Moe software version 2008

Molecular docking was performed using Molecular Operating Environment (MOE) software version 2008.10 (Chemical Computing Group, Montreal, Canada) according to reported process^{28 (link)}. The X-ray crystallographic complex of PDGFRA (PDB ID: 5GRN), c-KIT (PDB ID: 1T46) and CSF1R (PDB ID: 3LCO) with respective bound ligand were used as templates. All water molecules in PDB files were removed and hydrogen atoms were subsequently added to each protein structure. The 3-D structure of E5 was built using the builder interface of MOE program and energy minimized using MMFF94x force field. Then, E5 was docked into the active site of each protein and the best 5 poses of the molecules were retained and scored.

Molecular modeling calculations and docking studies were performed using Molecular Operating Environment (MOE) software version 2008.10 (Chemical Computing Group, Montreal, Canada)43 (link). The X-ray crystallographic structures of AChE (PDB code 1EVE) and Aβ (1–42) (PDB code PDB 1IYT) were obtained from the Protein Data Bank. All water molecules in PDB files were removed and hydrogen atoms were subsequently added to the protein. The compound 5l was built using the builder interface of the MOE program and energy minimized using MMFF94x force field. Then the 5l was docked into the active site of the protein by the “Triangle Matcher” method, which generated poses by aligning the ligand triplet of atoms with the triplet of alpha spheres in cavities of tight atomic packing. The Dock scoring in MOE software was done using ASE scoring function and force field was selected as the refinement method. The best 10 poses of molecules were retained and scored. After docking, the geometry of resulting complex was studied using the MOE’s pose viewer utility.

Molecular operating environment (MOE) software, version 2008.10 (Chemical Computing Group, Montreal, Canada) was used to perform in silico docking simulations. Default settings in the MOE docking simulation tool were used for docking using the London Gibbs free energy scoring function. Before docking simulations were performed, ligands and proteins were prepared, and the docking method was validated.