Machine learning and molecular simulation-based protocols to identify novel potential inhibitors for reverse transcriptase against HIV infections

Abstract

Acquired immunodeficiency syndrome (AIDS) is a potentially fatal condition affecting the human immune system, which is attributed to the human immunodeficiency virus (HIV). The suppression of reverse transcriptase activity is a promising and feasible strategy for the therapeutic management of AIDS. In this study, we employed machine learning algorithms, such as support vector machines (SVM), k-nearest neighbor (k-NN), random forest (RF), and Gaussian naive base (GNB), which are fast and effective tools commonly used in drug design. For model training, we initially obtained a dataset of 5,159 compounds from BindingDB. The models were assessed using tenfold cross-validation to ensure their accuracy and reliability. Among these compounds, 1,645 compounds were labeled as active, having an IC50 below 0.49 µM, while 3,514 compounds were labeled “inactive against reverse transcriptase. Random forest achieved 86% accuracy on the train and test set among the different machine learning algorithms. Random forest model was then applied to an external ZINC dataset. Subsequently, only three hits-ZINC1359750464, ZINC1435357562, and ZINC1545719422-were selected based on the Lipinski Rule, docking score, and good interaction. The stability of these molecules was further evaluated by deploying molecular dynamics simulation and MM/GBSA, which were found to be −38.6013 ± 0.1103 kcal/mol for the Zidovudine/RT complex, −59.1761 ± 2.2926 kcal/mol for the ZINC1359750464/RT complex, −47.6292 ± 2.4206 kcal/mol for the ZINC1435357562/RT complex, and −50.7334 ± 2.5713 kcal/mol for the ZINC1545719422/RT complex. Communicated by Ramaswamy H. Sarma