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The Company’s DELVE™ Platform combines computation and high-throughput biology to systematically discover the therapeutic potential of proteins tuned through millennia of viral evolution

The company emerges after three years of platform development with an initial commitment of $50 million from Flagship Pioneering

CAMBRIDGE, Mass., May 7, 2024 – Flagship Pioneering, the bioplatform innovation company, today unveiled Prologue Medicines, a company unlocking the therapeutic potential of the viral proteome for the creation of powerful new medicines. Flagship has initially committed $50 million to advance the company’s Decoding Evolutionary Logic of Variant Ensembles (DELVE)™ Platform and harness its power to develop a pipeline of medicines for a wide range of diseases, with an initial focus in immunological, oncology and metabolic indications.

"We asked, what if we could expand beyond the functional boundaries of the human proteome by harnessing viral evolution,” said Noubar Afeyan, Ph.D., Founder and CEO of Flagship Pioneering and Co-Founder and Chairman of the Strategic Oversight Board of Prologue. “By exploring the viral proteome, we can discover novel proteins with enhanced or completely unique therapeutic properties to develop medicines for optimal patient outcomes.”

Prologue is unlocking viral proteome-assisted drug discovery with its novel DELVE Platform. DELVE combines computation and high-throughput biology to continually mine the expanding viral proteome to uncover viral proteins and their unique features and evaluate their potential to modulate human physiology for the treatment of disease. The platform contains the largest known database of viral protein structures layered both with detailed data from known human proteins and annotations of previously uncharacterized viral proteins predicted through Prologue’s proprietary computational frameworks. By applying the learned rules of natural viral evolution, Prologue creates enhanced therapeutic proteins programmed to have properties, some previously unique to viruses, that expand the functional boundaries of human proteins.

“The viral proteome dwarfs the human proteome by orders of magnitude, enabling us to reveal a trove of powerful new proteins that can be used as medicines across nearly any therapeutic area,” said Lovisa Afzelius, Ph.D., MBA, Co-Founder and CEO of Prologue and Origination Partner at Flagship Pioneering. “Nature has evolved proteins with unique characteristics across the viral proteome. Advances in machine learning are enabling us to quickly characterize and select those that can precisely regulate human physiology to create powerful new medicines with impeccable precision.”

In addition to Afeyan and Afzelius, Prologue is led by Theonie Anastassiadis, Ph.D., Founding President of Prologue and Senior Principal at Flagship Pioneering, and Hozefa Bandukwala, Ph.D., Founding Chief Scientific Officer of Prologue and Science Partner at Flagship Pioneering.

About Prologue Medicines

Prologue is designing powerful new medicines by unlocking the viral proteome. The Company’s state-of-the-art DELVE™ Platform systematically identifies and evaluates viral proteins and their unique features for their potential to precisely regulate human physiology. By co-opting viral evolution, Prologue is expanding the functional boundaries of proteins encoded by the human genome to create new programmable medicines. Prologue was founded by Flagship Pioneering in 2021.

About Flagship Pioneering

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $70 billion in aggregate value. To date, Flagship has deployed over $3.7 billion in capital toward the founding and growth of its pioneering companies alongside more than $28 billion of follow-on investments from other institutions. The current Flagship ecosystem comprises over 40 companies, including Denali Therapeutics (NASDAQ: DNLI), Foghorn Therapeutics (NASDAQ: FHTX), Generate:Biomedicines, Inari, Indigo Agriculture, Moderna (NASDAQ: MRNA), Omega Therapeutics (NASDAQ: OMGA), Sana Biotechnology (NASDAQ: SANA), Seres Therapeutics (NASDAQ: MCRB) and Tessera Therapeutics.