AI predicts the shape of molecules, in a boon for medicine and drug design

DeepMind has given 3-D structure to 350,000 proteins, including every one made by humans

For some years now John McGeehan, a biologist and the director of the Centre for Enzyme Innovation in Portsmouth, England, has been searching for a molecule that could break down the 150 million tonnes of soda bottles and other plastic waste strewn across the globe.

Working with researchers on both sides of the Atlantic, he has found a few good options. But his task is that of the most demanding locksmith: to pinpoint the chemical compounds that on their own will twist and fold into the microscopic shape that can fit perfectly into the molecules of a plastic bottle and split them apart, like a key opening a door.

Determining the exact chemical contents of any given enzyme is a fairly simple challenge these days. But identifying its three-dimensional shape can involve years of biochemical experimentation. So last fall, after reading that an artificial intelligence lab in London called DeepMind had built a system that automatically predicts the shapes of enzymes and other proteins, McGeehan asked the lab if it could help with his project.

Toward the end of one workweek, he sent DeepMind a list of seven enzymes. The following Monday, the lab returned shapes for all seven. “This moved us a year ahead of where we were, if not two,” McGeehan said.

Now, any biochemist can speed their work in much the same way. On Thursday, DeepMind released the predicted shapes of more than 350,000 proteins — the microscopic mechanisms that drive the behaviour of bacteria, viruses, the human body and all other living things. This new database includes the three-dimensional structures for all proteins expressed by the human genome, as well as those for proteins that appear in 20 other organisms, including the mouse, the fruit fly and the E coli bacterium.

This vast and detailed biological map — which provides roughly 250,000 shapes that were previously unknown — may accelerate the ability to understand diseases, develop new medicines and repurpose existing drugs. It may also lead to new kinds of biological tools, like an enzyme that efficiently breaks down plastic bottles and converts them into materials that are easily reused and recycled.

“This can take you ahead in time — influence the way you are thinking about problems and help solve them faster,” said Gira Bhabha, an assistant professor in the department of cell biology at New York University. “Whether you study neuroscience or immunology — whatever your field of biology — this can be useful.”

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