Ligand channel in pharmacologically stabilized rhodopsin

Significance A substantial number of known genetic disorders have their origin in mutations that cause misfolding or dysfunction of G protein-coupled receptors (GPCRs). Pharmacological chaperones can rescue such mutant receptors from the endoplasmic reticulum by stabilizing protein conformations that support trafficking into the target membrane. Rhodopsin-mediated retinitis pigmentosa is a misfolding disease that might be targeted by PCs. Here we present a structure-based drug design approach to identify nonretinal compounds that bind and stabilize the receptor. Surprisingly, selected hits induce a previously unknown conformation of the seven-transmembrane helix bundle. Our study thus provides a remarkable example for compound class discovery and for the adaptability of GPCRs to chemically diverse ligands. In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2.4 Å resolution using one of the stabilizing hits (S-RS1). Chemical modification of S-RS1 and further structural analysis revealed the core binding motif of this class of rhodopsin stabilizers bound at the orthosteric binding site. Furthermore, previously unobserved conformational changes are visible at the intradiscal side of the seven-transmembrane helix bundle. A hallmark of this conformation is an open channel connecting the ligand binding site with the membrane and the intradiscal lumen of rod outer segments. Sufficient in size, the passage permits the exchange of hydrophobic ligands such as retinal. The results broaden our understanding of rhodopsin’s conformational flexibility and enable therapeutic drug intervention against rhodopsin-related retinitis pigmentosa.