Synthetic DNA Approach is Key to Startup’s New Drug
By Lisa Howard
The way Justin Siegel describes it, ordering synthetic DNA is almost as easy as ordering a pair of shoes online.
“You just type it in — or if the protein has been sequenced at one point, we can copy and paste — order it, and it shows up five days later.”
Siegel is an assistant professor of chemistry, biochemistry and molecular medicine at UC Davis. Synthetic DNA – the ability to create DNA sequences to order and use them to make useful products – is key to his work on a potential new treatment for celiac disease, a digestive disorder triggered by consuming gluten from wheat, barley or rye.
He is also a co-founder of PvP Biologics, a startup company that is seeking U.S. Food and Drug Administration approval for phase I trials of KumaMax, a possible new treatment for celiac disease. KumaMax is an enzyme, created with synthetic DNA technology, that digests gluten. The idea is that the enzyme breaks down gluten in food before it can hit the small intestine and set off a reaction.
Enzymes that can digest gluten are not a new idea for treating celiac disease. You can buy food supplements in health food stores that claim to do that, and there have also been credible therapeutic versions, including an oral treatment that combined two enzymes, SC PEP and EP-B2, created in Chaitan Khosla’s lab at Stanford University.
But there’s a big difference between breaking down gluten in a test tube and the human digestive system.
Siegel points out that people don’t just eat gluten; they eat a meal. In addition to a bun, they might also eat a hamburger with cheese and some fries and maybe drink a beer or a big chocolate milkshake, all in one sitting. It is extremely difficult for an enzyme supplement to zero in on just the gluten mixed up in a slurry of food. And the gluten needs to be digested in the stomach, before it reaches the small intestines where it triggers an immune reaction in people with celiac disease.
“The immunogenic portion of gluten is just a tiny piece of the protein. It’s this little peptide,” said Siegel. “The needle-in-a-haystack analogy is perfect because this peptide looks just subtly different from all the other proteins present in a meal, but that subtle difference is what triggers a whole immune response for people with celiac disease.”
Undergraduate competition launches new enzyme
During the summer of 2011, Siegel and Ingrid Swanson Pultz, then both pursuing doctorates at the University of Washington, advised an undergraduate team competing at the International Genetically Engineered Machine (iGEM) competition.
Held every year in Boston, iGEM is the Olympics of synthetic biology. Teams of undergraduates are expected to solve real-world challenges by building genetically engineered biological systems.
The UW team selected gluten intolerance. They found a naturally occurring enzyme called kumamolisin that could survive the stomach’s acidity and set out to engineer it to digest the small sequence of protein thought to be responsible for triggering gluten intolerance.
First they created about 100 variations of kumamolisin using an online multiuser video game called Foldit, which is based on a software program called Rosetta created in the lab of David Baker at the University of Washington. Then they created synthetic DNA for those variations, put them into E. coli cells and tested the proteins made by the microbes for ability to break down the motif associated with gluten sensitivity.
The team ended up with an enzyme that was significantly better at breaking down gluten under stomach conditions than SC PEP, which at that time had been licensed to Alvine Pharmaceuticals for consideration as an oral therapy for celiac disease.
And the students managed to do all of this in just one summer. Perhaps not surprisingly, the University of Washington team walked away with the grand prize.
Synthetic DNA melds engineering with biology
The enzyme they created, now named KumaMax, would not exist without synthetic biology. One way to think about synthetic biology is that it’s a discipline that melds engineering (what a piece of DNA can do) with biology (what an organism can produce). DNA can be synthesized with the exact code to produce the protein you require. Introduced into a cell such as E. coli, and the cell becomes a little factory producing what you want, making vaccines or insulin for diabetics or collagen for an artificial leather. Synthetic DNA has even been used to encode and storing digital information that could one day replace computer hard drives.
Getting DNA wasn’t always this easy. “Before synthetic DNA, you had to go out into nature and clone genes directly from the naturally occurring organism, and then hope the way the organism genetically encoded the protein of interest would be functional in easy-to-use model organisms,” said Siegel. “It had low success rates, and it was very difficult. It would commonly be an entire Ph.D. project to clone one gene and characterize it.”
These days, working with synthetic DNA is much easier. Order online and it arrives at the lab in a clear plastic tube.
Gluten-free diet is only treatment for celiac disease
KumaMax may end up being the first viable treatment for celiac disease. When people with celiac disease eat gluten – protein found in wheat, barley and rye — their immune system goes on the attack and the resulting inflammation damages the lining of the small intestine.
Sooraj Tejaswi, M.D., an associate clinical professor in UC Davis’ Division of Gastroenterology and Hepatology, uses a carpet analogy to describe the result of this immune system assault.
“Under a microscope, the villi in the small intestines, which help with nutrient absorption, should look like a shag carpet. But in people with celiac disease, the villi get destroyed faster than they can regenerate, so you end up with pretty flat mucosa,” essentially more like some nubby Berber carpet, “that can no longer absorb nutrients,” said Tejaswi.
As many as one percent of the world’s population may have the disease, but many go undiagnosed, Tejaswi said.
Breaking down gluten before it can cause a reaction could be a true breakthrough for the disease. That has to happen in the stomach, before the gluten enters the intestines where it causes so much damage.
In addition to intestinal damage, celiac disease is associated with a wide variety of health problems including vitamin and mineral deficiencies (which lead to other health problems, like osteoporosis and anemia) lactose intolerance, infertility, nervous-system disorders, a failure to thrive in children and other complications. In rare cases, celiac disease can lead to small intestinal lymphomas.
The only current treatment is to completely avoid gluten, meaning patients with celiac disease are on a special diet for the rest of their lives.
Tejaswi sees tremendous potential for a therapeutic enzyme. “It would be a miracle drug if it were to happen,” he said. “For me it is something we badly need as clinicians taking care of patients. It would be very useful for patients to improve their overall quality of life. Even when patients are being careful, gluten intake does happen — it’s everywhere — and a drug like this might actually help with that.”
From prototype to promising therapeutic drug
The work done by the University of Washington iGEM team was just the start. The enzyme was still a prototype, nowhere near ready to be a commercial product. Before Siegel left Washington to become a faculty member at UC Davis, had and Pultz formed a startup company, PvP Biologics.
“Most of these undergraduate student projects that get to the prototype stage are then left to languish on the shelves because the students move on to their next big thing. It’s difficult to see a project with so much promise stall because there is no one to push the work forward,” said Pultz. “I sat down with Justin before he left and we made a plan for how to pursue the development of this enzyme in the short term through academia, and then in the long term with PvP Biologics.”
Pultz is now a faculty member at UW’s Institute for Protein Design, where she continues to work on the enzyme. Siegel, Pultz, the student team members and a few others share credit for creating the enzyme, which PvP Biologics has licensed from the Unversity of Washington. (Most of the patents are owned by the University of Washington plus one owned jointly by University of Washington and UC Davis.)
In January 2017, PvP Biologics announced a deal with Takeda Pharmaceuticals, which invested $35 million to move the enzyme through phase one trials with an exclusive option for purchase.
The company is currently conducting safety testing with animals. The next step for getting Food and Drug Administration approval of the enzyme is human clinical trials, which will test for safety, efficacy and any possible side effects. The trials are scheduled to start this year.
“The real possibility to affect millions of people around the world has really driven my research in new directions,” said Siegel. “We are just starting to understand the complex relationship between our health and the food we eat. I think this will be a major step forward in developing a new paradigm for how we interact with our food.”
Lisa Howard is a writer with the UC Davis Office of Research.