Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies

• Published in: Nature communications Vol. 15; no. 1; pp. 4611 - 10
• Main Authors: Schlimgen, Roman R., Peterson, Francis C., Heukers, Raimond, Smit, Martine J., McCorvy, John D., Volkman, Brian F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.05.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 101/1; 101/6; 119/118; 13/95; 631/154/51/1568; 631/45/535/878/1263; 631/45/612/194; 82/83; Animals; Antibodies; Chemokine receptors; Chemokines; Complementarity-determining region 3; Development strategies; Drug development; G protein-coupled receptors; HEK293 Cells; Humanities and Social Sciences; Humans; Inactivation; multidisciplinary; Nanobodies; Protein Binding; Receptors, CXCR - antagonists & inhibitors; Receptors, CXCR - chemistry; Receptors, CXCR - genetics; Receptors, CXCR - metabolism; Receptors, G-Protein-Coupled - antagonists & inhibitors; Receptors, G-Protein-Coupled - chemistry; Receptors, G-Protein-Coupled - metabolism; Science; Science (multidisciplinary); Single-Domain Antibodies - chemistry; Single-Domain Antibodies - metabolism; Therapeutic targets
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49000-x

G protein-coupled receptors (GPCRs) are pivotal therapeutic targets, but their complex structure poses challenges for effective drug design. Nanobodies, or single-domain antibodies, have emerged as a promising therapeutic strategy to target GPCRs, offering advantages over traditional small molecules and antibodies. However, an incomplete understanding of the structural features enabling GPCR-nanobody interactions has limited their development. In this study, we investigate VUN701, a nanobody antagonist targeting the atypical chemokine receptor 3 (ACKR3). We determine that an extended CDR3 loop is required for ACKR3 binding. Uncommon in most nanobodies, an extended CDR3 is prevalent in GPCR-targeting nanobodies. Combining experimental and computational approaches, we map an inhibitory ACKR3-VUN701 interface and define a distinct conformational mechanism for GPCR inactivation. Our results provide insights into class A GPCR-nanobody selectivity and suggest a strategy for the development of these new therapeutic tools. Nanobodies are promising GPCR-targeting therapeutics. Here, the authors investigate a nanobody targeting atypical chemokine receptor 3 (ACKR3), and map trends in GPCR nanobody structure, mechanism, and selectivity.