Polish computational chemistry outfit Molecule. One has raised $4.6M to expand its quest to bring theoretical drug molecules to reality. Its machine learning systems predict the best ways to synthesize potentially valuable molecules, a crucial part of creating new drugs and treatments.
Molecule. One went on stage at Disrupt SF 2019’s Startup Battlefield. They explained the difficulty faced by the drug discovery industry, basically that they come up with many theoretical treatments but can’t make the molecules.
Molecule. The company’s system enters play when you have some exotic new compound you want to make to test in real life but don’t know how to make it. After all, these molecules are brand new to science — no one has created them before, so why should anyone know? One establishes a workflow starting with ordinary off-the-shelf chemicals and provides step-by-step instructions for going from A to B… and to C, D, and so on (rarely simple). The company leverages machine learning and a large body of knowledge about chemical reactions to create these processes, though as CSO Stanisław Jastrzębski explained, they do it backward.
“Synthesis planning can be characterized as a game,” he said. “In each move of this game, instead of moving a piece on a board, we break a chemical bond between a pair of atoms. The game aims to break down a target molecule into molecules that can then be bought on the market and used to synthesize the target. We use algorithms similar to the ones used by DeepMind to master Go or chess to find the synthesis pathway.”
Co-founders Piotr Byrski and Paweł Włodarczyk-Pruszyński note that predicting organic reactions is no cakewalk and that they have dedicated many resources towards making their system efficient and verifiable. The theoretical pathways they produce seem plausible but still need to be tested, something they do regularly internally. Hence, companies see Molecule. One selling good but workable ideas.
Since their debut at Disrupt, the company has acquired several customers with annual contracts, Byrski said and rolled out many features on the platform. Włodarczyk-Pruszyński said that their efficiency had increased as well.
“Our system has matured, and we have extended our platform to support planning synthesis for thousands of molecules per hour,” he said. “This feature is handy when combined with AI systems for drug discovery that generate huge numbers of candidate drug molecules. All these improvements helped us gain trust in the industry and initiate collaborations with relevant parties.”
Indeed the problem becomes one of scaling as your customers ask about pathways for hundreds of thousands of possible therapeutic molecules rather than a handful. If they are to bear the manufacturing cost, it’s worth the outlay at the start to see if one of the compounds they’re looking at is considerably easier to make than another with a similar effect. Without simulating the entire process, that’s difficult to say for sure, so they can send the list to Molecule. one and get the report back a few days later.
The team can’t share any of their customers’ successes (though presumably there have been some) because all this work is highly confidential. But they did say that, like many companies in biotech, they are doing what they can to support COVID-related therapies.
“We made part of our platform free to eligible researchers working on COVID drug discovery. This has resulted in a lasting collaboration with the LambdaZero project at MILA, which Prof. Yoshua Bengio advises,” said Byrski.
This also offered the opportunity to test their new scaling methods. For such a project, many candidate molecules must be evaluated for efficacy andthe capability of being manufactured easily.
“We are incredibly excited about this area in general because it enables traversing novel regions of the chemical space, which offers enormous promise in looking for drugs that have not yet been synthesized,” Byrski said.
The funding round was led by Atmos Ventures, with a long list of participating investors: AME Cloud Ventures, Cherubic Ventures, Firlej Kastory, Inventures, Luminous Ventures, Sunfish Partners, and individuals including Bayer executive Sebastian Guth.
The company plans to use the money to expand the team and continue expanding generally; it also plans to open new offices in the U.S. and Western Europe (based in Poland).
