Identification of toxifying and detoxifying moieties for mutagenicity prediction by priority assessment

Journal of Chemical Information and Modeling

Volumn 51, Issue 7, 2011, Pages 1564-1574

  Casalegno, Mose ^a   Benfenati, Emilio ^b   Sello, Guido ^c  

^a Department of Chemistry Materials and Chemical Engineering Giulio Natta   (Italy)

^b MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TOXICITY;

DATA SPACE; LARGE DATABASE; MUTAGENICITY; PRIORITY ASSESSMENT; STRUCTURAL DIVERSITY;

DATABASE SYSTEMS;

MUTAGENIC AGENT;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE;

DATABASES, FACTUAL; MODELS, CHEMICAL; MOLECULAR STRUCTURE; MUTAGENS;

EID: 79960701365     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200075g     Document Type: Article

References (45)

1. National Research Council (NRC). Toxicity Testing in the 21st century: A Vision and a Strategy; National Academies Press, Washington, DC, 2007.
2. Ames, B. N.; McCann, H.; Yamasaki, E. Methods for detecting carcinogens and mutagens with the Salmonella/mammalian microsome mutagenicity test Mutat. Res. 1975, 31, 347-364
3. Josephy, P. D.; Cruz, P.; Nohmi, T. Recent advances in the construction of bacterial genotoxicity assays Mutat. Res. 1997, 386, 1-23 (Pubitemid 27195022)
4. Piegorsch, W. W.; Zeiger, E. Measuring intra-assay agreement for the Ames Salmonella assay. In Lecture Notes in Medical Informatics; Springer-Verlag: Heidelberg, 1991; pp 35-41.
5. Ariens, E. J. Domestication of chemistry by design of safer chemicals: Structure-activity relationships Drug Metab. Rev. 1984, 15 (3) 425-504 (Pubitemid 14011857)
6. Benigni, R.; Bossa, C. Structural alerts of mutagens and carcinogens Curr. Comput.-Aided Drug Des. 2006, 2, 1-19
7. Ashby, J. Fundamental structural alerts to potential carcinogenicity and non-carcinogenicity Environ. Mutagen. 1985, 7, 919-921 (Pubitemid 16180586)
8. Ashby, J.; Tennant, R. 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. 1988, 204 (1) 17-115 (Pubitemid 18057809)
9. Tennant, R.; Ashby, J. 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. 1991, 257 (3) 209-227 (Pubitemid 121007618)
10. Ashby, J.; Tennant, R. Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP Mutat. Res. 1991, 257 (3) 229-306 (Pubitemid 121007619)
11. Kazius, J.; McGuire, R.; Bursi, R. Derivation and validation of toxicophores for mutagenicity prediction J. Med. Chem. 2005, 48 (1) 312-320 (Pubitemid 40105270)
12. Sanderson, D.; Earnshaw, C. Computer prediction of possible toxic action from chemical structure: The DEREK system Hum. Exp. Toxicol. 1991, 10 (4) 261-273
13. Ridings, J. E.; Barratt, M. D.; Cary, R.; Earnshaw, C. G.; Eggington, C. E.; Ellis, M. K.; Judson, P. N.; Langowski, J. J.; Marchant, C. A.; Payne, M. P.; Watson, W. P.; Yih, T. D. Computer prediction of possible toxic action from chemical structure: An update on the DEREK system Toxicology 1996, 106 (1-3) 267-279 (Pubitemid 26038295)
14. Woo, Y.-T.; Lai, D. Y.; Argus, M. F.; Arcos, J. C. Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals Toxicol. Lett. 1995, 79 (1-3) 219-228
15. Singer, B.; Kusmierek, J. Chemical mutagenesis Annu. Rev. Biochem. 1982, 51, 655-693 (Pubitemid 12024692)
16. Klopman, G.; Frierson, M.; Rosenkranz, H. The structural basis of the mutagenicity of chemicals in Salmonella typhimurium: The Gene-Tox Data Base Mutat. Res. 1990, 228, 1-50 (Pubitemid 20046324)
17. Rozenkranz, H.; Klopman, G. The structural basis of the mutagenicity of chemicals in Salmonella typhimirium: The National Toxicological Program Data Base Mutat. Res. 1990, 228, 51-80 (Pubitemid 20046325)
18. Dearden, J.; Barrat, M.; Benigni, R.; Bristol, D.; Combes, R.; The development and validation of expert systems for predicting toxicity. ATLA 1997, 25, 223-252; http://www.frame.org.uk/page.php?pg-id=18 (accessed October, 13, 2009).
19. Greene, N. Computer systems for the prediction of toxicity: An update Adv. Drug Delivery Rev. 2002, 54, 417-431 (Pubitemid 34260961)
20. Pearl, G.; Livingston-Carr, S.; Durham, S. Integration of computational analysis as a sentinel tool in toxicological assessments Curr. Top. Med. Chem. 2001, 1, 247-255
21. Johnson, D.; Wolfgang, G. Predicting human safety: Screening and computational approaches Drug Discovery Today 2000, 5, 445-454
22. Benfenati, E.; Gini, G. Computational predictive programs (expert systems) in toxicology Toxicology 1997, 119, 213-225 (Pubitemid 27187493)
23. Cronin, M.; Jaworska, J.; Walker, J.; Comber, M.; Watts, C. Use of QSARs in international decision-making frameworks to predict health effects of chemicals substances Environ. Health Perspect. 2003, 111, 1391-1401 (Pubitemid 37021144)
24. Benigni, R.; Richard, A. Quantitative structural-based modeling applied to characterization and prediction of chemical toxicity Methods 1998, 14, 264-276
25. Benigni, R.; Guliani, A. QSAR studies in genetic toxicology: Congeneric and non-congeneric chemicals Arch. Toxicol. Suppl. 1992, 15, 228-237
26. Richard, A. Application of SAR methods to non-congeneric data bases associated with carcinogenicity and mutagenicity: Issues and approaches Mutat. Res. 1994, 305, 73-97 (Pubitemid 24062618)
27. Enslein, K.; Borgstedt, H.; Tomb, M.; Blake, B.; Hart, H. A structure-activity prediction model of carcinogenicity based on NCI/NTP assays and food additives Toxicol. Ind. Health 1987, 3, 267-287 (Pubitemid 17108667)
28. Enslein, K. An overview of structure-activity relationships as an alternative to testing in animals for carcinogenicity, mutagenicity, dermal and eye irritation, and acute oral toxicity Toxicol. Ind. Health 1988, 4, 479-498 (Pubitemid 18268463)
29. Klopman, G. MULTICASE. 1. A hierarchical computer automated structure evaluation program Quant. Struct.-Act. Relat. 1992, 11 (2) 176-184
30. Schultz, T. W.; Cronin, M. T. D.; Netzeva, T. I. The present status of QSAR in toxicology J. Mol. Struct. (THEOCHEM) 2003, 622, 23-38
31. Purdy, R. 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. 1996, 104, 1085-1094 (Pubitemid 26402354)
32. Lewis, D. F. V.; Ioannides, C.; Parke, D. V. Validation of a novel 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. 1993, 291, 61-77 (Pubitemid 23036271)
33. Mekenyan, O. G.; Ivanov, J. M.; Karabunarliev, S. H.; Bradbary, S. P.; Ankley, G. T.; Karcher, W. A computationally-based hazard identification algorithm that incorporates ligand flexibility. 1. Identification of potential androgen receptor ligands Environ. Sci. Technol. 1997, 31, 3702-3711 (Pubitemid 28008231)
34. Mekenyan, O.; Nikolova, N.; Schmieder, P.; Veith, G. COREPA-M: A multi-dimensional formulation of COREPA QSAR Comb. Sci. 2004, 23 (1) 5-18 (Pubitemid 39490229)
35. Mekenyan, O.; Dimitrov, S.; Pavlov, T.; Veith, G. A systematic approach to stimulating metabolism in computational toxicology. I. The TIMES heuristic modelling framework Curr.Pharm. Des. 2004, 10 (11) 1273-1293 (Pubitemid 38425906)
36. Kazius, J.; Nijssen, S.; Kok, J.; Baeck, T.; Ijzerman, A. P. Substructure mining using elaborate chemical representation J. Chem. Inf. Model. 2006, 46, 597-605
37. Serafimova, R.; Todorov, M.; Pavlov, T.; Kotov, S.; Jacob, E.; Aptula, A.; Mekenyan, O. Identification of the structural requirements for mutagencitiy, by incorporating molecular flexibility and metabolic activation of chemicals. II. General Ames mutagenicity model Chem. Res. Toxicol. 2007, 20, 662-676 (Pubitemid 46762101)
38. Langham, J. J.; Jain, A. N. Accurate and interpretable computational modeling of chemical mutagenicity J. Chem. Inf. Model. 2008, 48, 1833-1839
39. Casalegno, M.; Sello, G.; Benfenati, E. Top-priority fragment QSAR approach in predicting pesticide aquatic toxicity Chem. Res. Toxicol. 2006, 19, 1533-1539 (Pubitemid 44863496)
40. Khüne, R.; Ebert, R.-U.; Schüürmann, G. Model selection based on structural similarity-method description and application to water solubility prediction J. Chem. Inf. Model 2006, 46, 636-641
41. Khüne, R.; Ebert, R.-U.; Schüürmann, G. Chemical domain of QSAR models from atom-centered fragments J. Chem. Inf. Model 2009, 49, 2660-2669
42. Casalegno, M.; Benfenati, E.; Sello, G. An automated group contribution method in predicting aquatic toxicity: The diatomic fragment approach Chem. Res. Toxicol. 2005, 18, 740-746 (Pubitemid 40563288)
43. Fawcett, T. An introduction to ROC analysis Pattern Rec. Lett. 2006, 27, 861-874
44. Young, S. S.; Gombar, V. K.; Emptage, M. R.; Cariello, N. F.; Lambert, C. Mixture-deconvolution and analysis of Ames mutagenicity data Chem. Int. Lab. Sys. 2002, 60, 5-11 (Pubitemid 34098916)
45. TOXNET. United States National Library of Medicine. http://toxnet.nlm. nih.gov/cgi-bin/sis/htmlgen?CCRIS (accessed May, 5, 2011).