3.4. Molecular Docking

All the molecular modeling studies were performed using Molecular Operating Environment (MOE, 2018) software. The partial charges were calculated automatically. All minimizations were performed with MOE until an RMSD gradient of 0.2534 kcal/molÅ with AMBER10 force field (a value below 2.0 kcal/molÅ indicates that the docking protocol was validated).

The X-ray crystallographic structure of MDM2 co-crystalized with Nutlin-3a (PDB ID:5C5A) was downloaded from the protein data bank available at the RCSB Protein Data Bank https://www.rcsb.org/. For each co-crystallized enzyme, water molecules and ligands that were not involved in the binding were removed. The Protonate 3D protocol in MOE with its default options was used to prepare the protein. The co-crystallized ligand (Nutlin-3a) was used to define the binding site for docking. The Triangle Matcher method was used, where 1000 poses were analyzed together with also redocking 1000 poses (to optimize docked structures) using the AMBER10 force field. From each obtained molecular docking result, five poses with the lowest energy were selected. Then one pose was selected that had the most interactions with amino acids in the MDM2 protein binding pocket. The choice of poses also took into account the number of interactions with the amino acids with which the known MDM2 (pdb: 5C5A) Nutlin-3a protein inhibitor binds. The docking scores, types of interactions and the bond lengths are shown in Table 3.