Preview

Toxicological Review

Advanced search
Open Access Open Access  Restricted Access Subscription Access

Prognostic systems in preventive toxicology (literature review)

https://doi.org/10.47470/0869-7922-2025-33-2-134-143

EDN: fxrxwa

Abstract

Introduction. Currently, the world scientific community recommends the increasing use of in silico methods in assessing the hazard of chemicals. Of the computer modeling methods, the most popular are predictive systems based on structure-activity (QSAR) methods, used in complex hazard assessment and forecasting.

The purpose of this study is to review the capabilities of prognostic systems to identify the most informative one when solving issues of preventive toxicology.

Material and methods. The analysis of the OECD QSAR Toolbox software, VEGA Qsar, AMBIT, Toxtree, CAESAR software, TEST, Danish (Q)SAR Database, Syntelly, as well as articles on the practice of using predictive systems in toxicology, was conducted.

Results. QSAR predictive models allow to assess various types of hazards. The data on the specific and long-term effects of chemicals, which in classical toxicology require a significant material and time resource, are of the greatest importance. For a deeper study of the possibility of using predictive systems in solving preventive toxicology issues, according to the criteria of informativeness and reliability of positive results, the OECD QSAR Toolbox, VEGA Qsar, AMBIT, Toxtree, CAESAR software, TEST, Danish (Q)SAR Database, Syntelly were selected.

Limitations. The study was conducted through the study of databases Scopus, Web of Science, PubMed, ResearchGate, Cyberleninka, RSCI, eLibrary.

Conclusion. The analysis showed that most software products merge and “exchange” (integrate) QSAR models. The largest number of hazard indicators of chemicals allows to evaluate the QSAR Toolbox, while providing the opportunity to set the necessary toxicity indicators for the researcher.

Authors’ contribution:
Khamidulina Kh.Kh.
– the concept and design of the study, editing, approval of the final version of the article, responsibility for the integrity of all parts of the article;
Tarasova E.V.
– writing and editing the text;
Lastovetskiy M.L.
– collection and processing of materials, writing and editing the text.

Conflict of interest. The authors declare no conflicts of interest.

Funding. Carried out as part of the research project «Validation of alternative research methods in assessing the hazard and risk of exposure to chemicals on human health as a tool for regulating the safety of chemical factors».

Received: February 23, 2025 / Accepted: February 25, 2025 / Published: April 30, 2025

About the Authors

Khalidya Kh. Khamidulina
Scientific Information and Analytical Center “Russian Register of Potentially Hazardous Chemical and Biological Substances” of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor; Russian Medical Academy of Continuous Professional Education, RF Ministry of Health
Russian Federation

Doctor of Medical Sciences, Head of the Scientific Information and Analytical Center "Russian Register of Potentially Hazardous Chemical and Biological Substances" of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor, 121087, Moscow, Russian Federation; Professor, Head of the Department of Hygiene, Russian Medical Academy of Continuous Professional Education, RF Ministry of Health, 125993, Moscow, Russian Federation

e-mail: rpohbv@fncg.ru



Elena V. Tarasova
Scientific Information and Analytical Center “Russian Register of Potentially Hazardous Chemical and Biological Substances” of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor
Russian Federation

Candidate of Chemical Sciences, Deputy Head of the Scientific Information and Analytical Center "Russian Register of Potentially Hazardous Chemical and Biological Substances" of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor, 121087, Moscow, Russian Federation

e-mail: rpohbv@fncg.ru



Mikhail L. Lastovetskiy
Scientific Information and Analytical Center “Russian Register of Potentially Hazardous Chemical and Biological Substances” of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor
Russian Federation

Chemist-expert of the Scientific Information and Analytical Center "Russian Register of Potentially Hazardous Chemical and Biological Substances" of the F.F. Erisman Federal Scientific Center of Hygiene, Rospotrebnadzor, 121087, Moscow, Russian Federation

e-mail: rpohbv@fncg.ru



References

1. QSAR Toolbox. Available at: https://qsartoolbox.org/ (Accessed 18 March 2025).

2. Emilio Benfenati (2023). In silico models: theory, guidance and applications within VEGAHUB. Pharmacological Research Institute "Mario Negri": 163.

3. General Manual for Predicting the Toxic Properties of Chemicals. Available at: https://www.rpohv.ru/files/QSAR.pdf (Accessed 18 March 2025). (in Russian)

4. Krasnov L., Khokhlov I., Fedorov M.V., et al. Transformer-based artificial neural networks for the conversion between chemical notations. Sci Rep. 2021; 11: 14798.

5. Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. Available at: https://eur-lex.europa.eu/eli/reg/2006/1907/oj (Accessed 19 March 2025)

6. VEGA HUB. Available at: https://www.vegahub.eu/ (Accessed 17 March 2025)

7. AMBIT. Available at: https://ambit.sourceforge.net/ (Accessed 14 March 2025)

8. Toxicity Estimation Software Tool (TEST). Available at: https://www.epa.gov/comptox-tools/toxicity-estimation-software-tool-test (Accessed 14 March 2025)

9. Toxtree. Available at: https://toxtree.sourceforge.net/index.html (Accessed 14 March 2025)

10. Danish (Q)SAR Database. Available at: https://qsarmodels.food.dtu.dk/index.html (Accessed 14 March 2025)

11. CAESAR software. Available at: https://www.caesar-project.eu/ (Accessed 14 March 2025)

12. Syntelly. Available at: https://syntelly.ru/ (Accessed 19 March 2025)

13. Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface. Journal of Cheminformatics. 2011; 3(1): 18. https://doi.org/10.1186/1758-2946-3-18

14. Pandey S.K., Roy K. Development of hybrid models by the integration of the read-across hypothesis with the QSAR framework for the assessment of developmental and reproductive toxicity (DART) tested according to OECD TG 414. Toxicology Reports. 2024; 13: 101822. https://doi.org/10.1016/j.toxrep.2024.101822

15. Myden A., Cayley A., Davies R., et al. A developmental and reproductive toxicity adverse outcome pathway network to support safety assessments. Computational Toxicology. 2024; 31: 100325. https://doi.org/10.1016/j.comtox.2024.100325

16. Iyer P.R., Makris S.L. Chapter 9 – Guidelines for reproductive and developmental toxicity testing and risk assessment of chemicals. Reproductive and Developmental Toxicology (Third Edition). 2022; 31: 147–64. https://doi.org/10.1016/B978-0-323-89773-0.00009-6

17. Menz J., Götz M.E., Gündel U., et al. Genotoxicity assessment: opportunities, challenges and perspectives for quantitative evaluations of dose-response data. Archives of Toxicology. 2023; 97(5): 1–26, 2303–2328. https://doi.org/10.1007/s00204-023-03553-w

18. Steiblen G., Benthem J. van, Johnson G. Strategies in genotoxicology: Acceptance of innovative scientific methods in a regulatory context and from an industrial perspective. Mutation Research/Genetic Toxicology and Environmental Mutagenesis. 2020; 853: 503171. https://doi.org/10.1016/j.mrgentox.2020.503171

19. Thomas D.N., Wills J.W., Tracey H., et al. Ames test study designs for nitrosamine mutagenicity testing: qualitative and quantitative analysis of key assay parameters. Mutagenesis. 2024; 39(2): 78–95. https://doi.org/10.1093/mutage/gead033

20. Ladeira C., Møller P., Giovannelli L., et al. The Comet assay as a tool in human biomonitoring studies of environmental and occupational exposure to chemicals-a systematic scoping review. Toxics. 2024; 12(4): 270. https://doi.org/10.3390/toxics12040270

21. Steinbach T., Gad-McDonald S., Kruhlak N., Powley M., Greene N. (Q)SAR: A Tool for the Toxicologist. International Journal of Toxicology. 34(4): 352–4. https://doi.org/10.1177/1091581815584914

22. OECD iLibrary. Available at: https://www.oecd-ilibrary.org/ (Accessed 18 March 2025)

23. Honarvar N., Urbisch D., Mehling A., Kolle S., Teubner W., Guth K., Landsiedel R., et al. Peptide reactivity associated with skin sensitization – A comparison of the DPRA with the QSAR Toolbox and TIMES SS. Toxicology Letters. 2015; 238(2): S178. https://doi.org/10.1016/j.toxlet.2015.08.518

24. Kolle S.N., Natsch A., Gerberick G.F., Landsiedel R. A review of substances found positive in 1 of 3 in vitro tests for skin sensitization. Regulatory Toxicology and Pharmacology. 2019; 106: 352–68. https://doi.org/10.1016/j.yrtph.2019.05.016

25. Kim J., Seo J.K., Kim T., Kim H.K., Park S., Kim P.J. Prediction of Human Health and Ecotoxicity of Chemical Substances. Using the OECD QSAR Application Toolbox. Korean Journal of Environmental Health Sciences. 2013; 39(2): 130–7. https://doi.org/10.5668/JEHS.2013.39.2.130

26. Benigni R., In silico assessment of genotoxicity. Combinations of sensitive structural alerts minimize false negative predictions for all genotoxicity endpoints and can single out chemicals for which experimentation can be avoided. Regulatory Toxicology and Pharmacology. 2021; 126: 105042. https://doi.org/10.1016/j.yrtph.2021.105042

27. Amberg A., Andaya R.V., Anger L.T., Barber C., Beilke L., Bercu J., et al. Principles and procedures for handling out-of-domain and indeterminate results as part of ICH M7 recommended (Q)SAR analyses. Regul Toxicol Pharmacol. 2019; 102: 53–64.

28. Benigni R., Serafimova R., Parra Morte J.M., Battistelli C.L., Bossa C., Giuliani A., et al. Evaluation of the applicability of existing (Q)SAR models for predicting the genotoxicity of pesticides and similarity analysis related with genotoxicity of pesticides for facilitating of grouping and read across: An EFSA funded project. Regul Toxicol Pharmacol. 2020; 114: 104658.

29. Hoffmann S., Kleinstreuer N., Alepee N., et al. In silico mechanistically-based profiling module for acute oral toxicity. Computational Toxicology. 2019; 12(102–103): 100109. https://doi.org/10.1016/j.comtox.2019.100109

30. Khamidulina Kh.Kh., Tarasova E.V., Lastovetskiy M.L. Application of OESR QSAR Toolbox software for calculating the parameters of acute toxicity of chemicals. Toksikologicheskiy vestnik (Toxicological Review). 2022; 30(1): 45–54. https://doi.org/10.47470/0869-7922-2022-30-1-45-54 (in Russian)

31. Khamidulina Kh.Kh., Tarasova E.V., Lastovetskiy M.L. Prediction of the biodegradation of chemicals using OECD QSAR Toolbox software. Toksikologicheskiy vestnik. 2024; 32(1): 20–30. https://doi.org/10.47470/0869-7922-2024-32-1-20-30 https://elibrary.ru/lcywkx (in Russian)

32. Kutsarova S., Mehmed A., Cherkezova D., Stoeva S., Georgiev M., Petkov T., et al. Automated read-across workflow for predicting acute oral toxicity: I. The decision scheme in the QSAR toolbox. Regulatory Toxicology and Pharmacology. 2021: 125: 105015. https://doi.org/10.1016/j.yrtph.2021.105015

33. Hoffmann S., Kinsner-Ovaskainen A., Prieto P., Mangelsdorf I., Bieler C., Cole T. Acute oral toxicity: Variability, reliability, relevance and interspecies comparison of rodent LD50 data from literature surveyed for the ACuteTox project. Regulatory Toxicology and Pharmacology. 2010; 58: 395–407.

34. Yang J.Y., Lim J.H., Park S.J., Jo Y., Yang S.Y., Paik M.K., Hong S.H. Potential endocrine-disrupting effects of iprodione via estrogen and androgen receptors: evaluation using in vitro assay and an in silico model. Applied Biological Chemistry. 2024; 67(1): 8. https://doi.org/10.1186/s13765-024-00932-4

35. Dorne J.L.C.M., Richardson J., Livaniou A., Carnesecchi E., Ceriani L., et al. EFSA’s OpenFoodTox: An open source toxicological database on chemicals in food and feed and its future developments. Environ Int. 2021; 146: 106293. https://doi.org/10.1016/j.envint.2020.106293

36. Jurowski K., Niznik Ł. ˙Toxicity of the New Psychoactive Substance (NPS) Clephedrone (4-Chloromethcathinone, 4-CMC): Prediction of Toxicity Using In Silico Methods for Clinical and Forensic Purposes. Int. J. Mol. Sci. 2024; 25: 5867. https://doi.org/10.3390/ijms25115867

37. Patlewicz G., Jeliazkova N., Safford R.J., Worth A.P., Aleksiev B. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR and QSAR in Environmental Research. 2008; 19(5–6): 495–524. https://doi.org/10.1080/10629360802083871

38. Adiga G.P., Ranjan B., Venkataramulu D., Krishnappa D.M., Ahuja V. Predicting genotoxicity, carcinogenicity and skin sensitization of agrochemicals using OECD QSAR toolbox, Toxtree, Predskin and TEST. EUROTOX 2023. 2023; 702: 1–2.

39. Frydrych A., Jurowski K. The comprehensive prediction of carcinogenic potency and tumorigenic dose (TD50) for two problematic N-nitrosamines in food: NMAMPA and NMAMBA using toxicology in silico methods. Chemico-Biological Interactions, 2024; 110864–4. https://doi.org/10.1016/j.cbi.2024.110864

40. Cassano A., Manganaro A., Martin T., Young D., Piclin N., Pintore M., Benfenati E., et al. CAESAR models for developmental toxicity. Chemistry Central Journal. 2010; 4(1): S4. https://doi.org/10.1186/1752-153x-4-s1-s4

41. Basketter D.A., Alépée N., Ashikaga T., Barroso J., Gilmour N., Goebel C., et al. Categorization of Chemicals According to Their Relative Human Skin Sensitizing Potency. Dermatitis. 2014; 25(1): 11–21. https://doi.org/10.1097/der.0000000000000003

42. Hoffmann S., Kleinstreuer N., Alepee N., et al. Nonanimal methods to predict skin sensitization (I): The Cosmetics Europe database. Crit Rev Toxicol. 2018; 48: 344–58. https://doi.org/10.1080/10408444.2018.1429385

43. Kleinstreuer N.C., Hoffmann S., Alépée N., et al. Nonanimal methods to predict skin sensitization (II): An assessment of defined approaches. Crit Rev Toxicol. 2018; 48: 359–74. https://doi.org/10.1080/10408444.2018.1429386

44. Urbisch D., Mehling A., Guth K., et al. Assessing skin sensitization hazard in mice and men using non-animal test methods. Regul Toxicol Pharmacol. 2015; 71: 337–51. https://dpoi.org/10.1016/j.yrtph.2014.12.008

45. Golden E. “Evaluation of the global performance of eight in silico skin sensitization models using human data”. ALTEX – Alternatives to animal experimentation, 2021; 38(1): 33–48. https://doi.org/10.14573/altex.1911261


Review

For citations:


Khamidulina Kh.Kh., Tarasova E.V., Lastovetskiy M.L. Prognostic systems in preventive toxicology (literature review). Toxicological Review. 2025;33(2):134-143. (In Russ.) https://doi.org/10.47470/0869-7922-2025-33-2-134-143. EDN: fxrxwa

Views: 340


ISSN 0869-7922 (Print)
ISSN 3034-4611 (Online)