Impact of Remdesivir Incorporation Along the Primer Strand on SARS-CoV-2 RNA-dependent RNA polymerase

Remdesivir was the first antiviral drug that received emergency use authorization from the United States Food and Drug Administration and is now formally approved to treat COVID-19. Remdesivir is a nucleotide analogue that targets the RNA-dependent RNA polymerase (RdRp) of coronaviruses, including SARS-CoV-2. The solution of multiple RdRp structures has been one of the main axes of research in the race against the SARS-CoV-2 virus. Several hypotheses of the mechanism of inhibition of RdRp by remdesivir have been proposed, although open questions remain. This work uses molecular dynamics (MD) simulations to explore the impact of remdesivir and two analogues as incoming nucleotides, and of up to four incorporations of remdesivir along the primer strand on RdRp. The simulation results suggest that the overall structure and dynamical behavior of RdRp is destabilized by remdesivir and the two analogues in the incoming position. The incorporation of remdesivir along the primer strand im- pacts specific non-bonded interactions between the nascent RNA and the polymerase subunit, as well as overall dynamical networks on RdRp. The strongest impact on the structure and dynamics are observed after three incorporations, when remdesivir is located at position -A3, in agreement with previously reported experimental and computational results. Our results provide atomic-level detail on the role played by remdesivir on the disruption of RNA synthesis by RdRp, and the main drivers of these disruptions.