2016 Archived Content

Targeting the Ubiquitin Proteasome System Header

The ubiquitin proteasome system (UPS) is an essential and highly regulated mechanism operating to tightly control intracellular protein degradation and turnover. While the concept of targeting specific components of the UPS to modulate protein degradation has been around for some time now, recent advances in our understanding of the role and molecular mechanisms of UPS components in disease – mainly DUBs and E3 ligases, the development of high-quality chemical tools and novel inhibitors, as well as preclinical studies demonstrating chemical tractability and therapeutic potential – have dramatically taken the ubiquitin proteasome system from an improbable target class, to one of the most robust and exciting arenas for the discovery of novel drugs. Indeed, over the past year, we have seen the generation of several DUB inhibitors poised for clinical development, novel approaches and inhibitors disrupting the protein-protein interactions of E3 ligases and UPS-mediated degradation of target proteins.

Cambridge Healthtech Institute’s fourth annual Targeting the Ubiquitin Proteasome System will once again gather an interdisciplinary collection of leaders working to advance the rapidly expanding field of UPS drug discovery.

Final Agenda

Best Value

• September 19 Short Course: RNA as a Small Molecule Drug Target

• September 20-21 Conference: Targeting the Ubiquitin Proteasome System

• September 21-22 Conference: Targeting Epigenetic Readers and Chromatin Remodelers

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Tuesday, September 20

7:00 am Registration Open and Morning Coffee



8:05 Chairperson’s Opening Remarks

Tauseef R. Butt, Ph.D., President and CEO, Progenra, Inc.

8:10 FEATURED PRESENTATION: Mechanism and Specificity of Deubiquitinating Enzyme USP14

Daniel_FinleyDaniel Finley, Ph.D., Professor, Cell Biology, Harvard Medical School

The deubiquitinating enzyme USP14 is a key regulator of proteasome activity. USP14 can suppress degradation of a subset of proteasome substrates, raising the question of USP14 specificity. We studied this using the N-terminus of cyclin B as an in vitro model. Surprisingly, what seems to be the dominant aspect of USP14 specificity is that it will not remove ubiquitin groups from substrates, or will do so only quite slowly, when only a single ubiquitin chain is present on the substrate. Multichain specificity could possibly bias degradation towards single-chain substrates produced by highly processive ubiquitin ligases. We hypothesize that the specificity for substrates bearing multiple chains reflects a role of proteasomal ubiquitin receptors in presenting conjugates to USP14.

8:50 Developing a Quantitative Profiling Platform to Evaluate Endogenous Deubiquitinase Activity

Ingrid_WertzIngrid E. Wertz, M.D., Ph.D., Senior Scientist, Discovery Oncology and Early Discovery Biochemistry, Genentech, Inc.

Deubiquitinases (DUBs) are important regulators of cell physiology and are emerging drug targets. However, the exact function and regulation of the majority of human DUBs remains largely enigmatic. DUB activity-based probes (ABPs) are engineered ubiquitin variants conjugated to a cysteine-reactive chemical group. We envisioned that DUB ABPs, coupled with mass spectrometry, could provide a highly sensitive and unbiased means to aid our understanding of DUB function and thus identify routes of therapeutic intervention in pathogenic processes controlled by DUBs. Recent developments in mass spectrometry and chemistry now allow for powerful multiplexing and quantitation of proteins in single experimental runs. However, current protocols are still limited by the number of samples that can be quantitatively compared with efficient throughput. Here we describe the development of an analysis platform that combines DUB ABPs with chemical multiplexing, targeted mass spectrometry, novel internal reaction standards, and a customized statistical analysis program. Our strategy allows us to quantitate changes in DUB activity across a theoretically unlimited number of samples in a high-throughput manner. We illustrate the efficacy of this technology by evaluating the activity of disease-relevant DUBs, in analyzing DUB inhibitor selectivity, and in evaluating how compounds that target other components of the ubiquitin/proteasome system impact DUB activity. 

9:20 Chemical Proteomics in the Ubiquitin System – DUBs Take Center Stage

Benedikt_KesslerBenedikt Kessler, Ph.D., Professor, Biochemistry and Life Science Mass Spectrometry, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford

Selection of molecular targets relevant for human diseases and converting lead compounds into drug candidates are crucial steps in drug development. Recently, enzymes that recognize and process ubiquitin, a small 76 amino acid protein that is tagged onto protein substrates, have been recognized as pharmacological targets in the context of cancer. The ubiquitin-specific protease USP7 was suggested as a potential drug target for a variety of cancers, in particular for Multiple Myeloma, where the treatment with small molecule USP7 inhibitors overcomes resistance to clinical proteasome inhibitors. We have utilized ubiquitin-based active site probes in combination with chemical proteomics workflows to determine the potency and selectivity of deubiquitylating enzyme (DUB) inhibitors in cancer cell culture models. 

9:50 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing



10:35 Ubiquitin Pathway: A New Frontier in Cancer Immunotherapy

Tauseef_ButtTauseef R. Butt, Ph.D., President and CEO, Progenra, Inc.

The host immune system is a powerful tool in the fight against cancer. Unfortunately, however, only a fraction of patients benefit from current biological therapies. Understanding and exploiting the role of ubiquitin in immune regulation will revolutionize cancer immunotherapy. Progenra has identified ubiquitin pathway enzymes that control pivot points of immune regulation. Small molecules discovered at Progenra suppress Treg function and unleash anti-tumor T-effector cell responses to melt the tumors in immune competent mice. Detailed mechanisms of the deubiquitylase USP7 that are critical for the activity of Tregs will be described. These inhibitors synergistically augment the activity of anti-PD1 antibody, CAR T cell therapy, and cancer vaccines. These studies provide a strong rationale that small molecules act as potent immunotherapeutic agents on their own and also synergize with biologicals to change the face of cancer therapy. 

11:05 Development and Exploitation of Ubi-Plex™, an Innovative Purpose-Built Drug Discovery Platform for Deubiquitinating Enzymes (DUBs)

Gerald_GavoryGerald Gavory, Ph.D., Director, Head of Biology, Almac Discovery

With increasing implications in the etiology of pathological conditions including cancer and neurodegeneration, DUBs are emerging as a promising target class for the development of first-in-class innovative medicines with high therapeutic impact. However, despite 15 years of intense research, DUBs have proved largely refractory to drug discovery efforts. Herein, we describe the design and implementation of Ubi-Plex™, a purpose-built drug discovery platform for the identification and optimization of DUB inhibitors. We will highlight the versatility and robustness of Ubi-Plex™ by describing a new case study spanning de novo target identification, focused library screening and hit finding to the development of novel, potent and selective inhibitors ready for lead optimization.

11:35 Discovery of Highly Selective Macrocyclic Inhibitors of DUBs: USP9x as a Case Study

Deborah_DodgeDeborah Dodge, Senior Scientist, Ensemble Therapeutics

Modulating protein homeostasis is an emerging and advancing approach to treat cancer. We have developed a productive discovery engine based on DNA-encoded libraries of macrocycles that has successfully identified novel lead compounds against a number of ubiquitin-specific proteases. Compounds targeting USP9x exemplify the potency, selectivity, and “drug likeness” potential of this class of inhibitors. Specifically, these highly selective compounds targeting USP9x exhibit mixed non-competitive and competitive modes of inhibition and possess cytotoxic cellular activity. Lead optimization is underway to optimize ADME properties and deliver a novel class of orally bioavailable USP9x inhibitors.

12:05 Comprehensive Profiling of DUB Inhibitors

Mark_AlbertellaMark Albertella, D.Phil., Director, Biology, Medivir

Deubiquitinases (DUBs) have potential roles in a number of disease processes. Although they represent targets of therapeutic interest, they have not been well characterized pharmacologically to date. A variety of small molecule inhibitors have been reported in the literature, and used to probe the consequences of pharmacological inhibition of DUBs in order to assess their therapeutic value. As part of our internal drug discovery efforts, we have comprehensively characterized a number of publically disclosed DUB inhibitors in our in-house biochemical and biophysical assays. We outline some of our observations, highlighting the low specificity or high chemical reactivity of a number of these compounds, and the caution that should be exercised when interpreting data obtained using these molecules as pharmacological tools.

12:35 Session Break

12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing



2:05 Chairperson’s Remarks

Gerald Gavory, Ph.D., Director, Head of Biology, Almac Discovery


Craig_CrewsCraig M. Crews, Ph.D., Lewis B. Cullman Professor of Molecular, Cellular, and Developmental Biology; Professor, Chemistry & Pharmacology, Yale University

The current “inhibitor-/binder-based” paradigm of pharmaceutical control has inherent limitations: 1) the need to achieve/maintain high systemic exposure to insure sufficient in vivo protein inhibition, 2) potential off-target side effects due to high in vivo concentrations, and 3) the need to bind to an active site, thus limiting the potential “drug target space” to a fraction of the proteome. Alternatively, induced protein degradation lacks these limitations. Based on an “event-driven” paradigm, this approach offers a novel, catalytic mechanism to irreversibly inhibit protein function, namely, the intracellular destruction of target proteins. This is achieved via recruitment of target proteins to the cellular quality control machinery, i.e., the ubiquitin proteasome system (UPS) using PROTACs (Proteolysis Targeting Chimeras) that can achieve “degradation concentrations” (DC50 values) in the picomolar range. 

2:45 Targeted Protein Degradation by Small Molecules

Alessio_CiulliAlessio Ciulli, Ph.D., Associate Professor, Chemical & Structural Biology, School of Life Sciences, University of Dundee

The application of small molecules to induce selected protein degradation is emerging as a transformative new modality of chemical intervention in drug discovery. We have previously shown that linking a VHL ligand that we had discovered with a pan-BET inhibitor creates highly selective PROTAC molecule MZ1. MZ1 triggers preferential intracellular degradation of Brd4, leaving the homologous BET members untouched, and exhibits greater anti-proliferative activity in leukemia cell lines than pan-BET inhibition.

Avacta Life Sciences3:15 Linkage-Specific, Affimer-Based Tools for the Study of Atypical Ubiquitin Chains

Michel_Martin (2)Martin Michel, Ph.D. Candidate - MRC Laboratory, Molecular Biology, University of Cambridge

Ubiquitin modifications encode a variety of distinct cellular signals due to a unique ability to assemble into differently-linked polyubiquitin chains. The lack of linkage-specific research tools has hindered elucidation of the biological roles for less common, so-called atypical chain types. Here, we describe the development and characterisation of such linkage-specific tools based on the Affimer scaffold from Avacta Life Sciences. These tools have widespread applications allowing investigations into the biological roles of atypical chain types.

3:45 Refreshment Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced

4:25 A New Paradigm in Drug Action: Differentiated Gain of Function among IMiD Structural Analogues Binding the E3 Ubiquitin Ligase, CRL4CRBN

Brian_CathersBrian Cathers, Ph.D., Executive Director, Co-Leader & Head, Drug Discovery, Protein Homeostasis Thematic Center of Excellence, Celgene

Definition of the CRL4CRBN E3 ligase as the target of lenalidomide opens a new chapter in mechanisms of drug action. Distinct cereblon-binding molecules evoke different phenotypic and molecularly defined responses, yet bind the same target. Solution of the ligand bound CRBN target complex provides a rationale for distinguishing “gain of function” targeting of key substrates, including the transcription factors aiolos (IKZ3) and ikaros (IKZ1) or the protein kinase CK1alpha. Is it possible to harness the action of a single E3 ligase and direct its actions toward new and different substrates? The presentation will explain distinctions among existing drugs, address guiding concepts applicable to determining new therapeutic applications, and point to the therapeutic power of harnessing protein homeostatic mechanisms.

4:55 PANEL DISCUSSION: Hijacking the UPS for Targeted Protein Degradation 
The design of small molecules to hijack the UPS has received significant attention over the past year, with several groups working on various strategies, and biotech spinouts formed. Collectively, this has formed a new paradigm in drug action, and is poised to have broad application and utilization in drug discovery. This panel, comprised of experts at the forefront of this field, will discuss these approaches, applications, and challenges for further development.


Craig M. Crews, Ph.D., Lewis B. Cullman Professor of Molecular, Cellular, and Developmental Biology; Professor, Chemistry & Pharmacology, Yale University

Andrew Phillips, Ph.D., CSO, C4 Therapeutics

Alessio Ciulli, Ph.D., Associate Professor, Chemical & Structural Biology, School of Life Sciences, University of Dundee

Brian Cathers, Ph.D., Executive Director, Co-Leader & Head, Drug Discovery, Protein Homeostasis Thematic Center of Excellence, Celgene

5:45 Welcome Reception in the Exhibit Hall with Poster Viewing

6:25 End of Day

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Wednesday, September 21

7:30 am Registration Open and Morning Coffee



8:00 Chairperson’s Opening Remarks

Benedikt Kessler, Ph.D., Professor, Biochemistry and Life Science Mass Spectrometry, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford

8:10 Discovery of Novel Protein Homeostasis Inhibitors Utilizing FORMA’s Drug Discovery Engine

Stephanos_IoannidisStephanos Ioannidis, Ph.D., Director, Medicinal Chemistry, FORMA Therapeutics

The ubiquitin pathway is most prevalent and illustrative of the protein degradation process. Ubiquitin is a small, 76 amino acid protein that attaches to other proteins as a single ubiquitin “tag” or in groups of ubiquitin molecules. These ubiquitin tags mark proteins for degradation. Polyubiquitination of substrates provides additional recognition/control elements to the protein degradation process. Ubiquitination is a three-step process involving ubiquitin-activating enzymes, ubiquitin conjugating enzymes and ubiquitin ligase (commonly referred to as E1, E2, E3). Deubiquitinating enzymes (DUBs) reverse the ubiquitination/polyubiquitination process, providing a tool for manipulating protein homeostasis. Protein homeostasis is important in oncology, neurodegenerative and other medical disorders involving a network of pathways controlling the biogenesis, folding, transport and degradation of proteins. Using FORMA’s innovative chemical libraries approach has led to the discovery of novel protein homeostasis inhibitors which allowed the understanding of pathways and targets associated with excessive protein degradation. The discovery of novel protein homeostasis inhibitors provides the potential for widespread clinical applications

8:40 Inhibition of an E2/E3 Protein-Protein Interaction as a Novel Strategy to Interfere with E3 Ligase Activity

Kamyar_HadianKamyar Hadian, Ph.D., Principal Investigator & Head, Assay Development and Screening Platform, HelmholtzZentrum München

This lecture will give insights into the discovery of a novel E2/E3 protein-protein interaction small molecule inhibitor that we were able to validate and characterize in a variety of biochemical as well as cell-based assays including primary mouse and human cells. More importantly, we can show that this first-in-class inhibitor is effective in preclinical autoimmune mouse models for psoriasis as well as rheumatoid arthritis.

9:10 SUMOylation in Cancer Biology

Sai_PulukuriSai Pulukuri, Ph.D., Senior Scientist & Project Team Leader, Millennium: The Takeda Oncology Company

SUMOylation has been implicated in many cellular processes that are important for cancer cell survival, including cell cycle, chromosome structure and segregation, nuclear and subnuclear organization, transcription and DNA damage repair. However, a potent and selective inhibitor to target the SUMO pathway has been lacking. The SUMO-activating enzyme (SAE) is an essential enzyme in the pathway that initiates the SUMOylation process. Here we report the identification of the first mechanism-based SAE inhibitor with nanomolar potency in cellular assays. Inhibition of SAE impacts numerous biological pathways relevant to cancer cell survival.

9:40 Coffee Break in the Exhibit Hall with Poster Viewing



10:25 UbFluor: A Novel Tool for HTS and FBDD Screening to Discover Chemical Probes for HECT and RBR E3 Ubiquitin Ligases

Alexander_SatsyukAlexander Statsyuk, Ph.D., Assistant Professor, Department of Pharmacological and Pharmaceutical Sciences, University of Houston

We present our work toward the rational and systematic approaches to develop small molecule inhibitors of HECT E3 and RBR E3s ubiquitin ligases. These are single subunit ligases that harbor the catalytic cysteine and form the obligatory HECT E3/RBR E3~Ub thioesters prior to ligation of the ubiquitin onto the lysines of protein substrates. Members of HECT and RBR E3s include Nedd4-1, Nedd4-2, ITCH, Parkin, and E6-AP. We used UbFluor to screen 50,000 compounds against two HECT E3s, and identified promiscuous and selective inhibitors. We also screened 2,000 water soluble fragments at 200 uM against three HECTs using UbFluor probe, and we will be presenting our results.

10:55 Stealing Secrets from the Germline: Alterations of Tumor Metabolism by a Testis-Specific Ubiquitin Ligase Hijacked in Cancer

Ryan_PottsRyan Potts, Ph.D., Associate Member, Faculty, Cell & Molecular Biology, St. Jude Children’s Research Hospital

AMP-activated protein kinase (AMPK) is a tumor suppressor and master regulator of cellular energy. Here, we describe a widespread mechanism to suppress AMPK through its ubiquitination and degradation by the cancer-specific MAGE-A3/6-TRIM28 ubiquitin ligase. MAGE-A3/6 are highly similar proteins normally expressed only in the male germline but frequently re-activated in human cancers. MAGE-A3/6 are necessary for cancer cell viability and are sufficient to drive tumorigenic properties of non-cancerous cells. Screening for targets of MAGE-A3/6-TRIM28 revealed that it ubiquitinates and degrades AMPKα1. This leads to inhibition of autophagy, activation of mTOR signaling, and hypersensitization to AMPK agonists. These findings elucidate a germline mechanism commonly hijacked in cancer to suppress AMPK.

11:25 Enjoy Lunch on Your Own

2:40 Refreshment Break in the Exhibit Hall with Poster Viewing

3:20 End of Conference

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