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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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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: https://doi.org/10.1021/jm500422b
  • Primary Citation of Related Structures:  
    4M3B, 4M3D, 4M3E, 4M3F, 4M3G

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator EthR216Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: etaRethRMT3970Rv3855
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMC1 
Go to UniProtKB:  P9WMC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMC1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2D1

Download Ideal Coordinates CCD File 
B [auth A]N-(3-methylbutyl)-4-(2-methyl-1,3-thiazol-4-yl)benzenesulfonamide
C15 H20 N2 O2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.089α = 90
b = 121.089β = 90
c = 33.854γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations