Infectious Disease / en Fri, 15 Aug 25 09:02:05 -0400 Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria /news/using-ai-researchers-design-new-compounds-kill-antibiotic-resistant-bacteria <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" title="Friday, August 15, 2025 - 09:02" class="datetime">August 15, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source 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type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=pwWzdLq2 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc" alt="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." title="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NIAID </div> <div class="media-caption__description"> Methicillin-resistant Staphylococcus aureus (MRSA) </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2301/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use 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block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/bios/james-collins">James Collins</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image 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media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Fri, 15 Aug 2025 13:02:05 +0000 tulrich@broadinstitute.org 5559321 at Sentinel program among finalists for the $100 Million 100&Change competition /news/sentinel-program-among-finalists-100-million-100change-competition <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created 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class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" 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class="field__item"><article about="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/longstory/24661308922_3eb66388f6_o.jpg?itok=a-A7AnUn 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b" alt="Microscope image showing E. coli." title="Microscope image showing E. coli." typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Scientists identify a unique combination of bacterial strains that could treat antibiotic-resistant gut infections</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=Yt7lhUBz 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7 1x" media="all and (max-width: 539px)" type="image/png" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7" alt="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" title="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">With AI, researchers identify a new class of antibiotic candidates</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=O_pwabKw 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS" alt="Carbapenem-resistant Enterobacteriaceae bacteria" title="Carbapenem-resistant Enterobacteriaceae bacteria" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Study finds new patterns of antibiotic resistance spread in hospitals</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/artificial-intelligence-yields-new-antibiotic" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Tue, 29 Apr 2025 20:22:58 +0000 kzusi@broadinstitute.org 5558516 at Simple test for flu could improve diagnosis and surveillance /news/simple-test-flu-could-improve-diagnosis-and-surveillance <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" title="Friday, August 15, 2025 - 09:02" class="datetime">August 15, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=LOIVChyr 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=P14nvfJp 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=pwWzdLq2 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc" alt="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." title="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NIAID </div> <div class="media-caption__description"> Methicillin-resistant Staphylococcus aureus (MRSA) </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2301/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2301/feed" target="_blank" title="Share to X" aria-label="Share to X" 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text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/bios/james-collins">James Collins</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" 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class="field__item"><article about="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/longstory/24661308922_3eb66388f6_o.jpg?itok=a-A7AnUn 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b" alt="Microscope image showing E. coli." title="Microscope image showing E. coli." typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Scientists identify a unique combination of bacterial strains that could treat antibiotic-resistant gut infections</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=Yt7lhUBz 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7 1x" media="all and (max-width: 539px)" type="image/png" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7" alt="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" title="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">With AI, researchers identify a new class of antibiotic candidates</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=O_pwabKw 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS" alt="Carbapenem-resistant Enterobacteriaceae bacteria" title="Carbapenem-resistant Enterobacteriaceae bacteria" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Study finds new patterns of antibiotic resistance spread in hospitals</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/artificial-intelligence-yields-new-antibiotic" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Tue, 18 Jun 2024 15:00:00 +0000 adicorat 5557056 at A new viral surveillance system in West Africa is showing the world how to prevent the next pandemic /news/new-viral-surveillance-system-west-africa-showing-world-how-prevent-next-pandemic <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" title="Friday, August 15, 2025 - 09:02" class="datetime">August 15, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source 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(max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc" alt="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." title="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NIAID </div> <div class="media-caption__description"> Methicillin-resistant Staphylococcus aureus (MRSA) </div> </div> </article> </div> </div> </div> </div> </div> </div> <div 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text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/bios/james-collins">James Collins</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a 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type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/longstory/24661308922_3eb66388f6_o.jpg?itok=a-A7AnUn 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b" alt="Microscope image showing E. coli." title="Microscope image showing E. coli." typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Scientists identify a unique combination of bacterial strains that could treat antibiotic-resistant gut infections</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=Yt7lhUBz 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7 1x" media="all and (max-width: 539px)" type="image/png" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7" alt="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" title="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">With AI, researchers identify a new class of antibiotic candidates</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=O_pwabKw 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS" alt="Carbapenem-resistant Enterobacteriaceae bacteria" title="Carbapenem-resistant Enterobacteriaceae bacteria" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Study finds new patterns of antibiotic resistance spread in hospitals</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/artificial-intelligence-yields-new-antibiotic" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Thu, 25 Apr 2024 15:00:00 +0000 adicorat 5556791 at A close research partnership with African scientists helps solve the mystery of malaria-like illnesses /news/close-research-partnership-african-scientists-helps-solve-mystery-malaria-illnesses <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" title="Friday, August 15, 2025 - 09:02" class="datetime">August 15, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=LOIVChyr 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=P14nvfJp 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=pwWzdLq2 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc" alt="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." title="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NIAID </div> <div class="media-caption__description"> Methicillin-resistant Staphylococcus aureus (MRSA) </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2301/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2301/feed" target="_blank" title="Share to X" aria-label="Share to 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text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/bios/james-collins">James Collins</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/p_aeruginosa_main.png?itok=sGBQc2Hr 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/p_aeruginosa_main.png?itok=Lno0VDmy 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" 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srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/GoPhAST-R_pilot_news_main.jpg?itok=lpX0JLCP 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/GoPhAST-R_pilot_news_main.jpg?itok=lpX0JLCP" alt="Hands wearing purple lab gloves use a multi-pipettor to transfer liquids into a multi-well plate." title="Hands wearing purple lab gloves use a multi-pipettor to transfer liquids into a multi-well plate." typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/new-diagnostic-approach-bacterial-infections-shows-promise-clinic-0" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">New diagnostic approach for bacterial infections shows promise in the clinic</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/longstory/24661308922_3eb66388f6_o.jpg?itok=IGMTFlT4 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/longstory/24661308922_3eb66388f6_o.jpg?itok=4eKOwV_f 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/longstory/24661308922_3eb66388f6_o.jpg?itok=a-A7AnUn 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/longstory/24661308922_3eb66388f6_o.jpg?itok=spOez19b" alt="Microscope image showing E. coli." title="Microscope image showing E. coli." typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Scientists identify a unique combination of bacterial strains that could treat antibiotic-resistant gut infections</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=Yt7lhUBz 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7 1x" media="all and (max-width: 539px)" type="image/png" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7" alt="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" title="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">With AI, researchers identify a new class of antibiotic candidates</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=O_pwabKw 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS" alt="Carbapenem-resistant Enterobacteriaceae bacteria" title="Carbapenem-resistant Enterobacteriaceae bacteria" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Study finds new patterns of antibiotic resistance spread in hospitals</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/artificial-intelligence-yields-new-antibiotic" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Fri, 08 Mar 2024 15:00:00 +0000 chenders@broadinstitute.org 5556586 at With AI, researchers identify a new class of antibiotic candidates /news/researchers-use-ai-identify-new-class-antibiotic-candidates <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" class="datetime">August 15, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>Using artificial intelligence, researchers design new compounds that kill antibiotic-resistant bacteria</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>AI-based approaches yield novel antibiotics that show promise against gonorrhea and MRSA.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Anne Trafton, MIT News </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-08-15T09:02:05-04:00" title="Friday, August 15, 2025 - 09:02" class="datetime">August 15, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=vNDL6n47 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=LOIVChyr 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=P14nvfJp 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=pwWzdLq2 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/longstory/MRSA_Staphylococcus_aureus_bacteria_NIAID_54149261148_2300d9f946_c.jpg?itok=q_Wi7kEc" alt="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." title="An electron microscope image of methicillin-resistant Staphylococcus aureus, also called MRSA." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NIAID </div> <div class="media-caption__description"> Methicillin-resistant Staphylococcus aureus (MRSA) </div> </div> </article> </div> </div> </div> </div> </div> </div> <div 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class="field__item"><a href="/infectious-disease-microbiome">Infectious Disease and Microbiome Program</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-articles sidebar-articles"> <div class="sidebar-articles__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related news</p> </div> <div class="field field--name-field-content-reference field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><article about="/news/making-antibiotics-more-potent-against-drug-resistant-bacteria" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a 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media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1921px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=sy_kAEnW 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=K8BQgHSR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=Yt7lhUBz 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7 1x" media="all and (max-width: 539px)" type="image/png" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/Scanning%20electron%20micrograph%20MRSA_crop.png?h=ae0fde30&itok=0bmkgsY7" alt="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" title="Methicillin-resistant Staphylococcus aureus (gold) on the remains of an immune cell (red)" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/researchers-use-ai-identify-new-class-antibiotic-candidates" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">With AI, researchers identify a new class of antibiotic candidates</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=i-DdytQi 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=pIHLJgdR 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=O_pwabKw 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2022/Hung-antibiotic-resistance_main.jpg?itok=QBgnkrRS" alt="Carbapenem-resistant Enterobacteriaceae bacteria" title="Carbapenem-resistant Enterobacteriaceae bacteria" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/study-finds-new-patterns-antibiotic-resistance-spread-hospitals" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Study finds new patterns of antibiotic resistance spread in hospitals</span> </a> </div> </article> </div> <div class="field__item"><article about="/news/artificial-intelligence-yields-new-antibiotic" class="node"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"><article class="media media--type-image media--view-mode-multiple-ct-sidebar-link-with-image"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <a href="/news/artificial-intelligence-yields-new-antibiotic"><picture> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop_xl/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=2Oh8TkmM 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="104" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_desktop/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=lvS73u77 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="87" height="104"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_tablet/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=ik4f-UbQ 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="285" height="186"/> <source srcset="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q 1x" media="all and (max-width: 539px)" type="image/jpeg" width="220" height="186"/> <img loading="eager" width="220" height="186" src="/files/styles/multiple_ct_sidebar_link_with_image_phone/public/news/images/2020/DrugHub_v2%20%281%29.jpg?h=d3e04ee7&itok=_4b5S24Q" alt="Susanna Hamilton, ӳý Communications" typeof="foaf:Image" /> </picture></a> </div> </article> </div> <div class="node__content"> <a href="/news/artificial-intelligence-yields-new-antibiotic" class="node__title"><span class="field field--name-title field--type-string field--label-hidden">Artificial intelligence yields new antibiotic</span> </a> </div> </article> </div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>With help from artificial intelligence, researchers from MIT, the Whitehead Institute for Biomedical Research, the Wyss Institute for Biologically Inspired Engineering, and the ӳý of MIT and Harvard have designed novel antibiotics that can combat two hard-to-treat infections: drug-resistant <em>Neisseria gonorrhoeae</em> and multi-drug-resistant <em>Staphylococcus aureus</em> (MRSA).</p> <p>Using generative AI algorithms, the research team designed more than 36 million possible compounds and computationally screened them for antimicrobial properties. The top candidates they discovered are structurally distinct from any existing antibiotics, and they appear to work by novel mechanisms that disrupt bacterial cell membranes.</p> <p>This approach allowed the researchers to generate and evaluate theoretical compounds that have never been seen before — a strategy that they now hope to apply to identify and design compounds with activity against other species of bacteria.</p> <p>“We’re excited about the new possibilities that this project opens up for antibiotics development. Our work shows the power of AI from a drug design standpoint, and enables us to exploit much larger chemical spaces that were previously inaccessible,” said <a href="/node/7015">James Collins</a>, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, a founding core faculty member at the Wyss Institute, and an institute member in the <a href="/node/8543">Infectious Disease and Microbiome Program</a> at the ӳý.</p> <p>Collins is the senior author of the study, which appears in <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank"><em>Cell</em></a>. The paper’s lead authors are MIT postdoc Aarti Krishnan of the Whitehead and ӳý institutes; former postdoc Melis Anahtar of the ӳý, Whitehead, and Wyss institutes and Mass General Brigham; and Jacqueline Valeri of the ӳý and Wyss institutes.</p> <h2>Exploring chemical space</h2> <p>Over the past 45 years, a few dozen new antibiotics have been approved by the FDA, but most of these are variants of existing antibiotics. At the same time, bacterial resistance to many of these drugs has been growing. Globally, it is estimated that drug-resistant bacterial infections cause nearly 5 million deaths per year.</p> <p>In hopes of finding new antibiotics to fight this growing problem, Collins and others at MIT’s Antibiotics-AI Project have harnessed the power of AI to screen huge libraries of existing chemical compounds. This work has yielded several promising drug candidates, including halicin and abaucin.</p> <p>To build on that progress, Collins and his colleagues decided to expand their search into molecules that can’t be found in any chemical libraries. By using AI to generate hypothetically possible molecules that don’t exist or haven’t been discovered, they realized that it should be possible to explore a much greater diversity of potential drug compounds.</p> <p>In their new study, the researchers employed two different approaches: First, they directed generative AI algorithms to design molecules based on a specific chemical fragment that showed antimicrobial activity, and second, they let the algorithms freely generate molecules, without having to include a specific fragment.</p> <p>For the fragment-based approach, the researchers sought to identify molecules that could kill <em>N. gonorrhoeae</em>, a Gram-negative bacterium that causes gonorrhea. They began by assembling a library of about 45 million known chemical fragments, consisting of all possible combinations of 11 atoms of carbon, nitrogen, oxygen, fluorine, chlorine, and sulfur, along with fragments from Enamine’s REadily AccessibLe (REAL) space.</p> <p>Then, they screened the library using machine-learning models that Collins’ lab has previously trained to predict antibacterial activity against N. gonorrhoeae. This resulted in nearly 4 million fragments. They narrowed down that pool by removing any fragments predicted to be cytotoxic to human cells, displayed chemical liabilities, and were known to be similar to existing antibiotics. This left them with about 1 million candidates.</p> <p>“We wanted to get rid of anything that would look like an existing antibiotic, to help address the antimicrobial resistance crisis in a fundamentally different way. By venturing into underexplored areas of chemical space, our goal was to uncover novel mechanisms of action,” Krishnan said.</p> <p>Through several rounds of additional experiments and computational analysis, the researchers identified a fragment they called F1 that appeared to have promising activity against <em>N. gonorrhoeae</em>. They used this fragment as the basis for generating additional compounds, using two different generative AI algorithms.</p> <p>One of those algorithms, known as chemically reasonable mutations (CReM), works by starting with a particular molecule containing F1 and then generating new molecules by adding, replacing, or deleting atoms and chemical groups. The second algorithm, F-VAE (fragment-based variational autoencoder), takes a chemical fragment and builds it into a complete molecule. It does so by learning patterns of how fragments are commonly modified, based on its pretraining on more than 1 million molecules from the ChEMBL database.</p> <p>Those two algorithms generated about 7 million candidates containing F1, which the researchers then computationally screened for activity against <em>N. gonorrhoeae</em>. This screen yielded about 1,000 compounds, and the researchers selected 80 of those to see if they could be produced by chemical synthesis vendors. Only two of these could be synthesized, and one of them, named NG1, was very effective at killing <em>N. gonorrhoeae</em> in a lab dish and in a mouse model of drug-resistant gonorrhea infection.</p> <p>Additional experiments revealed that NG1 interacts with a protein called LptA, a novel drug target involved in the synthesis of the bacterial outer membrane. It appears that the drug works by interfering with membrane synthesis, which is fatal to cells.</p> <h2>Unconstrained design</h2> <p>In a second round of studies, the researchers explored the potential of using generative AI to freely design molecules, using Gram-positive bacteria, <em>S. aureus</em> as their target.</p> <p>Again, the researchers used CReM and VAE to generate molecules, but this time with no constraints other than the general rules of how atoms can join to form chemically plausible molecules. Together, the models generated more than 29 million compounds. The researchers then applied the same filters that they did to the <em>N. gonorrhoeae</em> candidates, but focusing on <em>S. aureus</em>, eventually narrowing the pool down to about 90 compounds.</p> <p>They were able to synthesize and test 22 of these molecules, and six of them showed strong antibacterial activity against multi-drug-resistant S. aureus grown in a lab dish. They also found that the top candidate, named DN1, was able to clear a methicillin-resistant <em>S. aureus</em> (MRSA) skin infection in a mouse model. These molecules also appear to interfere with bacterial cell membranes, but with broader effects not limited to interaction with one specific protein.</p> <p>Phare Bio, a nonprofit that is also part of the Antibiotics-AI Project, is now working on further modifying NG1 and DN1 to make them suitable for additional testing.</p> <p>“In a collaboration with Phare Bio, we are exploring analogs, as well as working on advancing the best candidates preclinically, through medicinal chemistry work,” Collins said. “We are also excited about applying the platforms that Aarti and the team have developed toward other bacterial pathogens of interest, notably <em>Mycobacterium tuberculosis</em> and <em>Pseudomonas aeruginosa</em>.”</p> <p><em>Adapted from <a href="https://news.mit.edu/2025/using-generative-ai-researchers-design-compounds-kill-drug-resistant-bacteria-0814" target="_blank"> a story published by MIT News</a></em>.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Krishnan A, Anahtar MN, Valeri JA, et al. <a href="https://www.cell.com/cell/fulltext/S0092-8674(25)00855-4" target="_blank">A generative deep learning approach to de novo antibiotic design.</a> <em>Cell</em>. Online August 14, 2025. DOI: 10.1016/j.cell.2025.07.033.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study was provided by U.S. Defense Threat Reduction Agency, the National Institute of Allergy and Infectious Diseases, the Audacious Project, Flu Lab, the Sea Grape Foundation, Rosamund Zander and Hansjorg Wyss for the Wyss Foundation, the ӳý of MIT and Harvard, an anonymous donor, and other sources.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/infectious-disease-and-microbiome-0" hreflang="en">Infectious Disease and Microbiome Program</a></div> <div class="field__item"><a href="/broad-tags/antibiotic-resistance" hreflang="en">Antibiotic resistance</a></div> <div class="field__item"><a href="/broad-tags/infectious-disease" hreflang="en">Infectious Disease</a></div> <div class="field__item"><a href="/broad-tags/jim-collins" hreflang="en">Jim Collins</a></div> </div> </div> </div> </div> </div> Wed, 20 Dec 2023 16:30:46 +0000 tulrich@broadinstitute.org 5556221 at