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TitleStructural basis of vilazodone dual binding mode to the serotonin transporter.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 10119, Year 2025
Publish dateNov 18, 2025
AuthorsIris E Kalenderoglou / Andreas Nygaard / Caleb D Vogt / Anton Turaev / Tillmann Pape / Nathan B P Adams / Amy Hauck Newman / Claus J Loland /
PubMed AbstractThe serotonin transporter (SERT) plays a pivotal role in regulating serotonin (5-HT) signaling and is a key target in the treatment of psychiatric disorders. SERT has a binding site (S1) for 5-HT ...The serotonin transporter (SERT) plays a pivotal role in regulating serotonin (5-HT) signaling and is a key target in the treatment of psychiatric disorders. SERT has a binding site (S1) for 5-HT that also serves as a high-affinity binding site for antidepressants. The antidepressant vilazodone has been shown to inhibit SERT by binding to an allosteric site. Here, we present the cryo-EM structure of SERT with vilazodone bound to the S1 site and extending towards the allosteric site. We systematically dissect the vilazodone molecule into fragments and find that the terminal indole ring is the key determinant of its high affinity to SERT. Further, unlike typical Na-dependent SERT-selective antidepressants, vilazodone exhibits a dissociation constant (K) for purified SERT in the nanomolar range both in the presence and absence of Na. We substantiate this binding mode by exploring the conformational impact of vilazodone binding to SERT using site-specific insertion of the fluorescent non-canonical amino acid Anap. Our results offer molecular insight into the distinct pharmacological profile of a clinically used polymodal antidepressant.
External linksNat Commun / PubMed:41253806 / PubMed Central
MethodsEM (single particle)
Resolution2.78 Å
Structure data

52050

9hco

EMDB-52050, PDB-9hco:
Outward-open structure of human serotonin transporter bound to vilazodone
Method: EM (single particle) / Resolution: 2.78 Å

Chemicals

ChemComp-YG7:
5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide

ChemComp-NA:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
KeywordsMEMBRANE PROTEIN / Monoamine transporter / LeuT fold / antidepressant binding / Inhibitor complex

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