Alzheimer’s disease (AD) is an irreversible and progressive brain disorder that slowly destroys memory and cognitive skills. The current treatment of AD mainly focused on the restoring of ACh levels through acetylcholinesterase (AChE) inhibition. Peptides are a unique class of pharmaceutical compounds that have privilege over small molecules, especially in the realm of protein–protein interactions and G protein-coupled receptor (GPCR) inhibitors. We applied a rational structure-based virtual design approach to discover new peptidic inhibitors of AChE. In this regard, conformational space in the fasciculin II (Fas) and AChE complex was evaluated utilizing MD simulation, principal component analysis and clustering to figure out possible interactions of Fas and AChE. Assessment of Fas–AChE interactions by visual evaluation and alanine scanning led to the design of 10 peptides. The highest scored peptide (p2) was selected and synthesized using SPPS. Based on Ellman's test, the inhibitory activity of p2 against AChE was 51.2 ± 8.1 µM. The kinetics study of the enzyme inhibition in accompany with molecular modeling results revealed that p2 was a mixed-type reversible inhibitor of AChE. The DNRMLRTTRY peptide was considerable inhibitor of AChE. Peptides have the merit of being big enough to inhibit PPI and GPCR class B with a wide binding site. But possible peptidic chemical space is too large to be evaluated by the classical peptide synthesis methods. In the present contribution, we introduced a rational in silico peptide design approach that led to the considerable peptidic inhibitor of AChE.

阿尔茨海默氏病（AD）是一种不可逆的进行性脑部疾病，会逐渐破坏记忆力和认知能力。目前对AD的治疗主要集中在通过乙酰胆碱酯酶（AChE）抑制来恢复ACh水平。肽是一类独特的药物化合物，在小分子方面具有优势，尤其是在蛋白质-蛋白质相互作用和G蛋白偶联受体（GPCR）抑制剂领域。我们应用了基于合理结构的虚拟设计方法来发现新的AChE肽抑制剂。在这方面，利用MD模拟，主成分分析和聚类分析法确定Fasculin II（Fas）和AChE复合物中的构象空间，以找出Fas和AChE可能的相互作用。通过视觉评估和丙氨酸扫描评估Fas–AChE相互作用，从而设计了10种肽。得分最高的多肽（选择p2）并使用SPPS合成。根据Ellman检验，p2对AChE的抑制活性为51.2±8.1 µM。伴随分子模型结果对酶抑制作用的动力学研究表明，p2是AChE的混合型可逆抑制剂。DNRMLRTTRY肽是AChE的重要抑制剂。肽具有足够大的优点，可以抑制具有宽结合位点的PPI和GPCR B类。但是可能的肽化学空间太大，无法通过经典的肽合成方法进行评估。在目前的贡献中，我们介绍了一种合理的计算机模拟肽设计方法，该方法导致了相当多的AChE肽抑制剂。