2016 Archived Content

Targeting Epigenetic Readers and Chromatin Remodelers Header

Cambridge Healthtech Institute has extensively covered the progression of second-generation epigenetic inhibitor discovery and development by establishing the first and longest-running series of meetings specifically focused on enhancing epigenetic drug discovery. We are once again excited to host the industry’s largest drug discovery event focused on targeting the chromatin-modifying enzymes of histone methyltransferases, demethylases and bromodomain-containing proteins. The back-to-back Targeting Histone Methyltransferases and Demethylases and Targeting Epigenetic Readers and Chromatin Remodelers meetings will once again unite academic and industry researchers to discuss novel tools and strategies for targeting these proteins, share the discovery and development of novel inhibitors, and provide updates on preclinical and clinical findings. 

Part 2 - Targeting Epigenetic Readers and Chromatin Remodelers

The second part of this series focuses on one of the most exciting areas of discovery research, targeting chromatin modifying proteins, particularly those responsible for the recognition of the histone code written in acetyl and methyl marks. With several clinical trials underway, and many discovery programs initiated, particular interest has been given to targeting the BET family of proteins across a diverse range of therapeutic indications. Widespread efforts have also begun to develop novel chemical matter targeting non-BET bromodomain proteins to assess their therapeutic potential. Most recently, interest and success in developing chemical tools targeting methyl-lysine readers have substantially expanded the possibilities of modulating chromatin states by disrupting epigenetic reading.

Final Agenda

Best Value

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

• September 20-21 Conference: Targeting Histone Methyltransferases and Demethylases

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

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Wednesday, September 21

11:20 am Conference Registration Open

11:25 Enjoy Lunch on Your Own

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


3:20 Chairperson’s Opening Remarks

Claes Wahlestedt, M.D., Ph.D., Leonard M. Miller Professor & Associate Dean, Therapeutic Innovation, Miller School of Medicine, University of Miami

3:25 FEATURED PRESENTATION: Targeting BET Protein Degradation for New Cancer Therapeutics

Shaomeng_WangShaomeng Wang, Ph.D., Warner-Lambert/Parke-Davis Professor, Medicine; Professor, Medicine, Pharmacology and Medicinal Chemistry; Director, Center for Therapeutics Innovation, University of Michigan

BET proteins have emerged as exciting new therapeutic targets for cancer and other human conditions. Several classes of potent and selective small-molecule inhibitors of BET proteins have been discovered and a number of them are now in clinical development. Preclinical and clinical data have demonstrated both the promises and limitations of BET inhibitors as new therapeutics. Recently, a new small-molecule approach has been employed to target degradation of BET proteins through the design of bifunctional, Proteolysis-Targeting Chimera (PROTAC) molecules. Based upon our new classes of highly potent small-molecule BET inhibitors, we have designed and optimized highly potent and efficacious small-molecule degraders of BET proteins. We have performed critical and extensive evaluation of our BET degraders for their therapeutic potential and mechanism of action in models of acute leukemia and solid tumors.

4:05 Structure-Based Design of an in vivo BRD9 Probe

Laetitia_MartinLaetitia Martin, Ph.D., Research Laboratory Head & Project Leader, Medicinal Chemistry, Boehringer Ingelheim

Components of the chromatin remodeling switch/sucrose nonfermentable (SWI/SNF) complex are recurrently mutated in tumors, suggesting that altering the activity of the complex plays a role in oncogenesis. However, the role that the individual subunits play in this process is not clear. We set out to develop an inhibitor compound targeting the bromodomain of BRD9. The discovery and structure-based optimization of a potent and selective BRD9 bromodomain inhibitor series will be presented. These compounds modulate BRD9 bromodomain cellular function and display antitumor activity in an AML xenograft model. Two chemical probes, BI-7273 and BI-9564, were identified that should prove useful in further exploring BRD9 bromodomain biology in both in vitro and in vivo settings.

4:35 Development of Cell-Active Low Nanomolar, Selective CREBBP Bromodomain Inhibitors

Dimitrios_SpiliotopoulosDimitrios Spiliotopoulos, Ph.D., SNF SystemsX.ch Postdoctoral Fellow, Department of Biochemistry, University of Zurich

A fragment-based docking campaign led to identification of novel ligands of the CREBBP bromodomain, which were efficiently derivatized into potent inhibitors. These compounds displayed remarkable selectivity for the CREBBP inhibitors over other human bromodomain subfamilies (Xu et al., J Med Chem, 2016, Unzue et al., J Med Chem, 2016). Recently, the combination of computational methods (viz. docking and molecular dynamics) and protein X-ray crystallography has guided the development of inhibitors with double-digit nanomolar affinity coupled with more than 1,000-fold selectivity for the CREBBP bromodomain over the most promiscuous bromodomain, BRD4(1). Importantly, activity in a cellular context was confirmed by FRAP and further evaluations of the inhibitors are currently ongoing in suitable biological models.

5:05 Refreshment Break in the Exhibit Hall with Poster Viewing

5:40 Inducible Binding Conformations that Enabled the Identification of Selective in vitro Bromodomain Inhibitors from a Common Scaffold

Terry_CrawfordTerry Crawford, Senior Scientific Researcher, Medicinal Chemistry, Genentech, Inc.

To help elucidate the biological role of non-BET bromodomain inhibitors, we endeavored to identify potent and selective bromodomain inhibitors as in vitro tool compounds suitable for phenotypic screening. Through a fragment screening approach we identified 6-methyl pyrrolopyridone as a highly ligand efficient scaffold. We discovered that lipophilic substitutions on this scaffold directed towards the conserved water network found in the bromodomain binding pocket were able to induce two distinct binding conformations, either through rearrangement of the conserved water network or the formation of a hydrophobic channel directed below the waters. These inducible conformations led to the identification of selectivity handles for BRD7/9, CECR2, and TAF1-BD2. In this talk we will discuss the induced conformations and our in vitro tool compounds identified from this effort.

6:10 FEATURED PRESENTATION: Bromodomain Chemical Probes to Explore Epigenetic Pathways

Oleg_FederovOleg Fedorov, Ph.D., Group Leader, Biophysics and Biochemical Screening, Structural Genomics Consortium and Target Discovery Institute, University of Oxford

The regulation of chromatin structure and gene expression is governed by a multitude of proteins that “write,” “read” and “erase” histone marks. To better understand this process and the pharmacological relevance of potential targets, Structural Genomics Consortium (Universities of Oxford and Toronto) together with major pharmaceutical companies initiated the program of developing chemical tool compounds for these proteins. We developed more than 30 chemical probes which are released to the academic community without restriction of use. I will highlight the recent progress in the field of bromodomain inhibitors, especially outside the BET subfamily. We achieved a good coverage of the family and identified the potential application in multiple disease areas such as inflammation and osteoporosis.

6:40 End of Day

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Thursday, September 22

7:30 am Registration Open and Morning Coffee


8:30 Chairperson’s Remarks

Norman C.W. Wong, M.D., FRCPC, Professor of Medicine and Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary; CSO & Co-Founder, Resverlogix

8:35 Mechanism-Based Combination Strategies for BET Inhibitors in Solid and Hematologic Cancers

Anastasia_WyceAnastasia Wyce, Ph.D., Investigator, R&D Oncology, GlaxoSmithKline

BET (bromodomain and extra-terminal) family proteins are transcriptional regulators known to control expression of genes involved in cell growth and oncogenesis. Selective small molecule BET inhibitors prevent binding of BET proteins to acetylated histones and inhibit transcriptional activation of BET target genes. BET inhibitors attenuate cell growth and survival in a number of hematologic and solid tumor cancer models. Data will be presented characterizing the single agent activity, mechanisms of action, and potential combination strategies for GSK525762, a potent and selective pan-BET inhibitor in early clinical development.

9:05 Tumor-Intrinsic and Immune Modulatory Activities of the BET Inhibitor INCB054329

Phillip_LiuPhillip Liu, Ph.D., Associate Director, Applied Technology, Incyte Corporation

BET proteins may play a role in shaping the tumor environment in addition to direct inhibition of malignant cells. We have investigated the efficacy of INCB054329, a novel BET inhibitor currently in Phase I clinical studies, as monotherapy and in combination with targeted agents and immune checkpoint blockade. Data will be presented from syngeneic tumor models using immunocompetent mice that characterize the effect of INCB054329 on markers of immune cell function. The results support a model in which BET inhibition can block tumor growth by complementary tumor-intrinsic and immune modulatory mechanisms.

9:35 Novel Bromodomain Inhibitors with Broad Activities

Claes_WahlestedtClaes Wahlestedt, M.D., Ph.D., Leonard M. Miller Professor & Associate Dean, Therapeutic Innovation, Miller School of Medicine, University of Miami

A collaborative effort between the University of Miami, Epigenetix Inc. and the NeoMed Institute has resulted in the generation of a range of novel bromodomain inhibitors. Some of these molecules showed unexpected efficacy and potency in in vitro and in vivo in cancer models. Notably, unlike reference compounds, these compounds bind to not only the BET bromodomains but also to several other bromodomain-containing proteins. Some of the resulting synergies will be discussed.

10:05 Speaker has Cancelled Novel BET Bromodomain Inhibitors to Treat Disease

 Chris_BurnsChristopher Burns, Ph.D., Laboratory Head, ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research

We have identified chemically novel series of BET bromodomain proteins based on a novel benzodiazpine scaffold, that are readily prepared and possess potent activity in cells. Studies to improve their molecular and ADME properties will be presented. We have also explored apoptosis mechanisms involved in BET bromodomain inhibitor activity as well as their potential in osteosarcoma.

10:05 Selected Presentation (Late-Breaking Research): Development of Dual‐Activity Small Molecules that Target BRD4 and Dopamine Receptor D2

Jeffrey W. Strovel, Ph.D., President and CEO, ConverGene

ConverGene has developed a series of small molecule inhibitors of BET family of bromodomain-containing proteins. BET family includes BRD4, an epigenetic reader protein that mediates expression of MYC oncogene. Thus, BRD4 is considered a cancer therapeutic target to indirectly suppress MYC expression. Our compounds showed high activity in a binding test against BRD4; exhibited long half-lives and 100% bioavailability upon oral administration; profoundly suppressed MYC expression both in vitro and in vivo; and strongly inhibited growth of AML cells in a mouse xenograft model. Importantly, a lead candidate has been developed from a subclass of our BET inhibitors that showed additional activity against dopamine receptor D2 (DRD2). In addition to being a therapeutic target for psychiatric diseases, DRD2 is emerging as a therapeutic target for cancer/leukemia stem cells. Therefore, our dual activity BET inhibitors may hold promise as a therapeutic that inhibits MYC pathway and maintenance of cancer stem cells.

10:15 Coffee Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced

11:10 BET Bromodomain Inhibitors in Prostate Cancer

Ifran_AsanganiIrfan A. Asangani, Ph.D., Assistant Professor, Cancer Biology, Perelman School of Medicine, University of Pennsylvania

Next-generation antiandrogen therapies, such as enzalutamide and abiraterone, have had a profound impact on the management of metastatic castration-resistant prostate cancer (mCRPC). However, mCRPC patients invariably develop resistance to these agents. BET bromodomain inhibitors were shown previously to attenuate AR signaling in mCRPC; here, we demonstrate the efficacy of bromodomain and extraterminal (BET) inhibitors in enzalutamide-resistant prostate cancer models. Interestingly, AR-variant 7 (AR-v7), which has been reported to be associated with resistance to antiandrogen treatments, was markedly repressed by BET inhibitors. AR antagonists, enzalutamide, and ARN509 exhibit enhanced prostate tumor growth inhibition when combined with BET inhibitors, JQ1 and OTX015, respectively. Taken together, these data provide a compelling preclinical rationale to combine BET inhibitors with AR antagonists to subvert resistance mechanisms.

11:40 FEATURED PRESENTATION: Bromodomain Inhibition of the Transcriptional Coactivators CBP/EP300 as a Therapeutic Strategy to Target the IRF4 Network in Multiple Myeloma

Andrew_ConeryAndrew Conery, Ph.D., Senior Scientist II, Constellation Pharmaceuticals

Pharmacological inhibition of chromatin co-regulatory factors represents a clinically validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Selective targeting of multiple myeloma cell lines through CBP/EP300 bromodomain inhibition is the result of direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4, which is essential for the viability of myeloma cells, and the concomitant repression of the IRF4 target gene c-MYC. Ectopic expression of either IRF4 or MYC antagonizes the phenotypic and transcriptional effects of CBP/EP300 bromodomain inhibition, highlighting the IRF4/MYC axis as a key component of its mechanism of action. These findings suggest that CBP/EP300 bromodomain inhibition represents a viable therapeutic strategy for targeting multiple myeloma and other lymphoid malignancies dependent on the IRF4 network.

12:10 pm Selected Presentation (Late-Breaking Research): NUE7770 - A BET-BD1 Selective Chemical Probe with Potent Cellular and in vivo Anti-Inflammatory Activity

Jimmi Seitzberg, Ph.D., Research Scientist & Project Manager, Nuevolution AS

Several inhibitors of BET proteins are in clinical development primarily for oncology indications but inhibition of the BET BDs has also proven efficacious in numerous animal models of inflammatory diseases. As most BET inhibitors reported in the literature are pan-BET inhibitors, the contribution of individual BDs to the biological activity of BET proteins is currently unclear, and domain-specific inhibition (intra- and/or inter-BET) remains largely unexplored. We have developed NUE7770, a chemical probe with high potency and pronounced selectivity towards the first BD (BD1) of the BET family. We have characterized this compound in various cellular assays of inflammation. In the BioMap Diversity Plus system, NUE7770 shows potent and very selective quenching of markers in the BT system with very little activity outside of immune-related systems. In pharmacokinetic experiments, NUE7770 shows good rodent exposure with dose-proportionality up to super-therapeutic doses and high oral bioavailability. We will present the results of in vivo efficacy studies conducted with NUE7770 in several mouse models of inflammatory disease.

12:40 Session Break

12:50 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:30 Refreshment Break in the Exhibit Hall with Poster Viewing


2:15 Chairperson’s Remarks

Andrew Conery, Ph.D., Senior Scientist II, Constellation Pharmaceuticals

2:20 Apabetalone (RVX-208); Actions of a Selective BET Inhibitor that Lowers Cardiovascular Risk in Humans  

Norman_WongNorman C.W. Wong, M.D., FRCPC, Professor of Medicine and Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary; CSO & Co-Founder, Resverlogix

Apabetalone (RVX-208) is a selective inhibitor with affinity for the second ligand binding domain in BET proteins. This feature of RVX-208 gives it unique activity compared to a pan BET inhibitor like JQ-1. For example, in liver cells, JQ-1 affects gene expression of more than 700 genes while RVX-208 modulates activity of less than 50. The actions of RVX-208 have been tested in clinical trials that have enrolled nearly 1000 patients, many of whom have cardiovascular disease (CVD). The results arising from these trials point to a variety of beneficial effects of RVX-208 in affecting the complement, coagulation, inflammatory, metabolic and lipid pathways. These actions of RVX-208 may underlie the observed improvement in CVD outcomes. Findings from our studies support the ongoing Phase III clinical trial called BETonMACE to examine the use of apabetalone (RVX-208) in CVD patients with diabetes mellitus receiving standard-of-care therapy. 

2:50 New BET Inhibitor Combination Strategies and Lessons Learned from Clinical Trials Conducted 25 Years Ago 

Jonas_NilssonJonas Nilsson, Ph.D., Professor, Experimental Cancer Surgery, Surgery, Sahlgrenska Cancer Center, University of Gothenburg

We have found new combination therapies of cancer. We also have strong evidence showing that BET inhibitors were already in Phase II trials in the 1980s. The BETi we disclose is a BD2-selective. During this presentation attendees will learn about the trial results from the first BETi in Phase II. They will also learn about the chemical starting point of BD2-selective BETi.

3:20 Session Break


3:25 Chairperson’s Remarks

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

3:30 PHD and YEATS Domains and Their Roles in Epigenetic Mechanisms

Tatiana_KutateladzeTatiana Kutateladze, Ph.D., Professor, Department of Pharmacology, Anschutz Medical Campus, University of Colorado

Plant homeodomain (PHD) fingers and YEATS domains are found in proteins involved in a wide array of fundamental biological processes including transcription, replication, DNA damage repair, cell differentiation and survival. These domains comprise the largest families of epigenetic readers, capable of recognizing PTMs (posttranslational modifications) of histones. Here, we detail the binding mechanisms and biological functions of the readers that select for methylated, acetylated, and unmodified histone H3 tails. We compare the specificities and discuss the significance of crosstalk between PTMs and the consequence of combinatorial readout for the recruitment of these readers to chromatin.

4:00 Targeting Chromatin Regulation via Methyl-Lysine Reader Chemical Probes

Lindsey_JamesLindsey Ingerman James, Ph.D., Research Assistant Professor, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill

The posttranslational modification of lysine by methylation has a central role in chromatin function, primarily through the creation of binding sites for proteins that recognize these marks. Aberrant methylation levels and ensuing changes in gene expression patterns resulting from the altered expression of methyl-lysine regulatory proteins is one mechanism by which such epigenetic factors contribute to disease. There are more than 200 such proteins that “read” methyl-lysine, and despite their significance in chromatin biology, this target class has been relatively unexplored to date. We are interested in modulating the activity of chromatin reader proteins with small-molecule ligands, specifically potent and selective chemical probes, in order to open new avenues of research in the field of chromatin biology and potentially translate to compounds of therapeutic value.

4:30 Speaker has Cancelled  Identification and Validation of CBX2 as a Therapeutic Target

Cheryl D. Helgason, Ph.D., Senior Scientist, Experimental Therapeutics, British Columbia Cancer Agency Research Centre

Our studies have identified the chromodomain protein CBX2, an epigenetic reader, as a potential oncogene and therapeutic target in numerous tumor types. In this presentation we will present data demonstrating the identification of CBX2 as an oncogene worthy of targeting. We will also demonstrate that targeting CBX2 in prostate cancer cells results in significant cell death. Future perspectives will focus on attempts to target CBX2, as well as to identify co-interactors that may serve as complimentary therapeutic targets.

4:30 Selected Presentation (Late-Breaking Research): Ultra-Sensitive Regulation of the Nucleosome Binding of FACT, a Chromatin Remodeler, through Multiple Phosphorylation to Its Intrinsically Disordered Regions (IDRs)

Shin-ichi Tate, Ph.D., Professor, Graduate School of Science, Hiroshima University

A chromatin remodeler, Facilitates Chromatin Transcription (FACT), engages in the transcription in the context of chromatin by destroying nucleosome structures. FACT comprises two subunits, SPT16 and SSRP1; SPT16 binds to H2A/H2B histone components, while SSRP1 binds to nucleosomal DNA. We reported the long IDR in SSRP1 is responsible for the DNA binding and IDR is subjected to multiple phosphorylation. The IDR in SSRP1 is divided into two parts. The N-terminal IDR is rich in acidic residues, thus called as AID, while the C-terminal part preferentially contains basic residues, names as BID. AID part has 10 potential phosphorylation sites, and actually 8 sites are phosphorylated by CKII. We found the extent of the phosphorylation to AID changes the binding ability of FACT to nucleosome and the binding ability changes according to the number of phosphate in a sigmoidal manner, 'ultra-sensitive' response. We reported the sensitivity is achieved by the scissoring motion to make the AID and BID folded; the increased level of the phosphorylation stabilizes intra-molecular AID-BID contact form to mask the basic resides in BID to diminish the binding ability of the IDR. In the scissoring motion, the Gly-rich region located at the junction between AID and BID should roles as a hinge. To explore if the scissoring motion is functionally relevant, we studied the regulatory roles of Gly-rich region in the scissoring motion by using the mutations to the part. The NMR structure and dynamics analyses in combination with biochemical assays revealed how the Gly-rich part participates in the ultra-sensitivity of FACT.

5:00 Close of Conference

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