Bridging the fields of chemistry and biology, Benjamin Cravatt and his research group have developed and applied technologies to discover biochemical pathways in mammalian biology and disease. Cravatt, who was elected to the National Academy of Sciences in 2014 and is chair of the Department of Chemical Physiology at The Scripps Research Institute, pioneered an approach to identify protein classes based on their activity. Since the introduction of the approach in 1999, Cravatt’s group has used this and related chemical proteomic technologies to conduct global analyses of protein activities and to elucidate the functions of several enzymes, including those linked to human cancers, neurological disorders, and the endocannabinoid system, which consists of lipid transmitters involved in appetite, pain sensation, mood, memory, and other physiological processes.
Benjamin Cravatt. Image courtesy of TSRI BioMedical Graphics.
From the outset, Cravatt was inspired to think about biology by his dentist father and dental hygienist mother. He also credits his high school mathematics teachers for nurturing his interest in the quantitative sciences. “These individuals made subjects like calculus interesting and relatable to the young mind,” Cravatt says. “They also challenged me to extend beyond my comfort zone in my education, which helped me gain confidence in my abilities.”
In 1988, Cravatt entered Stanford University with the aim of studying medicine. That goal began to change, however, when he studied under chemist John Griffin, now the chief scientific officer of the biotech company Numerate. Cravatt explains, “I had a great undergraduate research experience in John Griffin’s lab, and this certainly set me on a trajectory to pursue research at the interface of biology and chemistry.” Cravatt graduated in 1992 with bachelor’s degrees in biological sciences and history. He then earned his doctorate in macromolecular and cellular structure and chemistry at The Scripps Research Institute in 1996. That same year, he became an assistant professor. Cravatt says, “I started at Scripps, and never looked back.”
In 1996 Cravatt and his colleagues authored an influential paper concerning a key enzyme, FAAH, which is involved in the endocannabinoid system (1). Cravatt says he spent much of the last two years of graduate school in a laboratory cold room purifying the FAAH enzyme to sufficient homogeneity for its molecular characterization. “There were many days where I doubted whether I would succeed in the project, but the hard work ultimately paid off,” he says. “FAAH became the first of several important enzymes that have been discovered to regulate endocannabinoid metabolism and signaling in the mammalian brain, some of which are potential drug targets to treat human disease.”
The work of Cravatt and his colleagues on the endocannabinoid system led to interest in the then-nascent field of chemical proteomics, a multidisciplinary science that aims to develop and apply chemical tools to annotate the functions of proteins like FAAH within their native biological environment. Cravatt credits two major technological advances for laying the foundations of the field: DNA sequencing, which provided a near-complete molecular parts-list encoded by an organism’s genome, and the introduction of mass spectrometry instruments with remarkable accuracy and resolution. Cravatt also notes the achievements of his colleague John Yates, who developed a search algorithm called SEQUEST, which allows in-depth analysis of entire sets of proteins in a mass spectrometry-based proteomics experiment.
The chemical proteomic technology Activity-Based Protein Profiling (ABPP), pioneered by Cravatt and colleagues (2), employs chemical probes to directly measure enzyme function. For example, a fluorescent label may be used to tag enzymes with certain chemical properties, allowing researchers to survey all active enzymes in a cell at once. ABPP thus enables enrichment and identification of large classes of mechanistically related proteins directly from native biological systems. “The ABPP method has grown to be quite useful for protein and inhibitor discovery,” Cravatt says. In 2010, for example, Cravatt and colleagues used ABPP to investigate cysteines, which are amino acids that represent one of the 20 building blocks of protein (3). The researchers discovered that the intrinsic reactivity of cysteine residues varies greatly across the proteome. They further determined that cysteines with high reactivity are much more likely to perform important functions in cells.
Cravatt’s team, again working with native biological systems, has also shown that untargeted mass spectrometry methods can be used to discover natural substrates for enzymes (4, 5). In the past, such research would have been more commonly conducted in artificially reconstituted test-tube settings. “I have always been interested in unbiased, data-driven approaches to research,” Cravatt says.
ABPP has also provided functional insights into the burgeoning connections being made between human genome sequences and disease. Cravatt says, “Advances in DNA sequencing technologies are propelling us into an age where virtually all Mendelian genetic disorders [meaning rare diseases caused by a mutation in a single gene, such as sickle-cell anemia and cystic fibrosis] will be mapped to their causative mutational basis. However, many of these mutations occur in genes that code for proteins of uncharacterized function.”
To address the conundrum, Cravatt and his team have combined ABPP with metabolomics—the measurement and analysis of metabolites, such as sugars and fats—to study rare neurological disorders caused by mutations in poorly characterized enzymes (6, 7). The researchers were able to determine the biochemical functions of these enzymes in the brain, providing insights into disease mechanism and potential treatment strategies.
Such successful innovative research approaches have earned Cravatt several awards, including Technology Review’s TR100 Top 100 Young Innovators Award (2002), the Eli Lilly Award in Biological Chemistry, American Chemical Society (2004), the ASBMB-Merck Award (2014), and the Sato Memorial International Award, Pharmaceutical Society of Japan (2015). In 2009, Cravatt was granted a MERIT award from the National Cancer Institute in recognition of the important contributions that ABPP technologies have made to characterizing deregulated enzyme activities, as well as the drugs that target these enzymes, in cancer.
Cravatt and his team have more recently adapted their chemical proteomic methods to construct a global map of lipid-binding proteins and the drugs that interact with these proteins (8). To do so, they once again used ABPP, but in this case constructed chemical probes that resemble natural bioactive lipids conjugated to a photoreactive group to trap interacting proteins in cells upon exposure to light. The method provided a broad and deep portrait of lipid-binding proteins in human cells, and the resulting map not only shed light on the functions of lipid-binding proteins, but also helped profile the activities of drug compounds by revealing how they may interfere with lipid–protein binding events.
Cravatt’s Inaugural Article (9) investigates the function of enzymes called diacylglycerol lipases (DAGLs), which regulate the production of endocannabinoids. Understanding the full spectrum of functions for DAGL-endocannabinoid pathways, however, requires selective inhibitors to perturb these pathways in cell and animal models. “Our findings with DAGL inhibitors revealed that these enzymes make key contributions to a much larger brain lipid network that includes not only endocannabinoids, but also eicosanoids and other signaling lipids,” Cravatt says. “Consequently, blocking DAGLs impairs neuroinflammatory processes in vivo, suggesting that inhibitors of these enzymes may be useful for treating neurological disorders that have a strong inflammatory underpinning, such as neurodegeneration and autoimmune disorders of the central nervous system.”
Although Cravatt’s work holds tremendous potential for the creation of novel, effective treatments for many diseases, his laboratory does not select proteins for investigation based on therapeutic interest per se, but rather based on their potential relevance to human biology and disease. “This may seem like a subtle distinction, but it is not. I believe that gaining a fundamental understanding of a protein’s function will, by default, lead thoughtful and creative scientists to potential therapeutic strategies for treating disorders connected to that protein.”
Cravatt also says that he is a firm believer that technological advances pave the way for leaps in scientific discovery and understanding. He says, “Our lab feels very fortunate to live in an era where the genetics of human disease is being illuminated with such precision and completeness, as this knowledge base becomes a major source for our prioritization of poorly characterized proteins for functional investigation.”
This is a Profile of a recently elected member of the National Academy of Sciences to accompany the member’s Inaugural Article on page 26 in issue 1 of volume 113.
