The ubiquitin-proteasome system (UPS) is a well-controlled, selective mechanism for intracellular protein degradation and turnover. New understanding of the role and molecular mechanisms involved in the dysregulation of the UPS has led to its emergence as a key regulator of protein function and stability. Although implicated to play a role in cancer, CNS, infectious diseases and more, the multi-step processes involved, and the diversity of substrates makes it difficult to target the UPS. However, in recent years, the development of high-quality chemical probes and assay technologies has turned it into one of the most exciting targets for discovering novel drugs. In the UPS, the ligases and deubiquitinases (DUBs) have recently attracted a lot of attention as possible targets for clinical intervention. Cambridge Healthtech Institute’s Targeting the Ubiquitin-Proteasome System conference will bring together a diverse group of chemists and biologists to discuss the promise and challenges in modulating the UPS. This conference will be preceded by a symposium that focuses on targeting autophagy pathways and will draw on some of the synergies between these two areas of research.

Final Agenda

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Wednesday, September 26

7:00 am Registration Open and Morning Coffee (Foyer)

Emerging Assays & Approaches To Study And Modulate The Ubiquitin Cascade
Constitution A

8:00 Welcome Remarks

Tanuja Koppal, PhD, Conference Director, Cambridge Healthtech Institute

8:05 Chairperson’s Opening Remarks

Daniel Finley, PhD, Professor, Department of Cell Biology, Harvard Medical School

8:10 USP14: Mechanism, Specificity, and Inhibition

Daniel Finley, PhD, Professor, Department of Cell Biology, Harvard Medical School

USP14, a proteasomal deubiquitinating enzyme, can rapidly remove ubiquitin prior to substrate commitment to degradation, thus rescuing substrates from a fate of degradation. Accordingly, small-molecule USP14 inhibitors that we have identified can stimulate the degradation of specific proteasome targets. USP14 shows a novel principle of selectivity in that it only deubiquitinates proteins carrying multiple ubiquitin chains. USP14 is activated ~1000-fold by the proteasome. We will discuss interesting new mutants that prevent this activation.

8:40 Conformational Remodeling of USP7 Catalytic Domain to Promote Deubiquitinating Activity

Ayşegül Özen, PhD, Scientist II, Blueprint Medicines

USP7 catalytic domain (USP7cd) shows limited activity alone and is regulated by intramolecular domains. Structural features stabilizing the inactive state and atomistic mechanism of activation remain unclear. By comparative structural analyses, molecular dynamics simulations, and in silico sequence re-engineering, we identified key determinants of USP7cd activation, engineered USP7cd for improved activity, and show that electrostatics in a distal loop and local packing in the core together modulate USP7cd activation.

9:10 Targeting the Deubiquitinase STAMBP Inhibits Inflammasome Activity

Joseph S. Bednash, MD, Postdoctoral Scholar, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh

Inflammasomes regulate innate immune responses by facilitating maturation of inflammatory cytokines, interleukin (IL)-1β and IL-18. The deubiquitinase enzyme, STAM-binding protein (STAMBP) is necessary for inflammasome activation and IL-1β secretion after Toll-like receptor (TLR) agonism. A small-molecule inhibitor of STAMBP suppresses IL-1β release after TLR agonism in both cell and tissue models. These findings describe a unique pathway of inflammasome regulation with the identification of STAMBP as a potential therapeutic target.

9:40 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing (Grand Ballroom)

10:25 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

The Ubiquitin System has emerged as promising system for drug discovery. 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.

10:55 A Targeted Quantitative Proteomic Assay for Parkinson’s Disease That Measures the Dynamics of Ubiquitin Events on Mitochondria and Their Modulation by Small Molecules

Alban Ordureau, PhD, Postdoctoral Fellow, Laboratory of Dr. Wade Harper, Department of Cell Biology, Harvard Medical School

The kinase PINK1 and Ub ligase Parkin, both mutated in Parkinson’s disease, promote mitochondrial outer membrane ubiquitylation and mitophagy. We have developed a quantitative proteomics approach that allows the dynamics and site specificity of Parkin-dependent mitochondrial ubiquitylation to be assessed in model systems and ES cell-derived neurons. We demonstrate that this approach can be used to monitor the activity of activators, inhibitors and regulators of the pathway with precision.

11:25 Mass Spectrometry Analysis of Linkage-Specific Ubiquitin Sites in Response to Oxidative Stress

Gustavo M. Silva, PhD, Assistant Professor, Department of Biology, Duke University

Oxidative stress is a prevalent condition that can lead to cell death, causing a variety of human diseases. To combat the harmful effects of oxidative stress, protein ubiquitination plays a significant role in regulating function, location, and fate of the proteome. Although the ubiquitin system is highly complex, here we used mass spectrometry to tease out a distinct ubiquitin signal, revealing new pathways relevant for stress response.

11:55 Drugging the Undruggable: Discovering Novel Drugs for the Ubiquitin-Proteasome System

Peter Foote, PhD, Senior Scientist II, Research & Development, LifeSensors

While ubiquitin regulates critical disease pathways, few FDA-approved drugs target the UPS, due to a lack of physiological HTS tools and PD markers for cellular activity. We have developed assays enabled by Tandem Ubiquitin Binding Entities (TUBEs) to quantitate cellular substrate ubiquitylation and help accelerate successful compounds to the clinic.

12:25 pm Session Break

12:35 Enjoy Lunch on Your Own

1:15 Refreshment Break in the Exhibit Hall with Poster Viewing  (Grand Ballroom)

NOVEL STRATEGIES FOR TARGETING USP7 AND PROTEASOME
Constitution A

1:50 Chairperson’s Remarks

Jetze Tepe, PhD, Associate Professor of Chemistry, Department of Chemistry, Michigan State University

1:55 Targeting the Nrf1-mediated Proteasome Recovery Pathway in Cancer

Senthil K. Radhakrishnan, PhD, Assistant Professor, Department of Pathology, Virginia Commonwealth University

Inhibition of cellular proteasome results in transcriptional upregulation of proteasome subunit genes eventually leading to the recovery of proteasome activity. In mammalian cells, this recovery pathway is mediated by the transcription factor Nrf1. Consistent with this observation, depletion of Nrf1 enhances proteasome inhibitor-mediated apoptosis in multiple cancer cells. In this presentation, I will describe a strategy to target the Nrf1 pathway to potentiate the action of proteasome inhibitor drugs in cancer.

2:25 Small Molecule Activation of Proteasome Activity

Jetze Tepe, PhD, Associate Professor of Chemistry, Department of Chemistry, Michigan State University

Intrinsically disordered proteins are important, low-abundant signaling proteins targeted for degradation by the 20S proteasome. When over-expressed, these disordered proteins are directly implicated in many human diseases, including neurodegenerative diseases and cancer. Our work demonstrates that small molecules can enhance the catalytic degradation of intrinsically disordered proteins by the 20S proteasome, which represents a new therapeutic strategy to combat human diseases.

2:55 Ubiquitination-Deubiquitination: A Friend and foe in Cellular Homeostasis

Sayantanee Niyogi, PhD, Scientist, Membrane Biology Section, National Institutes of Health (NIH)

We performed a screen knocking down about 100 deubiquitinating enzymes to screen for DUBs that had an effect on traffic of proteins, upregulated during Cancer. We identified two DUBs; USP3 and USP6 that decreased the half-life of long-lived proteins routing them to degradation. We also discovered that over-expression of USP6 could counter the effect of an E3-Ligase MARCH8 induced degradation. This study demonstrates that cycles of ubiquitylation and deubiquitylation can determine whether specific proteins are degraded or recycled.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced (Grand Ballroom)

4:05 USP7 Inhibition Impairs FOXP3+ Treg Function and Promotes Antitumor Immunity

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

FOXP3+ T-regulatory (Treg) cells are present in increased numbers and display significantly enhanced suppressive function compared to Tregs isolated from adjacent lung, lymph node or blood of the same individual, leading to potent suppression of host anti-tumor immunity. USP7 inhibition is able to preferentially impair FOXP3+ Treg function while maintaining host-anti-tumor immunity, leading to beneficial effects when used alone or in conjunction with checkpoint blockade, vaccination or other therapeutic approaches.

4:35 Potent and Selective USP7 Inhibitors Target Multiple Tumor Types through Diverse Mechanisms

Paul Kassner, PhD, Vice President, FLX Bio, Inc.

USP7 is a deubiquitinase with multiple downstream targets. Inhibitors of USP7 are expected to decrease function of oncogenes, increase tumor suppressor function, enhance immune function and sensitize tumor cells to DNA damaging agents. FLX Bio has developed potent and selective inhibitors of USP7 as a novel approach to cancer therapy.

5:05 Interactive Breakout Discussion Groups - View Details
Room: Constitution A

Join a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Table 5: Novel Targets for Cancer in the Proteostasis Space

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

• Biological insights into the Ubiquitin-Proteasome System pathway
• Target validation approaches for novel proteostasis targets
• Emerging proteostasis targets

Table 6: Screening Tools to Identify PROTACS, Kinases and Other Molecules

Moderator: Davide Gianni, PhD, Team Leader, Discovery Sciences, AstraZeneca

• Biochemical, biophysical and cellular based approaches to monitor ternary complex formation
• Approaches to identify novel E3 ligases and E3 ligase ligands

6:05 Welcome Reception in the Exhibit Hall with Poster Viewing  (Grand Ballroom)

7:10 Close of Day

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Thursday, September 27

7:30 am Registration Open and Morning Coffee (Foyer)

NEW PROBES AND INHIBITORS TARGETING Dubs AND LIGASES
Constitution A

8:00 Chairperson’s Remarks

Stephanos Ioannidis, Ph.D., Head, Early Portfolio, FORMA Therapeutics

8:05 Novel Small Molecule-Dependent Substrates for Ubiquitin Ligases

Stephanos Ioannidis, Ph.D., Head, Early Portfolio, FORMA Therapeutics

8:35 Ubiquitin Code-Reading, Writing and Editing: Future of Breakthrough Therapies

Tauseef R. Butt, PhD, President and CEO, Progenra, Inc.

We are currently developing small molecules that inhibit the cancer-supporting DUBs and ubiquitin ligases. The DUB inhibitors are capable of both killing tumor cells directly and suppressing regulatory T cells, thereby unleashing effector T cells, which identify and kill tumor cells. These results constitute the first example of a small molecule single agent that works by targeting both the tumor itself and the tumor’s ability to escape surveillance and killing by the host immune system and, in addition, by eliminating tumor metastasis.

9:05 Reports from Wednesday Evening Breakout Discussions

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

10:20 Plate-Based Approach to Identify PROTACS Molecules and Protein Degraders

Davide Gianni, PhD, Team Leader, Discovery Sciences, AstraZeneca

PROTACS provide a new modality to drug previously challenging targets and much evidence indicates that protein degraders are a mode of inhibition that can be pursued post HTS. Western Blot is mostly used to characterize PROTACS molecules, but it has a number of obvious limitations. The adoption of plate-based approaches is essential in PROTACS and several options are available such as, antibody-based and non-antibody based approaches. We will present two case studies building plate-based, HTS-friendly protein degradation assays potentially applicable for PROTACS identification campaigns.

10:50 PROTACS: The Chemical Equivalent of CRISPR

Shanique Alabi, Graduate Student, Laboratory of Dr. Craig Crews, Department of Molecular, Cellular and Developmental Biology, Yale University

Induced protein degradation offers several advantages over traditional inhibition strategies and has emerged recently as a potential therapeutic option. For the past 16 years, we have helped develop this fast-growing field, shepherding our initial chemical biology concept into a drug development strategy that is on the verge of clinical validation. PROTACS with high target selectivity, potency, and oral bioavailability will be discussed as well as a system to address the ‘PROTACability’ of particular E3 ligases.

11:20 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

11:50 Conference Registration Open (Foyer)

12:20 pm Plenary Keynote Program (Constitution Ballroom)

2:00 Refreshment Break in the Exhibit Hall with Poster Viewing  (Grand Ballroom)

2:45 Close of Conference

Day 1