Sofia Ghironi, Edoardo Luca Viganò, Gianluca Selvestrel, Emilio Benfenati
{"title":"预测化学物质抗氧化电位的QSAR模型。","authors":"Sofia Ghironi, Edoardo Luca Viganò, Gianluca Selvestrel, Emilio Benfenati","doi":"10.3390/jox15030080","DOIUrl":null,"url":null,"abstract":"<p><p>Antioxidants are widely studied compounds with significant applications in the nutraceutical and dietary industries. To enable the rapid screening of large libraries of substances for antioxidant activity and to provide a useful tool for the initial evaluation of substances of interest with unknown activity, we developed Quantitative Structure-Activity Relationship (QSAR) models to predict the antioxidant potential of chemical substances. We started from a dataset of 1911 antioxidant substances, retrieved from the AODB database by selecting the DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity assay and the experimental value of the half-maximal inhibitory concentration. Different machine learning algorithms were applied to build regression models, and the goodness-of-fit of each model was assessed using the statistical parameters of R squared (R<sup>2</sup>), the Root-Mean-Squared Error, and the Mean Absolute Error. The Extra Trees model outperformed the other models in both internal and external validations, achieving the highest R<sup>2</sup> of 0.77 and the lowest RMSE on the test set. Gradient Boosting and eXtreme Gradient Boosting also achieved promising results with R<sup>2</sup> values of 0.76 and 0.75, respectively. Given these results, we developed an integrated method that not only outperformed the individual models, achieving an R<sup>2</sup> of 0.78 on the external test set, but also provided valuable insights into the range of predicted values.</p>","PeriodicalId":42356,"journal":{"name":"Journal of Xenobiotics","volume":"15 3","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12194667/pdf/","citationCount":"0","resultStr":"{\"title\":\"QSAR Models for Predicting the Antioxidant Potential of Chemical Substances.\",\"authors\":\"Sofia Ghironi, Edoardo Luca Viganò, Gianluca Selvestrel, Emilio Benfenati\",\"doi\":\"10.3390/jox15030080\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Antioxidants are widely studied compounds with significant applications in the nutraceutical and dietary industries. To enable the rapid screening of large libraries of substances for antioxidant activity and to provide a useful tool for the initial evaluation of substances of interest with unknown activity, we developed Quantitative Structure-Activity Relationship (QSAR) models to predict the antioxidant potential of chemical substances. We started from a dataset of 1911 antioxidant substances, retrieved from the AODB database by selecting the DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity assay and the experimental value of the half-maximal inhibitory concentration. Different machine learning algorithms were applied to build regression models, and the goodness-of-fit of each model was assessed using the statistical parameters of R squared (R<sup>2</sup>), the Root-Mean-Squared Error, and the Mean Absolute Error. The Extra Trees model outperformed the other models in both internal and external validations, achieving the highest R<sup>2</sup> of 0.77 and the lowest RMSE on the test set. Gradient Boosting and eXtreme Gradient Boosting also achieved promising results with R<sup>2</sup> values of 0.76 and 0.75, respectively. Given these results, we developed an integrated method that not only outperformed the individual models, achieving an R<sup>2</sup> of 0.78 on the external test set, but also provided valuable insights into the range of predicted values.</p>\",\"PeriodicalId\":42356,\"journal\":{\"name\":\"Journal of Xenobiotics\",\"volume\":\"15 3\",\"pages\":\"\"},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2025-05-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12194667/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Xenobiotics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/jox15030080\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"TOXICOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Xenobiotics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/jox15030080","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"TOXICOLOGY","Score":null,"Total":0}
QSAR Models for Predicting the Antioxidant Potential of Chemical Substances.
Antioxidants are widely studied compounds with significant applications in the nutraceutical and dietary industries. To enable the rapid screening of large libraries of substances for antioxidant activity and to provide a useful tool for the initial evaluation of substances of interest with unknown activity, we developed Quantitative Structure-Activity Relationship (QSAR) models to predict the antioxidant potential of chemical substances. We started from a dataset of 1911 antioxidant substances, retrieved from the AODB database by selecting the DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity assay and the experimental value of the half-maximal inhibitory concentration. Different machine learning algorithms were applied to build regression models, and the goodness-of-fit of each model was assessed using the statistical parameters of R squared (R2), the Root-Mean-Squared Error, and the Mean Absolute Error. The Extra Trees model outperformed the other models in both internal and external validations, achieving the highest R2 of 0.77 and the lowest RMSE on the test set. Gradient Boosting and eXtreme Gradient Boosting also achieved promising results with R2 values of 0.76 and 0.75, respectively. Given these results, we developed an integrated method that not only outperformed the individual models, achieving an R2 of 0.78 on the external test set, but also provided valuable insights into the range of predicted values.
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.