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Structures of the 5-HT2A receptor in complex with the antipsychotics risperidone and zotepine

Abstract

Many drugs target the serotonin 2A receptor (5-HT2AR), including second-generation antipsychotics that also target the dopamine D2 receptor (D2R). These drugs often produce severe side effects due to non-selective binding to other aminergic receptors. Here, we report the structures of human 5-HT2AR in complex with the second-generation antipsychotics risperidone and zotepine. These antipsychotics effectively stabilize the inactive conformation by forming direct contacts with the residues at the bottom of the ligand-binding pocket, the movements of which are important for receptor activation. 5-HT2AR is structurally similar to 5-HT2CR but possesses a unique side-extended cavity near the orthosteric binding site. A docking study and mutagenic studies suggest that a highly 5-HT2AR-selective antagonist binds the side-extended cavity. The conformation of the ligand-binding pocket in 5-HT2AR significantly differs around extracellular loops 1 and 2 from that in D2R. These findings are beneficial for the rational design of safer antipsychotics and 5-HT2AR-selective drugs.

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Data availability

The atomic coordinates and structure factors for the reported crystal structures have been deposited in the Protein Data Bank under accession codes 6A93 (5-HT2ARris) and 6A94 (5-HT2ARzot). Source data for Figs. 3c and 6c,d and Supplementary Figure 6a,b are available with the paper online. Other data are available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank K. Yamashita and the beamline staff for helping with the data collection at SPring-8. Data were collected at SPring-8 (Proposal nos. 2013A1379, 2013B1184, 2014A1301, 2014B1273, 2015A1044, 2015A1080, 2015B2080 and 2017A2524). This research was supported by the Information Core of the Platform Project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from the Japan Agency for Medical Research and Development (AMED), the Research Acceleration Program of the JST (S.I.), JSPS KAKENHI (grant nos. 24370044, 24121715, 26102725, 15H04338, 17K19349, and 18H02388 (T.S.), 26840021 (K.T.K.) and 17K08264 (A.I.)), the PRIME JP17gm5910013 (A.I.) and the LEAP JP17gm0010004 (A.I. and J.A.) from AMED, and the Mitsubishi Foundation (T.S).

Author information

K.T.K. screened, expressed, and purified the constructs, performed crystallization trials for the constructs, collected the data with the help of D.I. and K.H., and performed the docking study. H.A. performed binding assays. D.I. collected and processed the data and solved the structures. C.M. screened, expressed, and purified the constructs, performed crystallization trials, and determined and optimized the crystallization conditions for the constructs. T.A. screened, expressed, and purified the constructs and performed crystallization trials for the constructs. A.I. and F.M.N.K. designed, performed, and analyzed functional assays under the supervision of J.A. N.N. and Y.N. prepared the mutants. T.S. designed and supervised the project. S.I. advised T.S. T.S. and S.I. wrote the manuscript. All authors discussed the results and provided comments regarding the manuscript.

Competing interests

The authors declare no competing interests.

Correspondence to So Iwata or Tatsuro Shimamura.

Integrated supplementary information

Supplementary Figure 1 Structures of 5-HT2AR antagonists used in this study and electron density maps for the antagonists in the 5-HT2AR crystal structures.

a, Structures of risperidone, zotepine and pimavanserin. |Fo|-|Fc| omit maps (magenta mesh, contoured at 3.0 σ) and polder maps (blue mesh, contoured at 3.0 σ) for risperidone (b) and zotepine (c). The asymmetric unit contains two 5-HT2AR molecules (molecules A and B).

Supplementary Figure 2 Conservation of the bottom hydrophobic cleft in 5-HT2Rs, 5-HT1BR, D2R and H1R.

Vertical cross sections of the receptors. The bottom hydrophobic clefts in the structures are shown in red dotted circles.

Supplementary Figure 3 The side-extended cavity in 5-HT2Rs.

a, Vertical cross sections of 5-HT2Rs. b, The surface of 5-HT2Rs viewed from the right side of (a). The side chains of Phe2345.38x39 of 5-HT2AR, Phe2175.38x39 of 5-HT2BR and Phe2145.38x39 of 5-HT2CR are shown. 5-HT2AR, 5-HT2BR and 5-HT2CR are shown in pink, orange and green, respectively. Risperidone, ergotamine and ritanserin are shown in magenta, yelloworange and lightgreen, respectively.

Supplementary Figure 4 Comparison of the structures of 5-HT2AR and other aminergic receptors.

a, Superposition of 5-HT2ARzot and the 5-HT1BR-methiothepin structure. Top (b) and bottom (c) views of (a). d, The ligand-binding pocket of (a). 5-HT2AR and 5-HT1BR are shown in cyan and pale green, respectively. Zotepine and methiothepin are shown in green and salmon pink, respectively. e, Superposition of the ligand-binding pockets of 5-HT2ARzot and the H1R-doxepin structure. 5-HT2AR and H1R are shown in cyan and yellow, respectively. Zotepine and doxepin are shown in green and gray-white, respectively.

Supplementary Figure 5 Identification of a Zn ion.

a, The XAFS spectrum of 5-HT2ARris crystals. The yellow dotted line shows the absorption edge of Zn. b, The |Fo|-|Fc| map (blue mesh) and the anomalous difference map (magenta mesh) contoured at 4.0 σ of the data collected at wavelengths of 1.0000 Å (left) and 1.3000 Å (right).

Supplementary Figure 6 TGFα shedding response and the ligand binding assay.

a, Gq/11-dependent TGFα shedding response. The parental HEK293 cells or the Gq/11-deficient HEK293 cells transfected with an empty vector (Mock), WT 5-HT2AR-encoding plasmid or C322K6.34x34 mutant-encoding plasmid were subjected to the TGFα shedding assay in the presence (+) or absence (−) of the Gq/11 inhibitor (1 μM YM-254890). Data represent mean ± SEM from 4–8 independent experiments performed in duplicate or triplicate (see Source data for details). b, The displacement curves of 5-HT2AR-mIIG and the key mutants. The detailed values are shown in Supplementary Table 4. Data represent mean ± SEM from 3 independent experiments performed in triplicate (see Source data for details). Source Data

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Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Notes 1–2, Supplementary Tables 1–6

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Source Data

Source Data Fig. 3

Source Data Fig. 6

Source Data Supplementary Fig. 6

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Fig. 1: Structure of 5-HT2AR.
Fig. 2: The ligand-binding pocket of 5-HT2AR.
Fig. 3: Importance of the interactions with Ile1633.40x40, Phe3326.44x44, and Trp3366.48x48 for the inverse agonist activity of antipsychotics.
Fig. 4: Comparison of 5-HT2Rs.
Fig. 5: Comparison of the structures of 5-HT2AR and D2R.
Fig. 6: Docking study of 5-HT2AR.
Supplementary Figure 1: Structures of 5-HT2AR antagonists used in this study and electron density maps for the antagonists in the 5-HT2AR crystal structures.
Supplementary Figure 2: Conservation of the bottom hydrophobic cleft in 5-HT2Rs, 5-HT1BR, D2R and H1R.
Supplementary Figure 3: The side-extended cavity in 5-HT2Rs.
Supplementary Figure 4: Comparison of the structures of 5-HT2AR and other aminergic receptors.
Supplementary Figure 5: Identification of a Zn ion.
Supplementary Figure 6: TGFα shedding response and the ligand binding assay.