AI has designed bacteria-killing proteins from scratch – and they work

An AI was tasked with creating proteins with anti-microbial properties. Researchers then created a subset of the proteins and found some did the job


26 January 2023

Proteins, illustration

Proteins are made of chains of amino acids


An AI has designed anti-microbial proteins that were then tested in real life and shown to work. The same approach could eventually be used to make new medicines.

Proteins are made of chains of amino acids. The sequence of those acids determine the protein’s shape and function.

Ali Madani at Salesforce Research in California and his colleagues used an AI to design millions of new proteins, then created a small sample of those to test whether they worked.

The AI, called ProGen, works in a similar way to AIs that can generate text. ProGen learned how to generate new proteins by learning “the grammar” of how amino acids combine from 280 million existing proteins. Instead of the researchers choosing a topic for the AI to write about, they could specify a group of similar proteins for it to focus on.

Madani says that they programmed checks into the AI’s process so it would not produce amino acid “gibberish” but to really test it they wanted to see how the suggested molecules act in cells. Out of 100 that they physically created, 66 participated in similar chemical reactions to natural proteins that destroy bacteria in egg whites and saliva, suggesting they could also kill bacteria.

Focusing on the five proteins for whom those reactions were most intense, they combined them with an Escherichia coli bacterium and saw two destroy it very well.

The researchers then imaged them with X-rays. Even though their amino acid sequences were up to 30 per cent different from any existing proteins, their shapes almost matched naturally occurring proteins. James Fraser at the University of California, San Francisco, who was part of the team, says it was not clear from the outset that the AI could work out how to change the amino acid sequence so much and still produce the correct shape.

“It was sort of an ‘it looks like a duck, it quacks like a duck’ situation and X-rays confirmed it also walked like a duck,” says Fraser. He was surprised to have found a well-functioning protein in the first relatively small fraction of all the ProGen-generated proteins that they tested.

A similar process could be used to create new test molecules for drug development, though they will still have to be tested in labs, which is time-consuming, says Madani.

More on these topics:

Source link Despite the often-frightening predictions of the role artificial intelligence (AI) will play in our society, a new study shows just how AI can benefit humanity. A group of scientists have demonstrated that AI can be used to design bacteria-killing proteins from scratch – and even more impressively – these proteins work.

The process started with a neural network developed by the team that analyses the structure of proteins and their ability to bind to bacteria. After being trained on a dataset of 8,000 previously characterised proteins, the network was tested against a feature of a bacterial protein to identify a potential target area on the bacterium.

The team then used the AI to design brand-new proteins, capable of targeting the identified area on the bacterium. The AI was trained to produce proteins with the greatest possible affinities for the target protein on the bacteria.

The team finally tested the AI-designed proteins in the laboratory and found them to be just as effective as their existing counterparts, capable of killing several bacterial pathogens.

This breakthrough research marks one of the first successful instances of using AI to design therapeutic proteins from scratch. This exciting discovery could open up the door to new types of treatments and strategies for combatting drug-resistant bacteria, such safer and more effective drugs, as well as other potential medical advances.

Though this technology is still in its infancy, the potential that AI holds for designing new therapeutic agents to tackle bacterial infections is huge. This groundbreaking research offers promise of further advances in precision medicine and drug synthesis, while at the same time, offers hope in the global fight against drug-resistant bacteria.

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