Editor’s note: This series profiles six of the Seattle region’s “Uncommon Thinkers”: inventors, scientists, technologists and entrepreneurs transforming industries and driving positive change in the world. They will be recognized Dec. 11 at the GeekWire Gala. Uncommon Thinkers is presented in partnership with Greater Seattle Partners.

Before he launched a venture-backed biotech startup, prior even to landing a research role in one of the world’s premier academic labs, Anindya Roy arrived in the U.S. with two suitcases and $2,000 in the bank.

Roy grew up in rural India in a home that lacked electricity and running water during his childhood. A passion for science fueled his ambitions, leading him to earn degrees at the University of Calcutta and the Indian Institute of Technology in Kharagpur.

Then he made the bold leap in 2008 to pursue his PhD at Arizona State University, which led to a postdoctoral fellowship with David Baker, a University of Washington professor who last year won a Nobel Prize in Chemistry.

In 2023, Roy co-founded Seattle-based Lila Biologics, which uses the AI-powered protein design technology developed in the Baker lab to pursue cutting-edge medical therapies.

“Anindya is a brilliant and determined scientist and innovator who has made key contributions across diverse areas of science,” Baker said, “and is charting a most exciting path forward with Lila.”

Dr. Sheila Gujrathi, a biotech executive and chair of Lila’s board of directors, described Roy as “a thoughtful and creative problem-solver who approaches each challenge with genuine humility. He stands out not just for his innovative thinking, but also for his sincere kindness and integrity.”

Unlocking potential

In the lab at ASU, Roy focused on protein engineering for sustainable energy resources, but he was eager to apply those skills to medicine. He sent an email to Baker who invited him for an interview and tour of his protein creation lab, which delivered a kid-in-a-candy-shop kind of experience.

“That was the most exciting thing because it was such an amazingly diverse set of computational protein design problems, aiming to solve so many different kinds of things,” Roy recalled.

He jumped at the postdoc opportunity, joining the lab that is part of the UW’s Institute for Protein Design (IPD). There he began exploring the groundbreaking tools for creating proteins from scratch, ultimately pursuing a molecule that showed promise in cancer care and the treatment of fibrotic diseases that form scar tissue in various organs.

Roy eventually entered the IPD’s Translational Investigator Research Program, which gives entrepreneurial scientists the support and training to begin commercializing their discoveries. Two years ago, he and Jake Kraft, a fellow IPD postdoc, licensed the molecule they worked on at the UW and launched Lila.

While Roy has found success in his research, scientific inquiry can be slow-going and frustrating. To unwind he turns to intense weight training and goes to live shows — he caught Lady Gaga this summer and loves house music. Roy also whips up French pastries and tortes worthy of “The Great British Bake Off.”

And sometimes he reflects on the unlikely journey that led him to launching his own company.

“Whenever I get kind of discouraged or depressed about things, I look back at my career trajectory and how far I’ve come,” Roy said. “That does give me a lot of strength.”

The power of science

His startup is also making confidence-boosting progress. Lila has raised $10 million from investors and released two AI-powered platforms for creating therapeutic proteins. One is focused on targeted radiotherapy, generating proteins that precisely bind to tumors and carry radioactive isotopes that zap cancerous cells. The other platform is used to build long-acting injectable drugs that slowly release medicine over weeks or months.

In September, the seven-person startup announced a collaboration with pharmaceutical giant Eli Lilly to develop therapies for treating solid tumors.

Roy is grateful for U.S. support of the basic research that underpins the work being done at universities, institutions and companies nationwide. He’s also worried about federal funding cuts being pursued by the current administration that threaten America’s leadership in scientific innovation.

Because while he has been doing de novo protein design for more than a decade, Roy is still amazed by what the technology can do and how fast it’s evolving.

“This is almost like science fiction,” Roy said. “Years ago, you never imagined what we are doing right now. You are designing molecules in the computer, and you are putting them in actual living systems, and it’s doing what it’s supposed to do. It is pure science fiction.”

A Seattle biotech startup born from a Nobel laureate’s lab has landed $12.7 million and partnerships with pharmaceutical giants Pfizer and Kite Pharma by using AI to design proteins that mount a multi-pronged attack on diseases.

Accipiter Biosciences emerged from stealth today with a leadership team that includes researchers who worked at the University of Washington’s Institute for Protein Design under David Baker, a 2024 Nobel Prize in Chemistry winner for his breakthroughs in building proteins from scratch.

The company is using artificial intelligence tools developed at the institute to engineer de novo proteins that have the unusual ability to bind multiple cellular targets at once, potentially amplifying their illness-fighting impact.

“We want to establish this new modality,” said Matthew Bick, Accipiter Bio’s co-founder and CEO. The strategy, he added, could unlock new ways to more effectively treat complicated diseases.

There’s evidence that combinations of drugs sometimes perform better than single therapies, but the challenge has been coordinating their actions so they work together at the same location.

In some forms of cancer, for example, multiple cell functions need to be turned on simultaneously to produce helpful molecules that work synergistically to create an effect “that is not just additive, it’s multiplicative,” Bick said.

The approach could also speed U.S. Food and Drug Administration approval and cut costs. Typically, when two drugs are combined to treat a condition, each must undergo its own expensive Phase 1 safety trial, followed by an additional trial testing them together. A single multi-functional drug would need just one Phase 1 trial.

Multiple avenues to drug therapies

Accipiter Bio has entered into a collaboration and license agreement with Pfizer to research and engineer new molecules. The deal provides an upfront payment for the startup and the potential to earn more than $330 million if Accipiter Bio hits certain milestones and through royalties.

“With Accipiter’s platform technology and collaboration, Pfizer aims to solve complex therapeutic problems with biologics that may have previously been unattainable,” said Jeffrey Settleman, Pfizer Oncology R&D’s chief scientific officer.

Accipiter Bio also has an agreement with the oncology drug company Kite, which is owned by Gilead Sciences, to design proteins for use in cell therapies. The arrangement similarly includes initial funding with the possibility of milestone payments and royalties. Kite has the option of acquiring molecules created through the arrangement and develop them into therapeutics for global sales.

On top of those efforts, Accipiter Bio has four of its own drug-development programs. Two programs are preparing for formal FDA discussions about human testing — a stage called pre-IND .

Bick would not provide details on the efforts, but said the company is researching agents for treating cancers and irritable bowel syndrome, among other ailments.

Funding and leadership

Flying Fish Partners and Takeda co-led the seed round. Additional investors are Columbus Venture Partners, Cercano Capital, Washington Research Foundation, Alexandria Investments, Pack Ventures and Argonautic Ventures.

“We’ve reached the point where computation isn’t just speeding up biology,” said Heather Gorham, principal at Flying Fish Partners and Accipiter board member. “It’s expanding what’s biologically possible.”

The startup launched in March 2023 and previously raised about $800,000 to get off the ground. Bick was a senior fellow in Baker’s lab for more than seven years and later a senior director for Seattle’s Neoleukin Therapeutics.

Accipiter Bio has 17 employees. The leadership team has three members in addition to Bick.

• Javier Castellanos, co-founder and chief technologist, was a graduate student with Baker; co-founder and CTO of Cyrus Biotechnology, another protein design startup; and a past director at Neoleukin.
• Hector Rincon-Arano, co-founder and chief scientist, was with Seagen (now a division of Pfizer) for more than seven years where he helped take a therapeutic from proof-of-concept to the first step of getting a new drug approved. He was also briefly at Neoleukin.
• William Canestaro, chief operating officer and chief strategy officer, has worked on the business and investing side of biotech with roles at the UW’s Michael G. Foster School of Business, Washington Research Foundation, Pack Ventures, Pioneer Square Labs, Cyclera Therapeutics and others. He has served on the board of directors for multiple startups.

Building on experience

While the strategy of using AI to build a new class of proteins could open the door to groundbreaking therapies, drug development is a risky business.

Neoleukin was a biotech company co-founded by Baker that spun out of the UW in 2019. The startup’s lead drug candidate, an engineered protein used in cancer treatment, under-performed in a Phase 1 trial. Neoleukin laid off many of its employees before merging with another company.

The three co-founders met at the startup and gained valuable technical and strategic lessons from the experience, Bick said. That included the need to have multiple drug programs running at once and insights into preventing immunogencity, which is an unwanted immune response to foreign bodies.

“We were part of the team,” he said, “that took the first fully de novo protein into patients.”

Researchers from Nobel Laureate David Baker’s lab and the University of Washington’s Institute for Protein Design (IPD) have used artificial intelligence to design antibodies from scratch — notching another game-changing breakthrough for the scientists and their field of research.

“It was really a grand challenge — a pipe dream,” said Andrew Borst, head of electron microscopy R&D at IPD. Now that they’ve hit the milestone of engineering antibodies that successfully bind to their targets, the research “can go on and it can grow to heights that you can’t imagine right now.”

Borst and his colleagues are publishing their work in the peer-reviewed journal Nature. The development could supercharge the $200 billion antibody drug industry.

Before the advent of AI-based tools, scientists made antibodies by immunizing animals and hoping they would produce useful molecules. The process was laborious and expensive, but tremendously important. Many powerful new drugs for treating cancer and autoimmune diseases are antibody-based, using the proteins to hit specific targets.

Baker, who won the Nobel Prize in Chemistry last year, was recognized for his work unraveling the molecular design of proteins and developing AI-powered tools to rapidly build and test new ones. The technology learns from existing proteins and how they function, then creates designs to solve specific challenges.

In the new research, the team focused on the six loops of protein on the antibody’s arms that serves as fingers that grab its target. Earlier efforts would tweak maybe one of the loops, but the latest technology allows for a much bigger play.

“We are starting totally from scratch — from the loop perspective — so we’re designing all six,” said Robert Ragotte, a postdoctoral researcher at IPD. “But the rest of the antibody, what’s called the framework, that is actually staying the same.”

The hope is that by retaining the familiar humanness of most of the antibody, a patient’s immune system would ignore the drug rather than mount an offense against an otherwise foreign molecule.

The researchers tested their computer creations against multiple real-world targets including hemagglutinin, a protein on flu viruses that allow them to infect host cells; a potent toxin produced by the C. difficile bacteria; and others.

The lab tests showed that in most cases, the new antibodies bound to their targets as the online simulations predicted they would.

“They were binding in the right way with the right shape against the right target at the spot of interest that would potentially be useful for some sort of therapeutic effect,” Borst said. “This was a really incredible result to see.”

Borst added that the computational and wet lab biologists worked closely together, allowing the scientists to refine their digital designs based on what the real-life experiments revealed.

The software used to create the antibodies is freely available on GitHub for anyone to use. Xaira Therapeutics, a well-funded biotech startup led by IPD alumni, has licensed some of the technology for its commercial operations and multiple authors on the Nature paper are currently employed by the company.

While the antibodies created as part of the research demonstrated the software’s potential, there are many more steps to engineering a potential therapy. Candidate drugs need to be optimized for additional features such as high solubility, a strong affinity for a target and minimizing immunogenicity — which is an unwanted immune response.

Before joining IPD four years ago, Ragotte was a graduate student doing conventional antibody discovery and characterization using animals.

The idea that one day you could get on a computer, choose a target, and create a DNA blueprint for building a protein was almost unimaginable, he said. “We would talk about it, but it didn’t even seem like a tractable problem at that point.”

The Nature study is titled “Atomically accurate de novo design of antibodies with RFdiffusion.” The lead authors include Nathaniel Bennett, Joseph Watson, Robert Ragotte, Andrew Borst, DéJenaé See,
Connor Weidle and Riti Biswas, all of whom were affiliated with the UW at the time the research was conducted, and Yutong Yu of the University of California, Irvine. David Baker is the senior author.

Additional authors are: Ellen Shrock, Russell Ault, Philip Leung, Buwei Huang, Inna Goreshnik, John Tam, Kenneth Carr, Benedikt Singer, Cameron Criswell, Basile Wicky, Dionne Vafeados, Mariana Sanchez, Ho Kim, Susana Torres, Sidney Chan, Shirley Sun, Timothy Spear, Yi Sun, Keelan O’Reilly, John Maris, Nikolaos Sgourakis, Roman Melnyk and Chang Liu.