Tag: Chemistry

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Stealthy startup builds ‘Antibody Cages’ to fight diseases

Archon co-founders James Lazarovits and George Ueda
Archon Biosciences’ co-founders, James Lazarovits and George Ueda, lead a tour through their Seattle lab. (GeekWire Photo / Alan Boyle)

Three weeks after University of Washington biochemist David Baker won a Nobel Prize, the latest venture to spin out from his lab — Archon Biosciences — has emerged from stealth mode with $20 million in financing for a technology that uses computationally designed protein structures to treat cancer and other diseases.

The seed funding round was led by Madrona Ventures, with participation from DUMAC Inc., Sahsen Ventures, WRF Capital, Pack Ventures, Alexandria Venture Investments and Cornucopian Capital.

Archon’s proprietary protein structures, known as Antibody Cages or AbCs, have been years in the making. Archon’s CEO and co-founder, James Lazarovits, said the Nobel Prize that Baker won for his pioneering work in the field of protein design confirms his view that the newly unveiled startup is on the right track.

“It’s reaffirmed our conviction for why we’re in this place to begin with,” Lazarovits told me during a tour of Archon’s Seattle lab. “It’s doing things that were not possible before. … You could not do anything that we’re doing unless there was the convergence of all these different fields at this moment in time.”

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Scientists turn to the cloud for computational chemistry

Illustration: Fanciful view of cloud containing molecular structures, circuitry and test tubes
Researchers are finding ways to speed up computational chemistry through cloud computing. (Illustration by Nathan Johnson / PNNL)

A team led by researchers from the Pacific Northwest National Laboratory is finding new ways to accelerate the pace of computational chemistry, by making tools for quantum computing and AI-assisted data analysis available via the cloud.

Their effort to make supercomputer-scale resources more widely available through cloud computing could aid in the search for methods to break down toxic “forever chemicals” that are currently hard to get rid of. And that’s just one example.

The researchers describe their progress on the project — known as Transferring Exascale Computational Chemistry to Cloud Computing Environment and Emerging Hardware Technologies, or TEC4 — in a study published today in the Journal of Chemical Physics.

“This is an entirely new paradigm for scientific computing,” PNNL computational chemist Karol Kowalski, who led the cross-disciplinary effort, said in a news release. “We have shown that it’s possible to bundle software as a service with cloud computing resources. The initial proof of concept shows that cloud computing can provide a menu of options to complement and supplement high-performance computing for solving complex scientific problems.”

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Nobel Prize in chemistry puts protein design in spotlight

Biochemist David Baker at home
Biochemist David Baker chats with a journalist online about his Nobel Prize. (Photo by Ian C Haydon / UW Medicine Institute for Protein Design)

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.

In a news release, 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.

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Scientists take a freeze-frame look at excited electrons

Illustration: X-ray pulses blasting water molecules
Scientists used a pair of X-ray pulses (shown in pink and green) to study the energetic response of electrons (gold) in liquid water on attosecond time scales, while the hydrogen (white) and oxygen (red) atoms are ‘frozen’ in time. (Pacific Northwest National Laboratory / Nathan Johnson)

An international team of scientists has blazed a new trail for studying how atoms respond to radiation, by tracking the energetic movement of electrons when a sample of liquid water is blasted with X-rays.

The experiment, described in this week’s issue of the journal Science, required “freezing” the motion of the atoms with which the electrons were associated, on a scale of mere attoseconds. An attosecond is one-quintillionth of a second — or, expressed another way, a millionth of a trillionth of a second.

Attosecond-scale observations could provide scientists with new insights into how radiation exposure affects objects and people.

“What happens to an atom when it is struck by ionizing radiation, like an X-ray? Seeing the earliest stages of this process has long been a missing piece in understanding how radiation affects matter,” Xiaosong Li, a chemistry professor at the University of Washington and a laboratory fellow at the Pacific Northwest National Laboratory, said in a UW news release. “This new technique for the first time shows us that missing piece and opens the door to seeing the steps where so much complex — and interesting — chemistry occurs!”

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Scientists visit the kind of lake where life may have arisen

Scientists walking across Last Chance Lake
Researchers walk across Last Chance Lake’s crusty surface in September 2022. (UW Photo / Zack Cohen)

Several years ago, scientists at the University of Washington theorized that key ingredients for life could have built up billions of years ago in special kinds of environments known as soda lakes.

At the time, their hypothesis was based on previously published research, computer modeling and lab experiments. But now the same scientists say they’ve found a shallow lake that just might fit the requirements — and it happens to be just a few hundred miles north of their home base in Seattle.

Their findings, focusing on Last Chance Lake in British Columbia, were published this month in Communications Earth & Environment, an open-access, peer-reviewed scientific journal.

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Scientists say Saturnian moon has all of life’s essentials

Illustration: Cutaway view of Enceladus, highlighting water geysers that rise through ice layer
A cutaway view shows water rising up from Enceladus’ ice-covered ocean. (NASA / JPL-Caltech Illustration)

Phosphorus, an essential ingredient for life as we know it, has been detected for the first time in water samples that can be traced back to Enceladus, an ice-covered moon of Saturn.

The discovery, reported today in the journal Nature, lends further support to suggestions that life could lurk within Enceladus’ ice-covered oceans — and perhaps in similar environments elsewhere in the solar system.

Phosphorus-containing compounds, known as phosphates, provide the molecular backbone for DNA and RNA molecules. Adenosine triphosphate, or ATP, serves as the source of energy for living cells. This research marks the first time that phosphates have been traced to an extraterrestrial ocean. The Nature paper suggests that phosphate levels in Enceladus’ hidden seas could be hundreds or even thousands of times higher than what exists in Earth’s oceans.

“By determining such high phosphate concentrations readily available in Enceladus’ ocean, we have now satisfied what is generally considered one of the strictest requirements in establishing whether celestial bodies are habitable,” study co-author Fabian Klenner, a postdoctoral researcher at the University of Washington, said in a news release.

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Azure Quantum joins the hunt for new fuel-cell catalysts

A hydrogen-powered car fills up at a refueling station
A hydrogen-powered car fills up at a refueling station. (Johnson Matthey via YouTube)

Chemists at Microsoft Azure Quantum are teaming up with Johnson Matthey, a British-based clean-tech company, to identify new types of catalysts for hydrogen fuel cells.

The project demonstrates how quantum information science could help reduce the automobile industry’s carbon footprint and address the challenge of climate change.

“So far, Johnson Matthey has seen a twofold acceleration in quantum chemistry calculations, and we’re just getting started,” Nathan Baker, senior director of partnerships for chemistry and materials at Microsoft, said today in a blog posting. “Both companies recognize that the discoveries needed to create a zero-carbon future will require significant breakthroughs in chemical and materials science, and are enthusiastic about the difference we can make in the world together.”

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A new type of salt crystal could exist on Europa

Galileo's view of Europa's surface
An image from NASA’s Galileo orbiter shows Europa’s surface of salt-streaked ice. (Credit: NASA / JPL / Ted Stryk)

A prime target in the search for extraterrestrial life is Europa, a moon of Jupiter that’s covered with a sheet of salty ice. But what kind of salt is there? Researchers say they’ve created a new kind of salt crystal that could fill the bill, and perhaps raise hopes for finding life under the ice.

This salt crystal is both exotic and common: It’s actually table salt — also known as sodium chloride, with the chemical formula NaCl — but bound up with water molecules to form a hydrate that doesn’t exist naturally on Earth.

Earthly sodium chloride hydrates are composed of one salt molecule linked by hydrogen bonds with two water molecules. In contrast, the hydrates created in the lab consist of two NaCl molecules to 17 water molecules, or one NaCl molecule to 13 water molecules. (The structure for a third type of “hyperhydrated hydrate” couldn’t be determined.)

That’s promising news for scientists who study Europa and other ice-covered worlds — including two other Jovian moons, Callisto and Ganymede; and the Saturnian moons Enceladus and Titan. Spectral observations indicate that Europa’s surface ice contains salts, including sodium chloride, but the observed levels of concentration don’t match up well with Earth’s run-of-the-mill NaCl hydrates.

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Synthetic peptide molecules open the way for new drugs

Peptides slipping through cell membrane
An illustration shows how peptide molecules can slip through a cell membrane. (Image by Ian C. Haydon / UW IPD)

Researchers at the University of Washington have discovered how to create peptide molecules that can slip through membranes to enter cells — and they’ve also created a company to take advantage of the discovery for drug development.

The findings, which were published today in the journal Cell, could eventually lead to new types of oral medications for health disorders ranging from COVID-19 to cancer.

“This new ability to design membrane-permeable peptides with high structural accuracy opens the door to a new class of medicines that combine the advantages of traditional small-molecule drugs and larger protein therapeutics,” senior study author David Baker, a biochemist at the University of Washington School of Medicine, said in a news release.

Small-molecule drugs — for example, aspirin — are small enough to slip through cell membranes to do their work. Protein therapeutics — for example, monoclonal antibodies — can target more complex ailments, but the protein molecules are typically too big to wedge their way through lipid-based cell walls.

Peptide drugs are made from the same building blocks as protein, and offer many of the advantages of protein-based drugs. They can bind protein targets in the body more precisely than small-molecule drugs, promising fewer side effects.

“We know that peptides can be excellent medicines, but a big problem is that they don’t get into cells,” said study lead author Gaurav Bhardwaj, an assistant professor of medicinal chemistry at the UW School of Pharmacy. “There are a lot of great drug targets inside our cells, and if we can get in there, that space opens up.”

The newly reported experiments used a couple of molecular design techniques to create types of peptide molecules that can get into cells more easily.

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Protein designers get a $45 million boost

David Baker and Neil King
University of Washington biochemists David Baker and Neil King show off molecular models of proteins at UW’s Institute for Protein Design. (UW IPD Photo / Ian Haydon)

The era of engineering proteins for medical applications just got a lot closer, thanks to a five-year, $45 million grant from The Audacious Project at TED to the Institute for Protein Design at the University of Washington School of Medicine.

The institute, headed by UW biochemist David Baker, is among eight recipients of Audacious grants announced today at the annual TED conference in Vancouver, B.C.

“We’re really thinking of this as a protein design revolution, parallel to the digital revolution at Bell Labs. … If you can design proteins exactly to order from first principles, you can solve a lot of problems that are facing humans today — primarily in medicine, but also in materials and energy,” Baker told GeekWire.

Among the potential products are a universal flu vaccine, non-addictive painkillers, smart proteins capable of identifying and treating cancer cells or the out-of-control cells that cause autoimmune disorders, potential treatments for neurodegenerative disorders and self-assembling proteins for solar cells or nanofabrication.

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