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

Authors

Stefan Nebl
Wesam Alwan
Martin Williams
Gaurav Sharma
Ashley Taylor
Bradley Doak
Karyn Wilde
Roisín McMahon
Maria Halili
Jennifer L. Martin, University of WollongongFollow
Ben Capuano
R Fenwick
Biswaranjan Mohanty
Martin Scanlon

RIS ID

144888

Publication Details

Nebl, S., Alwan, W., Williams, M., Sharma, G., Taylor, A., Doak, B., Wilde, K., McMahon, R., Halili, M., Martin, J., Capuano, B., Fenwick, R., Mohanty, B. & Scanlon, M. (2020). NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfide–dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei. Journal of Biomolecular NMR, Online First

Abstract

© 2020, Springer Nature B.V. 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.