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.

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