Macrocyclic Peptide Tools for Huntingtin-bound HAP40

Huntington's disease is a fatal neurodegenerative disorder caused by expansion of a cytosine-adenosine-guanine repeat in exon 1 of the Huntingtin (HTT) gene, resulting in a polyglutamine-expanded HTT protein. Although the genetic cause of Huntington's is well defined, the molecular functions of HTT and the mechanisms linking polyglutamine expansion to neurodegeneration remain incompletely understood. Huntingtin Associated Protein 40 kDa (HAP40) is a key HTT interaction partner that forms a stable complex with HTT and is increasingly recognized as an important player in the HTT structure-function paradigm. However, investigation of HAP40 biology has been limited by a lack of tools capable of directly targeting endogenous protein. Here, we report the discovery and characterization of a panel of nanomolar-affinity macrocyclic peptides targeting HAP40 identified using Random nonstandard Peptide Integrated discovery platform. We characterized macrocycle binding in vitro using surface plasmon resonance, fluorescence polarization, and hydrogen-deuterium exchange mass spectrometry, revealing selective, high-affinity engagement of distinct epitopes on HAP40. We further demonstrate that these macrocycles engage endogenous HAP40 in cellular lysates, enable selective isolation of HAP40-containing protein complexes using macrocycle precipitations and insights into interaction partners of distinct HTT and HAP40 proteoforms. Together, these macrocycles establish a new toolkit for investigating HTT-HAP40 biology and provide a framework for Dissecting HAP40-specific functions relevant to Huntington's disease pathogenesis.