Cambridge Healthtech Institute’s 4th Annual

PROTACs and Molecular Glues – Part 1

Design and Optimization of Protein Degraders

October 18 - 19, 2022 EDT

The ubiquitin-proteasome system (UPS) and the autophagy-lysosome system are responsible for protein degradation and maintenance of proteostasis. They consist of well-controlled, selective mechanisms for intracellular protein degradation and hold a lot of promise in seeking out previously “undruggable” targets for therapeutic intervention. However, their diversity and complexity make it difficult to target these pathways for therapeutic intervention. Cambridge Healthtech Institute’s conference on PROTACs and Molecular Glues discusses the progress that has been made and the challenges that are yet to be overcome. The first part of the proteolysis-targeting chimeras (PROTACs) and Molecular Glues conference will discuss the design and optimization of new small molecule degraders, E3 ligase and deubiquitinating enzyme (DUB) modulators, and monovalent degraders. Challenges that exist in terms of stability, biodistribution and penetration of these molecules for better in vitro to in vivo translation will be discussed.

Tuesday, October 18

Registration and Morning Coffee (Grand Ballroom Foyer)7:00 am

NEXT-GENERATION PROTEIN DEGRADERS

ROOM LOCATION: Constitution A

7:55 amWelcome Remarks
8:00 am

Chairperson's Remarks

Scott Eron, PhD, Senior Research Scientist II, Biochemistry Biophysics and Crystallography Group, C4 Therapeutics, Inc.

8:05 am

Where Next in the Search for Next-Generation Protein Degraders?

Andrea Testa, PhD, Head, Chemistry, Amphista Therapeutics Ltd.

Rapid progress has been made advancing novel TPD therapies in recent years, highlighting their huge clinical potential but also identifying opportunities where further enhancements can increase their impact further. This presentation will reflect on where there is the biggest opportunity for next-generation TPD approaches to achieve clinical impact and Amphista's own progress in identifying new degrading mechanisms and warheads which are directly expanding the potential of the TPD field.

8:35 am

Novel Monovalent Protein Degraders and Molecular Glues in Cancer Drug Discovery

Simon Bailey, PhD, MBA, Executive Vice President & Head of Drug Discovery, Plexium, Inc.

Degradation of pathogenic protein represents an important new modality in drug discovery. Here we describe the discovery of novel monovalent protein degraders and molecular glues using Plexium's approach. These monovalent degraders extend the options for targeted protein degradation beyond bivalent degraders and cereblon IMIDs.

9:05 am

The Arvinas PROTAC Discovery Engine: Insights from Discovering and Developing Molecules that Induce Targeted Protein Degradation

Miklos Bekes, PhD, Associate Director, Degrader Mechanisms Group, Platform Biology, Arvinas, Inc.

Targeted protein degradation (TPD) is an emerging therapeutic modality with promise across diverse diseases.  In the ~20 years since the idea of using bifunctional small molecules that recruit ubiquitin ligases to induce target degradation, 10+ TPD drug candidates have entered clinical trials, spawning a mini-biotech industry based on molecules that induce ‘proximity’ to impact target biology. Arvinas is a pioneer in the field and continues pushing the boundaries of TPD. This presentation will highlight recent developments in the Arvinas PROTAC Discovery Engine, focusing on the mechanistic and structural basis of small molecule degrader discovery highlighting recruitment of new ubiquitin ligases.

Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing (Grand Ballroom)9:35 am

10:25 am

Monofunctional Degradation Activating Compounds: From Platform Development to the Clinic

Scott Eron, PhD, Senior Research Scientist II, Biochemistry Biophysics and Crystallography Group, C4 Therapeutics, Inc.

This presentation highlights C4T’s platform build to enable rational and efficient discovery of Monofunctional Degradation Activating Compounds (MonoDACs) through the design and evolution of a diverse chemical library combined with various screening approaches. Leveraging this platform, we will discuss a snapshot of the key SAR advancements leading to the discovery of IKZF1/3 degrader, CFT7455, currently in clinical development, as well as the identification of the first MonoDAC hit to a novel therapeutic target.

10:55 am

PANEL DISCUSSION: Translational Challenges Developing PROTACs and Molecular Glues

PANEL MODERATOR:

Scott Eron, PhD, Senior Research Scientist II, Biochemistry Biophysics and Crystallography Group, C4 Therapeutics, Inc.

PANELISTS:

Simon Bailey, PhD, MBA, Executive Vice President & Head of Drug Discovery, Plexium, Inc.

Miklos Bekes, PhD, Associate Director, Degrader Mechanisms Group, Platform Biology, Arvinas, Inc.

Andrea Testa, PhD, Head, Chemistry, Amphista Therapeutics Ltd.

Chris De Savi, PhD, Senior Vice President & Head, Drug Discovery, Kymera Therapeutics

Jim Henderson, PhD, Vice President, Chemistry, C4 Therapeutics, Inc.

Transition to Lunch12:25 pm

12:35 pm LUNCHEON PRESENTATION:Accelerate the Discovery of PROTACs and Molecular Glues from Lead Identification to Protein Degradation Validation

Zachary Gurard-Levin, PhD, Chief Scientific Officer, SAMDI Tech

Katherine Jones, PhD, Senior Research Leader, Charles River

This presentation will describe innovative tools to initiate and advance drug discovery efforts focused on PROTACs and Molecular Glues. Through a series of case studies, we will describe a novel affinity selection mass spectrometry technique with distinct advantages over traditional approaches to accelerate hit finding efforts. We will then describe medicinal chemistry efforts to advance leads towards functional modalities and highlight assays to validate target degradation in multiple models.

Session Break1:05 pm

DEGRADATION STRATEGIES FOR ONCOLOGY

1:25 pm

Chairperson's Remarks

Behnam Nabet, PhD, Assistant Professor, Human Biology Division, Fred Hutchinson Cancer Center

1:30 pm

Strategies for Dynamic Protein Control to Advance Oncology Drug Discovery

Behnam Nabet, PhD, Assistant Professor, Human Biology Division, Fred Hutchinson Cancer Center

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 recent advances of the dTAG technology platform and will highlight case studies demonstrating utility for preclinical target discovery and validation in refractory cancers.

2:00 pm

A First-in-Class RIPK1 Degrader Sensitizes Immune Checkpoint Blockades

Jin Wang, PhD, Professor, Pharmacology & Chemical Biology, Baylor College of Medicine

Receptor-interacting protein kinase 1 (RIPK1) is a master regulator of cell fate and controls proinflammatory signaling downstream of multiple innate immune pathways. Leveraging the Proteolysis targeting chimera (PROTAC) technology, we developed a first-in-class RIPK1 degrader, which sensitizes ICBs by not only overcoming the intrinsic resistance in cancer cells but also activating a B cell subpopulation to contribute to antitumor immunity.

2:30 pm Building a Comprehensive Platform for Discovery and Optimization of Bifunctional Molecules

Dave Madge, PhD, Vice President, WuXi AppTec

Therapeutic strategies that are based on using a multi-functional molecule to induce the proximity of two proteins, or indeed an oligonucleotide and a protein, have become increasingly well validated. In this presentation we will discuss some of the chemical and biological tools that have been developed to enable the discovery, characterization and optimization of such bifunctional, proximity-inducing, molecules and show how these tools can dramatically accelerate drug discovery in this area.

2:45 pm Overcome common roadblocks during the characterization of your PROTAC candidates with Spectral Shift technology

Amit Gupta, PhD, MBA, Senior Product Manager, Product, NanoTemper

To develop effective PROTAC candidates, you need a method that tackles common challenges while screening small compound molecules and characterizing ternary complex, cooperativity, and hook effect. With Dianthus — a plate-based affinity screening platform — you succeed at binary and ternary complex characterizations with in-solution, mass-independent measurements that result in high-quality data for reliable affinity constants, cooperativity values, and hook effect characterization.

Refreshment Break in the Exhibit Hall with Poster Viewing (Grand Ballroom)3:00 pm

ROOM LOCATION: Constitution A

TARGETED DEGRADATION FOR INTRACELLULAR CANCER TARGETS

3:40 pm

FEATURED PRESENTATION: Development of a STAT3 Targeted Protein Degrader

Chris De Savi, PhD, Senior Vice President & Head, Drug Discovery, Kymera Therapeutics

Signal Transducer and Activator of Transcription 3 (STAT3) plays important roles in the transduction of signals from growth factors and cytokines in both normal and malignant cells. Aberrant activation of STAT3 has been observed in many cancers including lymphomas and leukemias through activating mutations, hyper-signaling through upstream regulators, or loss of negative feedback regulation. STAT3 has been historically considered “undruggable”. Here we introduce a first-in-class, potent, and selective STAT3 heterobifunctional degrader KT-333 that is being developed for the treatment of hematologic malignancies and solid tumors.  

4:10 pm

Discovery and Optimization of CBL-B Inhibitors for Immune-Cell Mediated Tumor Rejection

Frederick Cohen, PhD, Vice President, Medicinal Chemistry, Nurix Therapeutics, Inc.

Casitas B-lineage lymphoma b (CBL-B) is an E3 ligase that functions as a negative regulator of T, NK, and myeloid cells. Mice deficient in CBL-B reject tumors in syngeneic models, suggesting that inhibition of CBL-B may be a novel therapeutic strategy. We present discovery and optimization of compounds including NRX-8 (KD=20nM) that glue CBL-B into an inactive conformation. NRX-8 increases T cell activation in response to TCR stimulation and inhibits tumor growth in syngeneic models of cancer when dosed orally. We present preclinical data on NX-1607, a more potent CBL-B inhibitor being evaluated in a Phase I trial in multiple oncology indications.

4:40 pm

Characterization of the Molecular Glue-Induced Interactions of IO Target IKZF2 with Cereblon

Charles A. Wartchow, PhD, Associate Director, Global Discovery Chemistry, Novartis Institutes for BioMedical Research

Formation of ternary complexes between a ligase, a molecular glue, and a disease-modulating protein is the first step in a sequence of events leading to protein degradation.  In this presentation, we discuss the SPR and X-ray crystallographic characterization of ternary complexes involving a molecular glue that binds to the ligase Cereblon and induces the binding of the zinc finger-containing transcription factor IKZF2.

Interactive Discussions5:10 pm

Interactive Discussions are informal, moderated discussions, allowing participants to exchange ideas and experiences and develop future collaborations around a focused topic. Each discussion will be led by a facilitator who keeps the discussion on track and the group engaged. To get the most out of this format, please come prepared to share examples from your work, be a part of a collective, problem-solving session, and participate in active idea sharing. Please visit the conference website's Interactive Discussions page for a complete listing of topics and descriptions.

IN-PERSON INTERACTIVE DISCUSSION:

Degrader Strategies for Cancer and Beyond 

Miklos Bekes, PhD, Associate Director, Degrader Mechanisms Group, Platform Biology, Arvinas, Inc.

Chris De Savi, PhD, Senior Vice President & Head, Drug Discovery, Kymera Therapeutics

  • Why is oncology especially well-suited for targeted protein degradation (TPD) strategies?
  • What are the TPD approaches most likely to succeed in cancer?
  • What areas and which approaches show the most promise for non-cancer indications? ​​

Welcome Reception in the Exhibit Hall with Poster Viewing (Grand Ballroom)5:55 pm

Close of Day6:55 pm

Wednesday, October 19

Registration and Morning Coffee (Grand Ballroom Foyer)7:30 am

EMERGING DEGRADER MODALITIES

ROOM LOCATION: Constitution A

7:55 am

Chairperson's Remarks

Jessica Friedman, PhD, Director, Molecular & Cellular Pharmacology, EMD Serono

8:00 am

Targeted Degradation of Extracellular Proteins with ATACs (ASGPR-Targeting Chimeras)  

Kevin Lumb, DPhil, Vice President, Biology, Avilar Therapeutics

Targeted protein degradation of disease-causing proteins is a promising new therapeutic modality. Established protein degradation technologies using PROTACs or molecular glues utilize the ubiquitin proteasome system to degrade intracellular proteins.  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.

8:30 am Quantitative Analysis of Binding Affinities for Small Molecules Targeting STAT Transcription Factors

Jean Bernatchez, PhD, Senior Scientist and San Diego R&D Group Leader, Research & Development, Eurofins Discovery

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.

8:45 am Rationally Design PROTACs and Molecular Glues

Karteek Kadimisetty, Ph.D., Director, R&D, LifeSensors, Inc.

PROTACs have emerged as new class of drugs that can target the “undruggable” proteome by hijacking the ubiquitin proteasome system. Traditional methods are prone to artifacts. New methods that can monitor PROTAC function on endogenous targets at physiological expression levels are essential to accelerate the PROTAC discovery process. Current study highlights use of TUBE technology to rationally design molecular glue and PROTAC mediated ubiquitination and degradation of targets.

9:00 am

Nanobodies for Targeted Degradation of the RNA Binding Protein HNRNPA2B1

Yongku Cho, PhD, Associate Professor, Chemical & Biomolecular Engineering, University of Connecticut

Development and validation of high-specificity nanobodies for intracellular targeting remain a bottleneck. Here we describe a yeast surface display based nanobody screening approach that led to high specificity nanobodies against several intracellular targets in parallel. We also present a comprehensive comparison of nanobody-ubiquitin ligase F-box fusions for targeted degradation of intracellular proteins. Using these approaches, we demonstrate robust degradation of the RNA-binding protein HNRNPA2B1, implicated in multiple cancers and neurodegenerative diseases.

9:30 am

TPD2 – Dual Precision Target Protein Degradation: Antibody-Enabled GSPT1 Degraders for Breast Cancer and AML

Peter Park, PhD, CSO, Orum Therapeutics

TPD² approach merges the power of targeted protein degraders with the precision of antibodies to deliver molecular glues or PROTACs intracellularly with cell-specificity, overcomes many of the challenges of small molecule degraders, and increases the therapeutic index of degraders. Using the TPD² approach, the Antibody neoDegrader Conjugate (AnDC) platform has been developed using highly specific GSPT1 degraders that show promising efficacy against hematological malignancies and solid tumors. Two AnDCs in clinical/late preclinical testing, ORM-5029 for breast cancer and ORM-6151 for AML will be discussed. Furthermore, a second TPD² platform PROTAB used to deliver hetero-bifunctional PROTACs will also be highlighted.

Coffee Break in the Exhibit Hall with Poster Viewing (Grand Ballroom)10:00 am

PLENARY KEYNOTE PROGRAM

ROOM LOCATION: Constitution A + B

11:00 am

Plenary Chairperson’s Remarks

An-Dinh Nguyen, Team Lead, Discovery on Target, Cambridge Healthtech Institute

11:05 am

PLENARY: Pirating Biology to Detect and Degrade Extracellular Proteins

James A. Wells, PhD, Professor, Departments of Pharmaceutical Chemistry and Cellular & Molecular Pharmacology, University of California, San Francisco

In contrast to intracellular PROTACs, approaches to degrade extracellular proteins are just emerging. I’ll describe our recent progress to harness natural mechanisms such as transmembrane E3 ligases to degrade extracellular proteins using fully genetically encoded bispecific antibodies we call AbTACs. We have also engineered a peptide ligase which can be tethered to cells to detect proteolysis events and target them with recombinant antibodies for greater selectivity for the tumor microenvironment.

11:50 am

PLENARY: Therapeutic Modalities for Neuroscience Diseases

Anabella Villalobos, PhD, Senior Vice President, Biotherapeutics & Medicinal Sciences, Biogen

Many effective medicines exist to treat neurological diseases, but medical need remains high. We have a unique multi-modality approach to discover novel therapies and our goal is to find the best modality regardless of biological target. With a multi-modality approach, we aim to expand target space, leverage synergies across modalities, and offer options to patients. Opportunities and challenges associated with small molecules, biologics, oligonucleotides, and gene therapy will be discussed.

Enjoy Lunch on Your Own12:35 pm

Refreshment Break in the Exhibit Hall with Poster Viewing (Grand Ballroom Foyer)1:25 pm

Close of PROTACs and Molecular Glues – Part 1 Conference2:05 pm