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Structural and biochemical evidence for a boat-like transition state in β-mannosidases

Nature Chemical Biology volume 4, pages 306–312 (2008)Cite this article

Abstract

Enzyme inhibition through mimicry of the transition state is a major area for the design of new therapeutic agents. Emerging evidence suggests that many retaining glycosidases that are active on α- or β-mannosides harness unusual B2,5 (boat) transition states. Here we present the analysis of 25 putative β-mannosidase inhibitors, whose Ki values range from nanomolar to millimolar, on the Bacteroides thetaiotaomicron β-mannosidase BtMan2A. B2,5 or closely related conformations were observed for all tightly binding compounds. Subsequent linear free energy relationships that correlate log Ki with log Km/kcat for a series of active center variants highlight aryl-substituted mannoimidazoles as powerful transition state mimics in which the binding energy of the aryl group enhances both binding and the degree of transition state mimicry. Support for a B2,5 transition state during enzymatic β-mannosidase hydrolysis should also facilitate the design and exploitation of transition state mimics for the inhibition of retaining α-mannosidases—an area that is emerging for anticancer therapeutics.

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Figure 1: The conformational agenda of glycosidases.
Figure 2: Putative mannosidase inhibitors used in this study.
Figure 3: Active center of wild-type BtMan2A, in complex with substituted mannoimidazole 1c.
Figure 4: Observed electron density for compounds 1a, 1c, 2a, 2c, 4a, 5 and 6 bound to BtMan2A in “side-on” and “end-on” views.
Figure 5: Linear free energy relationships.

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Acknowledgements

The Biotechnology and Biological Sciences Research Council (BBSRC) is thanked for funding. G.J.D. is the recipient of a Royal Society-Wolfson Research Merit Award. S. Withers (University of British Columbia) is thanked for provision of 4-nitrophenyl 2-deoxy-β-D-arabino-hexopyranoside. A.V. thanks the Swiss National Science Foundation, Hoffmann-La Roche (Basle) and Syngenta (Basle) for generous support. This work is dedicated by M.-P.H., A.V. and J.G. to the memory of C. Mioskowski (deceased on June 2, 2007).

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Author notes

  1. Louise E Tailford, Wendy A Offen and Nicola L Smith: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK

    Louise E Tailford, Nicola L Smith, Claire Dumon, Carl Morland & Harry J Gilbert

  2. Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, YO10 5YW, York, UK

    Wendy A Offen & Gideon J Davies

  3. Commissariat à l'Energie Atomique Centre de Saclay, Direction des Sciences du Vivant, Institut de Biologie et de Technologies de Saclay, Service de Chimie Bioorganique et de Marquage, Bâtiment 547, Gif Sur Yvette cedex, 91191, France

    Julie Gratien & Marie-Pierre Heck

  4. Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia

    Robert V Stick

  5. Université Pierre et Marie Curie (Paris 6), Institut de Chimie Moléculaìre (Federation of Research 2769), Laboratoire de Chimie Organique (Unìté Mixte de Recherche Centre National de la Recherche Scientifique 7611), 4 place Jussieu, C. 181, Paris, 75005, France

    Yves Blériot

  6. Laboratorium für Organische Chemie, HCI H317, ETH Zürich, Wolfgang Paulistrasse 10, Zürich, CH-8093, Switzerland

    Andrea Vasella

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Correspondence to Harry J Gilbert or Gideon J Davies.

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Tailford, L., Offen, W., Smith, N. et al. Structural and biochemical evidence for a boat-like transition state in β-mannosidases. Nat Chem Biol 4, 306–312 (2008). https://doi.org/10.1038/nchembio.81

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