Bill Gates and the Gates Foundation are raising the alarm over the deadly impacts of international funding cuts in global health. Slashed budgets are projected to reverse decades of progress, causing the number of children dying before their fifth birthday to rise for the first time this century. An estimated 4.8 million children are expected to die this year, an increase of 200,000 deaths compared to last year.

“That is something that we hope never to report on, but it is a sad fact. And there are many causes, but clearly one of the key causes has been significant cuts in international development assistance from a number of high-income countries,” said Mark Suzman, CEO of the Gates Foundation, in a briefing with media this week.

Suzman specifically called out the U.S., the United Kingdom, France and Germany for “making significant cuts” to their support. Internationally, funding plunged 26.9% below last year’s levels, according to the philanthropy.

The Gates Foundation today released its annual Goalkeepers Report, which tracks progress on measures including poverty, hunger, access to clean water and energy, environmental benchmarks and other metrics.

The Seattle-based foundation worked with the University of Washington’s Institute for Health Metrics and Evaluation to model the effects of reduced assistance. The researchers found that if the cuts to aid persist or worsen, an additional 12 million to 16 million children could die over the next 20 years.

While offering dire projections, the document aims to be a call to action for governments and philanthropists large and small.

“This report is a roadmap to progress,” Gates writes, “where smart spending meets innovation at scale.”

The billionaire Microsoft co-founder calls out some specific areas that could yield the most benefit, including primary healthcare, routine immunizations, the development of improved vaccines and new uses of data.

Modeling in the report predicts that by 2045, better vaccines for respiratory syncytial virus (RSV) and pneumonia could save 3.4 million children, while new malaria tools could save an additional 5.7 million kids. Shots of lenacapavir could successfully prevent and treat HIV.

The foundation calls attention to the life-saving benefits of vaccinations as the U.S. Secretary of Health Robert F. Kennedy Jr. continues to undercut public support of vaccines.

With the backdrop of reduced federal funding for global humanitarian causes and backpedaling on vaccinations, Gates earlier this year announced plans to give away $200 billion — including nearly all of his wealth — over the next two decades through the Gates Foundation.

The Seattle-based organization, which celebrates its 25th anniversary this year, will sunset its operations on Dec. 31, 2045. The philanthropy is the world’s largest and has already disbursed $100 billion since its founding.

“If we do more with less now — and get back to a world where there’s more resources to devote to children’s health — then in 20 years, we’ll be able to tell a different kind of story,” Gates writes in the report. “The story of how we helped more kids survive childbirth, and childhood.”

David Baker’s lab at the University of Washington is announcing two major leaps in the field of AI-powered protein design. The first is a souped-up version of its existing RFdiffusion2 tool that can now design enzymes with performance nearly on par with those found in nature. The second is the release of a new, general-purpose version of its model, named RFdiffusion3, which the researchers are calling their most powerful and versatile protein engineering technology to date.

Last year, Baker received the Nobel Prize in Chemistry for his pioneering work in protein science, which includes a deep-learning model called RFdiffusion. The tool allows scientists to design novel proteins that have never existed. These machine-made proteins hold immense promise, from developing medicines for previously untreatable diseases to solving knotty environmental challenges.

Baker leads the UW’s Institute for Protein Design, which released the first version of the core technology in 2023, followed by RFdiffusion2 earlier this year. The second model was fine-tuned for creating enzymes — proteins that orchestrate the transformation of molecules and dramatically speed up chemical reactions.

The latest accomplishments are being shared today in publications in the leading scientific journals Nature and Nature Methods, as well as a preprint last month on bioRxiv.

A better model for enzyme construction

In the improved version of RFdiffusion2, the researchers took a more hands-off approach to guiding the technology, giving it a specific enzymatic task to perform but not specifying other features. Or as the team described it in a press release, the tool produces “blueprints for physical nanomachines that must obey the laws of chemistry and physics to function.”

“You basically let the model have all this space to explore and … you really allow it to search a really wide space and come up with great, great solutions,” said Seth Woodbury, a graduate student in Baker’s lab and author on both papers publishing today.

In addition to UW scientists, researchers from MIT and Switzerland’s ETH Zurich contributed to the work.

The new approach is remarkable for quickly generating higher-performing enzymes. In a test of the tool, it was able to solve 41 out of 41 difficult enzyme design challenges, compared to only 16 for the previous version.

“When we designed enzymes, they’re always an order of magnitude worse than native enzymes that evolution has taken billions of years to find,” said Rohith Krishna, a postdoctoral fellow and lead developer of RFdiffusion2. “This is one of the first times that we’re not one of the best enzymes ever, but we’re in the ballpark of native enzymes.”

The researchers successfully used the model to create proteins calls metallohydrolases, which accelerate difficult reactions using a precisely positioned metal ion and an activated water molecule. The engineered enzymes could have important applications, including the destruction of pollutants.

The promise of rapidly designed catalytic enzymes could unleash wide-ranging applications, Baker said.

“The first problem we really tackled with AI, it was largely therapeutics, making binders to drug targets,” he said. “But now with catalysis, it really opens up sustainability.”

The researchers are also working with the Gates Foundation to figure out lower-cost ways to build what are known as small molecule drugs, which interact with proteins and enzymes inside cells, often by blocking or enhancing their function to effect biological processes.

The most powerful model to date

While RFdiffusion2 is fine-tuned to make enzymes, the Institute for Protein Design researchers were also eager to build a tool with wide-ranging functionality. RFdiffusion3 is that new AI model. It can create proteins that interact with virtually every type of molecule found in cells, including the ability to bind DNA, other proteins and small molecules, in addition to enzyme-related functions.

“We really are excited about building more and more complex systems, so we didn’t want to have bespoke models for each application. We wanted to be able to combine everything into one foundational model,” said Krishna, a lead developer of RFdiffusion3.

Today the team is publicly releasing the code for the new machine learning tool.

“We’re really excited to see what everyone else builds on it,” Krishna said.

And while the steady stream of model upgrades, breakthroughs and publications in top-notch journals seems to continue unabated from the Institute for Protein Design, there are plenty of behind-the-scenes stumbles, Baker said.

“It all sounds beautiful and simple at the end when it’s done,” he said. “But along the way, there’s always the moments when it seems like it won’t work.”

But the researchers keep at it, and so far at least, they keep finding a path forward. And the institute continues minting new graduates and further training postdocs who go on to launch companies or establish their own academic labs.

“I don’t surf, but I sort of feel like we’re riding a wave and it’s just fun,” Baker said. “I mean, it’s so many, so many problems are getting solved. And yeah, it’s really exhilarating, honestly.”

The Nature paper, titled “Computational design of metallohydrolases,” was authored by Donghyo Kim, Seth Woodbury, Woody Ahern, Doug Tischer, Alex Kang, Emily Joyce, Asim Bera, Nikita Hanikel, Saman Salike, Rohith Krishna, Jason Yim, Samuel Pellock, Anna Lauko, Indrek Kalvet, Donald Hilvert and David Baker.

The Nature Methods paper, titled “Atom-level enzyme active site scaffolding using RFdiffusion2,” was authored by Woody Ahern, Jason Yim, Doug Tischer, Saman Salike, Seth Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus Bauer, Regina Barzilay, Tommi Jaakkola, Rohith Krishna and David Baker.

Seattle biotech startup Curi Bio, which enables the screening of new drugs using cells and 3D tissue models derived from human cells, announced $10 million in new funding.

Curi Bio’s customers include large biopharmaceutical and biotech companies such Novo Nordisk, Eli Lilly, Astrazeneca, Pfizer, Boehringer Ingelheim, UCB, Novartis and others. Its Series B round was led by Seoul-based DreamCIS, which supports biopharma R&D through extensive research services.

“We are thrilled to partner with DreamCIS, who shares our conviction that drug discovery urgently needs more human-relevant data at the preclinical stage,” said Michael Cho, Curi Bio’s chief strategy officer, in a statement. “The vast majority of new drugs fail in human clinical trials because preclinical animal and 2D cell models have failed to be good predictors of human outcomes.”

Curi Bio’s platform integrates bioengineered tissues created from induced pluripotent stem cells (iPSCs) with data collection and analysis. The additional funding will expedite its development of new platforms for cardiac, skeletal muscle, metabolic, smooth muscle and neuromuscular diseases, the company said.

The Seattle area is a hub of life science and biotech companies, including numerous efforts focused on AI-assisted research. Researchers have emphasized the need to test computer-generated drug candidates in the lab to verify their capabilities and impacts.

“Curi Bio’s unique integration of cells, systems, and data is a paradigm shift for preclinical drug discovery,” said Jeounghee Yoo, CEO of DreamCIS. “We were incredibly impressed by the company’s innovative platforms and their ability to generate functional data from 3D human tissues at scale.”

Curi Bio has raised $20 million from investors and $12 million from federal grants.

The company spun out of the University of Washington a decade ago as NanoSurface Biomedical. In April, Curi Bio celebrated the opening of its new 13,942-square-foot headquarters and research facility on the Seattle waterfront.

In an unusual act of philanthropy, an anonymous donor has committed more than $50 million to the University of Washington to support the little-known field of medical laboratory science. The funds will be distributed over the next half-century.

UW leaders called the gift “transformational,” noting it’s the largest gift they’re aware of for this particular specialty.

The donation will immediately impact the current class of 35 students in the Medical Laboratory Science Undergraduate Program by covering their tuition costs — waiving about $9,000 per student — during the two quarters of clinical rotations in their senior year.

When the students learned the news at an event Monday at the UW’s Seattle campus, many began to cry.

Students who graduate with a four-year degree in medical laboratory sciences are essential, behind-the-scenes healthcare workers. They collect biological samples, process the material, help interpret the results, and provide necessary data for individual patients and public health institutions.

Dr. Geoff Baird, chair of the Department of Laboratory Medicine and Pathology at UW Medicine, praised the program for training these healthcare professionals.

“No one really ever pays attention to the glue that holds the whole thing together,” Baird said of their critical role.

Dr. Tim Dellit, UW Medicine CEO and the dean of the School of Medicine Tim Dellit, echoed the sentiment in sharing news of the gift with the students. “In many ways, you are the unsung heroes,” he said. “You work behind the scenes that allow all of the healthcare machinery to continue to work.”

The field, however, is facing a challenge. Despite its importance, the workforce is aging, and there aren’t enough students graduating with the needed expertise, said Baird. The new gift is designed to help address that shortage by expanding the two-year medical laboratory sciences program from the current 70 students to 100 over the next decade.

Graduates earn a four-year bachelor’s degree and professional certifications, ready for employment at clinics and hospitals.

The university didn’t share details about the donor, except to say that he is a Washington resident and a big fan of the longtime, local burger franchise, Dick’s Drive-In. To celebrate the news, he requested that the students were served burgers at the announcement.

For the students, the financial relief felt profound.

Senior Lily Koplowitz-Fleming was grateful that she won’t have to juggle an additional job on top of the nine-hours, five-days a week that’s required by the clinical rotation. Instead, she’ll be able to focus on the training for her future career, which she said is a meaningful blend of “skills-based and knowledge-based” work.

Another senior, Keila Uchimura, also said she enrolled in the program because she “really likes being able to see the direct impact you make.”

While medical lab scientists typically work in the background, their roles became more noticeable during the pandemic as people rushed to get tested and waited anxiously for results.

Baird praised the donor and his gift in an earlier GeekWire interview.

“The morality, the righteousness of it — it’s just really impressive that someone was able to find that generosity,” he said. “And we’re all in the state of Washington forever indebted — not just the students.”

Creating a virtual brain may sound like a science-fiction nightmare, but for neuroscientists in Japan and at Seattle’s Allen Institute, it’s a big step toward a long-held dream.

They say their mouse-cortex simulation, run on one of the world’s fastest supercomputers, could eventually open the way to understanding the mechanisms behind maladies such as Alzheimer’s disease and epilepsy — and perhaps unraveling the mysteries of consciousness.

“This shows the door is open,” Allen Institute investigator Anton Arkhipov said today in a news release. “It’s a technical milestone giving us confidence that much larger models are not only possible, but achievable with precision and scale.”

Arkhipov and his colleagues describe the project in a research paper being presented this week in St. Louis during the SC25 conference on high-performance computing. The simulation models the activity of a whole mouse cortex, encompassing nearly 10 million neurons connected by 26 billion synapses.

To create the simulation, researchers fed data from the Allen Cell Types Database and the Allen Connectivity Atlas into Supercomputer Fugaku, a computing cluster developed by Fujitsu and Japan’s RIKEN Center for Computational Science. Fugaku is capable of executing more than 400 quadrillion operations per second, or 400 petaflops.

The massive data set was translated into a 3-D model using the Allen Institute’s Brain Modeling ToolKit. A simulation program called Neulite brought the data to life as virtual neurons that interact with each other like living brain cells.

Scientists ran the program in different scenarios, including an experiment that used the full-scale Fugaku configuration to model the entire mouse cortex.

“In our simulation, each neuron is modeled as a large tree of interacting compartments — hundreds of compartments per neuron,” Arkhipov said in comments emailed to GeekWire. “That is, we are capturing some sub-cellular structures and dynamics within each neuron.”

During the full-scale simulation, it took no more than 32 seconds to simulate one second of real-time activity in a living mouse brain. “This level of performance — 32 times slower than real time — is quite impressive for a system of this size and complexity,” Arkhipov said. “It is not uncommon to see a factor of thousands of times slower for such very detailed simulations (even much smaller than ours).”

The researchers acknowledge that much more work is needed to turn their simulation into a model capable of tracing the progress of a neurological disease. For example, the model doesn’t reflect brain plasticity — that is, the brain’s ability to rewire its own connections.

“If we want to mention something specific besides plasticity, then one aspect that is missing is the effects of neuromodulators, and the other is that we currently do not have a very detailed representation of sensory inputs in our whole-cortex simulations,” Arkhipov said. “For all of these, we need much more data than currently available to make much better models, although some approximations or hypotheses could be implemented and tested now that we have a working whole-cortex simulation.”

Arkhipov said the project’s long-term goal is to simulate an entire brain, not just the cortex. “There’s a distinction between whole-cortex and whole-brain,” he pointed out. “The mouse cortex (and our model of it) contains about 10 million neurons, whereas the whole mouse brain contains about 70 million neurons.”

A human-brain simulation would require an even greater leap. The human cortex alone contains not just 10 million neurons, but 21 billion.

The good news is that a sufficiently powerful supercomputer might be up to the task. “Our work shows that very detailed microscopic-level simulations of larger brains may be possible sooner than previously expected,” Arkhipov said. “The results suggest that a simulation of the whole monkey brain (such as that of a macaque monkey with 6 billion neurons) can fit on the full-scale Fugaku system.”

Arkhipov said it was important to point out that creating a brain model on a supercomputer “does not mean that such a model is complete or accurate.”

“Here we are talking about technical feasibility of simulations, and it looks like such simulations even at the scale of the monkey brain are now within reach,” he said. “But to make such simulations biologically realistic, much more experimental data production and model building work would need to happen.”

Rin Kuriyama and Kaaya Akira of the University of Electro-Communications in Tokyo are the principal authors of the paper presented at SC25, titled “Microscopic-Level Mouse Whole Cortex Simulation Composed of 9 Million Biophysical Neurons and 26 Billion Synapses on the Supercomputer Fugaku.” In addition to Arkhipov, authors from the Allen Institute include Laura Green, Beatriz Herrera and Kael Dai. The study’s other authors are Tadashi Yamazaki and Mari Iura of the University of Electro-Communications; Gilles Gouaillardet and Asako Terasawa of the Research Organization for Information Science and Technology in Hyogo, Japan; Taira Kobayashi of Yamaguchi University; and Jun Igarashi of the RIKEN Center for Computational Science.

The Allen Institute in Seattle has released the Brain Knowledge Platform, a research aid described as the most comprehensive artificial intelligence tool available for neuroscience.

The project aims to unify brain information from dozens of collaborators, species (such as humans, other primates and mice), and samples that span early development to old age, encompassing diverse data including cell types and disease indicators.

Using AI, this data has been translated into a shared scientific language or format, allowing for “apples-to-apples” comparisons across institutions and organisms to create a much larger dataset for new insights.

“Understanding the brain is not a single institute’s effort,” said Shoaib Mufti, the Allen Institute’s head of data and technology. “So you have to bring the community together in order to understand it.”

There’s an urgent need to better prevent, diagnose and treat neurological conditions. The number of people worldwide living with or dying from conditions like stroke, Alzheimer’s disease and other dementias, and meningitis has increased significantly over recent decades, according to the Institute for Health Metrics and Evaluation.

In 2021, an estimated 3.4 billion people experienced a nervous system condition, which also includes brain injuries and migraines.

To create the Brain Knowledge Platform, the Allen Institute recruited participants to voluntarily share their data. Contributors include the Allen Institute for Brain Science, the Michael J. Fox Foundation for Parkinson’s Research, teams at the University of Washington and Harvard University, the Seattle Alzheimer’s Disease Brain Cell Atlas, or SEA-AD, and others.

Amazon Web Services engineered the tool’s core computing infrastructure while Google developed AI models for the neuroscience. Funding came from the Allen Institute as well as the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies Initiative, or BRAIN Initiative.

Mufti said the resource is designed to be a “discovery platform,” not a traditional research tool where a scientist has a clear idea of what they are looking for. “How you can get to the ‘aha moments’ so you find something unexpected?” he asked.

Using the platform, scientists will be able to look across diseases. Studying the differences and similarities between people diagnosed with Alzheimer’s or Parkinson’s, for example, was previously laborious to make the data comparable.

With the Brain Knowledge Platform, “you can literally line those up side by side in the tool,” said Tyler Mollenkopf, associate director of data and technology at the Allen Institute.

While much of the data comes from research animals, information gathered from human brains — including 84 postmortem donors — is also available, stripped from identifying details.

The resource is offered to scientists for free. The team hopes more organizations contribute data and they’re devising a mechanism to provide attribution to credit researchers for their information, which could encourage sharing.

Given the massive societal impact of brain diseases “a real breakthrough is needed” to better understand them, said Mufti. “Let’s bring all the information together and make it discoverable. I’m hoping that [we] can really move the ball forward in a single community.”

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.”

Seattle’s Parse Biosciences is teed up for an acquisition by Qiagen, a Netherlands-based holding company, in a $225 million cash deal announced this week.

The transaction is expected to close in December.

Parse was co-founded in 2018 by Alex Rosenberg, who was a University of Washington postdoctoral fellow at the time, and Charles Roco, who was a UW graduate student. The company was an early entrant in the nascent field of single-cell RNA sequencing.

Rosenberg and his colleagues discovered a new way to profile RNAs while working in the lab of UW synthetic biology professor Georg Seelig. The business initially launched as Split Biosciences, later changing its name and growing to 110 employees.

Parse has raised more than $50 million from investors, including a $41.5 million Series B round announced in 2022.

Parse launched its first products in 2021 and currently serves 3,000 customers in more than 40 countries. The company is expected to add about $40 million in sales to Qiagen’s 2026 fiscal year.

Parse stated on its website that it will operate as a Qiagen subsidiary and “will maintain full operations in our Seattle headquarters and all other locations around the world.”

There’s a vast range of research questions that RNA profiling can help answer. Understanding which RNAs are present in a cell gives scientists a read-out of active genes. That helps distinguish different cell types, for instance in a blood sample or a petri dish of stem cells turning into heart cells.

Parse touts the accessibility of its technology, which does not require specialized lab equipment to use.

“As our team joins Qiagen, we want to accelerate that mission and extend the reach of our technology to more customers around the world,” said CEO Rosenberg in a statement, adding that Qiagen’s global infrastructure makes it “an ideal partner for our next stage of growth.”

Qiagen has developed technologies to isolate and analyze DNA, RNA and proteins from sources including blood, tissue and other materials. The company has about 5,700 employees in 35 locations. It serves 500,000 customers globally.

The acquisition is subject to clearance under the U.S. Hart-Scott-Rodino Antitrust Improvements Act and other conditions.

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.

Philips Ultrasound is laying off 33 employees from its Bothell, Wash., facility, which serves as a hub for the engineering and manufacturing of ultrasound equipment and other healthcare devices.

The cuts were disclosed in a new filing from the Washington Employment Security Department and will take effect Dec. 31.

Production operators, warehouse operators and technicians were affected by the cuts.

The layoff “is part of a limited restructuring of specific Philips Ultrasound activities within an ongoing strategic transition plan that was announced in 2024,” Mario Fante, Philips’ global external relations director told GeekWire via email.  

The Netherlands-based company has around 1,500 employees in the Seattle area, according to LinkedIn.

In a separate incident, the U.S. Food and Drug Administration in September issued a warning letter to the CEO of Royal Philips citing oversight concerns at the Bothell facility as well as a location in Pennsylvania and another in the Netherlands.

The issues at the Bothell site relate to a lack of documentation regarding the company’s response when ultrasound devices are reported to be defective and either break or perform incorrectly.

“We are not able to determine the adequacy of the proposed corrective actions for your responses for the Bothell and Reedsville facilities. We understand that Philips Ultrasound has revised their complaint procedures and have updated the corresponding complaint records to include additional information and to address the inspectional findings,” states the FDA letter.

The layoffs are “completely unrelated to any regulatory action,” Fante added.

Editor’s note: Story updated to clarify that the FDA warning is unrelated to the reduction in force and to add comment from Fante.

Inventprise, a Redmond, Wash.–based biotechnology company developing vaccines for infectious diseases, is laying off 76 workers, according to a new filing from the Washington Employment Security Department.

GeekWire has reached out to the company for additional details.

The layoffs impact employees across the company’s Redmond and Woodinville facilities, as well as some remote workers. The first separations are effective Dec. 31.

Job titles affected span a wide range of roles, including manufacturing, quality control, R&D, and technical staff, according to the filing.

The company has nearly 200 employees, according to LinkedIn.

Founded in 2012, Inventprise focuses on addressing global health challenges in low- and middle-income countries. Its pipeline includes lead candidate IVT-PCV-25, a pneumococcal conjugate vaccine candidate that is in Phase 2 trials, according to the company’s website.

Inventprise was founded by Dr. Subhash Kapre, who previously worked on vaccine initiatives with the Gates Foundation. The Seattle-based foundation has provided more than $13 million to Inventprise.

Kapre is currently chairman of Inventprise, which is led by CEO Yves Leurquin, a former Takeda exec who joined the company in 2021.