Disulfide constrained peptides (DCPs) show great potential as templates for drug discovery. We developed DCPs binding to membrane-bound E3 ubiquitin ligases. They can be used to develop strategies for targeted protein degradation at the plasma membrane. These DCPs can be produced synthetically or recombinantly, providing great versatility compared with large biologics or small molecules.

Only a handful of ligands are available for > 600 known E3 ligases. Using fragment-based methods and structure-based design, we have discovered ligands for additional E3 ligases that are tissue specific and are only present in cancer cells but not normal tissue. We are using these ligands to create less toxic PROTACS for cancer therapy.

Downregulation and mutation of E3 ligase substrate receptors such as CRBN, VHL, MDM2, and IAP will reduce the effectiveness of PROTACs, which necessitates addition of new substrate receptors and E3 ligases to the repertoire to avoid resistance. DCAF1 is a substrate receptor of EDVP and CUL4 E3 ligases with diverse substrate specificity. We will discuss structural insights into a mechanism by which DCAF1 could gain such diverse substrate specificity and describe why it could be a reliable and possibly better alternative to the commonly used E3 substrate receptors for development of PROTACs. 

Generating therapeutic targeting hypothesis for drugging proteins lacking traditional binding pockets is critical for tackling unprecedented targets. We describe a proximity labeling proteomics approach for revealing putative regulatory E3 ligases as a strategy-generating platform by targeting existing complexes via induced proximity. Furthermore, we discuss considerations for deploying this approach and bioinformatics strategies for increased confidence of putative hits.

Transcription factors are known to bind to cereblon in the presence of molecular glues and some reports implicate interactions with multiple zinc fingers. We present biophysical and structural assessments of the minimal binding domains of IKZF2 and other transcription factors, revealing that multiple zinc fingers interact with cereblon:glue complexes. In these examples, the binding modes are distinct and may have implications for the design of selective degraders.

Highly potent, exquisitely selective, and orally bioavailable inhibitor of SMARCA2 degrader identified using proprietary platform technology DNsD (Directed Neo-Substrate Degradation). Potential candidate has been identified for the treatment of SMARCA4 mutated cancers. In vitro and in vivo profile of potential candidate molecule will be presented.

Development of Degrader Antibody Conjugates (DACs) represents a novel therapeutic modality combining antibody specificity with targeted protein degradation. Our DAC has a GSPT1 molecular glue as the payload, enabling selective protein degradation in cancer cells. Different linker chemistries were compared for GSPT1 degradation efficiency and cellular potency. This dual-targeting approach demonstrates potent anti-tumor activity with improved therapeutic window compared to traditional ADCs.

The application of biophysical methods in the discovery of molecular glue degraders will be presented. By leveraging techniques such as Surface Plasmon Resonance and Spectral Shift assays and putting emphasis on ternary complex affinity and kinetic characterization, novel molecular glues to an important oncology target protein have been identified and validated.

PROTACs are an emerging class of therapeutics for many disease areas including oncology. We recently developed a novel chemical genetics-based method to selectively label existing proteins and newly synthesized proteins (CG-SLENP) in living cells. Using this method, we found that existing proteins and newly synthesized proteins have drastically different responses to small molecule inhibitors and PROTACs. We further found that combining PROTACs and small molecule inhibitors show synergistic anticancer activities.