2nd Annual

Epigenetic Inhibitor Discovery

Chemically Modulating Gene Expression

April 21-22, 2015


Epigenetic drug discovery is one of the fastest growing and potentially groundbreaking target spaces for developers. Over the past few years, a significant increase in small molecule inhibitors chemically modulating enzymatic activity of Histone Methyltransferases (HMTs), Histone Demethylases (HDMs), and disrupting interactions of the BET family bromodomains have rapidly translated into clinical investigation. Now, with apparent safety and efficacy being demonstrated in clinical trials, the opportunity to develop novel chemical tools and inhibitors against the wealth of epigenetic modifiers is ever present. 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. Join fellow drug discovery scientists for this day-and-a-half meeting that is in the first half of CHI’s larger Drug Discovery Chemistry event.

Great opportunity to share and discuss cutting-edge approaches/aspects in drug discovery.

Fabrizio G., Principal Scientist, AstraZeneca

Tuesday, April 21

7:00 am Registration and Morning Coffee


8:00 Chairperson’s Opening Remarks

Alison O'Mahony, Ph.D., Senior Director, Biology Research, BioSeek®, A Division of DiscoveRx Corp.

8:10 FEATURED PRESENTATION: A Bump-and-Hole Approach to Engineer Controlled Selectivity of BET Bromodomain Chemical Probes

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

BET proteins Brd2, Brd3, Brd4 and BrdT have attracted interest as drug targets because of their roles in transcriptional regulation, epigenetics, and cancer. The BET bromodomains have been targeted by potent pan-selective small-molecule inhibitors, but these inhibitors lack selectivity for individual family members because of the high conservation of the target binding sites. We developed an ethyl derivative of an existing small-molecule inhibitor, I-BET/JQ1, and showed that it binds leucine/alanine mutant bromodomains with nanomolar affinity and achieves up to 540-fold selectivity relative to wild-type bromodomains. Cell culture studies showed that blockade of the first bromodomain alone is sufficient to displace a specific BET protein, Brd4, from chromatin. Expansion of this approach could help identify the individual roles of single BET proteins in human physiology and disease, and aid association of the pharmacology of BET bromodomain inhibitors to particular targets within their different therapeutic applications.

8:40 In silico Discovery and Experimental Validation of Selective Bromodomain Inhibitors

Amedeo-CaflischAmedeo Caflisch, Ph.D., Professor and Chair, Computational Structural Biology, Department of Biochemistry, University of Zurich

We have discovered in silico, validated by X-ray crystallography, and optimized by chemical synthesis a series of nM potent and selective ligands of the CREBBP bromodomain. Fragment-based, high-throughput docking was employed for the identification of novel scaffolds whose affinity was enhanced in a straightforward manner by incorporating interactions within the ZA channel. The specificity and easy synthetic availability of our compounds will be useful to unravel the biological role(s) that CREBBP plays in several types of solid tumors as well as in haematological malignancies. Using the same approach, we have recently identified potent inhibitors of representatives of five different families of bromodomains.

9:10 Using Biophysics to Target Methyl Transferases (HKMTs) with Small Molecules

GreggSiegalGregg Siegal, Ph.D., CEO, ZoBio

HKMTs are an important class of targets, yet it has proven challenging to develop drug-like inhibitors against them. We have used our TINS NMR technology to screen a diversity fragment collection which has lead to SPR validated, novel hit matter against for 4 HKMTs. The hits target both the SAM and substrate sites. We find differences in the small molecule binding of the HKMTs. This allows us to 1) prioritize HKMTs on ligandability, 2) redefine family relationships based on pharmacology and 3) select specific or pan-family ligands as starting points for drug development efforts.

9:40 Coffee Break


10:05 Discovery of Dual PI3K/BRD4 Inhibitors

Donald-DurdenDonald Durden, M.D., Ph.D., Professor, Vice Chair, Pediatrics, University of California, San Diego School of Medicine; CEO and President, SignalRx Pharmaceuticals

A novel thienopyranone molecular scaffold has been discovered to selectively inhibit PI3 kinase as well as the bromodomain protein BRD4. Molecular modeling studies will be presented to describe how these single small molecules can bind to inhibit such distinctly different proteins and their functions. As a cancer therapeutic this dual inhibition mechanism allows for a unique and powerful way to modulate critical components of cancer cells. Inhibition of PI3K for example enhances the degradation of the cancer promoting transcription factor MYC and inhibition of BRD4 blocks the production of MYC thus maximal MYC extinction is achieved with a dual inhibitor. Key in vitro and animal proof-of-concept efficacy studies will be presented for the lead compound SF2523.

10:35 Discovery and Development of a Potent Dual TRIM24/BRPF1 Bromodomain Inhibitor, IACS-9571, Using Structure-Based Drug Design

Wylie-PalmerWylie Palmer, Ph.D., Institute Research Scientist, Institute of Applied Cancer Science, MD Anderson Cancer Center

We have developed a potent cellular dual TRIM24/BRPF1 bromodomain inhibitor which will be useful for interrogating the biological role of the bromodomains of these two proteins. We employed three different approaches for finding a starting point, including; virtual screening, assembling an acetyl-lysine mimetic library, and an HTS screen which led to the identification of a lead series. Iterative use of X-ray crystallography and observation of an unexpected binding-mode guided further optimization of this series towards single-digit nM potencies.

11:05 Translating Chromatin Biology into Drug Discovery

Alex-TaylorAlex Taylor, Ph.D., Senior Scientists, Medicinal Chemistry, Constellation Pharmaceuticals

There continues to be considerable interest in drugging epigenetic targets due to the profound potential to have an impact on disease. Constellation is interested in the readers, writers and erasers of histone modifications. Our drug discovery efforts towards identifying inhibitors of these therapeutic targets will be discussed.

DiscovRx11:35 Luncheon Presentation: Homogeneous Quantitative Biochemical Assay Platform Enabling Discovery and Optimization of Inhibitors for Diverse Therapeutic Targets

Treiber_DanDaniel Treiber, Ph.D., Vice President & Site Head, KINOMEscan, DiscoveRx Corporation
It is well established that ligand binding protects proteins from thermal denaturation; however, the broad application of this concept to high-throughput screening has been hindered by a lack of facile HTS-compatible protocols and sensitive, quantitative and precise readout methodologies. Here we describe a novel denaturation-based method that overcomes limitations of current denaturation-based screening methods, in addition to providing benefits over standard non-denaturation-based screening methods. Data generated using this format to query bromodomains, kinases, and more shall be presented.

12:05 pm Session Break


1:15 Chairperson’s Remarks

Brian Lohse, Ph.D., Associate Professor, Drug Design and Pharmacology, University of Copenhagen

1:20 Discovery of EPZ015666: A First-In-Class PRMT5 Inhibitor with Potent In Vitro and In Vivo Activity

Kenneth-DuncanKenneth W. Duncan, Ph.D., Associate Director, Molecular Discovery, Epizyme

We describe the identification and characterization of EPZ015666 (GSK3235025), a potent, selective and orally available inhibitor of Protein Arginine Methyltransferase-5 (PRMT5). This novel inhibitor is SAM-uncompetitive, peptide-competitive and interacts with the PRMT5:MEP50 complex through a unique inhibition mode not previously observed for any SAM-dependent enzyme. Treatment with EPZ015666 on Mantle Cell Lymphoma (MCL) cells leads to inhibition of PRMT5 mediated methylation and cell killing. Robust activity was also observed upon oral dosing of EPZ015666 in multiple MCL xenografts.

1:50 Discovery of a Potent and Specific Drug to Inhibit PRMT5 in Hematologic and Solid Tumors

Chenglong-LiChenglong Li, Ph.D., Associate Professor, Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University Comprehensive Cancer Center

Through our lab developed novel fragment-based drug design strategy, MLSD (multiple ligand simultaneous docking), we have optimized a class of drug-like small molecules in three iterative rounds. These PRMT5 inhibitors are potent and specific with favorable PK/PD properties. This presentation will discuss a novel lead in this series on the design process and demonstrate its efficacies in various hematologic and solid tumor models, such as lymphoma, AML and high grade astrocytomas. In addition, our data cross-validate that PRMT5 is a master epigenetic regulator that governs expression of its own target genes and those regulated by PRC2 of which a popular epigenetic target EZH2 is a component.

2:20 Selected Poster Presentation: Methylation and Cancer - Inhibiting the PRMTs and Looking for New Epigenetic Markers

Amy Varney, Research Scientist, Chemistry Research Laboratory, Department of Chemistry, University of Oxford

The Protein Arginine Methyltransferases (PRMTs) are a family of epigenetic regulating proteins that are implicated in various different cancers; inhibiting individual PRMTs is thus a potential therapeutic route for cancer therapy and the search for potent and selective PRMT inhibitors is ongoing. The PRMTs transfer methyl groups from the cofactor S-adenosyl-L-methionine to the guanidine group in arginine residues; the resultant specific methylation patterns have different downstream effects on the cell but as yet these have not been clearly defined. An improved understanding of arginine methylation patterns and their phenotypic effects could help inform design of a selective and potent PRMT inhibitor. Together these could have a profound impact on the cancer therapeutic field. 

 The presentation will describe work towards: 

I. Synthesis of PRMT inhibitors 

II. Design of a new robust mass spectrometry-based assay for PRMTs 

III. Investigation of possible novel epigenetic markers involving arginine modification 

The first aim of this work was to design and synthesise potent PRMT inhibitors, building on existing work in our laboratories. The presentation will describe the synthesis and testing of a series of bis-aryl and tricyclic structures against a panel of PRMTs, and the subsequent bioinformatic analyses towards identification of a new PRMT inhibitor scaffold. A second objective, to run concurrently with the design and synthesis of new inhibitors, was to develop a more robust PRMT assay to enable consistent and reliable structure-activity relationship data collection. We describe a mass spectrometry-based assay that is optimised to provide kinetic data and for inhibitor screening. The third part of this work looks at the PRMTs in the broader epigenetic context by exploring the possible existence of novel methylation patterns. In particular it investigated the ability of PRMTs to recognise peptides containing novel arginine methylation patterns as either substrates or inhibitors. The synthesis of peptides containing bespoke methylated forms of arginine amino acids and experiments to test their properties as epigenetic markers are underway.

2:35 Refreshment Break in the Exhibit Hall with Poster Viewing


3:20 Discovery of First-in-Class Reversible Dual Inhibitors of DNA Methyltransferase and Histone Methyltransferase G9a

Julen-OyarzabalJulen Oyarzabal, Ph.D., Director, Translational Sciences, Center for Applied Medical Research (CIMA), University of Navarra

We have designed and synthesized a new series of small molecules that act as potent, selective and reversible DNMT and G9a inhibitors. The most potent molecules inhibit both targets in the nanomolar range (IC50<100nM) and their functional responses, in vitro cellular, clearly show the corresponding impact on their epigenetic marks (2meH3K9 and 5-methylcytosine) with EC50 values of around 100nM, thus, confirming their mode of action. Off-target profiling shows that these molecules are selective against a panel of 37 additional epigenetic targets (<50% inhibition at 10uM).In addition, these molecules show high efficacy in inhibiting cell proliferation and apoptosis using different ALL, AML and MM cell lines, better than current standard of care (e.g. decitabine or 5-azacitidine); in fact, their GI50 values are between 50nM and 1mM. Optimization of these molecules led to a compound, CM-272, with adequate pharmacokinetics and therapeutic window to perform in-vivo efficacy assays. Details about this synergistic effect between G9a and DNMT in epigenetic mechanistic pathway will be discussed together with CM-272 in-vivo activity (3 different models) and potential therapeutic applications.

3:50 The Discovery and Characterization of A-366, a Potent and Selective Inhibitor of Histone Methyltransferase G9a

Ramzi Sweis, Ph.D., Research Investigator, Discovery Chemistry, AbbVie, Inc.

This talk highlights the discovery of a new class of inhibitors for G9a that are among the most potent and selective known for this methyltransferase. Physical and biological characterization of A-366, a representative compound from this class of inhibitors, has highlighted the utility of using this compound as a probe for studying G9a function. Further characterization has demonstrated efficacy of A-366 in particular models of leukemia.

4:20 Session Break


4:30 Plenary Keynote Introduction

Gregg Siegal, Ph.D., CEO, ZoBio


Chemotype Coverage in Fragment, Phenotypic, & Deorphanization Screens

Brian K. ShoichetBrian K. Shoichet, Ph.D., Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco

The numbing size of chemical space shouldn’t prevent us from asking what screening libraries are missing relative to what we know to be biologically relevant. I explore the impact of chemotype representation on inhibitor discovery, fragment-based screens, whole organism phenotypic screens, and screens to deorphanize enzymes and GPCRs. Each case is framed by rough calculation and illustrated by specific experimental results. The libraries that result differ as much as the goals of the screen, but specific limits and optimization strategies emerge.

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

6:30 Close of Day

Wednesday, April 22

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.

Topic: Developing Bromodomain Inhibitors

Moderator: Wylie S. Palmer, Ph.D., Institute Research Scientist, Institute for Applied Cancer Science, MD Anderson

  • Is it too easy to find BET inhibitors and BET biology?
  • What are the resulting selectivity implications for BET inhibitors? Would selectivity within the family be useful? How about domain 1 vs. domain 2 inhibition?
  • What are the prospects for other bromodomain inhibitors and working out their phenotypes? Why haven’t we seen phenotypes reported for other bromodomain inhibitors?
  • What are people’s experiences in finding new templates for other bromodomains?
  • Are other bromodomains as druggable as BET?

Topic: Considerations for Histone Methyltransferase Assay Development

Moderator: Karen Maegley, Ph.D., Associate Research Fellow, Integrative Biology and Biochemistry, Oncology, Pfizer, Inc.

  • What are the options (direct enzymatic/binding assays vs. indirect assays)?
  • What are the limitations and opportunities of each approach?
  • How do different substrates or changes in nucleosome structure alter the enzyme active site?

Topic: How Can We Identify New Inhibitors & Biomarkers for Epigenetic Proteins to Expand the Epigenetic Toolbox?

Moderator: Brian Lohse, Ph.D., Associate Professor, Drug Design and Pharmacology, University of Copenhagen

  • Are our worldwide screening libraries obsolete and exhausted and if so, where do we look for new libraries?
  • DNA-encoded libraries (Phage Display) peptides and small molecules
  • Fluorescent labeling of peptides or labeling of small molecules, as tools in cell studies, how can we improve?
  • Screening and investigating targets: full length vs truncated proteins
  • Biopharmaceuticals vs. small molecules
  • Can we achieve (subtype) selective inhibitors and biomarkers through allosteric binding sites?


8:40 Chairperson’s Remarks

Karen Maegley, Ph.D., Associate Research Fellow, Biochemistry and Primary Screening, Pfizer Oncology

8:45 Overcoming Drug Resistance through Small Molecule Epigenetic Modulation

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

Recent results will be described that establish the use of epigenetic inhibitors to overcome the transcriptional reprogramming that facilitates drug resistant phenotypes.

9:15 Epigenetic Inhibitors are Potentially Useful Therapeutics for Acute Leukemia

Yongcheng-SongYongcheng Song, Ph.D., Associate Professor, Pharmacology, Baylor College of Medicine

Mixed lineage leukemia (MLL) gene translocations are found in ~75% infant and 10% adult acute leukemia, showing a poor prognosis. Onco-MLL loses the H3K4 methyltransferase. Lysine specific demethylase 1 (LSD1), a H3K4 demethylase, is one of the members in MLL transcription complex. These cause imbalanced H3K4 methylation states, which might be corrected by LSD1 inhibition. We synthesized several potent LSD1 inhibitors and found they exhibited strong activity against MLL-rearranged leukemia cells, while these compounds are non-cytotoxic to several other tumor cells. One compound showed significant in vivo activity in a systemic leukemia mouse model without overt toxicities. The mechanistic studies of LSD1 inhibitors as well as their synergy with other epigenetic compounds against MLL leukemia are discussed.

9:45 Coffee Break in the Exhibit Hall with Poster Viewing


10:30 Histone Binding Mechanisms and Specificities of PHD Fingers

Tatiana-KutateladzeTatiana Kutateladze, Ph.D., Professor, Department of Pharmacology, Anschutz Medical Campus, University of Colorado

Plant homeodomain (PHD) fingers comprise one of the largest families of epigenetic effectors capable of recognizing PTMs (posttranslational modifications) of histones. Here, I summarize the structures and binding mechanisms of the PHD fingers that select for modified and unmodified histone H3 tails. I will compare the specificities of PHD fingers, Tudor and other histone readers, and discuss the significance of crosstalk between PTMs and the consequence of combinatorial readout for the selective recruitment of these effectors to chromatin.

11:00 Discovery of Novel Small Molecules and Small Cyclic Peptides as Chemical Tools and Inhibitors, Using DNA Encoded Peptide Libraries for HDMs and HMTs

Brian-LohseBrian Lohse, Ph.D., Associate Professor, Drug Design and Pharmacology, University of Copenhagen

EpiDiscoverY has previously shown new strategies and is continuously searching for alternative ways to identify new tool compounds for epigenetic targets, primarily HDMs (KDM4 and KDM1) and HMTs (EHMT and PRMTs). Here we present how we have used DNA encoded peptide libraries to identify both small molecule inhibitors and recently small cyclic peptide inhibitors for KDM4 and KDM1 and for EHMT and PRMTs. The entire strategy and timeline is presented along with two new assays.

11:30 Mechanistic Characterization of PRMT5 Enzyme Complexes

Karen Maegley, Ph.D., Associate Research Fellow, Biochemistry and Primary Screening, Pfizer Oncology

PRMT5 methylates arginine residues on protein substrates. Many different PRMT5 complexes have been described and different complexes are suggested to have different substrate preferences. We have enzymatically characterized PRMT5 complexes and will compare and contrast mechanism of action and inhibition and suggest a potential regulation mechanism.

12:00 pm Close of Track