Das Chandan Kumar, Nair Nisanth N
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
Phys Chem Chem Phys. 2017 May 24;19(20):13111-13121. doi: 10.1039/c6cp08769h.
Emergence of antibiotic resistance due to New Delhi metallo-β-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.
由于新德里金属β-内酰胺酶（NDM-1）细菌酶能够水解多种抗生素，其导致的抗生素耐药性的出现备受关注。目前正在努力获取水解机制的原子细节，以便开发针对NDM-1的抑制剂。特别是，不同抗生素家族的药物分子如何被NDM-1高效水解仍然不清楚。在此，我们报告了NDM-1催化头孢氨苄（一种头孢菌素家族药物）和美罗培南（一种碳青霉烯家族药物）水解的详细分子机制。本研究采用基于密度泛函理论（DFT）水平的混合量子力学/分子力学（QM/MM）方法进行分子动力学（MD）模拟，据此获得反应途径和相关自由能。我们发现，两种药物分子的开环步骤的机制和自由能垒相同，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的情况下发生烯丙基碳质子化，其中Lys211是质子供体，质子转移通过（仅）在开环中间结构形成的水链发生。基于自由能分布，讨论了药物水解的整体动力学。最后，我们表明所提出的机制和自由能分布可以解释各种实验观察结果。
