Paper: https://www.nature.com/articles/s41564-025-02142-0
New antibiotic targets IBD and AI predicted how it would work
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New antibiotic targets IBD and AI predicted how it would work
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Re: New antibiotic targets IBD and AI predicted how it would work
#2Here is the original study published in nature microbiology.
https://www.nature.com/articles/s41564-025-02142-0
Wanted to share what I thought the interesting parts. From the university press release.
"To date, AI has been leveraged as a tool for predicting which molecules might have therapeutic potential, but this study used it to describe what researchers call “mechanism of action” (MOA) — or how drugs attack disease.
MOA studies, he says, are essential for drug development. They help scientists confirm safety, optimize dosage, make modifications to improve efficacy, and sometimes even uncover entirely new drug targets. They also help regulators determine whether or not a given drug candidate is suitable for use in humans... A thorough MOA study can take up to two years and cost around $2 million; however, using AI, his group did enterololin’s in just six months and for just $60,000.
Indeed, after his lab’s discovery of the new antibiotic, Stokes connected with colleagues at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL) to see if any of their emerging machine learning platforms could help fast-track his upcoming MOA studies.
In just 100 seconds, he was given a prediction: his new drug attacked a microscopic protein complex called LolCDE, which is essential to the survival of certain bacteria.
“A lot of AI use in drug discovery has been about searching chemical space, identifying new molecules that might be active,” says Regina Barzilay, a professor in MIT’s School of Engineering and the developer of DiffDock, the AI model that made the prediction. “What we’re showing here is that AI can also provide mechanistic explanations, which are critical for moving a molecule through the development pipeline.”
Re: New antibiotic targets IBD and AI predicted how it would work
#3Is it well-established that IBD is caused by E Colli? Is it like a sensitivity to E Colli?
Re: New antibiotic targets IBD and AI predicted how it would work
#4Is it well-established that IBD is caused by E Colli? Is it like a sensitivity to E Colli?
We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!"
All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to find the right one, or even cocktail, that adequately manages the disease.
Re: New antibiotic targets IBD and AI predicted how it would work
#5Is it well-established that IBD is caused by E Colli? Is it like a sensitivity to E Colli?
We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…
It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful!
During my own IBD journey, I've managed to stump the heck out of two different teams of GIs. I had been diagnosed with UC by biopsy during colonoscopy, and then at my last colonoscopy, despite not having been on medication for more than two years, they determined not only that I don't have it now, but that I never did. They told me "remission" would look different from "this bowel has never had IBD." But they also insisted I had not been misdiagnosed.
And yet they told me with a straight face that it is incurable. I had it in the past, confirmed by pathology. I don't have it now. And it's incurable. I give up.
In the end, I don't care enough to fight them about the contradiction, because the part I most care about is the "I don't have it now" part, and we're all in agreement on that.
(Note for any who are interested: I stopped medication after successfully reducing my inflammation markers within normal limits by eating the exact same thing for every single meal for 20 months with no cheating of any kind. They told me that shouldn't have been possible either, but it worked. And yes, it was as miserable as it sounds, but less miserable than living with UC.)
Re: New antibiotic targets IBD and AI predicted how it would work
#6Earlier quoted context omitted.
We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…
It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…
Any hypothesis for why eating only one thing would solve IBD ?
Would that select for a particular biota / micro-fauna environment ? or cause less mechanical / chemical inflammation ?
glad it worked in your case.
Re: New antibiotic targets IBD and AI predicted how it would work
#7Is it well-established that IBD is caused by E Colli? Is it like a sensitivity to E Colli?
Not directly since we all have it. It’s a bit confusing from the article but basically they discovered an antibiotic which can target a narrower spectrum than before which will minimize messing up your natural flora and allow drug resistant enterobacter (e coli is a main species, but not the only one) to be over represented. There is an association with ibd and. microbiomes that have e coli over-represented. And there are some subtypes of e coli that appear to be associated, see:
Re: New antibiotic targets IBD and AI predicted how it would work
#8Earlier quoted context omitted.
We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…
It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…
Have you checked your Calprotectin levels?
Re: New antibiotic targets IBD and AI predicted how it would work
#9Earlier quoted context omitted.
We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…
It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…
Doctors are the only people I’ve encountered who are ready to inform you of their poorly supported contradictory conclusions with full confidence, and are fully ready to meet any pushback with gaslighting or the dreaded “difficult patient” label.
They approach the phenomenon of dropping trust and respect for their profession in much the same way.
It’s really frustrating. I don’t get why they feel entitled to acting this way when no one else does.
Re: New antibiotic targets IBD and AI predicted how it would work
#10Earlier quoted context omitted.
It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…
Doctors are the only people I’ve encountered who are ready to inform you of their poorly supported contradictory conclusions with full confidence, and are fully ready to meet any pushback with gaslighting or the dreaded “difficult patient” label. They approach the phenomenon of dropping trust and respect for their profession in much the same way. It’s really frustrating. I don’t get why they feel entitled to acting t…
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