Design of amyloidogenic peptide traps

Area of Science:

• Protein engineering
• Biochemistry
• Structural biology

Background:

• Amyloid fibrils, formed by protein segments with high β-strand propensity, are linked to various diseases.
• Developing inhibitors for amyloid formation is crucial for therapeutic intervention.

Purpose of the Study:

• To develop a general strategy for designing protein scaffolds that bind and stabilize β-strand and β-hairpin conformations of amyloidogenic peptides.
• To create potent inhibitors of amyloid fibril formation, specifically targeting transthyretin, tau, serum amyloid A1, and amyloid β_1-42 (Aβ42).

Main Methods:

• De novo protein design of scaffolds with deep peptide-binding clefts.
• In vitro binding assays to determine peptide affinities.
• X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy for structural characterization.
• Inhibition assays for amyloid fibril assembly and cell-based toxicity studies.

Main Results:

• Designed scaffolds demonstrated nanomolar binding affinities for their cognate peptide segments.
• Structural analysis confirmed the designed protein-peptide complex architecture.
• NMR studies elucidated the protective mechanism of the binding cleft in the unbound state.
• Amyloid β_1-42 (Aβ42) binders effectively inhibited Aβ fibril formation and protected cells from Aβ42-induced toxicity, comparable to leading antibodies.

Conclusions:

• A versatile de novo protein design approach enables the creation of high-affinity binders for β-strand-rich peptide segments.
• This strategy provides a promising platform for developing novel therapeutics against amyloid-related diseases.
• The designed Aβ binders represent a significant advancement in targeting toxic amyloid species.