High-Affinity, Structure-Validated and Selective Macrocyclic Peptide Tools for Chemical Biology Studies of Huntingtin

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the Huntingtin (HTT) gene, with no disease-modifying therapies currently available. The precise molecular function of the HTT protein is unclear, and the lack of selective chemical tools has limited functional studies. We have identified and characterized macrocyclic peptide binders targeting HTT. These binders exhibit low-nanomolar affinity in vitro and engage distinct HTT and HTT-HAP40 interfaces, as revealed by hydrogen-deuterium exchange mass spectrometry and cryo-electron microscopy. Chemoproteomics confirmed selective binding in cell extracts from wildtype but not HTT-null cell lines. HAP40 consistently and stoichiometrically co-purified with HTT across cell lines, including with HTT variants containing different CAG repeat lengths, highlighting the broad presence of the HTT-HAP40 complex. Significance StatementHuntingtin (HTT) is a large, essential protein with conserved roles in development, intracellular trafficking, and protein homeostasis, yet its precise molecular functions remain incompletely defined. Here, we report the first high-affinity, selective, and structurally validated macrocyclic peptide ligands for HTT. These chemical tools bind HTT and its complex with HAP40 across polyglutamine repeat lengths, enabling direct interrogation of HTT structure and function in health and disease contexts. By overcoming longstanding barriers to studying HTT at the molecular level, these ligands open new avenues for discovery in neurobiology, cell biology, and offer opportunities for therapeutic development. This study delivers urgently needed tools to both the Huntingtons disease field and the broader scientific community seeking to understand this elusive and biologically fundamental protein.