• A Corrigendum to this article was published on 12 July 2017

Abstract

Glucagon-like peptide 1 (GLP-1) regulates glucose homeostasis through the control of insulin release from the pancreas. GLP-1 peptide agonists are efficacious drugs for the treatment of diabetes. To gain insight into the molecular mechanism of action of GLP-1 peptides, here we report the crystal structure of the full-length GLP-1 receptor bound to a truncated peptide agonist. The peptide agonist retains an α-helical conformation as it sits deep within the receptor-binding pocket. The arrangement of the transmembrane helices reveals hallmarks of an active conformation similar to that observed in class A receptors. Guided by this structural information, we design peptide agonists with potent in vivo activity in a mouse model of diabetes.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Protein Data Bank

References

  1. 1.

    & Incretins and other peptides in the treatment of diabetes. Diabet. Med. 24, 223–232 (2007)

  2. 2.

    , & Glucagon-like peptide-1 receptor agonists favorably address all components of metabolic syndrome. World J. Diabetes 7, 441–448 (2016)

  3. 3.

    , & Dipeptidyl-peptidase IV hydrolyses gastric inhibitory polypeptide, glucagon-like peptide-1(7-36)amide, peptide histidine methionine and is responsible for their degradation in human serum. Eur. J. Biochem. 214, 829–835 (1993)

  4. 4.

    , & Degradation of glucagon-like peptide-1 by human plasma in vitro yields an N-terminally truncated peptide that is a major endogenous metabolite in vivo. J. Clin. Endocrinol. Metab. 80, 952–957 (1995)

  5. 5.

    , & Small molecule drug discovery at the glucagon-like peptide-1 receptor. Exp. Diabetes Res. 2012, 709893 (2012)

  6. 6.

    et al. Peptide binding at the GLP-1 receptor. Biochem. Soc. Trans. 35, 713–716 (2007)

  7. 7.

    et al. Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor. J. Biol. Chem. 285, 723–730 (2010)

  8. 8.

    , , , & Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain. J. Biol. Chem. 283, 11340–11347 (2008)

  9. 9.

    et al. Structure of the human glucagon class B G-protein-coupled receptor. Nature 499, 444–449 (2013)

  10. 10.

    et al. Extra-helical binding site of a glucagon receptor antagonist. Nature 533, 274–277 (2016)

  11. 11.

    et al. Identification of potent 11mer glucagon-like peptide-1 receptor agonist peptides with novel C-terminal amino acids: homohomophenylalanine analogs. Peptides 31, 950–955 (2010)

  12. 12.

    et al. Exploration of structure-activity relationships at the two C-terminal residues of potent 11mer glucagon-like peptide-1 receptor agonist peptides via parallel synthesis. Peptides 31, 1353–1360 (2010)

  13. 13.

    et al. Eleven amino acid glucagon-like peptide-1 receptor agonists with antidiabetic activity. J. Med. Chem. 52, 7788–7799 (2009)

  14. 14.

    , , & Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form. Proc. Natl Acad. Sci. USA 105, 877–882 (2008)

  15. 15.

    et al. Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation. Nature 474, 521–525 (2011)

  16. 16.

    et al. Structure of the agonist-bound neurotensin receptor. Nature 490, 508–513 (2012)

  17. 17.

    et al. Conformational states of the full-length glucagon receptor. Nat. Commun. 6, 7859 (2015)

  18. 18.

    et al. Structure of class B GPCR corticotropin-releasing factor receptor 1. Nature 499, 438–443 (2013)

  19. 19.

    , , , & Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proc. Natl Acad. Sci. USA 110, 5211–5216 (2013)

  20. 20.

    ., ., & Modelling dynamics in protein crystal structures by ensemble refinement. eLife 2012, 1–29 (2012)

  21. 21.

    et al. Structural determinants of binding the seven-transmembrane domain of the glucagon-like peptide-1 receptor (GLP-1R). J. Biol. Chem. 291, 12991–13004 (2016)

  22. 22.

    & The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling. Biosci. Rep. 36, e00285 (2015)

  23. 23.

    et al. The extracellular surface of the GLP-1 receptor is a molecular trigger for biased agonism. Cell 165, 1632–1643 (2016)

  24. 24.

    et al. Residues within the transmembrane domain of the glucagon-like peptide-1 receptor involved in ligand binding and receptor activation: modelling the ligand-bound receptor. Mol. Endocrinol. 25, 1804–1818 (2011)

  25. 25.

    , & Characterization of glucagon-like peptide-1 receptor-binding determinants. J. Mol. Endocrinol. 25, 321–335 (2000)

  26. 26.

    et al. Second extracellular loop of human glucagon-like peptide-1 receptor (GLP-1R) has a critical role in GLP-1 peptide binding and receptor activation. J. Biol. Chem. 287, 3642–3658 (2012)

  27. 27.

    et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002)

  28. 28.

    et al. Ligand binding pocket formed by evolutionarily conserved residues in the glucagon-like peptide-1 (GLP-1) receptor core domain. J. Biol. Chem. 290, 5696–5706 (2015)

  29. 29.

    , , , & Met-204 and Tyr-205 are together important for binding GLP-1 receptor agonists but not their N-terminally truncated analogues. Protein Pept. Lett. 11, 15–22 (2004)

  30. 30.

    et al. Molecular basis for negative regulation of the glucagon receptor. Proc. Natl Acad. Sci. USA 109, 14393–14398 (2012)

  31. 31.

    et al. High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks. In Silico Pharmacol. 1, 23 (2013)

  32. 32.

    A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28, 849–857 (1985)

  33. 33.

    et al. High-throughput virtual screening of proteins using GRID molecular interaction fields. J. Chem. Inf. Model. 50, 155–169 (2010)

  34. 34.

    et al. Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature 477, 549–555 (2011)

  35. 35.

    & Structural insights into agonist-induced activation of G-protein-coupled receptors. Curr. Opin. Struct. Biol. 21, 541–551 (2011)

  36. 36.

    , , , & Unifying family A GPCR theories of activation. Pharmacol. Ther. 143, 51–60 (2014)

  37. 37.

    et al. Functional expression of the rat glucagon-like peptide-I receptor, evidence for coupling to both adenylyl cyclase and phospholipase-C. Endocrinology 133, 57–62 (1993)

  38. 38.

    , , & Similar elimination rates of glucagon-like peptide-1 in obese type 2 diabetic patients and healthy subjects. J. Clin. Endocrinol. Metab. 88, 220–224 (2003)

  39. 39.

    Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010)

  40. 40.

    et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011)

  41. 41.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  42. 42.

    et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011)

  43. 43.

    , & Low-resolution refinement tools in REFMAC5. Acta Crystallogr. D Biol. Crystallogr. 68, 404–417 (2012)

  44. 44.

    , , & Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010)

  45. 45.

    . et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010)

  46. 46.

    et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010)

  47. 47.

    & Better models by discarding data? Acta Crystallogr D Biol Crystallogr. 69, 1215–1222 (2013)

Download references

Acknowledgements

We thank various colleagues past and present who have helped with the project. In particular we would like to acknowledge the contribution of K. Hollenstein, M. Koglin and C. Larner. We thank G. Brown for his help with coordinating peptide synthesis and radio-labelling and C. Scully for his assistance with the GRID analysis. We are grateful to R. Owen, J. Waterman and D. Axford at I24, Diamond Light Source, Oxford, UK for technical support.

Author information

Author notes

    • Ali Jazayeri
    • , Mathieu Rappas
    •  & Alastair J. H. Brown

    These authors contributed equally to this work.

Affiliations

  1. Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK

    • Ali Jazayeri
    • , Mathieu Rappas
    • , Alastair J. H. Brown
    • , James Kean
    • , James C. Errey
    • , Nathan J. Robertson
    • , Cédric Fiez-Vandal
    • , Stephen P. Andrews
    • , Miles Congreve
    • , Andrea Bortolato
    • , Jonathan S. Mason
    • , Asma H. Baig
    • , Iryna Teobald
    • , Andrew S. Doré
    • , Malcolm Weir
    • , Robert M. Cooke
    •  & Fiona H. Marshall

Authors

  1. Search for Ali Jazayeri in:

  2. Search for Mathieu Rappas in:

  3. Search for Alastair J. H. Brown in:

  4. Search for James Kean in:

  5. Search for James C. Errey in:

  6. Search for Nathan J. Robertson in:

  7. Search for Cédric Fiez-Vandal in:

  8. Search for Stephen P. Andrews in:

  9. Search for Miles Congreve in:

  10. Search for Andrea Bortolato in:

  11. Search for Jonathan S. Mason in:

  12. Search for Asma H. Baig in:

  13. Search for Iryna Teobald in:

  14. Search for Andrew S. Doré in:

  15. Search for Malcolm Weir in:

  16. Search for Robert M. Cooke in:

  17. Search for Fiona H. Marshall in:

Contributions

J.K., N.J.R. and A.J. carried out the conformational thermostabilization of constructs and determined the stability of the StaR in a panel of reagents/additives. A.H.B. and I.T. carried out the in vitro pharmacology. A.J.H.B. managed the in vivo studies. M.C. and S.P.A. designed the novel peptides, aided by A.B. and J.S.M. who designed the homology models and carried out in silico analyses of peptide binding. M.R. and J.C.E. designed the crystallization construct, and with C.F.V. performed and optimized protein expression and purification. M.R. and C.F.V. performed and optimized protein crystallization. M.R. and A.S.D. harvested crystals, collected and processed X-ray diffraction data, and solved and refined the structure. Project management was carried out by A.J., R.M.C., F.H.M. and M.W. The manuscript was prepared by M.R., A.J., A.S.D., A.J.H.B., M.C., R.M.C. and F.H.M. All authors contributed to the final editing and approval of the manuscript.

Competing interests

All authors are employees of Heptares Therapeutics Ltd and are shareholders in Sosei Group Corporation.

Corresponding author

Correspondence to Fiona H. Marshall.

Reviewer Information Nature thanks T. Schwartz, C. Siebold and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary information

    This file contains Supplementary Text and Data, 2 Supplementary Tables and Supplementary references.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature22800

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.