Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

The neuromodulator melatonin synchronizes circadian rhythms and related physiological functions via actions at two G protein-coupled receptors: MT₁ and MT₂. Circadian release of high nighttime levels of melatonin from the pineal gland activates melatonin receptors in the suprachiasmatic nucleus of the hypothalamus, synchronizing physiology and behavior to the light-dark cycle. The two receptors are established drug targets for aligning circadian phase in disorders of sleep and depression. Despite their importance, few if any in vivo active MT₁ selective ligands have been reported, hampering both the understanding of circadian biology and the development of targeted therapeutics. Here we docked over 150 million virtual molecules against an MT₁ crystal structure, prioritizing structural fit and chemical novelty. Thirty-eight high-ranking molecules were synthesized and tested, revealing ligands in the 470 pM to 6 μM range. Structure-based optimization led to two selective MT₁ inverse agonists, topologically unrelated to previously explored chemotypes, that were tested in mouse models of circadian behavior. Unexpectedly, the MT₁-selective inverse agonists advanced the phase of the mouse circadian clock by 1.3-1.5 hrs when given at subjective dusk, an agonist-like effect eliminated in MT₁- but not in MT₂-knockout mice. This study illustrates opportunities for modulating melatonin receptor biology via MT₁-selective ligands, and for the discovery of new, in vivo-active chemotypes from structure-based screens of diverse, ultra-large libraries.