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Targeting the Motion of Shikimate Kinase: Development of Competitive Inhibitors that Stabilize an Inactive Open Conformation of the Enzyme

Lookup NU author(s): Paul Thompson, Professor Alastair Hawkins


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The large conformational changes observed by Molecular Dynamics simulation studies on the product release in the LID and shikimic acid binding (SB) domains of the shikimate kinase (SK) enzyme have been exploited in the development of reversible competitive inhibitors against SK from Mycobacterium tuberculosis and Helicobacter pylori. This enzyme is a recognized target for antibiotic drug discovery. The reported C5-substituted shikimic acid analogues interact with the dynamic apolar pocket that surrounds the C4 and C5 hydroxyl groups of the natural substrate, cause the opening of the LID and SB domains, and capture the essential arginine far from the ATP binding site as required for catalysis. The 3-nitrobenzyl 3e and 5-benzothiophenyl derivatives 3i proved to be the most potent inhibitors. An ester prodrug of 3i was the most efficient derivative in achieving good in vitro activity against H. pylori, having a MIC value of 4 mu g/mL.

Publication metadata

Author(s): Prado V, Lence E, Maneiro M, Vazquez-Ucha JC, Beceiro A, Thompson P, Hawkins AR, Gonzalez-Bello C

Publication type: Article

Publication status: Published

Journal: Journal of Medicinal Chemistry

Year: 2016

Volume: 59

Issue: 11

Pages: 5471-5487

Print publication date: 09/06/2016

Online publication date: 11/05/2016

Acceptance date: 02/04/2016

ISSN (print): 0022-2623

ISSN (electronic): 1520-4804

Publisher: American Chemical Society


DOI: 10.1021/acs.jmedchem.6b00483


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Funder referenceFunder name
European Regional Development Fund (ERDF)
GRC2013-041Xunta de Galicia
PI14/00059ISCIII General Subdirection of Assesment and Promotion of the Research
SAF2013-42899-RSpanish Ministry of Economy and Competiveness