Probing Cell Death Mechanisms with Small Molecules and Genomics Tools
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.
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.
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.
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.
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.