7PP0 image
Deposition Date 2021-09-10
Release Date 2022-03-16
Last Version Date 2024-01-31
Entry Detail
PDB ID:
7PP0
Keywords:
Title:
Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 28 (JMV-7038)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.73 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Metallo-beta-lactamase VIM-2-like protein
Chain IDs:A
Chain Length:240
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Primary Citation
1,2,4-Triazole-3-Thione Analogues with a 2-Ethylbenzoic Acid at Position 4 as VIM-type Metallo-beta-Lactamase Inhibitors.
Chemmedchem 17 e202100699 e202100699 (2022)
PMID: 35050549 DOI: 10.1002/cmdc.202100699

Abstact

Metallo-β-lactamases (MBLs) are increasingly involved as a major mechanism of resistance to carbapenems in relevant opportunistic Gram-negative pathogens. Unfortunately, clinically efficient MBL inhibitors still represent an unmet medical need. We previously reported several series of compounds based on the 1,2,4-triazole-3-thione scaffold. In particular, Schiff bases formed between diversely 5-substituted-4-amino compounds and 2-carboxybenzaldehyde were broad-spectrum inhibitors of VIM-type, NDM-1 and IMP-1 MBLs. Unfortunately, these compounds were unable to restore antibiotic susceptibility of MBL-producing bacteria, probably because of poor penetration and/or susceptibility to hydrolysis. To improve their microbiological activity, we synthesized and characterized compounds where the hydrazone-like bond of the Schiff base analogues was replaced by a stable ethyl link. This small change resulted in a narrower inhibition spectrum, as all compounds were poorly or not inhibiting NDM-1 and IMP-1, but showed a significantly better activity on VIM-type enzymes, with Ki values in the μM to sub-μM range. The resolution of the crystallographic structure of VIM-2 in complex with one of the best inhibitors yielded valuable information about their binding mode. Interestingly, several compounds were shown to restore the β-lactam susceptibility of VIM-type-producing E. coli laboratory strains and also of K. pneumoniae clinical isolates. In addition, selected compounds were found to be devoid of toxicity toward human cancer cells at high concentration, thus showing promising safety.

Legend

Protein

Chemical

Disease

Primary Citation of related structures