From left: Flagship Founding Partner Yann Echelard; Flagship Founding Partner and President of ProFound Therapeutics Kala Subramanian; Flagship Senior Associate Vini Mani; Flagship Principal Erica Weinstein; Flagship Vanguard General Partner/Co-Founder and CEO of ProFound Therapeutics Avak Kahvejian ; and Noubar Afeyan, Flagship co-founder and CEO and Chairman of ProFound.
So much understanding of disease comes down to proteins, the building blocks that are important for biological function throughout the body. Scientific research has revealed many proteins that cause disease, and many of the drugs available today have come from efforts to develop molecules that target them. In some cases, proteins in the body can be used as therapeutic agents.
The human proteome is the complete human proteome, estimated to be approximately 20,000, a number derived from the identification of 20,000 protein-coding genes by the Human Genome Project nearly 20 years ago. While the discovery has propelled the drug search effort across the biotech field, the scientists at ProFound Therapeutics aim to go even further. Avak Kahvejian, the startup’s co-founder and CEO, said his company has discovered thousands of previously undiscovered proteins.
“We are essentially elucidating the human genome in new ways to identify a universe of previously undiscovered proteins,” he said. “The discovery of new drugs, let alone the discovery of tens of thousands of new drugs, is very helpful 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, of which Kahvejian is also a general partner.Startup company in Cambridge, Massachusetts emerge from invisibility Thursday’s glimpse at its work to date and the $75 million in funding that will help the young company translate those protein discoveries into a pipeline of drugs.
ProFound started as a flagship project to see if there were more proteins than the 20,000 discovered by the Human Genome Project. Kahvejian says his team has focused on studying or ignoring new evidence of DNA spans in the genome. New technology enables ProFound to read the genome, and the startup’s focus has turned to the translationome, the complete collection of RNA sequences that are translated into proteins. This insight revealed new proteins that are now part of the expanded ProFound database documenting their functions and roles in health and disease.
At this point, ProFound is disease-agnostic, Kahvejian said, but the company’s research to date has identified proteins as promising cancer targets, as well as proteins with potential applications in immunology and metabolic disease. These disease areas cover rare and common diseases. The types of drugs that ProFound develops can also take different forms. Some may be small molecules. But noting the example of insulin and erythropoietin, Kahvejian added, in some cases the protein itself will have a therapeutic effect. Some of the startup’s protein discoveries have reached early preclinical development, although Kahvejian declined to provide a timeline for when the company expects to conduct human trials.
ProFound joins a small group of companies exploring the proteome. Nautilus Biotechnology is developing a proteomics technology platform that combines hardware and softwareThe Seattle-based company plans to offer the technology as a service, analyzing samples and providing protein insights to clients such as biopharmaceutical companies and research institutions. Redwood City, Calif.-based Seer operates a similar business model. Unlike some of its proteomics peers, Kahvejian said, ProFound aims to be a drug developer, not a tool or service provider.
The $75 million in ProFound announced on Thursday is not new funding, but represents investment in the startup since its inception in 2020. Kahvejian said some of the funds have been used to develop ProFound’s technology platform, but a large part of it is still used to support the company’s growth. The new moves include partnerships with big pharma companies that may want to use the startup’s technology to conduct protein research in various therapeutic areas.
Flagship Pioneer Photography
