Letter | Published:

Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure

Nature volume 548, pages 480484 (24 August 2017) | Download Citation

Abstract

G-protein-coupled receptors (GPCRs) pose challenges for drug discovery efforts because of the high degree of structural homology in the orthosteric pocket, particularly for GPCRs within a single subfamily, such as the nine adrenergic receptors. Allosteric ligands may bind to less-conserved regions of these receptors and therefore are more likely to be selective. Unlike orthosteric ligands, which tonically activate or inhibit signalling, allosteric ligands modulate physiologic responses to hormones and neurotransmitters, and may therefore have fewer adverse effects. The majority of GPCR crystal structures published to date were obtained with receptors bound to orthosteric antagonists, and only a few structures bound to allosteric ligands have been reported. Compound 15 (Cmpd-15) is an allosteric modulator of the β2 adrenergic receptor (β2AR) that was recently isolated from a DNA-encoded small-molecule library1. Orthosteric β-adrenergic receptor antagonists, known as beta-blockers, are amongst the most prescribed drugs in the world and Cmpd-15 is the first allosteric beta-blocker. Cmpd-15 exhibits negative cooperativity with agonists and positive cooperativity with inverse agonists. Here we present the structure of the β2AR bound to a polyethylene glycol-carboxylic acid derivative (Cmpd-15PA) of this modulator. Cmpd-15PA binds to a pocket formed primarily by the cytoplasmic ends of transmembrane segments 1, 2, 6 and 7 as well as intracellular loop 1 and helix 8. A comparison of this structure with inactive- and active-state structures of the β2AR reveals the mechanism by which Cmpd-15 modulates agonist binding affinity and signalling.

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References

  1. 1.

    et al. Allosteric ‘beta-blocker’ isolated from a DNA-encoded small molecule library. Proc. Natl Acad. Sci. 114, 1708–1713 (2017)

  2. 2.

    et al. Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature 504, 101–106 (2013)

  3. 3.

    et al. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature 540, 458–461 (2016)

  4. 4.

    et al. Intracellular allosteric antagonism of the CCR9 receptor. Nature 540, 462–465 (2016)

  5. 5.

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

  6. 6.

    et al. GPCR engineering yields high-resolution structural insights into β2-adrenergic receptor function. Science 318, 1266–1273 (2007)

  7. 7.

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

  8. 8.

    et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523, 561–567 (2015)

  9. 9.

    et al. Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation. Nature 535, 448–452 (2016)

  10. 10.

    et al. Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature 502, 575–579 (2013)

  11. 11.

    et al. Structure of a nanobody-stabilized active state of the β2 adrenoceptor. Nature 469, 175–180 (2011)

  12. 12.

    et al. Structural insights into μ-opioid receptor activation. Nature 524, 315–321 (2015)

  13. 13.

    Amino and carboxyl terminal modifications to facilitate the production and purification of a G protein-coupled receptor. Anal. Biochem. 231, 269–271 (1995)

  14. 14.

    & Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009)

  15. 15.

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

  16. 16.

    et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl Acad. Sci. 103, 8060–8065 (2006)

  17. 17.

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

  18. 18.

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

  19. 19.

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

  20. 20.

    Fast Fourier transform calculation of electron density maps. Methods Enzymol. 115, 324–337 (1985)

  21. 21.

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

  22. 22.

    Stock-based detection of protein oligomeric states in jsPISA. Nucleic Acids Res. 43 (W1), W314–W319 (2015)

  23. 23.

    et al. A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein. Proc. Natl Acad. Sci. 104, 7682–7687 (2007)

  24. 24.

    et al. Divergent transducer-specific molecular efficacies generate biased agonism at a G protein-coupled receptor (GPCR). J. Biol. Chem. 289, 14211–14224 (2014)

  25. 25.

    et al. The effect of pH on β2 adrenoceptor function. Evidence for protonation-dependent activation. J. Biol. Chem. 275, 3121–3127 (2000)

  26. 26.

    , & Insights into the role of Asp792.50 in β2 adrenergic receptor activation from molecular dynamics simulations. Biochemistry 53, 7283–7296 (2014)

  27. 27.

    , , & OPM: orientations of proteins in membranes database. Bioinformatics 22, 623–625 (2006)

  28. 28.

    & CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013)

  29. 29.

    et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830–7843 (2010)

  30. 30.

    et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586–3616 (1998)

  31. 31.

    et al. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles. J. Chem. Theory Comput. 8, 3257–3273 (2012)

  32. 32.

    , , & Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys. J. 103, 1045–1051 (2012)

  33. 33.

    et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31, 671–690 (2010)

  34. 34.

    , & Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 52, 3155–3168 (2012)

  35. 35.

    & Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model. 52, 3144–3154 (2012)

  36. 36.

    , , , & Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh ewald. J. Chem. Theory Comput. 9, 3878–3888 (2013)

  37. 37.

    et al. AMBER 2016. (2016)

  38. 38.

    , , & Long-time-step molecular dynamics through hydrogen mass repartitioning. J. Chem. Theory Comput. 11, 1864–1874 (2015)

  39. 39.

    , & VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)

  40. 40.

    , & LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions. Protein Eng. 8, 127–134 (1995)

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Acknowledgements

We thank K. Hirata at Beamline BL32XU of Spring-8 for assistance in data collection. A. Wall and T. Xu provided technical assistance. NuEvolution for constructive discussions in the course of the work. We acknowledge support from the National Institute of Health grants NS028471 and GM106990 (B.K.K.), HL16037 (R.J.L.) and T32HL007101 (A.W.K. and A.M.), Amgen-China Postdoc fellowship (X.L.) and the Mathers Foundation (B.K.K. and W.I.W.). R.J.L. is an investigator with the Howard Hughes Medical Institute.

Author information

Author notes

    • Xiangyu Liu
    •  & Seungkirl Ahn

    These authors contributed equally to this work.

Affiliations

  1. Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China

    • Xiangyu Liu
    •  & Brian K. Kobilka
  2. Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA

    • Seungkirl Ahn
    • , Alem W. Kahsai
    • , Biswaranjan Pani
    • , Ali Masoudi
    •  & Robert J. Lefkowitz
  3. Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, Jiangsu, China

    • Kai-Cheng Meng
    •  & Xin Chen
  4. Department of Computer Science, Stanford University, Stanford, California 94305, USA

    • Naomi R. Latorraca
    • , A. J. Venkatakrishnan
    •  & Ron O. Dror
  5. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, USA

    • Naomi R. Latorraca
    • , A. J. Venkatakrishnan
    •  & Ron O. Dror
  6. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA

    • A. J. Venkatakrishnan
    •  & Brian K. Kobilka
  7. Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • William I. Weis
  8. Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA

    • Robert J. Lefkowitz
  9. Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA

    • Robert J. Lefkowitz

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Contributions

X.L. expressed and purified β2AR–T4L, performed crystallization, data collection, data processing, structure determination and refinement. S.A. designed and performed in vitro radio ligand binding and mutagenesis studies. A.W.K. designed the chemical synthetic route for Cmpd-15PA. B.P. designed and performed the in vitro radio ligand binding experiments. A.M. assisted in the design of mutagenesis studies and the development of Cmpd-15PA. K.-C.M. synthesized Cmpd-15PA and analysed the spectral data. X.C. designed the chemical structure and synthetic route for Cmpd-15PA, analysed the spectral data and assisted in manuscript preparation. N.R.L. performed and analysed molecular dynamics simulations, with assistance from A.J.V. R.O.D. oversaw molecular dynamics simulations and analysis. W.I.W. oversaw data processing, structure determination and refinement. The manuscript was written by B.K.K. with assistance from X.L. R.J.L. and B.K.K. coordinated the experiments and supervised the overall research. All authors contributed to the editing of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Robert J. Lefkowitz or Brian K. Kobilka.

Reviewer Information Nature thanks T. Sakmar, P. Scheerer 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.

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https://doi.org/10.1038/nature23652

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