A protein structure-guided covalent scaffold selectively targets the B1 and B2 subclass metallo-β-lactamases

Abstract

We report the discovery of ebselen-based dual covalent inhibitors of metallo-β-lactamases. Fluorescence and MALDI-TOF analysis suggested that the scaffold could bind to NDM-1 by forming a S-Se bond with Cys221 and an amide bond with Lys224 of NDM-1, thereby exhibiting selective inhibition and labeling against B1 and B2 subclass enzymes in vitro and in vivo.

Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism

“…The compound is now in clinical trials for different diseases (Meniere disease, tobramycin induced ototoxicity and to prevent acute noise induced hearing loss). Ebselen inhibited B1 and B2 enzymes with IC 50 values in the low-μM range but was not active against the B3 subclass ( Table 1 ) [ 164 ]. The inhibitor acts by forming a covalent bond between the Se atom and Cys221 coupled to dissociation of the Zn(II) ion at site 2 [ 202 ].…”

Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry

“…41 Here, native UVPD-MS revealed only the parent modication and not the degradation product, supporting the proposed inactivation mechanism and suggesting that the MS method may give less ambiguous results. Finally, native UVPD-MS of ebselen (3)-treated NDM-1 conrms a prior report that one zinc ion is ejected, 15,47 and now reveals the identity of the ejected zinc as Zn2 and provides direct evidence that Cys208 is the modied residue. Unexpectedly, we also detected partial denaturation of the C-terminus of the protein, which provides structural information that helps explain decreased thermostability and inclusion body formation upon Zn2 loss and ebselen treatment.…”

“…42 Our results are also consistent with prior studies that show an overall decrease in thermostability upon loss of Zn2 and the formation of putative inclusion bodies upon ebselen treatment, but provide more specic structural details about how the structure of Zn2 ligands, surrounding residues, and the C-terminal domain of the protein are impacted by Zn2 ejection. 15,47 Examining structural changes in NDM clinical variants associated with Zn(II) binding residues Given the capability of UVPD-MS to detect structural changes in NDM-1 upon Zn2 ejection by ebselen (3), we reasoned that this MS technique may also be useful to detect and better understand the structural implications of sequence differences introduced by clinical variants of NDM. Many of the NDM variants (currently NDM-1 through NDM-29) have increased thermostability and increased affinity for Zn2, presumably indicating that the bla NDM gene is evolving in response to the dual selective pressures of antibiotic treatment and zinc depravation by host innate immune responses.…”

Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-β-Lactamase 2 (VIM-2) Inhibitor

“…The SβLs inhibitors, such as clavulanic acid, tazobactam, sulbactam, vaborbactam, and avibactam have been used clinically [4,5]. Although a large number of MβL inhibitors have been reported, including thiols [6][7][8][9], carboxylic acids [10,11], rhodanine [12][13][14], cyclic boronates [15,16], and ebselen [17,18], there are no MβL inhibitors for available clinical purposes to date. Consequently, it is an urgent need to develop novel MβL inhibitors and to investigate their action mechanism.…”

“…The SβLs inhibitors, such as clavulanic acid, tazobactam, sulbactam, vaborbactam, and avibactam have been used clinically [4,5]. Although a large number of MβL inhibitors have been reported, including thiols [6-9], carboxylic acids [10,11], rhodanine [12][13][14], cyclic boronates [15,16], and ebselen [17,18], there are no MβL inhibitors for available clinical purposes to date. Consequently, it is an urgent need to develop novel MβL inhibitors and to investigate their action mechanism.VIM-2, a B1 subclass MβL [19], was initially discovered in P. aeruginosa, which showed a high prelevance and broad substrate spectrum, including penicillins, cephalosporins, and carbapenems [20], it therefore reflects a significant drug target for the treatment of antibiotic-resistant bacterial infection.…”