Structures of the σ receptor enable docking for bioactive ligand discovery.

The σ receptor has attracted intense interest in cancer imaging, psychiatric disease, neuropathic pain and other areas of biology. Here we determined the crystal structure of this receptor in complex with the clinical candidate roluperidone and the tool compound PB28. 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 σ receptor. Crystal structures of two ligands bound to the σ receptor confirmed the docked poses. To investigate the contribution of the σ receptor in pain, two potent σ-selective ligands and one potent σ/σ 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 model, suggesting that the σ 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.