Identification of a natural product inhibitor of SARS-CoV-2 Mpro through integrated virtual screening, DFT, and molecular dynamics simulations

Abstract The emergence of vaccine-resistant SARS-CoV-2 variants demands the development of novel antivirals targeting conserved viral proteins, like the main protease (M pro ). For expediting drug discovery, CADD approach of integrating different computational tools have been employed in drug candidate identification. Based on computational analysis, our study aimed to identify potential M pro inhibitors from natural product databases by combining virtual screening, DFT calculations and MD simulations. From 224,205 molecules from ZINC15 natural product database, N-[[(2R,3S,4R,5S)-5-(2-anilino-2-oxoethyl)-3,4-dihydroxyoxolan-2-yl]methyl]-4-methoxybenzamide (Lig14) was a prospective candidate against SARS-CoV-2 M pro . It exhibited binding energy of − 8.2 kcal/mol (Paxlovid with − 7.6 kcal/mol). It showed dipole moment of 12.70 D, HOMO/LUMO energy gap of 123.00 kJ/mol. MD simulations revealed a consistent contact area interference of ~ 360 Å 2 . The binding free energy (MM-GBSA) of − 31.82 ± 6.64 kcal/mol suggested in proper binding. Moreover, MD analysis also exhibited strong sub-diffusive motion (α = 0.49) with 35.2 Å confinement within the M pro active site, demonstrating sustained binding interactions characteristic of competitive inhibitors. The alchemical free energy perturbation calculation gave solvation free energy (ΔG solv ) in water (− 41.22 to − 40.70 kJ/mol) across four methods indicating solubility. The C145Y and π-sulfur bonding with C145 in G143S, G143D, G143N and E166K could disrupt catalytic dyad formation with H41, potentially compromising enzymatic function. Through an integrated computational approach, we identified Lig14 as a promising lead compound for the inhibition of SARS-CoV-2 M pro . While these in silico methods are highly credible for initial screening, their inherent limitations warrant subsequent experimental investigation to validate these findings.