![]() ![]() Members of the Coronaviridae virus family often cause mild respiratory syndrome in humans. Our results could contribute to the development of potential drugs inhibiting SARS-CoV-2. Replacing Glu166 by an alanine residue leads to ∼2.0 kcal/mol decreases in the affinity of darunavir to SARS-CoV-2 Mpro. We also found that Glu166 forms H-bonds to all of the inhibitors. The binding free energy largely arises from van der Waals interaction. FEP results indicate that two natural compounds, cannabisin A and isoacteoside, and an HIV-1 PR inhibitor, darunavir, exhibit a large binding free energy to SARS-CoV-2 Mpro, which is larger than that of 13b, the most reliable SARS-CoV-2 Mpro inhibitor recently reported. Finally, FEP, the most accurate and precise method, was used to determine the absolute binding free energy of these five compounds. FPL simulations resulted in five potential inhibitors, including three natural compounds and two available HIV-1 PR inhibitors. Molecular docking resulted in a short list of 35 natural compounds, which was subsequently refined using the FPL scheme. Subsequently, we applied our approach on a database of ∼4600 natural compounds, as well as 8 available HIV-1 protease (PR) inhibitors and an aza-peptide epoxide. We first tested our approach with three reported inhibitors of SARS-CoV-2 Mpro, and our computational results are in good agreement with the respective experimental data. Therefore, in this context, we used rigorous computational methods, including molecular docking, fast pulling of ligand (FPL), and free energy perturbation (FEP), to investigate potential inhibitors of SARS-CoV-2 Mpro. The main protease (Mpro) of SARS-CoV-2 is one of the potential drug targets. As the disease is spreading rapidly all over the world, it is urgent to find effective drugs to treat the virus. The novel coronavirus (SARS-CoV-2) has infected several million people and caused thousands of deaths worldwide since December 2019. ![]()
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May 2023
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