A Better Way to Build Cancer Drugs?

Late last year, doctors at the Princess Margaret Cancer Centre in Toronto administered the first dose of an experimental drug to a cancer patient.

That dose marked the start of human trials for PQ203 – and a major milestone for ProteinQure, the biotechnology startup behind it. If successful, PQ203 could be the first in a new class of treatments for cancer and other diseases.

ProteinQure was co-founded by Lucas Siow (MBA 2018) and emerged from the Creative Destruction Lab – the Rotman School of Management’s technology-focused business accelerator – in 2017. Today, Siow serves as the company’s CEO.

ProteinQure’s drug is designed to treat triple-negative breast cancer, an aggressive form of the disease that accounts for 10 to 15 per cent of breast cancer cases and has poorer survival rates than other types. The most common therapies don’t work on these cancer cells, leaving patients with limited treatment options.

The hope is to change that – soon. Siow says if clinical trials go well, PQ203 could reach the market in five years.

A new toolbox

ProteinQure’s approach to drug development departs from traditional methods. Instead of modifying an existing molecule through years of trial and error, the company employs artificial intelligence and advanced computing to design new drugs from the “bottom up,” building small proteins engineered to treat a specific condition.

“We have a new toolbox,” says Siow, “which allows us to tackle problems in ways that would not have been possible earlier.”

Most medicines work by binding to a specific molecular target in the body and altering its function. For instance, aspirin attaches to and disables an enzyme involved in inflammation and pain transmission. Using computer-aided design, researchers choose a target and then design a molecule precisely shaped to bind to it.

At ProteinQure, that process begins with a supercomputer that simulates atomic-scale physics to generate a molecule with the desired structure and behaviour. AI programs then evaluate the compound, refining it through repeated iterations until it meets the required specifications.

How PQ203 works

PQ203 targets and kills cancer cells while largely sparing healthy tissue. The drug consists of a small protein that binds to another protein found abundantly on tumour cells but not on normal cells. Attached to the drug protein is a toxic “payload” that is absorbed by the tumour cell and kills it.

Targeted approaches like this help concentrate the toxin in the cancer cells where it’s needed, reducing the widespread damage to healthy cells that’s common with traditional chemotherapy.

In mouse studies using implanted human breast cancer cells, PQ203 slowed tumour growth without causing the general toxicity seen with many other chemotherapy treatments. Based partly on those results, ProteinQure received approval for Phase I trials last August. These early trials are designed to assess safety and gather basic information about how the drug behaves in the body. The company plans to enroll 70 to 100 patients in this phase.

Under the conventional approval process, moving from Phase I trials to final approval can take six to eight years and require hundreds or even thousands of patients to demonstrate effectiveness. But because triple-negative breast cancer has few effective treatments, PQ203 was granted fast-track status. This could shorten the trial process to five years, putting the drug on the market soon after if it is found to be safe and effective.

Simpler design

ProteinQure got its start in 2017, when Tomas Babej and Mark Fingerhuth were selected by the Creative Destruction Lab as participants to develop their idea for the company. Acting on advice they received there, they brought on Siow, along with Chris Ing, who holds a PhD in biochemistry from U of T.

Other companies were using computers to design drugs, and protein-based therapies such as antibodies were already available. ProteinQure’s insight was that peptides – short chains of amino acids – offered a valuable alternative. Smaller and simpler than antibodies and other proteins, peptides require far less time and computing power to design. At the same time, scientific interest and research into peptide-based drugs was accelerating, with drugs such as Ozempic hitting the market.

ProteinQure initially partnered with established pharmaceutical companies to help design drugs for them; those collaborations still account for about half of the company’s business. But its long-term goal, says Siow, is to develop its own roster of drugs. In addition to PQ203, the company has two other drugs in development. One targets glioblastoma, an aggressive type of brain cancer; details about the third are undisclosed.

Homegrown biotech

Siow says one of the exciting things about the field is how broadly the technology could be applied as knowledge of peptides expands and computing power grows. One promising use is delivering gene therapies to the brain. Because of the protective blood-brain barrier, it’s notoriously difficult to get drugs to the brain. But in early tests, ProteinQure has shown that genetic material attached to peptides can cross that barrier.

Today, ProteinQure employs about 30 people. It has offices at U of T’s Schwartz Reisman Innovation Campus and labs across the street at the MaRS Centre. Still in its startup phase, the company raised US$4 million in seed funding in 2019 and another US$11 million in May 2025 to support the Phase I trials.

Siow hopes to build a large, homegrown biotech company – a rarity in Toronto – that eventually designs, tests, manufactures and distributes its own drugs. It’s precisely the kind of domestic industrial capacity that many policymakers argue Canada needs, as the federal government pushes to reduce the country’s economic reliance on the U.S.

Taking PQ203 through full clinical trials could cost US$100 million or more, requiring substantially more investment. “If you want to become a very large company, the real value is in developing your own drugs rather than only being a vendor to pharmaceutical companies,” Siow says.

“Our goal is to be as ambitious as possible.”