3.4. Molecular Modelling and Molecular Dynamic Procedures

Molecular modeling was carried out in the Schrodinger Maestro visualization environment using applications from the Schrodinger Small Molecule Drug Discovery Suite 2016-1 package [60]. Three-dimensional structures of the derivatives were obtained empirically in the LigPrep application using the OPLS3 force field [61]. All possible tautomeric forms of compounds, as well as various states of polar protons of molecules in the pH range of 7.0 ± 2.0 were taken into account. For calculations, the XRD model of human AChE with PDB ID 6O4W (resolution 2.35 Å) was chosen [62]. To model a possible mechanism of inhibition of the selected target, molecular docking of new compounds was performed at the binding site of donepezil of AChE in the Glide application [63]. The search area for docking was selected automatically, based on the size and physico-chemical properties of the inhibitor. The extra precision (XP) algorithm of docking was applied. Docking was performed in comparison with donepezil. The molecular structure of the inhibitor was obtained in the PubChem database and prepared in the LigPrep application. Non-covalent interactions of compounds in the binding site were visualized using Biovia Discovery Studio Client [64].

The molecular dynamic simulation was performed by using NAMD v. 2.14 [65]. Topology files for the ligands were generated by using SwissParam [66], and simulations were performed by using the CHARMM force field [67]. The protein–ligand complexes were solvated using a cubic box with periodic boundary conditions, with the minimal distance from the protein to the boundary being 20 Å. Water molecules, located in the protein pocket and taken into the account during docking procedure, were added as well into the systems to be simulated. The systems were neutralized by the addition of sodium or chlorine ions. Simulations were performed in conditions of 0.15 M NaCl solution. The systems were minimized, annealed up to 310 K, and equilibrated during 1 nanosecond in an NPT ensemble with the movable of the backbone being constrained. The following simulations were performed during 100 nanoseconds in an NVT ensemble at 310 K. System generations and calculations of the ligand root-mean-square deviations (RMSD) were performed in VMD [68]. Plots of changes in the RMSD of atomic coordinates over simulation time, obtained as a result of molecular dynamics research, are given in Supplementary Materials, Figure S1A–D.