Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent
Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent
复制标题
DOI：
10.1039/c6cp08769h
复制
发表时间：
2017-05-28
影响因子：
3.3
通讯作者：
Nair, Nisanth N.
中科院分区：
文献类型：
--
作者：
Das, Chandan Kumar;Nair, Nisanth N.
由于新德里金属- β -内酰胺酶（NDM-1）细菌酶具有水解多种抗生素的能力，因此引起了人们的高度关注。为了开发NDM-1的抑制剂，人们正在努力获得水解机制的原子细节。特别是，不同抗生素家族的药物分子如何被NDM-1高效水解仍然是一个谜。本文报道了NDM-1催化水解头孢菌素家族药物头孢氨苄和碳青霉烯家族药物美罗培南的详细分子机制。本研究在密度泛函数理论（DFT）水平上采用混合量子力学/分子力学（QM/MM）方法进行分子动力学（MD）模拟，在此基础上获得了反应路径和相关的自由能。我们发现两种药物分子开环步骤的机制和自由能势垒是相同的，而随后的质子化步骤不同。特别是，我们观察到质子化步骤的机制取决于药物分子的R2基团。我们的模拟表明，在头孢氨苄药物分子中，烯丙基碳质子化发生在Lys211为质子供体的情况下，质子转移通过（仅）在开环的中间结构上形成的水链发生。基于自由能谱，讨论了药物水解的总体动力学。最后，我们证明了所提出的机制和自由能分布可以解释各种实验观察结果。
Emergence of antibiotic resistance due to New Delhi metallo-beta-lactamase (NDM-1) bacterial enzymes is of great concern due to their ability to hydrolyze a wide range of antibiotics. There are ongoing efforts to obtain the atomistic details of the hydrolysis mechanism in order to develop inhibitors for NDM-1. In particular, it remains elusive how drug molecules of different families of antibiotics are hydrolyzed by NDM-1 in an efficient manner. Here we report the detailed molecular mechanism of NDM-1 catalyzed hydrolysis of cephalexin, a cephalosporin family drug, and meropenem, a carbapenem family drug. This study employs molecular dynamics (MD) simulations using hybrid quantum mechanical/molecular mechanical (QM/MM) methods at the density functional theory (DFT) level, based on which reaction pathways and the associated free energies are obtained. We find that the mechanism and the free energy barrier for the ring-opening step are the same for both the drug molecules, while the subsequent protonation step differs. In particular, we observe that the mechanism of the protonation step depends on the R2 group of the drug molecule. Our simulations show that allylic carbon protonation occurs in the case of the cephalexin drug molecule where Lys211 is the proton donor, and the proton transfer occurs via a water chain formed (only) at the ring-opened intermediate structure. Based on the free energy profiles, the overall kinetics of drug hydrolysis is discussed. Finally, we show that the proposed mechanisms and free energy profiles could explain various experimental observations.