Structure-based discovery of conformationally selective inhibitors of the serotonin transporter

Isha Singh; Anubha Seth; Christian B Billesbølle; Joao Braz; Ramona M Rodriguiz; Kasturi Roy; Bethlehem Bekele; Veronica Craik; Xi-Ping Huang; Danila Boytsov; Vladimir M Pogorelov; Parnian Lak; Henry O'Donnell; Walter Sandtner; John J Irwin; Bryan L Roth; Allan I Basbaum; William C Wetsel; Aashish Manglik; Brian K Shoichet; Gary Rudnick

doi:10.1016/j.cell.2023.04.010

Structure-based discovery of conformationally selective inhibitors of the serotonin transporter

Cell. 2023 May 11;186(10):2160-2175.e17. doi: 10.1016/j.cell.2023.04.010. Epub 2023 May 2.

Authors

Isha Singh¹, Anubha Seth², Christian B Billesbølle¹, Joao Braz³, Ramona M Rodriguiz⁴, Kasturi Roy², Bethlehem Bekele², Veronica Craik³, Xi-Ping Huang⁵, Danila Boytsov⁶, Vladimir M Pogorelov⁷, Parnian Lak¹, Henry O'Donnell¹, Walter Sandtner⁶, John J Irwin¹, Bryan L Roth⁸, Allan I Basbaum⁹, William C Wetsel¹⁰, Aashish Manglik¹¹, Brian K Shoichet¹², Gary Rudnick¹³

Affiliations

¹ Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA.
² Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA.
³ Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
⁴ Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA.
⁵ Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
⁶ Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
⁷ Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA.
⁸ Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
⁹ Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: allan.basbaum@ucsf.edu.
¹⁰ Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: william.wetsel@duke.edu.
¹¹ Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA. Electronic address: aashish.manglik@ucsf.edu.
¹² Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA. Electronic address: bshoichet@gmail.com.
¹³ Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA. Electronic address: gary.rudnick@yale.edu.

PMID: 37137306
PMCID: PMC10306110 (available on 2024-05-11)
DOI: 10.1016/j.cell.2023.04.010

Abstract

The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.

Keywords: depression; docking; functional selectivity; serotonin transporter; ultra-large libraries.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Animals
Fluoxetine / pharmacology
Ibogaine* / chemistry
Ibogaine* / pharmacology
Mice
Molecular Conformation
Selective Serotonin Reuptake Inhibitors* / pharmacology
Serotonin / metabolism
Serotonin Plasma Membrane Transport Proteins* / chemistry
Serotonin Plasma Membrane Transport Proteins* / metabolism
Serotonin Plasma Membrane Transport Proteins* / ultrastructure
Small Molecule Libraries* / pharmacology

Substances

Fluoxetine
Ibogaine
Serotonin
Serotonin Plasma Membrane Transport Proteins
Selective Serotonin Reuptake Inhibitors
Small Molecule Libraries

Abstract

Publication types

MeSH terms

Substances

Grants and funding