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Structure of the human histamine H1 receptor complex with doxepin

Abstract

The biogenic amine histamine is an important pharmacological mediator involved in pathophysiological processes such as allergies and inflammations. Histamine H1 receptor (H1R) antagonists are very effective drugs alleviating the symptoms of allergic reactions. Here we show the crystal structure of the H1R complex with doxepin, a first-generation H1R antagonist. Doxepin sits deep in the ligand-binding pocket and directly interacts with Trp 4286.48, a highly conserved key residue in G-protein-coupled-receptor activation. This well-conserved pocket with mostly hydrophobic nature contributes to the low selectivity of the first-generation compounds. The pocket is associated with an anion-binding region occupied by a phosphate ion. Docking of various second-generation H1R antagonists reveals that the unique carboxyl group present in this class of compounds interacts with Lys 1915.39 and/or Lys 179ECL2, both of which form part of the anion-binding region. This region is not conserved in other aminergic receptors, demonstrating how minor differences in receptors lead to pronounced selectivity differences with small molecules. Our study sheds light on the molecular basis of H1R antagonist specificity against H1R.

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Figure 1: Structure of H 1 R complex with doxepin.
Figure 2: Comparison of the structures of H 1 R, β 2 -AR and D3R.
Figure 3: Binding interactions of doxepin.
Figure 4: Interactions of second-generation selective H 1 R antagonists with the H 1 R ligand-binding pocket.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and the structure factors have been deposited in the Protein Data Bank under the accession code 3RZE.

References

  1. Schwartz, J. C., Arrang, J. M., Garbarg, M., Pollard, H. & Ruat, M. Histaminergic transmission in the mammalian brain. Physiol. Rev. 71, 1–51 (1991)

    Article  CAS  Google Scholar 

  2. Hill, S. J. Distribution, properties, and functional characteristics of three classes of histamine receptor. Pharmacol. Rev. 42, 45–83 (1990)

    CAS  PubMed  Google Scholar 

  3. Hill, S. J. et al. International Union of Pharmacology. XIII. Classification of histamine receptors. Pharmacol. Rev. 49, 253–278 (1997)

    CAS  PubMed  Google Scholar 

  4. Yamashita, M. et al. Expression cloning of a cDNA encoding the bovine histamine H1 receptor. Proc. Natl Acad. Sci. USA 88, 11515–11519 (1991)

    Article  ADS  CAS  Google Scholar 

  5. Simons, F. E. Advances in H1-antihistamines. N. Engl. J. Med. 351, 2203–2217 (2004)

    Article  CAS  Google Scholar 

  6. Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there? Nature Rev. Drug Discov. 5, 993–996 (2006)

    Article  CAS  Google Scholar 

  7. Bakker, R. A., Wieland, K., Timmerman, H. & Leurs, R. Constitutive activity of the histamine H1 receptor reveals inverse agonism of histamine H1 receptor antagonists. Eur. J. Pharmacol. 387, R5–R7 (2000)

    Article  CAS  Google Scholar 

  8. Bakker, R. A., Schoonus, S. B., Smit, M. J., Timmerman, H. & Leurs, R. Histamine H1-receptor activation of nuclear factor-κB: roles for Gβγ- and Gαq/11-subunits in constitutive and agonist-mediated signaling. Mol. Pharmacol. 60, 1133–1142 (2001)

    Article  CAS  Google Scholar 

  9. Tashiro, M. et al. Dose dependency of brain histamine H1 receptor occupancy following oral administration of cetirizine hydrochloride measured using PET with [11C]doxepin. Hum. Psychopharmacol. 24, 540–548 (2009)

    Article  MathSciNet  CAS  Google Scholar 

  10. Woosley, R. L., Chen, Y., Freiman, J. P. & Gillis, R. A. Mechanism of the cardiotoxic actions of terfenadine. J. Am. Med. Assoc. 269, 1532–1536 (1993)

    Article  CAS  Google Scholar 

  11. Yap, Y. G. & Camm, A. J. Potential cardiac toxicity of H1-antihistamines. Clin. Allergy Immunol. 17, 389–419 (2002)

    CAS  PubMed  Google Scholar 

  12. Okamura, N. et al. Functional neuroimaging of cognition impaired by a classical antihistamine, d-chlorpheniramine. Br. J. Pharmacol. 129, 115–123 (2000)

    Article  CAS  Google Scholar 

  13. Cusack, B., Nelson, A. & Richelson, E. Binding of antidepressants to human brain receptors: focus on newer generation compounds. Psychopharmacology (Berl.) 114, 559–565 (1994)

    Article  CAS  Google Scholar 

  14. Sarker, S. et al. The high-affinity binding site for tricyclic antidepressants resides in the outer vestibule of the serotonin transporter. Mol. Pharmacol. 78, 1026–1035 (2010)

    Article  CAS  Google Scholar 

  15. Klabunde, T. & Hessler, G. Drug design strategies for targeting G-protein-coupled receptors. ChemBioChem 3, 928–944 (2002)

    Article  CAS  Google Scholar 

  16. de Graaf, C., Rognan, D. & Customizing, G. Protein-coupled receptor models for structure-based virtual screening. Curr. Pharm. Des. 15, 4026–4048 (2009)

    Article  CAS  Google Scholar 

  17. Palczewski, K. et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289, 739–745 (2000)

    Article  ADS  CAS  Google Scholar 

  18. Cherezov, V. et al. High-resolution crystal structure of an engineered human β2-adrenergic G protein-coupled receptor. Science 318, 1258–1265 (2007)

    Article  ADS  CAS  Google Scholar 

  19. Warne, T. et al. Structure of a β1-adrenergic G-protein-coupled receptor. Nature 454, 486–491 (2008)

    Article  ADS  CAS  Google Scholar 

  20. Jaakola, V. P. et al. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322, 1211–1217 (2008)

    Article  ADS  CAS  Google Scholar 

  21. Murakami, M. & Kouyama, T. Crystal structure of squid rhodopsin. Nature 453, 363–367 (2008)

    Article  ADS  CAS  Google Scholar 

  22. Wu, B. et al. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330, 1066–1071 (2010)

    Article  ADS  CAS  Google Scholar 

  23. Chien, E. Y. et al. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science 330, 1091–1095 (2010)

    Article  ADS  CAS  Google Scholar 

  24. Kolb, P. et al. Structure-based discovery of β2-adrenergic receptor ligands. Proc. Natl Acad. Sci. USA 106, 6843–6848 (2009)

    Article  ADS  CAS  Google Scholar 

  25. Katritch, V. et al. Structure-based discovery of novel chemotypes for adenosine A2A receptor antagonists. J. Med. Chem. 53, 1799–1809 (2010)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  27. Ratnala, V. R. et al. Large-scale overproduction, functional purification and ligand affinities of the His-tagged human histamine H1 receptor. Eur. J. Biochem. 271, 2636–2646 (2004)

    Article  CAS  Google Scholar 

  28. Ballesteros, J. A. & Weinstein, H. Integrated methods for the construction of three-dimensional models and computational probing of structure–function relations in G protein-coupled receptors. Methods Neurosci. 25, 366–428 (1995)

    Article  CAS  Google Scholar 

  29. Qanbar, R. & Bouvier, M. Role of palmitoylation/depalmitoylation reactions in G-protein-coupled receptor function. Pharmacol. Ther. 97, 1–33 (2003)

    Article  CAS  Google Scholar 

  30. Wieland, K. et al. Mutational analysis of the antagonist-binding site of the histamine H1 receptor. J. Biol. Chem. 274, 29994–30000 (1999)

    Article  CAS  Google Scholar 

  31. Ohta, K. et al. Site-directed mutagenesis of the histamine H1 receptor: roles of aspartic acid107, asparagine198 and threonine194 . Biochem. Biophys. Res. Commun. 203, 1096–1101 (1994)

    Article  CAS  Google Scholar 

  32. Nonaka, H. et al. Unique binding pocket for KW-4679 in the histamine H1 receptor. Eur. J. Pharmacol. 345, 111–117 (1998)

    Article  ADS  CAS  Google Scholar 

  33. Bruysters, M. et al. Mutational analysis of the histamine H1-receptor binding pocket of histaprodifens. Eur. J. Pharmacol. 487, 55–63 (2004)

    Article  CAS  Google Scholar 

  34. Peeters, M. C., van Westen, G. J., Li, Q. & Ijzerman, A. P. Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation. Trends Pharmacol. Sci. 32, 35–42 (2011)

    Article  CAS  Google Scholar 

  35. Gillard, M. et al. H1 antagonists: receptor affinity versus selectivity. Inflamm. Res. 52 (Suppl. 1). S49–S50 (2003)

    Article  CAS  Google Scholar 

  36. Kiss, R., Kovari, Z. & Keseru, G. M. Homology modelling and binding site mapping of the human histamine H1 receptor. Eur. J. Med. Chem. 39, 959–967 (2004)

    Article  CAS  Google Scholar 

  37. Jongejan, A. & Leurs, R. Delineation of receptor–ligand interactions at the human histamine H1 receptor by a combined approach of site-directed mutagenesis and computational techniques—or—how to bind the H1 receptor. Arch. Pharm. (Weinheim) 338, 248–259 (2005)

    Article  CAS  Google Scholar 

  38. Totrov, M. & Abagyan, R. Flexible protein–ligand docking by global energy optimization in internal coordinates. Proteins (Suppl. 1). 29, 215–220 (1997)

  39. Katritch, V. et al. Analysis of full and partial agonists binding to β2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J. Mol. Recognit. 22, 307–318 (2009)

    Article  CAS  Google Scholar 

  40. Katritch, V., Kufareva, I. & Abagyan, R. Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology 60, 108–115 (2011)

    Article  CAS  Google Scholar 

  41. Matsumoto, Y., Funahashi, J., Mori, K., Hayashi, K. & Yano, H. The noncompetitive antagonism of histamine H1 receptors expressed in Chinese hamster ovary cells by olopatadine hydrochloride: its potency and molecular mechanism. Pharmacology 81, 266–274 (2008)

    Article  CAS  Google Scholar 

  42. Gillard, M., Van Der Perren, C., Moguilevsky, N., Massingham, R. & Chatelain, P. Binding characteristics of cetirizine and levocetirizine to human H1 histamine receptors: contribution of Lys191 and Thr194 . Mol. Pharmacol. 61, 391–399 (2002)

    Article  CAS  Google Scholar 

  43. Leurs, R., Smit, M. J., Meeder, R., Ter Laak, A. M. & Timmerman, H. Lysine200 located in the fifth transmembrane domain of the histamine H1 receptor interacts with histamine but not with all H1 agonists. Biochem. Biophys. Res. Commun. 214, 110–117 (1995)

    Article  CAS  Google Scholar 

  44. Bakker, R. A. et al. 8R-lisuride is a potent stereospecific histamine H1-receptor partial agonist. Mol. Pharmacol. 65, 538–549 (2004)

    Article  CAS  Google Scholar 

  45. Xu, F. et al. Structure of an agonist-bound human A2A adenosine receptor. Science 332, 322–327 (2011)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  47. Newstead, S., Kim, H., von Heijne, G., Iwata, S. & Drew, D. High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 104, 13936–13941 (2007)

    Article  ADS  CAS  Google Scholar 

  48. Cherezov, V., Peddi, A., Muthusubramaniam, L., Zheng, Y. F. & Caffrey, M. A robotic system for crystallizing membrane and soluble proteins in lipidic mesophases. Acta Crystallogr. D 60, 1795–1807 (2004)

    Article  Google Scholar 

  49. Aishima, J. et al. High-speed crystal detection and characterization using a fast-readout detector. Acta Crystallogr. D 66, 1032–1035 (2010)

    Article  CAS  Google Scholar 

  50. Winter, G. xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Cryst. 43, 186–190 (2010)

    Article  CAS  Google Scholar 

  51. Leslie, A. G. W. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 ESF-EACMB Newslet. Protein Crystallogr. No. 26. (1992)

  52. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)

    Article  Google Scholar 

  53. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  54. Skubák, P., Murshudov, G. N. & Pannu, N. S. Direct incorporation of experimental phase information in model refinement. Acta Crystallogr. D 60, 2196–2201 (2004)

    Article  Google Scholar 

  55. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  56. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and Development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  57. Abagyan, R., Orry, A., Raush, E. & Totrov, M. ICM Manual v.3.0 (MolSoft LLC, 2011)

  58. Totrov, M. & Abagyan, R. Derivation of sensitive discrimination potential for virtual ligand screening. Proceedings of the third annual international conference on computational molecular biology 312–317. (1999)

  59. Abagyan, R. & Totrov, M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983–1002 (1994)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the ERATO Human Receptor Crystallography Project from the Japan Science and Technology Agency and by the Targeted Proteins Research Program of MEXT (S.I.), Japan; the NIH Common Fund grant P50 GM073197 for technology development (R.C.S.) and NIH PSI:Biology grant U54 GM094618 (R.C.S., V.C., V.K. and R.A.); R.A. was also partly funded by NIH R01 GM071872. The work was also partly funded by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/G023425/1 (S.I.), Grant-in-Aid for challenging Exploratory Research (T.S.), the Mochida Memorial Foundation for Medical and Pharmaceutical Research (T.S. and T.K.), Takeda Scientific Foundation (M.S.) and the Sumitomo Foundation (T.K.). A part of the work was performed in the Membrane Protein Laboratory funded by the Wellcome Trust (grant 062164/ Z/00/Z) at the Diamond Light Source Limited and at The Scripps Research Institute. We thank D. Axford, R. Owen and G. Evans for help with data collection at I24 of the Diamond Light Source Limited, H. Wu for help with the preparation of Supplementary Fig. 1 and Q. Xu for help on validation of data processing and A. Walker for assistance with manuscript preparation. The authors acknowledge Y. Zheng (The Ohio State University) and M. Caffrey, Trinity College (Dublin, Ireland), for the loan of the in meso robot (built with support from the NIH (GM075915), the National Science Foundation (IIS0308078), and Science Foundation Ireland (02-IN1-B266)). S.I. is thankful for the help of L. E. Johnson, a co-founder of the Diamond-MPL Project and R. Tanaka, the technical coordinator of the ERATO Human Receptor Crystallography Project.

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Authors and Affiliations

Authors

Contributions

T.S. purified and crystallized the receptor in LCP, optimized crystallization conditions, grew crystals for data collection, solved and refined the structure, and prepared the manuscript. M.S. designed, characterized and screened the constructs, purified the receptor, and prepared the manuscript. S.W. and S.I. collected the data and processed diffraction data with G.W.H. H.T. expressed the receptor, prepared the membrane, and performed the ligand-binding assay. V.K. and R.A. performed flexible ligand-receptor docking, and prepared the manuscript. V.C. assisted with the crystallization in LCP and prepared the manuscript. W.L. performed the thermal stability assay and assisted with the crystallization in LCP. G.W.H. refined the structure and assisted with preparing the manuscript. T.K. designed the receptor production strategy and assisted with preparing the manuscript. R.C.S. and S.I. were responsible for the overall project strategy and management and wrote the manuscript.

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Correspondence to Takuya Kobayashi, Raymond C. Stevens or So Iwata.

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The authors declare no competing financial interests.

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Shimamura, T., Shiroishi, M., Weyand, S. et al. Structure of the human histamine H1 receptor complex with doxepin. Nature 475, 65–70 (2011). https://doi.org/10.1038/nature10236

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