Nathanael Gray

Professor of Biological Chemistry and Molecular Pharmacology

Dana Farber Cancer Institute
Longwood Center 2209
450 Brookline Ave.
Boston, MA 02115
Tel: 617-582-8590

Lab Size: Between 10 and 15

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. 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.

Galkin AV, Melnick JS, Kim S, Hood TL, Li N, Li L, Xia G, Steensma R, Chopiuk G, Jiang J, Wan Y, Ding P, Liu Y, Sun F, Schultz PG, Gray NS, Warmuth M. Identification of NVP-TAE684, a potent, selective, and efficacious inhibitor of NPM-ALK. Proc Natl Acad Sci U S A 2007;104:270-5.

Pan S, Mi Y, Pally C, Beerli C, Chen A, Guerini D, Hinterding K, Nuesslein-Hildesheim B, Tuntland T, Lefebvre S, Liu Y, Gao W, Chu A, Brinkmann V, Bruns C, Streiff M, Cannet C, Cooke N, Gray N. A monoselective sphingosine-1-phosphate receptor-1 agonist prevents allograft rejection in a stringent rat heart transplantation model. Chem Biol 2006;13:1227-34.

Okram B, Nagle A, Adrian FJ, Lee C, Ren P, Wang X, Sim T, Xie Y, Wang X, Xia G, Spraggon G, Warmuth M, Liu Y, Gray NS. A general strategy for creating 'inactive-conformation' abl inhibitors. Chem Biol 2006;13:779-86.

Liu Y, Gray NS. Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2006;2:358-64.