Latest advances in computational genotoxicity prediction

Bibliography

• Ashby J, Tennant RW. Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP. Mutat Res 1991;257(3):229-306
   PubMed Web of Science ®Google Scholar
• Haworth S, Lawlor T, Mortelmans K, Salmonella mutagenicity test results for 250 chemicals. Environ Mutagen 1983;5(Suppl 1):1-142
   PubMedGoogle Scholar
• Mortelmans K, Haworth S, Lawlor T, Salmonella mutagenicity tests: II. Results from the testing of 270 chemicals. Environ Mutagen 1986;8(Suppl 7):1-119
   PubMedGoogle Scholar
• Zeiger E, Anderson B, Haworth S, Salmonella mutagenicity tests: IV. Results from the testing of 300 chemicals. Environ Mol Mutagen 1988;11(Suppl 12):1-157
   PubMed Web of Science ®Google Scholar
• Zeiger E, Anderson B, Haworth S, Salmonella mutagenicity tests: III. Results from the testing of 255 chemicals. Environ Mutagen 1987;9(Suppl 9):1-109
   PubMedGoogle Scholar
• Naven RT, Louise-May S, Greene N. The computational prediction of genotoxicity. Expert Opin Drug Metab Toxicol 2010;6(7):797-807
   PubMed Web of Science ®Google Scholar
• Lynch AM, Sasaki JC, Elespuru R, New and emerging technologies for genetic toxicity testing. Environ Mol Mutagen 2011;52(3):205-23
   PubMed Web of Science ®Google Scholar
• Kirkland D, Aardema M, Henderson L, Müller L. Evaluation of the ability of a battery of three in vitro genotoxicity tests to discriminate rodent carcinogens and non-carcinogens I. Sensitivity, specificity and relative predictivity. Mutat Res 2005;584(1-2):1-256
   PubMed Web of Science ®Google Scholar
• Gramatica P. Principles of QSAR models validation: internal and external. QSAR Comb Sci 2007;26(5):694-701
   Google Scholar
• Tropsha A, Gramatica P, Gombar VK. The Importance of Being Earnest: validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models. QSAR Comb Sci 2003;22(1):69-77
   Google Scholar
• Marchant CA, Briggs KA, Long A. In silico tools for sharing data and knowledge on toxicity and metabolism: derek for windows, meteor, and vitic. Toxicol Mech Methods 2008;18(2-3):177-87
   PubMed Web of Science ®Google Scholar
• Saiakhov RD, Klopman G. Benchmark performance of MultiCASE Inc. software in Ames mutagenicity set. J Chem Inf Model 2010;50(9):1521
   PubMed Web of Science ®Google Scholar
• Valerio LG Jr, Cross KP. Characterization and validation of an in silico toxicology model to predict the mutagenic potential of drug impurities*. Toxicol Appl Pharmacol 2012;260(3):209-21
   PubMedGoogle Scholar
• Benigni R, Bossa C, Tcheremenskaia O, Giuliani A. Alternatives to the carcinogenicity bioassay: in silico methods, and the in vitro and in vivo mutagenicity assays. Expert Opin Drug Metab Toxicol 2010;6(7):809-19
   PubMed Web of Science ®Google Scholar
• Hillebrecht A, Muster W, Brigo A, Comparative evaluation of in silico systems for ames test mutagenicity prediction: scope and limitations. Chem Res Toxicol 2011;24(6):843-54
   PubMed Web of Science ®Google Scholar
• McCarren P, Bebernitz GR, Gedeck P, Avoidance of the Ames test liability for aryl-amines via computation. Bioorg Med Chem 2011;19(10):3173-82
   PubMedGoogle Scholar
• Greene N, Judson PN, Langowski JJ, Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. SAR QSAR Environ Res 1999;10(2-3):299-314
   PubMed Web of Science ®Google Scholar
• Snyder RD, Pearl GS, Mandakas G, Assessment of the sensitivity of the computational programs DEREK, TOPKAT, and MCASE in the prediction of the genotoxicity of pharmaceutical molecules. Environ Mol Mutagen 2004;43(3):143-58
   PubMed Web of Science ®Google Scholar
• Kamber M, Flückiger-Isler S, Engelhardt G, Comparison of the Ames II and traditional Ames test responses with respect to mutagenicity, strain specificities, need for metabolism and correlation with rodent carcinogenicity. Mutagenesis 2009;24(4):359-66
   PubMedGoogle Scholar
• Snyder RD. Assessment of atypical DNA intercalating agents in biological and in silico systems. Mutat Res 2007;623(1-2):72-82
   PubMed Web of Science ®Google Scholar
• United States Food and Drug Administration. Guidance for Industry, Genotoxic and Carciniogenic Impurities in Drug Substance and Drug Products: recommended Approaches. 2008. Available from: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm079235.pdf
   Google Scholar
• European Medicines Agency. Guideline on the Limits of Genotoxic Impurities. 2006. Available from: http://www.emea.europa.eu/docs/en_GB/document_library/Scientific_guideline/2009/09/WC500002903.pdf
   Google Scholar
• Muller L, Mauthe RJ, Riley CM, A rationale for determining, testing, and controlling specific impurities in pharmaceuticals that possess potential for genotoxicity. Regul Toxicol Pharmacol 2006;44(3):198-211
   PubMed Web of Science ®Google Scholar
• Dobo KL, Greene N, Fred C, In silico methods combined with expert knowledge rule out mutagenic potential of pharmaceutical impurities: an industry survey. Regul Toxicol Pharmacol 2012;62(3):449-55
   PubMed Web of Science ®Google Scholar
• Dobo KL, Greene N, Cyr MO, The application of structure-based assessment to support safety and chemistry diligence to manage genotoxic impurities in active pharmaceutical ingredients during drug development. Regul Toxicol Pharmacol 2006;44(3):282-93
   PubMed Web of Science ®Google Scholar
• Glowienke S, Hasselgren C. Use of Structure Activity Relationship (SAR) evaluation as a critical tool in the evaluation of the genotoxic potential of impurities, in genotoxic impurities: strategies for identification and control. John Wiley & Sons, Inc; Hoboken, NJ, USA: 2011. p. 97-120
   Google Scholar
• McCarren P, Springer C, Whitehead L. An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential. J Cheminform 2011;3:51
   PubMedGoogle Scholar
• Ono A, Takahashi M, Hirose A, Validation of the (Q)SAR combination approach for mutagenicity prediction of flavor chemicals. Food Chem Toxicol 2012;50(5):1538-46
   PubMedGoogle Scholar
• Pearl GM, Livingston-Carr S, Durham SK. Integration of computational analysis as a sentinel tool in toxicological assessments. Curr Top Med Chem 2001;1(4):247-55
   PubMedGoogle Scholar
• White AC, Mueller RA, Gallavan RH, A multiple in silico program approach for the prediction of mutagenicity from chemical structure. Mutat Res 2003;539(1-2):77-89
   PubMed Web of Science ®Google Scholar
• Sushko I, Novotarskyi S, Körner R, Applicability domains for classification problems: benchmarking of distance to models for Ames mutagenicity set. J Chem Inf Model 2010;50(12):2094-111
   PubMed Web of Science ®Google Scholar
• Dragos H, Gilles M, Alexandre V. Predicting the predictability: a unified approach to the applicability domain problem of QSAR models. J Chem Inf Model 2009;49(7):1762-76
   PubMedGoogle Scholar
• Ellison CM, Sherhod R, Cronin MT, Assessment of methods to define the applicability domain of structural alert models. J Chem Inf Model 2011;51(5):975-85
   PubMed Web of Science ®Google Scholar
• Hewitt M, Ellison CM. Developing the applicability domain of in silico models: relevance, importance and methodology. In: Cronin MTD, Madden JC, editors. In silico toxicology: principles and applications. Royal Society of Chemistry; Cambridge, UK: 2010. p. 301-33
   Google Scholar
• Weaver S, Gleeson MP. The importance of the domain of applicability in QSAR modeling. J Mol Graph Model 2008;26(8):1315-26
   PubMed Web of Science ®Google Scholar
• Kuhne R, Ebert RU, Schuurmann G. Chemical domain of QSAR models from atom-centered fragments. J Chem Inf Model 2009;49(12):2660-9
   PubMedGoogle Scholar
• Sheridan RP, Feuston BP, Maiorov VN, Kearsley SK. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR. J Chem Inf Comput Sci 2004;44(6):1912-28
   PubMedGoogle Scholar
• Netzeva TI, Worth A, Aldenberg T, Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52. Altern Lab Anim 2005;33(2):155-73
   PubMed Web of Science ®Google Scholar
• Jaworska J, Nikolova-Jeliazkova N, Aldenberg T. QSAR applicabilty domain estimation by projection of the training set descriptor space: a review. Altern Lab Anim 2005;33(5):445-59
   PubMed Web of Science ®Google Scholar
• Fioravanzo E, Bassan A, Pavan M, Role of in silico genotoxicity tools in the regulatory assessment of pharmaceutical impurities. SAR QSAR Environ Res 2012;23(3-4):257-77
   PubMed Web of Science ®Google Scholar
• Ellison CM, Enoch SJ, Cronin MT, Definition of the applicability domains of knowledge-based predictive toxicology expert systems by using a structural fragment-based approach. Altern Lab Anim 2009;37(5):533-45
   PubMed Web of Science ®Google Scholar
• Harbach PR, Zimmer DM, Mazurek JH, Bhuyan BK. Mutagenicity of the antitumor antibiotic CC-1065 and its analogues in mammalian (V79) cells and bacteria. Cancer Res 1988;48(1):32-6
   PubMed Web of Science ®Google Scholar
• O'Donovan MR, Mee CD, Fenner S, Boronic acids-a novel class of bacterial mutagen. Mutat Res 2011;724(1-2):1-6
   PubMed Web of Science ®Google Scholar