Molecular Docking and Binding Energy Estimation

Grid boxes were centered at reported binding sites for each target, outer box edges were set to 10Å, thus resulting in a box volume of 10 × 10 × 10 ų for all the enzymes. Molecular docking was performed with the Glide software (Schrödinger, LLC, New York, NY, USA, 2020), using the standard precision (SP) mode, that uses hierarchical filters to find the best ligand poses in the protein binding site. The filters incorporate a systematic search of orientation space, positional and conformational, of the ligands before assessing the energetic interaction with the protein [34 (link)]. All docking were re-scored by binding free energy calculations using the MM-GBSA (molecular mechanics combined with the generalized Born surface area) method. The idea is to estimate more accurate binding free energies for ligand–protein complex and to get a more reliable ranking. The implementation of MM-GBSA was carried out with the Prime module from Schrodinger [32 (link)]. The PLIP server [35 (link)] were used to visualize interactions of ligand–protein complexes, and visualization was carried out with Pymol [36 ].