3SFI

Ethionamide Boosters Part 2: Combining Bioisosteric Replacement and Structure-Based Drug Design to Solve Pharmacokinetic Issues in a Series of Potent 1,2,4-Oxadiazole EthR Inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ethionamide Boosters. 2. Combining Bioisosteric Replacement and Structure-Based Drug Design To Solve Pharmacokinetic Issues in a Series of Potent 1,2,4-Oxadiazole EthR Inhibitors.

Flipo, M.Desroses, M.Lecat-Guillet, N.Villemagne, B.Blondiaux, N.Leroux, F.Piveteau, C.Mathys, V.Flament, M.P.Siepmann, J.Villeret, V.Wohlkonig, A.Wintjens, R.Soror, S.H.Christophe, T.Jeon, H.K.Locht, C.Brodin, P.Deprez, B.Baulard, A.R.Willand, N.

(2012) J.Med.Chem. 55: 68-83

  • DOI: 10.1021/jm200825u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterial transcriptional repressor EthR controls the expression of EthA, the bacterial monooxygenase activating ethionamide, and is thus largely responsible for the low sensitivity of the human pathogen Mycobacterium tuberculosis to this antibio ...

    Mycobacterial transcriptional repressor EthR controls the expression of EthA, the bacterial monooxygenase activating ethionamide, and is thus largely responsible for the low sensitivity of the human pathogen Mycobacterium tuberculosis to this antibiotic. We recently reported structure-activity relationships of a series of 1,2,4-oxadiazole EthR inhibitors leading to the discovery of potent ethionamide boosters. Despite high metabolic stability, pharmacokinetic evaluation revealed poor mice exposure; therefore, a second phase of optimization was required. Herein a structure-property relationship study is reported according to the replacement of the two aromatic heterocycles: 2-thienyl and 1,2,4-oxadiazolyl moieties. This work was done using a combination of structure-based drug design and in vitro/ex vivo evaluations of ethionamide boosters on the targeted protein EthR and on the human pathogen Mycobacterium tuberculosis. Thanks to this process, we identified compound 42 (BDM41906), which displays improved efficacy in addition to high exposure to mice after oral administration.


    Organizational Affiliation

    Université Lille Nord de France, F-59000 Lille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulatory repressor protein (TETR-family)
A
236Mycobacterium 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
3SF
Query on 3SF

Download SDF File 
Download CCD File 
A
5,5,5-trifluoro-1-{4-[3-(1,3-thiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one
C15 H17 F3 N4 O2 S
WIFDOUQOJULUSV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3SFIC50: 400 nM BINDINGMOAD
3SFIC50: 400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.760α = 90.00
b = 120.760β = 90.00
c = 33.570γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata scaling
XDSdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-25
    Type: Database references
  • Version 1.2: 2014-04-09
    Type: Source and taxonomy
  • Version 1.3: 2018-01-24
    Type: Structure summary