Discovery of Novel N-phenylphenoxyacetamide Derivatives as EthR Inhibitors and Ethionamide Boosters by Combining High-Throughput Screening and Synthesis

J Med Chem. 2012 Jul 26;55(14):6391-402. doi: 10.1021/jm300377g. Epub 2012 Jul 17.


In this paper, we describe the screening of a 14640-compound library using a novel whole mycobacteria phenotypic assay to discover inhibitors of EthR, a transcriptional repressor implicated in the innate resistance of Mycobacterium tuberculosis to the second-line antituberculosis drug ethionamide. From this screening a new chemical family of EthR inhibitors bearing an N-phenylphenoxyacetamide motif was identified. The X-ray structure of the most potent compound crystallized with EthR inspired the synthesis of a 960-member focused library. These compounds were tested in vitro using a rapid thermal shift assay on EthR to accelerate the optimization. The best compounds were synthesized on a larger scale and confirmed as potent ethionamide boosters on M. tuberculosis -infected macrophages. Finally, the cocrystallization of the best optimized analogue with EthR revealed an unexpected reorientation of the ligand in the binding pocket.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetamides / chemical synthesis*
  • Acetamides / chemistry
  • Acetamides / pharmacology*
  • Animals
  • Antitubercular Agents / pharmacology*
  • Cell Line
  • Chemistry Techniques, Synthetic
  • Drug Discovery*
  • Drug Synergism
  • Ethionamide / pharmacology*
  • High-Throughput Screening Assays*
  • Ligands
  • Macrophages / drug effects
  • Macrophages / microbiology
  • Mice
  • Models, Molecular
  • Mycobacterium tuberculosis / drug effects
  • Protein Conformation
  • Repressor Proteins / antagonists & inhibitors*
  • Repressor Proteins / chemistry


  • Acetamides
  • Antitubercular Agents
  • EthR protein, Mycobacterium tuberculosis
  • Ligands
  • Repressor Proteins
  • Ethionamide

Associated data

  • PDB/3Q3S
  • PDB/4DW6