The predominance of Alzheimer’s disease (AD) among the aged remains a global challenge. As such, the search for alternative and effective therapeutic options continuous unabated. Among the therapeutic targets explored over the years toward impeding the progression of AD is caspase-6 (Casp6), although selectively targeting Casp6 remains a challenge due to high homology with other members of the caspase family. Methyl 3-[(2,3-dihydro-1-benzofuran-2-yl formamido) methyl]-5-(furan-2-amido) benzoate (C13), a novel allosteric inhibitor, is reportedly shown to exhibit selective inhibition against mutant human Casp6 variants (E35K). However, structural and atomistic insights accounting for the reported inhibitory prowess of C13 remains unresolved. In this study, we seek to unravel the mechanistic selectivity of C13 coupled with the complementary effects of E35K single-nucleotide polymorphism (SNP) relative to Casp6 inhibition. Analyses of binding dynamics revealed that the variant Lysine-35 mediated consistent high-affinity interactions with C13 at the allosteric site, possibly forming the molecular basis of the selectivity of C13 as well as its high binding free energy as estimated. Analysis of residue interaction network around Glu35 and Lys35 revealed prominent residue network distortions in the mutant Casp6 conformation evidenced by a decrease in node degree, reduced number of edges and an increase short in path length relative to a more compact conformation in the wild system. The relatively higher binding free energy of C13 coupled with the stronger intermolecular interactions elicited in the mutant conformation further suggests that the mutation E35K probably favours the inhibitory activity of C13. Further analysis of atomistic changes showed increased C-α atom deviations consistent with structural disorientations in the mutant Casp6. Structural Insights provided could open up a novel paradigm of structure-based design of selective allosteric inhibition of Casp6 towards the treatment of neurodegenerative diseases.

中文翻译：

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一种新型变构抑制剂对 Caspase-6 的“多态性辅助”选择性靶向和抑制，可有效治疗阿尔茨海默氏病。

阿尔茨海默氏病 (AD) 在老年人中的发病率居高不下，这仍然是一个全球性挑战。因此，寻找替代和有效的治疗选择的努力有增无减。多年来探索的阻止 AD 进展的治疗靶点之一是 caspase-6 (Casp6)，尽管由于与 caspase 家族其他成员的高度同源性，选择性靶向 Casp6 仍然是一个挑战。3-[(2,3-dihydro-1-benzofuran-2-yl formamido) methyl]-5-(furan-2-amido) benzoate (C13) 甲酯是一种新型变构抑制剂，据报道显示出选择性抑制突变的人类 Casp6 变体 (E35K)。然而，解释所报告的 C13 抑制能力的结构和原子学见解仍未得到解决。在这项研究中，我们寻求揭示 C13 的机械选择性以及 E35K 单核苷酸多态性 (SNP) 相对于 Casp6 抑制的互补作用。结合动力学分析表明，变体 Lysine-35 在变构位点介导了与 C13 的一致高亲和力相互作用，可能形成了 C13 选择性及其估计的高结合自由能的分子基础。对 Glu35 和 Lys35 周围残基相互作用网络的分析揭示了突变体 Casp6 构象中显着的残基网络扭曲，这通过节点度的降低、边缘数量的减少以及相对于野生系统中更紧凑的构象的路径长度的增加得到证明。C13 相对较高的结合自由能与突变构象中引起的更强的分子间相互作用进一步表明突变 E35K 可能有利于 C13 的抑制活性。对原子变化的进一步分析表明，C-α 原子偏差增加与突变体 Casp6 中的结构定向障碍一致。提供的结构见解可以开辟一种新的基于结构的设计范例，该范例用于 Casp6 的选择性变构抑制以治疗神经退行性疾病。