A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases

Abstract

Carbapenem-resistant Enterobacteriaceae threaten human health, since carbapenems are last resort drugs for infections by such organisms. Metallo-β-lactamases (MβLs) are the main mechanism of resistance against carbapenems. Clinically approved inhibitors of MBLs are currently unavailable as design has been limited by the incomplete knowledge of their mechanism. Here, we report a biochemical and biophysical study of carbapenem hydrolysis by the B1 enzymes NDM-1 and BcII in the bi-Zn(II) form, the mono-Zn(II) B2 Sfh-I and the mono-Zn(II) B3 GOB-18. These MβLs hydrolyse carbapenems via a similar mechanism, with accumulation of the same anionic intermediates. We characterize the Michaelis complex formed by mono-Zn(II) enzymes, and we identify all intermediate species, enabling us to propose a chemical mechanism for mono and binuclear MβLs. This common mechanism open avenues for rationally designed inhibitors of all MβLs, notwithstanding the profound differences between these enzymes’ active site structure, β-lactam specificity and metal content.

Structural and biochemical analysis of the metallo‐β‐lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di‐metal scaffold for catalytic activity

“…However, other hydrolyzed imipenem (PDB IDs http://firstglance.jmol.org/fg.htm?mol=5YPI, http://firstglance.jmol.org/fg.htm?mol=5YPL, and http://firstglance.jmol.org/fg.htm?mol=5YPK), structures with NDM‐1 adopted the conformation of the hydrolyzed meropenem. Both pyrrolines of hydrolyzed imipenem and meropenem seem to adopt a similar Δ1β tautomer as the double bonds shift from C2‐C3 to C3‐N4 as evidenced by puckering of the pyrroline rings—the sulfanyl sulfur at position 2 is not in the C1‐C2‐C3 plane. This suggests that in the later catalytic steps, the hydrolytic intermediates are protonated from bulk solvent water molecule on the same side of the bridging water molecule and Zn1.…”

Approaches for the discovery of metallo‐β‐lactamase inhibitors: A review

“…Wherein, Zn1 is co‐ordinated to three conserved histidine residues (His116, His118, and His196) and bridged hydroxide tetrahedrons. The ligand group of Zn2 is different: In the B1 enzyme, it is provided by residues Asp120, Cys221, and His263 (DCH site, Figure b), while in B3 MBLs, it is involved in residues Asp120, His121, and His263 (DHH site, Figure c) (Lisa et al., ). The smaller subgroup B2 includes the single Zn 2+ enzyme and has the same ligand residues as the B1 enzyme, namely Asp120, Cys221, and His263, which only hydrolyzes carbapenem (Figure d) (Bebrone et al., ).…”

Synthesis and enzyme-based evaluation of analogues L-tyrosine thiol carboxylic acid inhibitor of metallo-β-lactamase IMP-1

“…The proposed mechanism in Figure 2 shows that how the activated water molecule starts the process of hydrolysis of b-lactam antibiotics and convert them to useless drugs. [20][21][22] One strategy to overcome this problem is to find a potent inhibitor that can attach to the active site of IMP-1 and prevent the hydrolysis of the b-lactam rings of antibiotics. Although numerous MBLs inhibitors have been reported in the literature, there is no clinically available inhibitor.…”