ProFound Therapeutics has quietly come up with technology that it says has discovered tens of thousands of previously unknown proteins, many of which held promise for new drug targets. The Flagship Pioneering-founded startup is backed with $75 million to support its drug research and development, as well as partnership plans with Big Pharma.

The Flagship Pioneering-founded startup is backed by $75 million

Much of the understanding of disease comes down to proteins, those building blocks that are important for biological functions throughout the body. Scientific research has revealed many pathogenic proteins, and many of the drugs available today have evolved 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 identification of 20,000 protein-coding genes by the Human Genome Project almost 2,000 years ago, almost Two decades. While this discovery has fueled drug discovery efforts in the biotech industry, scientists at ProFound Therapeutics aim to take things even further. Avak Kahvejian, co-founder and CEO of the startup, says his company has found thousands of previously unknown proteins.

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"We're basically shedding light on the human genome in new ways to identify a universe of previously unknown proteins," he said. "Finding new ones, let alone tens of thousands of new ones, can be very conducive to new drug discovery."
For the past two years, ProFound has been developing its technology in the labs of venture capital firm Flagship Pioneering, where Kahvejian is also a general partner.

The Cambridge, Massachusetts-based startup emerged from stealth on Thursday with a preview of its work so far and $75 million in funding that will help the young company turn these protein discoveries into drug development.

ProFound began as a flagship effort to see if there might be more proteins than the consensus of 20,000 found by the Human Genome Project. Kahvejian said his team focused on emerging evidence of stretches of DNA in the genome that have been poorly studied or ignored.

Avak Kahvejian, the startup’s co-founder and CEO

The new technology allowed ProFound to read the genome, and the startup focused on the translator, the entire collection of RNA sequences that are translated into proteins. This information revealed the new proteins that are now part of an expanding ProFound database that records their functions and roles in health and disease.

Kahvejian said that at this point ProFound is disease-independent, 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. These disease domains cover both rare and common disorders. The types of drugs developed by ProFound could also take different forms. Some could be small molecules.

But pointing to the examples of insulin and erythropoietin, Kahvejian added that in some cases the proteins themselves will be the therapy. Some of the startup's protein discoveries have reached early preclinical development, though Kahvejian declined to offer a timeline for when the company hopes to reach human testing.

ProFound joins a small but growing group of companies exploring the proteome. Nautilus Biotechnology is developing a proteomics technology platform, a combination of hardware and software.

The Seattle-based company plans to offer this technology as a service, analyzing samples and providing protein information to customers such as biopharmaceutical companies and research institutes. Seer, based in Redwood City, California, operates a similar business model. Kahvejian said that unlike some of its proteomics peers, ProFound aims to be a drug developer rather than a tool or service provider.

The $75 million unveiled Thursday by ProFound is not new money, but rather represents capital committed to the startup since its inception in 2020. Kahvejian said some of that money has already been used to develop the platform, a form of funding technology. ProFound, but Much remains to support the company in the future. t