Study the Inhibitory Effect of some Antiviral Flavonoids against Main Protease of COVID-19 by Molecular Docking

Document Type : Full Paper


Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran



The potential of 39 antiviral flavonoid for inhibition of main protease of coronavirus disease 2019 (COVID-19) was investigated using molecular docking approach. The studied flavonoids were protease inhibitor of human immunodeficiency viruses (HIV), severe acute respiratory syndrome (SARS), hepatitis C virus (HCV) or Ebola virus. The both affinity and similarity based molecular docking approach was applied to improve the reliability of proposition. The estimated binding energy proposed six flavonoids for COVID-19 therapy. Then the similarity based molecular docking arranged the candidate flavonoids respectively as Quercetin 3-O-(2¢¢-galloyl)-R-Larabinopyranoside from Acer okamotoanum, Tomentin D and Tomentin A from Paulownia tomentosa, Corylifol A and psoralidin from Psoralea and Ladanein from Lamiaceae. The values of similarity score for these phytochemicals respectively was -340, -225, -221, -213, -176 and -152 while the estimated binding energy was -9.52, -7.74, -7.67, -8.09, -8.58 and -8.02 (kcal/mol). Also, ligand map probing of native and six flavonoids was shown Phe 140, Gly 143, His 164, Glu 166, Gln 189, Thr 190, Thr 26, Cys 145 and Asn 142 amino acids of active site of main protease of Covid-19 commonly was in the hydrogen or steric interactions with these inhibitors. This study outstanding the inhibitor effect of some antiviral non-nutrient plant compounds against main protease of COVID-19.