Elaboration of a benzofuran scaffold and evaluation of binding affinity and inhibition of Escherichia coli DsbA: A fragment-based drug design approach to novel antivirulence compounds

Bioorg Med Chem. 2021 Sep 1:45:116315. doi: 10.1016/j.bmc.2021.116315. Epub 2021 Jul 22.


Bacterial thiol-disulfide oxidoreductase DsbA is essential for bacterial virulence factor assembly and has been identified as a viable antivirulence target. Herein, we report a structure-based elaboration of a benzofuran hit that bound to the active site groove of Escherichia coli DsbA. Substituted phenyl groups were installed at the 5- and 6-position of the benzofuran using Suzuki-Miyaura coupling. HSQC NMR titration experiments showed dissociation constants of this series in the high µM to low mM range and X-ray crystallography produced three co-structures, showing binding in the hydrophobic groove, comparable with that of the previously reported benzofurans. The 6-(m-methoxy)phenyl analogue (2b), which showed a promising binding pose, was chosen for elaboration from the C-2 position. The 2,6-disubstituted analogues bound to the hydrophobic region of the binding groove and the C-2 groups extended into the more polar, previously un-probed, region of the binding groove. Biochemical analysis of the 2,6-disubsituted analogues showed they inhibited DsbA oxidation activity in vitro. The results indicate the potential to develop the elaborated benzofuran series into a novel class of antivirulence compounds.

Keywords: Antivirulence; Benzofuran; DsbA; Enzyme inhibition; Fragment-based drug discovery; Oxidoreductase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benzofurans / chemical synthesis
  • Benzofurans / chemistry
  • Benzofurans / pharmacology*
  • Crystallography, X-Ray
  • Dose-Response Relationship, Drug
  • Drug Design*
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • Escherichia coli Proteins / antagonists & inhibitors*
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Molecular Structure
  • Protein Disulfide-Isomerases / antagonists & inhibitors*
  • Protein Disulfide-Isomerases / metabolism
  • Structure-Activity Relationship


  • Benzofurans
  • Enzyme Inhibitors
  • Escherichia coli Proteins
  • Protein Disulfide-Isomerases
  • dsbA protein, E coli
  • benzofuran