ISDA

Deposition Date 2012-02-24

Release Date 2013-03-27

Last Version Date 2024-02-28

Entry Detail

PDB ID:

4DW6

Keywords:

TRANSCRIPTION/INHIBITOR

Title:

Novel N-phenyl-phenoxyacetamide derivatives as potential EthR inhibitors and ethionamide boosters. Discovery and optimization using High-Throughput Synthesis.

Biological Source:

Source Organism:

Mycobacterium tuberculosis (Taxon ID: 1773)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.21

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HTH-type transcriptional regulator EthR
Chain IDs:A
Chain Length:236
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis

UniProt ID:P9WMC1 Pfam ID:PF00440, PF21313

Ligand Molecules

0MN

GOL

NH4

Primary Citation

Discovery of novel N-phenylphenoxyacetamide derivatives as EthR inhibitors and ethionamide boosters by combining high-throughput screening and synthesis.

Flipo, M, Willand, N, Lecat-Guillet, N, Hounsou, C, Desroses, M, Leroux, F, Lens, Z, Villeret, V, Wohlkonig, A, Wintjens, R, Christophe, T, Kyoung Jeon, H, Locht, C, Brodin, P, Baulard, A.R, Deprez, B.Show

J.Med.Chem. 55 6391 6402 (2012)

PMID: 22738293 DOI: 10.1021/jm300377g

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures