The Molecular dynamics (MD) simulations of the interaction of CCF0058981 with Mpros.

The main protease (Mpro) of SARS-CoV-2 is a pivotal target for antiviral drug development. The non-covalent inhibitor CCF0058981 shows high potency against Mpro, but its structural inhibition mechanism required further elucidation. This dataset supports our study reporting the first crystal structures of SARS-CoV-2 and SARS-CoV Mpro in complex with CCF0058981, and provides molecular dynamics (MD) simulation data to analyze the stability and interactions of CCF0058981 with SARS-CoV Mpro, SARS-CoV-2 Mpro, and the known SARS-CoV-2 Mpro mutants (M49I and V186F). MethodsAll-atom MD simulations were performed using GROMACS for a duration of 100 ns. The stability of the Mpro-CCF0058981 complex was assessed, and binding free energy was calculated using the MM-PBSA/GBSA methods. Data DescriptionThis repository contains the complete set of files to reproduce the molecular dynamics simulations and analyses. This includes:- The final simulated structure (PDB format)- The molecular dynamics trajectory files- All required GROMACS input parameter files (.mdp)- GROMACS output files from the simulation and subsequent analysis Potential for ReuseThis dataset is valuable for researchers investigating SARS-CoV-2 Mpro inhibition mechanisms, developing non-covalent inhibitors, or performing computational studies such as free energy calculations and molecular docking.