Cambridge Healthtech Institute’s 2^nd Annual

Modulating the Ubiquitin-Proteasome System

Novel Tools and Compounds to Target DUBs, Ligases and Other Proteins

April 10-11, 2019

The ubiquitin-proteasome system (UPS) is a complex, highly regulated network of proteins that is responsible for intracellular protein degradation and turnover. Advances in our understanding of the role and molecular mechanisms of the UPS components in disease and the development of high quality chemical tools and inhibitors have turned the previously “undruggable” UPS targets into an exciting opportunity for small molecule drug intervention. Over the past years, we have seen the development of a new generation of deubiquitinating enzymes (DUBs) and proteasome inhibitors poised for clinical development, as well as the discovery of novel inhibitors for disrupting the protein-protein interactions in ligases and hijacking the UPS for targeted protein degradation. Cambridge Healthtech Institute’s conference on Modulating the Ubiquitin-Proteasome System will bring together an expert group of chemists and biologists who are working to advance this rapidly growing field of ubiquitin drug discovery.

Final Agenda

Wednesday, April 10

12:30 pm Registration Open (20 C/D Foyer) 

12:45 Dessert Break in the Exhibit Hall with Poster Viewing

EXPLOITING THE UPS FOR TARGETED PROTEIN DEGRADATION
30 B/C

1:30 Welcome Remarks

Tanuja Koppal, PhD, Conference Director, Cambridge Healthtech Institute

1:35 Chairperson’s Opening Remarks

Eric Fischer, PhD, Assistant Professor, Cancer Biology, Dana-Farber Cancer Institute/Harvard Medical School

1:40 Principles of Small Molecule Mediated Ubiquitin Ligase Targeting

Eric Fischer, PhD, Assistant Professor, Cancer Biology, Dana-Farber Cancer Institute/Harvard Medical School

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. I will present recent work towards a better understanding of the molecular principles that govern neo-substrate recruitment and its application to the development of small molecule degraders.

2:10 New Screening Technologies and Chemical Probes Targeting the Ubiquitin System: Inhibitors, Activators, and Degraders

Alexander Statsyuk, PhD, Assistant Professor, Department of Pharmacological and Pharmaceutical Sciences, University of Houston

Two major principles of targeting the ubiquitin system have emerged: direct targeting of the enzymes that control protein ubiquitination and hijacking E3 ligases to induce protein degradation. In this lecture, I will outline novel screening tools and technologies to discover small molecule inhibitors/activators and hijackers for RBR/HECT E3 ligases. I will show how UbFluor technology can be used to identify nanomolar inhibitors of HECT E3 ligases, thus validating UbFluor technology as a tool to discover HECT E3 ligase inhibitors.

2:40 Expanding the Druggable Target Space - Degrading a Multi-Functional Transcriptional Regulator

Lara Gechijian, PhD, Scientist/Project Lead, Jnana Therapeutics; Former Graduate Student, Laboratory of Drs. James Bradner/Nathanael Gray, Harvard Medical School

There has been limited success targeting transcription with small organic molecules because many transcriptional regulators are not amenable to conventional therapeutic approaches, as their ligandable domain may not be functionally relevant in disease. Because potent ligands of the bromodomain of TRIM24 are ineffectual in contexts of TRIM24 genetic dependence, we repurposed the potent ligands of the TRIM24 bromodomain as the TRIM24 targeting-ligand component of heterobifunctional degraders to orchestrate the recruitment of TRIM24 to the E3 ubiquitin ligase machinery.

3:10 Solving a 60-Year Mystery: SALL4 Mediates Teratogenicity as a Thalidomide-Dependent Substrate of Cereblon

Mary Matyskiela, PhD, Principal Scientist, Structural and Chemical Biology, Celgene

Targeted protein degradation through small molecule modulation of cereblon offers vast potential for new therapeutics, but cereblon-binding molecules carry the safety risks of thalidomide, which caused an epidemic of severe birth defects in the 1950s. We identify SALL4 as a thalidomide-dependent cereblon substrate whose degradation phenocopies genetic embryopathies caused by SALL4 mutation. This work expands the scope of cereblon neosubstrates and offers a path towards safer therapeutics through understanding the molecular basis of thalidomide-induced teratogenicity.

3:40 Refreshment Break in the Exhibit Hall with Poster Viewing

4:30 SPOTLIGHT PRESENTATIONS: Development of Small Molecule Protein Degraders as New Therapeutic Modalities

Applying Enzymology Concepts to the Optimization of Targeted Protein Degraders

Stewart Fisher, PhD, CSO, C4 Therapeutics

Targeted Degradation of IRAK4 Protein Via Heterobifunctional Small Molecules for Treatment of MYD88 Mutant Lymphoma

Nan Ji, PhD, Executive Director, Head of Chemistry, Kymera Therapeutics

Protein Degradation Beyond Bi-functional Degraders

Michal Walczak, PhD, CSO, Captor Therapeutics

5:30 Breakout Discussions - View All Breakouts

6:15 Close of Day

6:30 Dinner Short Courses*

*Premium or separate registration required.

Thursday, April 11

8:00 am Morning Coffee

8:45 Plenary Session Welcome Remarks from Event Director

Anjani Shah, PhD, Senior Conference Director, Cambridge Healthtech Institute

8:50 Plenary Keynote Introduction

Timothy Craig, PhD, HarkerBio

8:55 PLENARY KEYNOTE:

New Ways of Targeting K-Ras

Frank McCormick, PhD, Professor, HDF Comprehensive Cancer Center, University of California San Francisco

Efforts to find drugs that bind K‐Ras directly have increased recently, enabled by NMR‐based fragment screening, di-sulfide tethering, in silico drug design and biophysical methods such as Second Harmonic Generation (SHG). We will report progress on attacking two sites in the K‐Ras protein; cysteine‐185 (the site of prenylation), and histidine‐95, a residue unique to K‐Ras, to develop covalent K‐Ras inhibitors, as well as compounds identified by SHG and other methods.

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

UNDERSTANDING AND OPTIMIZING THE USE OF PROTACs

10:40 Chairperson’s Remarks

Peter Dragovich, PhD, Staff Scientist, Discovery Chemistry, Genentech

10:45 FEATURED PRESENTATION: Small Molecule-Induced Protein Degradation with Proteolysis Targeting Chimeric Molecules (PROTACs)

Markus Queisser, PhD, Scientific Leader, Protein Degradation DPU, R&D Future Pipelines Discovery, GlaxoSmithKline

The advantages of the PROTAC technology lie in its modular, rationally designed molecules, capable of producing potent, selective and reversible cellular protein knock-down as demonstrated in both cellular and in vivo. The removal of a disease-causing protein is an attractive therapeutic option. This presentation aims to highlight the potential of PROTACs in drug discovery with a focus on their challenges from our perspective.

11:15 Lessons from Viral Hijacking of Ubiquitin-Mediated Protein Degradation

Yue Xiong, PhD, William R. Kenan Professor of the Biochemistry and Biophysics, University of North Carolina; Co-Founder, Cullgen

Virus has learned the use of ubiquitin-proteasome system to overcome the host cellular defense, which provides us insight into the small molecule design to induce target protein degradation for drug discovery. Understanding ternary structure of viral/E3 complex will enhance the success rate of degraders. Protein-protein interaction between viral protein and E3 ligases may also lead us to the discovery of new E3 ligand.

11:45 Targeting Deubiquitylases (DUBs): Opportunities for Collaborative Drug Discovery

Jason Brown, PhD, Scientific and Business Development Director, Ubiquigent Ltd.

We will discuss Ubiquigent’s deubiquitylase (DUB) enzyme targeting small molecule hit-to-lead platform featuring: Our in-house DUB-targeting computational and medicinal chemistry capability and a comprehensive small molecule assay workflow featuring our widely accessed DUBprofiler™ and REDOXprofiler™ service platforms.The company also has significant capabilities to target other ubiquitin system proteins – including E3 ligases – and is developing a platform to provide PROTAC hit-to-lead SAR support. Commercial access models: Ubiquigent is providing access to its comprehensive capabilities to execute early stage hit-to-lead projects via our Collaborative Drug Discovery programme. Individual services may also be accessed via Fee For Service (FFS) or FTE routes.

12:00 pm Antibody-Mediated Delivery of Protein Degraders

Peter Dragovich, PhD, Staff Scientist, Discovery Chemistry, Genentech

Chimeric Chemical Inducers of DEgradation (CIDEs) which effect intracellular degradation of target proteins via E3 ligase-mediated ubiquitination are currently of high interest in medicinal chemistry. However, these entities are relatively large compounds that often possess molecular characteristics which may compromise oral bioavailability, solubility, and/or in vivo pharmacokinetic properties. Accordingly, we explored whether conjugation of CIDEs to monoclonal antibodies using technologies originally developed for cytotoxic payloads might provide alternate delivery options for these novel agents.

12:30 Enjoy Lunch on Your Own

1:30 Dessert Break in the Exhibit Hall with Poster Awards Announced

Poster Awards Sponsored by Domainex

TARGETING DUBs AND LIGASES

2:15 Chairperson’s Remarks

Domagoj Vucic, PhD, Principal Scientist, Early Discovery Biochemistry, Genentech

2:20 Multiple Therapeutic Actions of USP7 Inhibitors: Impairment of FOXP3+ Treg Function and Direct Effects on Tumor Cell Metabolism and DNA Damage Responses

Wayne W. Hancock, MD, PhD, Professor, Pathology and Chief of Transplant Immunology, Children’s Hospital of Philadelphia and University of Pennsylvania

With relevance to a critical unmet need in immune-oncology, we have shown that USP7 is a key target for therapeutic regulation of Foxp3+ Treg cells through its regulation of Tip60 expression. We now provide evidence of direct effects of Tip60 inhibitors (Tip60i) and USP7 inhibitors (USP7i) on tumor cells, including modulation of tumor cell metabolism and impairment of the DNA damage response (DDR). These dual mechanisms of action provide a compelling rationale for USP7i use in oncology.

2:50 Pharmacological Assessment of Potent, Selective, and Orally Bioavailable USP7 Inhibitors

Dennis Hu, PhD, Senior Scientist, FLX Bio

USP7 is a deubiquitinase (DUB) that has been reported to regulate the levels of multiple proteins with roles in cancer progression and immune response, including MDM2 and FOXP3. Using a structure-based drug design strategy, we have identified reversible USP7 inhibitors that are highly potent in biochemical and cellular assays and are >10,000 fold selective for USP7 over other DUBs. Potent and selective USP7 inhibitors with excellent oral pharmacokinetic properties were used to assess the pharmacologic effects of USP7 inhibition in vitro and in vivo.

3:20 NEW: Structures of the Substrate-engaged Proteasome 

Andres Hernandez, PhD, Research Fellow, The Scripps Institute

As the primary eukaryotic proteolytic machine, the 26S proteasome is responsible for ubiquitin-mediated degradation of misfolded, damaged, or obsolete proteins. We determined several structures of the proteasome as it actively translocated substrate. These structures reveal the mechano-chemical coupling of ATP hydrolysis to substrate translocation. Additionally, these structures suggest a co-translocational deubiquitination mechanism that positions ubiquitin and its isopeptide scissile bond in the Rpn11 deubiquitinase.

3:50 Networking Refreshment Break

EMERGING UBIQUITIN TARGETS FOR THERAPEUTIC INTERVENTION

4:20 Engineered Ubiquitin Variants for Inhibition and Activation of the Ubiquitin Proteasome System

Sachdev Sidhu, PhD, Professor, Donnelly Centre and Department of Molecular Genetics, University of Toronto

Despite the central importance of the ubiquitin proteasome system in virtually every biological process, inhibitors for the hundreds of component enzymes are severely limited. We have devised a general strategy for using engineered ubiquitin variants to rapidly develop tight and specific binders for virtually any protein that associates with ubiquitin. This approach has yielded numerous inhibitors, and in some cases activators, for deubiquitinases, E2 enzymes, E3 ligases, and non-catalytic docking modules. These tools have proven valuable for cell biology, structural studies, and drug target validation.

4:50 Conformation, Complexation, and Catalysis in the AAA+ ATPase p97/VCP

Michelle Arkin, PhD, Professor, Department of Pharmaceutical Chemistry, University of California San Francisco

Valosin Containing Protein (VCP, p97) is an AAA+ ATPase involved in several aspects of protein homeostasis, including ER-associated degradation, segregation of proteins from complexes, and membrane remodeling. This spectrum of activities is governed by protein-protein interactions between p97, adaptor proteins, and ubiquitin-processing enzymes. p97 function is furthermore modulated by ATPase activity and conformational changes throughout the protein’s barrel structure. We will compare inhibitors of p97 that act through different mechanisms and consequently modulate different aspects of p97 function.

5:20 Targeting Ubiquitin Ligases in Inflammatory Diseases

Domagoj Vucic, PhD, Principal Scientist, Early Discovery Biochemistry, Genentech

Disbalance in cellular signaling and cell death lead to unregulated cell death and cytokine production and contribute to numerous inflammatory diseases. RIP2 ubiquitination is critically associated with NOD2 signaling and production of pro-inflammatory cytokines. Selective targeting of RIP2 E3 ligase XIAP or RIP2 kinase inhibition can efficiently block NOD2 signaling and cytokine production. Collectively, our studies define major events regulating cell death and inflammatory signaling and contribute to development of anti-inflammatory and tissue protective treatments.

5:50 Close of Conference