Molecular Docking for Target Identification

Based on the results of the PPI network and drug–compound–target gene network, we selected the top 3 ranked targets and components for molecular docking. The PubChem database (https://pubchem.ncbi.nlm.nih.gov/) provides components’ names, 2D structures, molecular formulas, and molecular weight. The top 3 ligands (2D format) were downloaded from the database, then the structures of ligands were optimized using the Chem 3D software and Auto Dock Tools 1.5.7 software, and then prepared for molecular docking. Protein Sequence Database (https://www.rcsb.org) provides proteins’ 3D structure, the structures of the core targets were downloaded, and then, excess chains, ions, and water molecules were removed by the PyMOL software. The Auto Dock Tools 1.5.7 software was utilized to add hydrogen atoms and convert their format for docking. Afterwards, the ligands and receptors were imported in sequence in the AutoDock Tools 1.5.7 software, grid box parameters were configured and saved, and molecular docking was accomplished through the AutoDock Vina software. Finally, the PyMOL software was utilized to display the molecular docking results. It is generally accepted that a docking score less than or equal to -5.0 kcal/mol indicates a strong affinity between the docked compound and the target.^{[19 (link)]}