Validation of Interaction between Plant Compounds and Coronavirus Proteins Based on Virtual Screening and Molecular Docking Studies

Abstract

Since the spread of the COVID-19 pandemic, researchers have tried to find a compound that can potentially inhibit the replication of the SARS-CoV-2 virus. The present study aimed to validate the reaction of plant compounds and proteins of coronavirus based on virtual screening and molecular docking studies. In the present study, 90 various plant compounds and 8 types of coronavirus types were studied. The Auto Dock Vina 1.5.6 was used for the evaluation of the molecular bond, the PvMol was used for validation, and the Biovia Discovery Studio 4.5 was used for analysis. The best protein-ligand complex was chosen through the determination of the docking score or the highest docking affinity (the most negative ∆G of Gibbs free energy of docking). Among the 720 dockings performed, 18 plant compounds with coronavirus receptors have an energy above -10 and a more favorable RMSD value. Regarding the docking mode, the values under 1 angstrom are acceptable. According to the obtained validation results, 18 compounds have been expressed among which 8 showed the best RMSD results which is indicative of the validity of the data.

Keywords: Coronavirus, SARS-CoV-2, plant compounds, molecular bond, Auto Dock Vina.