Prologue Medicines wants to build therapies from viral proteins

The human proteome consists of about 20,000 proteins—a paltry number compared with the 6.2 million or so proteins encoded by viruses. New biotech company Prologue Medicines has plans to harness the largely untapped therapeutic potential of this vast trove of viral proteins. The firm launched today with $50 million in initial funding from the life sciences investment company Flagship Pioneering.

Viruses have a knack for evolving rapidly to regulate complex biological processes. “They do that by conferring unique characteristics and features onto viral proteins,” says Theonie Anastassiadis, Prologue’s founding president and a senior principal at Flagship. Those features include “potency to a certain target, cell specificity, and immune stability,” which are precisely the things that companies seek to optimize when they develop new biologics or drugs, she adds.

Historically, researchers have studied viruses with the aim of preventing them from causing disease, Anastassiadis says. Prologue aims to “flip this dogma on its head” and look for viral proteins that are fine-tuned to modulate human biology, she says. “We are asking, ‘What are the optimized proteins that we can actually leverage to turn into life-changing therapies?’”

Most viral proteins have not been characterized but so far exist only as sequences stored in databases. Prologue intends to use artificial intelligence and machine learning to layer these sequencing data with a host of other information, such as the proteins’ predicted structure and possible relationships to known human proteins and the diseases associated with them.

What enables this data exploration is the Cambridge, Mass. based company’s platform, Decoding Evolutionary Logic of Variant Ensembles, or DELVE. “Our platform builds a complete road map for us, telling us what biology is important,” says Hozefa Bandukwala, the firm’s founding chief scientific officer and a science partner at Flagship. “This allows us to systematically explore the entire viral proteome.”

The idea isn’t just to identify proteins that can act as therapies, Bandukwala says. “These viral proteins can also help point us to completely novel biology that we never would have thought of going after.”

Prologue isn’t yet announcing plans for specific targets, but Anastassiadis says it intends to focus initially on immunology, oncology, and metabolic diseases. “The beauty of this platform is that we can point it to so many different therapeutic areas that we are excited to pursue,” she says.