Crystal structure of the GLP-1 receptor bound to a peptide agonist

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  • 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.

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Figure 1: The overall structure of GLP-1R in complex with peptide 5.
Figure 2: Molecular details of the agonist peptide binding site in GLP-1R.
Figure 3: Comparison of GLP-1R with GCGR and CRF1R.
Figure 4: Mouse in vivo OGTT.

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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

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.

Correspondence to Fiona H. Marshall.

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Competing interests

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

Additional information

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.

An erratum to this article is available online at https://doi.org/10.1038/nature23311.

Extended data figures and tables

Extended Data Figure 1 Peptide 5 and in vitro pharmacology of wild-type GLP-1R.

a, Two-dimensional chemical plot of peptide 5 used in this study. b, Pharmacological characterization of 3H-peptide 1 at the wild-type GLP-1R. Affinity of peptide 1 for wild-type GLP-1R construct was measured using homologous competition experiments against three different concentration of 3H-peptide 1. cpm, counts per minute. Data are representative of four independent experiments and the Kd values are calculated as the arithmetic mean and s.e.m. c, Heterologous competition binding of exendin-4 and exendin-3 at the wild-type GLP-1R determined using 3H-peptide 1. Affinity constants (Ki) were calculated from IC50 values, using the Cheng–Prusoff equation and results are given as the arithmetic mean ± s.e.m.

Extended Data Figure 2 Stability, pharmacological characterization and functional activity of GLP-1R StaR.

a, Thermal stability (Tm) comparison of GLP-1R wild-type and StaR (containing the following point mutations: T207E, Q211A, D215R, L232F, G295A, T298A, C329A, P358A, G361A, H363V and V405A). Thermal stability was measured following solubilization in n-dodecyl-β-d-maltopyranoside supplemented with cholesteryl hemisuccinate (see Methods). Data representative of two independent experiments with Tm values calculated as the arithmetic mean and the standard deviation of the mean. b, Pharmacological characterization of GLP-1R wild-type and StaR. Affinity of peptide 1 for wild-type and StaR constructs was measured using homologous competition experiments against three different concentrations of 3H-peptide 1. Data representative of three independent experiments and the Kd values calculated as the arithmetic mean and the standard deviation of the mean. The difference in the means is not statistically significant as analysed by two-tailed t-test. c, d, cAMP response of GLP-1R wild-type and StaR in the presence of the indicated peptide agonists. e, Reported pEC50 values for each peptide agonist. Data presented is the arithmetic mean of three independent experiments. Error bars represent s.e.m. P values are calculated by multi-parametric two-way ANOVA.

Extended Data Figure 3 The GLP-1R StaR B-factors and electron density.

a, b, B-factor putty representation of the GLP-1R–peptide-5 structure (rainbow spectrum, blue to red = lowest to highest B-factors). c, d, representative 2Fo − Fc electron density contoured at 1.0σ across the orthosteric peptide-binding pocket of GLP-1R.

Extended Data Figure 4 Walkthrough of peptide 5 interactions with GLP-1R StaR.

ak, Views moving from the N to C terminus of peptide 5. Four overlayed models generated by PHENIX ensemble refinement are shown in each panel to demonstrate the confidence that can be assigned to interactions with the receptor described in this study.

Extended Data Figure 5 Structural superposition of the GLP-1R peptide 5 crystal structure with the crystal structure of the isolated GLP-1R extracellular domain in complex with the GLP-1 peptide.

a, Tilted view from membrane of the GLP-1R represented as cartoon (cyan) with the peptide 5 agonist in stick representation and carbon, nitrogen and oxygen atoms coloured yellow, blue and red respectively; the ECD solved in isolation from the TMD of GLP-1R in cartoon representation is coloured orange, with the GLP-1 peptide coloured magenta. The superposition was achieved using equivalent residues from peptide 5 and the GLP-1 peptide. b, Rotation of the superposed structures in a to view from extracellular space, the relative difference in orientation of the ECD is denoted.

Extended Data Figure 6 Evaluation of the lipophilic hotspots on GLP-1R and interactions with peptide 5.

a, GRID hotspot analysis of the binding mode of peptide 5 showing the overlap of the Cap1, X2 and X3 groups of peptide 5 with lipophilic regions of the GLP-1R. GLP-1R is represented as cartoon (cyan) with the ECD coloured brown. The peptide 5 agonist is shown in stick representation with carbon, nitrogen and oxygen atoms coloured yellow, blue and red respectively. The c1 = GRID map is represented as mesh (orange) and contoured at −2.5 kcal mol−1. b, View as in a rotated by 180°.

Extended Data Figure 7 In vitro pharmacological and pharmacokinetic profiles of selected peptides.

ad, Insulinotropic activities of GLP-1 and selected peptides on isolated rat pancreatic islets. Results are presented as mean ± s.e.m. (n = 6 each group) and analysed using a one-way analysis of variance and Dunnett’s post hoc test. Significant differences from basal responses are indicated with an asterisk (*P < 0.05). e, Pharmacokinetics of peptide 2 (1 mg kg−1), peptide 5 (1 mg kg−1) and peptide 8 (0.5 mg kg−1) following intravenous administration in male Sprague Dawley rats. Results presented as mean ± s.e.m. (n = 3). f, Pharmacokinetics of peptide 8 following subcutaneous administration in male CD1 mice. Results presented as mean ± s.e.m. (n = 3).

Extended Data Table 1 Truncated GLP-1 peptide analogues and associated biological data
Extended Data Table 2 Data collection and refinement statistics for GLP-1R StaR complexed with peptide 5
Extended Data Table 3 Pharmacokinetic evaluation of peptide 2, 5 and 8 detailed in this study

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Jazayeri, A., Rappas, M., Brown, A. et al. Crystal structure of the GLP-1 receptor bound to a peptide agonist. Nature 546, 254–258 (2017) doi:10.1038/nature22800

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