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Structural and Kinetic Studies on the Potent Inhibition of Metallo-β-Lactamases by 6-Phosphonomethylpyridine-2-Carboxylates

DOI: 10.1021/acs.biochem.7b01299 DOI Help

Authors: Philip Hinchliffe (University of Bristol) , Carol A. Tanner (University of Waterloo) , Anthony P. Krismanich (University of Waterloo) , Geneviève Labbé (University of Waterloo) , Valerie J. Goodfellow (University of Waterloo) , Laura Marrone (University of Waterloo) , Ahmed Desoky (University of Waterloo) , Karina Calvopina (University of Bristol) , Emily E. Whittle (University of Bristol) , Fanxing Zeng (University of Waterloo) , Matthew Avison (University of Bristol) , Niels C. Bols (University of Waterloo) , Stefan Siemann (Laurentian University) , James Spencer (University of Bristol) , Gary I. Dmitrienko (University of Waterloo)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Biochemistry

State: Published (Approved)
Published: February 2018
Diamond Proposal Number(s): 12342

Abstract: There are currently no clinically available inhibitors of metallo-β-lactamases (MBLs), enzymes which hydrolyze β-lactam antibiotics and confer resistance on Gram-negative bacteria. Here we present 6-phosphonomethylpyridine-2-carboxylates (PMPCs) as potent inhibitors of subclass B1 (IMP-1, VIM-2, NDM-1) and B3 (L1) MBLs. Inhibition followed a competitive, slow-binding model without an isomerization step (IC50 values 0.3 – 7.2 µM; Ki 0.03 – 1.5 µM). Minimum inhibitory concentration assays demonstrated potentiation of β-lactam (meropenem) activity against MBL-producing bacteria, including clinical isolates, at concentrations where eukaryotic cells remain viable. Crystal structures revealed unprecedented modes of inhibitor binding to B1 (IMP-1) and B3 (L1) MBLs. In IMP-1, binding does not replace the nucleophilic hydroxide and the PMPC carboxylate and pyridine nitrogen interact closely (2.3 and 2.7 Å, respectively) with the Zn2 ion of the binuclear metal site. The phosphonate group makes limited interactions, but is 2.6 Å from the nucleophilic hydroxide. Furthermore, the presence of a water molecule interacting with the PMPC phosphonate and pyridine N-C2 π-bond, as well as the nucleophilic hydroxide, suggests that the PMPC binds to the MBL active site as its hydrate. Binding is markedly different in L1, with the phosphonate displacing both Zn2, forming a monozinc enzyme, and the nucleophilic hydroxide, while also making multiple interactions with the protein main chain and Zn1. The carboxylate and pyridine nitrogen interact with Ser221/223, respectively (3 Å distance). The potency, low toxicity, cellular activity and amenability to further modification of PMPCs indicate these and similar phosphonate compounds can be further considered for future MBL inhibitor development.

Subject Areas: Biology and Bio-materials, Chemistry, Medicine

Instruments: I02-Macromolecular Crystallography