Chemical biology and proteomic strategies have rapidly emerged as cost effective yet powerful preclinical approaches for the discovery and identification of novel drugs and targets. Advances in the development and combination of novel chemical tools, bioorthogonal techniques, disease-relevant phenotypic systems, chemoinformatics, and chemical proteomics now provide robust and high-throughput workflows for interrogating drug-target-phenotype relationships. These efforts are poised to significantly enrich preclinical discovery programs and are illuminating a new paradigm for the development of novel drugs modulating novel targets.

Cambridge Healthtech Institute’s Chemical Biology in Drug Discovery will once again gather an interdisciplinary collection of leaders to discuss these emerging tools and strategies to de-risk novel discovery initiatives.

Final Agenda

Thursday, June 16

11:00 am Registration

12:00 pm Bridging Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

12:30 Session Break

1:00 Coffee and Dessert in the Exhibit Hall with Poster Viewing

1:45 PLENARY KEYNOTE SESSION

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

ADVANCES IN CHEMICAL BIOLOGY

4:15 Chairperson’s Opening Remarks

Ivan Cornella Taracido, Ph.D., Senior Principal Scientist, Merck Research Laboratories

4:55 Measuring Compound Residence Time and Exploring Kinetic Selectivity at Select Targets in Living Cells

Matthew Robers, Senior Research Scientist & Group Leader, Research & Development, 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 hundreds of selected protein kinases and epigenetic targets in living cells. Analysis of intracellular residence time reveals kinetic selectivity profiles for various kinase, HDAC, and bromodomain inhibitors.

5:25 Drug-Target Occupancy Determination in Living Cells Using Thermal Stability and Affinity-Based Profiling

Lyn Jones, Ph.D., Head, Rare Diseases Chemistry; Head, Chemical Biology, Pfizer

I will describe recent advances in our lab that have led to the successful development of biophysical and chemical methods for the interrogation of drug-target engagement in human primary cells. These studies are essential for the successful validation of therapeutically-relevant targets. Thermal shift and sulfonyl fluoride labeling technologies will be directly compared for the first time – our findings will be of broad interest to the chemical biology community.

5:55 What Is Your MOA? Target Deconvolution of a Phenotypic Screen

Erik Hett, Ph.D., Team Leader and Senior Scientist, Chemical Biology, Biogen

Cellular phenotypic screens are a powerful way to uncover novel biology and discover druggable targets and chemical matter. One of the main bottlenecks for this approach, as opposed to target-based screening, is determining the mechanism of action of lead hits. Our group is developing approaches to determine the MOA of lead hits. These approaches include using proteomics, RNAi, RNA-seq, chemical probes, and in silico studies. We have utilized chemical proteomics and RNAi to unveil the mechanism of a lead series for the project to be inhibition of a kinase that was not previously known to be involved in the pathway. This finding reveals unexpected biology in regards to regulation of this pathway.

6:25 Close of Day

6:30 Dinner Short Course Registration

7:00 - 9:30 Dinner Short Courses

Friday, June 17

7:15 am Registration

TECHNOLOGICAL ADVANCES ENABLING TARGET VALIDATION

8:35 Chairperson’s Remarks

Jing (Jeannie) Li, Ph.D., Senior Scientist, Medicinal Chemistry Chemical Biology, Pfizer

8:45 Chemogenomic Approaches to Spatiotemporal Regulation of HDAC Activity

Ralph Mazitschek, Ph.D., Assistant Professor, Center for Systems Biology, Chemical Biology Platform, Massachusetts General Hospital

HDACs are master regulators of chromatin structure and function. Beyond modulating histones acetylation, they are recognized as regulators of non-histone proteins. HDAC inhibitors have been used as tool compounds to study basic biology and recognized as promising therapeutics. However, systemic exposure is often not well tolerated, or does not provide the required resolution in biological model systems. To address these shortcomings we have developed a new approach to control HDAC activity with greater spatial and temporal resolution.

9:15 Intracellular Delivery of Membrane Impermeable Small Molecules Using CellSqueeze

 Jing (Jeannie) Li, Ph.D., Senior Scientist, Medicinal Chemistry Chemical Biology, Pfizer

Biochemical screening is a major source of lead generation for novel targets. One drawback of biochemical screening is that “hits” identified from this approach may not be able to reach their protein target to show activity in cellular assays. The poor translation from biochemical to cellular assays is usually attributed to lack of cell permeability, the presence of efflux pumps or native ligand competition. To our knowledge, there is no quick and robust method available for us to understand the discrepancy observed between these assays. In order to tackle this challenge, we employed a newly discovered vector-free microfluidic platform, which enables us to deliver membrane impermeable small molecules into cells and subsequently assess their cellular activity by various functional assays. We believe that this approach has the potential to not only allow better understanding of why some biochemically potent small molecules fail to elicit cellular responses, but it also provides a platform for delivering membrane impermeable chemical probes into cells to facilitate further target engagement and mechanism of action studies.

Selected Presentations:

9:45 Target Identification of Label-Free Small Molecules with DARTS and LC/MS/MS

Ho Jeong Kwon, Ph.D., Professor, Department of Biotechnology, Director, Chemical Genomics GRL, College of Life Science & Biotechnology, Yonsei University

10:00 Global LC-MS/MS Investigation of LTP-Nanoparticles for the Treatment of Neurodegenerative Disease

Celina Cahalane, Research Scientist, Department of Chemistry, The University of Akron

10:15 Coffee Break in the Exhibit Hall. Last Chance for Poster Viewing.

PHENOTYPIC SCREENING, MOA AND TARGET DECONVOLUTION

11:00 Prioritizing Chemical Tool Compounds for Phenotypic Drug Discovery

Yuan Wang, Ph.D., Investigator II, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research

Phenotypic screens are increasingly employed in drug discovery both for lead and tool compound finding. The use of potent and selective chemical tools (probes) in phenotypic screens can help drive elucidation of underlying biological processes. The identification of such compounds is nontrivial and biases towards famous compounds should be avoided. Here we investigated large-scale potency data integrated from diverse sources to create a compound tool score, which we used to systematically rank tool compounds. We then confirmed target-phenotype profiles of these compounds in a cell-based panel comprised of 41 reporter gene assays. We demonstrated that selected tool compounds with high tool scores specifically revealed their on-target biology. These useful tools in phenotypic screens are included in the Novartis MOA box.

11:30 Small Molecules-Driven Chemical Biology and Target Deconvolution Strategies

M. Paola Castaldi, Ph.D., Head, Chemical Biology Team, Discovery Sciences, R&D Boston, AstraZeneca

A Wnt pathway screen identified a series of compounds with sub-μM potency. We designed and synthesized chemical probes towards a comprehensive target deconvolution effort through a combination of chemoproteomics, cell biology, and biochemical techniques. Proteome-wide analysis identified putative targets, and while interesting, validation with siRNA knockdown did not yield conclusive evidence for these proteins being responsible for the observed phenotype. Rather, we found, through probing metabolic effects, that this chemical series inhibits oxidative phosphorylation in the mitochondria, with Wnt inhibition being a secondary phenotype. Additionally, we have identified a previously unreported phenotype for this series, through measuring oxygen consumption rates, detecting that these compounds uncouple the mitochondrial proton gradient. 

12:00 Case Study: Inhibitors of VPS34 Provide Chemical Tools to Modulate Autophagy In Vivo and Enable a Proteomics Strategy to Identify Autophagy Substrates 

Erin Keaney, Ph.D., Investigator III, Novartis Institutes for BioMedical Research

Autophagy is a dynamic process that regulates lysosomal-dependent degradation of cellular components. Until recently the study of autophagy has been hampered by the lack of reliable pharmacological tools, but selective inhibitors are now available to modulate the PI 3-kinase VPS34, which is required for autophagy. Here we describe the discovery of potent and selective VPS34 inhibitors, their pharmacokinetic (PK) properties, and ability to inhibit autophagy in cellular and mouse models. In addition, given that many known autophagy substrates are ubiquitylated, our VPS34 inhibitors enabled a ubiquitin-affinity proteomics strategy leading to the identification of autophagy substrates, including ​NCOA4.

12:30 Luncheon Presentation (Sponsorship Opportunity Available)

1:00 Session Break

CHEMICAL TOOLS AND STRATEGIES TO EXPAND PHARMACOLOGICAL MODULATION OF BIOLOGICAL PROCESSES

1:30 Chairperson’s Remarks

Lyn Jones, Ph.D., Head, Rare Diseases Chemistry; Head, Chemical Biology, Pfizer

1:35 Sequence-Based Design of Small Molecules Targeting RNA

Matthew David Disney, Ph.D., Professor, Department of Chemistry, The Scripps Research Institute

A challenge in biomedical research is to rapidly convert genome sequence into lead drugs. The Disney group has developed methods that can quickly and accurately convert genome sequence, namely the RNA products of the genome, into lead therapeutic targets. The general approach described herein is very different from typical drug discovery efforts that often rely on screening of a single drug target to identify lead compounds. It is an attempt to advance a rational, predictable approach to drug disease-causing RNAs with small molecules. In this talk, we will describe various aspects of this technology. This includes the development of rapid screening assays to assess and score the binding of small molecules to RNA fold. By using this information and RNA secondary structure prediction, a target-agnostic approach is used to selectively drug an oncogenic RNA from sequence, providing in vivo modulators of oncogenic microRNAs.

2:05 Novel Antibiotics Targeting Bacterial Adenylation Enzymes

Derek S. Tan, Ph.D., Chairman, Member, and Tri-Institutional Professor, Chemical Biology Program, Memorial Sloan Kettering Cancer Center

Tuberculosis is a massive problem in global public health, estimated to infect one-third of the world population, with increasing incidence of multidrug resistance. Accordingly, there is an urgent need for new antibiotics with novel mechanisms of action. To address this problem, our laboratory is developing small-molecule inhibitors of bacterial adenylation enzymes that are involved in the biosynthesis of natural products required for growth and virulence of pathogenic bacteria such as Mycobacterium tuberculosis. We use a rational design platform that leverages mechanistic and structural information about these targets to develop novel sulfonyladenosine inhibitors. Among these is salicyl-AMS, a first-in-class inhibitor of bacterial siderophore biosynthesis, which exhibits in vivo efficacy in a mouse model of tuberculosis. 

2:35 Covalent Reversible Inhibition of Mcl-1 through Modification of a Non-Catalytic Lysine Side Chain

Qibin Su, Ph.D., Senior Scientist, Chemistry Department, Oncology iMED, AstraZeneca

Myeloid cell leukemia 1 (Mcl-1) has emerged as a key resistance factor in human cancers by antagonizing signals that would normally induce tumor cell death. Restoring apoptotic signals by inactivating Mcl-1 protein interactions will have widespread utility in cancer treatment. We report here the structure-based design, synthesis and evaluation of first potent, covalent inhibitors of Mcl-1 and specific targeting of a non-catalytic Lysine residue to modulate a protein-protein interaction. Our covalent binders will be useful as a starting point for the development of therapeutically relevant Mcl-1 inhibitors and as probes to interrogate Mcl-1 dependent cellular phenomena.

3:05 Refreshment Break

CHEMICAL PROTEOMICS AND QUANTITATIVE MASS SPECTROMETRY
IN DRUG DISCOVERY

3:20 Defining the Consequences of Genetic Variation on a Proteome-Wide Scale

Steven P. Gygi, Ph.D., Professor, Cell Biology, Harvard Medical School

Genetic variation can influence protein expression through transcriptional and post-transcriptional mechanisms. To characterize the consequences of genetic diversity on the proteome, we combined a multiplexed, mass spectrometry-based method for protein quantification with an emerging mouse model harboring extensive genetic variation from eight founder strains. We measured genome-wide transcript and protein expression in liver tissue of 192 Diversity Outbred (DO) mice. We observed nearly 3,700 protein quantitative trait loci (pQTL) with equal proportions of local and distant genetic variants that affect protein expression. Among other things, we demonstrate that genotype can provide accurate predictions of protein abundance; allelic effects derived from the DO population mirrored protein expression levels measured in the founder strains and were predictive of protein levels in an independent cohort of Collaborative Cross mice.

3:50 An In Vivo Multiplexed Screening Platform Identifies a Pro-Metastatic Factor in Pancreatic Cancer

Christopher Schulze, Ph.D., Postdoctoral Research Fellow, Pathology (Bogyo Lab), Stanford University School of Medicine

Phenotype-based small molecule screening is a powerful method to identify regulators of cellular function. However, such screens are generally performed in vitro using conditions that do not allow modeling of complex physiological conditions or disease states. Here, we report the development of a technology that uses molecular cell barcoding to enable direct in vivo phenotypic screening of libraries of small molecules. The multiplexed nature of this approach allows rapid in vivo analysis of hundreds to thousands of compounds. Using this platform, we screened >700 covalent inhibitors directed towards hydrolases for their effect on pancreatic cancer metastatic seeding. We identified multiple hits and confirmed the relevant target of one compound as the lipase ABHD6. Pharmacological and genetic studies confirmed the role of this enzyme as a regulator of metastatic fitness. Our results highlight the applicability of this multiplexed screening platform for investigating complex processes in vivo using a chemical biology approach.

4:20 Mass Spectrometry-Based Proteomics in Preclinical Drug Discovery

Hannes Hahne, Ph.D., CEO, OmicScouts GmbH

Preclinical stages in the drug discovery process require a multitude of biochemical and genetic assays in order to characterize the effects of drug candidates on cellular systems and model organisms. Dramatic technological improvements in mass spectrometry-based proteomic and chemical proteomic strategies substantially facilitate decision-making throughout the drug discovery process. Here, we highlight proteomic approaches such as phosphoproteomics and chemical proteomics as well as emerging technologies like proteome-wide Cellular Thermal Shift assays and bioinformatic approaches to study the complex interactions of genomes, proteomes and drugs. These case studies illustrate the potential of proteomics in preclinical drug discovery.

4:50 Close of Conference