Abstract

β-amyloid precursor protein cleaving enzyme1 (BACE1) has prominently been an important drug design target implicated in Alzheimer’s disease pathway. The failure rate of most of the already tested drugs at different clinical phases remains a major concern. Recently, AM-6494 was reported as a novel potent, highly selective, and orally effective inhibitor against BACE1. AM-6494 displayed no alteration of skin/fur colour in animal studies, an adverse effect common to previous BACE1 inhibitors. However, the atomistic molecular mechanism of BACE1 inhibition by AM-6494 remains unclear. To elucidate the binding mechanism of AM-6494 relative to umibecestat (CNP-520) as well as the structural changes when bound to BACE1, advanced computational techniques such as accelerated MD simulation and principal component analysis have been utilised. The results demonstrated higher binding affinity of AM-6494 at BACE1 with van der Waals as dominant energy contributor compared to umibecestat. Conformational monitoring of the β-hairpin flap covering the active site revealed an effective flap closure when bound with AM-6494 compared to CNP-520, which predominantly alternates between semi-open and closed conformations. The observed effective flap closure of AM-6494 explains its higher inhibitory power towards BACE1. Besides the catalytic Asp32/228 dyad, Tyr14, Leu30, Tyr71 and Gly230 represent critical residues in the potency of these inhibitors at BACE1 binding interface. The findings highlighted in this research provide a basis to explain AM-6494 high inhibitory potency and might assist in the design of new inhibitors with improved selectivity and potency for BACE1.

摘要

β-淀粉样蛋白前体蛋白裂解酶1（BACE1）一直是阿尔茨海默氏病疾病途径中重要的药物设计目标。大多数已经测试的药物在不同临床阶段的失败率仍然是一个主要问题。最近，据报道AM-6494是一种针对BACE1的新型有效，高选择性和口服有效的抑制剂。在动物研究中，AM-6494的皮肤/皮毛颜色没有变化，这是以前BACE1抑制剂常见的不良反应。但是，尚不清楚AM-6494抑制BACE1的原子分子机理。为了阐明AM-6494相对于umibecestat（CNP-520）的结合机制以及与BACE1结合时的结构变化，已利用了先进的计算技术，例如加速MD模拟和主成分分析。结果表明，与umibecestat相比，AM-6494在BACE1上具有更高的结合亲和力，其中范德华斯是主要的能量贡献者。覆盖活性位点的β-发夹状襟翼的构象监测显示，与CNP-520相比，与AM-6494结合时，襟翼闭合是有效的，后者主要在半开放和闭合构象之间交替。观察到的AM-6494的有效襟翼闭合说明了其对BACE1的更高抑制能力。除催化性Asp32 / 228 dyad外，Tyr14，Leu30，Tyr71和Gly230还在BACE1结合界面的这些抑制剂的效能中代表了关键残基。这项研究中突出的发现为解释AM-6494的高抑制效力提供了基础，并可能有助于设计对BACE1具有更高选择性和效力的新型抑制剂。