4.5. Ligand preparation

PubChem is a chemical substance and biological activity repository, composed of three databases, including substances, compounds, and bioassay databases, which provide useful comprehensive chemical information for drug discovery [41]. The ligand structures were taken from PubChem databases server in 2D or 3D sdf format (https://pubchem.ncbi.nlm.nih.gov/). Then the sdf files of 2D were converted to mol2 files using Chemdraw software. After that, all the sdf files of 3D and mol2 were converted to pdb files using Pymol software and carry out hydrogenation and water removal treatment. After optimization, these files were loaded into AutoDock software for the final preparation of ligands and the standard process was run to obtain the pdbqt file.