A Complementarity-Based Approach to De Novo Binder Design.

Area of Science:

• Computational biology
• Protein engineering
• Drug discovery

Background:

• Designing protein binders for specific epitopes is challenging.
• Current methods often require extensive empirical optimization or in vitro screening.

Purpose of the Study:

• To present a generalizable computational strategy for de novo design of site-specific protein binders.
• To bypass the need for extensive empirical optimization or in vitro screening.

Main Methods:

• A dock-and-design pipeline was developed, retrieving complementary scaffolds and mutating them to create binding sites.
• A novel fingerprint was utilized to simplify and accelerate surface complementarity evaluation.
• The method was validated by designing binders against epitopes on vascular endothelial growth factor (VEGF) and interleukin-7 receptor-α (IL-7Rα).

Main Results:

• Experimental characterization of 24 candidates yielded nanomolar binders for each target epitope, with diverse protein folds.
• Several designed binders demonstrated in vitro activity.
• Anti-VEGF binders exhibited tumor-inhibiting activity in vivo.

Conclusions:

• The presented computational strategy is effective for de novo design of site-specific protein binders.
• The designed binders show therapeutic potential for oncogenic targets.
• This approach accelerates the discovery of novel therapeutic proteins.