Journal Article

Noncanonical roles of chemokine regions in CCR9 activation revealed by structural modeling and mutational mapping

Tan, Gavin, Dawson, John R. D., Calo, Nicolas, Hartley, Oliver, Kufareva, Irina, Akondi, Kalyana Bharati, Paolini-Bertrand, Marianne, De Magalhaes Pinheiro, Inês, Handel, Tracy M.

2025

Overview

The G protein-coupled chemokine receptor CCR9 plays a major role in inflammatory bowel disease and is implicated in cancer. Despite its therapeutic relevance, the mechanism by which CCR9 is activated by its endogenous chemokine CCL25 remains poorly understood. Here, we combine structural modeling with multimodal pharmacological analysis of CCR9 mutants to map the CCR9–CCL25 interface and delineate key determinants of binding, G protein versus arrestin signaling, and constitutive activity. We show that unlike other chemokines which drive receptor activation through their N-termini, CCL25 activates CCR9 via a distinct region, its 30s loop. Supporting this non-canonical mechanism, CCR9 signaling tolerates alanine mutations in the CCL25 N-terminus but is strongly affected by 30s loop modifications. Engineered N-terminally modified CCL25 analogs remain full agonists, consistent with signaling determinants lying outside the N-terminus. This non-canonical activation signature provides insights for CCR9 drug discovery and may inform structure-based design for other chemokine receptors. CCR9 is chemokine receptor involved in gut inflammation and cancer. Here, the authors use AI-based modeling, protein engineering and pharmacological experiments to reveal the unusual anatomy of CCR9 activation by its endogenous chemokine agonist CCL25.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 119/118 / 13/21 / 631/45/535/1267 / 631/92/611 / 82/75 / 96/95 / Agonists / Alanine / Arrestin / Cancer / CC chemokine receptors / Chemokine receptors / Chemokines / Chemokines, CC - chemistry / Chemokines, CC - genetics / Chemokines, CC - metabolism / Drug development / HEK293 Cells / Humanities and Social Sciences / Humans / Inflammatory bowel diseases / Ligands / Modelling / Models, Molecular / multidisciplinary / Mutagenesis / Mutation / N-Terminus / Peptide mapping / Pharmacology / Protein Binding / Protein engineering / Proteins / Receptor mechanisms / Receptors, CCR - chemistry / Receptors, CCR - genetics / Receptors, CCR - metabolism / Regulatory approval / Science / Science (multidisciplinary) / Signal Transduction