Latest news with #DavidBaker
Geek Wire
5 days ago
- Health
- Geek Wire
UW researchers discover AI-powered breakthrough that could boost precision cancer treatment
The co-lead authors of a study publishing today in Science describing AI-designed proteins for target health theraphies, from left: Julia Bonzanini, Nathan Greenwood and Bingxu Liu. All are researchers with UW Medicine's Institute for Protein Design. (IPD Photo) A breakthrough in the science used to customize the treatment of cancer and other diseases is so promising that researchers at the University of Washington are planning to launch a company to commercialize the technology. The strategy uses artificial intelligence to create proteins that recognize and bind to specific markers on diseased cells, creating what are essentially biological neon signs that attract immune cells to destroy the targets. The research comes from the lab of Nobel laureate David Baker and UW Medicine's Institute for Protein Design, which Baker leads, and is being published today in the journal Science. Additional study authors come from multiple UW departments, the Garcia Lab at Stanford University, and the Scheinberg Lab at Memorial Sloan Kettering Cancer Center. 'Detecting unhealthy cells is one of the main jobs of the immune system, but it doesn't always notice the subtle signs of cancer or viral infection,' Baker said in a statement. 'In this study, we show that computer-designed proteins can help human immune cells spot the right targets and function more effectively.' The work could lead to significant advancements in precision immunotherapy, which delivers disease-fighting drugs that are crafted for individual patients. The key to this personalized approach lies in understanding how cells display their identity on their surfaces. The outside membrane of a cell is studded with molecules that include small proteins called peptides that reveal a cell's inner workings, including if it's cancerous or infected by a virus such as HIV. The scientists used RFdiffusion and ProteinMPNN — AI-tools built by the Institute for Protein Design — to efficiently and cheaply engineer proteins that recognize the unique peptides. University of Washington biochemist and Nobel Prize laureate David Baker at his office in Seattle. (GeekWire Photo / Lisa Stiffler) The custom-made proteins can then be integrated into chimeric antigen receptors (CARs), which are engineered molecules that attract and activate immune-system warriors called T cells to attack specific targets. In their study, the researchers designed proteins for 11 peptide targets and eight successfully triggered a T-cell response. Of those eight, two produced such a strong immune response that the T cells killed the targeted cells. The peptide targets included HIV fragments and tumor-related protein mutations. 'We've shown how advances in protein design could make personalized cancer therapy possible, and we intend to start a company to turn these results into real therapies that benefit patients,' said Bingxu Liu, co-lead author of the study and postdoctoral scholar in the Baker Lab. Since 2014, the Institute for Protein Design has spun off 10 startups, and Baker has co-founded 21 tech companies. When Baker won the Nobel Prize in October, the Royal Swedish Academy of Sciences noted that '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 researchers involved in the latest study explained that the strategy can be easily adapted to new scenarios. Within days, the team was able to take one of its successful proteins and use AI to modify it to target new cancer and virus-associated peptides. The process could make it much cheaper to create personalized treatments. 'I'm hopeful that this will lead to new therapies that are more accessible to patients around the world who do not benefit from current state-of-the-art cancer treatments,' said Julia Bonzanini, a co-lead author and Baker Lab graduate student. Researchers worldwide can access online the open-source software used in the research. Other authors of the Science paper, titled 'Design of high-specificity binders for peptide–MHC-I complexes,' are Nathan Greenwood, Amir Motmaen, Jeremy Meyerberg, Tao Dao, Xinyu Xiang, Russell Ault, Jazmin Sharp, Chunyu Wang, Gian Marco Visani, Dionne Vafeados, Nicole Roullier, Armita Nourmohammad, David Scheinberg and Christopher Garcia. RELATED:
Geek Wire
17-07-2025
- Health
- Geek Wire
UW scientists use AI to crack ‘undruggable' proteins, opening door to new treatments
A protein engineered by University of Washington scientists wraps around its target. (Institute for Protein Design Image) The wiggly targets known to scientists as 'intrinsically disordered proteins' have for decades eluded capture by custom-made drugs and antibodies. But they played such important biological roles — activating opioid receptors; triggering protein misbehavior associated with neurodegeneration; killing insulin producing cells — that researchers kept after them. Now scientists in a University of Washington lab led by Nobel laureate David Baker have cracked the challenge, using generative AI to create proteins that grab hold of the shapeshifting molecules. The discovery could unlock a suite of new drugs and diagnostic tools. Almost half of the proteins found in humans are intrinsically disordered, 'yet we've had no reliable way to drug [them],' Baker said in a statement. 'These studies change that by giving scientists everywhere new tools for binding the unstructured half of biology.' University of Washington biochemist and Nobel Prize laureate David Baker at his office in Seattle. (GeekWire Photo / Lisa Stiffler) Unlike typical proteins that fold into defined, set shapes, intrinsically disordered proteins are more like cooked spaghetti — they're floppy and lack a stable structure. The UW scientists built a library of protein parts that can be stitched together and applied to diverse targets, zeroing in on short stretches of amino acids for binding. The researchers tested their custom-made proteins with promising results: one successfully blocked pain signals in cultured human cells, while another dissolved protein clumps linked to type 2 diabetes. The technique also proved useful for detecting and tagging scarce but important molecules, including a disease marker screened for in newborns. The results were striking — designer proteins successfully latched onto 39 out of 43 targets tested, a 91% success rate. Each protein folds precisely around its intended target, creating a tight, specific embrace. The new approach to engineering proteins is described in two papers, one published today in the journal Science, and a second available as a preprint. The majority of more than two-dozen authors are from the UW's Department of Biochemistry and the university's Institute for Protein Design, which is led by Baker. Researchers worldwide can access the open-source software online. Kejia Wu, a co-author on a Science paper describing a new technology for protein design, at her thesis defense in 2024 at the University of Washington. (IPD Photo) Kejia Wu, a former graduate student with the Baker lab and now a post-doctoral fellow, was a co-lead author of the newly published Science paper alongside Hanlun Jiang and Derrick Hicks. The project was exciting, Wu said, because it was so difficult and provided 'space to have creative thoughts.' Most of those ideas are nonsense and will fail, Wu said. 'But then you will be able to narrow [it] down — one of your thoughts might make sense, and you just start working on it,' she continued. 'So that's the part I like the most. You're able to come up with untraditional methods, untraditional thinking.' And while it was difficult initially to strategize a solution for the intrinsically disordered proteins given their shapeless nature, that fluidity has an upside. A structured, folded protein typically has just one solution for a binding protein, Wu said. 'But the conformational plasticity … actually gives us freedom to target [the molecule] many different ways — and we only need one of them to work.'
Economist
09-07-2025
- Science
- Economist
Scientists are using AI to invent proteins from scratch
Proteins are the molecular machines that make life work. Each one in your body has a specific task—some become muscles, bones and skin. Others carry oxygen in the blood or get used as hormones or antibodies. Yet more become enzymes, helping to catalyse chemical reactions inside our bodies. Given proteins can do so many things, what if scientists could design bespoke versions to order? Novel proteins, never seen before in nature, could make biofuels, say, or clean up pollution or create new ways to harvest power from sunlight. David Baker, a biochemist and recent Nobel laureate in chemistry, has been working on that challenge since the 1980s. Now, powered by artificial intelligence and inspired by living cells, he is leading scientists around the world in inventing a whole new molecular world.
Rhyl Journal
03-07-2025
- Automotive
- Rhyl Journal
Over 500 Denbighshire staff trained to use EV fleet
Denbighshire County Council has trained more than 500 staff through its Electric Vehicle (EV) Fleet programme, which supports the authority's transition to a cleaner, low-emission fleet. Martin Griffiths, fleet mobility lead officer at Denbighshire County Council, said: "As part of our council climate change and nature recovery strategy, we are committed to reducing carbon emissions across the local authority, which includes our fleet. "We have been transitioning our end-of-life fossil fuel-powered vehicles over to electric with significant support from Welsh and UK government departments to help us cut down on emissions produced and also reduce long-term costs for miles and maintenance across all services our fleet supplies to." The council's efforts follow its declaration of a Climate and Nature Emergency in 2019 and have resulted in more than 20 per cent of its fleet now being made up of zero-emission vehicles—one of the highest proportions in Wales. To ensure staff can operate the vehicles safely and efficiently, the in-house training covers the use of EV charging infrastructure, regenerative braking, and selecting the correct driving mode for different conditions. Four qualification levels are offered, covering cars and small vans through to LGVs, buses, plant machinery, and instructor certification. David Baker, senior driver training and assessment officer, said: "A key part of this is helping staff actually learn more about what an EV can do positively for travel and for the environment and coaching them to get the best out of this equipment. "Our in-house trainer supports with getting to grips with how regenerative braking works to extend range and reduce conventional wear and tear on normal brakes. "They look at how to smooth out driving to avoid harsh acceleration which impacts on battery performance." The council says the scheme is not only reducing emissions, but also lowering running costs and helping staff become more confident with EV technology. Mr Baker said: "Effectively the training helps maximise the ability of these cars driven by staff to increase vehicle efficiency and reduce long-term costs. "It's also good to help individual staff as well to make their own decisions regarding moving to an EV for personal use." The programme has attracted interest from other Welsh authorities. Mr Griffiths said: "We are sharing our good practice and experiences with other Welsh councils and public sector bodies to help them with their own transition to zero emission."
San Francisco Chronicle
30-06-2025
- Business
- San Francisco Chronicle
Santa Rosa wants to build 7,000 apartments. This luxury project could make or break the plan
The new Felix apartment building is unlike anything downtown Santa Rosa has seen before. At eight stories and 168 units, the L-shaped mid-rise at 420 Mendocino Ave. is both the tallest and densest building in the city's downtown. And it's definitely the fanciest: There is a double height co-working space with a sleek fireplace and office pods, a wellness center with cedar wood sauna and private steam shower rooms, a rooftop 'sky lounge' with firepit, demonstration kitchen and views of downtown and the Sonoma Mountains. The luxury comes with a cost. Studios start at $2,400, one-bedroom apartments at $2,995 and two-bedrooms at $3,745. Rent prices in Santa Rosa average about $2,000 for a one-bedroom and $3,000 for a two-bedroom, according to Zillow. If the building seems like a slightly more laid-back version of the sort of plush, four-star residential buildings in cities like San Francisco and New York — project architect David Baker calls it 'the hotelization of apartments' — it's because the developer, Related California, has long built some of the most deluxe towers on both coasts. For Related, the shift from major urban centers to smaller cities like Santa Rosa is part of a conscious move to cater to a post-pandemic landscape in which remote work allows for more geographic flexibility. In Santa Rosa they saw a downtown with great bones — a SMART train station, central green space in Courthouse Square, historic buildings, lively 4th Street restaurant row — that would attract people who want to be in a city but close to the wineries and hiking trails and rustic towns that make Sonoma County enchanting. 'We recognized that our customer was moving here and we recognized that the quality of product they were looking for did not exist in this market,' said Matthew Keipper, senior vice president with Related. 'We really view this as an exciting opportunity to follow our customer.' While it's too soon to say how fast the building will fill up — it opened in late May and Related declined to say how many units have been leased — downtown Santa Rosa boosters say it will be closely watched as a barometer of whether the market can support the level of investment needed to realize the city's downtown plan, which calls for 7,000 new housing units to be built in the 720-acre neighborhood by 2040. Currently there are 2,445 housing units in the downtown area, predominantly older duplexes, triplexes and fourplexes in established residential neighborhoods. In recent decades the city has grown largely through sprawl, a trend that came under scrutiny after the 2017 Tubbs Fire wiped out 2,800 homes in the city. 'It's definitely a test case,' said Jen Klose, executive director of the North Bay advocacy group Generation Housing. 'Our downtown needs an infusion of activity and we also just need housing here for all levels, including our young professionals and folks who might be attracted to a place like the Felix.' One group that will be paying close attention to how the Felix performs is Cornerstone, a North Bay real estate investment firm that has a pipeline with six downtown Santa Rose projects totalling 2,000 units. Two of those projects were fully entitled in 2020: an eight-story, 118-unit building on a parking lot at 556 Ross St.; and a six-story, 114-unit complex on a former railroad yard at 34 6th St. Both projects have been stalled due to the usual mix of lofty construction costs and high interest rates, but they could break ground in the next 12 months if the Related project does well, according to Pauline Block, director of marketing and development for Cornerstone. 'We are really excited about Felix,' said Block. 'It's right downtown, next to our projects, and it's of the quality we are aiming for. We are definitely interested to see the demographics that move into that building and how quick they lease up.' Cornerstone is working on lining up construction financing for the first two buildings, and the Felix will help make that case to lenders. 'In a market like ours it can be challenging when you say you are going to build a building of that size and quality and there is nothing similar nearby you can point to,' she said. While the North Bay has a well-earned reputation for being anti-development, there seems to be little opposition to adding density in downtown Santa Rosa. The city recently cut impact fees and Related only had to pay fees on the first three stories of the eight-story building. Felix won approval in just 75 days, and Baker described the community meetings on the project as a 'lovefest.' 'Santa Rosa has a shockingly laid-back culture,' Baker said. 'I was surprised we didn't get people screaming at us trying to stop it. People we like, 'You want to build this downtown? That would be great.'' Part of the acceptance of downtown density may be a result of lessons learned from the 2017 wildfires, which destroyed about 5% of the city's housing stock. Damages in the city topped $1.2 billion and exposed the risks of concentrating development in wildlands-urban interface zones rather than downtown. 'It makes a lot of sense to put density downtown because of the fire situation on the outskirts,' said Baker. But it's also a question of Santa Rosa coming to terms with the reality that it's a midsized city, not a small town, according to Klose. Santa Rosa grew from about 168,000 people in 2010 to 176,000 in 2023, and is projected to grow to 204,000 by 2030, according to the Association of Bay Area Governments. It's the largest city between the Golden Gate Bridge and the Oregon border. Santa Rosa isn't much smaller, in population, than cities like Providence, R.I., or Fort Lauderdale, Fla. And it is about the same size as Eugene, Ore. and Shreveport, La. 'All these cities that are our size or slightly bigger, they have real skylines,' Klose said. 'Santa Rosa has been a little stuck in the past, but it's kind of time for us to grow up.' Santa Rosa Metro Chamber CEO Ananda Sweet said there is county-wide support for growing downtown Santa Rosa, but that it's been hard to attract capital in a post-pandemic world with high interest rates and rising construction costs. The chamber has established a housing trust fund that helps groups with pre-development costs that conventional lenders don't typically cover. The fund is focused on low- and moderate-income housing, and has already provided a loan to Phoenix Development, which is converting two under-utilized bank buildings on B Street to 72 workforce units. Sweet said downtown Santa Rosa 'has so much potential that we are on the cusp of capitalizing on.' 'Even our members who don't do business in Santa Rosa really care about a thriving downtown,' Sweet said. 'Seeing Felix generate so much interest really helps tell the story for other developers and employers of what is possible downtown.' For Baker, who also designed the pioneering Hotel Healdsburg in that city's downtown, Felix is the culmination of a decade of work. He was initially hired by previous property owners on earlier iterations of the project that stalled out several times. He said downtown Santa Rosa 'has always been on the verge of happening but never quite does.' Maybe that is changing, he said. To celebrate the Felix he also made a ceramic sculpture for the lobby, a seven-foot totem of giant stacked seed pods. 'Thinking about the fertile Sonoma area, we wanted to reflect ideas around seeds — optimistic, vergevital, burgeoning, putting down roots and supporting new growth,' he said.
