4M3E

Rapid and efficient design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging and linking approaches


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.109 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ligand Efficiency Driven Design of New Inhibitors of Mycobacterium tuberculosis Transcriptional Repressor EthR Using Fragment Growing, Merging, and Linking Approaches.

Villemagne, B.Flipo, M.Blondiaux, N.Crauste, C.Malaquin, S.Leroux, F.Piveteau, C.Villeret, V.Brodin, P.Villoutreix, B.O.Sperandio, O.Soror, S.H.Wohlkonig, A.Wintjens, R.Deprez, B.Baulard, A.R.Willand, N.

(2014) J.Med.Chem. 57: 4876-4888

  • DOI: 10.1021/jm500422b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tuberculosis remains a major cause of mortality and morbidity, killing each year more than one million people. Although the combined use of first line antibiotics (isoniazid, rifampicin, pyrazinamide, and ethambutol) is efficient to treat most patien ...

    Tuberculosis remains a major cause of mortality and morbidity, killing each year more than one million people. Although the combined use of first line antibiotics (isoniazid, rifampicin, pyrazinamide, and ethambutol) is efficient to treat most patients, the rapid emergence of multidrug resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. Mycobacterial transcriptional repressor EthR is a key player in the control of second-line drugs bioactivation such as ethionamide and has been shown to impair the sensitivity of the human pathogen Mycobacterium tuberculosis to this antibiotic. As a way to identify new potent ligands of this protein, we have developed fragment-based approaches. In the current study, we combined surface plasmon resonance assay, X-ray crystallography, and ligand efficiency driven design for the rapid discovery and optimization of new chemotypes of EthR ligands starting from a fragment. The design, synthesis, and in vitro and ex vivo activities of these compounds will be discussed.


    Organizational Affiliation

    Université Lille Nord de France , F-59044 Lille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulator EthR
A
216Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ethR (etaR)
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMC1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2B3
Query on 2B3

Download SDF File 
Download CCD File 
A
4-(2-{[(propylsulfonyl)amino]methyl}-1,3-thiazol-4-yl)-N-(3,3,3-trifluoropropyl)benzamide
C17 H20 F3 N3 O3 S2
YJYLYLYZLFRVRC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2B3IC50: 560 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.109 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.058α = 90.00
b = 122.058β = 90.00
c = 33.836γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release