Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function.

ABSTRACT: In order to evaluate the interactions between a potential drug candidate like inhibitor N3 and the residues in substrate binding site of SARS-CoV-2 main protease ( Mpro ), we used molecular docking and dynamics simulations. The structural features describing the degrees of folding states of Mpro formed by beta-barrels and alpha-helices were analyzed by means of root mean square deviation, root mean square fluctuation, radius of gyration, residue velocity, H-bonding, dihedral angle distributions and radial distribution function. All of the residues forming ligand binding domain (LBD) of Mpro lie within the allowed region of the dihedral angle distributions as observed from the equilibrating best pose of Mpro -N3 system. Sharp peaks of radial distribution function (RDF) for H-bonding atom pa

SUBMITTER: Lamichhane TR 

PROVIDER: S-EPMC8525048 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature