Conformation-Dependent Binding Affinity of Small Molecules to Aβ42 Fibrils: Mechanistic Insights into Tracer Design

The β-amyloid (Aβ) deposits in Alzheimer's disease (AD) are primarily composed of Aβ42-derived fibrils, and Aβ42 fibrils exhibit polymorphism with diverse molecular structures. While small-molecule-based targeting strategies have achieved phased progress in AD diagnosis and treatment, the distribution and quantity of binding sites on Aβ42 fibrils, as well as the dynamic interaction mechanisms between these sites and different tracers, remain unclear. Additionally, the binding efficacy of small molecules to Aβ42 fibrils with distinct structures and their conformational dependence have not yet been elucidated. In this study, five novel ligands were selected as tracers to investigate their interactions with four representative Aβ42 fibril conformations. The results demonstrated significant differences in the capacities of these molecules to bind Aβ fibrils with varying conformations, revealing a pronounced conformation-dependent relationship. Notably, small molecule 1 (SM1) and SM3 exhibited robust binding affinities across all four Aβ fibril conformations, highlighting their potential as tracers. Furthermore, the binding sites of the υ-type (8EZE) Aβ fibril accommodating small molecules were first identified, and U-type (2BEG), S-type (2NAO), and LS-type (5OQV) Aβ fibrils were found to align with the ones reported previously for other ligands. Notably, strongly bound molecules induce structural deformation of the fibril. These findings provide critical insights for the rational design and modification of existing Aβ42 fibril-targeting ligands, facilitating the development of tracers with enhanced specificity and selectivity.