PMC:7441777 / 49529-51434 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"Keeping in mind that RdRp inhibitors play a crucial role to combat the SARS-CoV-2 infection, in this work, we performed a comprehensive molecular docking study with a library of hundred natural polyphenols with potential antiviral properties that may inhibit the SARS-CoV-2 RdRp and prevent the RNA replication. We shortlisted eight natural polyphenols having binding energy −7.0 kcal/mol or less for molecular dynamics simulation. Further, we performed 150 ns molecular dynamics simulation of RdRp/EGCG, RdRp/TF1, RdRp/TF2a, RdRp/TF2b, RdRp/TF3, RdRp/hesperidin, RdRp/myricetin, RdRp/quercetagetin, along with RdRp/remdesivir complex and computed the binding energies by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) scheme from last 50 ns trajectories. Our study suggests that the complex formation of the SARS-CoV-2 RdRp and eight natural polyphenols is favoured by the intermolecular van der Waals and electrostatic interactions as well as nonpolar solvation free energy. We have also investigated the hotspot residues controlling the receptor-ligand binding. Finally, molecular dynamics simulation and MM-PBSA study reveals that EGCG, TF2a, TF2b, and TF3 possess a better binding affinity than the control drug remdesivir against the SARS-CoV-2 RdRp. Further, we also looked at the ADME prediction, toxicity prediction, and target analysis to assess their druggability of the five compounds. The obtained results strongly suggest that EGCG, TF2a, TF2b, and TF3 have a stable binding affinity towards RdRp of the SARS-CoV-2 with favourable pharmacokinetic properties. These bioactive compounds exhibit broad ranges of therapeutic properties. Therefore, we believe that these four natural polyphenols can act as potential inhibitors for the SARS-CoV-2 RdRp. However, further in vitro and in vivo studies need to be carried out to validate their efficacy against SARS-CoV-2 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