Letter

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators

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Accepted:
Published online:

Abstract

The glucagon-like peptide-1 receptor (GLP-1R) and the glucagon receptor (GCGR) are members of the secretin-like class B family of G-protein-coupled receptors (GPCRs) and have opposing physiological roles in insulin release and glucose homeostasis1. The treatment of type 2 diabetes requires positive modulation of GLP-1R to inhibit glucagon secretion and stimulate insulin secretion in a glucose-dependent manner2. Here we report crystal structures of the human GLP-1R transmembrane domain in complex with two different negative allosteric modulators, PF-06372222 and NNC0640, at 2.7 and 3.0 Å resolution, respectively. The structures reveal a common binding pocket for negative allosteric modulators, present in both GLP-1R and GCGR3 and located outside helices V–VII near the intracellular half of the receptor. The receptor is in an inactive conformation with compounds that restrict movement of the intracellular tip of helix VI, a movement that is generally associated with activation mechanisms in class A GPCRs4,5,6. Molecular modelling and mutagenesis studies indicate that agonist positive allosteric modulators target the same general region, but in a distinct sub-pocket at the interface between helices V and VI, which may facilitate the formation of an intracellular binding site that enhances G-protein coupling.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China grants 31330019 (Z.-J.L.), 31500593 (G.S.), 81373463 and 81573479 (D.Y.), the National Health and Family Planning Commission grants 2012ZX09304-011, 2013ZX09401003-005, 2013ZX09507001 and 2013ZX09507-002 (M.-W.W.), Shanghai Science and Technology Development Fund 15DZ2291600 (M.-W.W.), and Ministry of Science and Technology of China grants 2014CB910400 (Z.-J.L.) and 2015CB910104 (Z.-J.L.), the Netherlands eScience Center (NLeSC)/NWO Enabling Technologies project: 3D-e-Chem, grant 027.014.201 (C.d.G.), the European Cooperation in Science and Technology Action CM1207 GLISTEN (C.d.G.), and National Key Research and Development Program of China 2016YCF0905902 (S.Z.). We thank the Cloning, Cell Expression and Protein Purification Core Facilities of iHuman Institute for their support. We thank L. Qu, Y. Feng and C. Ji for their technical assistance, Y. Liu, H. Tao, S. Qin, W. Shui, F. Ni, C. Zhang, J. Cheng, Q. Zhao and V. Cherezov for discussions or contributions at the early stages of this project, and A. Walker and S. Reedtz-Runge for critical review of the manuscript. We thank the Shanghai Municipal Government, ShanghaiTech University and GPCR Consortium for financial support. The synchrotron radiation experiments were performed at the BL41XU of Spring-8 with approval of the Japan Synchrotron Radiation Research Institute (JASRI) (proposal no. 2016B2708 and 2016B2724), and beamline BL17U1 (Shanghai Synchrotron Radiation Facility [SSRF], China). Computational resources were supported by the Shanghai Supercomputer Center, and the Supercomputing Center of ShanghaiTech University.

Author information

Author notes

    • Dehua Yang
    • , Yuxia Wang
    •  & Chris de Graaf

    These authors contributed equally to this work.

Affiliations

  1. iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China

    • Gaojie Song
    • , Yuxia Wang
    • , Qingtong Zhou
    • , Kaiwen Liu
    • , Dongsheng Liu
    • , Fan Wu
    • , Yiran Wu
    • , Suwen Zhao
    • , Zhi-Jie Liu
    •  & Raymond C. Stevens
  2. The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China

    • Dehua Yang
    • , Xiaoqing Cai
    • , Antao Dai
    •  & Ming-Wei Wang
  3. Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands

    • Chris de Graaf
  4. School of Pharmacy, Fudan University, 826 Zhang Heng Road, Shanghai 201203, China

    • Shanshan Jiang
    • , Li Ye
    •  & Ming-Wei Wang
  5. School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China

    • Kaiwen Liu
    • , Guangyao Lin
    • , Fan Wu
    • , Suwen Zhao
    • , Beili Wu
    • , Zhi-Jie Liu
    • , Ming-Wei Wang
    •  & Raymond C. Stevens
  6. University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China

    • Kaiwen Liu
    • , Fan Wu
    •  & Beili Wu
  7. Department of Chemistry, Bridge Institute, University of Southern California, 3430 S. Vermont Avenue, Los Angeles, California 90089, USA

    • Gye Won Han
  8. Novo Nordisk, Måløv DK-2760, Denmark

    • Jesper Lau
  9. The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China

    • Beili Wu
  10. GPCR Consortium, San Marcos, California 92078, USA

    • Michael A. Hanson
  11. Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China

    • Zhi-Jie Liu

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Contributions

G.S., C.d.G. and M.A.H. designed constructs for crystallization. G.S., Y.W., S.J. and K.L. expressed, characterized and screened constructs and ligands for crystallization. G.S., Y.W., S.J. and F.W. purified and crystallized the receptor, optimized crystallization conditions and grew the crystals. G.S., Z.-J.L., M.A.H. and G.W.H. collected diffraction data and solved and refined the structure. G.S., D.Y. and C.d.G. designed and analysed the receptor mutagenesis studies. D.Y., X.C., A.D. and G.L. expressed the receptor, and performed the mutagenesis, functional and ligand-binding assays. Q.Z., Y.W., C.d.G. and S.Z. constructed the GLP-1R–agonist PAM model and performed and analysed MD-simulations on wild-type and mutant GLP-1R. B.W. provided advice on construct design. R.C.S. conceived of the project. R.C.S., M.-W.W., and Z.-J.L. were responsible for the overall project management and edited the manuscript. G.S., C.d.G. and M.A.H. wrote the manuscript with discussions and improvements from D.L., L.Y. and J.L.

Competing interests

J.L. is an employee of Novo Nordisk, a pharmaceutical company focused on GLP-1R for type 2 diabetes. R.C.S. is a founder and board member of Bird Rock Bio, a company focused on GPCR therapeutic antibodies. The remaining authors declare no competing financial interests.

Corresponding authors

Correspondence to Zhi-Jie Liu or Ming-Wei Wang or Raymond C. Stevens.

Reviewer Information Nature thanks G. Lebon, T. W. Schwartz and C. Siebold 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.

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