In Silico Substrate-Binding Profiling for SARS-CoV-2 Main Protease (M^pro) Using Hexapeptide Substrates.

ABSTRACT: The SARS-CoV-2 main protease (M^pro) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of M^pro (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of enco

SUBMITTER: Zabo S 

PROVIDER: S-EPMC10385622 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature