Structural basis for ligand recognition at the human MT(1) melatonin receptor

Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythm(1) by synchronization to environmental cues and is involved in diverse physiological processes(2) including blood pressure and core body temperature regulation, oncogenesis, and immune function(3). Formed in the pineal gland in a light-regulated manner(4) by enzymatic conversion from 5-hydroxytryptamine (5-HT, or serotonin), melatonin modulates sleep and wakefulness(5) by activating two high-affinity G protein-coupled receptors (GPCRs), type 1A (MT(1)) and type 1B (MT(2))(3,6). Shift work, travel, and ubiquitous artificial lighting can disrupt a natural circadian rhythm, leading to sleep disorders affecting a significant population in our modern society, posing a considerable economic burden(7). Widely used to alleviate jet lag and as safer alternative to benzodiazepines and other sleeping aids(8,9), over-the-counter melatonin is one of the most popular supplements in the United States(10). Here, we present high-resolution room-temperature X-ray free electron laser (XFEL) structures of MT(1) in complex with four agonists: the insomnia drug ramelteon(11), two melatonin analogues, and the mixed melatonin-serotonin antidepressant agomelatine(12,13). The structure of MT(2) is described in an accompanying paper(14). Despite similar endogenous ligands and dual action of agomelatine, MT(1) and 5-HT receptors differ dramatically in structure and composition of their ligand pockets, access to which in MT(1) is tightly sealed from solvent by extracellular loop 2, leaving only a narrow channel between transmembrane helices IV and V that connects it to the lipid bilayer. The binding site is extremely compact, and ligands interact with MT(1) mainly by strong aromatic stacking with F179 and auxiliary hydrogen bonds with N162 and Q181. Our structures provide an unexpected example of atypical ligand entry for a non-lipid receptor, lay the molecular foundation of ligand recognition by melatonin receptors, and will facilitate the design of future tool compounds and therapeutics, while their comparison to 5-HT receptors yields new insights into GPCR evolution and polypharmacology.