Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1

Thomas, Charles Swain; Cheng, Zishuo; Yang, Kundi; Hellwarth, Elle; Yurkiewicz, Cole J.; Baxter, Faith M.; Fullington, Sarah; Klinsky, Spencer A.; Otto, Jen L.; Chen, Allie Y.; Cohen, Seth M.; Crowder, Michael W.

doi:10.1016/j.jinorgbio.2020.111123

Cited by 23 publications

(23 citation statements)

References 41 publications

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“…). [29] The techniques used and results reported in the Crowder group's study with VIM-2 are complimentary to the methods we use and support well the findings here described in our comparative analysis of MBL inhibitors towards the NDM and IMP classes.…”

Section: Introductionsupporting

confidence: 78%

Mechanistic Investigations of Metallo-β-Lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition

Wade¹,

Tehrani²,

Brüchle³

et al. 2020

Preprint

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Metallo-β-lactamases (MBLs) are zinc-dependent bacterial resistance enzymes that can inactivate essentially all classes of β-lactam antibiotics. Infections due to multi-drug-resistant pathogens that express MBLs are difficult to treat and carry high mortality rates. At present there are no clinically approved MBL inhibitors underscoring the urgent need for pharmaceutical agents capable of counteracting the action of these enzymes. In order to develop effective MBL inhibitors it is essential to understand their inhibitory mechanisms. We here describe a comprehensive mechanistic study on a panel of structurally distinct MBL inhibitors drawn from the diverse collection of compounds reported to date in both the scientific and patent literature. Specifically, we determined the half-maximal inhibitory concentration value (IC50) for each inhibitor against purified NDM-1 and IMP-1 revealing clear differences in inhibitory potency among the compounds tested. Additional mechanistic insights into metal binding were also obtained by means of isothermal titration calorimetry (ITC) which was used to assess the affinity of the MBL inhibitors for Zn2+, Ca2+ and Mg2+. These investigations revealed clear differences in metal binding among the MBL inhibitors evaluated. In addition, we directly compared the ability of these compounds to resensitize an NDM-1-expressing E. coli strain to the last resort carbapenem antibiotic meropenem. Notably, indole carboxylate 12 proved to be the most potent inhibitor tested in its ability to synergize with meropenem and with IC50 values in the low nanomolar range against both enzymes. Interestingly, while compound 12 was found the most active MBL inhibitor, it exhibited no appreciable binding to any of the metals tested. These findings provide valuable insights into differences in mechanism and potency for the various classes of MBL inhibitors reported to date.

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Section: Introductionsupporting

confidence: 78%

Mechanistic Investigations of Metallo-β-Lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition

Wade¹,

Tehrani²,

Brüchle³

et al. 2020

Preprint

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“…As recently shown by our group and others, MBLs in the B1 class (NDM, VIM, and IMP) exhibit different inhibitory profiles when tested against known MBL inhibitors in vitro . 24 , 25 Clearly, the development of selective and broad-spectrum MBL inhibitors is not an easy task. In the case of ANT431 and its related analogues, for instance, there is a promising inhibitory activity against NDM-1 (IC 50 = 2.67 μM) and VIM-2 (IC 50 = 6.7 μM).…”

Section: Results and Discussionmentioning

confidence: 99%

Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases

et al. 2021

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In an attempt to exploit the hydrolytic mechanism by which β-lactamases degrade cephalosporins, we designed and synthesized a series of novel cephalosporin prodrugs aimed at delivering thiol-based inhibitors of metallo-β-lactamases (MBLs) in a spatiotemporally controlled fashion. While enzymatic hydrolysis of the β-lactam ring was observed, it was not accompanied by inhibitor release. Nonetheless, the cephalosporin prodrugs, especially thiomandelic acid conjugate ( 8 ), demonstrated potent inhibition of IMP-type MBLs. In addition, conjugate 8 was also found to greatly reduce the minimum inhibitory concentration of meropenem against IMP-producing bacteria. The results of kinetic experiments indicate that these prodrugs inhibit IMP-type MBLs by acting as slowly turned-over substrates. Structure–activity relationship studies revealed that both phenyl and carboxyl moieties of 8 are crucial for its potency. Furthermore, modeling studies indicate that productive interactions of the thiomandelic acid moiety of 8 with Trp28 within the IMP active site may contribute to its potency and selectivity.

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“…DPA has been used as alternative to EDTA to identify MBLs. ,, A thorough analysis of the inhibitory effect of different picolinic acid in MBLs by Galleni and co-workers was able to trap pyridine-2,4-dicarboxylic acid bound to the Zn(II) ion in CphA in a bidentate fashion . DPA was also identified as an MBL inhibitor in a fragment-based drug discovery approach. − A series of DPA derivatives were synthesized with inhibitory potencies ranging from μM to nM. The inclusion of additional metal binding groups did not necessarily result in better inhibition.…”

Section: Mbl Inhibitorsmentioning

confidence: 99%

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design

2021

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Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.

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Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1

Cited by 23 publications

References 41 publications

Mechanistic Investigations of Metallo-β-Lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition

Mechanistic Investigations of Metallo-β-Lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition

Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-β-Lactamases

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design

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