Journal ArticleDOI
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 Williams,Gaurav Sharma,Ashley Taylor,Bradley C. Doak,Karyn L. Wilde,Róisín M. McMahon,Maria A. Halili,Jennifer L. Martin,Jennifer L. Martin,Ben Capuano,R. Bryn Fenwick,Biswaranjan Mohanty,Martin J. Scanlon +14 more
TLDR
The identification of a small molecule binding site adjacent to the catalytic site of oxidized BpsDsbA is reported, and a fragment that binds at this site with an estimated affinity of KD ~ 500 µM inhibits BpsdsbA enzymatic activity in vitro.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.read more
Citations
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DSB proteins and bacterial pathogenicity
Begoña Heras,Stephen R. Shouldice,Makrina Totsika,Martin J. Scanlon,Mark A. Schembri,Jennifer L. Martin +5 more
TL;DR: This view of protein-folding machinery must now be adjusted to encompass the wider range of disulphide catalytic systems present in bacteria.
Structure and function of DsbA, a key bacterial oxidative folding catalyst
Stephen R. Shouldice,Begoña Heras,Patricia M. Walden,Makrina Totsika,Mark A. Schembri,Jennifer L. Martin +5 more
TL;DR: Current knowledge on DsbA, a bacterial periplasmic protein that introduces disulfide bonds into diverse substrate proteins and which may one day be the target of a new class of anti-virulence drugs to treat bacterial infection, is reviewed.
Journal ArticleDOI
Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9.
Dene R. Littler,Biswaranjan Mohanty,Biswaranjan Mohanty,Shea A. Lowery,Rhys N. Colson,Benjamin S. Gully,Stanley Perlman,Martin J. Scanlon,Jamie Rossjohn,Jamie Rossjohn +9 more
TL;DR: In this article, a base-mimicking compound identified from a small molecule fragment screen was used to engage Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers.
Journal ArticleDOI
NMR in pharmaceutical discovery and development.
Journal ArticleDOI
Selective binding of small molecules to Vibrio cholerae DsbA offers a starting point for the design of novel antibacterials
TL;DR: In this article , a fragment-based screening approach has identified novel compounds that bind to the active site groove of DsbA from Vibrio cholerae, which is a key mediator of bacterial virulence and an attractive target.
References
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