3.4. Docking Protocol

Molecular docking was performed for the most potent inhibitors using the Genetic Optimization for Ligand Docking (GOLD) package 5.4.1 [30,31,32]. The atomic coordinates of target inhibitors were obtained directly from previously reported X-ray crystallography data [10], except for ligand 2m, for which coordinates were constructed in the ChemBio3D workspace and were energy-minimized by MM2 force fields. The crystal structures of AChE (PDB ID: 1ACJ [33]) and BChE (PDB ID: 4BDS [34]) were isolated from Pteronarcys californica and Homo sapiens, respectively, with tacrine obtained from the Protein Data Bank ligand-protein binding space, and the conformational flexibility of the ligand inside the protein was explored by the Genetic Algorithm (GA). A spherical binding site with a radius of 15 Å was used, which lay around the binding site of the tacrine covering both the catalytic anionic and peripheral anionic sites. Runs were carried out (100 GA), and the top 100 ranked docking poses were scored using the Piecewise Linear Potential (PLP) scoring function. Default values were used for all other parameters. The intermolecular interactions of the best-scored pose of each ligand were analyzed and illustrated using Discovery Studio 4.5 software (Discovery Studio, v4.5.0.15071; San Diego, CA, USA, Accelrys Inc.; 2015).