RNA-Dependent RNA Polymerase From SARS-CoV-2. Mechanism Of Reaction And Inhibition By Remdesivir

Abstract

We combine sequence analysis, molecular dynamics and hybrid quantum mechanics/molecular mechanics simulations to obtain the first description of the mechanism of reaction of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and of the inhibition of the enzyme by Remdesivir. Despite its evolutionary youth, the enzyme is highly optimized to have good fidelity in nucleotide incorporation and a good catalytic efficiency. Our simulations strongly suggest that Remdesivir triphosphate (the active form of drug) is incorporated into the nascent RNA replacing ATP, leading to a duplex RNA which is structurally very similar to an unmodified one. We did not detect any reason to explain the inhibitory activity of Remdesivir at the active site. Displacement of the nascent Remdesivir-containing RNA duplex along the exit channel of the enzyme can occur without evident steric clashes which would justify delayed inhibition. However, after the incorporation of three more nucleotides we found a hydrated Serine which is placed in a perfect arrangement to react through a Pinner's reaction with the nitrile group of Remdesivir. Kinetic barriers for crosslinking and polymerization are similar suggesting a competition between polymerization and inhibition. Analysis of SARS-CoV-2 mutational landscape and structural analysis of polymerases across different species support the proposed mechanism and suggest that virus has not explored yet resistance to Remdesivir inhibition.

Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type

“…Therefore, to further illustrate the effects of RdRp mutations, using MD simulations, we extrapolated the free binding energies (∆G) of RDV bound to A97V and P323L and compared them to WT. The ∆G for RDV bound to WT-RdRp was 17.30 kcal/mol, similar to results described by Andra et al, where they predicted binding affinity of 17.4 kcal/mol with at 298 K. However, the temperature and the MD simulation environment differed from our study [62]. Interestingly, RDV binding to A97V-RdRp showed a weaker affinity than to WT at 14.37 kcal/mol, although the RMSD dynamics and RMSF fluctuations showed similar patterns for both structures bound to RDV (Figures 3 and 4).…”

Expanding the boundaries of ligand–target modeling by exascale calculations

“…As a result, MiMiC may reach sub‐ns time scale with current HPC architectures 99 . This may pave the way to highly efficient HPC‐based hybrid simulations of pharmaceutically relevant enzymatic reactions, such as those performed on SARS‐COV‐2 proteins 37 …”

“…99 This may pave the way to highly efficient HPC-based hybrid simulations of pharmaceutically relevant enzymatic reactions, such as those performed on SARS-COV-2 proteins. 37 3.2 | Structure-based virtual screening…”

“…MD‐based ligand binding free energies 13,28–32 allow to predict potency and residence times of drugs 30,33–35 . Examples of the impact of MD in pharmacology include (but are by no means limited to) the development of the FDA‐approved HIV‐1 lifesaving drugs nelfinavir and raltegravir, 36 the ongoing SARS‐CoV‐2 research 37–40 and the development of a variety of anti‐cancer drugs 41,42 …”

“…MD-based ligand binding free energies 13,[28][29][30][31][32] allow to predict potency and residence times of drugs. 30,[33][34][35] Examples of the impact of MD in pharmacology include (but are by no means limited to) the development of the FDA-approved HIV-1 lifesaving drugs nelfinavir and raltegravir, 36 the ongoing SARS-CoV-2 research [37][38][39][40] and the development of a variety of anti-cancer drugs. 41,42 The development of supercomputers, combined with the power of parallel algorithms, can greatly boost the investigations of ligand/target complexes and CSBDD.…”