Screening nucleotide and nucleoside analogues as potential inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase by the molecular docking method for the treatment of COVID-19

Abstract

The COVID-19 pandemic triggering acute respiratory syndrome is a major global health concern. The SARSCoV-2 RNA-dependent RNA polymerase (RdRp) enzyme regulating viral replication has been evaluated as a potential therapeutic target for inhibition of the infection of SARS-CoV-2. In this study, we evaluated the ability of RNA-dependent RNA polymerase drug inhibitors by using molecular docking in silico model. Lipinski’s rule of Five was used to evaluate drug - like properties of potential compound. Pharmacokinetic parameters of potential compounds were assessed using the pkCSM tool. Based on previous publications, we have collected 100 compounds. The results exhibited that 18  compounds have RdRp inhibitory activity stronger than the remdesivir as reference compounds. The Lipinski’s rule of Five showed that 17 among 18 compounds had proprietary drug-likenesss. Compounds including novuridine, didanosine, sofosbuvir, puromycin, defibrotite, gemcitabine, and nikkomycins are the most negative energies and have pharmacokinetic good absorption, not metabolised in the liver, excreted by the kidney and may have hepatotoxicity properties. Therefore, it is necessary to conduct the in vitro and in vivo assays to develop these compounds into drugs for COVID-19 treatment.