Comparative evaluation of 11 in silico models for the prediction of small molecule mutagenicity: role of steric hindrance and electron-withdrawing groups

References

• Ames BN, Gurney EG, Miller JA, Bartsch H. (1972). Carcinogens as frameshift mutagens: metabolites and derivatives of 2-acetylaminofluorene and other aromatic amine carcinogens. Proc Natl Acad Sci 69:3128–32.
   PubMed Web of Science ®Google Scholar
• Ayrton AD, Neville S, Ioannides C. (1992). Cytosolic activation of 2-aminoanthracene: implications in its use as diagnostic mutagen in the Ames test. Mutat Res 265:1–8.
   PubMed Web of Science ®Google Scholar
• Bajorath J. (2012). Modeling of activity landscapes for drug discovery. Expert Opin Drug Discov 7:463–73.
   PubMed Web of Science ®Google Scholar
• Bakhtyari NG, Raitano G, Benfenati E, et al. (2013). Comparison of in silico models for prediction of mutagenicity. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 31:45–66.
   PubMed Web of Science ®Google Scholar
• Boer DR, Canals A, Coll M. (2009). DNA-binding drugs caught in action: the latest 3D pictures of drug–DNA complexes. Dalton Trans 3:399–414.
   PubMed Web of Science ®Google Scholar
• Braun R, Jakel HP, Schoneich J. (1984). Genetic effects of isoniazid and the relationship to in vivo and in vitro biotransformation. Mutat Res 137:61–9.
   PubMed Web of Science ®Google Scholar
• Canals A, Purciolas M, Aymami J, Coll M. (2005). The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs. Acta Crystallogr D Biol Crystallogr 61:1009–12.
   PubMed Web of Science ®Google Scholar
• Chataigner I, Panel C, Gerard H, Piettre SR. (2007). Sulfonyl vs. carbonyl group: which is the more electron-withdrawing? Chem Commun 31:3288–90.
   Web of Science ®Google Scholar
• Cho B, Geacintov N, Broyde S. (2010). Structure–function characteristics of aromatic amine–DNA adducts. In: Geacintov NE, Broyde S, eds. The chemical biology of DNA damage. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
   Google Scholar
• Claxton LD, Matthews PP, Warren SH. (2004). The genotoxicity of ambient outdoor air, a review: Salmonella mutagenicity. Mutat Res 567:347–99.
   PubMed Web of Science ®Google Scholar
• Clive D, Flamm WG, Machesko MR, Bernheim NJ. (1972). A mutational assay system using the thymidine kinase locus in mouse lymphoma cells. Mutat Res 16:77–87.
   PubMed Web of Science ®Google Scholar
• Combes RD. (2012). In silico methods for toxicity prediction. Adv Exp Med Biol 745:96–116.
   PubMed Web of Science ®Google Scholar
• Dang LN, McQueen CA. (1999). Mutagenicity of 4-aminobiphenyl and 4-acetylaminobiphenyl in Salmonella typhimurium strains expressing different levels of N-acetyltransferase. Toxicol Appl Pharmacol 159:77–82.
   PubMed Web of Science ®Google Scholar
• Delaney EJ. (2007). An impact analysis of the application of the threshold of toxicological concern concept to pharmaceuticals. Regul Toxicol Pharmacol 49:107–24.
   PubMed Web of Science ®Google Scholar
• Demchuk E, Ruiz P, Chou S, Fowler BA. (2011). SAR/QSAR methods in public health practice. Toxicol Appl Pharmacol 254:192–7.
   PubMed Web of Science ®Google Scholar
• Dobo KL, Greene N, Fred C, et al. (2012). In silico methods combined with expert knowledge rule out mutagenic potential of pharmaceutical impurities: an industry survey. Regul Toxicol Pharmacol 62:449–55.
   PubMed Web of Science ®Google Scholar
• Ekins S, Ring BJ, Grace J, et al. (2000). Present and future in vitro approaches for drug metabolism. J Pharmacol Toxicol Methods 44:313–24.
   PubMed Web of Science ®Google Scholar
• El-Bayoumy K, Hecht SS. (1983). Identification and mutagenicity of metabolites of 1-nitropyrene formed by rat liver. Cancer Res 43:3132–7.
   PubMed Web of Science ®Google Scholar
• Fjodorova N, Vracko M, Novic M, et al. (2010). New public QSAR model for carcinogenicity. Chem Cent J 4:S3.
   PubMed Web of Science ®Google Scholar
• Fluckiger-Isler S, Baumeister M, Braun K, et al. (2004). Assessment of the performance of the Ames II assay: a collaborative study with 19 coded compounds. Mutat Res 558:181–97.
   PubMed Web of Science ®Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, et al. (2009). Gaussian 09, revision A.1. Wallingford, CT. Available at: http://www.gaussian.com/g_tech/g_ur/g09help.htm.
   Google Scholar
• Galloway SM, Vijayaraj Reddy M, McGettigan K, et al. (2013). Potentially mutagenic impurities: analysis of structural classes and carcinogenic potencies of chemical intermediates in pharmaceutical syntheses supports alternative methods to the default TTC for calculating safe levels of impurities. Regulat Toxicol Pharmacol 66:326–35.
   PubMed Web of Science ®Google Scholar
• Gholivand MB, Kashanian S, Peyman H. (2012). DNA-binding, DNA cleavage and cytotoxicity studies of two anthraquinone derivatives. Spectrochim Acta A Mol Biomol Spectrosc 87:232–40.
   PubMed Web of Science ®Google Scholar
• Glende C, Schmitt H, Erdinger L, et al. (2001). Transformation of mutagenic aromatic amines into non-mutagenic species by alkyl substituents. Part I. Alkylation ortho to the amino function. Mutat Res 498:19–37.
   PubMed Web of Science ®Google Scholar
• Guengerich FP. (2007). Cytochrome p450 and chemical toxicology. Chem Res Toxicol 21:70–83.
   PubMed Web of Science ®Google Scholar
• Hillebrecht A, Muster W, Brigo A, et al. (2011). Comparative evaluation of in silico systems for Ames test mutagenicity prediction: scope and limitations. Chem Res Toxicol 24:843–54.
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. (1996). VMD: visual molecular dynamics. J Mol Graph Model 14:33–8.
   Web of Science ®Google Scholar
• ICH. (2007). ICH guidance for industry S2B genotoxicity: a standard battery for genotoxicity testing of pharmaceuticals. Available at: http://www.ich.org.
   Google Scholar
• ICH. (2012). ICH guidance for industry S2A specific aspects of regulatory genotoxicity tests for pharmaceuticals, Step 5. U.S. Federal Register 77(110):33748–9.
   Google Scholar
• ICH. (2013). Draft ICH consensus guideline M7. Current Step 2, Feb 6. Assessment and control of DNA reactive (mutagenic) impurities in pharmaceuticals to limit potential carcinogenic risk. Available at: http://www.ich.org.
   Google Scholar
• Jemnitz K, Veres Z, Torok G, et al. (2004). Comparative study in the Ames test of benzo[a]pyrene and 2-aminoanthracene metabolic activation using rat hepatic S9 and hepatocytes following in vivo or in vitro induction. Mutagenesis 19:245–50.
   PubMed Web of Science ®Google Scholar
• Johnson GE. (2012). Mammalian cell HPRT gene mutation assay: test methods. Methods Mol Biol 817:55–67.
   PubMedGoogle Scholar
• Kadotani S, Arisawa M, Maruyama HB. (1984). Mutagenicity examination of several non-steroidal anti-inflammatory drugs in bacterial systems. Mutat Res 138:133–6.
   PubMed Web of Science ®Google Scholar
• Kamber M, Fluckiger-Isler S, Engelhardt G, et al. (2009). 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 24:359–66
   PubMed Web of Science ®Google Scholar
• Kazius J, McGuire R, Bursi R. (2005). Derivation and validation of toxicophores for mutagenicity prediction. J Med Chem 48:312–20.
   PubMed Web of Science ®Google Scholar
• Kitchin RM, Bechtold WE, Brooks AL. (1988). The structure–function relationships of nitrofluorenes and nitrofluorenones in the Salmonella mutagenicity and CHO sister-chromatid exchange assays. Mutat Res 206:367–77.
   PubMed Web of Science ®Google Scholar
• Klein M. (1997). Mutagenitätsuntersuchungen an Substituierten 4-Nitrobiphenylen, Diplomarbeit. Marburg: Philipps-Universtät.
   Google Scholar
• Klein M, Boche G. (1999). Regiospecific synthesis of substituted nitrofluorenes and aminofluorenes with the Negishi coupling reaction as key step. Synthesis 1999:1246–50.
   Google Scholar
• Klein M, Voigtmann U, Haack T, et al. (2000). From mutagenic to non-mutagenic nitroarenes: effect of bulky alkyl substituents on the mutagenic activity of 4-nitrobiphenyl in Salmonella typhimurium. Part I. Substituents ortho to the nitro group and in 2′-position. Mutat Res 467:55–68.
   PubMed Web of Science ®Google Scholar
• Kolář M, Kubař Ts, Hobza P. (2010). Sequence-dependent configurational entropy change of DNA upon intercalation. J Phys Chem B 114:13446–54.
   PubMed Web of Science ®Google Scholar
• Kroes R, Kleiner J, Renwick A. (2005). The threshold of toxicological concern concept in risk assessment. Toxicol Sci 86:226–30.
   PubMed Web of Science ®Google Scholar
• Krueger SK, Williams DE. (2005). Mammalian flavin-containing monooxygenases: structure/function, genetic polymorphisms and role in drug metabolism. Pharmacol Ther 106:357–87.
   PubMed Web of Science ®Google Scholar
• La DK, Swenberg JA. (1996). DNA adducts: biological markers of exposure and potential applications to risk assessment. Mutat Res 365:129–46.
   PubMed Web of Science ®Google Scholar
• Liber HL, Thilly WG. (1982). Mutation assay at the thymidine kinase locus in diploid human lymphoblasts. Mutat Res 94:467–85.
   PubMed Web of Science ®Google Scholar
• Liberman DF, Fink RC, Schaefer FL, et al. (1982). Mutagenicity of anthraquinone and hydroxylated anthraquinones in the Ames/Salmonella microsome system. Appl Environ Microbiol 43:1354–9.
   PubMed Web of Science ®Google Scholar
• Linget JM, du Vignaud P. (1999). Automation of metabolic stability studies in microsomes, cytosol and plasma using a 215 Gilson liquid handler. J Pharm Biomed Anal 19:893–901.
   PubMed Web of Science ®Google Scholar
• MacKerell AD, Banavali N, Foloppe N. (2001). Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56:257–65.
   Web of Science ®Google Scholar
• Matthews EJ, Kruhlak NL, Benz RD, et al. (2008). Combined use of MC4PC, MDL-QSAR, BioEpisteme, Leadscope PDM, and Derek for Windows Software to achieve high-performance, high-confidence, mode of action-based predictions of chemical carcinogenesis in rodents. Toxicol Mech Methods 18:189–206.
   PubMed Web of Science ®Google Scholar
• McCann J, Choi E, Yamasaki E, Ames BN. (1975). Detection of carcinogens as mutagens in the Salmonella/microsome test: assay of 300 chemicals. Proc Natl Acad Sci USA 72:5135–9.
   PubMed Web of Science ®Google Scholar
• McCoy EC, Rosenkranz EJ, Petrullo LA, Rosenkranz HS. (1981). Frameshift mutations: relative roles of simple intercalation and of adduct formation. Mutat Res 90:21–30.
   PubMed Web of Science ®Google Scholar
• McGovern T, Jacobson-Kram D. (2006). Regulation of genotoxic and carcinogenic impurities in drug substances and products. TrAC Trends Anal Chem 25:790–5.
   Web of Science ®Google Scholar
• Meneni SR, Shell SM, Gao L, et al. (2007). Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair. Biochemistry 46:11263–78.
   PubMed Web of Science ®Google Scholar
• Miller RB, Dugar S. (1984). Stoichiometric synthesis of unsymmetrical mononitrobiphenyls via the palladium-catalyzed cross-coupling of arylboronic acids with aryl bromides. Organometallics 3:1261–3.
   Web of Science ®Google Scholar
• Mortelmans K, Zeiger E. (2000). The Ames Salmonella/microsome mutagenicity assay. Mutat Res 455:29–60.
   PubMed Web of Science ®Google Scholar
• Muller L, Gocke E, Lave T, Pfister T. (2009). Ethyl methanesulfonate toxicity in Viracept – a comprehensive human risk assessment based on threshold data for genotoxicity. Toxicol Lett 190:317–29.
   PubMed Web of Science ®Google Scholar
• Nelson DL, Cox MM, Lehninger AL. (2008). Lehninger principles of biochemistry. New York: W. H. Freeman.
   Google Scholar
• Rescifina A, Chiacchio MA, Corsaro A, et al. (2006). Synthesis and biological activity of isoxazolidinyl polycyclic aromatic hydrocarbons: potential DNA intercalators. J Med Chem 49:709–15.
   PubMed Web of Science ®Google Scholar
• Ricci CG, Netz PA. (2009). Docking studies on DNA–ligand interactions: building and application of a protocol to identify the binding mode. J Chem Inform Model 49:1925–35.
   PubMed Web of Science ®Google Scholar
• Ridings JE, Barratt MD, Cary R, et al. (1996). Computer prediction of possible toxic action from chemical structure: an update on the DEREK system. Toxicology 106:267–79.
   PubMed Web of Science ®Google Scholar
• Sanderson DM, Earnshaw CG. (1991). Computer prediction of possible toxic action from chemical structure; the DEREK system. Hum Exp Toxicol 10:261–73.
   PubMed Web of Science ®Google Scholar
• Serafimova R, Fuart Gatnik M, Worth A. (2010). Review of QSAR models and software tools for predicting genotoxicity and carcinogenicity. JRC Scientific and Technical Report EUR 24427 EN-2010. Available at: http://publications.jrc.ec.europa.eu/repository/handle/JRC59068.
   Google Scholar
• Snyder RD, Ewing D, Hendry LB. (2006). DNA intercalative potential of marketed drugs testing positive in in vitro cytogenetics assays. Mutat Res 609:47–59.
   PubMed Web of Science ®Google Scholar
• Snyder RD, Holt PA, Maguire JM, Trent JO. (2013). Prediction of noncovalent Drug/DNA interaction using computational docking models: studies with over 1350 launched drugs. Environ Mol Mutagen 54:668–81.
   PubMed Web of Science ®Google Scholar
• Snyder RD, McNulty J, Zairov G, et al. (2005). The influence of N-dialkyl and other cationic substituents on DNA intercalation and genotoxicity. Mutat Res 578:88–99.
   PubMed Web of Science ®Google Scholar
• Sutter A, Amberg A, Boyer S, et al. (2013). Use of in silico systems and expert knowledge for structure-based assessment of potentially mutagenic impurities. Regul Toxicol Pharmacol 67:39–52.
   PubMed Web of Science ®Google Scholar
• Teasdale A, Elder D, Fenner S. (2011). Strategies for the evaluation of genotoxic impurity risk. In: Teasdale A, ed. Genotoxic impurities. Hoboken, NJ: John Wiley & Sons, Inc., 219–247.
   Google Scholar
• United Nations Department of Economic and Social Affairs (DESA). Consolidated List of Products Whose Consumption and/or Sale Have Been Banned, Withdrawn, Severely Restricted or not Approved by Governments. Fourteenth Issue (January 2005–October 2008). Pharmaceuticals. Nitrofurazone.
   Google Scholar
• Valencia A, Prous J, Mora O, et al. (2013). A novel QSAR model of Salmonella mutagenicity and its application in the safety assessment of drug impurities. Toxicol Appl Pharmacol 273:427–34.
   PubMed Web of Science ®Google Scholar
• Verghis SB, Essigmann JM, Kadlubar FF, et al. (1997). Specificity of mutagenesis by 4-aminobiphenyl: mutations at G residues in bacteriophage M13 DNA and G–>C transversions at a unique dG(8-ABP) lesion in single-stranded DNA. Carcinogenesis 18:2403–14.
   PubMed Web of Science ®Google Scholar
• Vernieulcn N. (1996). Role of metabolism in chemical toxicity. In: Ioannides C, ed. Cytochromes P450: metabolic and toxicological aspects. Boca Raton, FL: CRC Press.
   Google Scholar
• Vollhardt KPC, Schore NE. (2014). Organic chemistry, 7th edition. New York, NY: W. H. Freeman.
   Google Scholar
• Watson JD. (2007). Molecular biology of the gene. San Francisco/Cold Spring Harbor (NY): Pearson/Benjamin Cummings, Cold Spring Harbor Laboratory Press.
   Google Scholar
• Watson JD, Crick FH. (1953). Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–8.
   PubMed Web of Science ®Google Scholar
• Watt DL, Utzat CD, Hilario P, Basu AK. (2007). Mutagenicity of the 1-nitropyrene–DNA adduct N-(deoxyguanosin-8-yl)-1-aminopyrene in mammalian cells. Chem Res Toxicol 20:1658–64.
   PubMed Web of Science ®Google Scholar
• Worth A, Lapenna S, Lo Piparo E, et al. (2010). The applicability of software tools for genotoxicity and carcinogenicity prediction: case studies relevant to the assessment of pesticides. JRC Scientific and Technical Reports. EC Joint Research Centre Institute for Health and Consumer Protection, Ispra 18–9. Available at: http://publications.jrc.ec.europa.eu/repository/bitstream/JRC62109/eur_24640_en.pdf.
   Google Scholar
• Wynalda MA, Wienkers LC. (1997). Assessment of potential interactions between dopamine receptor agonists and various human cytochrome P450 enzymes using a simple in vitro inhibition screen. Drug Metab Dispos 25:1211–14.
   PubMed Web of Science ®Google Scholar
• Zeiger E, Haseman JK, Shelby MD, et al. (1990). Evaluation of four in vitro genetic toxicity tests for predicting rodent carcinogenicity: confirmation of earlier results with 41 additional chemicals. Environ Mol Mutagen 16:1–14.
   PubMed Web of Science ®Google Scholar