Heterobifunctional chimeric degraders are a class of ligands that recruit target proteins to E3 ubiquitin ligases to drive compound-dependent protein degradation. Critical to the mechanism of action is the formation of a ternary complex between the target, degrader and E3 ligase to promote ubiquitination and subsequent degradation. However, limited insights into ternary complex structures exist, including a near absence of studies on one of the most widely co-opted E3s, cellular inhibitor of apoptosis 1 (cIAP1). Our results reveal insights from unique ternary complex structures and show that increased ternary complex stability/rigidity need not always correlate with increased degradation efficiency.

Small molecules that induce protein degradation through ligase-mediated ubiquitination, have shown considerable promise as a new pharmacological modality. Thalidomide and related IMiDs provided the clinical proof of concept, while significant progress has recently been made towards chemically induced targeted protein degradation using heterobifunctional small molecule ligands. We will present recent work towards a better understanding of the molecular principles that govern neo-substrate recruitment, and other small molecule degraders.

Cellular chaperones not only mediate protein folding, but can also direct proteins towards the ubiquitin-proteasome system. Chaperone-mediated protein degraders (CHAMPs) are hetero-bifunctional small molecules that induce proximity between a target of interest and the chaperone machinery, thereby resulting in target degradation. Due to the highly activated state of chaperones in cancer cells, CHAMPs preferentially induce protein degradation in tumors relative to normal tissues.

Currently, PROTACs based on Cereblon, VHL, HDM2 and cIAPs degrade a limited set of therapeutic targets. Targeting membrane protein for degradation can open new applications for PROTAC drugs that will compete with monoclonal antibody therapies and yet have an advantage of small molecules. Progenra has established a novel membrane associated ubiquitin ligase that preferentially degrades membrane proteins. Importance of this ligase in selective regulation of membrane receptor provides new ways to regulate membrane receptor function with small molecules. This presentation will provide examples of PROTAC mediated degradation of membrane receptors.

PROTACs have emerged as a novel drug development platform. Through computational modelling of the entire NEDD8-VHL Cullin RING E3 ubiquitin ligase (CRLVHL)/PROTAC/BCL-xL/UbcH5B(E2)-Ub/RBX1 complex, we rationally designed of a new series of ABT263-derived and VHL-recruiting PROTACs and generated the first potent BCL-xL and BCL-2 (BCL-xL/2) dual degrader with significantly improved antitumor activity against BCL-xL/2-dependent leukemia cells. In addition, our studies provide the first experimental evidence that the accessibility of lysine(s) on a target protein plays an important role in determining the selectivity and potency of a PROTAC in inducing protein degradation.

Prostate cancer remains as an unmet medical need despite that there are androgen receptor (AR) inhibitors on market. PROTAC-targeting AR signaling emerges as a showcase of this revolutionary strategy, and a new approach to treat prostate cancers. Recent progress in oral PROTAC for prostate cancer from Hinova will be presented.

AssayQuant® has combined chelation-enhanced fluorescence with high-throughput peptide synthesis to create optimized physiological substrate sensors to monitor the activity of protein kinases and phosphatases. The result is a simple add & read method for continuous, quantitative and direct detection of activity using recombinant enzymes or crude lysates. A modified approach allows continuous monitoring of lipid kinases (DGKs). These enabling tools and services provide a quantum improvement to accelerate nextgen drug development.

The oncogene MYC presents a central unresolved challenge to drug discovery efforts. Being a transcription factor, MYC lacks catalytic activity and instead contains disordered regions that mediate macromolecular interactions. These features make it hard to develop compounds against MYC but offer the opportunity to inhibit MYC function by targeted degradation of MYC binding partners. We systematically identified MYC interacting proteins, analyzed their potential as cancer targets and developed bifunctional degraders.

PROteolytic TArgeting Chimeras (PROTACs) have emerged as a new class of protein degrader drug that can target the “undruggable” proteome for novel therapeutics. Currently, PROTAC discovery is hampered by large gap in understanding link between ubiquitination and degradation, and current methods to quantify this process are of limited utility in drug discovery. We addressed these gaps utilizing Tandem Ubiquitin Binding Entities (TUBEs) in high throughput biochemical and cell based assays.

We will discuss how scalable genome engineering platforms can empower Target ID to Lead Optimization studies for TPD. This will include the time- and cost-effective creation of disease-relevant cell lines to validate targets with inducible protein loss and for easy assessment of protein turnover.

Many diseases, including cancer, stem from aberrant activation or overexpression of oncoproteins that are associated with multiple signaling pathways. Although proteins with catalytic activity can be successfully drugged, the majority of other protein families, such as transcription factors, remain intractable due to their lack of ligandable sites. Here, we report the development of TRAnscription Factor TArgeting Chimeras (TRAFTACs) as a generalizable strategy for targeted transcription-factor degradation. TRAFTACs are chimeric oligonucleotides that can simultaneously bind to the transcription factor-of-interest and to E3 ligase resulting in an induced degradation of the former via the proteasomal pathway.

Overview of current state of targeted protein degradation and thoughts on where the field is heading with respect to clinical candidates, new degradation targets and different degradation strategies.

Constituent activation of the tropomyosin receptor kinases, through aberrant fusions, leads to the unrestrained signaling of the oncogenic RAS/RAF and PI3K/AKT kinase cascade.  NTRK mutations or fusions have been identified as the driver of many cancers making the NTRK family of proteins an attractive target for drug discovery.  Herein we will describe the discovery and optimization of NTRK degraders.

Molecular glue degraders are a novel therapeutic modality and induce destabilization of proteins that would otherwise be considered undruggable due to the lack of a ligandable pocket. Their discovery however has so far been serendipitous. The Proxygen glue degrader discovery platform enables rational screening for such molecules on an industrial scale. Here, we present a case study of the subsequent chemical optimization of the resulting hit molecules.

The recent development of successful CAR (chimeric antigen receptor) T cell therapies has been accompanied by a need to better control potentially fatal toxicities that can arise from adverse immune reactions. Here we present a ligand-controlled CAR system, based on the IKZF3 ZF2 b-hairpin IMiD-inducible degron, which allows for the reversible control of expression levels of type I membrane proteins, including CARs. Testing this system in an established mouse xenotransplantation model for acute lymphoblastic leukemia, we validate the ability of the CAR19-degron to target and kill CD19-positive tumor cells displaying complete control/clearance of the tumor. We also demonstrate that the activity of CAR19-degron can be regulated in vivo when dosing a FDA-approved drug, lenalidomide.