The Japanese pharma giant Takeda has signed a second research deal with the AI specialist Nabla Bio, expanding the scope of a collaboration that started three years ago.
The two companies announced the deal Tuesday, with Takeda agreeing to pay double-digit millions in upfront and research cost payments, along with possible milestones of more than $1 billion. Nabla’s leaders said there was mutual interest in expanding their work after seeing successes with Nabla’s AI models for generating and designing proteins.
There has been a flurry of small, AI-focused deals in the last few weeks as big drugmakers explore a range of AI approaches in R&D. Within the past month, Merck
expanded a partnership with Variational AI
on small molecules, AstraZeneca signed deals
with Algen Biotechnologies
and
Turbine
, and Sanofi announced a three-year deal
to use BenchSci’s AI platform
on disease biology.
Nabla, a Cambridge, MA-based biotech that spun out of George Church’s lab in 2020, has focused on pharma partnerships rather than building its own pipeline. The 20-person company
raised a $26 million Series A last year
, and plans to grow to 25 to 30 employees over the next couple of months, CEO Surge Biswas said. It has also partnered with AstraZeneca and Bristol Myers Squibb.
“One of the things that has been really exciting to us is the broad scope of impact,” Nabla’s president and co-founder Frances Anastassacos said in an interview. “We want to get the technology to influence as many programs as possible and as quickly as possible.”
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Since signing that first Takeda deal in 2022, Nabla and the broader AI bio field have made dramatic progress with AI models to generate and design proteins. Last year, Nabla
debuted its AI model called JAM
, which has made antibodies from scratch that bind to some hard-to-drug targets.
Biswas described it as “autocomplete for molecules.” Given context on a research problem, like the protein sequence and structure of the target, JAM “can autocomplete the biologic that binds to that target at a specific epitope location.”
Today, Biswas said they are seeing double-digit percent success rates in getting hits with JAM that bind fairly strongly to a target — often in the double-digit nanomolar and sometimes in the single-digit nanomolar range.
“That is one dimension that needs to improve,” Biswas said, adding they are “pushing hard” on getting down to picomolar binding affinities. The tighter drugs bind to their target, the better — it can lead to higher potency and less potential for off-target side effects.
JAM is a key part of the new deal, in which Nabla will work on a range of Takeda research projects. Focus areas include
de novo
biologics for antibodies and multispecifics. The work will include targets that can’t be hit using conventional methods, but also targets that “could be accessed with traditional discovery approaches but are very inefficient in that way,” Biswas said.
“With the same resources that it would ordinarily take to process a single target, we can process five to 10 in parallel,” he said.
Nabla will also work on optimizing some existing biologics that have severe developability issues, in what Biswas called rescuing programs and “bringing it out of the graveyard.”
Across its partnerships, Nabla has two programs “getting very close to IND-enabling studies,” Biswas said.
Entering the clinic “in the next year or two is not too crazy,” he said, although that decision will ultimately be made by the partnering pharma companies.
That may make Nabla potentially the first company to bring a
de novo
protein into the clinic. Other AI-focused biotechs like Generate:Biomedicines and Absci are advancing clinical-stage programs where AI played a role in their development, but that aren’t
de novo
efforts.
A key unknown for AI-made proteins is their immunogenicity in the human body, Biswas said. Oftentimes, anti-drug antibody responses appear in the clinic that are hard to predict with preclinical models or animal testing.
The immunogenicity question “is something the industry overall just doesn’t have a great grasp on yet, and is sort of the big question mark with computationally designed antibodies, because we have yet to see one of these really get into the clinic and see how they fare in humans,” Biswas said. “No one’s going to feel totally comfortable until we see these in a human.”
But Biswas said he’s encouraged by the preclinical data and in Nabla’s efforts to make its
de novo
proteins “indistinguishable from antibody sequences you would pull out of a human.”