Reimagining “Druggability”

November 5, 2019

Dan Nomura

Dan Nomura in his lab. Photo: Elena Zhukova

This story originally appeared in Breakthroughs magazine

Dan Nomura’s lab explores the human proteome for the development of next-generation therapeutics

In the modern age of pharmacology, some of the newest heroes in the war against human disease are biologists and chemists working in chemical proteomics. The term proteome is a portmanteau of protein and genome; roughly speaking, if genomics is focused on the genetic mapping of disease, proteomics identifies the proteins that can be targeted with drugs to actually fight disease. Chemical proteomics—also known as chemoproteomics—is the field in which chemical tools are combined with proteomics to help develop those drugs.

Among the leaders in this research is the Novartis-Berkeley Center for Proteomics and Chemistry Technologies (NB-CPACT), a joint venture linking Novartis, a large pharmaceutical company, and the world’s leading public research university. Launched in October 2017, the center is developing new technologies to further the discovery of next-generation therapeutics for cancer and other diseases.

“This collaboration has been a catalyst for our work on drug-discovery technologies,” says Dan Nomura, director of the center and a professor in the Departments of Nutritional Sciences and Toxicology (NST), Chemistry, and Molecular and Cell Biology. “It’s an opportunity to combine the brainpower, innovation, and infrastructure of a large pharmaceutical company with the creativity of academia to tackle blue-sky ideas.”

The proteome includes more than 20,000 human proteins. Roughly 90 percent appear to be molecularly inscrutable—or, in pharma terms, “undruggable.” Why? Because they seem to lack a “pocket” in which to insert a drug. In proteins that do have such a pocket, it could be a deep groove or a mere indentation—a physiological nuance. Imagine a tiny baseball glove waiting to catch a small-molecule drug that can disrupt the function of the protein. However, as Nomura notes, “many proteins are not enzymes or receptors that have nicely crafted pockets that are meant to bind to chemicals or metabolites.” In other words, their natural function doesn’t require them to have a pocket. Or maybe their protein “body type” bonds with another kind of interface altogether, one with a completely flat surface.

Using a chemoproteomic technology called activity-based protein profiling (ABPP), Nomura’s lab has started tackling the problem of undruggable proteins by locating new protein pockets, or “hotspots” that can be targets for disease therapy. One of these discoveries involved the use of an anticancer natural product called withaferin-A, which comes from the winter cherry tree (Withania somnifera) and has long been known to help in the treatment of arthritis and gout. In 2017, Nomura’s lab was able to use withaferin-A to target and activate a heretofore undruggable protein: a tumor-suppressing enzyme called protein phosphatase 2A, which impairs breast cancer.

And the team is confident it can do more. “It’s a big challenge,” says Nomura. “But we believe that we can help move the needle in the treatment of human disease by finding new ways to drug the ‘undruggable.’”

The Coltrane of Chemistry

Nomura grew up in a small town at the foot of the San Gabriel Mountains, in Southern California. He set out to become a jazz musician, awed by the complexity of the music of John Coltrane, and thought he could pursue science “on the side.” He was offered a scholarship to study saxophone at the Eastman School of Music but at the last moment veered away and came to Berkeley to begin a career as a chemical biologist. As an undergraduate, Nomura majored in molecular and cell biology and worked in the lab of the preeminent toxicologist and NST professor John Casida (1929–2018). He stayed on in the Casida lab as a graduate student, earning a PhD in molecular toxicology in 2008.

Next, Nomura began three years of postdoctoral work at Scripps Research in a lab run by Ben Cravatt, who invented ABPP. It was there that Nomura began to study chemical biology, cancer, and neurodegenerative diseases and to search for drugs that would slow or halt those potentially life-threatening conditions. One of his breakthroughs during this period, widely recognized in the neuroscience world, was finding a way to use inhibitors to block the activity of a particular enzyme in order to decrease brain inflammation and prevent neurodegeneration.

Building an Anticancer Arsenal

More recent iterations of ABPP have enabled Nomura to extend his research beyond enzymes and pathways to all proteins in a cell—work that is flourishing through the collaboration with Novartis. In June, one of the first papers to come out of NB-CPACT was published in Nature Chemical Biology. In the study, the team used ABPP to pinpoint how another natural compound, called nimbolide, which is derived from the neem tree (Azadirachta indica), could be used in cancer drug therapies.

The neem tree grows on the Indian subcontinent, as well as in China, Brazil, and West Africa. An evergreen in the mahogany family, it can grow to 65 feet tall and has a 200-year life span. Nowadays, neem oil is popularly known as an insect repellent. However, neem bark has been used to treat malaria and ulcers; the fruit has been used as a remedy for diabetes and leprosy; and the leaf has been used to help prevent cardiovascular disease and pancreatic cancer.

“People have been isolating natural products for centuries,” says Nomura. “It has become an obsession of mine to learn how these chemicals work and how to harness the enormous power of chemoproteomics to help cure human diseases.”

For Nomura’s purposes, nimbolide is a tenacious chemical that can bind to a cellular protein called RNF114. RNF114 is an E3 ligase—a protein whose function is to tag other proteins for elimination by the “cellular trash can,” naturally degrading proteins for which the cell no longer has a use. Nimbolide attaches to RNF114 and impairs its ability to degrade certain tumor suppressors, leading to an increase in the availability of anticancer proteins and the death of cancer cells.

Jessica Spradlin

Jessica Spradlin in the lab. Photo: Elena Zhukova

For Jessica Spradlin, a fourth-year graduate student in Nomura’s lab—and first author on the nimbolide study—the project began as a perfunctory effort to understand more about how nimbolide functions to kill cancer cells. But when Spradlin discovered that nimbolide targets an E3 ligase, the project took a unique turn.

She and Nomura—in collaboration with Tom Maimone’s lab in the Department of Chemistry and scientists from Novartis—hypothesized that they might be able to exploit nimbolide to recruit RNF114 to cancer-causing proteins to tag them for destruction. Known as targeted protein degradation, this approach of tagging specific proteins for destruction has taken off in pharmaceutical drug discovery over the past few years. According to Nomura, a major challenge is that there are very few recruiting molecules for E3 ligases that can be used to tag the proteins that cause cancer and other diseases. The team’s discovery adds nimbolide to the arsenal.

“In our training as chemical biologists, we are taught to approach problems with an interdisciplinary mind-set, so it can be frustrating to have an idea that we can’t follow up on due to the lack of necessary tools or experimental expertise,” says Spradlin, reflecting on the opportunities that NB-CPACT has created for her and the other scientists involved. “This collaboration has opened up doors for my research.” More than 35 researchers from across campus are currently involved in NB-CPACT, including faculty, postdocs, graduate students, and undergraduate assistants, notes Nomura.

Nomura is optimistic about future advances in the science, given the resources and knowledge-sharing avenues the collaboration has created for his team, and he’s confident that scientists will eventually be able to access 100 percent of the proteins within a cell. “We have the capability of finding molecules that bind to pockets for nearly any protein of interest,” he says. “The question is, how long will it take to find the individual molecules that would fit into individual pockets across every single protein? Right now, we’re prioritizing those targets or pathways that we know are major drivers of human disease. This will be game-changing.”