The pandemic COVID-19 caused by SARS-CoV-2 has raised global health concerns. However, there is still no targeted medicine available for treatment of this disease. It is reported that 3CLpro plays an important role for the life cycle of virus and this protein has also been proved as an effective drug target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Medicinal plantsare important resource for drug discovery. Therefore, we executed large scale virtual screening on the herbal medicine library and hoped to find a potential drug againstthe main protease. As a result, we obtained three available compounds derived from Chinese herbal medicines through the docking and binding free energy calculation.Then 100 ns molecular dynamic (MD) were employed to uncover the potential mechanisms which is helpful for further drug optimization.

The figure_data was collected from the trajectory using the Cpptraj tool with the script ‘rmsd.in’, ‘rmsf.in’, ‘h_bond.in’ respectively. And the figures were drawn by the Orgin2020b software.

The molecular data came from the database (ligand.zip) and the binding affinity was measured by Autodock vina.

The trajectories of nine compounds with excellent binding affinity. The trajectories were produced by amber using the input file (md.in).

The binding free energies were calculated by the script: mmpbsa.in.