Molecular docking study of hinokiflavone with RNA dependent RNA polymerase (NSP12) of SARS-CoV-2
Molecular docking study of hinokiflavone with RNA dependent RNA polymerase (NSP12) of SARS-CoV-2
Rahman Abdizadeh,1Tooba Abdizadeh,2,*
1. Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran 2. Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
Introduction: SARS-CoV-2 is caused a major outbreak of coronavirus disease 2019 (COVID-19) and threatening global health safety [1]. COVID-19 is an enveloped virus having four different structural proteins, N (nucleocapsid), M (membrane), E (envelope) and S (spike), whereas, non-structural proteins (NSPs) comprise of RNA dependent RNA polymerase protein (RdRp) that is coded by NSP12 gene [2]. The Nsp12 RNA-dependent RNA polymerase (RdRp) constitutes highly conserved regions in non-structural proteins among coronaviruses which can be targeted [3]. In this work, we present molecular docking of the potential hinokiflavone compound that specifically target vital protein of Nsp12 RNA polymerase of SARS-CoV-2.
Methods: The molecular docking process was performed using Molecular Operation Environment (MOE) software to predict the mode of interaction between the best possible biological conformations of hinokiflavone in the active site of NSP12 protein. The 2D structure of hinokiflavone was prepared by Chem Draw ultra 8.0 software and converted into PDB format by Hyper Chem7 using AM1 semiempirical method. The hinokiflavone was docked into the active site of NSP12 (PDB ID: 6m71) by MOE software. The best pose of compound with the higher score was selected for ligand-target interaction analysis by the LigX module in MOE software.
Results: The docking result showed a high potency of hinokiflavone with binding energy of −11.59 kcal mol−1. According to docking result, hinokiflavone binds strongly with some of the amino acid residues in the active site of NSP12 such as Ala550, Ser549, Ser682, Glu811 and Lys551.
Conclusion: Molecular docking analysis of the hinokiflavone showed that this compound could be significant in treatment of COVID-19. However, these finding may be further supported by experimental data for its possible clinical application.