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?:abstract
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The efforts towards developing a potential drug against the current global pandemic, COVID-19, has increased in the past few months Drug development strategies to target the RNA dependent RNA polymerase (RdRP) are being tried worldwide The gene encoding this protein, is known to be conserved amongst positive strand RNA viruses This enables an avenue to repurpose the drugs designed against earlier reported inhibitors of RdRP One such strong inhibitor is remdesivir which has been used against EBOLA infections The binding of remdesivir to RdRof SARS-CoV-2 has been studied using the classical molecular dynamics and ensemble docking approach A comparative study of the simulations of RdRin the apo and remdesivir-bound form revealed blocking of the template entry site in the presence of remdesivir The conformation changes leading to this event were captured through principal component analysis The conformational and thermodynamic parameters supported the experimental information available on the involvement of crucial arginine, serine and aspartate residues belonging to the conserved motifs in RdRfunctioning The catalytic site comprising of SER 759, AS760, and AS761 (SDD) was observed to form strong contacts with remdesivir The significantly strong interactions of these residues with remdesivir may infer the latter’s binding similar to the normal nucleotides thereby remaining unidentified by the exonuclease activity of RdRP The ensemble docking of remdesivir too, comprehended the involvement of similar residues in interaction with the inhibitor This information on crucial interactions between conserved residues of RdRwith remdesivir through iin-silicoapproaches may be useful in designing inhibitors b/b
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