Targeting the Ubiquitin Proteasome System header


About This Conference:

The ubiquitin proteasome system (UPS) is an essential and highly regulated mechanism operating to tightly control intracellular protein degradation and turnover. It is therefore no surprise that emerging strategies in drug discovery moving away from single-target approaches are shifting toward targeting multicomponent cellular machineries such as the UPS to elicit therapeutic response in complex disease. Following the approval of two proteasome inhibitors, significant progress has been made in our understanding of ubiquitin biology along with the emergence of novel technologies and strategies enabling the development of small molecules targeting specific UPS components. Thus, modulating ligases within the ubiquitination cascade and "rescue" deubiquitinases (DUBs) have gained significant interest in drug discovery.

Cambridge Healthtech Institute’s Targeting the Ubiquitin Proteasome System is one of the first meetings of its kind devoted to gather an interdisciplinary collection of leading development scientists to present and evaluate novel tool compounds/inhibitors to accelerate next-generation UPS therapies.


Wednesday, October 8

7:00am Registration and Morning Coffee


DIVERSE STRATEGIES MODULATING THE UPS & PROTEIN DEGRADATION

8:05 Chairperson’s Opening Remarks

Ben Nicholson, Ph.D., Senior Director, R&D, Progenra, Inc.

8:15 Featured Presentation: Inducing Protein Degradation as a Therapeutic Strategy

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

While consisting of successful drugs, the current pharmacopeia also has inherent limitations based on its ‘occupancy-based’ paradigm of pharmaceutical control. These limitations include: 1) the need to achieve/maintain high systemic exposure to insure sufficient in vivo protein inhibition, 2) the 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. As an alternative pharmaceutical strategy, 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). For the past decade, we have focused on developing different strategies for inducing selective protein degradation, including the PROTAC (Proteolytic Targeting Chimera) and HyT (Hydrophobic Tagging) technologies.

9:00 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.

9:30 Substrate-Assisted Inhibition of Ubiquitin-Like Protein Activation

Lawrence Dick, Ph.D., Director, Biochemistry, Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co.

We have identified small molecule inhibitors of ubiquitin-like protein (Ubl) activating enzymes (E1’s) that work by a novel form of mechanism-based inhibition. These molecules serve as tools to probe the biological functions of individual Ubl conjugation pathways, but more importantly they represent leads for the development of novel oncology therapeutics. To date our efforts have yielded two investigational drugs of this class that have entered into clinical trials; MLN4924, an inhibitor of the Nedd8 conjugation pathway; and MLN7243, an inhibitor of the ubiquitin conjugation pathway.

10:00 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing

10:45 Targeting Ring1B-Bmi1 E3 Ubiquitin Ligase Activity

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

Bmi1 is a central component of the Polycomb Repressive Complex 1 (PRC1) and interacts with Ring1B protein to form an active E3 ligase, which ubiquitinates histone H2A on lysine K119 to maintain the transcriptionally repressive state of many genes. Small molecule inhibitors of Ring1B-Bmi1 E3 ligase activity are highly desired as potential agents targeting cancer stem cells. Targeting the Ring E3 ligases with small molecules is a challenging task due to the lack of well-defined substrate binding pocket and a complex biochemical assay required for enzymatic activity studies. To identify small molecule inhibitors of Ring1B-Bmi1 we performed fragment-based screening using NMR spectroscopy. I will present development of potent Ring1B-Bmi1 inhibitors using medicinal chemistry and evaluation of their biological activity.

11:15 Discovery of a Selective p97 Inhibitor that Disrupts Protein Homeostasis In Vitro and Has Antitumor Activity In Vivo 

Han-Jie Zhou, Ph.D., Director, Chemistry, Cleave BioSciences

The AAA+ ATPase p97 (also known as VCP) plays an important role in the degradation of mis-folded or unneeded proteins by the ubiquitin proteasome system (UPS). The overexpression of p97 has been associated with poor outcomes in a number of tumor types. Herein we reported the discovery of a selective and potent p97 inhibitor which demonstrated effects on tumor cell markers of protein homeostasis related to UPS inhibition and survival in vitro. After oral dosing this compound affected pharmacodynamic markers of UPS activity in vivo as well as antitumor activity in a xenograft model. Together these studies validate p97 as a druggable target with potential antitumor activity.

11:45 Small Molecules Targeting Integrity of the 26S Proteasome Assembly

Pawel Osmulski, Ph.D., Assistant Research Professor, Molecular Medicine, The University of Texas Health Science Center at San Antonio

The 26S proteasome super-assembly is the most physiologically relevant among all proteases sharing the 20S proteasome catalytic core. So far, all clinically recognized inhibitors used to treat aggressive blood cancers are directly targeting catalytic sites of the core. These drugs do not perform well with solid cancers and in many cases resistance pose a problem. We developed a set of small molecules disabling the proteasome with an entirely different mechanism: by targeting interactions between the catalytic core and its regulatory modules and by allosterically inhibiting the core. In a proof-of principle studies one of our compounds disables degradation of polyubiquitinylated substrates and induces apoptosis in cancer cells, including triple-negative breast cancer.

12:15 pm Sponsored Presentations (Opportunities Available)

12:45 Session Break

1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:40 Session Break


TARGETING DUBs: NOVEL APPROACHES, CHEMICAL MATTER AND LEAD OPTIMIZATION

1:50 Chairperson’s Opening Remarks

Lawrence Dick, Ph.D., Director, Biochemistry, Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co.

2:00 Targeting DUBs by Chemoproteomic Inhibitor Profiling in Cancer Cells

Benedikt Kessler, Ph.D., University Research Lecturer, Ubiquitin Proteolysis Group, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford

Converting lead compounds into drug candidates is a crucial step in drug development, requiring early assessment of potency, selectivity and off-target effects, ultimately in cells. We have utilized chemical proteomics and ubiquitin-based active site probes to determine the potency and selectivity of deubiquitylating enzyme (DUB) inhibitors in cell culture models. This approach is now being combined with the application of unbiased molecular probes that allowed detection of endogenous active nucleophile-dependent enzymatic activities in cell extracts by direct isotope-label based mass spectrometric quantitation to discover a broad range of small molecule cellular targets. We demonstrate that both approaches allow the examination of specificity and selectivity properties of promising DUB inhibitor candidates in cancer cells. This information will accelerate the selection of novel lead compounds with complementary cellular effects for anti-cancer drug development.

2:30 A Selective USP1/UAF1 Deubiquitinase Inhibitor Modulates the DNA Damage Response In Humans

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 a number of human diseases. In line with the important function of DUBs in cells, the enzymatic activities of many DUBs are exquisitely controlled. Ubiquitin-specific protease 1 (USP1) in complex with a WD40-repeat protein, UAF1, is essential in the DNA damage response. DUBs, as a promising therapeutic target class, have attracted increasing interest in inhibitor discovery. We conducted a quantitative high-throughput screening (qHTS) against USP1/UAF1 and a subsequent lead optimization. We obtained a reversible inhibitor that displays nanomolar inhibition and excellent selectivity towards USP1/UAF1. The USP1/UAF1 inhibitor disrupts cellular DNA damage tolerance and repair pathways, i.e. Fanconi Anemia (FA) and DNA translesion synthesis (TLS). The USP1/UAF1 inhibitor also acts synergistically in potentiating non-small cell lung cancer (NSCLC) cells to cisplatin. Our study suggested a new strategy of inhibiting deubiquitinases and also demonstrated the utility of the USP1/UAF1 inhibitor in understanding the complex biology in the human DNA damage response.

3:00 Sponsored Presentations (Opportunities Available)

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

4:10 Identification of Selective DUB Inhibitors Targeting DDR Deficient Tumors

Niall Martin, Ph.D., COO, MISSION Therapeutics Ltd.

Loss of DNA damage response (DDR) pathways is an early event in tumourigenesis. In cancer cells, loss of one DDR pathway leads to dependency on the remaining DDR pathways for survival. Inhibition of these remaining pathways causes synthetic lethality (SL), a powerful mechanism for selectively targeting cancer. By systematically knocking down all deubiquitylating enzymes (DUBs) in isogenic models of DDR deficiencies, we identified SL interactions in genetic backgrounds including ATM-, ATR- and BRCA2. These results have been “phenocopied” using novel inhibitors identified through MISSION’s DUB drug discovery platform. A robust cascade of assays has led to the identification of compounds that selectively target tumor cells deficient in specific DDR pathways.

4:40 Small Molecule Inhibitors of the Deubiquitinase USP7 Interfere with Ubiquitin Binding

Ingrid E. Wertz, Ph.D., Scientist & Project Team Leader, Department of Early Discovery Biochemistry, Genentech

5:10 Interactive Breakout Discussion Groups (see website for details)

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

Challenges and Opportunities for Ubiquitin System Drug Discovery 

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

  • How to select E3 enzymes for drug discovery purposes? For example in the kinase field, tyrosine kinase Src is important, yet selective Src-kinase inhibitors have never made it to the clinic. How do we select the right E3s as drug targets? Can we learn the lessons from the kinase field? How are kinases selected, and how do we not select Src-type E3s, but rather Abl/RAF/EGFR type E3s as drug targets?
  • E3 enzymes can perform two enzymatic functions: substrate monoubiquitination (polyubiquitin chain initiation) and substrate polyubiquitination (polyubiquitin chain elongation or processivity). It is becoming evident that protein monoubiquitination regulates protein localization, while polyubiquitination leads to protein degradation. Question: Will the inhibition of polyubiquitin chain elongation but not initiation be therapeutically useful? In other words will the inhibition of substrate polyubiquitination but not monoubiquitination be therapeutically useful? In what cases?
  • Are other components of UPS system such as E2 enzymes neglected as therapeutic targets? E2 enzymes are viewed as simple messengers that shuttle between E1 and E3 enzymes. Inhibition of E2 enzymes should inhibit the activity of all respective downstream E3s. Are E2 enzymes good drug targets? Can E2 enzymes cause human diseases?
  • Are E1 enzymes viable drug targets?
 

Discussing DUBs: Biological Rationale, Achieving Selectivity, and Non-Catalytic Targeting 

Co-Moderators:

Benedikt Kessler, Ph.D., University Research Lecturer, Ubiquitin Proteolysis Group, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford

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

  • Many DUBs have functional implications in biological processes such as the DNA Damage Response Pathway (USP7, USP1, USP2, USP10, USP 47, USP16, USP 22 and USP 29), endosomal trafficking or cell signalling. What are other pathways and associated DUBs that are emerging?
  • DUBs as drug targets: Given the highly conserved catalytic cleft, how do you achieve selectivity while targeting DUB enzymes?
  • Many DUBs exist in different conformations that are either functional or non-functional, in part determined by ligand binding. Which versions should you design inhibitors against?
  • What are novel and emerging tools to better understand the selectivity of DUBs for polyubiquitinated chain linkages? How can this knowledge be exploited for drug development?
  • What are opportunities for targeting DUBs outside of the catalytic site? Targeting interactions between DUBs and ubiquitin molecules? Other allosteric 'hotspots' for targeting?

Additional Group to be Announced

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

7:15 Close of Day

Thursday, October 9

7:30 am Registration and Morning Coffee


BEYOND ONCOLOGY: DISCOVERY OF BIOACTIVE COMPOUNDS

8:00 Chairperson’s Opening Remarks

Niall Martin, Ph.D., COO, MISSION Therapeutics Ltd.

8:10 Selective Inhibition of the Proteasome-Associated Deubiquitinating Enzyme USP14

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

Small-molecule inhibitors of the proteasome-associated deubiquitinating enzyme Usp14 were obtained via high-throughput screening. The compounds enhance degradation of various proteins and may have therapeutic applications for proteopathies. Proteasome substrates vary dramatically in their susceptibility to Usp14 inhibition, and surprisingly Usp14 will not act on tested substrates when only a single ubiquitin chain is present on the substrate. This principle of selectivity is to our knowledge novel for a deubiquitinating enzyme. The failure of Usp14 to deubiquitinate substrate is accompanied by failure to regulate substrate degradation. The attack on supernumerary chains may have an impact on the overall selectivity of protein degradation by the proteasome, biasing degradation towards single-chain substrates produced by highly processive ubiquitin ligases.

8:40 Small-Molecule Inhibition of JAK-STAT Signaling through the Deubiquitinase USP9X

Bridget Wagner, Ph.D., Director, Pancreatic Cell Biology, Center for the Science of Therapeutics, Broad Institute

Using phenotypic screening, we identified a small-molecule suppressor of beta-cell apoptosis. Mechanism-of-action studies revealed that our top compound binds USP9X and interferes with JAK-STAT signaling induced by IFN-gamma stimulation. However, unlike common JAK-STAT pathway inhibitors, BRD0476 does not have kinase inhibitory activity. Mutagenesis studies suggest a competition between phosphorylation and ubiquitination, rather than direct kinase inhibition, in small-molecule inhibition of JAK-STAT signaling. These results demonstrate that phenotypic screening, followed by comprehensive mechanism-of-action efforts, can provide novel mechanistic insights into ostensibly well-understood cell signaling pathways. Furthermore, this study suggests USP9X as a novel target for regulating JAK2 activity in cellular inflammation.

9:10 Idolizing Ubiquitin: Novel Therapies to Treat Cardiovascular Disease

Ben Nicholson, Ph.D., Senior Director, R&D, Progenra, Inc.

The ubiquitin-proteasome system provides a rich environment for drug discovery and E3 ubiquitin ligases in particular are considered attractive therapeutic targets in a wide variety of disorders including metabolic disorders. Here we report that using our UbiProTM drug discovery platform we have discovered novel inhibitors of the E3 ligase IDOL that modulate cellular cholesterol homeostasis. Specifically these compounds increase LDLR levels in various cellular models and biophysical characterization revealed direct binding of the compounds to IDOL as well as perturbation of IDOL:LDLR interactions. The most promising compounds were used as starting points to develop novel drug like molecules and the efficacy of the lead compounds is being evaluated in translational models of hypercholesterolemia. Data will be presented summarizing our progress to date targeting IDOL for the treatment of hypercholesterolemia.

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


DISRUPTING PPIs OF E3 LIGASES

10:30 The Discovery of Small Molecules Targeting the VHL E3 Ubiquitin Ligase and Disrupting its Protein-Protein Interaction with HIF-alpha Subunit

Alessio Ciulli, Ph.D., Reader, Chemical & Structural Biology, College of Life Sciences, University of Dundee

Targeting E3 Ubiquitin Ligases is an attractive strategy for selective pharmacological modulation of the Ubiquitin Proteasome System (UPS) by small molecule probes, with high potential to deliver quality therapeutic leads. However the approach is considered high-risk since it requires modulation of Protein-Protein Interactions (PPIs) within large multisubunit enzyme complexes that are deemed challenging to target. We have discovered drug-like small molecules that target the von Hippel-Lindau protein (VHL) Cullin RING E3 Ligase and disrupt its key interaction with the Hypoxia Inducible Factor alpha subunit (HIF-α) with nanomolar potencies. Structure-based design informed by co-crystal structures and biophysical binding characterisation guided medicinal chemistry optimization, which combined peptidomimetic strategies with fragment-based deconstructive analyses. We show using chemoproteomics that the compounds are on-target with high specificity for the native VHL E3 ligase complex and provide evidence of their biological activity inside living cells. I will then discuss the potential of the compounds to be developed in two distinct areas: 1) as HIF stabilisers to upregulate the hypoxic response by acting downstream of prolyl-hydroxylase (PHD)-catalyzed HIF hydroxylation; 2) as molecular templates to induce the degradation of target proteins of interest by recruiting the VHL E3 ligase activity inside cells.

11:00 Targeting the MDM2-p53 Protein-Protein Interaction for New Cancer Therapeutics

Shaomeng Wang, Ph.D., Director, Center for Discovery of New Medicines; Warner-Lambert/Parke-Davis Professor, Medicine, Pharmacology and Medicinal Chemistry, University of Michigan Comprehensive Cancer Center

Blocking the MDM2-p53 protein-protein interaction is being pursued as a new cancer therapeutic strategy. Our laboratory has designed and developed a class of highly potent and specific small-molecule inhibitors to block the MDM2-p53 PPI (MDM2 inhibitors). I will present our structure-based design and optimization of our MDM2 inhibitors and extensive preclinical studies of SAR405838 (MI-77301), which is now in phase I clinical development for the treatment of human cancers.

11:30 Enjoy Lunch on Your Own


1:00 pm Plenary Keynote Program 
 

Chas BountraChas Bountra, Ph.D., Professor of Translational Medicine & Head, Structural Genomics Consortium, University of Oxford

Martin TolarMartin Tolar, M.D., Ph.D., Founder, President & CEO, Alzheon, Inc.

Andrew L. Hopkins, Andrew L. Hopkins, D.Phil, FRSC, FSB, Chair of Medicinal Informatics and SULSA Research Professor of Translational Biology, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee


2:45 Refreshment Break in the Exhibit Hall with Poster Viewing

3:45 Close of Conference


Suggested Event Package:

October 7 Short Course: Targeting Protein-Protein Interactions 

October 7 Short Course: Introduction to Targeted Covalent Inhibitors 

October 8-9: Targeting the Ubiquitin Proteasome System

October 9-10: Maximizing Efficiency in Discovery Conference 

 


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SPONSORSHIPS & EXHIBITS 

The exhibit hall was sold out in 2013, so please contact us early to reserve your place. To customize your sponsorship or exhibit package for 2014, contact:

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CONFERENCES


October 8 – 9

Targeting Epigenetic Readers and
Chromatin Remodelers
 

Targeting the Ubiquitin Proteasome System  

Big Data Analytics and Solutions  

GPCR-Based Drug Discovery  

RNAi for Functional Genomics Screening
– Part 1
 

Protein-Protein Interactions as Drug Targets  

Antibodies Against Membrane Protein Targets
– Part 1
 


October 9 – 10

Targeting Histone Methyltransferases and Demethylases  

Screening Drug Transporter Proteins  

Maximizing Efficiency in Discovery  

GPCR-Targeted Therapeutics  

Genome Editing for Functional Genomics
Screens – Part 2
 

Cancer Metabolism  

Antibodies Against Membrane Protein Targets
– Part 2
 


SYMPOSIUM


October 7

Next Generation Histone Deacetylase Inhibitors  


SHORT COURSES


October 7

SC1: Designing Scalable Software Systems for Big Data Analytics  

SC2: Approaches for Biologically-Relevant Chemical Diversity  

SC3: Setting Up Effective RNAi Screens: From Design to Data to Validation  

SC4: Targeting Protein-Protein Interactions  

SC5: GPCR Structure-Based Drug Discovery  

SC6: Advances in Metagenomic Drug Discovery for New Anti-Infective Agents  

SC7: Targeting of GPCRs with Monoclonal Antibodies  

SC8: A Primer to Gene Editing: Tools and Applications  

SC9: Introduction to Targeted Covalent Inhibitors  


October 9

SC10: Setting Up Effective Functional Screens Using 3D Cell Cultures  

SC11: Integration of BDDCS and Extended Clearance Principles  

SC12: Introduction to Allosteric Modulators and Biased Ligands of GPCRs  

SC13: Introduction to Drug Metabolism