Molecular Docking and Binding Free-Energy Calculation

Molecular docking calculations were performed with the Glide software, using the Glide Standard Precision (SP) mode, which uses a series of hierarchical filters to find the best ligand binding poses in a space within the protein binding site, previously mapped and constructed (grid box).⁷⁸ The filters included a systematic search approach, which samples the ligands for a positional, conformational, and orientational space before evaluating the energetic interactions with the protein.⁷⁹ Default docking parameters were used, and the top-10 docking solutions (according to the glide score) for each ligand were kept for the postdocking process.⁸⁰ In addition, the scope of the employed docking protocol was also assessed through redocking using the cocrystallized ligands, retrieved from the starting templates used for the homology model building. Thus, the cocrystallized ligands were deeply minimized and, subsequently, docked using the same Glide-based protocol. The differences between cocrystallized and redocked ligands were found to be reasonable (RMSD < 1), indicating that the employed docking protocol was suitable to discriminate binders. Finally, all docking solutions were rescored using MM-GBSA (molecular mechanics combined with the generalized Born surface area) to calculate the binding free energy for each of the studied compounds with higher precision. This rescoring allows a more reliable pose ranked. The implementation of MM-GBSA was done with the Prime module from Schrodinger.