Spinning out science startups: UW’s Institute for Protein Design brings research beyond ivory tower

IPD’s commercial impact in Seattle. Spinouts are Monod Bio, Arzeda, Icosavax, Neoleukin Therapeutics, Cyrus Biotechnlogy, PvP Bio, A-Alpha Bio, and Mopac Bio. IPD scientists are co-founders and advisors at cell therapy companies Sana Biotechnology, Lyell Immunopharma and Outpace Bio. (IPD Image)

The Institute for Protein Design is an innovation factory.

Since launching a decade ago, the University of Washington institution has grown to about 200 researchers and spun out eight startups wielding protein-design software to forge new drugs, vaccines, and enzymes. IPD spinouts have collectively raised more than $1 billion and helped fuel a biotech boom in Seattle, where they have all landed.

IPD researchers also keep close ties to the institution after joining startups, forming a pool of advisors that nurture the next generation of companies within the bustling institution.

The IPD aims to fosters a culture of collaboration among its interdisciplinary mix of software engineers, drug development experts and other scientists, according to director David Baker, who won the prestigious “Breakthrough” award in the life sciences in 2021. His job, he said, is to bring the right people together and provide an environment for interaction.

“I just kind of stand back and let the magic happen,” said Baker.

It’s the human connections that foster entrepreneurship within an institution that has risen to the challenge of moving research beyond the ivory tower since its launch ten years ago.

“You’re surrounded by people who know some of the problems you’re running into,” said Anindya Roy, an IPD scientist and co-founder of Lila Biologics, an emerging spinout within the IPD. “You just go to them.”

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

Incubating a spinout

Lila’s journey to nascent startup began several years ago as a research project.

Roy was designing proteins to target integrins, a family of molecules involved in a range of conditions.

Software advances within the last two years or so finally enabled a breakthrough. Roy successfully built a drug-like protein targeting an integrin involved in a deadly condition that scars the lungs, idiopathic pulmonary fibrosis.

A minibinder in blue, bound to its target. (IPD Image / Anindya Roy)

Roy’s team found that the protein neutralizes the integrin in cells and counteracts disease in mouse models of the respiratory condition. The treatment is stable at room temperature and is delivered to the lungs via a nebulizer.

The researchers went on to design proteins to other integrins involved in cancer and metabolic disease. The proteins, called minibinders, are small, sleek and easily synthesized.

“With these really precise protein design methods you can now make compounds that can target many different members of the family,” said Baker of Roy’s research. “It just really wasn’t possible before.”

As Roy’s project matured, he moved into a separate arm of the IPD, its translational research program. That’s where IPD entrepreneurs go when they are ready to build a company.

Lila Biologics co-founders Jake Kraft (left) and Anindya Roy. (IPD Photo)

Encouraging entrepreneurship

Separating entrepreneurship into a distinct program takes the load off Baker and enables him and his team to focus on what they do best: basic research.

See also  Seattle startup raises $14M to fuel ambitious plan for a social network built on the blockchain

The translational program has its own head, Lance Stewart, and eases access to advice and funding. “It gives researchers a chance to feel some autonomy and their own personal responsibility, including fundraising of grants in their own lab space,” said Stewart. And that helps prepare scientists for the riskier task of launching a company.

Program advisors include Ingrid Swanson Pultz, co-founder of IPD spinout PvP Biologics, which was acquired by Takeda in 2020 for $330 million. Another is former PvP CEO Adam Simpson, now CEO of IPD vaccine spinout Icosavax. Both are part of Lila’s management team.

IPD chief strategy and operations officer Lance Stewart. (IPD Photo)

“There is an intoxicating culture here that creates so much energy, it’s a lot of smart people in one place,” said Jake Kraft, who is also a Lila co-founder, along with Xinru Wang and Hua Bai. “We are constantly encouraged to talk to each other and communicate and just bounce ideas off each other. David calls it the communal brain. That has been his philosophy and it works.”

Sources of seed funding include UW startup program WE-REACH and the nonprofit Washington Research Foundation, which together provided $640,000 for Lila.

Even IPD’s software is licensed with an eye to furthering innovation. The tools are available through the Rosetta Commons, which provides a mechanism for community-wide collaboration and access through 70 commercial and 30,000 academic licenses. The IPD also intentionally builds companies within Seattle, said Stewart, which helps build its network.

Baker aims to foster a creative, fun work environment where interactions happen spontaneously, he said. Twice-weekly research talks and happy hours help that along.

“I think part of what’s drawn people from all over the world here is the prospect of starting a company,” said Baker. “When those brilliant people come in, that leads to new scientific advances, which then enables new companies. It’s really a nice, feedback kind of thing.”

And there are more startups in the wings. “There are quite a few nascent companies in the works, in a very broad range of different areas,” said Baker.

Other IPD researchers in the translational program include George Ueda and James Lazarovits, who are engineering nanoparticles to regenerate blood vessels. Stephanie Berger recently fledged from the program: she co-founded Mopac Biologics, which is developing a minibinder treatment for inflammatory bowel disease, and is the company’s chief scientific officer.

A 5-year $45 million award from The Audacious Project at TED in 2019 also bolsters IPD’s science and helped it almost double in size.

The IPD’s emphasis on basic research seeds a lot of new ideas for companies. And the speed of innovation is accelerating, said Baker.

The Institute for Protein Design occupies the entire fourth floor of UW’s Molecular Sciences and Engineering building. (IPD Photo)

From software to startup

The IPD’s science is propelled by its software. And software is powering a shift in how new therapeutics are designed and developed.

See also  Tech Moves: Former Expedia exec named Remitly CFO; Beckett hires Seattle exec as CEO; more

This March, the IPD published a study in Nature showing how its Rosetta software could create drug-like “minibinders” like the ones made by Lila. In April, the IPD showcased proteins that act like miniature axle and rotor assemblies. A week later the IPD unveiled custom biosensors for detecting coronavirus antibodies in blood.

IPD researcher Minkyung Baek. (IPD Photo)

Last December, the IPD was lauded by Science magazine with its “Breakthrough of the Year” award for 2021. IPD researcher Minkyung Baek and her colleagues helped crack open a long-standing challenge: predicting how a protein folds based on the sequence of its amino acid building blocks. The IPD took home the award with Alphabet’s DeepMind for its software tool that accomplished the task with speed and unprecedented accuracy.

The new tools are already being deployed by biopharma companies to help design potential drugs.

“The research is advancing at just an incredibly rapid pace now. It seems like every couple of months, we can do something that we couldn’t do before,” said Baker. “That’s opening really large numbers of new company opportunities. It’s a really exciting time.”

Other IPD spinouts include industrial enzyme company Arzeda, which recently raised $33 million; drug development startup Cyrus Biotechnology, which has more than 90 industry partners; and A-Alpha Bio, which is helping develop therapies against COVID-19 variants.

Just last week, a vaccine designed by IPD and other UW researchers won approval in South Korea. The vaccine, licensed to SK bioscience, is the first approved medicine based on computational protein design — a milestone that stands to increase the confidence of investors, said IPD researcher Neil King in a previous interview with GeekWire.

And investors are already bullish on the field. Last spring, computationally-driven biotech company Insitro landed $400 million in venture funding and Recursion pulled in $436 million in its IPO. In November, Alphabet spun out Isomorphic Labs to leverage DeepMind’s software for drug design.

In Seattle, it’s not just IPD spinouts that benefit from the advice and influence of the institution — other biotech companies harness its expertise.

Baker, for instance, is a scientific co-founder of Seattle cell therapy giants Sana Biotechnology and Lyell Immunopharma. IPD postdoctoral fellows Marc Lajoie and Scott Boyken are also co-founders of Lyell, as well as Lyell spinout Outpace Bio. Baker has co-founded ten companies and advises eight more.

All that has helped make Seattle area the eighth largest life sciences market in the U.S. and fueled a surge in life sciences employment. Soon, IPD may rack up another successful startup.

Roy and Kraft will shop Lila to venture firms this summer. They aim to convince investors that they have a potential treatment for respiratory disease and a platform to develop similar drug-like proteins down the line.

See also  David Baker, head of Seattle’s Institute for Protein Design, launches London biotech startup

One day Lila’s founders may advise the next generation of entrepreneurs at IPD. Said Roy: “If we are successful, hopefully we can come back.”

See the list below for more info on IPD-linked spinouts, listed by date of launch.


Founded: 2008 (Founded with tech from the lab of director David Baker, prior to IPD’s formal launch)

Focus: Metabolic Engineering

CEO: Alexandre Zanghellini, a former UW graduate student in Baker’s lab and a company co-founder.

Related Coverage: Funding News: Enzyme design startup lands $33M

Inside Arzeda’s synthetic biology lab, where industrial ingredients are brewed like beer

Cyrus Biotechnology

Founded: 2014

Focus: Drug design and development.

CEO: Lucas Nivon, a former UW postdoctoral fellow in Baker’s lab and a company co-founder.

Related Coverage: Funding news: Cyrus lands $18M and buys startup developing COVID-19 therapeutic

Seattle startup Cyrus inks protein-design deal with immune biotech Selecta worth up to $1.5 billion

PvP Biologics (acquired by Takeda)

Founded: 2014, acquired 2020

Focus: Oral therapeutic for celiac disease.

CEO: IPD investigator Ingrid Swanson Pultz was a company co-founder and founding CEO. Long-term life sciences executive Adam Simpson later became CEO; he is now CEO of Icosavax.

Related Coverage: After buying Seattle startup PvP Biologics for $330M, Takeda to advance celiac disease treatment

A-Alpha Bio

Founded: 2018

Focus: Protein drug target screening.

CEO: David Younger, a company co-founder and former UW graduate student in the lab of David Baker.

Related Coverage: University of Washington spinout A-Alpha Bio snags $20M for protein-discovery platform


Founded: 2018

Focus: Nanoparticle protein vaccines

CEO: Adam Simpson, former CEO of IPD spinout PvP Biologics and an Icosavax co-founder.

Related Coverage: Icosavax stock skyrockets 200% on first day of trading for newly public Seattle biotech company

Icosavax posts COVID-19 vaccine data ‘below our expectations’ as shares plummet more than 60%

COVID-19 shots with Seattle origins reach regulatory milestones in South Korea, India

Neoleukin Therapeutics

Founded: 2018

Focus: Mimetics of protein regulators called cytokines, for oncology.

CEO: Jonathan Drachman, former chief medical officer and head of R&D at Seagen.

Related Coverage: Cancer-fighting startup Neoleukin merging with Aquinox in $40M deal, 8 months after UW spinout

Monod Bio

Founded: 2021

Focus: Custom biosensors

CEO: Daniel-Adriano Silva, company co-founder and former head of research at IPD spinout Neoleukin Therapeutics He is also a former UW postdoctoral fellow in David Baker’s lab.

Related Coverage: Biosensor startup Monod lands $6M and spins out of Univ. of Washington’s Institute for Protein Design

Mopac Biologics

Founded: 2022

Focus: Minibinder therapeutics for inflammation.

CEO: Acting CEO is Adam Simpson, currently Icosavax CEO.

Related Posts

Why are top accounting software for nonprofits necessary

The best top accounting software for nonprofits

Accounting software can help simplify and streamline bookkeeping and accounting tasks, ensuring that financial records are in order and reporting standards are met. msiu.info share you to…

Sea.citi merges with WTIA in combination of two civic-focused tech industry nonprofits in Seattle

Former Seattle Mayor Jenny Durkan announced the launch of Sea.citi in 2018. (GeekWire File Photo / Monica Nickelsburg) Sea.citi, a nonprofit that launched in 2018 with the…

Survey: 88% of U.S. startup leaders worried about fundraising, signaling slower growth ahead

Qualtrics / Delighted Graphic New research published Monday quantifies the growing sense of caution among U.S. startup leaders, as economic turmoil creates concerns about cash, and causes…

About to take early stage startup job? Amid concern of downturn, CEO says to ask these hard questions

Kieran Snyder of Textio at the 2019 GeekWire Awards. (GeekWire File Photo) In addition to the usual questions about pay and benefits and culture and so on,…

Why this Florida venture capitalist is touring Seattle’s tech scene

Pablo Casilimas. (Photos courtesy of Casimilias) When Pablo Casilimas gave his girlfriend, a travel nurse, a list of cities he would prefer to live in, he put…

Maveron raises $225M for its 8th fund to back more consumer-focused startups

The Maveron team. (Maveron Photo) The news: Maveron, a venture capital firm founded 24 years ago that invests in consumer-oriented startups, raised $225 million for its eighth…

Leave a Reply

Your email address will not be published. Required fields are marked *