A-Alpha Bio will build laboratory space in downtown Seattle and bolster its machine learning equipment with $ 20 million in new venture funding for its operation to identify therapeutic proteins, the company announced Thursday.
Seattle’s Madrona Venture Group, a technology-focused company branching out into the life sciences, led the Series A round.
The funding propels the company from a grant-funded spinoff of the University of Washington with $ 2.8 million in seed funding to a comprehensive biotechnology that supports the development of potential treatments for COVID-19 and other diseases.
And the more proteins the company tests, the better it does. A-Alpha Bio uses information from your data sets to train its algorithms to predict favorable protein interactions.
“Over time, we are accumulating these huge repositories of protein interaction data that we can also use with computational tools like machine learning to better understand and design protein interactions,” CEO David Younger said in an interview with GeekWire.
Younger founded the company in 2017 with CTO Randolph Lopez using the technology they helped develop while graduating as researchers at the UW Institute for Protein Design.
The drug development platform company combines computational tools with yeast experiments to identify potentially therapeutic proteins. It partners with pharmaceutical companies to help them find the best agents to try in a variety of conditions.
The technology is based on clumps of single-celled yeast designed to express various proteins or protein fragments. When two proteins interact, the yeast fuses and the interacting proteins are counted. The method can identify protein interactions, such as an antibody that sticks tightly to a viral protein.
A-Alpha Bio hits the sweet spot of high precision and high sample volume to measure protein interactions, Younger said.
“Historically there has been a really dramatic trade-off, where you either get high quality or you get high quantity, and it’s very difficult to maximize both,” he said.
A-Alpha Bio has partnerships with three big pharmaceutical companies and is aiming for more. It is also partnering with the Bill and Melinda Gates Foundation, Twist Biopharma, and Seattle-based Lumen Biosciences to help develop COVID-19 antibodies, among other projects. Lumen grows therapeutic proteins in spirulina algae and recently announced plans to build a new production facility in a former Seattle bakery.
The high precision and performance of A-Alpha Bio give it an edge over competing platform technology companies, Younger said. Other companies in the space include Adimab and Distributed Bio.
Younger and his colleagues recently demonstrated his technology in a study that identifies antibodies to variants of the COVID-19 virus. Such antibodies could potentially be used as therapies to treat disease.
The researchers started with yeast that expressed a variety of antibodies, as well as proteins from different variants of the virus. “And we throw them all in a pot, map all the interactions and then determine which antibodies are going to have the correct profile,” Younger said. The document appears on the BioRxiv prepress server and has not yet been peer reviewed.
In addition to identifying antibodies, A-Alpha Bio focuses on finding targets for “molecular glues.” Such “glues” connect a target protein to another type of protein that tells the cell to eliminate the target.
“It’s essentially a way of targeting particular proteins for degradation,” Younger said. And it is also the basis for the chemotherapy drug Revlimid. Revlimid has generated billions in revenue for Celgene, a Bristol Myers Squibb company, and has generated intense interest in the area of molecular “glues.”
A-Alpha Bio is also taking advantage of computational methods developed by IPD for its tool that predicts how proteins fold. IPD’s tool, called Rose TTAFold, and a similar one developed by DeepMind recently impressed the life science community with their speed and precision in predicting protein folding.
Those tools were made possible by existing massive data sets on known protein folding, while training sets for predicting protein-protein interactions are still limited. But A-Alpha Bio sees that change as it builds its databases.
A-Alpha Bio can measure millions of protein interactions in one Just experiment, Younger said, “And so with this volume of data we can begin to train machine learning models that essentially learn the rules of protein-protein binding.”
“Our vision is to get to a point where we can essentially make an in silico antibody prediction for a given target never seen before,” she added.
The combination of laboratory science and computational approaches is an emerging field of investment for Madrona, managing director Matt McIlwain previously told GeekWire.
The decades-old venture firm has traditionally invested in technology companies, but is increasingly backing companies at the “intersection of innovation.” These companies at the interface between biology and informatics and data science also include Nautilus Biotechnology, TwinStrand Biosciences, Ozette, and Terray Therapeutics.
“As machine learning, computing power, and wet lab automation advancements converge, we expect to see even more companies addressing research problems in paradigm-shifting ways,” said McIlwain and Madrona partner Chris. Picardo, in a blog post about the new financing.
A-Alpha Bio currently has 13 employees and expects to expand to about 50 in the next two years as it builds its machine learning team. Before the pandemic, “we had a pretty strong conviction around keeping the team as local as possible,” Younger said.
But like many operations, A-Alpha Bio has learned to operate effectively remotely and is open to off-site contracting. Said Younger: “We have recently learned that we do not want, under any circumstances, to sacrifice talent.”
The company is also converting existing office space in the Belltown neighborhood for its new laboratory for experiments on yeast, a creature that does not require much maintenance.
“One of the best things about working with yeast as a model organism is that our needs from an infrastructure perspective are very simple,” Younger said, “Instead of having to fight tooth and nail with other biotech companies for that 1% From the vacant lab space in Seattle, we can move into office space and do a complete conversion into a lab that meets all of our needs. ”
The company is the latest spin-off from IPD to raise new funding after the recent IPO of Icosavax, a company that develops vaccines for COVID-19 and other diseases.
The initial funding above was led by the OS Fund, and the company has also received grant support from the Gates Foundation and the US National Science Foundation. In addition to Madrona, participants in the Series A funding round include Perceptive Xontogeny Venture Fund and Lux Capital.
Ben Askew and McIlwain de Xontogeny, who also sits on the board of directors of the Fred Hutchinson Cancer Research Center, have joined the company’s advisory board.
