Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations

In the present study, the binding free energy of some classical inhibitors (DMT, DNP, GNT, HUP, THA) with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation (FEP) method based on hybrid quantum mechanics and molecular mechanics (QM/MM) potentials. The results highlight the key role of the van der Waals interaction for the inhibition process, since the contribution of this term to the binding free energy is almost as decisive as the electrostatic one. The analysis of the geometrical parameters and the interaction energy per residue along the QM/MM molecular dynamics (MD) simulations highlights the most relevant interactions in the different AChE–ligand systems, showing that the charged residues with a more prominent contribution to the interaction energy are Asp72 and Glu199, although the relative importance depends on the molecular size of the ligand. A correlation between the binding free energy and the number of cation−π interactions present in the systems has been established, DMT being the most potent inhibitor, capable of forming four cation−π interactions. A layer of water molecules surrounding the inhibitors has been observed, which act as bridges along a network formed by the ligands and the residues of the gorge and also between different residues. Although several hydrogen bonds between ligands and AChE do appear, no significant values of BIEs have been recorded. This behavior can be accounted for by the special features of AChE, such as the presence of several subsites of different natures in the gorge or the existence of several water molecules that act as bridges in the electrostatic interactions.The authors acknowledge the financial support of the following agencies: Generalitat Valenciana for PrometeoII/2014/022 and ACOMP/2014/270, ACOMP/2015/1202, Ministerio de Economía y Competitividad, project CTQ2015-65207-P, Universitat Jaume I for projects P1·1B2013-40 and P1·1B2013-58.E.C.M.N. is grateful to the Generalitat Valencia for Santiago Grisolia program 2011/040. K.S. acknowledge the Polish Ministry of Science and Higher Education (“Iuventus Plus ” program project no. 0478/IP3/2015/73, 2015-2016). J.B.L.M. thanks CNPq for project CNPq 306945/2015-0. We also wish to thank the Servei d’Informàtica, Universitat Jaume I, for the generous allocation of computer time