Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme

BackgroundInsulin-degrading enzyme (IDE) is an allosteric Zn+2 metalloprotease involved in the degradation of many peptides including amyloid-β, and insulin that play key roles in Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM), respectively. Therefore, the use of therapeutic agents that regulate the activity of IDE would be a viable approach towards generating pharmaceutical treatments for these diseases. Crystal structure of IDE revealed that N-terminal has an exosite which is ∼30 Å away from the catalytic region and serves as a regulation site by orientation of the substrates of IDE to the catalytic site. It is possible to find small molecules that bind to the exosite of IDE and enhance its proteolytic activity towards different substrates.
Methodology/Principal FindingsIn this study, we applied structure based drug design method combined with experimental methods to discover four novel molecules that enhance the activity of human IDE. The novel compounds, designated as D3, D4, D6, and D10 enhanced IDE mediated proteolysis of substrate V, insulin and amyloid-β, while enhanced degradation profiles were obtained towards substrate V and insulin in the presence of D10 only.
Conclusion/SignificanceThis paper describes the first examples of a computer-aided discovery of IDE regulators, showing that in vitro and in vivo activation of this important enzyme with small molecules is possible.

背景
胰岛素降解酶（Insulin-degrading enzyme, IDE）是一种变构锌金属蛋白酶（allosteric Zn²+ metalloprotease），可降解包括淀粉样β肽（amyloid-β）、胰岛素在内的多种多肽，这两类底物分别在阿尔茨海默病（Alzheimer's disease, AD）与2型糖尿病（type 2 diabetes mellitus, T2DM）中发挥关键作用。因此，开发调控IDE活性的治疗制剂，将为上述两类疾病的药物研发提供可行路径。晶体结构解析结果显示，IDE的N端存在一个与催化区域相距约30埃的异位位点（exosite），该位点通过将IDE底物定向至催化区域，从而实现酶活性的调控。据此，可筛选结合IDE异位位点并增强其对不同底物蛋白水解活性的小分子化合物。

方法与主要结果
本研究将基于结构的药物设计（structure based drug design）方法与实验手段相结合，成功发现4种可增强人源IDE活性的新型小分子化合物。上述被命名为D3、D4、D6与D10的新型化合物，均可介导IDE对底物V、胰岛素及淀粉样β肽的蛋白水解过程；而仅在添加D10的情况下，底物V与胰岛素的降解效果得到显著提升。

结论与意义
本研究首次通过计算机辅助手段发现IDE活性调控剂，证实借助小分子化合物在体外（in vitro）与体内（in vivo）激活这一重要酶类具备可行性。