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Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

Nature 2020, 579 (7800), 609-614

DOI: 10.1038/s41586-020-2027-0

Stein R.; Kang H.; McCorvy J.; Glatfelter G.; Jones A.; Che T.; Slocum S.; Huang X.; Savych O.; Moroz Y.; Stauch B.; Johansson L.; Cherezov V.; Kenakin T.; Irwin J.; Shoichet B.; Roth B.; Dubocovich M.

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.