Two Distinct Binding Modes Govern High-Affinity Ligand Interactions with Amyloid Fibrils

Fibrillar protein aggregates are a defining feature of neurodegenerative diseases and are attractive biomarkers and therapeutic targets. However, rational ligand design is limited by a poor mechanistic understanding of fibril binding. This work demonstrates that high-affinity binding to amyloid fibrils occurs via two topologically distinct binding modes, informing design changes that enhance ligand binding. Mathematical models were outlined that demonstrate these binding modes can be distinguished using diagnostic features from standard binding assays. Reanalysis of published binding data indicates that these binding modes are likely widespread amongst common ligand scaffolds. Guided by these binding modes, new ligands were designed with improved binding affinities and distinct fluorescence responses. Together, these findings support the presence of two prevalent binding modes and establish new design principles for enhancing interactions between ligands and amyloid fibrils.