Structural basis of μ-opioid receptor targeting by a nanobody antagonist

Article Article scientifique Article Structural basis of μ-opioid receptor targeting by a nanobody antagonist eng 2024-10-09 2024-10-09 author Yu Jun Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland. 924631 Département de biologie moléculaire et cellulaire (MOCEL) author Kumar Amit Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland. 924488 Département de physiologie cellulaire et métabolisme (PHYME) author Zhang Xuefeng 0000-0002-5222-7042 Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland. 402287 Département de biologie moléculaire et cellulaire (MOCEL) author Martin Charlotte Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium. author Van Holsbeeck Kevin 0000-0002-9345-4962 Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium. author Raia Pierre 0000-0003-3469-1922 Department of Plant Sciences, University of Geneva, Geneva, Switzerland. 930734 Département des sciences végétales (BIVEG) author Koehl Antoine Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA. author Laeremans Toon Confo Therapeutics N.V., Gent, Belgium. author Steyaert Jan 0000-0002-3825-874X Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium. author Manglik Aashish 0000-0002-7173-3741 Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA. author Ballet Steven 0000-0003-4123-1641 Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium. author Boland Andreas 0000-0003-1218-6714 Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland. andreas.boland@unige.ch. 912539 Département de biologie moléculaire et cellulaire (MOCEL) author Stoeber Miriam Carolin 0000-0002-5210-2864 Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland. miriam.stoeber@unige.ch. 930635 Département de physiologie cellulaire et métabolisme (PHYME) 8687 10.1038/s41467-024-52947-6 39384768 2041-1723 PMC11464722 https://www.nature.com/articles/s41467-024-52947-6 The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments. Analgesics, Opioid / chemistry Analgesics, Opioid / metabolism Analgesics, Opioid / pharmacology Animals Binding Sites Cryoelectron Microscopy HEK293 Cells Humans Ligands Models, Molecular Peptides, Cyclic / chemistry Peptides, Cyclic / metabolism Peptides, Cyclic / pharmacology Protein Binding Receptors, Opioid, mu / antagonists & inhibitors Receptors, Opioid, mu / chemistry Receptors, Opioid, mu / metabolism Single-Domain Antibodies / chemistry Single-Domain Antibodies / metabolism Single-Domain Antibodies / pharmacology Dewey 612 Dewey 580 Dewey 570 Swiss National Science Foundation Mechanisms Underlying Subcellular Location Bias of Opioid Receptor Signaling 181282 CH Careers Swiss National Science Foundation Structural studies of cytokine-mediated signal transduction 185235 CH Projects Swiss National Science Foundation Deciphering the molecular mechanisms underlying chromosome segregation 211581 CH Programmes 134 Département de physiologie cellulaire et métabolisme 21C 7daed2ee-1311-4824-9df9-2e51260a966a Département de biologie moléculaire et cellulaire 16484 45 Département des sciences végétales 163 false 1283 Contrôle subcellulaire des récepteurs de signalisation 1005 1277 Groupe Boland https://www.ebi.ac.uk/emdb/EMD-18541 https://www.wwpdb.org/pdb?id=pdb_00008qot https://www.wwpdb.org/pdb?id=pdb_00008v8k https://yareta.unige.ch/archives/e8fe7845-23ee-4379-8554-3fd3c15ea311 Nature communications 15 1 20c47301-6c24-4631-95c7-fc6878b7e8fd Article (Published version) Public Article_scientifique_from_crossref.pdf 2681487 application/pdf CC BY-NC-ND-4.0 e58f7aa50a90e72720c8a7e0bb690132056bc52e6e27f52751a8172b36319a7e 16b43146-37f5-4a2c-8527-7b5beae9cffe Supplemental data Public 41467_2024_52947_MOESM1_ESM.pdf 9368675 application/pdf a69b6e852e44701ceadbe9f0fb0e400fce9b464d689e73a2113b8710bc008b88 0c92f232-95da-4c49-a44d-4a092e80545e Supplemental data Public 41467_2024_52947_MOESM3_ESM.pdf 27061 application/pdf 2335bf5f1c92fa913d02c13c95eae372d861dbdc933203707981a204c84e58eb 9471b0a3-a79f-4229-a33d-5563d590a914 Supplemental data Public 41467_2024_52947_MOESM4_ESM.mp4 20617547 video/mp4 Movie 097f88ed3fba6e024a25616556177b8891b53ca85394793d5e277c6d97e43e82 0524c4cf-3565-46b3-b046-027ecd4d9d08 Supplemental data Public 41467_2024_52947_MOESM6_ESM.xlsx 28431 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Source Data 17ab0bc2e9cf300b96bfed899819889ef25bd03420b60cca3547f3e6fd1a8666 openAccess Faculté de médecine / Section de médecine fondamentale / Département de physiologie cellulaire et métabolisme Faculté des sciences / Section de biologie / Département de biologie moléculaire et cellulaire Faculté des sciences / Section de biologie / Département des sciences végétales

Title	Published in	Year	Views	Downloads

Structural basis of μ-opioid receptor targeting by a nanobody antagonist	Nature communications	2024	200	59
Extracellular Nanobody-Based Modulators of the μ-Opioid Receptor		2024	233	9
Structural Basis of μ-Opioid Receptor-Targeting by a Nanobody Antagonist	Cold Spring Harbor protocols	2023	85	53

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