Zuo Zhili, Gang Chen, Zou Hanjun, Mok Puah Chum, Zhu Weiliang, Chen Kaixian, Jiang Hualiang
Drug Discovery and Design Centre, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China.
Comput Biol Chem. 2007 Jun;31(3):186-95. doi: 10.1016/j.compbiolchem.2007.03.007. Epub 2007 Mar 30.
Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of other zymogens, is also partially active in cleaving APP. Hence, it is important to study on the mechanism of the zymogen's activation process. This study was to model the 3-D structure of the zymogen, followed by intensive molecular dynamics (MD) simulations to identify the most probable 3-D model and to study the dynamic structural behavior of the zymogen for understanding the effects of pro-segment on the function of the enzyme. The results revealed that the dropping in catalytic activity of the beta-secretase zymogen could be attributed to the occupation of the entrance of the catalytic site of the zymogen by its pro-segment. On the other hand, the partial catalytic activity of the zymogen could be explained by high fluctuation of the pro-segment in comparison with that of other zymogens, resulting in the occasionally exposure of the catalytic site for access its substrate APP. Indeed, steered MD (SMD) simulation revealed a weak pulling force at quasi-equilibrium state for the pro-segment of the zymogen leaving from the entrance, indicating that this swinging process could take place spontaneously. Furthermore, MM-PBSA calculation revealed a small change of free energy of 10.56 kal/mol between the initial and final states of the process of pro-segment swung outside the binding pocket of beta-secretase zymogen. These results not only account for the partial catalytic activity of beta-secretase zymogen, but also provide useful clues for discovering new potent ligands, as new type of drug leads for curing Alzheimer's disease, to prevent the pro-segment of the zymogen from leaving its catalytic site.
β-分泌酶是抗阿尔茨海默病抑制性药物的潜在靶点，因为它可切割淀粉样前体蛋白（APP），在大脑中形成不溶性淀粉样斑块和血管沉积物。β-分泌酶由其前体蛋白β-分泌酶酶原成熟而来，与大多数其他酶原不同的是，它在切割APP时也具有部分活性。因此，研究该酶原的激活过程机制很重要。本研究旨在对该酶原的三维结构进行建模，随后进行深入的分子动力学（MD）模拟，以确定最可能的三维模型，并研究该酶原的动态结构行为，从而了解前肽段对酶功能的影响。结果表明，β-分泌酶酶原催化活性的下降可归因于其前肽段占据了酶原催化位点的入口。另一方面，该酶原的部分催化活性可以通过与其他酶原相比前肽段的高波动性来解释，这导致催化位点偶尔暴露以接触其底物APP。事实上，引导分子动力学（SMD）模拟显示，在准平衡状态下，酶原的前肽段从入口离开时存在微弱的拉力，表明这种摆动过程可以自发发生。此外，MM-PBSA计算显示，在前肽段摆动到β-分泌酶酶原结合口袋外部的过程中，初始状态和最终状态之间的自由能变化很小，为10.56千卡/摩尔。这些结果不仅解释了β-分泌酶酶原的部分催化活性，还为发现新的有效配体提供了有用线索，作为治疗阿尔茨海默病的新型药物先导物，以防止酶原的前肽段离开其催化位点。
