NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfide–dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei

Stefan Nebl, Wesam S. Alwan, Martin L. Williams, Gaurav Sharma, Ashley Taylor, Bradley C. Doak, Karyn L. Wilde, Róisín M. McMahon, Maria A. Halili, Jennifer L. Martin, Ben Capuano, R. Bryn Fenwick, Biswaranjan Mohanty, Martin J. Scanlon

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1 Citation (Scopus)

Abstract

The presence of suitable cavities or pockets on protein structures is a general criterion for a therapeutic target protein to be classified as ‘druggable’. Many disease-related proteins that function solely through protein–protein interactions lack such pockets, making development of inhibitors by traditional small-molecule structure-based design methods much more challenging. The 22 kDa bacterial thiol oxidoreductase enzyme, DsbA, from the gram-negative bacterium Burkholderia pseudomallei (BpsDsbA) is an example of one such target. The crystal structure of oxidized BpsDsbA lacks well-defined surface pockets. BpsDsbA is required for the correct folding of numerous virulence factors in B. pseudomallei, and genetic deletion of dsbA significantly attenuates B. pseudomallei virulence in murine infection models. Therefore, BpsDsbA is potentially an attractive drug target. Herein we report the identification of a small molecule binding site adjacent to the catalytic site of oxidized BpsDsbA. 1HN CPMG relaxation dispersion NMR measurements suggest that the binding site is formed transiently through protein dynamics. Using fragment-based screening, we identified a small molecule that binds at this site with an estimated affinity of KD ~ 500 µM. This fragment inhibits BpsDsbA enzymatic activity in vitro. The binding mode of this molecule has been characterized by NMR data-driven docking using HADDOCK. These data provide a starting point towards the design of more potent small molecule inhibitors of BpsDsbA.

Original languageEnglish
Pages (from-to)595-611
Number of pages17
JournalJournal of Biomolecular NMR
Volume74
DOIs
Publication statusPublished - 6 Aug 2020

Keywords

  • BpsDsbA
  • Burkholderia pseudomallei
  • CPMG relaxation dispersion
  • Disulfide oxidoreductase
  • Fragment-based drug design (FBDD)
  • High ambiguity driven biomolecular docking (HADDOCK)
  • Methyl-NMR
  • Non-uniform sampling (NUS)
  • Protein dynamics
  • Protein–ligand complexes
  • Structure-based drug design (SBDD)

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