Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature

Area of Science:

• Biochemistry
• Computational Biology
• Neuroscience

Background:

• Donepezil is a key acetylcholinesterase (AChE) inhibitor used to treat Alzheimer's disease (AD).
• AChE plays a crucial role in neurotransmission by hydrolyzing acetylcholine.
• Existing X-ray models suggest a unique binding mode for donepezil, but its mixed inhibition mechanism requires further clarification.

Purpose of the Study:

• To elucidate the molecular mechanism behind the mixed competitive and noncompetitive inhibition of AChE by donepezil.
• To investigate the binding energetics and microscopic details of donepezil association using computational methods.
• To understand how enzyme conformation and substrate occupancy influence donepezil binding.

Main Methods:

• Molecular dynamics (MD) simulations at room temperature.
• Docking and free-energy calculations.
• Analysis of enzyme-ligand interactions in substrate-free and substrate-bound states.

Main Results:

• AChE exhibits dynamic transitions between 'open' and 'closed' conformations, regulating active site accessibility.
• Donepezil binding involves reversible axial displacement and reorientation within the active site, facilitated by water molecules.
• Donepezil interacts with multiple sites (PAS, acyl pocket, catalytic site) with varying orientations, showing preferential stability in the substrate-free enzyme state.

Conclusions:

• The study reveals a complex, physiologically relevant mechanism of AChE inhibition by donepezil.
• Multistable interaction modes at the molecular level underlie donepezil's therapeutic activity.
• Computational simulations provide crucial insights into the dynamic binding of donepezil to AChE.