Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold

Area of Science:

• Computational biology
• Protein engineering
• Biophysics

Background:

• Accurate protein-protein docking is crucial for biologics development, but challenging for engineered scaffolds.
• Existing methods like ProPOSE face limitations with protein backbone flexibility.

Purpose of the Study:

• To evaluate ProPOSE's effectiveness on engineered scaffolds with limited backbone flexibility, specifically DARPins.
• To demonstrate a computational screening protocol for identifying DARPin binders against a target protein.

Main Methods:

• Docking of sequence-diversified DARPin interfaces against the BCL-W protein epitope using ProPOSE.
• Application of a computational selection protocol based on binding scores and mode frequency.
• Experimental validation of top-ranked DARPin designs.

Main Results:

• Three out of 18 computationally selected DARPin designs showed nanomolar binding affinity to BCL-W.
• The binding affinities were comparable to known DARPin binders.
• The computational approach successfully enriched for binders.

Conclusions:

• ProPOSE is effective for docking rigid protein scaffolds like DARPins.
• This study validates a computational strategy for engineering and screening DARPins.
• The findings support future efforts in designing rigid scaffolds for targeted protein interactions.