7PP0

Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 28 (JMV-7038)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.2 of the entry. See complete history


Literature

1,2,4-Triazole-3-Thione Analogues with a 2-Ethylbenzoic Acid at Position 4 as VIM-type Metallo-beta-Lactamase Inhibitors.

Verdirosa, F.Gavara, L.Sevaille, L.Tassone, G.Corsica, G.Legru, A.Feller, G.Chelini, G.Mercuri, P.S.Tanfoni, S.Sannio, F.Benvenuti, M.Cerboni, G.De Luca, F.Bouajila, E.Vo Hoang, Y.Licznar-Fajardo, P.Galleni, M.Pozzi, C.Mangani, S.Docquier, J.D.Hernandez, J.F.

(2022) ChemMedChem 17: e202100699-e202100699

  • DOI: https://doi.org/10.1002/cmdc.202100699
  • Primary Citation of Related Structures:  
    7PP0

  • PubMed Abstract: 

    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 K i 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.


  • Organizational Affiliation

    Dipartimento di Biotecnologie Mediche, Università di Siena, 53100, Siena, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2-like protein240Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.071α = 90
b = 78.128β = 90
c = 79.599γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description