The ubiquitin proteasome system (UPS) is an essential and highly regulated mechanism operating to tightly control intracellular protein degradation and turnover. Recently, researchers have found new ways to chemically modulate this cellular machinery, thereby altering protein homeostasis as a therapeutic strategy to achieve phenotypic novelty and providing new avenues for pharmacological development. In particular, specific components of the UPS, such as E3 ligases, deubiquitinases (DUBs) and ubiquitin-like protein (Ubl) activating enzymes are quickly emerging as promising targets as they provide specificity for targeting with the ability to alter cellular processes within a wide range of disease indications. As new strategies and tools emerge, novel UPS inhibitors are rapidly being developed and are collectively setting the foundation for a new generation of therapeutics.

Cambridge Healthtech Institute’s third 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

Day 1 | Day 2Targeting The Unfolded Protein Response | Download Brochure 

Tuesday, September 22

7:00 am Registration and Morning Coffee


8:00 Chairperson’s Opening Remarks

Xavier Jacq, Ph.D., Head of Biology, MISSION Therapeutics

8:10 FEATURED PRESENTATION: Diverse Mechanisms of Allosteric Activation in DUB Enzymes

Titia Sixma, Ph.D., Professor, Head of Division and Group Leader, Biochemistry, Netherlands Cancer Institute

Deubiquitinating enzymes are frequently kept under tight control and only activated at the right time and the right site. For a number of different DUBs allosteric mechanisms of regulation have been identified and these present interesting new opportunities for targeting. Even in comparative similar USPs or UCHs, different regulatory mechanisms have been observed. We study the enzymology of different DUBs structurally and biophysically. Here we discuss how USP4 and USP7 have different regulatory mechanisms with a common catalytic switch. We also discuss how UCH-L5 can be switched on and off by structurally related regulators in the context of the proteasome and the INO80 chromatin remodeller respectively.

8:40 Parkin and USP30 Signaling in Parkinson’s Disease

Christian Cunningham, Ph.D., Scientist, Early Discovery Biochemistry Department, Genentech

Here we investigate the mechanism by which Parkin and USP30, a mitochondria-localized deubiquitinase, regulate mitophagy. We find that mitochondrial damage stimulates Parkin to assemble Lys6, Lys11, and Lys63 chains on mitochondria, and that USP30 is an ubiquitin-specific deubiquitinase with a strong preference for cleaving Lys6 and Lys11-linked multimers. Using mass spectrometry, we show that recombinant USP30 preferentially removes these linkage types from intact ubiquitinated mitochondria and counteracts Parkin-mediated ubiquitin chain formation in cells. These results, combined with a series of chimera and localization studies, afford insights into the mechanism by which a balance of ubiquitination and deubiquitination regulates mitochondrial homeostasis. Our model predicts that Parkin mutants with reduced activity could be therapeutically compensated by inhibition of USP30 and that inhibition of DUBs may have broader utility in counteracting autophagy impairment beyond mitophagy.

9:10 Investigating Deubiquitination with Small Molecule and Ubiquitin-Based Probes

Zhihao Zhuang, Ph.D., Associate Professor, Department of Chemistry & Biochemistry, University of Delaware

Deubiquitinases (DUBs) play essential roles in a number of cellular processes and are implicated in many human diseases. In cells individual DUBs are linked to specific cellular pathways, making them attractive targets for small molecule modulation. DUBs are also known to possess different types of ubiquitin chain linkage specificities. Understanding the DUB chain linkage specificity requires new probes to be developed. The probes can also be used to understand the different modes of ubiquitin chain binding and cleavage by DUBs.

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


10:25 Selective De-Ubiquitylase Inhibitors for Cancer Immunotherapy

Joseph Weinstock, Ph.D., Senior Director, Medicinal Chemistry, Progenra

Although the ubiquitin pathway remains a highly attractive drug target, no one has taken a de-ubiquitylase (DUB) drug to the clinic. This failure is attributed to poor screening technologies, the inability to develop selective compounds, and even to the notion that DUBs are “un-druggable”. Progenra has discovered selective USP7 inhibitors that demonstrate efficacy in a number of p53-positive and p53-negative animal tumor models. An interesting finding is that USP7 inhibitors block cancer growth in immunocompetent mice; these molecules impair Treg functions, thereby promoting T effector-mediated anti-tumor activity. USP7 is overexpressed in multiple myeloma, neuroblastoma, prostate, bladder, colon, liver and lung cancers, and its expression is inversely correlated with survival in multiple myeloma, and correlated with tumor grade in prostate cancer. In addition to their immune mediated antitumor role, the USP7 inhibitors have also demonstrated direct anti-tumor activity in several models. Molecular mechanisms of these dual-acting USP7 inhibitors will be discussed. These unexpected findings indicate that USP7 is an important node in cancer and a compelling target for tumor therapy. USP7 inhibitors could be combined with other cancer immunotherapies to achieve durable clinical responses.

10:55 Proteasome-Associated DUBs: Molecular Targets for Cancer Treatment

Martina Bazzaro, Ph.D., Assistant Professor, Masonic Cancer Center, University of Minnesota

Recent work from our laboratory has shown that pharmacological inhibition of the proteasome-associated USP14 and UCHL5 has preclinical efficacy in preclinical models without toxicity in the host. Furthermore, we have shown that primary ovarian cancer cells derived from patients with recurrent ovarian cancer are particularly sensitive to USP14/UCHL5 inhibition. Importantly, we have shown that exposure of cancer cells to sublethal concentration of USP14/UCHL5 inhibitors causes ER stress responses and activation of autophagy. This suggests that inhibition of this class of enzymes results with an attempt of cancer cells to activate alternative and compensatory pathways to protein degradation. This concept is supported by our most recent data showing that both pharmacological and genetic inhibition of autophagy, potentiate the cell killing effects of USP14/UCHL5 inhibitors in cancer cell lines. Thus, we believe in the significance of taking advantage of the new weakness of chemoresistant ovarian cancer cells (i.e higher dependency upon USP14/UCHL5 activity) AND the cellular responses to USP14/UCHL5 inhibition to design a rational combinatorial approach with autophagy inhibitor to treat recurrent ovarian cancer. Importantly the combination approach proposed here has potential to achieve significant anti-cancer activity using much lower doses of the individual compounds thus limiting off-target toxicity and ultimately side effects on patients. This aspect being particular important for the cancer patient population, which responds well to standard chemotherapy but is often too debilitated to undergo a much needed second round of effective treatment.

11:25 Characterization of the Biochemical and Biological Activities of Proteasome Deubiquitinase Inhibitors

Padraig D’Arcy, Ph.D., Associate Professor, Cancer Pharmacology, Department of Oncology and Pathology, Karolinska Institute

The proteasome has emerged as an important target for anti-cancer drug development. We previously identified the small molecule b-AP15 as a novel class of proteasome inhibitor that functions by abrogating the deubiquitinase (DUB) activity of the proteasome. An optimized lead of this compound, named VLX1570, has subsequently been developed. b-AP15/VLX1570 are reversible and competitive inhibitors of the USP14/UCHL5 proteasome deubiquitinases (DUBs). b-AP15/VLX1570 are electrophilic compounds, but nevertheless show specificity to proteasome DUBs. Exposure to these drugs results in blocking of proteasome function as evidenced by the accumulation of polyubiquitinated proteins at the proteasome. Treatment with b-AP15/VLX1570 generates a robust proteotoxic stress response characterized by up-regulation of chaperone expression, ER and oxidative stress followed by apoptosis and cell death. VLX1570 shows in vivo activity in models of multiple myeloma and has recently been improved for clinical studies.

PerkinElmer NEW 200911:55 Presentation to be Announced


12:25 pm Session Break

12:35 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:15 Refreshment Break in the Exhibit Hall with Poster Viewing


1:50 Chairperson’s Remarks

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

2:00 Discovery of Highly Selective DUB Inhibitors With in vivo Preclinical Anti-Tumour Activity

Xavier Jacq, Ph.D., Head, Biology, MISSION Therapeutics

Using a combination of synthetic lethality screens and isogenic cell line models, depletion of a number of deubiquitylating enzymes (DUB) was shown to selectively kill a range of different tumour types, including platinum-resistant ovarian cancers, DNA damage response pathway deficient tumours (e.g. ATM, ATR, BRCA2) and haematological tumours such as multiple myeloma. Illustrating our DUB target identification platform, USP11, was identified as an essential enzyme for the proliferation of platinum-resistant cells but not platinum-sensitive tumour cells in an isogenic model derived from patient tumours before and after development of resistance. Target validation of specific DUBs, like USP11, in genetic backgrounds corresponding to deficiencies found only in tumour cells associated with specific cancers, supported our rationale to develop DUB inhibitors for the treatment of cancers with unmet medical need. A broad drug discovery platform combining unique biochemical, cellular, biophysical and structural assays was designed to identify and optimise potent and selective DUB inhibitors. Early selective DUB hits have been successful in recapitulating synthetic lethality genetic evidences in matched isogenic backgrounds. Lead optimisation of early hits has recently been translated into compounds with adequate properties for in vivo proof-of-concept studies. The challenges and advances in demonstrating in vivo DUB target engagement will be discussed.

2:30 Development of Novel and Selective Inhibitors of USP7 with Cellular Activity

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

Novel, selective and potent USP7 inhibitors (e.g. IC50 < 10 nM) have been developed. These inhibitors exhibit potent target engagement in cells (e.g. EC50 < 30 nM) and affect p53, p21 and MDM2 levels in line with expectations. Initial studies aimed at identifying cell lines sensitive to these inhibitors will also be discussed.

3:00 Sponsored Presentation (Opportunity Available)

3:30 Refreshment Break in the Exhibit Hall with Poster Viewing and Poster Winner Announced


4:10 New Strategies for the Identification of Chemical Inhibitors of E2 Enzymes: The Problem with Ubc9

John ‘Jay’ Schneekloth Jr., Ph.D., Investigator, Chemical Biology Laboratory; Head, Chemical Genetics Section, Center for Cancer Research, National Cancer Institute, NIH

In this talk, I will discuss my group’s recent efforts to target E2 ubiquitin and ubiquitin-like conjugating enzymes, with a focus on Ubc9, the SUMO E2 enzyme. In addition to discussing the challenges associated with drugging E2 enzymes, I will describe the development and application of a high throughput electrophoretic mobility shift assay to screen for natural product inhibitors of sumoylation. Additionally, I will describe my group’s use of fragment-based inhibitor discovery techniques to develop inhibitors of Ubc9.

4:40 Pharmacological Activators of Tumor Suppressor PTEN

Alexander Statsyuk, Ph.D., Assistant Professor, Department of Chemistry, Northwestern University

Genetic deletion, inactivating mutation, or aberrant polyubiquitination and degradation of tumor suppressors p53 and PTEN contributes to the origins and progression of human cancers. To this end, pharmacological inhibitors of ubiquitin ligases that polyubiquitinate and degrade p53 and PTEN hold substantial promise as anticancer therapeutics. To discover such inhibitors we developed a novel fragment-based drug discovery platform, which we call irreversible tethering. We subsequently used this platform to discover covalent inhibitors of Nedd4-1 ligase, which ubiquitinates and degrades tumor suppressor PTEN. To further optimize discovered inhibitors we obtained a crystal structure of Nedd4-1-inhibitor complex, which revealed previously unknown druggable site present in this enzyme. We developed a novel fragment-based drug discovery platform, and used it to discover first in class mechanism based covalent inhibitor of Nedd4-1 ubiquitin ligase, which degrades tumor suppressor PTEN. The developed drug discovery platform is generally applicable to discover covalent drug leads for E1, E2, E3 enzymes and DUBs (~800 known enzymes). Our findings are conceptually novel and will be of significant interest to the drug discovery community.

5:10 Interactive Breakout Discussion Groups

6:10 Welcome Reception in the Exhibit Hall with Poster Viewing

7:15 Close of Day

Day 1 | Day 2 | Targeting The Unfolded Protein Response | Download Brochure 

Wednesday, September 23

7:30 am Registration and Morning Coffee


8:00 Chairperson’s Remarks

John ‘Jay’ Schneekloth Jr., Ph.D., Investigator, Chemical Biology Laboratory; Head, Chemical Genetics Section, Center for Cancer Research, National Cancer Institute, NIH

8:10 Strategies for Enhancing Proteasome Inhibitor Efficacy

Jonathan Blank, Ph.D., Senior Scientist, Biochemistry, Takeda Oncology

The 20S proteasome core particle contains two copies of three catalytic subunits, each with differing proteolytic specificity (β1: caspase-like; β2: trypsin-like and β5: chymotrypsin-like). Bortezomib (VELCADE®) and ixazomib (Takeda’s oral proteasome inhibitor, currently in clinical trials) primarily inhibit β5 (~5 nM IC50), with 10-fold lesser potency against β1, while β2 inhibition is much weaker (>1 µM IC50). We therefore investigated whether targeting of β2 could represent an alternate approach to inhibit the proteasome and have an anti-cancer effect. We describe a novel class of non-covalent dipeptide inhibitors possessing nano-molar potency for the β2 site in vitro with high selectivity over the β1 and β5 sites that can potentiate the effect of β5 inhibition with bortezomib or ixazomib, suggesting a strategy for combining proteasome inhibitors in disease settings with limited sensitivity to these agents.

8:40 In situ Generated Activity-Based Probes for Ub/Ubl E1-E2-E3 Enzymes: Structure, Activity and Biological Sensing

Farid El Oualid, Ph.D., CSO & COO, R&D, UbiQ

I will present the design and characterization of the first full-length Ub/Ubl-based activity-based probes (ABPs) for the E1-E2-E3 cascade. The ABPs are processed as native Ub/Ubl and at the same time allow covalent trapping of the active site cysteine of E1-E2-E3 enzymes (HECT and RBR type). I will discuss how these new ABPs can be used for activity-based protein profiling (of cell lysates and live cells) and structural biology experiments (of HECT, RBR and RING type ligases).

9:10 Inhibition of E2/E3 Protein-Protein Interaction as Novel Strategy to Interfere with E3 Ligase Activity

Kamyar Hadian, Ph.D., Head, Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, German Research Center for Environmental Health (GmbH)

This lecture will give insights into the discoveries of a novel E2/E3 protein-protein interaction inhibitor that we were able to validate and characterize in a variety of biochemical as well as cell-based assays. More importantly, we can show that this compound is also effective in an in vivo mouse model. Hence, we provide evidence that disrupting E2/E3 interactions may be a valid strategy to target E3 ligase activity.

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


10:25 FEATURED PRESENTATION: Targeting Protein-Protein Interactions and Surfaces of Cullin RING E3 Ubiquitin Ligases (CRLs) with Chemical Probes

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

This talk will describe current progress from the lab with developing and characterising small molecules targeting Cullin RING E3 Ubiquitin Ligases (CRLs). CRL-targeting chemical tools can be used alone as E3 ligase inhibitors or modulators of the biological pathway in which the specific CRL is involved. In addition, CRL-targeting ligands can be suitably tethered with a ligand for a given protein of interest, yielding bifunctional proteolysis targeting chimeras (PROTACs) to hijack the ubiquitin proteasome system and induce the intracellular degradation of the target protein.

10:55 Targeting Ubiquitination Activity of RING Domain in Cancer with Small Molecules

Tomasz Cierpicki, Ph.D., Assistant Professor, Pathology, University of Michigan

Targeting the Ring E3 ligases with small molecules is a very challenging task due to the lack of well-defined substrate binding pockets and a complex biochemical assays required for enzymatic activity studies. To identify small molecule inhibitors of Ring1B-Bmi1 we performed fragment-based screening using NMR spectroscopy. We identified a class of compounds that directly bind to Ring1B-Bmi1 and block its ubiquitination activity on H2A. We then performed extensive medicinal chemistry optimization of these compounds and substantially improved binding affinity, resulting in compounds that bind to Ring1B-Bmi1 with low micromolar affinities. Using structural studies we determined that these compounds induce significant conformational changes of the protein upon binding. We have performed characterization of in vitro and cellular activities of our best inhibitors and found that these compounds specifically inhibit Ring1B-Bmi1 ubiquitin ligase activity at low micromolar concentrations without inhibiting other RING E3 ligases that ubiquitinate histone H2A. Treatment of several cancer cell lines with Ring1B-Bmi1 inhibitors revealed robust downregulation of H2A K119 ubiquitination and increase in p16 expression. Furthermore, treatment with Ring1B-Bmi1 inhibitors impairs self-renewal of leukemia initiating cells. Our approach to target Ring1B-Bmi1 validates that RING ligases are ‘druggable’ targets.

11:25 Enjoy Lunch on Your Own

12:55 pm Plenary Keynote Program 

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

3:25 Close of Conference

Day 1 | Day 2Targeting The Unfolded Protein Response | Download Brochure 

Suggested Event Package: 

September 21 Short Course: Targeting Protein-Protein Interactions: Biophysical Approaches 

September 23 Short Course: Assays and High-Throughput Screening for Novel Epigenetic Inhibitors 

September 22-23 Conference: Targeting the Ubiquitin Proteasome System 

September 23-24 Conference: Targeting the Unfolded Protein Response 


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Molecular Sensing 

Rosa Drug Development Advisors







The exhibit hall was sold out in 2014, so please contact us early to reserve your place. To customize your sponsorship or exhibit package for 2015, contact:

Jon Stroup
Sr. Business Development Manager


September 21 

Next-Generation Histone Deacetylase Inhibitors Symposia 

Strategies for Rare Diseases Symposia 

September 22 

Developing CRISPR-Based Therapies Symposia 

September 22 - 23 

Targeting Epigenetic Readers and Chromatin Remodelers 

Targeting the Ubiquitin Proteasome System 

Targeting the Microbiome 

GPCR - Based Drug Discovery - Part 1 

Antibodies Against Membrane Protein Targets - Part 1 

RNAi for Functional Genomics Screening 

Gene Therapy Breakthroughs 

Targeting Ocular Disorders 

September 23 - 24 

Targeting Histone Methyltransferases and Demethylases 

Targeting the Unfolded Protein Response 

Kinase Inhibitor Discovery 

GPCR-Based Drug Discovery - Part 2 

Antibodies Against Membrane Protein Targets - Part 2 

New Frontiers in Gene Editing 

Quantitative Systems Pharmacology 

Short Courses 

SC1: Cancer Metabolism: Pathways, Targets and Clinical Updates 

SC2: Leveraging Data and Analytics for Drug DiSCovery 

SC3: Setting Up Effective Rnai SCreens: From Design to Data to Validation 

SC4: Phenotypic SCreening and Chemical Probe Development 

SC5: GPCR Structure-based Drug Discovery 

SC6: Targeting of GPCRs with Monoclonal Antibodies 

SC7: Setting Up Effective Functional SCreens Using 3D Cell Cultures 

SC8: Targeting Protein-protein Interactions: Biophysical Approaches 

SC9: Preclinical Animal Models for Ocular Indications 

SC10: Introduction to Allosteric Modulators and Biased Ligands of GPCRs 

SC11: Introduction to Targeted Covalent Inhibitors 

SC12: Assays and High-throughput SCreening for Novel Epigenetic Inhibitors 

SC13: Gamification and Drug Target Challenges 

SC14: A Primer to Gene Editing: Tools and Applications 

SC15: Using Mechanistic Physiological Models In Drug Development