The Enzyme Detective
Daniel Nomura Fights Disease by Manipulating Metabolism
“Cancer is the ultimate form of evolution,” Daniel Nomura said one day after we’d been talking about a news-making breakthrough he made back in 2010 in the potential treatment of that insidious disease. “Cancer cells are very smart. And there’s an elegance in the way they adapt so quickly.” For an instant he sounded like a World War I flyer, ever the gentleman, speaking respectfully of his enemy even after a murderous day in the sky.
If Nomura, an assistant professor who joined the Nutritional Sciences and Toxicology faculty in the fall of 2011, is respectful of cancer, he’s awestruck by the mysteries of his field — by the great unknown of how the body’s nearly infinite metabolic pathways work and are connected, especially those that were discovered, but not defined, with the sequencing of the human genome.
The focus of his work is how metabolism functions in disease. In a paper published in Science this past October, Nomura showed that blocking a particular enzyme — the same one he found to be effective in slowing cancer-cell growth — also suppresses brain inflammation and protects against neurodegeneration. The implications are vast.
“We’re talking about the potential for a drug that might act like a combination of marijuana and aspirin,” says Nomura, “but without the psychological side effects of cannabis and without the withering effect of aspirin on the lining of the gastrointestinal system.”
Applications may be able to stop or slow neuro-degenerative diseases as Parkinson’s — and there may well be others not yet apparent.
A Big View of an Infinitesimal World
Nomura, 30, received his B.A. in molecular and cell biology in 2003 from Berkeley, and his Ph.D. in molecular toxicology in 2008, from the same department where he now teaches. He is, strictly speaking, a chemical biologist, but he would rather be thought of as a chemical physiologist. The difference is one of scope: Nomura and his lab are focused not only on the properties and behaviors of molecules but of entire physiological systems — “the whole body,” as he puts it.
Nomura uses technology as a “theory-generating tool,” to narrow the possibilities in an area that's nearly infinite.
“And that’s the way I do science; I try to think of things in a macro way. I always look at the bigger picture, and of course all of our technologies are designed to look at the bigger picture.”
This bigger picture is of the infinitesimal world of molecular compounds, life’s most fundamental material — sugars, fats, acids, and other biological molecules — all caught in an endless drama of convolution and conversion, in among metabolic pathways, those hothouses of chemical reaction.
Imagine a single metabolic pathway as a long string of falling dominoes, a Rube Goldberg contraption using molecules. Every few feet, a falling string reaches a hub — call that an enzyme — which triggers another string to fall and then another and another, on and on, and each string is slightly different from the one before as it passes through these hubs. There might be 40 strings in a pathway, and at the very end, the last domino has a new identity and a different function from the domino at the beginning of the process.
To complete the rough metaphor, this last domino, with its new function, naturally affects other strings of dominoes. But now the result may be that a new string of dominoes stands up rather than falls down, which in turn sets off other reactions, accumulations, and conversions.
Nomura found that in a mouse model of Parkinson’s disease, when MAGL was blocked, the mice were protected against neurodegeneration and dopamine loss.
What Nomura is doing is trying to change the effect of particular pathways that cause inflammation in the brain, which is associated with many neurodegenerative diseases. In what might one day become the news story of the year, Nomura and his team have found a novel way to control brain inflammation, by using an inhibitor — a chemical compound that’s essentially a drug in preclinical trial form — to block a certain enzyme.
His hope is that the discovery will result in a drug that not only stops brain inflammation — thereby lessening pain and protecting against neurodegeneration — but does so in a safer manner than current anti-inflammatory drugs.
“It’s a very important breakthrough,” says Tarek Samad, head of neuroinflammation research at Pfizer Neuroscience. “Dr. Nomura has identified a relationship between two metabolic pathways whose ‘crosstalk’ modulates inflammation in the brain. He has characterized an enzyme critical for this new pathway to work, and he has used inhibitors to block the activity of the enzyme in order to decrease brain inflammation.”
The Right Tools
Nomura’s revelation was largely a matter of “brute force,” as he puts it, referring partly to his bag of chemical tools, including “activity-based probes” used to assess enzyme activity. But the real plow horse is his faithful mass spectrometer, a technology born in the late 19th century that essentially uses a magnetic field to reveal properties of various kinds of molecules.
“Technology is one of the huge advantages we have, because the truth is we know very little about metabolism,” Nomura says. The tools are lacking to study the unknown aspects of normal metabolism, he says, let alone metabolism in disease, so many biologists simply don’t go there. “But what we can do in my lab is use our technology to uncover the unknown by tracking changes in metabolites.”
Nomura uses technology as a “theory-generating tool,” to narrow the possibilities in an area that’s nearly infinite.
“We can agnostically go in and figure out what may be important in a disease or what the role of a pathway may be, without having a theory to start with.” As a scientist, he adds, you never get breakthroughs sitting around a table thinking about things. “In biology, we make our discoveries in the lab; it’s the hard data that drives us to revelations and inspirations.”
The Rosetta Stone Enzyme
In high school in Alta Loma, Calif., Nomura excelled in both science and music. He played the saxophone, performed, competed, and listened closely to the music of John Coltrane. He planned to accept a scholarship to the Eastman School of Music, but at the last minute changed his mind, concluding that he could never start a career in science on the side, as he could with music. He ended up at UC Berkeley, where in his freshman year, looking at a job board one day, he noticed an opening to do research in a lab run by a prominent professor of toxicology, John Casida.
Nomura started out as a volunteer in Casida’s lab, doing chemical inventory and cleaning glassware, but was soon assigned his own research project and eventually became almost completely independent. The project involved looking for “off-targets” — enzymes that are unintentionally blocked by agricultural insecticides that work by inhibiting, or targeting, a specific enzyme in insects.
He joined Berkeley’s molecular toxicology Ph.D. program, continuing his research in Casida’s lab. Over the next several years, collaborating with Casida and staff researcher Gary Quistad, Nomura began to focus on these pesticide off-targets. One of them was monoacylglycerol lipase (MAGL, pronounced mag-EL), which became something of a Rosetta stone for Nomura.
“That was certainly the most interesting enzyme we were working on,” remembers Casida, who became Nomura’s Ph.D. advisor. “It was known to be important, and it could be inhibited in a test tube and inside a living organism.”
The Cannabinoid Connection
Because this class of insecticides had the unintentional consequence of blocking MAGL, Nomura used them to study MAGL’s role in the brain. He was intrigued to find that blocking MAGL led to a dramatic rise in the level of endocannabinoids, molecules naturally produced in the brain that act similarly to the active components of marijuana, aka cannabis, by stimulating receptors in the brain, called cannabinoids, that cause a “high.”
Armed with this insight, in 2008 Nomura began his postdoc work at the Scripps Research Institute in La Jolla, Calif., in a lab directed by Ben Cravatt, a professor and chair of the Department of Chemical Physiology. There, using chemical tools developed in their lab, Nomura discovered that especially aggressive human cancer cells had elevated levels of MAGL.
In a headline-making study, he and Cravatt found that blocking MAGL in cancer cells slowed the spread of the disease by shutting off the release of fat in the affected cells.
Meanwhile, Nomura was also following up on his discoveries from graduate school, investigating the role of MAGL in the brain and how it might be involved in neuroinflammation.
Inflammation and Disease
In the last decade, biologists have become increasingly interested in inflammation as evidence mounts of its role in the pathogenesis of many diseases. In good times, inflammation, including fever, is part of a body’s elaborate defense against not only foreign material — the splinter in your toe — but also disease. Inflammation marks the rallying point where immune cells arrive, laden with toxins to dispatch an enemy. After the battle, the process “resolves” itself, as biologists say. The chemical landscape is stable once more.
But when things go awry, you get chronic inflammation. “For example, with neurodegenerative disease, inflammation becomes a self-propagating problem,” Nomura explains. “The immune cells die, which releases more toxins, which leads to more inflammation. The solution becomes the problem, unless you can shut off the faucet.”
Enter MAGL, this strange rascal of an enzyme that is constantly breaking down endocannabinoids in the body. Nomura found that blocking MAGL stops this breakdown. Halting the breakdown causes the endocannabinoids to accumulate and then stimulate cannabinoid receptors, which suppresses pain and inflammation. This is how marijuana works — it can directly stimulate the receptors. However, unlike marijuana, MAGL inhibitors are not likely to make you high.
The Aspirin Effect
The discoveries continued: Nomura also found that when MAGL breaks down endocannabinoids, that process generates a fatty acid that is, in turn, converted into molecules called prostaglandins. Prostaglandins signal the body to start the inflammation process. Nomura found that blocking MAGL reduces these prostaglandins, but only in the brain — not in the gut.
Anyone who’s popped an aspirin or ibuprofen has manipulated prostaglandins in their brain. These non-steroidal anti-inflammatory drugs lower prostaglandin production, thereby lowering fever, pain, and inflammation. But they can act on the stomach lining, leading to ulcers.
Thus, Nomura showed that with a little help — the blocking of MAGL with inhibitors — the body itself can provide the benefits of both marijuana and aspirin, without their side effects.
So the hypothesis for Nomura then became, if we can stop neuroinflammation by blocking MAGL, can this help alleviate neurodegeneration?
A series of experiments to test this theory yielded promising results. For example, Nomura found that in a mouse model of Parkinson’s disease, when MAGL was blocked, the mice were protected against neurodegeneration and dopamine loss. He is now following up on these discoveries, testing whether blocking MAGL can protect against other neurodegenerative diseases, like Alzheimer’s or multiple sclerosis.
Nomura’s lab is also branching out into new aspects of metabolism in cancer. While he now understands how cancer cells use MAGL to grow tumors that can metastasize, there’s work to be done exploring what other aspects of metabolism cancers use to fuel malignant tumors.
On sleepless nights, as the Agilent QQQ LC/mass spectrometer hums in a Morgan Hall lab, Nomura is at home in the quiet of his mind-lab, trying to see connections in the vast circuit board of metabolic pathways. Always, the questions remain: How are the pathways connected? How do the nodes work, and how can they be inhibited to stop inflammation or slow malignant tumors?
To him, one imagines, it’s all a little like exploring a new music score. You take the sound apart measure by measure, try to understand it, learn it, and then play it, see what it sounds like, try things on the fly, and try to get ever closer to an interpretation that transcends intellect. In that sense, perhaps, there’s something jazz-like in biology; the paradox of something that is at once orderly and chaotic, microscopic and cosmic, predictable and yet, on some days, unknowable.
“And that’s how you construct a hypothesis,” says Nomura, comparing the deconstruction of music to the deconstruction of, say, metabolic pathways. “In the end you take a leap of faith, that our bodies, down to the most minute chemical reactions, have some good reason for acting the way they do.”