The Two Enantiomers of Citalopram Bind to the Human Serotonin Transporter in Reversed Orientations

Abstract

The two enantiomers of the antidepressant citalopram inhibit the human serotonin transporter substantially differently. Previous studies revealed Tyr95 and Ile172 as important for citalopram binding, however, the overall orientation of the ligands in the binding site and the protein-ligand interaction points remain unknown. The binding of S- and R-citalopram to a human serotonin transporter homology model are herein examined via docking simulations including induced fit effects. For a better description of the formal charges of the ligand when bound inside the protein, polarization effects of the protein were included by additional quantum-polarized ligand docking calculations, where ligand charges are evaluated using QM/MM calculations. By this approach a much clearer picture emerged of the positions of the functional groups of citalopram. The two enantiomers are predicted to bind in the substrate binding pocket with opposite orientations of their aromatic groups. The predicted binding modes are experimentally validated using human wild type and 15 serotonin transporter mutants and 13 optically pure citalopram analogues. Important protein-ligand interaction points were identified validating one binding model for each enantiomer. In the validated model of the high affinity enantiomer, S-citalopram, the fluorine atom is located near Ala173 and Thr439 and the cyano group is in close proximity of Phe341; these contacts are found to be reversed for the R-enantiomer.

Binding and Orientation of Tricyclic Antidepressants within the Central Substrate Site of the Human Serotonin Transporter

“…Furthermore, the fact that TCA binding in hSERT and human norepinephrine transporter is competitive with substrate (9, 40, 41), sodium-dependent (32,42), and partially chloride-dependent (32,43,44) indicates that TCAs use the same site as the substrate, a site next to the cotransported ions in Na ϩ /Cl Ϫ -dependent transporters (12-14, 19, 45). The overlapping of TCA and substrate sites is in accordance with findings for other competitive inhibitors as well (22,24,34,35). We assert that the central TCA site modeled and biochemically validated in the present study is the site relevant for competitive high affinity inhibition of hSERT as well as Na ϩ /Cl Ϫ -dependent transporters in general.…”

X-ray structures and mechanism of the human serotonin transporter

“…These data are consistent with the fluorophenyl group of ( S )-citalopram occupying subsite B. The non-therapeutic R -enantiomer of citalopram has significantly weaker affinity for SERT, perhaps because the aromatic substituents swap subsites, relative to the S -enantiomer 33 . Inspection of F o -F c omit electron density maps allowed placement of paroxetine in the central binding site with the benzodioxol and fluorophenyl groups in subsites B and C (Fig.…”

Understanding the Molecular Activity of Alkaline Sphingomyelinase (NPP7) by Computer Modeling

“…Induced Fit Docking has been validated on 21 different test cases (20) and has been shown to generate viable binding modes in homology models (21)(22)(23). Briefly, the protocol involves three steps.…”