Flagship Pioneering Awarded First-Of-Its-Kind Contract by Department of War to Advance Next-Generation Medical Countermeasure Technologies Against Evolving Biological Threats

Agreement marks strategic shift in how Department of War partners with the private sector, with Flagship providing access to broad range of innovative platforms against evolving threats 

Award of up to $47 million over a five-year period; initial projects include Flagship-founded Apriori Bio and Prologue Medicines 

CAMBRIDGE, MA, September 23, 2026 – Flagship Pioneering, a scientific innovation engine for transformative platforms and products, has been awarded a first-of-its-kind contract by the Department of War (DoW) under the ONTARGET - Operationalizing Novel Technologies for Advanced Rapid Generation of Effective Medical Countermeasures (MCM) - program. The award of up to $47 million will be executed over a five-year period, beginning with a select set of initial projects and allowing for additional projects to be initiated throughout the contract term. 

The strategic partnership will leverage Flagship’s unique ecosystem of more than 40 pioneering companies and technological capabilities across translational science, platform engineering, drug development, enabling technologies, and AI/machine learning to support the rapid testing of tailored solutions across a broad range of DoW MCM priorities and evolving threats. The initial projects include Flagship-founded companies Apriori Bio and Prologue Medicines. The award will be administered by Flagship Health Security Corporation, a new subsidiary of Flagship Pioneering created specifically to facilitate government partnerships. 

“Through the ONTARGET program, we can harness our nation’s greatest strength – its unmatched capacity to invent and scale breakthrough technologies – to stay ahead of evolving threats and safeguard national security,” said Noubar Afeyan, Ph.D., Founder and CEO of Flagship Pioneering. “By mobilizing Flagship’s ecosystem of first-in-category, AI-enabled biotechnologies, we are not only advancing next-generation countermeasures, we will also be building the innovation infrastructure to define America’s strategic advantage for decades ahead.” 

The agreement marks a strategic shift in how DoW partners with the private sector, establishing a new, more agile model for defense solutions. Instead of contracting for a specific product, DoW and Flagship will evaluate a broad range of cutting-edge platform technologies from Flagship’s ecosystem of companies for their potential to accelerate and optimize medical countermeasure development and address an evolving range of DoW warfighter protection priorities. 

The ONTARGET program is managed by the Joint Science and Technology Office (JSTO) within the Department of War’s Chemical and Biological Defense Program. The ONTARGET program aims to stay ahead of evolving threats—adaptive and engineered—by partnering with the private sector in unique and powerful ways to enhance medical countermeasure performance, accelerate development timelines, and strengthen response effectiveness.  

“Ultimately, our goal is to get the best technology into the hands of our warfighters as quickly as possible. The ONTARGET agreement provides a new pathway to do just that, by identifying and maturing the most promising biotechnologies the private sector has to offer,” said Robert Kristovich, Ph.D., Director of JSTO at the Defense Threat Reduction Agency. “This keeps our military personnel equipped to face any biological challenge.”  

The program targets several priority capability areas essential for national defense preparedness: 

• Broad-spectrum countermeasures against emerging threats 
• Precision delivery technologies to improve efficacy and reduce side effects 
• Toxin-neutralizing platforms for enhanced protection 
• Novel approaches to immune enhancement and viral pathway disruption 
• Integration of AI/ML to optimize medical countermeasure discovery and development 

Initial Research Projects 

The award will provide proof-of-concept funding for a select set of cutting-edge projects, each leveraging distinct Flagship technologies. The Department of War will have the opportunity to advance additional projects throughout the five-year agreement with Flagship. 

Apriori Bio – Broadly Protective Medical Countermeasures 

Apriori Bio will apply its Octavia™ platform, a biology-enabled AI platform for the design of variant-resilient countermeasures, to rapidly generate one or more stable, cross-protective candidates. By anticipating viral evolution, the platform can enable faster, more resilient countermeasure development, reducing response timelines, and strengthening biological threat readiness against evolving and engineered threats. 

Prologue Medicines – Immunomodulatory Protein Discovery 

Prologue Medicines’ DELVE platform applies advanced AI approaches to mine millions of viral proteins and identify evolutionarily-optimized functions that can modulate and enhance human immune responses. This project seeks to leverage DELVE to strengthen immune resilience and enable rapid, adaptable countermeasures that can be deployed across a broad range of emerging and engineered threats. 

About Flagship Pioneering 

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, operating with $14 billion of assets under its direction as of its latest capital raise, announced in July 2024. The current Flagship ecosystem comprises more than 40 companies, including Generate Biomedicines, Inari, Lila Sciences, Moderna, Sana Biotechnology, Tessera Therapeutics and Valo Health. 

Flagship Health Security Corporation is a subsidiary of Flagship Pioneering created specifically to facilitate government partnerships.