Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1

作者：Hongmin Zhang, Guixing Ma, Yifan Zhu, Lingxiao Zeng, Ashfaq Ahmad, Changzhi Wang, Bo Pang, Huiyan Fang, Liqing Zhao, Quan Hao · 发表于：Antimicrobial Agents and Chemotherapy · 年份：2018 · DOI：10.1128/aac.01579-18 · 被引用次数：84 · 研究领域：Antibiotic Resistance in Bacteria、Tuberculosis Research and Epidemiology、Computational Drug Discovery Methods

β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all β-lactam antibiotics, has rapidly spread all over the world and poses serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs toward different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products and by using biochemical and biophysical studies, site-directed mutagenesis, and molecular dynamics computation. The structural studies reveal the consistency of the active-site conformations in NDM-1/product complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active-site fluctuation, with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active-site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism s...