University of Toronto spinoff firm helping to map COVID-19's molecular structure

Software developed by a University of Toronto spinoff firm has helped scientists produce the first atomic-scale, 3D structure of a critical part of the coronavirus (COVID-19) – a key step in creating a vaccine.

Structura Biotechnology’s software and associated algorithms are now being used worldwide, says CEO Ali Punjani, the UToronto computer science PhD student who co-founded the startup in 2016. Structura’s patented “cryoSPARC” platform optimizes a Nobel Prize-winning scientific imaging technique called cryogenic electron microscopy (cryo-EM).

“We have thousands of users in over 40 countries and more than 400 institutions, both academic and industrial, using our software,” Punjani told RE$EARCH MONEY. Large pharmaceutical companies, for example, are using the technology to accelerate development of vaccines, therapeutic antibodies and other new drugs.

“Cryo-EM is like a flashlight that lets us finally see areas and regions of biological molecular space that we just couldn’t see before,” Punjani says. “This ability is fundamentally game-changing for drug design and understanding the inner workings of biological life.”

“The whole world has started moving over to the use of cryo-EM, and Structura’s software and algorithms have been state-of-the-art,” says David Fleet, professor of computer science and associate director of the Vector Institute at UToronto, and Punjani’s PhD supervisor. “The field is still moving quickly and the impact will be profound.”

Cryo-EM produces electron microscopy images, and 3D reconstruction of those images, that reveal in atomic-scale detail the structure of single proteins and other biological molecules. The Nobel Prize in Chemistry 2017 was awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for developing the technique.

Last month, a research team from the University of Texas at Austin and the National Institutes of Health used Cryo-EM, along with Structura’s software, to produce a high-resolution, 3D molecular structure of the COVID-19 virus’s “spike proteins” that attach to and infect human cells. Their breakthrough was published in Science.

“Every protein functions because of its structure and because of the way it’s shaped to do some task at the molecular level,” Punjani notes. “Solving the structure of the coronavirus spike protein is in many ways a required precursor for developing a vaccine.”

Support crucial in taking research to commercialization

Fleet led the initial research team at UToronto, which included Punjani, then post-doctoral fellow Marcus Brubaker (now an assistant professor at York University and co-founder of Structura Biotechnology), and MSc student Haowei Zhang.

Funding for the research (including a paper published in Nature Methods) included Fleet’s Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, an NSERC grant for an undergraduate student, and support from the Canadian Institute for Advanced Research.

The Connaught Fund, the largest internal university research funding program in Canada, awarded the research group its Connaught Innovation Award, which helped drive the proof-of-concept technology into first-stage product and commercialization.

Punjani says Structura received a lot of help from UToronto’s intellectual property office and seed funding from UTEST, UToronto’s startup development program supported by the Connaught Fund and MaRS Innovation. The Ontario Centres of Excellence also provided funding.

Key mentors for the startup included Fleet, an expert in machine learning, and John Rubenstein, a professor in UToronto’s Department of Biochemistry and Medical Biophysics, and a Canada Research Chair in Electron Cryomicrosopy.

Structura’s market strategy includes providing its cryoSPARC platform free to all academic research groups. “Their validation of our tools has allowed us to get great traction within industry,” Punjani says.

Structura licenses its platform to commercial entities. The company’s list of large, high-profile industrial customers has grown so rapidly it hasn’t yet needed to look for outside capital.

Says Punjani: “Our aim is that Structura and cryoSPARC will be part of an evolution of cryo-EM into a technology that is so reliable and repeatable it becomes part of every biological insight-driving experimental technique.”

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