Docking study of naringin binding with COVID-19 main protease enzyme

Abstract

Recently the pandemic coronavirus disease 2019(COVID-19) has spread quickly all over the world caused by SAR-CoV2. In the present study, it has been used molecular docking to the binding affinity between COVID-19 main protease enzyme and flavonoids with evaluations based on docking scores calculated by AutoDock Vina. Results showed that naringin interacted with COVID-19 main protease, and it has the highest binding affinity than other flavonoids include quercetin, hesperetin, and naringenin. An important finding in this study is that naringin with poly hydroxyl groups can serve as an inhibitor of COVID-19 main protease bind to the pocket of the protein. It is shown that residues His163, Glu166, Asn142, His41and Gln189 participate in the hydrogen bonding interactions, the same as happened with decahydroisoquinoline as a novel structure as a protease inhibitor for SARS 3CL.On the other hand, some of the known protease inhibitors and anti-influenza drugs docked with COVID-19main protease, it has a low binding affinity than naringin.