| چکیده انگلیسی مقاله |
Spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic across the worldwide causing global effort for discovery of vaccine or drug. SARS-CoV-2 is a members of coronavirus large family which are enveloped, positive-sense and single-stranded RNA (+ssRNA) viruses that termed as coronavirus disease 2019 (COVID-19) [1]. The potential of 39 antiviral flavonoid for inhibition of main protease of 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. Firstly, the affinity based molecular docking approach was done using MGLTools (version 1.5.6) software. A grid box with 60 × 60 × 60 points was defined in the inhibitory site while the crystallography structure of maine protease of COVID-19 (6LU7) was taken from protein data bank (PDB). The predicted binding energy of flavonoids compare with co-crystalized inhibitor of protease for COVID-19 (N3) [2]. Then, the similarity screening was performed using Molegro Virtual Docker (MVD) against template N3 [2,3]. 6 hydrogen acceptor, 9 hydrogen donor, 9 steric criteria and 49 ring groups was considered as template group of native inhibitor N3 while a single atom may contribute to several centers in the several groups. The estimated binding energy proposed six flavonoids for COVID-19 therapy. The similarity screening 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 [4-7]. 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. |
