A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations.
A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations.
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DOI：
10.1371/journal.pone.0032397
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Cavalli A
中科院分区：
文献类型：
--
作者：
Lodola A;Branduardi D;De Vivo M;Capoferri L;Mor M;Piomelli D;Cavalli A
N末端亲核试剂（Ntn）水解酶是专门用于酰胺键水解断裂的酶超家族。尽管这个家族的几个成员正在成为癌症，炎症和疼痛的创新药物靶标，但它们催化酰胺水解的过程仍然知之甚少。特别是，半胱氨酸Ntn-水解酶的催化反应从未从机理的角度进行过研究。在本研究中，我们使用自由能模拟的量子力学/分子力学框架，以确定由原型半胱氨酸Ntn-水解酶，共轭胆汁酸水解酶（CBAH）催化的酰胺水解的反应机理。计算分析，这是在水中得到证实，并使用不同的CBAH突变体，揭示了椅子样过渡态的存在，这可能是一个具体的功能之一的Ntn-水解酶的催化循环。我们的研究结果为Ntn介导的水解提供了新的见解，并为创造治疗上有用的抑制剂提出了可能的策略。
The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.
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