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A-Alpha Bio team
The A-Alpha Bio team includes scientist Emily Engelhart, principal scientist David Colby, co-founder and CEO David Younger, co-founder and chief technology officer Randolph Lopez and engineering associate Charles Lin. (A-Alpha Bio Photo)

A Seattle startup that took root at the University of Washington has closed a $2.8 million seed round for a drug discovery platform that can sort through millions of protein interactions at once.

“We expect that we can go considerably further than that,” said David Younger, the co-founder and CEO of A-Alpha Bio.

A-Alpha Bio’s genetically engineered protein analysis technology, known as AlphaSeq, has the potential to speed up the process of evaluating drug candidates. That’s what attracted interest from investors including OS Fund, which led the seed round, plus AME Cloud Ventures, Boom Capital, Madrona Venture Group, Sahsen Ventures, Washington Research Foundation and a number of angel investors.

“We are inspired by the work that AAlpha Bio is doing at the intersection of biological and information sciences to help find treatments and cures to some of the hardest-to-address diseases,” Matt McIlwain, managing director of Madrona Venture Group, said in an emailed statement. “We have partnered with many UW companies and are excited to back this compelling team, our first out of the globally known Institute for Protein Design and Center for Synthetic Biology.“

A-Alpha Bio’s scientific advisers include Eric Klavins, the director of UW’s Center for Synthetic Biology; and David Baker, who heads the Institute for Protein Design. Both advised Younger in graduate school and collaborated with him on research that set the stage for A-Alpha Bio.

“While there are many methods available for screening large biomolecular libraries for a particular binding activity, there are few approaches for assessing in parallel the very large number of possible interactions between biomolecules in two large libraries,” Baker said in a news release.

That’s what AlphaSeq is designed to do.

The platform takes advantage of a common strategy for protein-based therapeutics. On the cellular level, proteins attach to each other like keys in locks. That’s how viruses such as HIV can gain entry into cells. It’s also how your immune system uses antibodies to recognize viruses, cancer cells and other invaders.

If there are millions of molecular keys, and millions of molecular locks, it can be devilishly difficult to find the right combination for blocking a disease or revving up your immune system.

“It’s referred to as ‘library-on-library,’ and it’s a massive scaling problem,” Younger said. To address the problem, A-Alpha Bio is developing a method that uses yeast cells to sort through all those molecular locks and keys. The technique should end up identifying a small number of “master keys” that can serve a number of therapeutic purposes.

“We have genetically engineered cells that we use as a test bed for measuring protein interactions at a massive scale, and our output is next-generation sequencing,” Younger said. “Once we have that data, there’s a ton we can do with it.”

AlphaSeq was invented by Younger and A-Alpha Bio’s other co-founder, chief technology officer Randolph Lopez. A-Alpha got its start at UW’s CoMotion innovation hub, and In the two years since its founding, the venture has added three more scientists to the team. It has also picked up support from the National Science Foundation and the Bill & Melinda Gates Foundation. A-Alpha’s work for the Gates Foundation focuses on optimizing AlphaSeq to identify drugs that can target many strains of intestinal pathogens at once.

Jeff Klunzinger, co-founder and general partner of OS Fund, said A-Alpha Bio should help its partners accelerate the discovery of multi-target protein drugs. “A-Alpha Bio’s platform is plug-and-play for partners, facilitating read-outs on drug potency and effectiveness in a much shorter time frame, solving an important challenge for pharma companies,” he said.

Younger said the seed funding will help A-Alpha Bio validate AlphaSeq’s application to high-impact disease targets, including cancer and infectious diseases.

“Our main priority in the short term is to form partnerships with pharmaceutical companies very early,” he said. “To have them work with us from the very get-go, to help them discover and optimize therapeutics against targets that they’ve identified. … We are in conversations with a number of partners, and we’re really excited about those prospects.”

Younger said A-Alpha Bio has been working closely with another Seattle-based venture, Olympic Protein Technologies, to “co-develop a service to characterize protein interactions.”

He expressed his appreciation to the seed-round investors, particularly OS Fund. “They have a mission, which is to invest in companies that lower barriers to scientific discovery,” Younger said. “That is just absolutely perfectly aligned with our own vision for the company.”

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