Structural-based Computational Screening of Enzyme Inhibitors

The following crystal structures of the target enzymes were retrieved from the protein data bank (https://www.rcsb.org/ (accessed on 1 June 2022)): AChE (PDB ID: 6O52) [57 (link)], BChE (PDB ID: 6EQP) [58 (link)], tyrosinase (PDB ID: 6QXD) [59 (link)], amylase (PDB ID: 2QMK) [60 (link)], and glucosidase (PDB ID: 7KBJ) [61 (link)]. In the absence of crystal structures of human tyrosinase and glucosidase, human sequences (UniProt IDs P14679 and P0DUB6, respectively) were used to build their homology models using these PDB structures as templates. The models were built using the ITASSER web-based tool (https://zhanggroup.org/I-TASSER/, accessed on 1 June 2022) [62 (link)] and validated using the PROCHECK server (https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/, accessed on 1 June 2022) [63 (link)].
Each protein was protonated using the predicted pKa of the titratable residues at a physiological pH of 7.4 using an online server “Playmolecule proteinPrepare” (https://playmolecule.com/proteinPrepare/, accessed on 1 June 2022) [64 (link)]. The three-dimensional structure of each study ligand was retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/, accessed on 1 June 2022), and its geometry was optimized using Frog2 [65 (link)].
Using Autodock Tools program (https://autodock.scripts.edu, accessed on 10 June 2022) [66 (link)], docking grid files were generated using the coordinates of the cocrystal ligand in each crystal. The details of the docking procedure have been described in our previous studies [67 (link),68 (link)]. The binding energy of the ligand poses were calculated, and protein–ligand interactions were examined using the Biovia DS Visualizer (Dassault Systèmes Biovia Software Inc, 2012, San Diego, CA, USA).