Abstract Targeted protein degradation (TPD) is a promising therapeutic modality, but its broader application is constrained by the lack of established strategies to select optimal E3 ligases for specific targets. Although many E3 ligases exist, only a few have been leveraged in degraders currently undergoing clinical trials, leaving much of the ligase space unexplored. To address this challenge, a proprietary TPD discovery platform enables rational E3 ligase selection in a high-throughput manner through a workflow that integrates fragment-based diversity-oriented synthesis (DOS) with phenotypic screening in relevant cell models. This workflow, supported by in-house capabilities for high-throughput compound synthesis, generates diverse chemical scaffolds and identifies degrader candidates with desired activity profiles. Phenotypic screening ensures functional relevance and facilitates the discovery of compounds that engage E3 ligases not previously applied in TPD, thereby expanding the scope of ligase-targeted degradation strategies. Lead compounds are refined through optimization and E3 ligase deconvolution to confirm ligase engagement and improve molecular properties such as potency, selectivity, and drug-likeness. Once novel E3 ligase binders are identified through this process, they open up new application opportunities. One path is to incorporate the binder into our internal E3 ligase toolbox and apply it to other targets as part of bifunctional degrader design. Another is to evaluate whether the binder can function as a molecular glue, enabling degradation through neo-substrate recruitment. Importantly, our phenotypic screening approach has led to the identification of proprietary E3 ligases with low expression in bone marrow and hematopoietic tissues. Degraders based on these E3 ligase binders demonstrate the potential to avoid bone marrow toxicity—a major concern for cancer targets—while maintaining robust activity. This strategy not only enables the development of orally bioavailable molecules with improved pharmacokinetics and broad target applicability, but also provides a path to safer TPD therapeutics. By expanding the usable E3 ligase toolbox, this proprietary platform unlocks new degrader modalities and supports the development of therapeutics with improved physicochemical properties, including orally bioavailable candidates. This presentation will highlight case studies demonstrating how this platform contributes to the advancement of novel E3 ligase-based TPD, offering a scalable, versatile, and forward-looking solution to a key bottleneck in the field. Citation Format: Kanae Gamo, Shinya Yokosaka, Michiko Watanabe, Tomoaki Hayashi, Shigeyuki Mori, Naomi Asahara, Noriyasu Sano, Shigeru Furukubo, Kazuteru Aoki. Expanding the landscape of targeted protein degradation: E3-agnostic discovery and proprietary ligand identification abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5168.
Gamo et al. (Fri,) studied this question.