A-Alpha Bio Awarded $800K to Develop Infectious Disease Drugs using AlphaSeq Platform

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Supported by the Bill & Melinda Gates Foundation, A-Alpha Bio and Lumen Bioscience will Leverage AlphaSeq Data to Optimize Therapeutic Antibodies with Machine Learning

A-Alpha Bio

A-Alpha Bio

This approach will have broad implications for the development of therapeutics for highly diverse and newly emerging infectious diseases, including enteric bacterial pathogens and respiratory viruses like COVID-19.

A-Alpha Bio, a biotechnology startup that partners with pharmaceutical companies to accelerate drug development with multiplexed measurements of protein interactions, today announced that it had been awarded an $800,000 grant to optimize therapeutics for infectious diseases. Awarded by the Bill & Melinda Gates Foundation, the grant work will be carried out by A-Alpha Bio in partnership with Lumen Bioscience using machine learning models built from data generated by A-Alpha Bio’s proprietary AlphaSeq platform. A-Alpha Bio has already completed a pilot study in partnership with Lumen Biosciences and supported by the Gates Foundation. This pilot study successfully demonstrated the AlphaSeq platform’s ability to characterize binding of therapeutic antibodies against multiple pathogen strains simultaneously. With the latest grant, the companies will utilize AlphaSeq data to train machine learning models for the development of potent and cross-reactive therapeutics against intestinal and respiratory pathogens.

Intestinal and respiratory pathogens each cause an enormous global health burden. In developing countries, intestinal bacterial pathogens cause over 500,000 deaths per year in children under the age of 5. Repeated infections in young children lead to lifelong health problems, including developmental delays and cognitive impairment. Respiratory pathogens can be equally damaging, as demonstrated by the ongoing pandemic. As of July 9, more than 11.8 million cases of COVID-19 have been confirmed worldwide and more than 540,000 people have died.

When it comes to developing therapeutics to address these global health issues, one major challenge for both bacterial and viral pathogens is strain diversity. Small differences between closely related pathogens can render a therapeutic non-effective. Additionally, new pathogenic strains are continually emerging for which existing therapeutics are ineffective, requiring the constant development of new drugs. There is a critical need for drug development platforms to rapidly optimize antibodies for cross-reactivity against multiple pathogenic strains and for neutralization of emerging pathogens that pose a significant global health threat.

“Due to strain diversity, treating infections caused by enteric pathogens requires broadly cross-reactive drugs and COVID-19 has highlighted the necessity for a more rapid drug development pipeline. We are excited to collaborate with A-Alpha Bio and incorporate machine learning models to enhance and expedite antibody development” said Dr. Jim Roberts, CSO of Lumen Bioscience. “By enabling a higher throughput of antibody-antigen binding characterization, AlphaSeq, coupled with machine learning, can make a meaningful difference in the development of new drugs for many high-impact disease targets.”

AlphaSeq is a ‘multi-target’ antibody screening platform, enabling the measurement of millions of interactions between proteins with high quantitative accuracy. With continued support from the Bill & Melinda Gates Foundation, A-Alpha Bio will use AlphaSeq to measure binding between antibody candidates and multiple strain variants simultaneously in collaboration with Lumen Bioscience. AlphaSeq datasets will then be used to train machine learning models and predict antibody sequences likely to neutralize a broad diversity of pathogenic strains.

“We’re honored to have the continued support of the Bill & Melinda Gates Foundation as we pursue this exciting partnership with Lumen Bioscience to develop high-impact infectious disease therapeutics,” said Dr. David Younger, Co-Founder and CEO of A-Alpha Bio. “This next phase of our work with Lumen is happening at a critical time. Our hope is that by continuing to scale drug development capabilities through the AlphaSeq platform, we can accelerate the development of new, life-saving drugs for enteric and respiratory infectious diseases.”

Unlike existing platforms for characterizing many antibodies at once, AlphaSeq generates quantitative information about protein interactions and measures interactions in two-dimensions, examining all combinatorial interactions between many antibodies and many pathogen strains in one experiment. These properties make AlphaSeq particularly well suited for training machine learning models.

“The AlphaSeq platform outputs datasets that are perfectly suited for building ML models,” said Randolph Lopez, Co-Founder and CTO of A-Alpha Bio. Prior to the founding of A-Alpha Bio, Lopez worked at Microsoft Research on their DNA data storage project. His PhD concentrated on molecular neural nets. “By multiplying the power of AlphaSeq’s datasets through machine learning models, we will be able to scale protein testing even further and improve the prediction of antibody sequences with desired properties, including affinity, specificity, and cross-reactivity.”

The machine learning models developed through the partnership will be used to predict potent antibodies against novel pathogen strains and antibodies demonstrating cross-reactivity to multiple strains. If successful, this approach will have broad implications for the development of therapeutics for highly diverse and newly emerging infectious diseases, including enteric bacterial pathogens and respiratory viruses like COVID-19.

For more information, please visit: https://www.aalphabio.com/.

About A-Alpha Bio
A-Alpha Bio leverages synthetic biology and next generation sequencing tools to characterize protein-protein interactions quantitatively and in enormous throughput. The company has developed a proprietary platform technology called AlphaSeq that uses genetically engineered yeast cells to measure millions of protein-protein interaction affinities simultaneously at a library-on-library scale, generating enormous amounts of data to inform the discovery and development of potent, specific, and cross-reactive drugs. A-Alpha Bio was founded in 2017 by a team of synthetic biologists from the University of Washington's Institute for Protein Design and Center for Synthetic Biology.

About Lumen
Lumen Bioscience is a clinical-stage biotechnology developing orally delivered antibodies and other biologics drugs for diseases of the gastrointestinal tract. This is made possible by Lumen’s unique cGMP manufacturing technology, which allows it to make orally delivered, therapeutic proteins for a small fraction of the traditional cost — cheap enough for mass-market, daily use. In addition to unlocking straightforward treatments for previously untreatable diseases, the novel approach enables faster, cheaper drug development, and the products have a better safety profile than traditional technologies. Lumen’s initial clinical programs target four high-prevalence infectious diseases, an area with well validated biological targets, significant unmet clinical need, readily available non-dilutive financing, and straightforward regulatory paths. For more information, please visit: http://www.lumen.bio.

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