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Structural basis for recognition of diverse antidepressants by the human serotonin transporter

Abstract

Selective serotonin reuptake inhibitors are clinically prescribed antidepressants that act by increasing the local concentrations of neurotransmitters at synapses and in extracellular spaces via blockade of the serotonin transporter. Here we report X-ray structures of engineered thermostable variants of the human serotonin transporter bound to the antidepressants sertraline, fluvoxamine, and paroxetine. The drugs prevent serotonin binding by occupying the central substrate-binding site and stabilizing the transporter in an outward-open conformation. These structures explain how residues within the central site orchestrate binding of chemically diverse inhibitors and mediate transporter drug selectivity.

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Fig. 1: Saturation and competition binding experiments.
Fig. 2: Antidepressant binding in the central binding site.
Fig. 3: Antidepressant recognition.
Fig. 4: Comparisons of SSRI binding poses and central-binding-site structures.

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Acknowledgements

We thank L. Vaskalis for assistance with figures, H. Owen for help with manuscript preparation, and members of the laboratory of E.G. for discussion. We acknowledge the staff of the Berkeley Center for Structural Biology at the Advanced Light Source and the Northeastern Collaborative Access Team at the Advanced Photon Source for assistance with data collection. J.A.C. is supported by a Banting postdoctoral fellowship from the Canadian Institutes of Health Research. We are particularly grateful to B. LaCroute and J. LaCroute for their generous support, as well as for funding from the National Institutes of Health (NIH) (5R37MH070039) to E.G. E.G. is supported as an Investigator of the Howard Hughes Medical Institute.

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J.A.C. and E.G. designed the project. J.A.C. performed protein purification, crystallography, and biochemical assays. J.A.C. and E.G. wrote the manuscript.

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Correspondence to Eric Gouaux.

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Integrated supplementary information

Supplementary Figure 1 Intracellular gate and C terminus

a, Positions of residues associated with the intracellular gate are shown and the Polder ‘omit’ electron density is shown in blue mesh (contoured at 6-8σ). b, Fit of C-terminal residues into 2Fo – Fc electron density map (blue mesh), contoured at 0.75σ. Density for most side chains of the SEC24C recognition sequence were observed except for Arg607.

Supplementary Figure 2 Fitting of paroxetine with fluorophenyl in subsite B and benzodioxol in subsite C

Shown is the 2Fo-Fc (blue mesh) and Fo-Fc (positive, green; negative red) electron density associated with paroxetine after refinement, contoured at 2σ and 2.5σ respectively. Shown in red to yellow to green disks are severe to significant to slight overlaps of van der Waals radii of residues within 5 Å of paroxetine. The size of the disk also indicates the degree of clashing.

Supplementary Figure 3 Electron density of drug-binding residues

a, Residues associated with paroxetine (magenta) binding are shown and the Polder ‘omit’ electron density is shown in blue mesh (contoured at 7σ). b, Residues associated with sertraline (yellow) binding are shown and the Polder ‘omit’ electron density is shown in blue mesh (contoured at 6-7σ). c, Residues associated with fluvoxamine (green) binding are shown and the Polder ‘omit’ electron density is shown in blue mesh (contoured at 5-6σ).

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Coleman, J.A., Gouaux, E. Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Nat Struct Mol Biol 25, 170–175 (2018). https://doi.org/10.1038/s41594-018-0026-8

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