Molecular Analysis of Potential Inhibitors Against SARS-CoV-2: Computational Approach

SARS-CoV-2 has endangered the health of notable population of the world and hence, it attracted the attention of many researchers. In this study, we introduce two potential antiviral compounds for the treatment COVID-19 and compare it with the current reference drug. Molecular dynamics simulation and quantum theory of atoms in molecules (QTAIM) were used to study the host-guest interaction and dynamics between the nCov protein and inhibitors. Results obtained after a triplicate run of 100 ns for each compound revealed that compound B2 showed better inhibitory potential with MM-GBSA binding energy of -40.05 kcal mol-1, compared to the referenced drug. It is worth noting that B1 had a comparable binding potential with B2, suggesting some similarity in their inhibitory features. The QTAIM results showed that Laplacian ∇2ρ(r) and ellipticity (ε) were positive, indicating a stable protein-ligand interaction. The order of stability was in agreement with the MM-GBSA energy trends. The results showed that B1 and B2 can be used as a hopeful therapeutic for the cure of Covid-19. Though, a crucial trial should be done to authenticate this conclusion © 2023, Physical Chemistry Research. All Rights Reserved.

Molecular docking and dynamic simulations of some medicinal plants compounds against SARS-CoV-2: an in silico study

COVID-19 pandemic has poses urgent health challenge, and this project aims to identify potential inhibitors to combat this virus. We screened 198 bioactive compounds from five selected medicinal plants previously reported to be antiviral against SARS-CoV-2 protease and two co-receptors followed by molecular dynamics simulations. From the screened compounds, Astragalin demonstrated very strong molecular interactions with the molecular docking binding energies -8.5, -8.0, -7.6 kcal/mol for 6LU7, 6LZG, and 6VXX proteins of SARS-CoV-2, respectively. Hydrogen bonding interaction with the active site catalytic residue HIS-41 or CYS-145 of the main protease SARS-CoV-2 was observed. Binding free energies (Delta G(bind)) from MM-GBSA after 50 ns MD simulations showed that Astragalin has the highest energy of -33.00 and -34.89 kcal/mol in complex with the main protease and spike glycoprotein of SARS-CoV-2, respectively. The study identifies Astragalin as a better inhibitor for the inactivation of COVID-19 and should be pursued as a potential drug candidate for this virus.