Building on our CoraFluor TR-FFRET technology, we have established a versatile assay platform for the comprehensive characterization of PROTACs and molecular glue degraders, including (a) detailed kinetic and thermodynamic analyses of ligand binding to both endogenous and recombinant proteins, (b) accurate quantification of ternary complex cooperativity, (c) facile measurements of cellular protein levels. This advancement provides a robust toolset for enhancing the understanding and development of targeted protein degradation technologies.

Targeted proteomics through parallel reaction monitoring (PRM) leverages high precision and quantitative accuracy for target protein(s), affording higher throughput as opposed to discovery proteomics. For degrader projects, targeted proteomics is invaluable for quantitatively understanding degradation in cells and in vivo. Here, we describe a case study where targeted proteomics impacted a protein degrader project at AstraZeneca, by providing a key orthogonal method to understand accurate DC50 and Dmax values.

The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a  combination of physics and machine learning methods for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. We will discuss the generalization of the approach for other TACs and ligases, and principles of molecular glue discovery.

Ubiquitin proteasome system (UPS) plays a critical role in removing aggregated proteins and damaged mitochondria (mitophagy) and building new mitochondria (mitobiogenesis). Parkinson’s disease (PD) and Alzheimer’s Disease (AD) share common neurodegenerative traits, inability to correct protein misfolding or remove aggregated proteins. Progenra has discovered a molecular glue that activates parkin ligase and phospho-poly-ubiquitinate target proteins in cells and animal models. Blood-based levels of phospho-ubiquitin are important biomarkers for neurodegeneration. Discovery and development of molecular glue for parkin ubiquitin ligase that induces mitophagy and improves neuronal health will be discussed.

Multiple sclerosis (MS) is characterized by inflammation and demyelination in the central nervous system, lacking effective treatments despite advancements. Bruton's tyrosine kinase (BTK) is crucial in B cell activation and MS autoimmunity. BTK degraders offer a fresh therapeutic path by specifically degrading BTK protein. This talk discusses the rationale for targeting BTK in MS and elucidates the mechanism of BTK degraders through preclinical characterization of selective and CNS-penetrant degraders.

Lysosome-mediated degradation is an emerging therapeutic strategy with clinical promise for catalytically depleting dysregulated proteins, both from the plasma membrane or from extracellular circulation. Small Molecule Lysosome-Targeting Chimeras (SMaLTACs) circumvent the requirement of expression of carbohydrate-based lysosome-targeting receptors. Using proteomics, we demonstrate how SMaLTACs enable the selective internalization and subsequent degradation of a therapeutically relevant extracellular protein and allow exploration of mechanistic insights.

PIM kinases have important pro-tumorigenic roles and mediate several oncogenic traits, including cell proliferation, survival, and chemotherapeutic resistance. We found that inhibition of PIM kinase activity stabilizes protein levels of all three PIM isoforms (PIM1/2/3), and this can promote resistance to PIM inhibitors and chemotherapy. To overcome this effect, we designed PIM proteolysis targeting chimeras (PROTACs) to target PIM for degradation. PIM PROTACs effectively downmodulated PIM levels through the ubiquitin-proteasome pathway. Importantly, degradation of PIM kinases was more potent than inhibition of catalytic activity at inducing apoptosis in prostate cancer cell line models.

The development of immune checkpoint inhibitors based on anti-CTLA-4, anti-PD-1/PD-L1 has revolutionized cancer treatment. However, many patients fail to respond, suggesting the existence of other immune checkpoints orthogonal to these well-established ones. Myeloid cell-associated Siglec (sialic acid-binding immunoglobulin-like lectin)-7 and -9 have recently been recognized as glycoimmune checkpoints. However, there is currently no antibody that can target both Siglecs on the cell surface. We have developed a degrader that induces efficient degradation of both Siglec-7 and -9 in primary cells and in vivo. Blocking Siglec-7/9 signaling showed excellent tumor control in several murine solid tumor models.

Description:Bi-functional degraders occupy beyond-rule-of-five chemical space where established rules for drug-likeness cannot easily be applied. In contrast to approved CNS drugs, bi-functional degraders violate most metrics, particularly molecular weight, yet we routinely observe brain penetrance in our programs. For example, NX-5948, a clinical stage orally bioavailable BTK degrader shows CNS exposure and activity both preclinically and clinically. This presentation will explore our evolving understanding of targeting the CNS using degraders.

The zinc finger transcription factor Helios (IKZF2) is highly expressed in Tregs and plays an important role in helping tumors evade a normal immune response. IKZF2 is a transcription factor that had been considered "undruggable." Here we disclose the discovery and preclinical evaluation of a selective molecular glue degrader of IKZF2 (PLX-4545) which reverses Treg suppression and is currently being evaluated in a Phase 1 trial of healthy volunteers.

CREB binding protein (CBP) and E1A binding protein (p300) are paralog histone acetyltransferases involved in many cellular processes via their activity as transcription factor co-activators. Dysregulation of one or both proteins has been implicated in a variety of cancers. Due to the high homology between CBP and p300, identification of selective chemical matter that specifically and directly targets CBP has proven challenging. Here, we describe potent, highly selective, CBP heterobifunctional degraders with selective biological activity in CBP-dependent cancer lines.