Microbe-Hacker Ginkgo Bioworks Pushes Further Into Medicine With Acquisition Of Genome Mining Platform And Antibiotics Discovery Deal With Roche

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Ginkgo Bioworks said today that it had acquired the genome mining platform of Warp Drive Bio, a subsidiary of Revolution Medicines, that will help it push ahead in the search for new antibiotics and other pharmaceutical applications. With the acquisition, Ginkgo will resume the work to find a new class of antibiotics with pharmaceutical giant Roche that Warp Drive had begun before being sold to Revolution, Ginkgo CEO Jason Kelly told Forbes.

Boston-based Ginkgo stands to receive a total $160 million from the Roche deal if it can locate antibiotics and bring them to clinical trials, he said, with royalties above that should it find something that becomes an approved drug. “This is our first big therapeutics deal,” Kelly said. “This is a big part of the future of Ginkgo.” Roche declined to comment.

With the acquisition, Ginkgo will get Warp Drive’s genomic database with more than 135,000 bacterial strains with the potential to encode more than 4 million biosynthetic gene clusters to be used in the development of novel antibiotics. Ginkgo will add that database to its vast codebase as it pushes ahead in its search for therapeutic applications. The purchase price was not disclosed.

A leader in synthetic biology, Ginkgo — an alumnus of Forbes 2017 Next Billion-Dollar Startups list now worth more than $1 billion — focused its early efforts on fragrances, and then food and agriculture as it opened automated foundries to engineer organisms at a speed and cost not possible in traditional scientific labs. With the opening last fall of its fourth foundry, known as BioWorks4, for genetic engineering of mammalian cells, Ginkgo has been moving further in therapeutics.

Warp Drive uses genomic mining to analyze and evaluate more than 100 classes of potential antibiotics to develop novel medicines. Antibiotics have been an increasingly important area of research because of growing antibiotics resistance, which threatens modern medicine’s ability to fight certain infections. Antibiotics typically had been discovered largely by chance, and there have been no major breakthroughs in antibiotics treatments since daptomycin was discovered in the 1980s, Kelly said.

Part of the difficulty in discovering new antibiotics is that the parts of the genome that make them may not turn on in the unnatural environment of a petri dish, Kelly said, allowing them to remain undiscovered. By sequencing genomes, Ginkgo and Warp Lab can more systematically examine microbes to find those hidden antibiotics. “The bet,” Kelly said, “is there are more antibiotics hiding in their genome. There was no way to see that in the ’70s or ’80s, but now we can.”

Warp Drive, founded in 2012, was a hot biotech of its time. It was cofounded by Harvard professors George Church and Greg Verdine and backed by $125 million in capital from French drug giant Sanofi and biotech investor ThirdRock Ventures. And it established collaborations with Big Pharma, including with GlaxoSmithKline on oncology and with Roche on antibiotics. The original deal with Roche offered Warp Drive $387 million in upfront fees and milestone payments.

But Warp Drive’s ambitious drug discovery goals didn’t pay off in its six years as an independent company, and last October it was acquired by Redwood City, California-based Revolution Medicines for an undisclosed sum. Revolution Medicines has focused its efforts on cancer treatments, especially those that block RAS proteins linked to cancer growth, and it was interested in Warp Drive’s related oncology work. From the beginning, Revolution was clear that Warp Drive’s genome mining platform and its antibiotics discovery deal with Roche did not fit with that focus on cancer. “It was very explicit in our discussions with the board and management of Warp Drive Bio,” said Revolution CEO Mark Goldsmith. “We indicated to employees internally that we would do everything possible to find a home for the genome mining platform.”

For Ginkgo, Kelly said, the database could prove useful for its projects in food, agriculture and fragrances, as well as for therapeutics. In fact, he said, the company had already located an enzyme for one of its fragrance projects. “For all of our projects, we can go looking in that database for interesting genes,” he said. “You never know where you are going to find interesting code.”

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