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David Baker
David Baker is the director of the University of Washington’s Institute for Protein Design. (UW Medicine Photo)

The University of Washington’s Institute for Protein Design has won an $11.3 million grant from the Open Philanthropy Project to cook up a public health breakthrough: a universal flu vaccine.

This marks the San Francisco-based nonprofit group’s first gift to a research effort in the Seattle area, and one of its largest gifts to date. Open Phil’s main funders are Facebook co-founder Dustin Moskovitz and philanthropist Cari Tuna, a husband-and-wife team.

The grant will accelerate the institute’s efforts to advance the field of protein design and put it to use in real-world applications. The institute is led by UW biochemist David Baker, who has pioneered protein-folding software platforms such as Rosetta and FoldIt.

“Our team can now custom-design proteins from scratch, creating entirely novel molecules that can be used for new treatments, new diagnostics and new biomaterials,” Baker said today in a news release. “We’ll improve all our tools and build out greater understanding of proteins as we explore paths to a universal flu vaccine.”

Baker said Open Phil’s gift “will allow us to go all in and focus on basic science.”

Today’s flu vaccines take aim at viral proteins that can change from year to year. Determining which flu strains to target, and making enough vaccine to fill the projected need, is an annual puzzle that epidemiologists and drug companies have to solve. And they don’t always get it completely right.

Baker and his colleagues are taking a different approach: They’re designing a vaccine with self-assembling protein nanoparticles that can be attached to specific bits of proteins common to many different strains of the flu virus.

Such a vaccine would trigger an immune response to a wide range of flu strains. Researchers think it could be administered every five years or so, rather than annually — dramatically reducing the cost, the hassle and the risk of infection.

About $5.6 million of the Open Philanthropy Project’s grant will support basic protein research. That part of the grant will go toward developing machine learning techniques to refine Rosetta’s protein-folding algorithms — and help the institute fine-tune the system for community sharing through the Rosetta Commons, a collaboration of more than 150 developers from 23 universities and labs.

The other $5.7 million will go specifically to the effort to develop a universal flu vaccine.

“The universal flu vaccine is a tough nut to crack, but David Baker has shown the ability to pioneer life-changing scientific research,” said Chris Somerville, a program officer for scientific research at Open Phil. “It’s exciting that whether a universal flu vaccine is developed or not, this gift will build techniques and technologies that will advance science and have a huge variety of implications in medicine and industry.”

Protein structure on computer
The Institute for Protein Design creates complex molecular structures using sofware. (UW Medicine Photo)

Principal investigators for the computational protein design effort are Baker and Frank DiMaio, a biochemist at the University of Washington School of Medicine.

Development of the universal flu vaccine will be a joint project involving Baker’s lab as well as the lab of Neil King, another biochemist at UW Medicine. They’ll work to design and test vaccine candidates with research groups headed by Barney Graham and Masaru Kanekiyo at the Vaccine Research Center of the National Institute of Allergy and Infectious Diseases at the National Institutes of Health.

The quest to create a universal flu vaccine is proceeding at other institutions as well. A British company called Vaccitech is in the midst of a two-year Phase 2 clinical trial of its vaccine candidate, and recently raised $27.1 million in a Series A financing round. Several other research groups are working on novel vaccines that can target multiple flu strains.

If the UW approach works, universal vaccines could be created not just for the flu, but for other infectious diseases as well, Baker said.

“We envision that in the future it may be possible to rapidly design vaccines to new pathogens that induce immunity against all strains of that pathogen,” he said.

Read more: Universal flu vaccine uses genetic tech

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