A Rapid Binder Discovery Workflow for Engineering Mini-Protein Degraders

Developing molecules that selectively bind targets of interest remains a critical bottleneck in biological research and biotechnology. Here, we present a workflow that leverages the Phage-Assisted Non-Continuous Selection for Binders (PANCS-Binders) technology for rapid de novo binder discovery. To directly assess the speed and utility of the approach, we pursued three cancer-related targets: NSD3, NMNAT2, and CSF1R. Within 26 days, the PANCS-Binders workflow yielded sequence- and function-verified binders for all three targets with nano-to-micromolar affinities. By incorporating an NSD3 binder into an engineered E3 ligase, RNF8, we developed an NSD3 degrader that potently depleted endogenous NSD3 and inhibited colorectal cancer cell proliferation. We then applied this degrader to reveal previously unknown NSD3 dependencies in ovarian cancer cell lines, uncovering new therapeutic vulnerabilities. Together, our work establishes a robust workflow for accelerated binder discovery and demonstrates how binders can expedite chemical biology discovery and biotechnology development.