Tricyclic antidepressant binding to the human serotonin transporter (hSERT)

Abstract

For more than 50 years tricyclic antidepressants (TCA) have been used to treat clinical depression and have been shown to be superior to SSRIs in treating severely depressed patients. Their mode of action can primarily be attributed to inhibition of hSERT but the exact binding site and its interaction with the inhibitor is not known despite extensive research efforts.

Recent crystallographic structures has identified a surprising low affinity noncompetitive binding site for TCAs in the cytoplasmic vestibule of the bacterial homolog LeuT_Aa.

Induced fit docking (IFD) of the TCA imipramine to a homology model of hSERT based on the LeuTAa template predict the imipramine binding site to be overlapping the 5-HT binding site. We find two probable orientational clusters of imipramine within the substrate binding site.

Several specific protein-ligand interaction points were identified by rational combination of imipramine analogs with point mutated hSERT in activity assays. It has allowed us to unequivocally identify the correct orientation of imipramine within the binding site. Based on the modeling and biochemical data we present an experimentally validated model of imipramine binding to the central binding site of hSERT, clearly distinct from the TCA site reported in LeuT_Aa.

Our experimentally validated model shows the differences in protein conformation between binding substrate (5-HT) and inhibitor (TCA) readily explaining why the inhibitor is not transported despite binding to the substrate site. The model has shown its validity and usefulness by supporting succesful rational drug design of novel TCAs with a hitherto unseen potency.