Tools version 4

The molecular docking approach was employed to analyze the interactions between the bioactive compounds of Tualang honey and the hub genes identified in the study. This computational method is commonly utilized in drug discovery as it enables predictions of binding modes and affinities between receptors and ligands. The crystal structures of the six hub genes—SRC (PDB ID: 1O43), PIK3R1 (PDB ID: 315R), PIK3CA (PDB ID: 6PYS), EGFR (PDB ID: 8A27), PTPN11 (PDB ID: 3B40), and AKT1 (PDB ID: IUNQ) were obtained from the RCSB Protein Data Bank (https://www.rcsb.org/, accessed on 13 February 2023) [38 (link)]. The 3D structure of the Tualang honey compounds (catechin, ethyl oleate, fisetin, hesperitin, kaempferol, and luteolin) was retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/, accessed on 14 February 2023) [39 (link)]. The compounds served as the ligands and the hub genes as the receptors. The receptors were prepared in Biovia Discovery Studio 2021 [40 ] by removing water molecules and existing ligand. The binding conformation between the ligand and receptor was predicted by AutoDockTools Version 4.2 (http://autodock.scripps.edu/, accessed on 16 February 2023) [41 (link)], and the binding energy, which is an outcome of molecular docking, was used to assess the potential of the ligand–receptor binding (typically, ≤−5 kcal/mol). Finally, the visualization of molecular interactions between the proteins and ligands was performed using Discovery Studio Visualizer 2021.