Project Background
A discovery-stage client wanted to establish whether a VHL-directed self-degradation strategy could serve as a chemical biology tool for probing ligase dependence in a hypoxia-related signaling project. The client had a known VHL-binding motif but lacked a clear plan for converting that binder into a productive homobivalent degrader.
Our Support
We began by comparing multiple attachment vectors on the VHL ligand and designed three linker families with different rigidity and spacing logic. Computational modeling was used to remove candidates likely to create steric clash or unproductive geometry. We then synthesized 18 Homo-PROTAC analogs and evaluated them through ligase activity, ubiquitination, and cell-based degradation studies. Early screening showed that several high-affinity compounds failed to induce meaningful ligase loss, so we shifted the design toward a narrower distance window and a less flexible linker architecture. This second-round optimization yielded 4 compounds with reproducible VHL degradation in the client's preferred cell system, including 1 lead that combined stronger degradation depth, clearer dose response, and more interpretable kinetic behavior than the initial series.
Project Outcome
The client obtained a ranked Homo-PROTAC tool set, a clear SAR map linking geometry to degradation output, and a lead compound suitable for follow-up pathway studies. Just as importantly, the project clarified which linker patterns were non-productive, reducing unnecessary chemistry in the next phase.
Project Background
A biotech partner was interested in exploring whether a CRBN-focused Homo-PROTAC strategy could complement its broader targeted protein degradation platform. The team had internal ligands and screening capability but needed support in converting early concepts into compounds with interpretable mechanistic data.
Our Support
We first reviewed the client's available ligands, assay format, and desired success criteria, then selected 2 chemotypes for homobivalent expansion. To improve design quality, we integrated linker topology planning with degradation-focused decision gates rather than relying on binding potency alone. Across the campaign, we designed 26 compounds, prioritized 12 for full synthesis, and advanced 7 into mechanistic testing. Initial results indicated acceptable engagement but weak degradation, pointing to a geometry issue rather than a ligand-affinity limitation. After redesigning the attachment position and reducing excessive linker flexibility, we identified 2 optimized compounds that showed markedly improved CRBN reduction in live-cell studies and stronger consistency across replicate assays.
Project Outcome
The client received optimized leads, a documented troubleshooting path explaining why the first series underperformed, and a more reliable framework for future Homo-PROTAC design around the same ligase class.
Directly Probes E3 Ligase Vulnerability
