Binding of serotonin to the human serotonin transporter. Molecular modeling and experimental validation

J Am Chem Soc. 2008 Mar 26;130(12):3853-65. doi: 10.1021/ja076403h. Epub 2008 Mar 4.


Molecular modeling and structure-activity relationship studies were performed to propose a model for binding of the neurotransmitter serotonin (5-HT) to the human serotonin transporter (hSERT). Homology models were constructed using the crystal structure of a bacterial homologue, the leucine transporter from Aquifex aeolicus, as the template and three slightly different sequence alignments. Induced fit docking of 5-HT into hSERT homology models resulted in two different binding modes. Both show a salt bridge between Asp98 and the charged primary amine of 5-HT, and both have the 5-HT C6 position of the indole ring pointing toward Ala173. The difference between the two orientations of 5-HT is an enantiofacial discrimination of the indole ring, resulting in the 5-hydroxyl group of 5-HT being vicinal to either Ser438/Thr439 or Ala169/Ile172/Ala173. To assess the binding experimentally, binding affinities for 5-HT and 17 analogues toward wild type and 13 single point mutants of hSERT were measured using an approach termed paired mutant-ligand analogue complementation (PaMLAC). The proposed ligand-protein interaction was systematically examined by disrupting it through site-directed mutagenesis and re-establishing another interaction via a ligand analogue matching the mutated residue, thereby minimizing the risk of identifying indirect effects. The interactions between Asp98 and the primary amine of 5-HT and the interaction between the C6-position of 5-HT and hSERT position 173 was confirmed using PaMLAC. The measured binding affinities of various mutants and 5-HT analogues allowed for a distinction between the two proposed binding modes of 5-HT and biochemically support the model for 5-HT binding in hSERT where the 5-hydroxyl group is in close proximity to Thr439.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cell Line
  • Cells, Cultured
  • Computer Simulation
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Structure
  • Protein Binding
  • Serotonin / analogs & derivatives
  • Serotonin / chemistry*
  • Serotonin / pharmacokinetics
  • Serotonin Plasma Membrane Transport Proteins / chemistry*
  • Stereoisomerism
  • Structure-Activity Relationship
  • Tissue Distribution


  • Ligands
  • Serotonin Plasma Membrane Transport Proteins
  • Serotonin