Cambridge Healthtech Instituteの第6回年次会議
Protein Degraders & Molecular Glues - Part 1
（タンパク質分解誘導剤・分子接着剤 - パート1）
2023年4月11 - 12日
*Premium Pricing or separate registration required. See Short Courses page for details.
Registration and Morning Coffee7:00 am
Welcome Remarks8:00 am
STRUCTURAL AND MECHANISTIC CHARACTERIZATION
Structural and Biophysical Studies of Protein Degrader Ternary Complexes
Protein degradation using heterobifunctional chimeras is a rapidly growing mechanism to alter protein function. Critical to this mechanism is the formation of a ternary complex in which the target protein is recruited to an E3 ligase. We report structural, biophysical, and cellular studies that expand our understanding of this process - shedding light on different degradation efficiencies for distinct recruitment mechanisms for Bruton’s Tyrosine Kinase.
CoraFluor-Enabled TR-FRET Assay Strategies for Facile PROTAC Profiling
The pace of progress in drug discovery is highly dependent on the availability of robust and quantitative assay platforms that allow for straightforward but accurate characterization of the underlying molecular interactions and target abundance. We have developed novel TR-FRET-based assay systems to facilitate the characterization of PROTACs and molecular glue degraders, including the facile measurements of endogenous protein levels, target affinity profiling, and quantitative determination of complex ternary cooperativity. It also allows kinetic and thermodynamic measurement of ligand binding with endogenous proteins, high-throughput quantification of endogenous target protein abundance in cell lysates, and measurement of absolute cooperativity of ternary complexes.
Structural and Mechanistic Understanding of Cereblon as a Target of Molecular Glues
Cereblon is both a substrate adaptor protein for CRL4-mediated protein destruction, and the target of several novel clinical compounds which redirect this destructive activity to degrade "undruggable" substrates of interest. Though previous crystallographic structures existed, we use Cryo-EM to study the cereblon apoenzyme and directly compare it with several liganded and substrate-engaged states. This ensemble analysis reveals important allosteric changes to the mechanistic cycle of cereblon.
Protein degradation is a novel modality with the potential to tackle therapeutically interesting proteins previously seen as undruggable. Pelago Biosciences AB will show how CETSA in combination with functional efficacy assays and quantitative proteomics can be applied in various stages of drug discovery to provide data that is both actionable and biologically relevant for targeting protein degradation.
Transcription factors, such as the STAT proteins, are critical for the regulation of gene expression in the cell; deregulation of the biochemical functions of these proteins can be important hallmarks of cancer and inflammation. Eurofins Discovery presents its new line of STAT binding assays, showing selective binding for published small molecules targeting the SH2 domains of the STAT proteins. This platform is ideal for accelerated screening and SAR analysis.
Networking Coffee Break10:10 am
EMERGING DEGRADER STRATEGIES
Chimeric BRM Degraders and Degrader-Antibody Conjugates
The BRG1 (SMARCA4) protein is mutated in a subset of NSCLC, and such alterations make the cancers highly dependent on the closely-related BRM (SMARCA2) paralog for growth. The detailed characterization of a potent, heterobifunctional, chimeric BRM degrader compound using NSCLC cells and tumor models will be discussed. The conjugation of a second chimeric BRM degrader molecule to monoclonal antibodies to enhance its in vivo activity will also be described.
Targeted Degradation of Extracellular Proteins with ATACs (ASGPR-Targeting Chimeras)
Targeted protein degradation of disease-causing proteins is a promising new therapeutic modality. A novel approach has emerged for extracellular protein degradation that utilizes the asialoglycoprotein receptor (ASGPR) to recruit pathogenic proteins for endolysosomal degradation. We describe the discovery of novel bifunctional compounds called ATACs (ASGPR-Targeting Chimeras) containing Avilar’s proprietary, high-affinity, small-molecule, ASGPR-binding ligands.
A Unique Covalent Strategy for Protein Degradation Which Co-Opts a Human DNA Repair Protein
Most strategies in protein degradation focus on co-opting E3 ligases directly. Another strategy would be to find a native protein which is potently degraded (naturally or induced) and then hitchhike on that protein. I will present our work on using such an approach to coax the DNA repair protein methylguanine methyltransferase (MGMT) into degrading other target proteins.
Transition to Lunch12:05 pm
Session Break12:45 pm
PURSUING DIFFICULT DRUG TARGETS
One-Carbon Pathway PROTACs
Methotrexate (MTX), a folate cofactor analog, is a potent inhibitor of dihydrofolate reductase (DHFR), where it is used as both an antineoplastic and an immunosuppressant therapeutic. MTX undergoes folylpolyglutamate synthetase (FPGS)-mediated g-glutamylation, which affects cellular retention and target specificity. Unfortunately, therapeutic resistance to MTX is a significant clinical barrier. Furthermore, the polypharmacological of MTX remains poorly understood. We developed a series of potent MTX-based PROteolysis TArgeting Chimeras (PROTACs) to investigate DHFR degradation pharmacology and one-carbon biochemistry.
A Functional Zinc Finger Transcription Factor Degrader
The zinc finger transcription factor SALL4 is an ideal target in cancer, but small-molecule therapies against SALL4 are not yet clinically available. We have deduced the crystal structure of the complex of SALL4 bound to DNA via zinc finger cluster 4 (ZFC4), followed by computational predictions and cell-based drug screening identification of a new lead molecule that preferentially targets SALL4 positive cancer cells.
Discover Protein Degraders for Cancer Therapy: Expect the Unexpected
PROTACs as a nascent technology have shown early promises and the field witnessed an explosion of discovery and development activities recently. In this presentation, we will share some learnings from multiple programs over the last 6 years, including our understanding of potential resistant mechanisms and some unexpected findings on selectivity, toxicity, etc.
Developing protein degraders is a multi-step and complex process. Using appropriate biochemical and biophysical methods is crucial to selecting the right candidates with confidence. Common roadblocks during the characterization of ternary complexes, cooperativity, and hook effect are low-quality data, immobilization of covalent binders or multimeric molecules, and complex protocols. In this talk, you’ll learn how Dianthus, a plate-based screening platform, overcomes these roadblocks from case studies representing difficult drug targets.
Refreshment Break in the Exhibit Hall with Poster Viewing3:20 pm
PLENARY KEYNOTE SESSION
Plenary Keynote Introduction (Sponsorship Opportunity Available)4:35 pm
Targeting Nodes and Edges in Protein Networks
Protein interaction networks consist of protein nodes and interaction edges. We aim to inhibit or stabilize specific protein-protein interactions to dissect these complex networks for chemical biology and therapeutics discovery. Through covalent fragment-based approaches, we discovered compounds that selectively stabilized the chaperone 14-3-3 bound to diverse client proteins and altered their function. Additionally, function-selective inhibitors for the multifunctional enzyme VCP/p97 are providing new tools and drug leads for cancer.
Welcome Reception in the Exhibit Hall with Poster Viewing5:30 pm
Close of Day6:30 pm
Registration Open7:00 am
In-Person Group Discussions with Continental Breakfast7:45 am
Tools for Structural and Mechanistic Characterization of Protein Degraders
- Structural, biophysical, and cellular studies to expand our understanding of protein degradation
- New assay systems to facilitate the characterization of PROTACs and molecular glue degraders
- Chemoproteomics method to discover additional E3 ligases
- Cryo-EM to study and compare ligand binding and conformational changes
FRAGMENTS AND TARGETED PROTEIN DEGRADATION APPROACHES
FEATURED PRESENTATION: Fragment Approaches for Discovering Tissue-Specific E3 Ligases and β-Catenin Degraders
I will present how we've applied fragment-based methods to discover ligands for tissue-specific E3 ligases. I will also cover our work on discovering bifunctional degraders for β-catenin. This highly sought-after but difficult-to-drug intracellular target is part of a multi-functional cellular signaling complex whose overactivity contributes to the development of specific cancers and other diseases.
Coffee Break in the Exhibit Hall with Poster Awards Announced9:35 am
Poster Award (Sponsorship Opportunity Available)
EXPLORING NEW E3 LIGASES
Discovery of Novel E3 Ligands for Targeted Protein Degradation
Three features separate the targeted protein degradation from previously drug discovery modalities; its catalytic mechanism to achieve higher efficacy, its ability to target previously undruggable proteins such as non-enzyme targets, and its potential to deliver drug activity to selective tissues. All three features depend on the E3 ligands. Human cells express estimated more than 600 E3 ubiquitin ligases, yet nearly all current advanced degraders use the same E3 ligand binding to cereblon. I will discuss our rationale and efforts in discovering novel E3 ligands for targeted protein degradation.
Expanding the Landscape of E3 Ligases for Targeted Protein Degradation
The field of small molecule-mediated protein degradation has grown tremendously over the past few years. Nonetheless, only a handful of E3 ligases have been identified to support this process. We have developed a chemoproteomic method to discover additional E3 ligases capable of supporting small molecule-mediated protein degradation and identified two novel E3 ligases, DCAF16 and DCAF11, as the targets of electrophilic bifunctional degraders that engage diverse protein substrates.
Explore the Target Scope of KEAP1 E3 Ligase-Based PROTACs
A major challenge in the TPD field is the lack of accessible E3 ligase ligands for developing degraders. To expand the E3 ligase toolbox, we sought to convert the KEAP1 inhibitor into a recruitment handle for several targets. We characterize tool compounds to explore KEAP1-mediated ubiquitination and delineate the challenges of exploiting new E3 ligases for generating bivalent degraders.
Close of Protein Degraders & Molecular Glues - Part 1 Conference12:00 pm