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

• Published in: Journal of biomolecular NMR 2020-11, Vol.74 (10-11), p.595-611
• Main Authors: Nebl, Stefan, Alwan, Wesam S., Williams, Martin L., Sharma, Gaurav, Taylor, Ashley, Doak, Bradley C., Wilde, Karyn L., McMahon, Róisín M., Halili, Maria A., Martin, Jennifer L., Capuano, Ben, Fenwick, R. Bryn, Mohanty, Biswaranjan, Scanlon, Martin J.
• Format: Article
• Language: English
• Subjects: Animal models; Binding sites; Biochemistry; Biological and Medical Physics; Biophysics; Burkholderia pseudomallei; Crystal structure; Enzymatic activity; Enzymes; Inhibitors; Molecular structure; NMR; Nuclear magnetic resonance; Physics; Physics and Astronomy; Protein interaction; Proteins; Screening; Spectroscopy/Spectrometry; Therapeutic targets; Thiol oxidoreductase; Virulence; Virulence factors
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1007/s10858-020-00339-5

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. 1 H N 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 K D  ~ 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.