A novel Bromine-containing paroxetine analog provides mechanistic clues for binding ambiguity at the central primary binding site of the serotonin transporter.

The serotonin transporter (SERT) is the primary target for the selective serotonin reuptake inhibitors (SSRIs). However, the structural basis for the extraordinarily high binding affinity of the widely-prescribed SSRI, paroxetine, to human SERT (hSERT) has not yet been fully elucidated. Our previous findings unveiled a plausible ambiguity in paroxetine's binding orientations that may constitute an integral component of this SSRI's high affinity for hSERT. Herein, we investigate factors contributing to paroxetine's high affinity by modifying both the ligand and the protein. We generated a series of Bromine (Br)-containing derivatives and found that the one in which the 4-F of paroxetine had been replaced with the chemically-similar but more electron-rich Br atom (13) has the highest affinity. By comparatively characterizing the binding of paroxetine and 13 to both WT and a construct harboring a paroxetine-sensitive mutation in the binding cavity, we identified a mechanistic determinant responsible for the pose ambiguity of paroxetine, which can guide future drug design.