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posted by janrinok on Monday February 24 2020, @03:22PM   Printer-friendly
from the genetic-algorithms dept.

Powerful antibiotic discovered using machine learning for first time:

A powerful antibiotic that kills some of the most dangerous drug-resistant bacteria in the world has been discovered using artificial intelligence. The drug works in a different way to existing antibacterials and is the first of its kind to be found by setting AI loose on vast digital libraries of pharmaceutical compounds.

Tests showed that the drug wiped out a range of antibiotic-resistant strains of bacteria, including Acinetobacter baumannii and Enterobacteriaceae, two of the three high-priority pathogens that the World Health Organization ranks as “critical” for new antibiotics to target.

“In terms of antibiotic discovery, this is absolutely a first,” said Regina Barzilay, a senior researcher on the project and specialist in machine learning at Massachusetts Institute of Technology (MIT).

“I think this is one of the more powerful antibiotics that has been discovered to date,” added James Collins, a bioengineer on the team at MIT. “It has remarkable activity against a broad range of antibiotic-resistant pathogens.”

Antibiotic resistance arises when bacteria mutate and evolve to sidestep the mechanisms that antimicrobial drugs use to kill them. Without new antibiotics to tackle resistance, 10 million lives around the world could be at risk each year from infections by 2050, the Cameron government’s O’Neill report warned.

To find new antibiotics, the researchers first trained a “deep learning” algorithm to identify the sorts of molecules that kill bacteria. To do this, they fed the program information on the atomic and molecular features of nearly 2,500 drugs and natural compounds, and how well or not the substance blocked the growth of the bug E coli.

Once the algorithm had learned what molecular features made for good antibiotics, the scientists set it working on a library of more than 6,000 compounds under investigation for treating various human diseases. Rather than looking for any potential antimicrobials, the algorithm focused on compounds that looked effective but unlike existing antibiotics. This boosted the chances that the drugs would work in radical new ways that bugs had yet to develop resistance to.

Jonathan Stokes, the first author of the study, said it took a matter of hours for the algorithm to assess the compounds and come up with some promising antibiotics. One, which the researchers named “halicin” after Hal, the astronaut-bothering AI in the film 2001: A Space Odyssey, looked particularly potent.

Writing in the journal Cell, the researchers describe how they treated numerous drug-resistant infections with halicin, a compound that was originally developed to treat diabetes, but which fell by the wayside before it reached the clinic.

Jonathan M. Stokes, Kevin Yang, Kyle Swanson, Wengong Jin, Andres Cubillos-Ruiz, Nina M. Donghia, Craig R. MacNair, Shawn French, et. al. A Deep Learning Approach to Antibiotic Discovery Cell, Vol. 180, Issue 4, p688–702.e13 DOI:https://doi.org/10.1016/j.cell.2020.01.021


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  • (Score: 2) by Freeman on Monday February 24 2020, @03:39PM (2 children)

    by Freeman (732) on Monday February 24 2020, @03:39PM (#961860) Journal

    This could be a really good thing for everyone. Then there's a part of me saying, the down side to this likely has military applications. Sure, we don't engage in biological warfare, and most other places also don't, most.

    --
    Joshua 1:9 "Be strong and of a good courage; be not afraid, neither be thou dismayed: for the Lord thy God is with thee"
    • (Score: 4, Interesting) by ikanreed on Monday February 24 2020, @04:46PM (1 child)

      by ikanreed (3164) Subscriber Badge on Monday February 24 2020, @04:46PM (#961882) Journal

      Please "we don't engage in biological warfare" is a steadfast american value that will last exactly as long as "we don't torture" did, when it becomes politically or militarily expedient. If we still have any values at all its gonna take some real goddamn effort to maintain that past the hooting and braying animals that constantly call for blood and the politicians whose main foreign policy goal is "looking strong".

      I still don't know if Obama actually ended the torture or the media just stopped reporting it.

      • (Score: 1, Informative) by Anonymous Coward on Monday February 24 2020, @07:12PM

        by Anonymous Coward on Monday February 24 2020, @07:12PM (#961940)

        Part of the dissolution currently happening.

        Hollywood did a great job of brainwashing acceptability of surveillance, law enforcement breaking the law is OK if done in pursuit of catching a REALLY BAD GUY, war crimes, and probably some other fucked up shit.

        Obama making a joke about droning his daughter's date was the most chilling example of dictatorship I'd seen in a long time. Dubya had so many problems I can't even call up a specific example, but he probably had some war crime material in there.

        Now we have Trump not even joking around and suggesting war crimes as a matter of course. Still waiting for the Superior Christian Morality to kick in. Jesus is watching y'all!

  • (Score: 3, Insightful) by Booga1 on Monday February 24 2020, @03:43PM (5 children)

    by Booga1 (6333) on Monday February 24 2020, @03:43PM (#961861)

    I hate to say this, but we need to keep this as restricted access to last lines of defense for humans only. Otherwise it'll be sold to farmers all over the world and we'll be back to where we are now in 10-15 years.
    It's a whole new class of antibiotics, and losing this one might ruin the whole line for use because of how quickly resistance can develop.

    • (Score: 2, Informative) by Anonymous Coward on Monday February 24 2020, @03:50PM

      by Anonymous Coward on Monday February 24 2020, @03:50PM (#961865)

      it will be sold to farmers all over the world. that's a given as long as growing food is a profit-oriented enterprise. hopefully future generations will be able to find new antibiotics.

    • (Score: 2) by ikanreed on Monday February 24 2020, @04:52PM (1 child)

      by ikanreed (3164) Subscriber Badge on Monday February 24 2020, @04:52PM (#961883) Journal

      It's time for a well actually.

      Well actually, we already do withhold the more potent antibiotics for only human use, and for the most powerful ones, only for use on antibiotic resistant cases. That's been the compromise for decades now. Farmers pretty much only use neomycin and penicillin for "growth promotion". The problem is that the resistance that develops from those also dramatically increases the resistance to the "good" ones, because they often antagonize the same biochemical pathways, just in different levels of specificity and intensity.

      • (Score: 2) by Azuma Hazuki on Tuesday February 25 2020, @02:54AM

        by Azuma Hazuki (5086) on Tuesday February 25 2020, @02:54AM (#962169) Journal

        Yeeee-up. Specifically, those are beta-lactams (penicillin) and aminoglycosides (neomycin) that are getting cross-resistance developed. This is especially troubling because some rather strong beta-lactams, the "monobactam" and "cephalosporin" classes, are used in hospitals.

        --
        I am "that girl" your mother warned you about...
    • (Score: 0) by Anonymous Coward on Monday February 24 2020, @06:51PM (1 child)

      by Anonymous Coward on Monday February 24 2020, @06:51PM (#961928)

      You're essentially saying that it should be restricted from use on Medicare patients and reserved for those with better genes?

      • (Score: 3, Insightful) by captain normal on Monday February 24 2020, @07:30PM

        by captain normal (2205) on Monday February 24 2020, @07:30PM (#961948)

        "You're essentially saying that it should be restricted from use on Medicare patients and reserved for those with deeper pockets?"
        TFTFY

        --
        When life isn't going right, go left.
  • (Score: 1, Funny) by Anonymous Coward on Monday February 24 2020, @04:06PM (5 children)

    by Anonymous Coward on Monday February 24 2020, @04:06PM (#961872)

    Who gave that antibiotic access to the machine learning lab?

    And how did they know it was it's first time?

    • (Score: 0) by Anonymous Coward on Monday February 24 2020, @04:22PM (3 children)

      by Anonymous Coward on Monday February 24 2020, @04:22PM (#961875)

      > Hal, the astronaut-bothering AI in the film 2001: A Space Odyssey
      Revisionist movie history? Seemed to me that HAL became an insane killing machine.

      Speaking of killing, isn't it a little early to declare success with this new drug before animal and human trials?

      • (Score: 2) by Freeman on Monday February 24 2020, @06:46PM (2 children)

        by Freeman (732) on Monday February 24 2020, @06:46PM (#961923) Journal

        It's too early to celebrate, perhaps, but the potential usefulness is astounding.

        Tests on bacteria collected from patients showed that halicin killed Mycobacterium tuberculosis, the bug that causes TB, and strains of Enterobacteriaceae that are resistant to carbapenems, a group of antibiotics that are considered the last resort for such infections. Halicin also cleared C difficile and multidrug-resistant Acinetobacter baumannii infections in mice.

        To hunt for more new drugs, the team next turned to a massive digital database of about 1.5bn compounds. They set the algorithm working on 107m of these. Three days later, the program returned a shortlist of 23 potential antibiotics, of which two appear to be particularly potent. The scientists now intend to search more of the database.

        Stokes said it would have been impossible to screen all 107m compounds by the conventional route of obtaining or making the substances and then testing them in the lab. “Being able to perform these experiments in the computer dramatically reduces the time and cost to look at these compounds,” he said.

        https://www.theguardian.com/society/2020/feb/20/antibiotic-that-kills-drug-resistant-bacteria-discovered-through-ai [theguardian.com]

        --
        Joshua 1:9 "Be strong and of a good courage; be not afraid, neither be thou dismayed: for the Lord thy God is with thee"
        • (Score: 2) by captain normal on Monday February 24 2020, @07:35PM (1 child)

          by captain normal (2205) on Monday February 24 2020, @07:35PM (#961951)

          Well that's all great and good, but now comes ten to fifteen years of testing and patent squabbles before any of these get to be used.

          --
          When life isn't going right, go left.
          • (Score: 2) by Freeman on Monday February 24 2020, @08:28PM

            by Freeman (732) on Monday February 24 2020, @08:28PM (#961977) Journal

            Still better than the "move fast and break things" motto.

            --
            Joshua 1:9 "Be strong and of a good courage; be not afraid, neither be thou dismayed: for the Lord thy God is with thee"
    • (Score: 2) by aristarchus on Monday February 24 2020, @06:49PM

      by aristarchus (2645) on Monday February 24 2020, @06:49PM (#961925) Journal

      Yes! Once the powerful antibiotics are discovered to be using machine learning, it can only mean one thing: amphiboly! Humanity is doomed.

  • (Score: 0) by Anonymous Coward on Monday February 24 2020, @08:50PM (1 child)

    by Anonymous Coward on Monday February 24 2020, @08:50PM (#961990)

    If it can't cure Ethanol Fueled's encephalitis then we need to keep searching!

    • (Score: 3, Informative) by Azuma Hazuki on Tuesday February 25 2020, @02:51AM

      by Azuma Hazuki (5086) on Tuesday February 25 2020, @02:51AM (#962168) Journal

      Eth's problem is chronic stage 4 rectocranial inversion, not encephalitis.

      --
      I am "that girl" your mother warned you about...
  • (Score: 2) by Gaaark on Tuesday February 25 2020, @12:34AM (1 child)

    by Gaaark (41) on Tuesday February 25 2020, @12:34AM (#962102) Journal

    Who is the patent owner?

    Computer? Mankind? MIT? Some guy who will Jack the price up?

    --
    --- Please remind me if I haven't been civil to you: I'm channeling MDC. ---Gaaark 2.0 ---
    • (Score: 0) by Anonymous Coward on Tuesday February 25 2020, @08:40AM

      by Anonymous Coward on Tuesday February 25 2020, @08:40AM (#962288)

      the people that now own the .org domain

  • (Score: 3, Interesting) by Azuma Hazuki on Tuesday February 25 2020, @03:25AM (3 children)

    by Azuma Hazuki (5086) on Tuesday February 25 2020, @03:25AM (#962187) Journal

    From the wiki article (I know, I know, "Wikipedia isn't a primary source," but the primaries are listed at the bottom): https://en.wikipedia.org/wiki/Halicin [wikipedia.org]

    It seems this has an entirely novel bacteriocidal mechanism. My worry about this is that it looks more like something a chemotherapy drug would do than an antibiotic. In particular: mitochondria are very similar to bacteria, and I can imagine a large systemic dose of this stuff could do some really awful things to you--think "cyanide" here--if it turns out the li'l guys are vulnerable :(

    This may make it a candidate for a targeted delivery system of some sort, though...

    --
    I am "that girl" your mother warned you about...
    • (Score: 2) by Booga1 on Tuesday February 25 2020, @04:19AM (2 children)

      by Booga1 (6333) on Tuesday February 25 2020, @04:19AM (#962217)

      Well, much like chemotherapy, I guess it's an alternative is to letting the infection kill you outright.

      • (Score: 0) by Anonymous Coward on Tuesday February 25 2020, @08:41AM (1 child)

        by Anonymous Coward on Tuesday February 25 2020, @08:41AM (#962289)

        everyone I know who did chemo, died quickly thereafter; within a month

        • (Score: 0) by Anonymous Coward on Tuesday February 25 2020, @04:48PM

          by Anonymous Coward on Tuesday February 25 2020, @04:48PM (#962432)

          i bet they breathed oxygen too.

  • (Score: 0) by Anonymous Coward on Tuesday February 25 2020, @05:22AM (1 child)

    by Anonymous Coward on Tuesday February 25 2020, @05:22AM (#962240)

    Wake me up when they discover a penis enlargement pill that works.

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