Molecular glue degraders have incredible therapeutic potential, particularly considering delivering on the promise of degrading “undruggable” proteins. However, their discovery has thus far been largely serendipitous. We have established a scalable strategy toward glue degrader discovery that is based on chemical screening in cell models where many E3 ligases are functionally impaired. Collectively, we outlined a versatile and broadly applicable strategy to identify molecular glues at scale and thus empower future drug discovery efforts.

During the talk Amphista's approaches to Targeted Protein Degradation (TPD) will be discussed. In particular, I will be highlighting the need for new degrading mechanisms to increase the reach of TPD approaches even further. I will also be sharing new data on bifunctional degraders with improved profiles over PROTACs and discussing future directions for next-generation TPD drug discovery.

Tag-based targeted protein degradation technologies including the degradation tag (dTAG) system have emerged as powerful approaches to control protein abundance using small molecule degraders. This talk will describe the development and advances of the dTAG technology platform and highlight case studies demonstrating utility for pre-clinical target discovery and validation.

Mutations to RAS are among the most common oncogenic drivers. To determine the advantages and feasibility of KRAS targeted degradation, we applied ‘Biodegraders’: chimeric proteins with a high-affinity target-binding domain fused to an engineered E3 ligase adapter. A series of anti-RAS biodegraders spanning different RAS isoform/nucleotide-state specificities and leveraging different E3 ligases provide evidence for KRAS degradability and its functional consequences. Furthermore, application of a GDP-state specific degrader uncovers the relative prevalence of the “off-state” of various KRAS mutants in the cellular context.

Recent advances in the development of small-molecule protein degraders, including molecular glues and heterobifunctional degraders, have made it possible to target many disease-causing proteins previously considered undruggable. The broad applicability of this approach is enabled by the plasticity of E3 ubiquitin ligases to interact with and ubiquitylate different (neo)substrates. The unique catalytic and assembly mechanism of the cullin-RING E3 ligases (CRLs) makes them particularly suitable for targeted protein degradation (TPD).

Finding new ways to target histone acetyltransferases, such as Tip60, is important for advances in immuno-oncology, and the PROTAC approach makes this possible. However, mice have a single amino acid substitution that blocks efficient iMID-dependent recruitment of the E3-ligase, Cereblon, limiting experimental studies. We report use of Tip60 PROTACs in WT vs. Cereblon knock-in mice in which PROTAC-dependent recruitment is now rendered active, allowing use of murine models for testing of this and other PROTAC molecules.

PROTACs are required to form ternary complexes to drive target ubiquitination and degradation at low catalytic concentrations. This presentation will demonstrate a novel trivalent PROTAC strategy to boost targeted protein degradation. We will show how the trivalent degrader we discovered exhibits enhanced potency and downstream activity in a series of biophysical and cellular assays.

PROTACs represents an exciting new modality in drug discovery that offers several potential advantages over traditional small-molecule inhibitors, including the potential to deliver pharmacodynamic (PD) efficacy which extends beyond the detectable pharmacokinetic (PK) presence of the PROTAC, driven by the synthesis rate of the protein. This disconnect between PK and PD, when coupled with low nanomolar potency, offers the potential for low human doses and infrequent dosing regimens with PROTAC medicines.

Accurate SAR insights to drive drug development cycles depend on using the right mathematical models to fit data. For PROTACs data with hook behaviour, the standard Hill equation often misestimates pharmacological parameters including potency and efficacy. We have developed an automated, flexible bell-shaped biphasic model that can apply double sigmoidal curve fitting at scale and delivers accurate parameter estimates, enabling faster and more robust DMTA cycles.

DNA encoded library technology is an optimal discovery tool for targeted protein degradation: 1) DEL screening is a very powerful way of identifying potent, selective POI and novel E3 ligase binders. 2) DEL molecule shares similar topological structure as PROTAC molecule with clearly defined linkage point; 3) it is proven that dual binding molecules can be directly identified from DEL screening; 4) DEL screening can be applied in molecular glue discovery.

Here I will discuss the latest targeted protein degradation developments from the Induced Proximity Platform at Amgen.

Eukaryotic proteins undergo proteasomal degradation as a means of maintaining protein homeostasis, quantity, and quality to regulate various biological processes. An emerging theme in the drug development field is to exploit ubiquitin (Ub)-mediated proteolysis for targeted degradation of disease-causing proteins. We employ structure-based combinatorial protein design and engineering strategies to develop Ub variants (UbVs) as high-affinity binders for novel E3 ligases to induce intracellular degradation of selective substrates. 

Ubiquitin (Ub)-dependent proteolysis drives the cell cycle. The behemoth anaphase-promoting complex/cyclosome (APC/C) is a 1.2 MDa Ub ligase responsible for regulating mitosis and G1 maintenance. Here, we will discuss how to optimize large complexes for cryo-EM studies using a new method called mass photometry and how multiple mechanisms activate the APC/C for a swift cell cycle transition.