Molecular Docking

Molecular docking is a method for drug design by exploring the interaction and recognition between receptors and ligands. It is a theoretical simulation method that focuses on the study of intermolecular interactions and the prediction of their binding patterns and affinities. In recent years, molecular docking methods have become an important technique in the field of computer-aided drug research (Chen et al., 2020). AutoDock Vina is an open-source molecular docking program designed by the Scripps Research Institute for the computation of semi-flexible molecular docking. AutoDock Vina uses a complex gradient algorithm and multi-threaded techniques to make more accurate and faster predictions than AutoDock4. Semi-flexible docking means that the conformation of the ligand molecule can be changed according to the receptor molecule and is flexible, while the receptor molecule does not change and is rigid. The SDF structure of the active ingredient was imported into Chem3D 18.0 for optimization. The main protein targets selected were passed through the PDB database (https://www.rcsb.org/). Therefore, we searched the PDB database for the 3D structures of the ten potential targets of Shan Ci Gu in the treatment of NSCLC and found 3D structures for ten of the targets (EGFR, SRC, ESR1, ERBB2, MTOR, MCL1, MMP2, MMP9, KDR, and JAK2.). Then, the best protein crystal structure was selected [images with lower resolution (A) with observable ligands and a relatively intact structure were more desirable] and downloaded from the PDB database. The PDB files of the active compound and ligand molecules were imported into AutoDock Tools. We removed these target proteins’ water molecules, added polar hydrogen, and built active pockets active pockets, which were saved as PDBQT format files for later use. By adjusting target protein X-Y-Z coordinates and grid size, optimizing the position of protein structure-binding sites for molecular docking. AutoDock Vina was run to dock the treated active compound to the target protein ten times, and the lowest binding energy for each docking was taken as the final result. The complexes were then observed and plotted using PyMOL.