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In Silico Methods for Carcinogenicity Assessment

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In Silico Methods for Predicting Drug Toxicity

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2425))

Abstract

Screening compounds for potential carcinogenicity is of major importance for prevention of environmentally induced cancers. A large sequence of predictive models, ranging from short-term biological assays (e.g., mutagenicity tests) to theoretical models, has been attempted in this field. Theoretical approaches such as (Q)SAR are highly desirable for identifying carcinogens, since they actively promote the replacement, reduction, and refinement of animal tests. This chapter reports and describes some of the most noted (Q)SAR models based on human expert knowledge and statistical approaches, aiming at predicting the carcinogenicity of chemicals. Additionally, the performance of the selected models has been evaluated, and the results are interpreted in details by applying these predictive models to some pharmaceutical molecules.

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References

  1. Arcos JC (1995) Chemical induction of cancer: modulation and combination effects. In: An inventory of the many factors which influence carcinogenesis. Springer Science & Business Media, Berlin

    Google Scholar 

  2. Woo Y, Lai D (2003) Mechanisms of action of chemical carcinogens, and their role in structure-activity relationships (SAR) analysis and risk assessment. In: Benigni R (ed) Quantitative structure-activity relationship (QSAR) models of mutagens and carcinogens. CRC Press, Boca Raton, FL, pp 41–80

    Google Scholar 

  3. Jacobs MN, Colacci A, Louekari K, Luijten M, Hakkert BC, Paparella M, Vasseur P (2016) “International regulatory needs for development of an IATA for non-genotoxic carcinogenic chemical substances”. ALTEX – Alternatives to animal experimentation 33(4): 359–392. https://doi.org/10.14573/altex.1601201

  4. Miller EC, Miller JA (1981) Searches for ultimate chemical carcinogens and their reactions with cellular macromolecules. Cancer 47(10):2327–2345

    Article  CAS  Google Scholar 

  5. Ames BN (1979) Identifying environmental chemicals causing mutations and cancer. Science 204(4393):587–593

    Article  CAS  Google Scholar 

  6. OECD Test no. 487: in vitro mammalian cell micronucleus test. OECD Publishing, Paris

    Google Scholar 

  7. Benfenati E (2013) Theory, guidance and applications on QSAR and REACH. http://ebook.insilico.eu/insilico-ebook-orchestra-benfenati-ed1_rev-June2013.pdf. Accessed 30 Apr 2021

  8. Dearden JC, Barratt MD, Benigni R, Bristol DW, Combes RD, Cronin MT, Judson PN, Payne MP, Richard AM, Tichy M, Worth A, Yourick J (1998) The development and validation of expert systems for predicting toxicity. Altern Lab Anim 25:223–252

    Article  Google Scholar 

  9. Benigni R, Bossa C, Tcheremenskaia O, Giuliani A (2010) Alternatives to the carcinogenicity bioassay: in silico methods, and the in vitro and in vivo mutagenicity assays. Expert Opin Drug Metab Toxicol 6(7):809–819. https://doi.org/10.1517/17425255.2010.486400

    Article  CAS  PubMed  Google Scholar 

  10. Kirkland D, Zeiger E, Madia F, Corvi R (2014) Can in vitro mammalian cell genotoxicity test results be used to complement positive results in the Ames test and help predict carcinogenic or in vivo genotoxic activity? II. Construction and analysis of a consolidated database. Mutat Res Genet Toxicol Environ Mutagen 775-776:69–80. https://doi.org/10.1016/j.mrgentox.2014.10.006

    Article  CAS  PubMed  Google Scholar 

  11. Toropov AA, Toropova AP, Benfenati E (2009) Additive SMILES-based carcinogenicity models: probabilistic principles in the search for robust predictions. Int J Mol Sci 10(7):3106–3127

    Article  CAS  Google Scholar 

  12. Benigni R, Bossa C, Jeliazkova N, Netzeva T, Worth A (2008) The Benigni/Bossa Rulebase for mutagenicity and carcinogenicity—a module of Toxtree. EUR 23241 EN. Luxembourg (Luxembourg): OPOCE, JRC43157. https://publications.jrc.ec.europa.eu/repository/handle/JRC43157

  13. Rositsa S, Mojca FG, Andrew W (2010) Review of QSAR models and software tools for predicting genotoxicity and carcinogenicity. In: JRC scientific and technical reports- EUR 24427 EN. Publications Office of the European Union, Luxembourg

    Google Scholar 

  14. Benfenati E, Benigni R, Demarini DM, Helma C, Kirkland D, Martin TM, Mazzatorta P, Ouédraogo-Arras G, Richard AM, Schilter B, Schoonen WG, Snyder RD, Yang C (2009) Predictive models for carcinogenicity and mutagenicity: frameworks, state-of-the-art, and perspectives. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 27(2):57–90. https://doi.org/10.1080/10590500902885593

    Article  CAS  PubMed  Google Scholar 

  15. Ferrari T, Gini G (2010) An open source multistep model to predict mutagenicity from statistical analysis and relevant structural alerts. Chem Cent J 4:S2

    Article  Google Scholar 

  16. Ferrari T, Gini G, Bakhtyari NG, Benfenati E (2011) Mining toxicity structural alerts from SMILES: a new way to derive structure activity relationships. Computational intelligence and data mining (CIDM). IEEE Symposium 2011:120–127. https://doi.org/10.1109/cidm.2011.5949444

    Article  Google Scholar 

  17. IdeaConsult (2009) Toxtree software. http://toxtree.sourceforge.net/. Accessed 30 Apr 2021

  18. Woo Y-T, Lai DY, Argus MF, Arcos JC (1995) Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals. Toxicol Lett 79(1):219–228

    Article  CAS  Google Scholar 

  19. OECD (2010) OECD QSAR Toolbox. http://www.oecd.org/chemicalsafety/risk-assessment/theoecdqsartoolbox.htm . Accessed 30 Apr 2021

  20. Helma C (2006) Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and salmonella mutagenicity. Mol Divers 10(2):147–158

    Article  CAS  Google Scholar 

  21. Klopman G, Rosenkranz HS (1994) Approaches to SAR in carcinogenesis and mutagenesis. Prediction of carcinogenicity/mutagenicity using MULTI-CASE. Mutation Res 305(1):33–46

    Article  CAS  Google Scholar 

  22. Enslein K, Gombar VK, Blake BW (1994) Use of SAR in computer-assited prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program. Mutation Res 305(1):47–61

    Article  CAS  Google Scholar 

  23. Smithing MP, Darvas F (1992) HazardExpert: an expert system for predicting chemical toxicity. ACS Symposium series American Chemical Society, Springfield, Ohio

    Book  Google Scholar 

  24. Sanderson D, Earnshaw C (1991) Computer prediction of possible toxic action from chemical structure; the DEREK system. Hum Exp Toxicol 10(4):261–273

    Article  CAS  Google Scholar 

  25. Ridings J, Barratt M, Cary R, Earnshaw C, Eggington C, Ellis M, Judson P, Langowski J, Marchant C, Payne M (1996) Computer prediction of possible toxic action from chemical structure: an update on the DEREK system. Toxicology 106(1):267–279

    Article  CAS  Google Scholar 

  26. Leadscope Inc (2019). https://www.leadscope.com/carcinogenicity_model_suite/. Accessed 30 Apr 2021

  27. Helma C (2005) In silico predictive toxicology: the state-of-the-art and strategies to predict human health effects. Curr Opin Drug Discov Devel 8(1):27–31

    CAS  PubMed  Google Scholar 

  28. Helma C, Cramer T, Kramer S, De Raedt L (2004) Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds. J Chem Inf Comput Sci 44(4):1402–1411. https://doi.org/10.1021/ci034254q

    Article  CAS  PubMed  Google Scholar 

  29. Yi Wang NC, Venkatapathy R, Bruce RM, Moudgal C (2011) Development of quantitative structure–activity relationship (QSAR) models to predict the carcinogenic potency of chemicals. II. Using oral slope factor as a measure of carcinogenic potency. Regul Toxicol Pharmacol 59(2):215–226

    Article  Google Scholar 

  30. Kar S, Deeb O, Roy K (2012) Development of classification and regression based QSAR models to predict rodent carcinogenic potency using oral slope factor. Ecotoxicol Environ Saf 82:85–95

    Article  CAS  Google Scholar 

  31. VEGA software (2021). https://www.vegahub.eu/. Accessed 30 Apr 2021

  32. The Carcinogenic Potency Database (CPDB). https://www.nlm.nih.gov/databases/download/cpdb.html. Accessed 30 Apr 2021

  33. Fjodorova N, Vračko M, Novič M, Roncaglioni BE (2010) New public QSAR model for carcinogenicity. Chem Cent J 4(Suppl 1):S3

    Article  Google Scholar 

  34. Golbamaki Bakhtyari A, Benfenati E, Golbamaki Bakhtyari N, Manganaro A, Merdivan E, Roncaglioni A, Gini G (2016) New clues on carcinogenicity-related substructures derived from mining two large datasets of chemical compounds. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 34:97–113

    Article  Google Scholar 

  35. ISS database on chemical carcinogens (ISSCAN) (2008). https://www.iss.it/isstox. Accessed 30 Apr 2021

  36. Kirkland D, Aardema M, Henderson L, Müller L (2005) 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 584(1):1–256

    CAS  PubMed  Google Scholar 

  37. Toma C, Manganaro A, Raitano G, Marzo M, Gadaleta D, Baderna D, Roncaglioni A, Kramer N, Benfenati E (2021) QSAR models for human carcinogenicity: an assessment based on Oral and inhalation slope factors. Molecules 26(1):127

    Google Scholar 

  38. Mayer J, Cheeseman MA, Twaroski ML (2008) Structure-activity relationship analysis tools: validation and applicability in predicting carcinogens. Regul Toxicol Pharmacol 50(1):50–58. https://doi.org/10.1016/j.yrtph.2007.09.005

    Article  CAS  PubMed  Google Scholar 

  39. EPA Environmental Protection Agency. https://www.epa.gov/tsca-screening-tools/oncologictm-expert-system-evaluate-carcinogenic-potential-chemicals. Accessed 30 Apr 2021

  40. Edler L, Hart A, Greaves P, Carthew P, Coulet M, Boobis A, Williams GM, Smith B (2014) Selection of appropriate tumour data sets for benchmark dose modelling (BMD) and derivation of a margin of exposure (MoE) for substances that are genotoxic and carcinogenic: considerations of biological relevance of tumour type, data quality and uncertainty assessment. Food Chem Toxicol 70:264–289

    Article  CAS  Google Scholar 

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Acknowledgments

The research for this chapter was financially supported by the LIFE VERMEER project (LIFE16 ENV/IT/OOO167).

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Correspondence to Alessandra Roncaglioni .

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Golbamaki, A., Benfenati, E., Roncaglioni, A. (2022). In Silico Methods for Carcinogenicity Assessment. In: Benfenati, E. (eds) In Silico Methods for Predicting Drug Toxicity. Methods in Molecular Biology, vol 2425. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1960-5_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1960-5_9

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  • Publisher Name: Humana, New York, NY

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