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Decoding ligand recognition and constitutive activation of histamine H3 and H4 receptors

Acta Pharmacologica Sinica (2025)Cite this article

Abstract

Histamine H3 receptor (H3R) and H4 receptor (H4R) are key members of the histamine receptor family, with H3R as a potential target for narcolepsy treatments and H4R as a candidate for next-generation antihistamines for inflammatory and allergic diseases. Although progress has been made in understanding the structure of histamine receptors, the detailed mechanisms of ligand recognition and receptor antagonism for H3R and H4R remain unclear. In this study, using cryo-electron microscopy, we present an inactive structure of H4R bound to a selective antagonist, adriforant, and two Gi-coupled structures of H3R and H4R in complex with histamine. Our structural and mutagenesis analyses provide insights into the selective binding of adriforant to H4R and the recognition of histamine across histamine receptors. Our findings also uncovered distinct antagonistic mechanisms for H3R and H4R and identified the role of aromatic amino acids on extracellular loop 2 in modulating the constitutive activity of H3R and H4R. These findings advance our knowledge of the functional modulation of histamine receptors, providing a foundation for the development of targeted therapeutics for neurological and immune-related disorders.

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Fig. 1: Cryo-EM structures of histamine receptors H3R and H4R.
Fig. 2: Recognition and selectivity of adriforant for H4R.
Fig. 3: Histamine recognition in histamine receptors.
Fig. 4: Antagonism mechanism of H3R and H4R.
Fig. 5: ECL2b in histamine receptors.

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Acknowledgements

The cryo-EM data were collected at the Advanced Center for Electron Microscopy, Shanghai Institute of Materia Medica. We thank all staff at the institution for their assistance with cryo-EM data collection. This work was partially supported by the National Key R&D Program of China (2022YFC2703105 to HEX); the Lingang Laboratory (LG-GG-202204-01 to YJ); the National Natural Science Foundation of China (32171187 to YJ; 82121005 to YJ, HEX and DHY; 32130022 to HEX; 82273985 to DHY; 82273961 to MWW); the CAS Strategic Priority Research Program (XDB37030103 to HEX); the Shanghai Municipal Science and Technology Major Project (2019SHZDZX02 to HEX); the National Key Basic Research Program of China (2023YFA1800804 to DHY); the Shanghai Municipality Science and Technology Development Fund (21JC1401600 to DHY); the Program of Shanghai Academic/Technology Research Leader (23XD1400900 to DHY); Sanya Science and Technology Innovation Special Project (2022KJCX77 to DHY).

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  1. These authors contributed equally: San-shan Jin, Heng Zhang, Jia-hui Yan

Authors and Affiliations

  1. Lingang Laboratory, Shanghai, 200031, China

    San-shan Jin & Yi Jiang

  2. School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

    San-shan Jin & Yi Jiang

  3. State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Heng Zhang, Can-rong Wu, Kai Wu & H. Eric Xu

  4. National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Jia-hui Yan, Xiao-qing Cai & De-hua Yang

  5. University of Chinese Academy of Sciences, Beijing, 100049, China

    Jia-hui Yan, H. Eric Xu & De-hua Yang

  6. Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China

    Can-rong Wu, Ming-Wei Wang & H. Eric Xu

  7. State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Xiao-qing Cai & De-hua Yang

  8. The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Kai Wu & H. Eric Xu

  9. Research Center for Deepsea Bioresources, Sanya, 572025, China

    Ming-Wei Wang

  10. School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China

    Yi Jiang

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Contributions

SSJ screened constructs and purification conditions, prepared the protein samples for final structure determination, participated in cryo-EM grid inspection and data collection, analyzed structures and performed some of the functional studies, and prepared the Figs. and wrote the initial manuscript. HZ performed cryo-EM data collection and structure determination, built and refined structure models, prepared Figs. and manuscript draft. JHY and XQC prepared the constructs for functional assays and conducted functional studies and functional data analysis. CRW. participated in protein sample optimization and purification, participated in grid preparation, cryo-EM grid inspection, and gave advice to the functional study. KW participated in data collection and analysis. DHY. and MWW conceived and supervised the functional study. HEX conceived and supervised the structure determination. YJ initiated, conceived, and supervised the project, analyzed structures, prepared the Figs. and wrote the manuscript with inputs from all authors.

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Correspondence to H. Eric Xu, De-hua Yang or Yi Jiang.

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Jin, Ss., Zhang, H., Yan, Jh. et al. Decoding ligand recognition and constitutive activation of histamine H3 and H4 receptors. Acta Pharmacol Sin (2025). https://doi.org/10.1038/s41401-025-01633-4

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