The fidelity control of nucleotide selectivity in SARS-CoV-2 RdRp through amino acid mutations via molecular dynamics simulations

Abstract

The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 (CoV2-RdRp) is a promising antiviral drug target for nucleotide analogue drugs such as the remdesivir nucleotide analogue (RTP). In this study, based on the most recently identified new substrate-bound insertion state of CoV-2-RdRp with ATP or RTP, we used all-atom molecular dynamics simulations to investigate the nucleotide selectivity or fidelity control of CoV2-RdRp upon the effects of multiple-point amino acid mutations, namely, K551A/R553A/R555A and T687A/N691A/S759A. We found that RTP exhibited greater binding stability than the natural substrate ATP in both the pre-insertion and insertion states for both the wild-type and mutated CoV2-RdRp complexes. In addition, multiple-point amino acid mutation K551A/R553A/R555A mainly effected the stability of CoV2-RdRp in the pre-insertion state for ATP and RTP and had a greater influence on the stability of ATP than RTP. In addition, the multiple-point amino acid mutations T687A/N691A/S759A mainly effected the stability of CoV2-RdRp-RTP in both the pre-insertion state and insertion state through the interactions between RTP and residues T687/N691/S759. The binding interaction between RTP and residues S759/T687/N691 revealed that the binding of the 1′-cyano group of the RTP ribose within the pocket formed by key residues T687, N691, and S759 was a critical factor in the RTP insertion process.