Computational and in vitro evaluation of sumac-derived ©Rutan compounds towards Sars-CoV-2 Mpro inhibition.

Abstract

The emergence of the SARS-CoV-2 virus caused the COVID-19 outbreak leading to a global pandemic. Natural substances started being screened for their antiviral activity by computational and in-vitro techniques. Here, we evaluated the anti-SARS-CoV-2 main protease (M^pro) efficacy of ^©Rutan, which contains five polyphenols (R5, R6, R7, R7', and R8) extracted from sumac Rhus coriaria L. We obtained three fractions after large-scale purification: fraction 1 held R5, fraction 2 consisted of R6, R7 and R7', and fraction 3 held R8. In vitro results showed their anti-M^pro potential: IC₅₀ values of R5 and R8 made 42.52 µM and 5.48 µM, respectively. Further, we studied M^pro-polyphenol interactions by in silico analysis to understand mechanistic extrapolation of Rutan binding nature with M^pro. We extensively incorporated a series of in silico techniques. Initially, for the docking protocol validation, redocking of the co-crystal ligand GC-376* to the binding pocket of M^pro was carried out. The representative docked complexes were subjected to long-range 500 ns molecular dynamics simulations. The binding free energy (BFE in kcal/mol) of components were calculated as follows: R8 (-104.636) > R6 (-93.754) > R7' (-92.113) > R5 (-81.115) > R7 (-67.243). In silico results of R5 and R8 correspond with their in vitro outcomes. Furthermore, the per-residue decomposition analysis showed C145, E166, and Q189 residues as the hotspot residues for components contributing to maximum BFE energies. All five components effectively interact with the catalytic pocket of M^pro and form stable complexes that allow the estimation of their inhibitory activity. Assay kit analyses revealed that Rutan and its components have effective anti-SARS-CoV-2 M^pro inhibitory activity.