2015 Chemical Biology for Target Validation and Chemical Proteomics for Target Validation Banner

The development and utilization of high-quality chemical tools in combination with disease-relevant phenotypic systems provides a powerful approach to interrogate target-phenotype relationships – now a critical component to preclinical drug discovery. By systematically perturbing and interrogating biological pathways with synthetically novel chemical tools, preclinical validation of target biology is beginning to illuminate a more cost effective and efficient paradigm for the development of novel drugs modulating novel targets.


Cambridge Healthtech Institute’s second annual Chemical Biology for Target Validation will once again gather an interdisciplinary collection of leaders developing novel tools and approaches enhancing target validation.

Wednesday, June 10



7:00 am Registration and Morning Coffee



8:00 Chairperson’s Opening Remarks

Advances and Hurdles in Target Discovery with Small Molecule Probes

Ivan_Cornella-TaracidoIván Cornella-Taracido, Ph.D., Senior Principal Scientist, Discovery Chemistry, Merck Research Laboratories

Chemical Biology and Proteomics approaches have become an integral part of the identification and validation of novel therapeutic targets, particularly enabling small molecule mechanism of action studies. Yet, in spite of the published successes and high expectations over the last decade, the rate of discovery of new druggable targets with clinical translational success has been, so far, apparently disappointing. As a general introduction to the symposium, and to highlight the contributions of invited speakers and the topics of the 2015 edition, in these opening remarks we will introduce some potential contributing factors to these shortcomings to seed discussions and brainstorm during the “Interactive Breakout Discussion Groups” sessions of the event.

8:15 Identification of HIV Reactivation Agents through Phenotypic Screening: Synergy, Mechanism, and Education

David-TellerDavid Tellers, Ph.D., Principal Scientist, Discovery Chemistry, Merck Research Laboratories

Only a limited number of mechanisms have been identified which induce latent HIV expression in vitro in latently infected cell lines, primary cell models and ex vivo cells from suppressed HIV infected subjects. To identify novel mechanisms with the potential for use in combination therapy to induce latent HIV, we conducted an ultra-high throughput screen using a T-cell HIV latency model system. Results from this screen identified known mechanisms of action and a larger subset of unknown pathways. Our progress in elucidating these mechanisms will be detailed.

8:35 A Trigger Based Selectivity Mechanism of Cell Death Identified through Chemical Genetics

Deborah-RothmanDeborah Rothman, Ph.D., Investigator III, Chemical Genetics, Novartis Institutes of Biomedical Research

Phenotypic drug discovery has gained momentum as a complementary approach to target based drug discovery in the last decade. Though a phenotypic drug discovery approach, we have identified the N-BICs series of small molecules, which selectively kill a subset of cancer cells. Using multiple profiling tools and techniques, we identified the mechanism of selectivity to be activation of the compounds by high cellular expression of a phase II metabolic enzyme. Additionally, we show that the compounds covalently modify cellular proteins as part of their efficacy mechanism yet are efficiently cleared from animal models.

9:05 Sulfonyl Fluoride Chemistry for Target Validation, Identification and Other Applications in Chemical Biology

Lyn-JonesLyn Jones, Ph.D., Head, Chemistry, Chemical Biology & Rare Diseases, Pfizer

I will describe the first rational design and synthesis of sulfonyl fluoride covalent probes that specifically target reactive tyrosine residues in a protein binding site. Subsequent development of a clickable covalent inhibitor of the mRNA/miRNA metabolizing enzyme DcpS enabled the measurement of target engagement in human primary cells for the first time. This technology validated DcpS as a bona fide target protein of a series of diaminoquinazoline derivatives that modulate RNA levels and the broader utility of sulfonyl fluoride chemical probes in chemical biology will be described.

PromegaNEW9:35 Correlating Intracellular Drug Affinity and Residence Time with Phenotypic Outcomes Using Bioluminescence Resonance Energy Transfer (BRET)

Robers_Matt2Matt Robers, MSc, Senior Research Scientist 2, Research & Development, Integrated Biology, Promega Corporation

Bioluminescence energy transfer (BRET) enables a real-time, biophysical assessment of intracellular target engagement. This technique has enabled a quantitative analysis of compound binding against selected chromatin modifying enzymes, and has uncovered a mechanism of action for a class of HDAC prodrug inhibitors involving slow binding and long residence time.

9:50 Sponsored Presentation (Opportunity Available)

10:05 Coffee Break in the Exhibit Hall with Poster Viewing



10:50 Featured Presentation: Targeted Protein Degradation of Pathological Proteins

Andy-CrewAndy Crew, Ph.D., Vice President, Chemistry, Arvinas

While consisting of successful drugs, the current pharmacopeia 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 target engagement, 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 mechanistic strategy, targeted protein degradation lacks these limitations. Based on an ‘event-driven’ paradigm, this approach offers a novel and broad mechanism to irreversibly inhibit protein function, namely, the intracellular destruction of target proteins. This is achieved via small molecule mediated recruitment of the target proteins in question to the E3 ligase component of the UPS cellular quality control machinery. The application of the Arvinas degradation platform to identification of potent degraders of TBK1 will be described.

11:20 Targeting the Stress Chaperome in Disease, Diagnosis and Treatment

Gabriela-ChiosisGabriela Chiosis, Ph.D., Associate Member and Lab Head, Molecular Pharmacology and Chemistry, Sloan Kettering Institute; Associate Attending, Department of Medicine, Memorial Sloan Kettering Cancer Center

Normal cellular physiology is maintained by the coordinated action of the chaperome, a network of molecular chaperones as well as co-chaperones and folding enzymes that assist in their function. When under the insult of stress, such as is malignant transformation, the chaperome becomes modified to appease, in each tumor, the specific demand of proteome malfunctions. As such, tumors express, in addition to the housekeeping chaperome, a stress chaperome species dedicated to controlling the altered proteome. By using innovative methods, we develop small molecule chemical tools specifically targeted to the stress chaperome; these act as “sensors” of the chronic stress, and in turn, of the chronic stress-associated proteome. We will discuss how by the use of these unique tools we aim to understand, diagnose and treat cellular processes associated with chronic stress.

11:50 Targeting Epigenetic Proteins for Cancer Therapy

Jun-QiJun Qi, Ph.D., Lead Scientist, Bradner Lab, Department of Medical Oncology, Dana-Farber Cancer Institute

In cancer, epigenetic proteins are intensely studied targets for drug discovery owing to the general view that it is not just the DNA sequence that is altered in epigenetics-based diseases. We have been focusing on developing small molecule inhibitors of the BET (for bromodomain and extraterminal domain) epigenetic readers, which recognizes the acetylated lysine side chain on histones. The small molecule inhibitor we developed, JQ1, exhibits excellent inhibition against the BET subfamily with low nanomolar binding potency, especially targeting the BET protein, BRD4. It also exhibited excellent efficacy in a murine xenograft model without obvious toxicity. While we further developed our prototype drug towards a pre-clinical candidate, we have also established a series of chemical biology tools that can be utilized to further develop small molecule inhibitors for epigenetic targets, such as epigenetic writers and erases. Together with the small molecule inhibitors we developed, these tools have been used to understand the mechanism of epigenetic target inhibition cancers.

12:20 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall with Poster Viewing



1:30 Chairperson’s Remarks

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

1:35 Small Molecules to Engineer and Explore Human Immunity

David-SpiegelDavid A. Spiegel, Ph.D., M.D., Professor, Department of Chemistry, Yale University

Research in the Spiegel Laboratory utilizes techniques and insights from organic chemistry to modulate and/or create immunological function, an area termed “Synthetic Immunology.” This talk will discuss our recent work toward novel paradigms for immunotherapy by developing and characterizing synthetic constructs that harness immune responses. Specific topics to be discussed will include the rational design and biological characterization of immunomodulatory small molecules, as well as applications in areas ranging from cancer to infectious disease.

2:05 Spliceosome Modulation for the Treatment of Mutant SF3B1 Cancers

Gregg-KeaneyGregg F. Keaney, Ph.D., Senior Scientific Investigator, Medicinal Chemistry, H3 Biomedicine

H3 Biomedicine is an oncology-focused drug discovery company aimed at translating cancer patients’ genomes into powerful precision therapeutics. H3 Biomedicine’s lead drug discovery program is focused on targeting cancer cells which have mutations in SF3B1, a component of the U2 snRNP complex of the spliceosome which is involved in the recognition of splice sites during early spliceosomal assembly. This presentation will describe how the pladienolide natural products were originally identified to interact with the spliceosome through target identification cross-linking experiments, and how recently-discovered SF3B1 mutations in chronic lymphocytic leukemia (CLL) and myelodysplastic syndrome (MDS) represent a novel biological target for therapeutic intervention. The total synthesis of 6-deoxypladienolide D, a structurally-complex macrocyclic natural product, along with its biological activity in a suite of mutant SF3B1 assays will be described.

2:35 Discovering and Validating Drug Targets Using Synthetic Binding

Shohei-KoideShohei Koide, Ph.D., Professor, Department of Biochemistry and Molecular Biology, The University of Chicago

Advances in our knowledge of protein structure-function and directed evolution technologies have enabled us to rapidly engineer highly selective and potent binding proteins to diverse targets. We have developed "Monobodies," synthetic binding proteins that can be introduced into cells as genetically encoded protein. Remarkably, Monobodies to diverse target proteins are almost always inhibitors of their functions. Like small-molecule drugs, Monobodies modulate endogenous targets by binding them. Therefore, investigation of cellular effects of Monobodies and of the structural basis of Monobody-target interactions accelerates target validation and the discovery of potentially druggable sites. I will discuss our approach as applied to signal transduction and epigenetics.

3:05 High-Throughput Generation of Synthetic Peptides Modulating Enzyme Function

Sachdev-SidhuSachdev Sidhu, Ph.D., Professor, Donnelly Centre for Cellular & Biomolecular Research, Department of Molecular Genetics, University of Toronto

Peptide ligands are promising small-molecule therapeutic candidates for devastating diseases such as cancer. In principle, some natural proteins could be used as therapeutic agents, but their target binding affinities often precludes their use in a clinical setting. Using a phage display strategy and libraries of variant proteins designed based on crystal structure information, we can evolve high affinity variants that show increased binding affinity and improved activity compared to the wild type proteins.

3:35 Modeling Peptide Therapeutics/A Case Study

Villacañas_OscarOscar Villacañas, Ph.D., Head, Computational Chemistry, Intelligent Pharma

The identification of small molecules which can mimic peptides has great potential in overcoming difficulties associated with synthesis, or unfavorable physical properties. Through a case study we applied our ligand-based virtual screening to determine the similarity of a peptide to a set of small molecules that were experimentally validated.

3:50 Sponsored Presentation (Opportunity Available)

4:05 Refreshment Break in the Exhibit Hall with Poster Viewing

5:00 PLENARY KEYNOTE PANEL - click here for detailed agenda

6:00 Welcome Reception in the Exhibit Hall with Poster Viewing

7:00 Close of Day>

Thursday, June 11

7:30 am Interactive Breakout Discussion Groups with Continental Breakfast

Each discussion group in this session is led by a moderator/s who ensures focused conversations around key issues. Attendees join a specific group and the small, informal setting facilitates sharing of ideas and active networking.  

TABLE 19: Recent Advances and Hurdles in Phenotypic Screening and Target Discovery


Iván Cornella-Taracido, Ph.D., Senior Principal Scientist, Discovery Chemistry, Merck

Erik Hett, Ph.D., Principal Scientist, Chemical Biology & Medicinal Chemistry, Pfizer

  • Latest strategies for MoA annotated sets and phenotypic screening
  • Latest techniques in on/off-target identification - in particular label-free techniques
  • Techniques for identifying mechanisms not based on a single target protein or that are not protein in nature at all, such as targeting miRNA or riboswitches or ROS
  • Avoiding potential blind spots in target identification with regards to non-protein mechanisms


TABLE 20: Expanding Target Space Utilizing Chemical Diversity


Gregg F. Keaney, Ph.D., Senior Scientific Investigator, Medicinal Chemistry, H3 Biomedicine

  • Resurgence of natural product discovery
  • Diversity-oriented synthesis
  • DNA-encoded libraries
  • Recent developments in synthetic organic chemistry


TABLE 21: Novel Approaches Targeting Protein-Protein Interactions


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

  • Covalent drug leads for protein-protein interaction inhibitors
  • Mapping protein-protein interaction interfaces in vitro using MS methods
  • Photoreactive chemoproteomic reagents
  • What is the equivalent of Lipinski rules for covalent drugs?


Keynote Session: Chemical Biology Driving Discovery  


8:35 Chairperson’s Remarks

Laura Benitez, Ph.D., Sales and Business Development Manager, Intelligent Pharma


8:45 From Yeast to Human Neurons and Back Again: Powerful Platforms for Chemical Biology and Target Validation

SusanLindquistSusan Lindquist, Ph.D., Professor, Biology, MIT; Investigator, Howard Hughes Medical Institute

Taking advantage of the highly conserved biology of protein folding and trafficking in eukaryotic cells, we have created yeast models of human neurodegenerative diseases that recapitulate the basic pathological processes disrupting protein homeostasis. Significantly, each yeast model exhibits cellular toxicity through a different mechanism. The unique advantage of these models is the ability to perform ultra-highthroughput screening of chemical compound libraries. Hits from these yeast screens rescue patient-derived neurons. With this validation, we return to yeast and use the power of yeast genetics to identify targets. This lecture will discuss recent successes and the future promise of these yeast-to-neurons-to-yeast platforms.

9:30 FITGE-Based Target Identification for the Connection of Rational Drug Discovery with Phenotypic Screening

SeungBumParkSeung Bum Park, Ph.D., Professor, Chemistry, Seoul National University

We developed a new target identification platform, FITGE, which aims to preserve protein-small molecule interactions under the intact cellular environment. After a series of failures using conventional target ID methods, we successfully identified the protein target of anti-proliferative compound with FITGE only under the live cell condition and observed the environment-dependent binding events of a functional small molecule by direct comparison between live cells and cell lysates. In this presentation, I will report a phenotype-based discovery of initial hits that enhance the cellular glucose uptake in myotubes and adipocytes. The early-stage target identification and rational optimization of initial hits can generate lead compounds with high potency for PPARγ transactivation and cellular glucose uptake. At the end of my presentation, I will present our current effort on the development of novel neuroinflammatory agents via specific perturbation of post-translational modification of HMGB1 and HMGB2 from phenotypic screening and early stage FITGE-based target identification.

10:15 Covalent Inhibitors of Oncogenic Signaling Pathways

Nathanael GrayNathanael Gray, Ph.D., Professor, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Professor, Cancer Biology, Dana-Farber Cancer Institute

Tumour oncogenes include transcription factors that co-opt the general transcriptional machinery to sustain the oncogenic state, but direct pharmacological inhibition of transcription factors has so far proven difficult. However, the transcriptional machinery contains various enzymatic cofactors that can be targeted for the development of new therapeutic candidates, including cyclin-dependent kinases (CDKs). Here we present the discovery and characterization of a covalent CDK7 inhibitor, THZ1, which has the unprecedented ability to target a remote cysteine residue located outside of the canonical kinase domain, providing an unanticipated means of achieving selectivity for CDK7. Cancer cell-line profiling indicates that a subset of cancer cell lines, including human T-cell acute lymphoblastic leukaemia (T-ALL), neuroblastoma and small cell lung cancer have exceptional sensitivity to THZ1.

10:45 Selected Poster Presentation: Improving ALS Phenotypes by Targeting Aging Pathways: A Chemical Biology Approach 

Sunitha Rangaraju, Ph.D., Research Associate & MDA Development Grant Fellow, The Scripps Research Institute

11:00 Coffee Break in the Exhibit Hall with Poster Viewing



11:30 Novel Probes for E3 Ligases: pH Cleavable Photocrosslinkers to Map E2/E3 Ligase PPI Interface and UbiFlu Novel Fluorescent Probes

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

We will present our work toward the development of chemical probes to study the biochemistry and pharmacology of E3 ubiquitin ligases. First we have developed a novel class of pH-cleavable, minimalist photocrosslinkers that can be installed anywhere on the surface of the E2 enzyme using cysteine chemistry. Purified photoreactive E2 enzyme is incubated with the second protein (E3 ligase) and irradiated with UV-light. Photocrosslinked protein complexes are purified, and photocrosslinked sites identified. The unique features of the method include a pH-cleavable nature of photocrosslinkers, and a novel sample preparation protocol that includes electroelution step. Using this robust approach we have discovered catalytically relevant residues on E6AP ubiquitin ligase. The second part of this presentation will outline the invention of a novel class of fluorescent activity based probes for E3 ligases called UbiFlu. We discovered that fluorescent C-terminal ubiquitin thioesters cat undergo the direct transthiolation reaction with the catalytic cysteine of HECT and RBR E3s producing catalytically active E3~Ub thioester, which is accompanied by the release of the fluorescein. Based on this discovery we will discuss the development of HTS methods to screen for inhibitors/activators of E3 ligases, which require only 2 reagents instead of currently used 8 reagents.

12:00 pm Not All mGluR PAMs Are Created Equal: Designing the Right Allosteric Ligand for Your Clinical Indication

Dario-DollerDario Doller, Ph.D., Director, Discovery Chemistry & DMPK, Global Head of Chemical Biology, Lundbeck Research USA

Glutamate is a major neurotransmitter in mammal brain, its synaptic concentration being very tightly regulated through a network of ion channels, GPCRs and transporters. Allosteric modulation of glutamate-sensing metabotropic receptors (mGluRs) has the potential to provide new therapies for the most debilitating CNS diseases (AD, PD, MS). Advances in our understanding of the chemical biology of these receptors has enabled the characterization of ligands with distinct phenotype. We will disclose new results in the area of mGlu4 positive allosteric modulation, including careful characterization of different tool compounds.

12:30 Close of Conference