Probing Cell Death Mechanisms with Small Molecules and Genomics Tools

  • Genetic-like Screens with Small Molecules and Genomic Reagents
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Approach: The Stockwell lab sits at the interface of chemistry and biology and is systematically using small molecules to discover mechanisms underlying cellular processes. Our approach is interdisciplinary, combining chemical design and synthesis with genomics, biochemistry and cell biology, with the ultimate goal of revealing new basic biological mechanisms and disease pathophysiology. (Click top-right corner of each figure to enlarge.)

Discovery of Genotype-Selective Anti-Tumor Agents: Towards Personalized Cancer Therapy

  • Personalized Cancer Therapy
  • RAS-selective lethal (RSL) compounds
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We have sought to design small molecules that are programmed to be lethal to tumor cells of a specific genotype. We refer to such compounds as “genotype-selective compounds”. One approach is to use synthetic lethal screening, so named by analogy to model organism synthetic lethal screens. Such compounds have increased potency and activity in the presence of specific genetic alterations. We have screened more than a million compounds for synthetic lethality with oncogenic RAS, and have identified two compounds: erastin and RSL3. We are pursuing the mechanism of action of these compounds and translating them into potential therapeutic agents.

New Small Molecule Design Approaches to Tackle Undruggable Proteins

  • 15% of Proteins Potentially Druggable
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We are developing in silico design strategies, coupled with biophysical, biochemical, cell-based assays and in vivo models to discover small molecules that target intractable proteins previously viewed as undruggable. Only 15% of human proteins are considered viable targets of small molecules (druggable). By tackling these undruggable protein families, we can significantly expand the range of targets for drug discovery and potentially impact currently incurable diseases.

Probing Cell Death in Neurodegeneration

  • What is the mechanism connecting protein misfolding to neuronal cell death?
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Cell death mechanisms are poorly defined in neurodegeneration, which is often caused by mis-folded proteins. In the case of Huntington Disease (HD), expansion of a CAG repeat in the huntingtin gene causes expression of a polyglutamine (polyQ)-containing protein that mis-folds. Mutant-huntingtin-induced cell death involves, at least in part, apoptotic death. Expression of mutant huntingtin causes apoptosis in cells, in mouse and nematode HD models, and in HD patients. We have discovered small molecules that block cell death in models of neurodegeneration and are exploring these compounds both as mechanistic probes and as potential therapeutic agents.

Other technologies

  • Other ongoing research in the Stockwell Lab
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We have also pioneered methods for screening compounds in cell-based and in vitro assays and for defining the mechanism of action of active compounds: we created, with our collaborators, a polymer-based microarray screening system for cell-based assays1, methods of testing millions of pairwise combinations of compounds2,3, a synthetic lethal screening system using engineered human tumor cells 4 , the first library of thousands of biologically active, annotated compounds for revealing mechanisms underlying cellular phenotypes5 , and a genome-wide RNAi collection6. Because purification of target proteins for moderate potency compounds is challenging; we are developing a photolabeling strategy to identify such target proteins7. We have focused on using these tools to reveal proteins and pathways involved in cancer and neurodegeneration.

 Reference

  1. Bailey SN, Sabatini DM, Stockwell BR. Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens. Proc Natl Acad Sci USA 2004 Nov;101(46):16144 -16149. [pubmedpdf]

  2. Borisy AA, Elliott PJ, Hurst NW, Lee MS, Lehár J, Price ER, Serbedzija G, Zimmermann GR, Foley MA, Stockwell BR, Keith CT. Systematic discovery of multicomponent therapeutics. Proc Natl Acad Sci USA 2003 Jun;100(13):7977 -7982. [pubmedpdf]

  3. Keith CT, Borisy AA, Stockwell BR. Multicomponent therapeutics for networked systems. Nat Rev Drug Discov 2005 Jan;4(1):71-78. [pubmedpdf]

  4. Dolma S, Lessnick SL, Hahn WC, Stockwell BR. Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells. Cancer Cell 2003 Mar;3(3):285-296. [pubmedpdf]

  5. Root DE, Flaherty SP, Kelley BP, Stockwell BR. Biological Mechanism Profiling Using an Annotated Compound Library. Chemistry & Biology 2003;10(9):881-892. [pubmedpdf]

  6. Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK. A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen. Cell 2006;124(6):1283-1298. [pubmedpdf]

  7. Smukste I, Bhalala O, Persico M, Stockwell BR. Using small molecules to overcome drug resistance induced by a viral oncogene. Cancer Cell 2006;9(2):133-146. [pubmedpdf]