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The modulation of biological processes with light-sensitive chemical probes promises precise temporal and spatial control. Yet, the design and synthesis of suitable probes is a challenge for medicinal chemists. This article introduces a photocaging strategy designed to modulate the pharmacology of histamine H₃ receptors (H₃R) and H₄ receptors (H₄R). Employing the photoremovable group BODIPY as the caging entity for two agonist scaffolds—immepip and 4-methylhistamine—for H₃R and H₄R, respectively, we synthesized two BODIPY-caged compounds, <b>5</b> (VUF25657) and <b>6</b> (VUF25678), demonstrating 10–100-fold reduction in affinity for their respective receptors. Notably, the caged H₃R agonist, VUF25657, exhibits approximately a 100-fold reduction in functional activity. The photo-uncaging of VUF25657 at 560 nm resulted in the release of immepip, thereby restoring binding affinity and potency in functional assays. This approach presents a promising method to achieve optical control of H₃R receptor pharmacology.