Making lethal molecules with machine learning

• Published date: 02 March 2023
• Publication title: The Korea Times

"We are but one very small company (among) many hundreds of companies using AI software for drug discovery and de novo design. How many of them have ... the know-how to find the pockets of chemical space that can be filled with molecules predicted to be orders of magnitude more toxic than VX?" This is a warning that requires a little explanation.

VX is a variety of "nerve gas," first synthesized by Britain's chemical warfare lab at Porton Down in the 1950s. Just 8 milligrams (two grains of salt) will kill an adult human being if it comes into contact with their skin. Half a milligram if it is inhaled or swallowed. It's odorless and tasteless, and it comes in a mist so fine that it's practically invisible.

It took Porton Down almost a decade to develop it from the German nerve gases that the British discovered at the end of the Second World War, but with machine learning, you can now come up with something similar in practically no time.

The "very small company" that issued the above warning, published in the scientific journal Nature Machine Learning, is "Collaborations Pharmaceuticals, Inc.," based in Raleigh, North Carolina. Their business model is discovering new drugs, or more precisely designing them, and they have nothing whatsoever to do with poisoning people.

Like everybody in the drug discovery business these days, their primary tool is "machine learning" ? not exactly Artificial Intelligence as it was originally conceived, but a sub-category of AI that simply ingests vast quantities of data and searches it for resemblances.

Those resemblances will suggest possible new ('de novo') molecules that may not exist in nature but might be useful in treating disease. So you synthesize them, test them, and once in a while you come up with one that really does fill a gap in the existing pharmaceutical arsenal. But they might serve other purposes, too.

Two years ago four research scientists working for Collaborations Pharmaceuticals ? Fabio Urbina, Filippa Lentzos, Cedric Invernizzi and Sean Ekins ? were asked to speak at the biennial conference hosted by the Swiss Institute for the Protection of the Population against Nuclear, Biological and Chemical Threats and Dangers ? the Spiez Laboratory, for short.

The Spiez Lab is one of five in the world certified by the Organization for the Prohibition of Chemical Weapons to identify developments in chemistry, biology and enabling technologies that have implications for the Chemical and Biological Weapons Conventions. It...