NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfideâ??dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei
NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfideâ??dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei
The presence of suitable cavities or pockets on protein structures is a general criterion for a therapeutic target protein to be classified as â??druggableâ??. Many disease-related proteins that function solely through proteinâ??protein interactions lack such pockets, making development of inhibitors by traditional small-molecule structure-based design methods much more challenging. The 22Â*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 KDâ??~â??500Â*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.
[NMR paper] A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.
A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.
A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.
Bioorg Med Chem. 2018 Feb 22;:
Authors: Nagatoishi S, Yamaguchi S, Katoh E, Kajita K, Yokotagawa T, Kanai S, Furuya T, Tsumoto K
Abstract
19F NMR has recently emerged as an efficient,...
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[NMR paper] Dual Labeling of the CBP/p300 KIX domain for 19F NMR leads to identification of a new small molecule binding site.
Dual Labeling of the CBP/p300 KIX domain for 19F NMR leads to identification of a new small molecule binding site.
Dual Labeling of the CBP/p300 KIX domain for 19F NMR leads to identification of a new small molecule binding site.
Chembiochem. 2018 Feb 11;:
Authors: Gee CT, Arntson KE, Koleski EJ, Staebell RL, Pomerantz WCK
Abstract
Protein-Observed Fluorine NMR Spectroscopy (PrOF NMR) is an emerging technique for screening and characterizing small molecule-protein interactions. The choice of which amino acid to label for PrOF...
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[NMR paper] Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41.
Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41.
Related Articles Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41.
Org Biomol Chem. 2017 Jun 07;:
Authors: Chu S, Zhou G, Gochin M
Abstract
Small molecule inhibitors of glycoprotein-41 (gp41) are able to prevent HIV infection by binding to a hydrophobic pocket (HP) contained within the gp41 ectodomain, and preventing progression of fusion. There is little...
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[NMR paper] Automated resonance assignment of the 21kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA
Automated resonance assignment of the 21kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA
Publication date: December 2014
Source:Journal of Magnetic Resonance, Volume 249</br>
Author(s): Elena Schmidt , Teppei Ikeya , Mitsuhiro Takeda , Frank Löhr , Lena Buchner , Yutaka Ito , Masatsune Kainosho , Peter Güntert</br>
The automated chemical shift assignment algorithm FLYA has been extended for use with stereo-array isotope labeled (SAIL) proteins to determine the sequence-specific resonance assignments of large proteins. Here we present the...
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[NMR paper] NMR reveals double occupancy of quinone-type ligands in the catalytic quinone binding site of the Na+-translocating NADH:Quinone oxidoreductase from Vibrio cholerae.
NMR reveals double occupancy of quinone-type ligands in the catalytic quinone binding site of the Na+-translocating NADH:Quinone oxidoreductase from Vibrio cholerae.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_final.gif Related Articles NMR reveals double occupancy of quinone-type ligands in the catalytic quinone binding site of the Na+-translocating NADH:Quinone oxidoreductase from Vibrio cholerae.
J Biol Chem. 2013 Oct 18;288(42):30597-606
Authors: Nedielkov R,...
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[NMR paper] Screening protein-small molecule interactions by NMR.
Screening protein-small molecule interactions by NMR.
Related Articles Screening protein-small molecule interactions by NMR.
Methods Mol Biol. 2013;1008:389-413
Authors: Davis B
Abstract
Nuclear magnetic resonance (NMR) is well suited to probing the interactions between ligands and macromolecular receptors. It is a truly label-free technique, requiring only the presence of atoms (usually (1)H or (19)F) which give rise to observable resonances on either the ligand or the receptor. A number of parameters associated with these resonances can...
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[NMR paper] (1)H, (13)C, (15)N backbone and side chain NMR resonance assignments of BPSL1050 from Burkholderia pseudomallei.
(1)H, (13)C, (15)N backbone and side chain NMR resonance assignments of BPSL1050 from Burkholderia pseudomallei.
Related Articles (1)H, (13)C, (15)N backbone and side chain NMR resonance assignments of BPSL1050 from Burkholderia pseudomallei.
Biomol NMR Assign. 2013 Apr 25;
Authors: Gaudesi D, Quilici G, Musco G
Abstract
BPSL1050 is a 13.9*kDa protein produced by the Gram-negative bacterium Burkholderia pseudomallei, the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1050...
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Novel Small Molecule Inhibitors of MDR Mycobacterium tuberculosis by NMR Fragment Scr
Novel Small Molecule Inhibitors of MDR Mycobacterium tuberculosis by NMR Fragment Screening of Antigen 85C.
Related Articles Novel Small Molecule Inhibitors of MDR Mycobacterium tuberculosis by NMR Fragment Screening of Antigen 85C.
J Med Chem. 2010 Nov 12;
Authors: Scheich C, Puetter V, Schade M
Protein target-based discovery of novel antibiotics has been largely unsuccessful despite rich genome information. Particularly in need are new antibiotics for tuberculosis, which kills 1.6 million people annually and shows a rapid increase in...
NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfideâ??dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei
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