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Comparative Study of Machine Learning-Based QSAR Modeling of Anti-inflammatory Compounds from Durian Extraction.

ABSTRACT: Quantitative structure-activity relationship (QSAR) analysis, an in silico methodology, offers enhanced efficiency and cost effectiveness in investigating anti-inflammatory activity. In this study, a comprehensive comparative analysis employing four machine learning algorithms (random forest (RF), gradient boosting regression (GBR), support vector regression (SVR), and artificial neural networks (ANNs)) was conducted to elucidate the activities of naturally derived compounds from durian extraction. The analysis was grounded in the exploration of structural attributes encompassing steric and electrostatic properties. Notably, the nonlinear SVR model, utilizing five key features, exhibited superior performance compared to the other models. It demonstrated exceptional predictive accuracy for both the training and external test datasets, yielding R² values of 0.907 and 0.812, respectively; in addition, their RMSE resulted in 0.123 and 0.097, respectively. The study outcomes underscore the significance of specific structural factors (denoted as shadow ratio, dipole z, methyl, ellipsoidal volume, and methoxy) in determining anti-inflammatory efficacy. Thus, the findings highlight the potential of molecular simulations and machine learning as alternative avenues for the rational design of novel anti-inflammatory agents.

SUBMITTER: Wiriyarattanakul A

PROVIDER: S-EPMC10882656 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Comparative Study of Machine Learning-Based QSAR Modeling of Anti-inflammatory Compounds from Durian Extraction.

Wiriyarattanakul Amphawan A Xie Wanting W Toopradab Borwornlak B Wiriyarattanakul Sopon S Shi Liyi L Rungrotmongkol Thanyada T Maitarad Phornphimon P

ACS omega 20240207 7

Quantitative structure-activity relationship (QSAR) analysis, an <i>in</i> silico methodology, offers enhanced efficiency and cost effectiveness in investigating anti-inflammatory activity. In this study, a comprehensive comparative analysis employing four machine learning algorithms (random forest (RF), gradient boosting regression (GBR), support vector regression (SVR), and artificial neural networks (ANNs)) was conducted to elucidate the activities of naturally derived compounds from durian e ...[more]

PMID: 38405441

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Project description:Due to their multiple beneficial effects, antioxidant peptides have attracted increasing interest. Currently, the screening and identification of bioactive peptides, including antioxidative peptides based on wet-chemistry methods are time-consuming and highly rely on many advanced instruments and trained personnel. Quantitative structure-activity relationship (QSAR) analysis as an in silico method can be more efficient and cost-effective. However, model performance of QSAR studies on antioxidant peptides was still poor due to limited attempts in model development approaches. The objective of this study was to compare popular machine learning methods for antioxidant activity modeling and screening of tripeptides and identify the critical amino acid features that determine the antioxidant activity. 533 numerical indices of amino acids were adopted to characterize 130 tripeptides with known antioxidant activity from the published literature, and then 7 feature selection strategies plus pairwise correlation were used to screen the most important indices for antioxidant activity and model building. 14 machine learning methods were used to build models based on the feature selection strategies, respectively. Among the 98 models, non-linear regression methods tended to perform better, and the best model with an R 2 Test of 0.847 and RMSETest of 0.627 for tripeptide antioxidants was obtained by combining random forest for feature selection and tree-based extreme gradient boost regression for model development. Based on the predicted antioxidant values of 7870 unknown tripeptides, potentially high antioxidant activity tripeptides all have a tyrosine, tryptophan, or cysteine residue at the C-terminal position. Furthermore, the predicted antioxidant activity of six synthesized tripeptides was confirmed through experimental determination, and for the first time, the cysteine or tyrosine residue at the C-terminal was found to be critical to the antioxidant activity based on both QSAR models and experimental observations.

Project description:BackgroundMachine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR data sets often encompass tens of thousands of compounds and the size of proprietary, as well as public data sets, is rapidly growing. Hence, there is a demand for computationally efficient machine learning algorithms, easily available to researchers without extensive machine learning knowledge. In granting the scientific principles of transparency and reproducibility, Open Source solutions are increasingly acknowledged by regulatory authorities. Thus, an Open Source state-of-the-art high performance machine learning platform, interfacing multiple, customized machine learning algorithms for both graphical programming and scripting, to be used for large scale development of QSAR models of regulatory quality, is of great value to the QSAR community.ResultsThis paper describes the implementation of the Open Source machine learning package AZOrange. AZOrange is specially developed to support batch generation of QSAR models in providing the full work flow of QSAR modeling, from descriptor calculation to automated model building, validation and selection. The automated work flow relies upon the customization of the machine learning algorithms and a generalized, automated model hyper-parameter selection process. Several high performance machine learning algorithms are interfaced for efficient data set specific selection of the statistical method, promoting model accuracy. Using the high performance machine learning algorithms of AZOrange does not require programming knowledge as flexible applications can be created, not only at a scripting level, but also in a graphical programming environment.ConclusionsAZOrange is a step towards meeting the needs for an Open Source high performance machine learning platform, supporting the efficient development of highly accurate QSAR models fulfilling regulatory requirements.

Project description:BackgroundICU-acquired weakness (ICU-AW) is a common complication among ICU patients. We used machine learning techniques to construct an ICU-AW inflammatory factor prediction model to predict the risk of disease development and reduce the incidence of ICU-AW.MethodsThe least absolute shrinkage and selection operator (LASSO) technique was used to screen key variables related to ICU-AW. Eleven indicators, such as the presence of sepsis, glucocorticoids (GC), neuromuscular blocking agents (NBAs), length of ICU stay, Acute Physiology and Chronic Health Evaluation (APACHE II) II score, and the levels of albumin (ALB), lactate (LAC), glucose (GLU), interleukin-1β (IL-1β), interleukin-6 (IL-6), and interleukin-10 (IL-10), were used as variables to establish the prediction model. We divided the data into a dataset that included inflammatory factors and a dataset that excluded inflammatory factors. Specifically, 70% of the participants in both datasets were used as the training set, and 30% of the participants were used as the test set. Three machine learning methods, logistic regression (LR), random forest (RF), and extreme gradient boosting (XGB), were used in the 70% participant training set to construct six different models, which were validated and evaluated in the remaining 30% of the participants as the test set. The optimal model was visualized for prediction using nomograms.ResultsThe logistic regression model including the inflammatory factors demonstrated excellent performance on the test set, with an area under the curve (AUC) of 82.1% and the best calibration curve fit, outperforming the other five models. The optimal model is represented visually in the nomograms.ConclusionThis study used easily accessible clinical characteristics and laboratory data that can aid in early clinical recognition of ICU-AW. The inflammatory factors IL-1β, IL-6, and IL-10 have high value for predicting ICU-AW.Trial registrationThe trial was registered at the Chinese Clinical Trial Registry with the registration number ChiCTR2300077968.

Dataset Information

Comparative Study of Machine Learning-Based QSAR Modeling of Anti-inflammatory Compounds from Durian Extraction.

Publications

Comparative Study of Machine Learning-Based QSAR Modeling of Anti-inflammatory Compounds from Durian Extraction.

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