Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation.

ABSTRACT: We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (M^pro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in M^pro. The frequently accessed sites on M^pro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex s

SUBMITTER: Komatsu TS 

PROVIDER: S-EPMC7550358 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature