New Flagship Pioneering startup expands the protein universe to fuel drug discovery

So much about the understanding disease comes down to proteins, these building blocks that are important to biological functions throughout the body. Scientific research has revealed many disease-causing proteins, and many of the drugs available today came from efforts to develop molecules that target them. In some cases, a protein in the body can be harnessed as a therapeutic.

The human proteome, which is the complete set of proteins in humans, is estimated to be around 20,000, a figure that comes from the Human Genome Project’s identification of 20,000 protein-coding genes nearly two decades ago. While that discovery has fueled drug hunting efforts throughout the biotechnology sector, scientists at ProFound Therapeutics aim to go even further. Avak Kahvejian, the startup’s co-founder and CEO, says his company has found thousands of previously undiscovered proteins.

“We’re essentially illuminating the human genome in new ways to identify a universe of previously undiscovered proteins,” he said. “Unearthing new ones, let alone unearthing tens of thousands of new ones, can be very enabling for the discovery of new drugs.”

For the past two years, ProFound has been developing its technology within the labs of venture capital firm Flagship Pioneering, where Kahvejian is also a general partner. The Cambridge, Massachusetts-based startup emerged from stealth Thursday with a glimpse at its work so far and $75 million in financing that will help the young company turn those protein discoveries into a drug pipeline.

ProFound started as a Flagship effort to see if there might be more proteins than the consensus 20,000 found by the Human Genome Project. Kahvejian said that his team focused on emerging evidence of spans of DNA in the genome that was understudied or ignored. New technology enabled ProFound to read the genome, and the startup’s focus turned to the translatome, the full collection of RNA sequences that are translated into proteins. This insight revealed the new proteins that are now part of an expanding ProFound database that logs their functions and roles in health and disease.

Kahvejian said that at this point, ProFound is disease agnostic but the company’s research so far has found proteins that are promising targets for cancer, as well as proteins with potential applications in immunology and metabolic diseases. Those disease areas span both rare and common disorders. The types of drugs that ProFound develops could also take on different forms. Some could be small molecules. But noting the examples of insulin and erythropoietin, Kahvejian added that in some cases the proteins themselves will be the therapeutic. Some of the startup’s protein discoveries have reached early preclinical development, though Kahvejian declined to offer a timeline for when the company expects to reach human testing.

ProFound joins a small but growing group of companies that are exploring the proteome. Nautilus Biotechnology is developing a proteomics technology platform, a combination of both hardware and software. The Seattle-based company plans to offer this technology as a service, analyzing samples and providing protein insights to customers such as biopharmaceutical companies and research institutions. Redwood City, California-based Seer operates a similar business model. Kahvejian said that unlike some of its proteomics peers, ProFound aims to be a drug developer rather than a tools or service provider.

The $75 million unveiled Thursday ProFound is not new money, rather it represents capital committed to the startup since its 2020 inception. Kahvejian said some of that money has already been used to develop ProFound’s technology platform but a large portion of it remains to support the company going forward. New initiatives include pursuing partnerships with large pharmaceutical companies that may want to tap into the startup’s technology for protein research in various therapeutic areas.

Photo by Flagship Pioneering