• Researcher Profile

    Nathanael Gray, PhD

     
    Nathanael Gray, PhD
     
    Professor of Biological Chemistry and Molecular Pharmacology, Harvard Medical School

    Office phone: 617-582-8590
    Fax: 617-582-8615
    Email: nathanael_gray@dfci.harvard.edu
    Website: Gray Laboratory

    Preferred contact method: email
     
     

    Research Department

    Cancer Biology

    Area of Research

    Synthetic Chemistry/Functional Small Molecule Discovery

    Dana-Farber Cancer Institute
    450 Brookline Avenue
    Seeley G. Mudd 628A
    Boston, MA 02215

    Biography

    Nathanael Gray received his PhD in chemistry from the University of California at Berkeley in 1999. He then moved to the Genomics Institute of the Novartis Research Foundation in San Diego, where after serving as a staff scientist and group leader of kinase inhibitor chemistry, he was named director of biological chemistry in 2001. Dr. Gray recently joined the faculty of Harvard Medical School and DFCI to continue his research using synthetic chemistry and functional small molecule discovery to modulate biological pathways important in cancer.

    Research

    Synthetic Chemistry/Functional Small Molecule Discovery

    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. For more information, please visit our Web site at http://research.dfci.harvard.edu/gray_lab/home.htm.

    Select Publications

    • 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.
    • Melnick JS, Janes J, Kim S, Chang JY, Sipes DG, Gunderson D, Jarnes L, Matzen JT, Garcia ME, Hood TL, Beigi R, Xia G, Harig RA, Asatryan H, Yan SF, Zhou Y, Gu XJ, Saadat A, Zhou V, King FJ, Shaw CM, Su AI, Downs R, Gray NS, Schultz PG, Warmuth M, Caldwell JS. An efficient rapid system for profiling the cellular activities of molecular libraries. Proc Natl Acad Sci USA 2006;103:3153-8.
    • Adrian FJ, Ding Q, Sim T, Velentza A, Sloan C, Liu Y, Zhang G, Hur W, Ding S, Manley P, Mestan J, Fabbro D, Gray NS. Allosteric inhibitors of Bcr-abl-dependent cell proliferation. Nat Chem Biol 2006;2:95-102.
    • Han S, Zhou V, Pan S, Liu Y, Hornsby M, McMullan D, Klock HE, Haugen J, Lesley SA, Gray N, Caldwell J, Gu XJ. Identification of coumarin derivatives as a novel class of allosteric MEK1 inhibitors. Bioorg Med Chem Lett 2005;15:5467-73.
    • 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;11:247-59.
    • Wignall SM, Gray NS, Chang YT, Juarez L, Jacob R, Burlingame A, Schultz PG, Heald R. Identification of a novel protein regulating microtubule stability through a chemical approach. Chem Biol 2004;11:135-46.
    • Sanna MG, Liao J, Jo E, Alfonso C, Ahn MY, Peterson MS, Webb B, Lefebvre S, Chun J, Gray N, Rosen H. Sphingosine 1-phosphate (S1P) receptor subtypes S1P1 and S1P3, respectively, regulate lymphocyte recirculation and heart rate. J Biol Chem 2004;279:13839-48.

    Trainees

    • Choi, Yongmun, PhD
    • Deng, Xian-Ming, PhD
    • Miduturu, Chandrasekhar, PhD
    • Sim, Taebo, PhD
    • Zhang, Jianming, PhD
    • Zhou, Wenjun, PhD
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