Structures of the σ₂ receptor enable docking for bioactive ligand discovery

The σ₂ receptor has attracted intense interest in cancer imaging¹, psychiatric disease², neuropathic pain^3-5 and other areas of biology^6,7. Here we determined the crystal structure of this receptor in complex with the clinical candidate roluperidone² and the tool compound PB28⁸. These structures templated a large-scale docking screen of 490 million virtual molecules, of which 484 compounds were synthesized and tested. We identified 127 new chemotypes with affinities superior to 1 μM, 31 of which had affinities superior to 50 nM. The hit rate fell smoothly and monotonically with docking score. We optimized three hits for potency and selectivity, and achieved affinities that ranged from 3 to 48 nM, with up to 250-fold selectivity versus the σ₁ receptor. Crystal structures of two ligands bound to the σ₂ receptor confirmed the docked poses. To investigate the contribution of the σ₂ receptor in pain, two potent σ₂-selective ligands and one potent σ₁/σ₂ non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands showed time-dependent decreases in mechanical hypersensitivity in the spared nerve injury model⁹, suggesting that the σ₂ receptor has a role in nociception. This study illustrates the opportunities for rapid discovery of in vivo probes through structure-based screens of ultra large libraries, enabling study of underexplored areas of biology.