Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

Abstract

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature

“…In spite of the fact that other physiological structural aspects of the AChE function including isoforms, oligomerization states, and post-translational modifications were not addressed here, we may conclude that multistable modes of interaction at room temperature must underlie the physiologically relevant mechanism of AChE inhibition by donepezil at the level of the reactive gorge of the enzyme. That conclusion is highly consistent with a recent metadynamics study by Ganguly and co-workers showing that donepezil must bind the ∼20 Å long enzymatic cavity of AChE at multiple spots with favorable and comparable free-energies either at inward or outward orientations and, further supported by independent structural studies showing multisubsites, at different residue compositions along the enzyme gorge that ensure equally important van der Waals and electrostatic free-energy contributions for the inhibition process of AChE by a variety of inhibitors. , …”

“…That conclusion is highly consistent with a recent metadynamics study by Ganguly and co-workers 18 showing that donepezil must bind the ∼20 Å long enzymatic cavity of AChE at multiple spots with favorable and comparable free-energies either at inward or outward orientations and, further supported by independent structural studies showing multisubsites, at different residue compositions along the enzyme gorge that ensure equally important van der Waals and electrostatic free-energy contributions for the inhibition process of AChE by a variety of inhibitors. 10,11 We thus believe the results are of broad interest as they provide an important clarification about the reversible and mixed inhibition mechanism of AChE by donepezil. Particularly insightful for guiding novel experiments for further characterization of donepezil action, we anticipate our study must inspire rational design of new AChE's inhibitors in general.…”

“…In this regard, as successfully applied to other systems, , the combination of docking calculations against an ensemble of equilibrium structures of the enzyme to handle protein flexibility and MM/PBSA calculations to estimate solvation energies is critical for technical aspects of the adopted approach to minimize such drawbacks. It is worth emphasizing that MM/PBSA estimates ⟨ W *­( r , ω )⟩ in Table overestimate binding energies as computed either from QM/MM-based free energy perturbation , or umbrella sampling for a variety of AChE inhibitors, including huperzine A, tacrine, galantimine, phenserine, rivastigmine, dichlorvos, soman, huprines, and Cordyceps derivatives. Correction of the estimated potential of mean force W *­( r , ω ) by means of a scaling factor α in order to reproduce the experimental equilibrium dissociation constant is therefore another critical aspect of the applied methodology devised to minimize such error, allowing for proper comparison of free energy stabilities of basins 1, 2, and 3–indeed, scaled free-energies ⟨ W *­( r , ω )⟩ in Table are comparable to independent binding estimates for donepezil in the range of one or two dozens of kcal per mol, as determined by means of metadynamics using more accurate force fields .…”

“…9 Consistent with a mechanism large in complexity, recent QM/MM based free energy calculations show equally important van der Waals and electrostatic free-energy contributions for the inhibition process of AChE by a variety of inhibitors, implying that the enzyme features a large gorge with ligand subsites at different residue compositions. 10,11 The experimental facts then suggest a more complex binding mechanism beyond the molecular view in X-ray structures 7 resolved at cryogenic temperatures that show a unique binding mode of donepezil in the active site of the enzyme. More specifically, by revealing bound donepezil at the catalytic site CAS of the enzyme, the very same binding region for acetylcholine, the available X-ray models are consistent with the competitive nature of the ligand in the sense that it competes for the catalytic site blocking substrate reaction.…”