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Chen Y, van den Nieuwendijk AMC, Wu L, Moran E, Skoulikopoulou F, van Riet V, Overkleeft HS, Davies GJ, Armstrong Z. Molecular Basis for Inhibition of Heparanases and β-Glucuronidases by Siastatin B. J Am Chem Soc 2024; 146:125-133. [PMID: 38118176 PMCID: PMC10785800 DOI: 10.1021/jacs.3c04162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Siastatin B is a potent and effective iminosugar inhibitor of three diverse glycosidase classes, namely, sialidases, β-d-glucuronidases, and N-acetyl-glucosaminidases. The mode of inhibition of glucuronidases, in contrast to sialidases, has long been enigmatic as siastatin B appears too bulky and incorrectly substituted to be accommodated within a β-d-glucuronidase active site pocket. Herein, we show through crystallographic analysis of protein-inhibitor complexes that siastatin B generates both a hemiaminal and a 3-geminal diol iminosugar (3-GDI) that are, rather than the parent compound, directly responsible for enzyme inhibition. The hemiaminal product is the first observation of a natural product that belongs to the noeuromycin class of inhibitors. Additionally, the 3-GDI represents a new and potent class of the iminosugar glycosidase inhibitor. To substantiate our findings, we synthesized both the gluco- and galacto-configured 3-GDIs and characterized their binding both structurally and kinetically to exo-β-d-glucuronidases and the anticancer target human heparanase. This revealed submicromolar inhibition of exo-β-d-glucuronidases and an unprecedented binding mode by this new class of inhibitor. Our results reveal the mechanism by which siastatin B acts as a broad-spectrum glycosidase inhibitor, identify a new class of glycosidase inhibitor, and suggest new functionalities that can be incorporated into future generations of glycosidase inhibitors.
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Affiliation(s)
- Yurong Chen
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300
RA Leiden, The Netherlands
| | | | - Liang Wu
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, U.K.
| | - Elisha Moran
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, U.K.
| | - Foteini Skoulikopoulou
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300
RA Leiden, The Netherlands
| | - Vera van Riet
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300
RA Leiden, The Netherlands
| | - Hermen S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300
RA Leiden, The Netherlands
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, U.K.
| | - Zachary Armstrong
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300
RA Leiden, The Netherlands
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, U.K.
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