2.5. Molecular docking with Autodock Vina

The molecular docking was performed using Autodock Vina software (Trott and Olson, 2010). The X-ray structure of SARS-CoV-2 PL^Pro WT (RCSB ID: 6W9C), as well as the modeled 3D structures with indicated mutations by the 3D DynaMut protein modeling tool, were utilized in this study. The protein structure was cleaned by removing co-crystallized water molecules and saved in PDB format using BIOVIA Discovery Studio Visualizer 2019. The three-dimensional structure of GRL0617 was retrieved from PubChem (PubChem CID: 24941262) in PDB format. Before docking, the polar hydrogen atoms of protein and ligand were added by Autodock Tools (Huey et al., 2012) and structures were then saved in PDBQT format. The auto-grid tool was used for the determination of the docking grid map with 1.00 Å spacing and box dimensions of 20 X  × 20 Y × 20 Z Å and centers of 43.186 X  × -8.55 Y × 7.144 Z Å. The interactions between the SARS-CoV-2 PL^Pro and the inhibitor GRL0617 were visualized and analyzed by PyMOL (DeLano, 2002) and UCSF Chimera 1.14 (Pettersen et al., 2004).