8HY6

Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding.

Yan, Y.H.Zhang, T.T.Li, R.Wang, S.Y.Wei, L.L.Wang, X.Y.Zhu, K.R.Li, S.R.Liang, G.Q.Yang, Z.B.Yang, L.L.Qin, S.Li, G.B.

(2023) J Med Chem 66: 13746-13767

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01189
  • Primary Citation of Related Structures:  
    8HX5, 8HXE, 8HXI, 8HXN, 8HXO, 8HXP, 8HXU, 8HXV, 8HXW, 8HY1, 8HY2, 8HY6, 8HYD, 8JAO

  • PubMed Abstract: 

    Metallo-β-lactamases (MBLs) are zinc-dependent enzymes capable of hydrolyzing all bicyclic β-lactam antibiotics, posing a great threat to public health. However, there are currently no clinically approved MBL inhibitors. Despite variations in their active sites, MBLs share a common catalytic mechanism with carbapenems, forming similar reaction species and hydrolysates. We here report the development of 2-aminothiazole-4-carboxylic acids (AtCs) as broad-spectrum MBL inhibitors by mimicking the anchor pharmacophore features of carbapenem hydrolysate binding. Several AtCs manifested potent activity against B1, B2, and B3 MBLs. Crystallographic analyses revealed a common binding mode of AtCs with B1, B2, and B3 MBLs, resembling binding observed in the MBL-carbapenem product complexes. AtCs restored Meropenem activity against MBL-producing isolates. In the murine sepsis model, AtCs exhibited favorable synergistic efficacy with Meropenem, along with acceptable pharmacokinetics and safety profiles. This work offers promising lead compounds and a structural basis for the development of potential drug candidates to combat MBL-mediated antimicrobial resistance.


  • Organizational Affiliation

    Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2
A, B
241Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5ZX (Subject of Investigation/LOI)
Query on 5ZX

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid
C12 H12 N2 O2 S
JARXXMAFINZHLY-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.313α = 90
b = 79.301β = 90
c = 133.698γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81874291
National Natural Science Foundation of China (NSFC)China82122065
National Natural Science Foundation of China (NSFC)China82073698

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release