., Magee, P. N., and Michejda, C. J. (1981) α-Hydroxylation pathway in the in vitro metabolism of carcinogenic nitrosamines: N-nitrosodimethylamine and N-nitroso-N- methylaniline. Proc. Natl. Acad. Sci. U.S.A. 78 (10), 6489-6493.
39. Lenk, W., and Rosenhauer-Thilmann, R. (1993) Metabolism of 2-acetylaminofluorene. I. Metabolism in vitro of 2-acetylaminofluorene and 2-acetylaminofluoren-9-one by hepatic enzymes. Xenobiotica 23, 241-257.
40. Lynn, R. K., Gould, C. C., Milam, D. F., Eastman, C. L., and Rodgers, R. M. (1983) Metabolism of the human carcinogen, benzidine, in the isolated perfused rat liver. Drug Metab. Dispos. 11, 109-114.
41. McKay, S., Farmer, P. B., Cary, P. D., and Grover, P. L. (1987) The metabolism of 7-ethylbenz[a]anthracene by rat liver microsomal preparations. Drug Metab. Dispos. 15, 682-694.
42. Williams, J. A., and Phillips, D. H. (2000) Mammary expression of xenobiotic metabolizing enzymes and their potential role in breast cancer. Cancer Res. 60, 4667-4677.
43. Lu, O. G., and Guethner, T. M. (1994) Detoxication of the 2′,3′-epoxide metabolites of allylbenzene and estragole. Conjugation with glutathione Drug Metab. Dispos. 22, 731-737.
44. Nakajama, M., Iwata, K., Yamamoto, T., Funae, Y., Yoshida, T., and Kurowa, Y. (1998) Nicotine metabolism in liver microsomes from rats with acute hepatitis or cirrhosis. Drug Metab. Dispos. 26(1), 36-41.
45. Low, L. K. (1998) Metabolic changes of drugs and related compounds. In Textbook of Organic Medicinal and Pharmaceutical Chemistry (Delgado, J. N., and Remers, W. A., Eds.) pp 43-109, Lippincott-Raven Publishers, Philadelphia, New York.
46. Mays, D. C., Hecht, S. G., Unger, S. E., Pacula, C. M., Climie, J. M., Sharp, D. E., and Gerber, N. (1987) Disposition of 8-methoxypsoralen in the rat. Induction of metabolism in vivo and in vitro and identification of urinary metabolites by thermospray mass spectrometry. Drug Metab. Dispos. 15, 318-328.
47. Noguchi, M., Nitoh, S., Mabuchi, M., and Kawai, Y. (1996) Effects of phenobarbital on aniline metabolism in primary liver cell culture of rats with ethionine-induced liver disorder. Exp. Anim. 45 (2), 161-170.
48. Mekenyan, O., Ivanov, J., Karabunarliev, S., Bradbury, S., Ankley, G., and Karcher, W. (1997) A computationally-based hazard identification algorithm that incorporates ligand flexibility. 1. Identification of potential androgen receptor ligands. Environ. Sci. Technol. 31, 3702-3711.
49. Bradbury, S., Kamenska, V., Schmieder, P., Ankley, G., and Mekenyan, O. (2000) A computationally-based identification algorithm for estrogen receptor ligands, part I. Predicting hER binding affinity. Toxicol. Sci. 58, 253-269.
50. Mekenyan, O., Kamenska, V., Schmieder, P., Ankley, G., and Bradbury, S. (2000) A computationally based identification algorithm for estrogen receptor ligands: Part 2. Evaluation of a hERα binding affinity model. Toxicol. Sci. 58, 270-281.
51. Mekenyan, O., Dimitrov, D., Nikolova, N., and Karabunarliev, S. (1999) Conformational coverage by a genetic algorithm. Chem. Inf. Comput. Sci. 39, 997-1016.
52. Todorov, M., Pavlov, T., Serafimova, R., Aladjov, H., and Mekenyan, O. Conformational coverage by genetic algorithm: Saturation of conformational space J. Chem. Inf. Model. In press.
53. Steward, J. (1990) MOPAC: A semiempirical molecular orbital program. J. Comput.-Aided Mol. Des. 4, 1-105.
54. Steward, J. (1993) MOPAC 93, Fujitsu Limited, Chiba-City, Japan, and Stewart Computational Chemistry, Colorado Springs, CO.
55. Mekenyan, O., Nikolova, N., and Schmieder, P. (2003) Dynamic 3D QSAR techniques: Applications in toxicology. J. Mol. Struct. (THEOCHEM) 622, 147-165.
56. Connoly, M. (1983) J. Appl. Crystallogr. 16, 548.
57. Stanton, D. T., and Jurs, P. C. (1990) Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Anal. Chem. 62 (21), 2323-2329.
58. Mekenyan, O., Nikolova, N., Schmieder, P., and Veith, G. (2004) COREPA-M: A multi-dimensional formulation of COREPA. QSAR Comb. Sci. 23 (1), 5-18.
59. Serafimova, R., Todorov, M., Nedelcheva, D., Pavlov, T., Akahori, Y., Nakai, M., and Mekenyan, O. (2006) QSAR and mechanistic interpretation of estrogen receptor binding. SAR QSAR Environ. Res. In press.
60. Dimitrov, S., Dimitrova, G., Pavlov, T., Dimitrova, N., Patlewicz, G., Niemela, J., and Mekenyan, O. (2005) A stepwise approach for defining the applicability domain of SAR and QSAR models. J. Chem. Inf. Model. 45 (4), 839-849.
61. Dimitrov, S., Pavlov, T., Vasilev, R., and Mekenyan, O. (2005) Simulation of abiotic molecular transformations by CATABOL, poster presented at SETAC Europe 15th Annual Meeting, Lille, France, May 21-26.
62. IARC (1987) Evaluation of the Carcinogenic Risk of Chemicals to Humans - Views and Expert Opinions of an IARC Working Group, IARC, Lyon, France (Russian ed.).
63. Hemminki, K. (1981) Reactions of β-propiolactone, β-butyrolactone and γ-butyrolactone with nucleic acids. Chem.-Biol. Interact. 34 (3), 323-331.
64. http://potency.berkeley.edu/chempages/beta-BUTYROLACTONE.html.
65. Sawatari, K., Nakanishi, Y., and Matsushima, T. (2001) Relationships between chemical structures and mutagenicity: A preliminary survey for a database of mutagenicity test results of new work place chemicals. Ind. Health 39 (4), 341-345.
66. http://www.oehha.ca.gov/prop65/pdf/BCMEEf.pdf.
67. http://www.biolab.co.uk/dna.html.
68. Couch, D., Forbes, N., and Hsie, A. (1978) Comparative mutagenicity of alkylsulfate and alkanesulfonate derivatives in Chinese hamster ovary cells. Mutat. Res. 57 (2), 217-224.
69. www.uic.edu/classes/pcol/pcol425/restricted/Tiruppathi/Carcinogenst-.PDF.
70. Kovacic, P., and Jacintho, J. (2001) Reproductive toxins: Pervasive theme of oxidative stress and electron transfer. Curr. Med. Chem. 8 (7), 863-892.
71. Wiaderkiewicz, R., Walter, Z., and Reimschussel, W. (1986) Sites of methylation of DNA bases by the action of organophosphorus insecticides in vitro. Acta Biochim. Pol. 33 (2), 73-85.
72. Hecht, S., McIntee, E., and Wang, M. (2001) New DNA adducts of crotonaldehyde and acetaldehyde. Toxicology 166 (1-2), 31-36.
73. http://monographs.iarc.fr/htdocs/monographs/vol60-11.htm.
74. http://www.inchem.org/documents/cicads/cicads/cicad_19.htm#Part Number:.
75. Sabboni, G. (1994) Hemoglobin binding of arylamines and nitroarenes: Molecular dosimetry and quantitative structure-activity relationships. Environ. Health Perspect. 102 (6), 61-67.
76. Bartsch, H. (1981) Metabolic activation of aromatic amines and azo dyes. IARC Sci. Publ. 40, 13-30.
77. http://linkage.garvan.unsw.edu.au//public/gerham/macsos/public/thesis/ NitreniumIons.html.
78. Glatt, H., and Meini, W. (2004) Use of genetically manipulated Salmonella typhimurium strains to evaluate the role of sulfotransferases and acetyltransferases in nitrofen mutagenicity. Cancer Causes Control 15 (3), 225-236.
79. Westwood, I., Holton, S., Rodriges-Lima, F., Dupret, J., Bhakta, S., Noble, M., and Sim, E. (2005) Expression, purification, characterization and structure of Pseudomonas aeruginosa arylamine N-acetyltransferase. Biochem. J. 385 (2), 605-612.
80. Guengerich, F., Parikh, A., Johnson, E., Richardson, T., von Wachenfeldt, C., Cosme, J., Jung, Fr., Strassburg, C., Mannis, M., Tukey, R., Prichard, M., Fournel-Gigleux, S., and Burchell, Br. (1997) Heterologous expression of human drug-metabolizing enzymes. Drug Metab. Dispos. 25 (11), 1234-1241.
81. Kiese, M., and Renner, G. (1966) The hydrolysis of acetanilide and some of its derivatives by enzymes in the microsomal and soluble fraction prepared from livers of various species. Naunyn-Schmiedeberg's Arch. Pathol. Pharmacol. 252 (5), 480-500.