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New antibiotic targets IBD and AI predicted how it would work

healthsci.mcmaster.ca

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Re: New antibiotic targets IBD and AI predicted how it would work

#11

Post by pazimzadeh »

Ifkaluva wrote: post #3

Is it well-established that IBD is caused by E Colli? Is it like a sensitivity to E Colli?

not exactly but E. coli and other Enterobacteriaceae can actually use the inflammation to their advantage

Inflammation release nitrates, which Enterobacteriaceae can use as a replacement for oxygen as a terminal electron acceptor

They can also encroach more easily on the protective mucus layers, which are thinner and more porous during inflammatory conditions (which itself may be a result of a messed up microbiota, which is why broad-spectrum antibiotics are not a solution)

These Enterobacteriaceae blooms in turn can cause inflammation, makes remission harder

There has been some success in reducing inflammation levels in IBD by blocking some of the binding factors that E. coli uses to attach to the epithelium/mucus

Re: New antibiotic targets IBD and AI predicted how it would work

#12

Post by blauervogel »

smeej wrote: post #5
voxl wrote: post #4

Earlier 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…

Great to hear this worked for you! What was in the the meal? And how did you decide on exactly that meal?

Re: New antibiotic targets IBD and AI predicted how it would work

#13

Post by zaptheimpaler »

KLK2019 wrote: post #2

Here 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 disea…

> 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.

It must be so cool to work at a university. You can just walk across campus to meet with experts and learn about or apply the cutting edge of any given field to solve whatever problem you're interested in.

Re: New antibiotic targets IBD and AI predicted how it would work

#14

Post by bongodongobob »

zaptheimpaler wrote: post #13
KLK2019 wrote: post #2

Here 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 disea…

> 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. It must be so cool to work at a university. You can just walk across campus to meet with experts and learn about or apply the cutting edge of any given fie…

That's only if there are experts there. The average college is not really what you're thinking it is.

Re: New antibiotic targets IBD and AI predicted how it would work

#15

Post by Izikiel43 »

KLK2019 wrote: post #2

Here 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 disea…

> 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.

Beautiful, finally something for ai/machine learning that is not a coding autocomplete or image generation usage.

It would be very interesting to keep track of this area for the next 10 years, between alpha fold for protein folding and this to predict how it will behave, how cost is reduced and trials get fast tracked

Re: New antibiotic targets IBD and AI predicted how it would work

#16

Post by hkt »

smeej wrote: post #5
voxl wrote: post #4

Earlier 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…

As someone with IBD who is on their fifth trip to the toilet since midnight (BST) I'd love to get the recipe. I've got a few months of steroids ahead and anything more long term and high impact is of enormous interest.

Re: New antibiotic targets IBD and AI predicted how it would work

#17

Post by azinman2 »

smeej wrote: post #5
voxl wrote: post #4

Earlier 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…

Which markers? What meal? Why that meal?

Note it also could return; looks can be deceiving.

Re: New antibiotic targets IBD and AI predicted how it would work

#18

Post by Fomite »

zaptheimpaler wrote: post #13
KLK2019 wrote: post #2

Here 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 disea…

> 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. It must be so cool to work at a university. You can just walk across campus to meet with experts and learn about or apply the cutting edge of any given fie…

Can confirm it is often very cool to be able to do this.

Re: New antibiotic targets IBD and AI predicted how it would work

#19

Post by marginalia_nu »

jgord wrote: post #6
smeej wrote: post #5

Earlier 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…

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.

Not the person you're replying to, but my own IBD went away completely after I did keto for an extended period. This was a decade ago and it hasn't come back even as my diet returned to normal.

In my n=1 experience, it seems maybe significant dietary changes can perturb the gut ecosystem out of whatever state corresponds to IBD.

Re: New antibiotic targets IBD and AI predicted how it would work

#20

Post by Zafira »

Izikiel43 wrote: post #15
KLK2019 wrote: post #2

Here 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 disea…

> 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. Beautiful, finally something for ai/machine learning that is not a coding autocomplete or image generation usage. It would be very interesting to keep track of this area for the next 10 years, between alpha fold for protein folding and this to predict how…

Based on the paper for DiffDock (https://arxiv.org/abs/2210.01776) it looks like it was a great use case for a diffusion model.

> We thus frame molecular docking as a generative modeling problem—given a ligand and target protein structure, we learn a distribution over ligand poses.

I just hope work on these very valid use cases doesn’t get negatively impacted when the AI bubble inevitably bursts.

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