How can we fight diseases that no longer respond to available treatments?

Groundbreaking Protein-based Drugs Being Developed on SOSCIP Systems:

By Susan Hickman


A computer scientist and a biochemist at Carleton University have teamed up to start a company that designs therapeutic peptides derived from human proteins – drugs that may offer a new way of treating complex diseases that no longer respond to current treatments.

After working together for a decade and a half, Frank Dehne, a Chancellor’s Professor of Computer Science who runs the Parallel Computing and Data Science Research Lab, and Ashkan Golshani, an award-winning biochemist who leads a molecular biology and genetics lab, registered Designed Biologics in February. The company will push development of special small peptides that can target specific proteins involved in various human diseases.

When he and Golshani first put their heads together at the graduate pub on campus 15 years ago, Golshani was a new faculty member working in the novel field of systems biology looking for a way to speed up his costly time- and energy-consuming protein interaction experiments. Dehne, who loves looking into other fields, was searching for bigger and better problems to solve.

The problem? If you consider each human being has 20,000 proteins, there are 200 million possible combinations of interaction.

“I started trying to predict these protein interactions using computation,” says Dehne, “and to come up with a way to be more precise.”

They developed a hypothesis that smaller sequences of molecules could facilitate some of the protein interactions, which became the basis for the prediction algorithm that Dehne later developed.

“It turns out there are a lot of these different types of interactions that were being missed,” explains Dehne. “Our method is the only one that works on these types of interactions, which represent about 40 per cent of human protein interactions.” Several students in Biochemistry and Computer Science have since completed doctoral theses on this hypothesis.

The pair’s findings, as well as those of their students and research teams, may impact a pharmaceutical industry that has traditionally focused on antibody- and chemical-based therapies. Their early work was undertaken in partnership withSOSCIP, a collaborative R&D consortium of Ontario academic institutions, OCEand IBM Canada Ltd., with a mandate to drive innovation by providing state-of-the-art advanced computing facilities and expertise to industry-academic collaborative projects. Now that they have calculated the entire 200 million human protein interactions, they believe they are at the forefront of designing new pharmaceuticals using significantly smaller molecules that can attach to specifically targeted proteins — the culprits causing illnesses.

Designed Biologics continues to leverage the high-performance computing power of SOSCIP and will contract out its services to develop small peptides containing between 30 and 75 amino acids that can hit targets not responding to traditional drugs. These “smart biologics” will focus on alternative binding characteristics to engage disease-fighting mechanisms in the human body in a new way that should result in fewer side effects for the patient.

The company will start by focusing on cancer, says Golshani, who lost his mother to breast cancer last year after all the traditional therapies failed to cure the disease.

“In theory, we can target all kinds of cancer with these new designed drugs,” Golshani adds, “as well as inflammation and any complex human disease such as diabetes or Alzheimer’s. We are hoping this new platform could actually treat a lot of diseases, and that we can provide new drugs that can extend the lifespan by several years or even cure the disease.”

Dehne notes that for those illnesses that currently have no treatment, “we can offer new possibilities. For companies that have problems finding the target protein that has gone haywire . . . we can help them find it with our new methodology.”

The company is in its early stages and the co-founders say what they have discovered is simply one piece of the puzzle required to take a newly designed drug to market.

But they say their partnership is resulting in important interdisciplinary work that can benefit not only the health of Canadians, but research by students.

“We had to learn each other’s fields,” notes Dehne. “In fact, that’s part of our strength, because it’s not so easy for people from different disciplines to work together.”

Golshani, whose passion to know the meaning of life led him to his field of study, adds that he and Dehne interact really well, which happened organically in true interdisciplinary fashion.

For more information about Designed Biologics, please refer to

SOSCIP is a research and development consortium that pairs academic and industry researchers with advanced computing tools to fuel Canadian innovation. SOSCIP supports projects that have the potential to have a considerable impact on the lives of Canadians, within areas such as water, cities, health and cybersecurity. The consortium includes 15 universities as well as the Ontario Centres of Excellence and the IBM Canada Research and Development Centre.