Investigation of Antiviral Drugs with Direct Effect on RNA Polymerases and Simulation of Their Binding to SARS-CoV-2 (COVID-19) RNA-Dependent RNA Polymerase by Molecular Docking Method

Abstract

Background: Following the outbreak of SARS-CoV (Severe Acute Respiratory Syndrome coronavirus) in 2002 and the outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, we are facing the rapid spread of SARS-CoV-2 (COVID-19) in the world in 2019. Several outbreaks of the virus and its widespread prevalence have necessitated the design of drugs and vaccines in the shortest possible time. This is not possible except by using bioinformatics tools. In this study, the binding of drugs affecting RNA Polymerases to SARS-CoV-2 RNA-dependent RNA polymerase structure was simulated by molecular docking method. Methods: The structure of drugs used to treat COVID-19 and their similar structures from the drugbank database received. It was then subjected to molecular docking by AutoDock Vina software, and the structure with the most negative affinity was docked to reconsider its connection location. Finally, the amino acids involved in binding were investigated by Discovery Studio software. Results: In the test with in silico status, the Rifabutin had the best performance for SARS-CoV-2 RNA-dependent RNA polymerase binding, and the binding site identified for this drug was different from the binding site shown in the PDB database. Conclusion: Further research on the Rifabutin could be the key to discovering new drugs for COVID-19.