3rd Annual

Epigenetic Inhibitor Discovery

Targeting Histone Methyltransferases, Demethylases and Bromodomains

April 19-20, 2016

Epigenetic Inhibitor Discovery icon

Targeting epigenetic modifiers and readers, particularly histone methyltransferases, demethylases and bromodomain-containing proteins have recently set the foundation for a new generation of anti-cancer drugs. Over the past few years, several companies have developed and successfully moved novel compounds targeting EZH2, DOT1L, LSD1, and a collection of BET bromodomain inhibitors into clinical studies. As these compounds continue to progress, developers are now focused on the discovery of new targets and designing novel inhibitors to expand into this robust target space. Of particular interest for discovery are non-BET bromodomain proteins and JmjC-domain containing demethylases.

Cambridge Healthtech Institute will once again convene leaders in Epigenetic Inhibitor Discovery to bring forth novel and emerging strategies for inhibition, new bioactive tools and inhibitors, as well as strategies for lead optimization to obtain clinically relevant small molecules.

Tuesday, April 19

7:00 am Registration and Morning Coffee


8:00 Chairperson’s Opening Remarks

Kip Harry, Director, Conferences, Cambridge Healthtech Institute

8:10 New Synthetic Routes to Triazolo-Benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective Bromo and Extra-Terminal (BET) Bromodomain Inhibition

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

We describe new synthetic routes developed toward a range of substituted analogues of bromo and extra-terminal (BET) bromodomain inhibitors I-BET762/JQ1 based on the triazolo-benzodiazepine scaffold. These new routes allow for the derivatization of the methoxyphenyl and chlorophenyl rings, in addition to the diazepine ternary center and the side chain methylene moiety. Substitution at the level of the side chain methylene afforded compounds targeting specifically and potently engineered BET bromodomains designed as part of a bump and hole approach.

8:40 FEATURED PRESENTATION: The Design and Development of Bromodomain Ligands

Stuart_ConwayStuart Conway, Ph.D., Professor, Department of Chemistry, University of Oxford

Bromodomains are protein modules that bind to N-ε-acetyl-L-lysine (acetyl lysine) and facilitate the assembly of multiprotein scaffolds by mediating protein–protein interactions. It is only comparatively recently that bromodomains have been viewed as therapeutically important targets, but subsequent progress in the development of drug-like bromodomain ligands has been rapid. This presentation will discuss advances in the development of BET bromodomain ligands and progress in the identification of non-BET bromodomain ligands.

PerkinElmer NEW 20099:10 Novel Bromodomain & Extra Terminal Domain (BET) Family Bromodomain Assays Utilizing AlphaLISA Technology

Jen_CarlstromJen Carlstrom, PhD Application Scientist, Global Discovery Applications Group, PerkinElmer, Inc Global Discovery Applications Group PerkinElmer, Inc.

We have developed novel biochemical bromodomain AlphaLISA assays suitable for screening compounds against BRD4 using Histone 4 peptides of differing acetylation states. Assay specificity was confirmed by IC-50 determination of commercially available compounds. In collaboration with EpiCypher, PerkinElmer now offers kits to study modulators of bromodomain activity in vitro.

9:40 Coffee Break

10:05 In silico Design of Dual PI-3 Kinase/BET Bromodomain Inhibitors; Structural Details for Binding BD1

Adam Burgoyne, M.D., Ph.D., Chief Fellow, Division of Hematology/Oncology, Department of Medicine, University of California San Diego

We will present in silico drug discovery of a lead compound which inhibits PI-3 kinase isoforms and BRD4. Specificity and potency are to be presented as well as biological data on the inhibition of tumor growth, metastasis, M1-M2 transition and the activation of the immune checkpoint response to activate immunity.

10:35 Preclinical Characterization of ZEN-3694, a Novel BET Bromodomain Inhibitor Entering Phase I Studies for Metastatic Castration-Resistant Prostate Cancer (mCRPC)

Eric_CampeauEric Campeau, Ph.D., PMP, Director of Biology, Zenith Epigenetics

Targeting of proteins involved in the epigenetic regulation of oncogenesis has been motivated by the elucidation of their pivotal roles in various cancer programs, as well as the recent discovery of small molecules that could potently inhibit these proteins. Of these, inhibition of the bromodomain and extra-terminal (BET) proteins has shown potent inhibition of several transcriptional programs known to promote tumorigenesis, and promising evidence of clinical activities in leukemia and lymphoma have been presented. ZEN-3694 is a novel pan-BET bromodomain inhibitor displaying anti-tumor activity in various preclinical models. In vitro and in vivo characterization of ZEN-3694 will be presented, as well as evidence of activities in various models of CRPC that are resistant to current therapies. An overview of the planned phase I clinical trial in mCRPC with ZEN-3694 will also be discussed.

11:05 Structure-Guided Discovery of Potent and Selective Bromodomain Inhibitors and Their Application to Phenotype Discovery

Alexandre Côté, Ph.D., Senior Scientist, Constellation Pharmaceuticals

We describe the construction of a broad platform designed to interrogate the bromodomain family of acetyl lysine binding proteins. The platform produced multiple potent, selective and cell active bromodomain inhibitors that were then used to probe the biology of these epigenetic targets. Examples taken from our work with PCAF/GCN5 and CBP/EP300 bromodomain inhibitors will be described.

11:35 Enjoy Lunch on Your Own

12:05 pm Session Break


1:15 Chairperson’s Remarks

Elisabeth Martinez, Ph.D., Assistant Professor, Pharmacology, University of Texas Southwestern Medical Center

1:20 Novel Dual Inhibitors of LSD1-HDAC for Treatment of Multiple Myeloma and Other Cancers

Dhanalakshmi Sivanandhan, Ph.D., Principal Scientist & Assistant Director, Jubilant Biosys

We have developed a set of molecules having dual activity on LSD1 and HDAC. Multiple compounds with dual activity show an in vitro potency of <0.05 µM against LSD1 with more than 1000 fold selectivity against MAOs. On HDAC, these dual inhibitors showed different isoform selectivity and molecules with LSD1/HDAC1, LSD1/HDAC6/8 and LSD1/pan HDAC activities have been identified. JBI-097, one of the dual molecules with LSD1/HDAC/6/8 selectivity showed an IC50 of µM on LSD1 and an IC50 of 0.04 and µM on HDAC6 and HDAC8, respectively with about 100 fold selectivity over other HDAC isoforms.

1:50 Small Molecule Modulators of Gene Expression for Use in Multiple Diseases

Patrick_WosterPatrick M. Woster, Ph.D., Endowed Chair, Drug Discovery; Professor, Pharmaceutical and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina

We have identified multiple series of small molecules and peptides that act as potent and selective LSD1 inhibitors. Because of their relatively low toxicity, we have explored the use of these molecules in diseases other than cancer, where cytotoxicity is not a desirable endpoint. In this presentation, we will describe the optimization of this new series of LSD1 inhibitors, and present evidence that LSD1 inhibitor-mediated correction of aberrant gene silencing can have therapeutic potential in a variety of disease states.

2:20 Discovery of Histone Lysine Demethylase Inhibitors with Anticancer Activity

Takayoshi_SuzukiTakayoshi Suzuki, Ph.D., Professor, Graduate School of Medical Science, Kyoto Prefectural University of Medicine

Recent studies have revealed that histone lysine demethylases (KDMs) are involved in transcriptional activation or silencing and associated with several disease states such as cancer. Since 2004, two classes of KDMs have been identified. One class includes lysine-specific demethylase 1 (LSD1, also known as KDM1A) and LSD2 (also known as KDM1B), which are flavin-dependent amine oxidase domain-containing enzymes. The other class comprises the recently discovered Jumonji domain-containing protein (JMJD) histone demethylases, which are Fe(II) and a-ketoglutarate-dependent enzymes. To date, we have identified several classes of KDM inhibitors including LSD1 inhibitors and JMJD inhibitors, and the feasibility of using KDM inhibitors as anticancer agents has been suggested. In this meeting, the design, synthesis, and evaluation of our most recent KDM inhibitors and their possibility as anticancer agents will be presented.

2:50 Jumonji Inhibitors Target Surprising Cancer Pathways

Elisabeth-MartinezElisabeth Martinez, Ph.D., Assistant Professor, Pharmacology, University of Texas Southwestern Medical Center

During this lecture, I will discuss the use of small molecule inhibitors of Jumonji demethylases to modulate the lung and prostate cancer transcriptome and to interfere with Gli-1 driven signaling.



3:20 Selected Presentation: Aspartyl(Asparaginyl)-Beta-Hydroxylase Inhibitors for the Treatment of Hepatocellular Carcinoma

Mark Olsen, Ph.D., Associate Professor of Medicinal Chemistry, College of Pharmacy, Midwestern University

3:35 Refreshment Break in the Exhibit Hall with Poster Viewing


A Chemist's Foray into Translational Research

Peter SchultzPeter G. Schultz, Ph.D., Professor, Department of Chemistry, The Scripps Research Institute and Director, California Institute for Biomedical Research

Our research program combines the tools and principles of chemistry with the molecules and processes of living cells to synthesize new molecules and molecular assemblies with novel physical, chemical and biological functions. By studying the structure and function of the resulting molecules, new insights can be gained into the mechanisms of complex biological and chemical systems.

5:30 Welcome Reception in the Exhibit Hall with Poster Viewing

6:30 Close of Day

Wednesday, April 20

7:30 am Continental Breakfast Breakout Discussions

In this session, attendees choose a specific roundtable discussion to join. Each group has a moderator to ensure focused conversations around key issues within the topic. The small group format allows participants to informally meet potential collaborators, share examples from their work and discuss ideas with peers. Check our website in February to see the full listing of breakout topics and moderators.

Next-Generation BET Bromodomain Inhibitors

Moderator: Eric Campeau, Ph.D., PMP, Director of Biology, Zenith Epigenetics Non-BET

  • Do bromodomain-1 or bromodomain-2 specific inhibitors provide advantages over pan-BET bromodomain inhibitors?
  • What advantages do pan-BET inhibitors provide?
  • What are the prospects for other bromodomain inhibitors and working out their phenotypes?
  • Designing combination therapies with BET bromodomain inhibitors

How Can We Identify New Inhibitors and Biomarkers for Histone Methyltransferases?

Moderator: Matthew Fuchter, Ph.D., Reader, Chemistry, Department of Chemistry, Imperial College London

  • Are our worldwide screening libraries obsolete and exhausted and if so, where do we look for new libraries?
  • Why is substrate identification for histone methyltransferases hard, and why is it important?
  • How can we define cancer subtypes/treatment regimes and PD biomarkers suitable for histone methyltransferase inhibitors?
  • Can we achieve selective inhibitors and biomarkers through allosteric binding sites?

Challenges in Targeting Histone Demethylases

Moderator: Takayoshi Suzuki, Ph.D., Professor, Graduate School of Medical Science, Kyoto Prefectural University of Medicine

  • What is the optimal strategy for selective inhibition of histone demethylases?
  • What critical challenges still remain in designing potent and selective KDM inhibitors?
  • What other opportunities exist for KDM inhibitors outside of oncology?


8:30 Chairperson’s Remarks

Matthew Fuchter, Ph.D., Reader, Chemistry, Department of Chemistry, Imperial College London

8:35 FEATURED PRESENTATION: Profiling the ‘Methylome’ Targets of the Histone Lysine Methyltransferases: DOT1L

Matthew FuchterMatthew Fuchter, Ph.D., Reader, Chemistry, Department of Chemistry, Imperial College London

Indeed to date, no suitable technologies exist for defining the specific contribution of a given HKMT to the protein ‘methylome’. In currently unpublished work, we have gained proof-of-concept data towards the development a unique proteomic technology, via a traceable HKMT-cofactor system, that will allow cellular methylome profiling. We have initially applied our approach to DOT1L and in this talk I will present the underlying science of the method, the technological validation obtained so far, and the early insight we have gained on DOT1L biochemistry/biology.

9:05 Identification of a Novel Potent Selective SMYD3 Inhibitor with Oral Bioavailability

Ann_Boriack-SjodinAnn Boriack-Sjodin, Ph.D., Senior Director, Protein and Structural Sciences, Lead Discovery, Epizyme, Inc.

SMYD3 (Set and Mynd Domain containing 3) is a lysine methyltransferase overexpressed in several cancer types including breast, prostrate, pancreatic, and lung, and this overexpression is associated with poor clinical prognosis. Genetic knockdown of SMYD3 by shRNA has been shown to decrease proliferation in a range of cancer cell lines suggesting that inhibition of SMYD3 may have therapeutic utility. In this presentation we describe the discovery and optimization of a novel series of oxindole sulfonamides and sulfamides with SMYD3 inhibitory activity. One of these compounds, EPZ030456, has a SMYD3 biochemical IC50 of 4 nM and is active in cells with an IC50 of 48 nM in a trimethyl MAP3K2 (MEKK2) in-cell western (ICW) assay. The crystal structure of this compound was solved with SMYD3 and the nucleotide substrate, S-adenosylmethionine and shows the oxindole portion of the molecule extends into the SMYD3 lysine binding channel. EPZ030456 shows less than 30% inhibition at a 10 uM screening concentration against 17 histone methyltransferase targets tested, including SMYD2. Further optimization within the series resulted in EPZ031686 which has similar potency to EPZ030456 with a biochemical IC50 of 3 nM and an ICW IC50 of 36 nM and in addition exhibits good bioavailability following oral dosing in mice. Hence, EPZ031686 is a suitable tool to study the role of SMYD3 in cancer and other therapeutic areas, using both in vitro and in vivo models.

9:35 Coffee Break in the Exhibit Hall with Poster Viewing

10:30 Discovery of A-196, a Novel Chemical Probe for SUV420H1/H2

William_PappanoWilliam Pappano, Ph.D., Senior Scientist, Oncology Discovery, AbbVie, Inc.

11:00 Fragments Enable a New Mechanism of Inhibiting Lysine Methyl Transferases

Gregg Siegal, Ph.D., Lecturer, Faculty of Science, Leiden Institute of Chemistry, Leiden University

We set out to discover KMT inhibitors with a fundamentally different mechanism of action, that is compounds that bound in the presence of SAM, but not at the peptide substrate site. By doing so, we expected to address issues of ligandability, specificity and structural biology simultaneously. Here we present progress on a model program targeting Dot1L. Screening of the ZoBio fragment library using both ZoBio’s proprietary TINS technology and Biacore has led to a large number of hits. All hits were titrated using SPR to yield affinity and ligand efficiency. Using simple competition binding experiments with ligand observed NMR or SPR as the readout, SAM competitive, partially competitive and non-competitive ligands could be defined. Simple analoging experiments have yield more potent, ligand efficient molecules and the best behaved (stoichiometry, ligand efficiency and kinetics) were soaked into crystals of the Dot1L-SAH complex (SAH is the des-methyl product of SAM). We will present the first known structures of KMT inhibitors that bind in the presence of SAH, but not in the substrate site and how we are using the structural information to guide elaboration of biochemically active, Dot1L selective compounds. We feel this approach opens a new paradigm in KMT inhibitor development.

11:30 Chemical Tools to Modulate Gene Expression by Targeting DNA Methylation

Paola_ArimondoPaola B. Arimondo, Ph.D., Director, Research, ETaC - Epigenetic Targeting of Cancer, CNRS

A challenge to develop new anticancer strategies consists in designing chemical molecules able to modulate gene expression. To this aim we have designed inhibitors of DNA methyltransferases to reactive tumor suppressor genes. In order to identify novel inhibitors of DNA methylation, we applied three chemical strategies: High-Throughput Screening of chemical libraries, rational drug design based on molecular modeling and the pharmacomodulation of known inhibitors. The discovery and the biological activity of the compounds will be illustrated as the study of their mechanism of action.

12:00 pm Close of Track