A Rapid Binder Discovery Workflow for Engineering Mini-Protein Degraders

Area of Science:

• Biotechnology
• Molecular Biology
• Cancer Research

Background:

• Developing selective binding molecules is a key challenge in biological research and biotechnology.
• Existing methods for de novo binder discovery can be time-consuming.

Purpose of the Study:

• To present and validate a rapid workflow for de novo binder discovery using Phage-Assisted Non-Continuous Selection for Binders (PANCS-Binders) technology.
• To demonstrate the utility of this workflow for identifying binders against cancer-related targets.
• To showcase the application of discovered binders in chemical biology and biotechnology.

Main Methods:

• Utilized the PANCS-Binders technology for rapid de novo binder discovery.
• Targeted three cancer-related proteins: NSD3, NMNAT2, and CSF1R.
• Incorporated a discovered NSD3 binder into an engineered E3 ligase (RNF8) to create a degrader.

Main Results:

• Successfully identified sequence- and function-verified binders for all three targets within 26 days.
• Achieved nano- to micromolar affinities for the discovered binders.
• Developed a potent NSD3 degrader that depleted endogenous NSD3 and inhibited colorectal cancer cell proliferation.
• Uncovered novel NSD3 dependencies in ovarian cancer cell lines using the developed degrader.

Conclusions:

• The PANCS-Binders workflow provides a robust and accelerated method for binder discovery.
• Discovered binders can be effectively utilized to create molecular degraders for chemical biology research.
• This approach facilitates the identification of new therapeutic vulnerabilities and accelerates biotechnology development.