4B1F

Design of Inhibitors of Helicobacter pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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This is version 1.3 of the entry. See complete history


Literature

Design of Inhibitors of Helicobacter Pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles Onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty.

Basarab, G.S.Hill, P.Eyermann, C.J.Gowravaram, M.Kack, H.Osimoni, E.

(2012) Bioorg Med Chem Lett 22: 5600

  • DOI: https://doi.org/10.1016/j.bmcl.2012.07.004
  • Primary Citation of Related Structures:  
    4B1F

  • PubMed Abstract: 

    Structure-activity relationships are presented around a series of pyrazolopyrimidinediones that inhibit the growth of Helicobacter pylori by targeting glutamate racemase, an enzyme that provides d-glutamate for the construction of N-acetylglucosamine-N-acetylmuramic acid peptidoglycan subunits assimilated into the bacterial cell wall. Substituents on the inhibitor scaffold were varied to optimize target potency, antibacterial activity and in vivo pharmacokinetic stability. By incorporating an imidazole ring at the 7-position of scaffold, high target potency was achieved due to a hydrogen bonding network that occurs between the 3-position nitrogen atom, a bridging water molecule and the side chains Ser152 and Trp244 of the enzyme. The lipophilicity of the scaffold series proved important for expression of antibacterial activity. Clearances in vitro and in vivo were monitored to identify compounds with improved plasma stability. The basicity of the imidazole may contribute to increased aqueous solubility at lower pH allowing for improved oral bioavailability.


  • Organizational Affiliation

    Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. greg.basarab@astrazeneca.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE RACEMASE
A, B
255Helicobacter pyloriMutation(s): 0 
EC: 5.1.1.3
UniProt
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZLT0 
Go to UniProtKB:  Q9ZLT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZLT0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DGL BindingDB:  4B1F Ki: 5800 (nM) from 1 assay(s)
KRH BindingDB:  4B1F IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.933α = 90
b = 75.974β = 90
c = 108.935γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2018-05-02
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other