Molecular docking simulation

A total of 8 key genes which have good correlation with other genes, active components, and pathways including SRC, PIK3R1, TP53, HSP90AA1, MAPK8, JAK2, CASP3, and ERBB2 were included in the molecular docking simulation. The PDB-ID of these target genes were accessed from Protein Data Bank (PDB) database. In brief, Discovery studio software (version 4.5.0, Biovea Inc., Omaha, NE, USA) was employed, and the screened active components were prepared using “Prepare Ligands” module to obtain an effective three-dismensional conformation. After removing crystallographic water molecules, the “Prepare Protein” module was used to remove the polyconformation of target protein and to supplement the incomplete amino acid residues. Subsequently, molecular docking was performed in “LibDock” module, and LibDockScore was required to evaluate affinity of the target proteins and active components. The LibDockScore of the target protein and its corresponding prototype ligand was viewed as the threshold, and the components with higher scores were regarded as the active ones for interacting with this protein.