Department of
Biological Chemistry & Molecular Pharmacology

Nathanael Gray

Seeley G. Mudd Bldg., 628A
250 Longwood Ave.
Boston MA 02115

Our lab is interested in the following general questions: 1. How can small molecule inhibitors with selectivity towards a desired wild-type or drug-resistant kinase be efficiently developed? 2. How can we use kinase inhibitors to dissect the molecular wiring of signaling pathways? 3. What are the most efficient ways to develop small molecule modulators for protein targets for which no ligand is currently known? 4. How do you develop a small molecule modulator for biological pathways for which very little is known? 5. What are new methods for identifying the biological targets for small molecules of unknown mechanism?

Synthetic Chemistry: Our lab uses synthetic organic chemistry to make combinatorial gene-family targeted libraries. We typically base the libraries on close variants of scaffolds that have been previously shown to have interesting biological activity (so called "privileged scaffolds"). We use solution and solid-phase chemistry and employ "directed-sorting" technology to enable efficient library production. We also perform medicinal chemistry to improve the potency, cellular activity, specificity, stability and pharmacological properties of our initial "lead" compounds.

Functional Small Molecule Discovery: Following synthesis of new compounds, we use three distinct but complementary approaches to discover and optimize their biological function: (1) target-based biochemical screening (2) functional target-based cellular assays and (3) cellular or organismal "phenotypic" screening. Target-based screening supported by cellular assays that precisely monitor the activity of interest and that can guide chemical optimization is the most direct means to obtain functional inhibitors. The target-based cellular screens present a significant advantage over biochemical assays because the kinases are expressed in an appropriate cellular context allowing compounds to be identified that may possess a number of distinct mechanisms including: direct inhibition of the active kinase, binding to the inactive form of the kinase, inhibiting activating phosphorylations, or interacting with negative regulators. We are in the process of creating a battery of such cellular assays that will allow us to more fully annotate the kinase selectivity of a given compound which can then be used as a chemical probe in various biological systems. We have used target-based enzymatic and cellular screening to develop cyclin-dependent kinase inhibitors (purvalanols), tubulin depolymerizers (myoseverins), kinase inhibitors selective for plasmodial kinases (with potential application as antimalarials), selective agonists of sphingosine-1-phosphate receptors (SEW02871), and a large variety of tyrosine kinase inhibitors (Abl, Src, PDGFR, FLT3, c-Kit, Ephrins, EGFR, etc). In contrast, phenotypic screening provides a means to interrogate a pathway in an unbiased fashion with small molecules. Provided that the molecular target(s) of the compound can be identified (usually by affinity chromatography, genetic complementation, or expression profiling), phenotypic screening can deliver new biological insight in addition to yielding useful small molecules. We have used phenotypic screening to identify a small molecule (diminutol) capable of inducing a shrunken mitotic spindle phenotype in Xenopus extracts and used the compound to identify the potential target as a ubiquinone oxidoreductase (Nqo1). We have also identified small molecules capable of inducing cardiomyogenesis, compounds that are agonists(purmorphamine) and antagonist of the hedgehog and Wnt signaling pathways, and compounds that can induce keratinocyte differentiation.

1. Wan Y, Hur W, Cho CY, Liu Y, Adrian FJ, Lozach O, Bach S, Mayer T, Fabbro D, Meijer L, Gray NS*: Synthesis and target identification of hymenialdisine analogs. Chem Biol. 2004 , 11(2): 247-59.

2. Ding S, Gray NS*, Wu X, Ding Q, Schultz PG*: A combinatorial scaffold approach toward kinase-directed heterocycle libraries. J Am Chem Soc. 2002, 124 : 1594-1596.

3. Gray NS, Wodicka L, Thunnissen AM, Norman TC, Kwon S, Espinoza FH, Morgan DO, Barnes G, LeClerc S, Meijer L, Kim SH, Lockhart DJ, Schultz PG*: Exploiting Chemical Libraries, Structure, and Genomics in the Search for New Kinase Inhibitors. Science . 1998, 281 : 533-538.