Discovery of Potential Prion Fibril Inhibitors From Curcumin‐Like Compounds via Structure‐Based Virtual Screening and Molecular Dynamics Simulations

Abstract

Prion diseases are neurodegenerative disorders characterized by the conformational conversion of the cellular prion protein (PrP C ) into its pathogenic fibrillar form (PrP Sc ). Recent cryo‐electron microscopy studies revealed that the mouse‐adapted RML prion fibril adopts an infectious single‐filament architecture with distinct N‐ and C‐terminal lobes, providing a structurally defined target for inhibitor design. Curcumin has been reported to interfere with amyloid aggregation through hydrophobic and π–π interactions; however, its structural determinants in prion fibril inhibition remain unclear. Here, curcumin‐like compounds were systematically explored to elucidate structure–activity relationships and identify potential inhibitors targeting the single‐filament RML prion fibril using structure‐based virtual screening, molecular docking, and molecular dynamics (MD) simulations. Five compounds were identified to preferentially bind to a hotspot region within the N‐terminal lobe. MD simulations revealed increased structural fluctuations upon ligand binding, as reflected by elevated root‐mean‐square deviation (RMSD) values (~20–25 Å), representing a structural relaxation toward a stable steady state while maintaining local dynamic features consistent with cryo‐EM data. Binding energy analysis indicated that van der Waals interactions dominate ligand–fibril association, consistent with ligand localization within a hydrophobic hotspot, suggesting a mechanism that modulates fibril dynamics rather than directly disrupting the fibril core. These findings suggest that curcumin‐like compounds modulate fibril stability through binding to a specific hydrophobic hotspot rather than directly disrupting β‐sheet structures, providing mechanistic insights into their potential as prion fibril inhibitors.