Using AI to design peptide molecules in record time.

IBM AI Peptides Breakthrough Could Lead to Covid Medicine in Days Instead of Years

IBM has announced another exciting breakthrough for antibiotics and their possible use in fighting Covid-19, as reported by Sigal Samuel for 

The majority of news reports this week talk about how the Johnson and Johnson vaccine was being paused due to severe reactions in six people from the vaccine they were given. And the questions about testing and the rush to produce these vaccines have been asked again and again. Was the vaccine put in arms too soon?

Typically, you’d have to test lots and lots of different molecules in the lab until you find the right one  You might find some contenders that are good at killing the bacteria only to realize that you can’t use them because they also prove toxic to humans. It’s a very long, very expensive, and probably very aggravating process.

But what if, instead, you could just type into your computer the properties you’re looking for and have your computer design the perfect molecule for you?

That’s the general approach IBM researchers are taking, using an AI system that can automatically generate the design of molecules for new antibiotics.

In a new paper, published in Nature Biomedical Engineering, the researchers detail how they’ve already used it to quickly design two new antimicrobial peptides — small molecules that can kill bacteria — that are effective against a bunch of different pathogens in mice.

The more we overuse antibiotics, the more bacteria have a chance to adapt to our drugs, morphing into antibiotic-resistant superbugs that render our drugs ineffective.

And according to a new report from the Pew Charitable Trusts, the Covid-19 pandemic has aggravated the problem. Doctors have been even more inclined to unnecessarily prescribe antibiotics to patients. Even though Covid-19 is a viral illness and antibiotics don’t work on viruses, doctors have been giving patients these drugs to protect against secondary infections while they’re in the hospital — even before they know if the patients have infections or not.

With the overuse of antibiotics, we are entering a post-antibiotic era in medicine. We must find new ways to treat these viruses and the use of AI will be a big part of finding answers.

IBM Shines a Light on Its Process

First, the researchers start with a massive database of known peptide molecules.

Then the AI pulls information from the database and analyzes the patterns to figure out the relationship between molecules and their properties. It might find that when a molecule has a certain structure or composition, it tends to perform a certain function. This allows it to “learn” the basic rules of molecule design.

Finally, researchers can tell the AI exactly what properties they want a new molecule to have. They can also input constraints (for example: low toxicity, please!). Using this info on desirable and undesirable traits, the AI then designs new molecules that satisfy the parameters. The researchers can pick the best one from among them and start testing on mice in a lab.

As one of the co-authors of the IBM paper, Aleksandra Mojsilović, said,  “You have the knobs to turn, and you get the molecule that satisfies the properties.”

In a blog post, the IBM researchers noted that while they’re excited about how the AI system can potentially accelerate antibiotic discovery and keep antibiotic-resistant bacteria at bay, they’re also hopeful that the system can have much broader applications.

In addition, the AI could help create medication to treat Covid-19.

“Right now, for example, her team is working to figure out how the AI system might design treatments for Covid-19. When the pandemic came along, she explained, “We continued to say, we can use the same algorithms, but now we’re going to search a little differently — for something that looks like a molecule that can bind to a Covid target.”