As he was testing new antivirals to halt a future pandemic, John Chodera encountered an unlikely set of new problems that ultimately helped lead to his new job.
The computational chemist won
a $68 million grant in 2022
from the National Institutes of Health to help lead a five-year effort to develop new antivirals. That work
ended prematurely
when Congress decided in 2023 to effectively abandon that initiative.
“We found out a five-year program to discover drugs was really going to be a three-year halfway bridge to nowhere,” Chodera said in an interview. “If you give up halfway across the river, you don’t get a useful bridge with half the capacity. You don’t get anything useful at all, unfortunately.”
After a decade-plus of running a computational biology lab at Memorial Sloan Kettering, Chodera is now venturing out on his own as a first-time CEO. The antiviral experience wasn’t just a lesson in whimsical pandemic funding, but it brought Chodera closer to the process of discovering drugs. The 47-year-old had previously developed software to simulate molecules,
most notably OpenMM
, but the drug-hunting effort showed how today’s tools — even AI-powered ones — lacked the accuracy or scalability to do what’s needed in finding, testing and making drugs.
Chodera is now CEO and president of Achira, a biotech startup incorporated last summer that launched Friday with a $33 million seed round. Achira is aiming to build the next generation of these computational tools for drug discovery, which Chodera calls “atomistic foundation simulation models.” That’s a complicated way of saying his team is blending AI- and physics-based methods together to try to improve drug discovery.
Chodera’s co-founders are Theofanis Karaletsos, head of AI at the Chan Zuckerberg Institute and formerly an AI leader at the biotech insitro, and Zavain Dar, a co-founder and managing partner of Dimension. Dimension led the seed round, which exceeded an initial $15 million target and included Amplify Partners, Compound, and NVentures, Nvidia’s VC arm.
Dar said Dimension spoke with over 50 biotechs on the theme of combining machine learning and molecular dynamics, ultimately deciding to start a new company with Chodera and Karaletsos. Those two have known each other for about a decade, and have long discussed the ideas that turned into Achira.
“We want to turn drug discovery into 90% compute and 10% experiment,” Karaletsos said. “This is the domain where we can do it based on first principles.”
Achira’s view is that neither physics-based methods nor machine-learning models are enough on their own in drug discovery.
ML models still don’t have enough drug discovery data, Chodera said. And physics methods, like molecular dynamic simulations that power Schrödinger’s ubiquitous software, are powerful but limited. Those calculations need tons of compute power to show molecules wriggling, moving and interacting with each other. Scientists face a trade-off in how many molecules and how long those simulations can be.
Chodera, who previously served on Schrödinger’s scientific advisory board, said the computational framework known as force fields that power those simulations has effectively gone unchanged for over four decades. In the meantime, compute power has grown exponentially.
“This stuff has not changed fundamentally in 45 years, which is crazy because those models were built for a PDP-11, a late 1970s-era computer,” he said. “The cost per FLOP [floating-point operation, a cost-effectiveness metric for compute power] is now 160 billion times less than it was at that time, and we still are using the same functional form.”
Achira is developing a type of AI model called neural network potentials that rely on the physical laws of nature to simulate molecules. Achira plans to then generate synthetic data by using these models, making large biological datasets that are in short supply today.
“The foundation simulation models that we are building are going to be extremely general,” Chodera said, meaning they could subsequently be trained for a range of tasks like predicting a molecule’s binding affinities, selectivity or stability.
The 10-employee company has hired several notable scientists, including CTO Daniel Smith, a co-founder of Iambic Therapeutics and most recently head of computation at a
Flagship Pioneering startup called Abiologics
, and a mix of computational biologists, theoretical chemists, biophysicists and chemical engineers. Achira expects to grow around the hubs of AI talent in San Francisco and New York.
Achira’s leaders declined to specify what business model it may pursue, but won’t start by building its own pipeline of drugs. Chodera said he expects to have “some fun stuff to share later this year” on its first generation of its simulation models.