In silico Prediction of Novel SARS-CoV 3CL pro Inhibitors: a Combination of 3D-QSAR, Molecular Docking, ADMET Prediction, and Molecular Dynamics Simulation

Abstract

The Chymotrypsin-like protease (3CLpro) is a drug target in the coronavirus because of its role in processing the polyproteins that are translated from the viral RNA. This study applied 3D quantitative structure-activity relationship (3D-QSAR), molecular docking, and ADMET prediction on a series of SARS-CoV 3CLpro inhibitors. The 3D-QSAR study was applied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods, which gave the cross-validation coefficient (Q2) values of 0.64 and 0.80, the determination coefficient (R2) values of 0.998 and 0.993 and the standard error of the estimate (SEE) values of 0.046 and 0.091, respectively. The acceptable values of the determination coefficient (R2 test) to CoMFA and CoMSIA respectively corresponding to values of 0.725 and 0.690 utilizing a test set of seven molecules prove the high predictive ability of this model. Molecular docking analysis was utilized to validate 3D-QSAR methods and explain the binding site interactions and affinity between the most active ligands and the SARS-CoV 3CLpro receptor. Based on these results, a novel series of compounds were predicted, and their pharmacokinetic properties were verified using drug-likeness and ADMET prediction. Finally, the best-docked candidate molecules were subjected to molecular dynamics (MD) simulation to affirm their dynamic behavior and stability.