University of Washington’s David Baker wins Nobel Prize for designing proteins

University of Washington biochemist David Baker has won a share of this year’s Nobel Prize in chemistry for more than two decades of discoveries about the molecular structure of proteins — discoveries that have led to new medical therapies, new materials and new startups.

“I’m very, very excited about the future,” Baker, who is the director of the UW Medicine Institute for Protein Design, said today during a Seattle news briefing. “I think protein design has huge potential to make the world a better place, and I really do think we’re just at the very, very beginning.”

Baker shares the prize with Demis Hassabis and John Jumper of Google DeepMind, who have also pioneered computational techniques for predicting protein structure. They will be awarded their medals at a ceremony in Stockholm, Sweden, on Dec. 10.

The Royal Swedish Academy of Sciences said Baker “has succeeded with the almost impossible feat of building entirely new kinds of proteins.”

“His research group has produced one imaginative protein creation after another, including proteins that can be used as pharmaceuticals, vaccines, nanomaterials and tiny sensors,” the academy said in a news release.

Proteins serve as the foundation for biological processes, literally unlocking the workings of the cell. But determining the 3D structure of those molecular “keys” is a devilishly complex task. “Life could not exist without proteins. That we can now predict protein structures and design our own proteins confers the greatest benefit to humankind,” the Swedish academy said.

Baker and his colleagues developed an early protein design tool and made the code available through a consortium called Rosetta Commons. That code was leveraged into a game-like crowdsourcing campaign called Foldit, which enlisted hundreds of thousands of computer users to help unravel the twists and turns of proteins.

The advent of artificial intelligence tools accelerated the pace of protein structure prediction — and today, the Institute for Protein Design and Google DeepMind are recognized as the world’s leaders. Microsoft’s chief scientific officer, Eric Horvitz, noted on LinkedIn that “we made the decision to go all-in with David” five years ago and work together on accelerating the development of vaccines and drugs with AI.

Half of this year’s Nobel Prize in chemistry, which comes with a $1 million cash prize, will go to Baker. Hassabis and Jumper will share the other half.

Baker’s research contributed to the development of the world’s first computationally designed protein medicine, a vaccine for COVID-19 that was pioneered by colleagues at UW Medicine. UW says Baker holds more than 100 patents and has co-founded 21 biotech companies — some of which have already been acquired.

Takeda Pharmaceuticals bought one of the Institute for Protein Design’s spinouts, PvP Biologics, for $330 million. AstraZeneca paid $1.1 billion to acquire a different spinout, Icosavax, which develops synthetic vaccines that target naturally occurring viruses. Other spinouts associated with the institute include Cyrus Biotechnology, Sana Biotechnology, A-Alpha Bio and Xaira Therapeutics.

In 2020, Baker won the Breakthrough Prize in Life Sciences. “Being able to design proteins from scratch, to do exactly what you want to do rather than modifying what we find around us, is kind of like the transition out of the stone age,” he told GeekWire at the time.

Today, Baker said the technology could be harnessed to synthesize new treatments for maladies including cancer, Alzheimer’s disease and autoimmune disease; to produce chemicals that break down plastics and other pollutants; and to create new materials for applications that might be considered close to the lunatic fringe.

“You can imagine all kinds of hybrid materials that could be superior in many ways to any of the materials that we have today, including semiconductor materials,” he said. “So, it could be a new way of patterning things for electronics. I’d say that still qualifies as lunatic fringe.”

During a panel discussion in June about the Seattle tech ecosystem, Ken Horenstein, general partner at Pack Ventures — which invests in startups with ties to the UW — said Baker’s lab was “transformational to the world.”

“It is a matter of when he will win a Nobel Prize, not if he will win a Nobel Prize,” Horenstein said at the time.

In the wake of today’s announcement, David Younger, CEO of A-Alpha-Bio, called Baker a “brilliant and visionary biochemist.” Nikesh Parekh, who was CEO of Bio Architecture Lab, another startup spun out from Baker’s lab, said he’s “a true pillar of the Seattle tech community.”

“David is an inspirational and incredibly supportive academic co-founder to work with, in that he understands that both the opportunities and the challenges of commercialization,” Parekh told GeekWire in an email.

Baker is the eighth UW faculty member to receive a Nobel.

“Let’s be honest: This is about as good as it gets,,” UW President Ana Mari Cauce said at today’s news briefing. “We are so proud to be the home of some of the most remarkable, creative, innovative and talented faculty, and we don’t have a better example of that than David.”

Baker, 62, was born in Seattle and grew up not far from the UW campus. Both his parents were UW faculty members, and he graduated from Seattle’s Garfield High School. “He really is a local kid, and he ‘s having a global impact,” Cauce said.

Baker completed his undergraduate studies at Harvard in 1984, and earned his doctorate in biochemistry in 1989 at the University of California at Berkeley. He’s been a faculty member in the Department of Biochemistry at the UW School of Medicine since 1993. “I’ve been here for quite a long time, and I never thought for a nanosecond about leaving,” Baker said.

His wife, UW Medicine biochemist Hannele Ruohola-Baker, is a noted stem-cell biology researcher. Baker told The Associated Press that Ruohola-Baker was beside him when he got the news about the Nobel early this morning, and that she immediately started screaming.

“It was a little deafening,” Baker told AP.

GeekWire’s Taylor Soper contributed to this report.