Crystal Structures of Metallo-β-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester

Abstract

The emergence and rapid spread of carbapenemresistant pathogens producing metallo-β-lactamases such as IMP-1 and NDM-1 have been of great concern in the global clinical setting. The X-ray crystal structures of IMP-1 from Serratia marcescens and its single mutant, D120E, in complexes with citrate were determined at resolutions of 2.00 and 1.85 Å, respectively. Two crystal structures indicate that a single mutation at position 120 caused a structural change around Zn1, where the geometry changes from a tetrahedron in the native IMP-1 to a square pyramid in D120E. Based on these two complex structures, the authors synthesized citrate monobenzyl ester 1 to evaluate the structural requirement for the inhibitory activity against IMP-1 and compared the inhibitory activities with nonsubstituted citrate. The introduction of a benzyl group into citrate enhanced the inhibitory activity in comparison to citrate (IC 50 > 5 mM).

Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-β-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution

“…When superposed, the two structures closely match, with an rmsd of 0.25 Å for the Cα atoms. Significantly, the conformation of loop 1 in both IMP-1 and IMP-6 takes the closed form, which is analogous to the closed forms found in the crystal structures of IMP-1–inhibitor and −citrate complexes. ,,− …”

Structure and Mechanism-Guided Design of Dual Serine/Metallo-Carbapenemase Inhibitors

“…However, DBO and VAB do not inhibit any metallo-carbapenemases. Compared with the clinical success of SβL inhibitors, there are no equivalent inhibitors in the clinic for MβLs, − which can hydrolyze almost all β-lactams including carbapenems and the first-generation β-lactamase inhibitors clavulanate, tazobactam, and sulbactam. ,, The continuous emergence and dissemination of MDR Gram-negative pathogens with acquired serine and metallo-carbapenemase genes has led to an urgent need for the development of broad-spectrum, dual-action inhibitors to conquer carbapenem resistance. ,, …”

Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-β-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding

“…PDB codes: 8HX5 (VIM-2:15), 8HXE (L1:18), 8HXI (L1: 19), 8HXN (Sfh-I:24), 8HXO (VIM-2:32), 8HXP (VIM-2:34), 8HXU (VIM-2:35), 8HXV (VIM-2:36), 8HXW (VIM-2:37), 8HY1 (VIM-2:39), 8HY2 (VIM-2:41), 8HY6 (NDM-1:41), 8JAO (IMP-1:41), 8HYD (VIM-2:45).…”

“…1 H NMR (400 MHz, DMSO-d 6 ) δ: 7.14−7.09 (m, 4H), 6.91 (s, 2H), 4.29 (s, 2H), 2.51 (t, J = 7.6 Hz, 2H), 1.60−1.51 (m, 2H), 0.87 (t, J = 7.6 Hz, 3H) ppm. 13 2-Amino-5-(4-isopropylbenzyl)thiazole-4-carboxylic Acid (19). The title compound was prepared in a manner similar to that for compound 10, 22% yield for four steps, 98.7% HPLC purity.…”

“…MBLs are zinc-dependent metalloenzymes, which utilize Zn­(II)-bound hydroxyl for β-lactam hydrolysis . Various inhibitor chemotypes have been reported to target MBLs, − which can be broadly classified as type I–V inhibitors based on the proposed mechanisms of MBL-mediated β-lactam hydrolysis (Figure ). The potent and broad-spectrum MBL inhibitors typically achieve their efficacy by mimicking key features of complexes involved in β-lactam binding and reactions, albeit at different phases of catalysis. , Currently, three drug candidates, namely VNRX-5133 (taniborbactam), QPX7728 (xeruborbactam), and QPX7831, which are dual MBL/SBL inhibitors, are undergoing evaluation in clinical trials.…”