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The Skaggs Institute
for Chemical Biology

Scientific Report 2008

Chemical Physiology

B.F. Cravatt, D. Bachovchin, J. Blankman, M. Dix, S. Ji, F. Kopp, W. Li, J. Long, B. Martin, K. Masuda, M. McKinney, D. Nomura, G. Simon, J. Thomas, S. Tully, E. Weerapana

We are interested in understanding complex physiology and behavior at the level of chemistry and molecules. At the center of cross talk between different physiologic processes are endogenous compounds that provide a molecular mode for intersystem communication. However, many of these molecular messages remain unknown, and even in the instances in which the participating molecules have been defined, the mechanisms by which these compounds function and their modes of regulation are for the most part still a mystery.

One family of chemical messengers we study is the endogenous cannabinoids ("endocannabinoids"), a class of lipid signaling molecules that activate cannabinoid receptors in the nervous system and peripheral tissues. The levels and signaling function of endocannabinoids are tightly regulated by enzymes to maintain proper control over the influence of the endocannabinoids on brain and body physiology. One of our major goals is to identify endocannabinoid biosynthetic and degradative enzymes and develop selective genetic and pharmacologic tools to perturb the function of these enzymes in vivo. An example is fatty acid amide hydrolase (FAAH), which terminates the signaling function of the endocannabinoid anandamide, as well as several other amidated lipid transmitters.

We are using transgenic and synthetic chemistry techniques to study the role of FAAH in regulating fatty acid amide levels in vivo. We found that transgenic mice that lack FAAH have highly elevated levels of fatty acid amide in the brain that correlate with reduced pain behavior, suggesting that FAAH may be a new therapeutic target for the treatment of pain and related neural disorders. In collaboration with R.C. Stevens, Scripps Research, we solved the first 3-dimensional structure of FAAH. We are using this information to design potent and selective inhibitors of the enzyme. In studies with D.L. Boger, the Skaggs Institute, we have identified potent FAAH inhibitors and using a functional proteomic screen developed by us, have shown that these inhibitors are highly selective for this enzyme. We are also interested in proteins responsible for the biosynthesis of endocannabinoids.

A second major focus in the laboratory is the design and use of chemical probes for the global analysis of protein function. The evolving field of proteomics, defined as the simultaneous analysis of the complete protein content of a given cell or tissue, encompasses considerable conceptual and technical challenges. We hope to enhance the quality of information obtained from proteomics experiments by using chemical probes that indicate the collective catalytic activities of entire classes of enzymes. Using activity-based probes that target the serine and metallo hydrolases, we have identified several enzymes with altered activities in human cancers. Using a combination of pharmacologic and molecular biology approaches, we are now testing the role that these enzymes play in cancer pathogenesis.

Finally, we are developing proteomic and metabolomic platforms to map endogenous substrates of enzymes in native biological systems. These large-scale technologies are intended to provide a global, unbiased portrait of the physiologic activities of enzymes, thereby aiding in the functional annotation and assessment of the enzymes as potential therapeutic targets for a range of human diseases.


Ahn, K., Johnson, D.S., Fitzgerald, L.R., Liimatta, M., Arendse, A., Stevenson, T., Lund, E.T., Nugent, R.A., Nomanbhoy, T.K., Alexander, J.P., Cravatt, B.F. Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity. Biochemistry 46:13019, 2007.

Ahn, K., McKinney, M.K., Cravatt, B.F. Enzymatic pathways that regulate endocannabinoid signaling in the nervous system. Chem. Rev. 108:1687, 2008.

Blankman, J.L., Simon, G.M. Cravatt, B.F. A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol. Chem. Biol. 14:1347, 2007.

Carlson, E.E., Cravatt, B.F. Enrichment tags for enhanced-resolution profiling of the polar metabolome. J. Am. Chem. Soc. 129:15780, 2007.

Cravatt, B.F., Simon, G.M., Yates, J.R. III. The biological impact of mass-spectrometry-based proteomics. Nature 450:991, 2007.

Cravatt, B.F., Wright, A.T., Kozarich, J.W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77:383, 2008.

Dix, M.M., Simon, G.M., Cravatt, B.F. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 134:679, 2008.

Salisbury, C.M., Cravatt, B.F. Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes. J. Am. Chem. Soc. 130:2184, 2008.

Simon, G.M., Cravatt, B.F. Anandamide biosynthesis catalyzed by the phosphodiesterase GDE1 and detection of glycerophospho-N-acyl ethanolamine precursors in mouse brain. J. Biol. Chem. 283:9341, 2008.

Weerapana, E., Simon, G.M., Cravatt, B.F. Disparate proteome reactivity profiles of carbon electrophiles. Nat. Chem. Biol. 4:405, 2008.


Benjamin F. Cravatt, Ph.D.
Director, Helen L. Dorris Child and Adolescent Neuro-Psychiatric Disorder Institute

Cravatt Web Site