Identifying 124 new anti-HIV drug candidates in a 37 billion-compound database: An integrated approach of machine learning (QSAR), molecular docking, and molecular dynamics simulation

Cobre, Alexandre de Fátima; Ara, Anderson; Alves, Alexessander Couto; Maia Neto, Moisés; Fachi, Mariana Millan; Beca, Laize Sílvia dos Anjos Botas; Tonin, Fernanda Stumpf; Pontarolo, Roberto

doi:10.1016/j.chemolab.2024.105145

Chemometrics and Intelligent Laboratory Systems

2024

DOI: 10.1016/j.chemolab.2024.105145

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Identifying 124 new anti-HIV drug candidates in a 37 billion-compound database: An integrated approach of machine learning (QSAR), molecular docking, and molecular dynamics simulation

Alexandre de Fátima Cobre,

Anderson Ara,

Alexessander Couto Alves

et al.

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Optimizing Hepatitis C Virus Inhibitor Identification with LightGBM and Tree-structured Parzen Estimator Sampling

Noviandy,

Idroes,

Maulana

et al. 2024

Eng. Technol. Appl. Sci. Res.

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Identifying potent inhibitors against the Hepatitis C Virus (HCV) is crucial due to the continuous emergence of drug-resistant strains. Traditional drug discovery methods, including high-throughput screening, are often resource-intensive and time-consuming. Machine Learning (ML) approaches, particularly Quantitative Structure-Activity Relationship modeling, have been increasingly adopted to address this. This study utilized LightGBM, an efficient gradient-boosting framework, to predict the activity of potential HCV inhibitors. Additionally, the Tree-structured Parzen Estimator (TPE) was employed for hyperparameter optimization to enhance model performance. The optimized LightGBM-TPE model outperformed other ML models, including standard LightGBM, XGBoost, Random Forest, K-Nearest Neighbors, and Support Vector Machines, achieving an accuracy of 86.27%, a precision of 85.47%, a recall of 87.50%, a specificity of 85.03%, and an F1-score of 86.47%. Feature importance analysis identified critical molecular descriptors contributing to the model's predictive power. The results underscore the potential of advanced ML techniques and robust optimization methods to accelerate drug discovery, particularly for challenging targets such as HCV.

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Optimizing Hepatitis C Virus Inhibitor Identification with LightGBM and Tree-structured Parzen Estimator Sampling

Noviandy,

Idroes,

Maulana

et al. 2024

Eng. Technol. Appl. Sci. Res.

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show abstract

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Identifying 124 new anti-HIV drug candidates in a 37 billion-compound database: An integrated approach of machine learning (QSAR), molecular docking, and molecular dynamics simulation

Cited by 1 publication

References 60 publications

Optimizing Hepatitis C Virus Inhibitor Identification with LightGBM and Tree-structured Parzen Estimator Sampling

Optimizing Hepatitis C Virus Inhibitor Identification with LightGBM and Tree-structured Parzen Estimator Sampling

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