Potential of Inhibiting the Receptor Binding Mechanism of SARS-COV-2 using Phytochemicals contained in Paspanguwa Water Extract: Molecular Docking and Dynamic Studies

Abstract

This study is focused on the SARS-CoV-2 virus by in silico screening of phytochemicals contained in ‘Paspanguwa’ water extract, targeting ACE2 receptors using molecular docking. Phytochemicals of the five herbal ingredients contained in ‘Paspanguwa’ were extracted into water and were identified based on the literature reviews. Ligands geometries were optimized using Avogadro software and transformed to PDBQT format files by detecting torsion root using AutoDock Tools 1.5.6. SWISS-MODEL server was used to model the structure of the ACE2 receptor based on the UniProt ID Q9BYF1. The stereochemical quality of the protein model was assessed using SAVES v 6.0 and ProSA servers. Finally, potential ligands were docked to the ACE2 receptor protein by considering all variants of this virus and their interactions with the ACE2 receptor. The highest binding energy (BE) (-10.42 kcal/mol) was given by carpesterol phytochemical with allosteric site-2 and allosteric site-3 in the ACE2 receptor and this complex was subjected to molecular dynamic (MD) analysis using a CHARMM36 force field. According to the radius of gyration (Rg), root mean square deviation (RMSD) and root mean square fluctuation (RMSF) results, the studied protein-ligand complex was stable throughout the simulation time.