Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations

A Publisher Correction to this article was published on 19 August 2022

This article has been updated

Abstract

Enzymes achieve high substrate and product selectivities by orientating and activating the substrate(s) appropriately inside a confined and finely optimized binding pocket. Although some basic aspects of enzymes have already been mimicked successfully with man-made catalysts, substrate activation by proton wires inside enzyme pockets has not been recreated with man-made catalysts so far. A proton wire facilitates the dual activation of a nucleophile and an electrophile via a reciprocal proton transfer, enabling highly stereoselective reactions under mild conditions. Here we present evidence for such an activation mode inside the supramolecular resorcin[4]arene capsule and demonstrate that it enables catalytic and highly β-selective glycosylation reactions—still a major challenge in glycosylation chemistry. Extensive control experiments provide very strong evidence that the reactions take place inside the molecular container. We show that this activation strategy is compatible with a broad scope of glycoside donors and nucleophiles, and is only limited by the cavity size.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Proton wire activation mode and prototypical glycosylation mechanism.
Fig. 2: Summary of the screening results.
Fig. 3: Control experiments concerning the role of the capsule catalyst.
Fig. 4: Experimental and computational mechanistic investigations.
Fig. 5: Application of the methodology to the synthesis of two known β-saccharides.

Data availability

The data that support the findings of this study are available in the Supplementary Information (experimental procedures, characterization data, copies of the NMR spectra of novel compounds). The source data for Figs. 15 and Table 1 have been deposited on Zenodo (https://zenodo.org/record/6337480#.YidH8ZYo8cQ). Simulation input files for Fig. 4f,g are provided on the PLUMED-NEST repository (https://www.plumed-nest.org/eggs/22/009/).

Change history

References

  1. Kirby, A. J. Enzyme mechanisms, models and mimics. Angew. Chem. Int. Ed. 35, 707–724 (1996).

    CAS  Article  Google Scholar 

  2. Motherwell, W. B., Bingham, M. J. & Six, Y. Recent progress in the design and synthesis of artificial enzymes. Tetrahedron 57, 4663–4686 (2001).

    CAS  Article  Google Scholar 

  3. Breslow, R. & Dong, S. D. Biomimetic reactions catalyzed by cyclodextrins and their derivatives. Chem. Rev. 98, 1997–2012 (1998).

    CAS  PubMed  Article  Google Scholar 

  4. Hof, F., Craig, S. L., Nuckolls, C. & Rebek, J. J. Molecular encapsulation. Angew. Chem. Int. Ed. 41, 1488–1508 (2002).

    CAS  Article  Google Scholar 

  5. Koblenz, T. S., Wassenaar, J. & Reek, J. N. H. Reactivity within a confined self-assembled nanospace. Chem. Soc. Rev. 37, 247–262 (2008).

    CAS  PubMed  Article  Google Scholar 

  6. Rebek, J. Molecular behavior in small spaces. Acc. Chem. Res. 42, 1660–1668 (2009).

    CAS  PubMed  Article  Google Scholar 

  7. Yoshizawa, M., Klosterman, J. K. & Fujita, M. Functional molecular flasks: new properties and reactions within discrete, self-assembled hosts. Angew. Chem. Int. Ed. 48, 3418–3438 (2009).

    CAS  Article  Google Scholar 

  8. Wiester, M. J., Ulmann, P. A. & Mirkin, C. A. Enzyme mimics based upon supramolecular coordination chemistry. Angew. Chem. Int. Ed. 50, 114–137 (2011).

    CAS  Article  Google Scholar 

  9. Conn, M. M. & Rebek, J. Self-assembling capsules. Chem. Rev. 97, 1647–1668 (1997).

    CAS  PubMed  Article  Google Scholar 

  10. Hong, C. M., Bergman, R. G., Raymond, K. N. & Toste, F. D. Self-assembled tetrahedral hosts as supramolecular catalysts. Acc. Chem. Res. 51, 2447–2455 (2018).

    CAS  PubMed  Article  Google Scholar 

  11. Zhang, Q., Catti, L. & Tiefenbacher, K. Catalysis inside the hexameric resorcinarene capsule. Acc. Chem. Res. 51, 2107–2114 (2018).

    CAS  PubMed  Article  Google Scholar 

  12. Gaeta, C. et al. The hexameric resorcinarene capsule at work: supramolecular catalysis in confined spaces. Chem. Eur. J. 25, 4899–4913 (2019).

    CAS  PubMed  Article  Google Scholar 

  13. Mouarrawis, V., Plessius, R., van der Vlugt, J. I. & Reek, J. N. H. Confinement effects in catalysis using well-defined materials and cages. Front. Chem. https://doi.org/10.3389/fchem.2018.00623 (2018).

  14. Ward, M. D., Hunter, C. A. & Williams, N. H. Coordination cages based on bis(pyrazolylpyridine) ligands: structures, dynamic behavior, guest binding and catalysis. Acc. Chem. Res. 51, 2073–2082 (2018).

    CAS  PubMed  Article  Google Scholar 

  15. Némethová, I., Syntrivanis, L.-D. & Tiefenbacher, K. Molecular capsule catalysis: ready to address current challenges in synthetic organic chemistry? Chimia 74, 561–568 (2020).

    PubMed  Article  CAS  Google Scholar 

  16. Kang, J. & Rebek, J. Acceleration of a Diels–Alder reaction by a self-assembled molecular capsule. Nature 385, 50–52 (1997).

    CAS  PubMed  Article  Google Scholar 

  17. Yoshizawa, M., Tamura, M. & Fujita, M. Diels-Alder in aqueous molecular hosts: unusual regioselectivity and efficient catalysis. Science 312, 251–254 (2006).

    CAS  PubMed  Article  Google Scholar 

  18. Ajami, D. & Rebek, J. More chemistry in small spaces. Acc. Chem. Res. 46, 990–999 (2012).

    PubMed  Article  CAS  Google Scholar 

  19. Leenders, S. H. A. M., Gramage-Doria, R., de Bruin, B. & Reek, J. N. H. Transition metal catalysis in confined spaces. Chem. Soc. Rev. 44, 433–448 (2015).

    CAS  PubMed  Article  Google Scholar 

  20. Raynal, M., Ballester, P., Vidal-Ferran, A. & van Leeuwen, P. W. N. M. Supramolecular catalysis. Part 2: artificial enzyme mimics. Chem. Soc. Rev. 43, 1734–1787 (2014).

    CAS  PubMed  Article  Google Scholar 

  21. Catti, L., Zhang, Q. & Tiefenbacher, K. Advantages of catalysis in self-assembled molecular capsules. Chem. Eur. J. 22, 9060–9066 (2016).

    CAS  PubMed  Article  Google Scholar 

  22. Morimoto, M. et al. Advances in supramolecular host-mediated reactivity. Nat. Catal. 3, 969–984 (2020).

    CAS  Article  Google Scholar 

  23. Percástegui, E. G., Ronson, T. K. & Nitschke, J. R. Design and applications of water-soluble coordination cages. Chem. Rev. 120, 13480–13544 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  24. Frank, R. A. W., Titman, C. M., Pratap, J. V., Luisi, B. F. & Perham, R. N. A molecular switch and proton wire synchronize the active sites in thiamine enzymes. Science 306, 872–876 (2004).

    Google Scholar 

  25. Cukierman, S. Et tu, Grotthuss! and other unfinished stories. Biochim. Biophys. Acta Bioenerg. 1757, 876–885 (2006).

    CAS  Article  Google Scholar 

  26. Nakamura, A. et al. ‘Newton’s cradle’ proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. Sci. Adv. 1, e1500263 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  27. MacGillivray, L. R. & Atwood, J. L. A chiral spherical molecular assembly held together by 60 hydrogen bonds. Nature 389, 469–472 (1997).

    CAS  Article  Google Scholar 

  28. Shivanyuk, A. & Rebek, J. Reversible encapsulation by self-assembling resorcinarene subunits. Proc. Natl Acad. Sci. USA 98, 7662–7665 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. Avram, L. & Cohen, Y. Spontaneous formation of hexameric resorcinarene capsule in chloroform solution as detected by diffusion NMR. J. Am. Chem. Soc. 124, 15148–15149 (2002).

    CAS  PubMed  Article  Google Scholar 

  30. Avram, L., Cohen, Y. & Rebek, J. Recent advances in hydrogen-bonded hexameric encapsulation complexes. Chem. Commun. 47, 5368–5375 (2011).

    CAS  Article  Google Scholar 

  31. Bianchini, G., La Sorella, G., Canever, N., Scarso, A. & Strukul, G. Efficient isonitrile hydration through encapsulation within a hexameric self-assembled capsule and selective inhibition by a photo-controllable competitive guest. Chem. Commun. 49, 5322–5324 (2013).

    CAS  Article  Google Scholar 

  32. Cavarzan, A., Scarso, A., Sgarbossa, P., Strukul, G. & Reek, J. N. H. Supramolecular control on chemo- and regioselectivity via encapsulation of (NHC)-Au catalyst within a hexameric self-assembled host. J. Am. Chem. Soc. 133, 2848–2851 (2011).

    CAS  PubMed  Article  Google Scholar 

  33. Zhang, Q. & Tiefenbacher, K. Hexameric resorcinarene capsule is a Brønsted acid: investigation and application to synthesis and catalysis. J. Am. Chem. Soc. 135, 16213–16219 (2013).

    CAS  PubMed  Article  Google Scholar 

  34. Köster, J. M. & Tiefenbacher, K. Elucidating the importance of hydrochloric acid as a cocatalyst for resorcinarene-capsule-catalyzed reactions. ChemCatChem 10, 2941–2944 (2018).

    Article  CAS  Google Scholar 

  35. Merget, S., Catti, L., Piccini, G. & Tiefenbacher, K. Requirements for terpene cyclizations inside the supramolecular resorcinarene capsule: bound water and its protonation determine the catalytic activity. J. Am. Chem. Soc. 142, 4400–4410 (2020).

    CAS  PubMed  Article  Google Scholar 

  36. Tanaka, Y., Khare, C., Yonezawa, M. & Aoyama, Y. Highly stereoselective glycosidation of ribose solubilized in apolar organic media via host-guest complexation1. Tetrahedron Lett. 31, 6193–6196 (1990).

    CAS  Article  Google Scholar 

  37. Zhu, X. & Schmidt, R. R. New principles for glycoside-bond formation. Angew. Chem. Int. Ed. 48, 1900–1934 (2009).

    CAS  Article  Google Scholar 

  38. Nigudkar, S. S. & Demchenko, A. V. Stereocontrolled 1,2-cis glycosylation as the driving force of progress in synthetic carbohydrate chemistry. Chem. Sci. 6, 2687–2704 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Jensen, K. J. O-Glycosylations under neutral or basic conditions. J. Chem. Soc. Perkin Trans. 1, 2219–2233 (2002).

    Article  CAS  Google Scholar 

  40. Davis, B. G. Recent developments in oligosaccharide synthesis. J. Chem. Soc. Perkin Trans. 1, 2137–2160 (2000).

    Article  Google Scholar 

  41. Das, R. & Mukhopadhyay, B. Chemical O-glycosylations: an overview. ChemistryOpen 5, 401–433 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. Ling, J. & Bennett, C. S. Recent developments in stereoselective chemical glycosylation. Asian J. Org. Chem. 8, 802–813 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  43. Nielsen, M. M. & Pedersen, C. M. Catalytic glycosylations in oligosaccharide synthesis. Chem. Rev. 118, 8285–8358 (2018).

    CAS  PubMed  Article  Google Scholar 

  44. McKay, M. J. & Nguyen, H. M. Recent advances in transition metal-catalyzed glycosylation. ACS Catal. 2, 1563–1595 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. Li, W. & Yu, B. Gold-catalyzed glycosylation in the synthesis of complex carbohydrate-containing natural products. Chem. Soc. Rev. 47, 7954–7984 (2018).

    CAS  PubMed  Article  Google Scholar 

  46. Williams, R. & Galan, M. C. Recent advances in organocatalytic glycosylations. Eur. J. Org. Chem. 2017, 6247–6264 (2017).

    CAS  Article  Google Scholar 

  47. Crich, D. Mechanism of a chemical glycosylation reaction. Acc. Chem. Res. 43, 1144–1153 (2010).

    CAS  PubMed  Article  Google Scholar 

  48. Adero, P. O., Amarasekara, H., Wen, P., Bohé, L. & Crich, D. The experimental evidence in support of glycosylation mechanisms at the SN1-SN2 interface. Chem. Rev. 118, 8242–8284 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. Park, Y. et al. Macrocyclic bis-thioureas catalyze stereospecific glycosylation reactions. Science 355, 162–166 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. Kwan, E. E., Park, Y., Besser, H. A., Anderson, T. L. & Jacobsen, E. N. Sensitive and accurate 13C kinetic isotope effect measurements enabled by polarization transfer. J. Am. Chem. Soc. 139, 43–46 (2017).

    CAS  PubMed  Article  Google Scholar 

  51. Mukaiyama, T. & Jona, H. Glycosyl fluoride A superb glycosyl donor in glycosylation. Proc. Jpn. Acad. B Phys. Biol. Sci. 78, 73–83 (2002).

    Article  Google Scholar 

  52. Gerkensmeier, T. et al. Self-assembly of 2,8,14,20-tetraisobutyl-5,11,17,23-tetrahydroxyresorc[4]arene. Eur. J. Org. Chem. 8, 2257–2262 (1999).

    Article  Google Scholar 

  53. Zhang, Q., Catti, L., Kaila, V. R. I. & Tiefenbacher, K. To catalyze or not to catalyze: elucidation of the subtle differences between the hexameric capsules of pyrogallolarene and resorcinarene. Chem. Sci. 8, 1653–1657 (2017).

    CAS  PubMed  Article  Google Scholar 

  54. Crich, D. & Chandrasekera, N. S. Mechanism of 4,6-O-benzylidene-directed β-mannosylation as determined by α-deuterium kinetic isotope effects. Angew. Chem. Int. Ed. 43, 5386–5389 (2004).

    CAS  Article  Google Scholar 

  55. Matsui, H., Blanchard, J. S., Brewer, C. F. & Hehre, E. J. α-Secondary tritium kinetic isotope effects for the hydrolysis of α-D-glucopyranosyl fluoride by exo-α-glucanases. J. Biol. Chem. 264, 8714–8716 (1989).

    CAS  PubMed  Article  Google Scholar 

  56. Chan, J., Sannikova, N., Tang, A. & Bennet, A. J. Transition-state structure for the quintessential SN2 reaction of a carbohydrate: reaction of α-glucopyranosyl fluoride with azide ion in water. J. Am. Chem. Soc. 136, 12225–12228 (2014).

    CAS  PubMed  Article  Google Scholar 

  57. Slovak, S. & Cohen, Y. The effect of alcohol structures on the interaction mode with the hexameric capsule of resorcin[4]arene. Chem. Eur. J. 18, 8515–8520 (2012).

    CAS  PubMed  Article  Google Scholar 

  58. Wang, K. et al. Electrostatic control of macrocyclization reactions within nanospaces. J. Am. Chem. Soc. 141, 6740–6747 (2019).

    CAS  PubMed  Article  Google Scholar 

  59. Cai, X., Kataria, R. & Gibb, B. C. Intrinsic and extrinsic control of the pKa of thiol guests inside yoctoliter containers. J. Am. Chem. Soc. 142, 8291–8298 (2020).

    CAS  PubMed  Article  Google Scholar 

  60. Barducci, A., Bussi, G. & Parrinello, M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys. Rev. Lett. 100, 020603 (2008).

    PubMed  Article  CAS  Google Scholar 

  61. Grifoni, E., Piccini, G. & Parrinello, M. Microscopic description of acid-base equilibrium. Proc. Natl Acad. Sci. USA 116, 4054–4057 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  62. La Manna, P. et al. Mild Friedel-Crafts reactions inside a hexameric resorcinarene capsule: C-Cl bond activation through hydrogen bonding to bridging water molecules. Angew. Chem. Int. Ed. 57, 5423–5428 (2018).

    Article  CAS  Google Scholar 

  63. Grifoni, E., Piccini, G. & Parrinello, M. Microscopic description of acid-base equilibrium. Proc. Natl Acad. Sci. USA 116, 4054–4057 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. Doubleday, C., Bolton, K. & Hase, W. L. Direct dynamics quasiclassical trajectory study of the thermal stereomutations of cyclopropane. J. Phys. Chem. A 102, 3648–3658 (1998).

    CAS  Article  Google Scholar 

  65. Xu, L., Doubleday, C. E. & Houk, K. N. Dynamics of 1,3-dipolar cycloadditions: energy partitioning of reactants and quantitation of synchronicity. J. Am. Chem. Soc. 132, 3029–3037 (2010).

    CAS  PubMed  Article  Google Scholar 

  66. Fu, Y., Bernasconi, L. & Liu, P. Ab initio molecular dynamics simulations of the SN1/SN2 mechanistic continuum in glycosylation reactions. J. Am. Chem. Soc. 143, 1577–1589 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  67. Xu, L., Doubleday, C. E. & Houk, K. N. Dynamics of 1,3-dipolar cycloaddition reactions of diazonium betaines to acetylene and ethylene: bending vibrations facilitate reaction. Angew. Chem. Int. Ed. 48, 2746–2748 (2009).

    CAS  Article  Google Scholar 

  68. Jiménez-Osés, G., Liu, P., Matute, R. A. & Houk, K. N. Competition between concerted and stepwise dynamics in the triplet di-π-methane rearrangement. Angew. Chem. Int. Ed. 53, 8664–8667 (2014).

    Article  CAS  Google Scholar 

  69. Baldwin, J. E. & Fleming, R. H. Allene-olefin and allene-allene cycloadditions methylenecyclobutane and 1,2-dimethylenecyclobutane degenerate rearrangements. Dynamic Sterochem. https://doi.org/10.1007/BFb0050819 (2006).

  70. Patel, A. et al. Dynamically complex [6 + 4] and [4 + 2] cycloadditions in the biosynthesis of spinosyn A. J. Am. Chem. Soc. 138, 3631–3634 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. Venkatasubban, K. S. & Schowen, R. L. The proton inventory technique. Crit. Rev. Biochem. Mol. Biol. 17, 1–44 (1984).

    CAS  Google Scholar 

  72. Schowen, R. L. The use of solvent isotope effects in the pursuit of enzyme mechanisms. J. Labelled Compd Radiopharm. 50, 1052–1062 (2007).

    CAS  Article  Google Scholar 

  73. Bennett, C. S. & Galan, M. C. Methods for 2-deoxyglycoside synthesis. Chem. Rev. 118, 7931–7985 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. Yao, H., Vu, M. D. & Liu, X.-W. Recent advances in reagent-controlled stereoselective/stereospecific glycosylation. Carbohydr. Res. 473, 72–81 (2019).

    CAS  PubMed  Article  Google Scholar 

  75. Singh, M. K., Jayaraman, N., Rao, D. S. S. & Prasad, S. K. Effect of the C-2 hydroxyl group on the mesomorphism of alkyl glycosides: synthesis and thermotropic behavior of alkyl 2-deoxy-d-arabino-hexopyranosides. Chem. Phys. Lipids 155, 90–97 (2008).

    CAS  PubMed  Article  Google Scholar 

  76. Marino-Albernas, J. R., Bittman, R., Peters, A. & Mayhew, E. Synthesis and growth inhibitory properties of glycosides of 1-O-hexadecyl-2-O-methyl-sn-glycerol, analogs of the antitumor ether lipid ET-18-OCH3 (Edelfosine). J. Med. Chem. 39, 3241–3247 (1996).

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Swiss National Science Foundation as part of the NCCR Molecular Systems Engineering. We thank M. Pfeffer for HR-MS analysis and T. R. Ward for helpful discussions. Molecular dynamics calculations were carried out on the ETH Zurich cluster Euler.

Author information

Authors and Affiliations

Authors

Contributions

K.T. conceived and supervised the project. K.T. and T.-R.L. planned the project. T.-R.L. carried out all the experiments except the mechanistic investigations concerning SKIE and reaction order, which were performed by F.H. T.-R.L. and K.T. compiled the first draft of the manuscript. G.M.P. conceived and modelled the simulation of the system, carried out the simulations, interpreted the results, and wrote the first draft of the molecular dynamics section. All authors contributed to the final version of the manuscript.

Corresponding author

Correspondence to Konrad Tiefenbacher.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Chemistry thanks Alessandro Laio and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary experimental details, Figs. 1–18 and schemes 1–9.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Li, TR., Huck, F., Piccini, G. et al. Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations. Nat. Chem. 14, 985–994 (2022). https://doi.org/10.1038/s41557-022-00981-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41557-022-00981-6

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing