College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China.
Research Center for Material Genome Engineering, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
J Mol Model. 2020 Mar 7;26(4):71. doi: 10.1007/s00894-020-4330-y.
Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of O-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
金属β-内酰胺酶（MβLs）能够水解和失活含有β-内酰胺的抗生素，这是导致细菌感染治疗中药物耐药性的主要机制。由于迄今为止缺乏临床批准的抑制剂，这已成为全球关注的问题。变色沙雷氏菌（Serratia marcescents）来源的 SMB-1 是一种新型 B3 亚类 MβL，几乎可以灭活所有含有β-内酰胺的抗生素，例如头孢菌素和碳青霉烯类抗生素。它代表了新一轮令人担忧的细菌耐药性。在这项工作中，使用组合量子力学和分子力学方法模拟了 SMB-1 与氨苄西林复合物的米氏模型。与其他二锌 MβLs 类似，模拟了一个 Zn 桥连的氢氧根离子作为 D120 辅助水解反应的亲核试剂。D120 的质子化会导致 O-Zn2 配位键的丢失，而 C3 羧酸根向下移动成为 Zn2 的新配体。初始β-内酰胺开环反应导致保守的氮阴离子中间物形成，该中间物在生成的氮阴离子和 Zn2 之间形成新的配位键。计算得到β-内酰胺开环反应第一步的反应自由能垒为 19.2 kcal/mol。在反应过程中，Q157 充当了假定的“氧阴离子空穴”，而不是 L1 酶中的 Zn1，这通过 Q157A 定点突变模拟得到了证实。我们的理论研究为 SMB-1 金属β-内酰胺酶的底物结合和催化机制提供了一些见解。
