Warp Drive Bio has secured another lucrative partnership for its genome mining drug discovery platform. Roche will pay up to $87 million in preclinical milestones and fees as part of a pact to explore new classes of natural products targeting gram-negative bacteria.
Researchers have long relied on molecules made by soil bacteria as the starting point for antibiotics development. But despite decades of trying, in the lab they can only coax bacteria into making a limited range of compounds.
As a result, “we continue to mine in the same field,” says Warp Drive Chief Scientific Officer Alan Rigby. “Even the most current molecules are really rip-offs of what’s out there in terms of chemical backbones and, thus, mechanisms.”
Warp Drive is trying to overcome those limitations by mining bacterial genomes for sequences that encode for novel molecules. During the company’s first few years, that meant searching for gene clusters that encode for key components of known drugs.
The approach allowed the company to unearth novel, built-by-nature analogues of familiar classes of antibiotics. These included β-lactams and aminoglycosides, the later of which it licensed to Sanofi.
With the Roche pact, Warp Drive will now search for novel classes of antibiotics. To do that, Warp Drive scientists use their database of bacterial genomes two different ways. One effort involves looking for genomic signatures that suggest a molecule is related to the synthesis of a polyketide, a huge class of compounds whose structures can be translated from their gene sequences.
“We can look in the genome for gene clusters that we can predict with pretty high confidence will encode natural products that have not historically been analyzed,” says Warp Drive CEO Laurence Reid.
The second effort involves digging for gene clusters where something “looks amiss,” Rigby says. For example, extra copies of a housekeeping gene embedded in a cluster could be a clue to the recipe for a natural product that would overcome a resistance mechanism.
The deal gives Roche an option for global rights to certain antibiotic classes that come out of the collaboration, while Warp Drive gets to keep any other promising molecules discovered. Warp Drive is eligible for an additional $300 million if certain milestones are reached.
For Roche, the pact ties into a broader strategy of building an antibiotics portfolio through partnerships rather than significant internal research. After a lengthy hiatus from antibiotics, Roche re-entered the space in 2014 and has since established deals with firms including Spero Therapeutics, Discuva, Meiji Seika Pharma, and Fedora Pharmaceuticals.