Structure-based Discovery of Conformationally Selective Inhibitors of the Serotonin Transporter

Singh, I.; Seth, A.; Billesbolle, C. B.; Braz, J.; Rodriguiz, R. M.; Roy, K.; Bekele, B.; Craik, V.; Huang, X.-P.; Boytsov, D.; Lak, P.; O'Donnell, H. R.; Sandtner, W. R.; Roth, B. L.; Basbaum, A.; Wetsel, W. C.; Manglik, A.; Shoichet, B. K.; Rudnick, G.

doi:10.1101/2022.06.13.495991

bioRxiv · 10.1101/2022.06.13.495991

Structure-based Discovery of Conformationally Selective Inhibitors of the Serotonin Transporter

Singh, I.·Seth, A.·Billesbolle, C. B.·Braz, J.·Rodriguiz, R. M.·Roy, K.·Bekele, B.·Craik, V.·Huang, X.-P.·Boytsov, D.·Lak, P.·O'Donnell, H. R.·Sandtner, W. R.·Roth, B. L.·Basbaum, A.·Wetsel, W. C.·Manglik, A.·Shoichet, B. K.·Rudnick, G.

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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 an unusual anti-depressant profile and stabilizes the inward-open conformation. Unfortunately, ibogaine is promiscuous and cardiotoxic, limiting understanding of inward-open state ligands. We computationally docked over 200 million small molecules against the ibogaine stabilized inward-open state of SERT. Thirty-six top-ranking compounds were synthesized and thirteen inhibited with potencies ranging from 29 to 5000 nM. Structure-based optimization led to two novel inhibitors with Ki values down to 3 nM. The new molecules stabilized an outward-closed state of the transporter and had little activity against off-targets. A cryo-EM structure of one of these bound to SERT confirmed the predicted geometry. In mouse behavioral assays, both had anxiolytic and anti-depressant activity, with potencies up to 200 better than fluoxetine.

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Singh, I., Seth, A., Billesbolle, C. B., Braz, J., Rodriguiz, R. M., Roy, K., Bekele, B., Craik, V., Huang, X.-P., Boytsov, D., Lak, P., O'Donnell, H. R., Sandtner, W. R., Roth, B. L., Basbaum, A., Wetsel, W. C., Manglik, A., Shoichet, B. K., Rudnick, G.. 2022-06-13. Structure-based Discovery of Conformationally Selective Inhibitors of the Serotonin Transporter. https://doi.org/10.1101/2022.06.13.495991

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