Phenotypic Screening and Chemical Biology

Chemical biology has rapidly emerged as a cost-effective yet powerful preclinical approach for the discovery and identification of novel drugs and targets. Advances in the development and combination of high-quality chemical tools, bio-orthogonal techniques, disease-relevant models, proteomics and quantitative mass spectrometry 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 Phenotypic Screening and Chemical Biology conference will once again gather an interdisciplinary collection of leaders to discuss these emerging tools and strategies to de-risk novel discovery initiatives.

Final Agenda

Tuesday, June 13

7:00 am Registration Open and Morning Coffee


8:25 Chairperson’s Opening Remarks

Matt Lucas, Ph.D., Director, Medicinal Chemistry, Yumanity Therapeutics

8:35 Yeast-Based Phenotypic Screening to Identify Brain Penetrant Inhibitors

Matt_LucasMatt Lucas, Ph.D., Director, Medicinal Chemistry, Yumanity Therapeutics

Phenotypic screening has undergone a revival in the last decade. In this presentation, I will share some of our learnings from Yumanity’s phenotypic screening platform to bias towards the identificatation of scaffolds that are brain penetrant with potential utility to treat protein misfolding diseases.

9:05 Phenotypic Drug Discovery in SMA: Parallel Efforts in Preclinical Development and Target Identification

Atwood Cheung, Ph.D., Investigator III, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Inc. 

Phenotypic drug discovery has been a mainstay of drug development, enabling the discovery of numerous therapeutic molecules. A key challenge, however, has always been the determination of the efficacy target. A recent success story will be presented, where our team progressed a small-molecule preclinical candidate to treat Spinal Muscular Atrophy (SMA) while simultaneously elucidating the molecular mechanism of action.

9:35 Massive Parallelization of Rare Disease Drug Discovery

Ronald Alfa, Ph.D., Director, Translational Biology, Recursion Pharmaceuticals

I will discuss methods to leverage computational biology to perform phenotypic screens in parallel for discovery of therapeutic candidates for dozens of rare genetic diseases.

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


10:50 Linking High-Throughput Screens to Identify MOAs and Novel Inhibitors of Mycobacterium Tuberculosis Dihydrofolate Reductase

John Santa Maria, Ph.D., Research Fellow, Cheminformatics, Merck

I describe a framework for joining high-throughput phenotypic and target-based data coupled with machine learning to identify efficacy targets of bioactive compounds. We validate this approach on data from a set of 55,000 compounds in 24 historical Merck antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Our models revealed relationships between phenotype, target, and chemotype and recapitulated mechanisms for known antibacterials.

11:20 Chemical Biology Informatic Approaches to Enable High-Throughput Screening: Focused Compounds Sets, Target Enrichment, and Hit Expansion

Peter_KutchukianPeter Kutchukian, Ph.D., Associate Principal Scientist, Cheminformatics, Merck

A suite of integrated data repositories and tools have been developed to empower phenotypic screening at our company. A chemogenomics database CHEMGENIE that captures compound-target interactions has been implemented by integrating and harmonizing internal and external data sources, and an algorithm to identify tool compounds has been designed to harness this information. We describe use cases of screening such tools in phenotypic screens, and the ability to identify targets and pathways that perturb a phenotype through “target enrichment”.

11:50 Kinome-Wide Profiling of Target Engagement and Residence Time in Living Cells Using NanoBRET

Matthew Robers, Senior Research Scientist, Research & Development, Promega Corporation

NanoBRET is the first technology enabling quantitative, real-time assessment of intracellular compound engagement without disruption of cell membrane integrity. NanoBRET enables profiling of intracellular selectivity for clinically relevant kinase inhibitors against >200 selected full-length protein kinases. Of note, residence time analysis via NanoBRET reveals surprisingly durable binding for various tyrosine kinase inhibitors in living cells.

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

12:50 Session Break


1:40 Chairperson’s Remarks

Ceren Korkut, Ph.D., Scientist, Chemical Biology, Biogen

1:50 What Is Your MOA? Target Deconvolution of a Phenotypic Screen

Ceren Korkut, Ph.D., 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.

2:20 Selective Downregulation of JAK2 and JAK3 by an ATP-Competitive Pan-JAK Inhibitor

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

PF-956980 has been used previously as a JAK3-selective chemical probe in numerous cell-based experiments. Here, we report that not only is PF-956980 a pan-JAK ATP-competitive inhibitor but it also causes selective reduction of endogenous JAK2 and JAK3 protein levels in human primary immune cells (in a time-dependent manner), leaving the other JAK family members (JAK1 and TYK2) unchanged. We found that PF-956980 selectively downregulated JAK2 and JAK3 mRNA, corresponding to changes observed at the protein level. This work highlights therapeutic opportunities for the development of pharmacological inhibitors that also modulate the expression of their cognate binding proteins.

Psycho Genics2:50 High Throughput In Vivo Phenotypic Drug Discovery

Emer LeahyEmer Leahy, Ph.D., President & CEO, PsychoGenics Inc.

PsychoGenics’ phenotypic screening approach employs SmartCube®, an in vivo, high throughput, behavioral testing platform that combines robotics, computer vision, and machine learning algorithms to capture and analyze data that can be distilled into a “behavioral signature” for a compound. Working in partnership with pharmaceutical/biotech companies, PsychoGenics has been instrumental in identifying therapeutic potential for novel first-in-class compounds resulting in several compounds now in clinical trials or advanced preclinical development.

3:20 Refreshment Break in the Exhibit Hall with Poster Viewing

4:05 New Chemical Biology Technologies for Target Identification and High-Throughput Screening: Chemical Glycobiology and Beyond

Henning Stockmann, Ph.D., Senior Scientist, Chemical Biology, AbbVie Inc.

Improved strategies for reliable drug target identification and target engagement studies are urgently needed, whereby cell-surface receptors present particular challenges. We have developed new chemical biology approaches to link probes and reporters to cell-surface receptors and cytosolic proteins in live cells. Our sugar-based cell-surface engineering methods not only enable receptor visualization, isolation, and proteomics-based characterization, but also facilitate target engagement studies and high-throughput ligand binding assays in intact cells.

4:35 Prioritizing Chemical Tool Compounds for Phenotypic Drug Discovery

Yuan_WangYuan Wang, Ph.D., Investigator III, Chemical Biology & Therapeutics, 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. The identified selective and non-selective tool compounds have applications in phenotypic assays for target hypothesis validation as well as assay development, and are included in the Novartis MOA box.

5:05 Chemical Synthesis of Activity Based Probes and Inhibitors

Ian Foe, Ph.D., Research Scientist, Bogyo Lab, Department of Pathology, Stanford University School of Medicine

5:35 Welcome Reception in the Exhibit Hall with Poster Viewing

6:45 Close of Day

Wednesday, June 14

7:00 am Registration Open

7:30 Interactive Breakout Discussion Groups with Continental Breakfast

This session features various discussion groups that are led by a moderator/s who ensures focused conversations around the key issues listed. Attendees choose to join a specific group and the small, informal setting facilitates sharing of ideas and active networking. Continental breakfast is available for all participants.

Recent Advances and Hurdles in Phenotypic Screening and Target Discovery  


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

Ceren Korkut, Ph.D., Scientist, Biogen

  • 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

Uncovering Current Challenges and Technical Limitations in Chemical Proteomics

Moderator to be Announced

  • What is the accessible target space, what can be covered with these techniques and what are we missing?
  • Target and off-target engagement in live primary cells and tissues, aren’t we there yet?
  • Impact of chemical proteomics on toxicology, and safety predictions
  • The challenge of linking the binding of a drug to a target or off-target to a clinical, toxicological, cellular phenotype



8:35 Chairperson’s Remarks

Kieran F. Geoghegan, Ph.D., Research Fellow, Pfizer Worldwide Research

8:45 A Probe-Centered Analysis of γ-Secretase Photolabeling Reveals the Binding Site of Avagacestat

Kieran_GeogheganKieran F. Geoghegan, Ph.D., Research Fellow, Pfizer Worldwide Research

Photoaffinity labeling frequently identifies the protein targets of drugs, but specifying their binding sites by this method is challenging. In photolabeling γ-secretase, a target in Alzheimer's disease, our previous efforts to detect probe-labeled peptides were unsuccessful. Reconsideration of the chromatographic properties of our probes led us to design benzophenone derivatives of the clinical candidate avagacestat incorporating a cleavable link between the photoprobe and biotin. The intention was to minimize the hydrophobicity of labeled peptides. Competition effects showed that γ-secretase was selectively photolabeled, and proteomic LC-MS detected a peptide derivatized at Leu-282 of presenilin-1. The results indicated that avagacestat binds near the enzyme's active site, were supported by results from molecular dynamics, and aligned well with emerging data from cryo-electron microscopy.

9:15 Selected Poster Presentation: HepatoPearls: 3D Liver Micro-Tissues for High-Throughput Drug-Drug Interaction Assays

Raif Eren Ayata, Ph.D., MSc, Topical Drug Delivery/Formulations and Percutaneous Absorption Specialist & Postdoctoral Fellow, Skin/Liver Tissue Engineering, PSL Research University

9:30 Selected Poster Presentation: Validation of a Cellular BRET Platform Using the Bruton's Tyrosine Kinase Model System for High-Throughput Cellular Target Engagement and Residence Time

Charu Chaudhry, Ph.D., Senior Research Investigator, Mechanistic Biochemistry, Lead Discovery & Optimization, Bristol-Myers Squibb

10:15 Coffee Break in the Exhibit Hall with Poster Viewing

11:00 Proteomics-Based Methods for In-Depth Analysis of Key Molecular Events in Tumorogenesis

Jarrod Marto, Ph.D., Associate Professor, Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute

Proteomics-based methods provide a highly parallel readout of multiple biologically relevant events in a single experiment. Collectively, these data provide a detailed view of key molecular mechanisms in cancer initiation and progression and can also facilitate drug target discovery and improved characterization of small molecule-based therapeutics.

11:30 CASE STUDY: Chemical Biology Tools for Target Identification and Target Engagement Studies

Hua Xu, Ph.D., Principal Scientist, Pfizer

Phenotypic screening is a major source for the discovery of first-in-class small molecule drugs, thanks to its ‘target agnostic’ feature. Recent technology advances and utilization of patient-derived cells have facilitated the design of sophisticated phenotypic assays that recapitulate the disease relevant biology. However, it remains quite challenging to elucidate the mechanism of action and identify the target(s) for compounds of interest from these assays. In this talk, I will present our efforts to use various tools to identify and subsequently validate the target for a phenotypic program.

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


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

4:15 Close of Conference

Download Brochure