Investigation of Dipicolinic Acid Isosteres for the Inhibition of Metallo‐β‐Lactamases

Abstract

New Delhi metallo‐β‐lactamase‐1 (NDM‐1) poses an immediate threat to our most effective and widely prescribed drugs, the β‐lactam‐containing class of antibiotics. There are no clinically relevant inhibitors to combat NDM‐1, despite significant efforts toward their development. Inhibitors that use a carboxylic acid motif for binding the ZnII ions in the active site of NDM‐1 make up a large portion of the >500 inhibitors reported to date. New and structurally diverse scaffolds for inhibitor development are needed urgently. Herein we report the isosteric replacement of one carboxylate group of dipicolinic acid (DPA) to obtain DPA isosteres with good inhibitory activity against NDM‐1 (and related metallo‐β‐lactamases, IMP‐1 and VIM‐2). It was determined that the choice of carboxylate isostere influences both the potency of NDM‐1 inhibition and the mechanism of action. Additionally, we show that an isostere with a metal‐stripping mechanism can be re‐engineered into an inhibitor that favors ternary complex formation. This work provides a roadmap for future isosteric replacement of routinely used metal binding motifs (i.e., carboxylic acids) for the generation of new entities in NDM‐1 inhibitor design and development.

Iminodiacetic Acid as a Novel Metal‐Binding Pharmacophore for New Delhi Metallo‐β‐lactamase Inhibitor Development

“…The N ‐donor atom in the MBPs were either a tertiary amine ( 1 ), secondary amine (IDA, 2–4 ), or aromatic amine ( 5 – 10 ). These MBPs were screened at a single concentration of 200 μM by using an enzymatic assay which monitored the NDM‐1 mediated hydrolysis of the substrate meropenem . Evaluation of this library revealed IDA to be the only MBP with a secondary amine N ‐donor atom to yield significant inhibition activity (48 %).…”

“…The purity of all compounds used in assays was determined to be ≥95 % by high‐performance liquid chromatography. Enzymatic assays were performed via monitoring the hydrolysis of substrate meropenem on Synergy H4 Hybrid Microplate Reader using 96‐well UV‐transparent microplates #3635 (Corning) according to previously published procedures . Thermal shift assays were performed on QuantStudio 3 real‐time PCR machines (Applied Biosystems) using 96‐well 0.2 mL optical MicroAmp thermocycler plates and SYPRO orange Thermal Shift dye (ThermoFisher).…”

“…Inhibition screening and IC 50 determination : A soluble truncation of NDM‐1 was over‐expressed and purified as described previously . IC 50 values were determined using 11 concentrations of compound that span the IC 50 value, and were assayed using meropenem as described previously except that total assay volumes were increased to 200 μL. Final DMSO concentrations (derived from compound stock solutions) were 1 % ( v/v ).…”

Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery

“…5 and S17 †). 51,58 Considering the library as an entirety, a hit rate (percent inhibition > 50%) of approximately $40% was achieved against PA N and NDM-1, while Hsp90 had a hit rate of $15% (Fig. S16 †).…”

MBLinhibitors.com, a Website Resource Offering Information and Expertise for the Continued Development of Metallo-β-Lactamase Inhibitors

“…The numbers of MBL inhibitors and publications describing MBL inhibitors have increased over the last decade ( Figures 1B and 1C). The four major approaches to identify MBL inhibitors include: (1) high-throughput screening (HTS) of large chemical libraries [18]; (2) fragment-based drug discovery (FBDD) [27,28]; (3) computer-based virtual screening [29,30]; and (4) screening of natural products [31]. The typical "hit" rates of these approaches are very low (<1%) [32].…”