Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil.
J Chem Inf Model. 2020 Jul 27;60(7):3463-3471. doi: 10.1021/acs.jcim.9b01073. Epub 2020 Mar 5.
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. 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 -- 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.
多奈哌齐是一种第二代乙酰胆碱酯酶（AChE）抑制剂，用于治疗阿尔茨海默病（AD）。AChE 在神经肌肉接头和胆碱能脑突触中通过将乙酰胆碱水解为乙酸和胆碱对神经传递很重要。数据支持多奈哌齐是 AChE 的可逆、混合竞争性和非竞争性抑制剂。实验事实表明，在低温下解析的 X 射线模型中，除了分子观点之外，还存在一种更复杂的结合机制，该模型显示了多奈哌齐在酶活性部位的独特结合模式。为了阐明抑制剂的这种混合竞争性和非竞争性性质背后的机制，我们应用分子动力学（MD）模拟和对接以及自由能计算来研究无底物和有底物状态下酶的微观细节和多奈哌齐结合的能量学。室温下的液相 MD 模拟表明，AChE 在“开放”和“关闭”构象之间转变，以控制对活性部位和配体结合的可及性。如对接和自由能计算所示，多奈哌齐的结合涉及到它在酶的活性部位的可逆轴向位移和重定向，这是由水分子辅助的。多奈哌齐通过分别采用 -- 取向，同样可以很好地结合主门阴离子结合位点 PAS、酰口袋和催化位点 CAS，而不管底物的占有率如何——该反应过程的整体稳定性取决于酶的共占据，酶的无底物状态更有利于其优先占据。总之，我们的研究结果支持了多奈哌齐抑制 AChE 的一种生理相关的机制，该机制涉及抑制剂活性的分子起源处的多稳态相互作用模式。
