Influence of SARS-CoV-2 variants’ spike glycoprotein and RNA-dependent RNA polymerase (nsp12) mutations on remdesivir docking residues

Abstract

Rapid emergence and evolution of novel SARS-CoV-2 variants has raised concerns about their potential impact on efficiency of currently available vaccines. Among the most significant target mutations in the virus are those of the spike glycoprotein. Remdesivir, which inhibits the polymerase activity of the RNAdependent RNA polymerase RdRp, is the only medicine approved by FDA for treatment of COVID-19 (nsp12). The docking features of the flexible ligand (remdesivir) with the stiff receptors was investigated in the present study (S protein and RdRp interaction). In various studies, the spike glycoprotein and RdRp mutations were found to have a significant influence upon viral behaviour and, as a result, affect human health. The docking position of remdesivir with the S and RdRp proteins was shown to be unaffected by mutations in the missing loops. The remdesivir can only bind the B and C chains of S protein. Some mutations can be transferred between variations, without changing the type of amino acid, such as K417N, L452R, N501Y, D614G, T716I, and S982A.