Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature

Abstract

Donepezil is a second generation acetylcholinesterase (AChE) inhibitor for treatment of Alzheimer’s disease (AD). AChE is important for neurotransmission at neuromuscular junctions and cholinergic brain synapses by hydrolyzing acetylcholine into acetate and choline. In vitro data support that donepezil is a reversible, mixed competitive and noncompetitive inhibitor of AChE. The experimental fact then suggests a more complex binding mechanism beyond the molecular view in X-ray models resolved at cryogenic temperatures that show a unique binding mode of donepezil in the active site of the enzyme. Aiming at clarifying the mechanism behind that mixed competitive and noncompetitive nature of the inhibitor, we have applied molecular dynamics (MD) simulations and docking and free-energy calculations to investigate microscopic details and energetics of donepezil association for conditions of substrate-free and -bound states of the enzyme. Liquid-phase MD simulation at room temperature shows AChE transits between “open” and “closed” conformations to control accessibility to the active site and ligand binding. As shown by docking and free-energy calculations, association of donepezil involves its reversible axial displacement and reorientation in the active site of the enzyme, assisted by water molecules. Donepezil binds equally well the main-door anionic binding site PAS, the acyl pocket, and the catalytic site CAS by respectively adopting outward–inward–inward orientations regardless of substrate occupancy–the overall stability of that reaction process depends however on co-occupancy of the enzyme being preferential for its substrate-free state. All together, our findings support a physiologically relevant mechanism of AChE inhibition by donepezil involving multistable interactions modes at the molecular origin of the inhibitor’s activity.

In Silico Design of Dual-Binding Site Anti-Cholinesterase Phytochemical Heterodimers as Treatment Options for Alzheimer’s Disease

“…The heterodimers were compared directly with the binding affinities of the synthetic drug, donepezil, since donepezil is a potent FDA approved ChEIs and is also capable of binding both the PAS and CS of AChE [3,4,26,52]. However, a limitation of this molecular docking approach is that it only provides a snapshot of the ligand to protein interaction, whereas in nature, this is a dynamic process.…”

“…The peripheral anionic site (PAS) has a gorge-like entrance with several aromatic amino acids that mediate ACh trapping and lead down to the catalytic site (CS), at which a catalytic triad of Ser200, Glu327, and His440 mediate substrate hydrolysis [23][24][25]. ChEIs, such as donepezil, can inhibit AChE activity via transitory binding to the PAS and/or the catalytic site of the enzyme [25,26]. Potential control of AChE activity via dual inhibitory binding site occupancy has led to the generation of hybrid ligands separated by suitable linkers or spacers.…”

Neuroprotective Effects of Cholinesterase Inhibitors: Current Scenario in Therapies for Alzheimer’s Disease and Future Perspectives

“…Donepezil is widely prescribed for mild, moderate, and severe AD and has been considered a first-line treatment against this disease since 1996 [ 38, 39 ]. It is a reversible, mixed inhibitor that exhibits competitive and non-competitive AChE activity [ 40, 41 ]. Donepezil is capable of simultaneously inhibiting both CAS and PAS sites of AChE [ 40 ].…”

“…It is a reversible, mixed inhibitor that exhibits competitive and non-competitive AChE activity [ 40, 41 ]. Donepezil is capable of simultaneously inhibiting both CAS and PAS sites of AChE [ 40 ]. It has a selective activity for AChE, but only a modest effect on BuChE, unlike other compounds such as rivastigmine and tacrine [ 41 ].…”

Pd-Catalyzed Direct Modification of an Anti-Alzheimer’s Disease Drug: Synthesis and Biological Evaluation of α-Aryl Donepezil Analogues

“…5 Up to now, only five drugs have been approved by FDA for the treatment of AD, including tacrine, rivastigmine, galantamine, donepezil, and menantine (Figure 1). Donepezil is a second-generation specific reversible central acetylcholinesterase (AChE) inhibitor 6,7 for AD therapy with many side effects, such as nausea, vomiting, diarrhea, fatigue, muscle cramps, lack of appetite, and so forth. Thus, the development of donepezil derivatives with high AChE inhibitory activity and low cell toxicity has drawn immense attention.…”