Effects of flavonoids on SARS–CoV–2 main protease (6W63): A molecular docking study

Abstract

Public health is still under attack by a worldwide pandemic caused by a coronavirus which is known to cause mainly respiratory and enteric disease in humans. Currently, still limited knowledge exists on the exact action mechanism and biology of SARS‒CoV‒2 although there are several effective vaccines and antiviral treatment. Besides, there is a considerable amount of 3D protein structures for SARS–CoV–2, related to its main protease resolved by X–ray diffraction. Here, we used molecular docking strategy to predict possible inhibitory activities of flavonoids on SARS–CoV–2 Mpro enzyme. For this, 800 flavonoids were retrieved from the ZINC database. Results suggested that avicularin was the lead flavonoid which docked to Mpro with the best binding energy. However, most of flavonoids showed H–bond interactions with Hie–41 and Cys–145 catalytic dyad, which were important residues for the catalytic activity of SARS–CoV–2 Mpro. Strong hydrogen bonding (2.36 Å) with Sγ atom of Cys145 residue was observed. This might suggest an initial formation of covalent bonding. Findings showed that selected flavonoids could be promising inhibitors of this enzyme and have the potential for future therapeutic drugs against COVID–19 after immediate experimental validation and clinical approvals.