Alla P Toropova, Andrey A Toropov, Emilio Benfenati
{"title":"Monte Carlo Simulation of Pesticide Toxicity for Rainbow Trout (<i>Oncorhynchus mykiss</i>) Using New Criteria of Predictive Potential.","authors":"Alla P Toropova, Andrey A Toropov, Emilio Benfenati","doi":"10.3390/jox15030082","DOIUrl":null,"url":null,"abstract":"<p><p><i>Background</i>: The toxicity of pesticides for fish in general and Rainbow Trout (<i>Oncorhynchus mykiss</i>) in particular is an important ecological indicator required by regulations, and it implies the use of a large number of fish. The number of animals needed would be even higher to evaluate metabolites and pesticide impurities. Considering ethical issues, the costs, and the necessary resources, the use of in silico models is often proposed. <i>Aim of the study</i>: We explore the use of advanced Monte Carlo methods to obtain improved results for models testing Rainbow Trout (<i>Oncorhynchus mykiss</i>) acute toxicity. Several versions of the stochastic Monte Carlo simulation of pesticide toxicity for Rainbow Trout, carried out using CORAL software, were studied. The set of substances was split into four subsets: active training, passive training, calibration, and validation. Modeling was repeated five times to enable better statistical evaluation. To improve the predictive potential of models, the index of ideality of correlation (IIC), correlation intensity index (CII), and coefficient of conformism of correlation prediction (CCCP) were applied. <i>Main results and novelty</i>: The most suitable results were observed in the case of the CCCP-based optimization for SMILES-based descriptors, achieving an R<sup>2</sup> of 0.88 on the validation set, in all five random splits, demonstrating consistent and robust modeling performance. The relationship of information systems related to QSAR simulation and new ideas is discussed, assigning a key role to fundamental concepts like mass and energy. The study of the mentioned criteria of predictive potential during the conducted computer experiments showed that even though they are all aimed at improving the predictive potential, their values do not correlate, except for the CII and the CCCP. This means that, in general, the information impact of the considered criteria has a different nature, at least in the case of the simulation of toxicity for Rainbow Trout (<i>Oncorhynchus mykiss</i>). The applicability domain of the model is specific for pesticides; the software identifies potential outliers by looking at rare molecular fragments.</p>","PeriodicalId":42356,"journal":{"name":"Journal of Xenobiotics","volume":"15 3","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12193767/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Xenobiotics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/jox15030082","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"TOXICOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Background: The toxicity of pesticides for fish in general and Rainbow Trout (Oncorhynchus mykiss) in particular is an important ecological indicator required by regulations, and it implies the use of a large number of fish. The number of animals needed would be even higher to evaluate metabolites and pesticide impurities. Considering ethical issues, the costs, and the necessary resources, the use of in silico models is often proposed. Aim of the study: We explore the use of advanced Monte Carlo methods to obtain improved results for models testing Rainbow Trout (Oncorhynchus mykiss) acute toxicity. Several versions of the stochastic Monte Carlo simulation of pesticide toxicity for Rainbow Trout, carried out using CORAL software, were studied. The set of substances was split into four subsets: active training, passive training, calibration, and validation. Modeling was repeated five times to enable better statistical evaluation. To improve the predictive potential of models, the index of ideality of correlation (IIC), correlation intensity index (CII), and coefficient of conformism of correlation prediction (CCCP) were applied. Main results and novelty: The most suitable results were observed in the case of the CCCP-based optimization for SMILES-based descriptors, achieving an R2 of 0.88 on the validation set, in all five random splits, demonstrating consistent and robust modeling performance. The relationship of information systems related to QSAR simulation and new ideas is discussed, assigning a key role to fundamental concepts like mass and energy. The study of the mentioned criteria of predictive potential during the conducted computer experiments showed that even though they are all aimed at improving the predictive potential, their values do not correlate, except for the CII and the CCCP. This means that, in general, the information impact of the considered criteria has a different nature, at least in the case of the simulation of toxicity for Rainbow Trout (Oncorhynchus mykiss). The applicability domain of the model is specific for pesticides; the software identifies potential outliers by looking at rare molecular fragments.
期刊介绍:
The Journal of Xenobiotics publishes original studies concerning the beneficial (pharmacology) and detrimental effects (toxicology) of xenobiotics in all organisms. A xenobiotic (“stranger to life”) is defined as a chemical that is not usually found at significant concentrations or expected to reside for long periods in organisms. In addition to man-made chemicals, natural products could also be of interest if they have potent biological properties, special medicinal properties or that a given organism is at risk of exposure in the environment. Topics dealing with abiotic- and biotic-based transformations in various media (xenobiochemistry) and environmental toxicology are also of interest. Areas of interests include the identification of key physical and chemical properties of molecules that predict biological effects and persistence in the environment; the molecular mode of action of xenobiotics; biochemical and physiological interactions leading to change in organism health; pathophysiological interactions of natural and synthetic chemicals; development of biochemical indicators including new “-omics” approaches to identify biomarkers of exposure or effects for xenobiotics.