2.7. Docking Studies

Molecular docking studies were carried out for simulating the interaction of WO₃ NPs and WO₃-AAs into three important cancer developing proteins, namely, Bcl-2, p53, and E2F2. The crystal structures of the three aforementioned proteins were downloaded from the protein data bank (PDB) website with ID 2W3L, 3ZME, and 5TUU, respectively. Molecular operating environment (MOE) software was used to conduct molecular docking. The downloaded protein was prepared by 3D protonation, deletion of water molecules and unwanted peptide chains, and energy minimization. The pocket was obtained by isolating the molecular surface around the binding site (within 4.5 Å near the ligand atom). Validation was carried out by redocking the crystallized ligand. Rigid protocol docking (default protocol) was selected. The docking protocol is considered valid when the root mean square deviation (RMSD) of the docking pose compared to the co-crystal ligand position is about 1.5 Å or less. To prepare WO₃ NPs and modified WO₃-AAs for docking, the structure of the studied compound was built on MOE. 3D protonation was selected, then energy minimization (force field: MMFF94x) was applied. The prepared compounds were added to the created database, which was then selected for docking according to the default protocol in which the bond rotation method generated ligand conformations. The conformers are placed on the site with the Triangle matcher method [51].