ArticleCell2025
A generative deep learning approach to de novo antibiotic design.
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Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29citing papers in PubMed
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29 citing papers in PubMed.
- Combating antimicrobial resistance through multimodal data via artificial intelligence.One health (Amsterdam, Netherlands) · 2026Review
- Coupling continuous directed evolution with base editors identifies combinatorial antibiotic resistance.Biotechnology letters · 2026Article
- Artificial Intelligence-Guided Phenotypic Drug Repurposing Against Streptococcus pneumoniae.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Evolutionary Convergence on a Dihydrofolate Reductase Mutation Drives Trimethoprim-Sulfamethoxazole Resistance in Burkholderia thailandensis.ACS infectious diseases · 2026Article
- Random Forest Modeling to Predict Small Molecule Accumulation in Gram-Negative Bacteria.ACS infectious diseases · 2026Article
- Conformational hijacking of lipoprotein transporter LolDF enables precision antimicrobial activity against Acinetobacter baumannii.Nature communications · 2026Article
- The use of artificial intelligence (AI) in neuropsychiatric drug discovery: current challenges and future directions.Translational psychiatry · 2026Review
- Medical artificial intelligence and the right to health.BMC medical ethics · 2026Article
- Deep learning-enabled discovery of antibiotics effective againstScience translational medicine · 2026Article
- SyntheMol-RL: a flexible reinforcement learning framework for designing easily synthesizable antibiotics.Molecular systems biology · 2026Article
- Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery.PLoS computational biology · 2026Article
- Current State of the Fight Against Antimicrobial Resistance: What Are the Different Strategies for Tomorrow?Antibiotics (Basel, Switzerland) · 2026Review
- Harnessing artificial intelligence for antimicrobial discovery and optimization.Current opinion in microbiology · 2026Review
- AI is taking on antibiotic resistance - here's how.Nature · 2026Article
- Quorum Sensing and Quorum Quenching in Periodontal Disease: Mechanisms and Therapeutic Potential.Current issues in molecular biology · 2026Review
- Structure-Based Strategy Reveals a Novel Ligand Binding Site inACS omega · 2026Article
- Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis.Pharmacological research · 2026Article
- Immortal AI, Mortal Life: Long-Term Perspectives on AI and Human Knowledge.Journal of medical Internet research · 2026Article
- FRAIL: fragment-based reinforcement learning for molecular design and benchmarking on fatty acid amide hydrolase 1 (FAAH-1).Molecular diversity · 2026Article
- Reprogrammed SimCells for antimicrobial therapy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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Authors and funding
32 authors.
Aarti KrishnanInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Melis N AnahtarInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Departments of Pathology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Jacqueline A ValeriInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Wengong JinEric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA.
Nina M DonghiaWyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Leif SiebenInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
Andreas LuttensInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Yu ZhangInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Seyed Majed ModaresiInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Andrew HennesInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
Jenna FromerDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Parijat BandyopadhyayInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Jonathan C ChenInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Danyal RehmanMila-Quebec AI Institute, Montréal, QC H2S 3H1, Canada.
Ronak DesaiInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard Medical School, Boston, MA 02115, USA.
Paige EdwardsInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Ryan S LachIntegrated Biosciences, Inc., Redwood City, CA 94065, USA.
Marie-Stéphanie AschtgenDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden.
Margaux GaborieauDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden.
Massimiliano GaetaniDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17 177 Stockholm, Sweden; Chemical Proteomics Unit, Science for Life Laboratory (SciLifeLab), 171 77Stockholm, Sweden.
Samantha G PalaceDepartment of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
Satotaka OmoriIntegrated Biosciences, Inc., Redwood City, CA 94065, USA.
Lutete KhondeCenter for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Yurii S MorozEnamine Ltd., 67 Winston Churchill Street, Kyiv 02094, Ukraine; Chemspace LLC, 85 Winston Churchill Street, Kyiv 02094, Ukraine; Department of Chemistry, Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv 01601, Ukraine.
Bruce BloughCenter for Drug Discovery, RTI International, Research Triangle Park, Durham, NC 27713, USA.
Chunyang JinCenter for Drug Discovery, RTI International, Research Triangle Park, Durham, NC 27713, USA.
Edmund LohDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden.
Yonatan H GradDepartment of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
Amir Ata SaeiDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden.
Connor W ColeyDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Felix WongInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Integrated Biosciences, Inc., Redwood City, CA 94065, USA.
James J CollinsInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. Electronic address: jimjc@mit.edu.
Funding
Chemistry Center for Combatting Antibiotic-Resistant Bacteria (CC4CARB)75N93021C00002 · NIAID · RESEARCH TRIANGLE INSTITUTE · PI BLOUGH, BRUCE · 2021 to 2025
$19.6MMedical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7MGenetic, Metabolic and Regulatory Control of MIC and Relapse in M. tuberculosisR01AI146194 · NIAID · UNIVERSITY OF WASHINGTON · PI ALLAND, DAVID, SHERMAN, DAVID R · 2020 to 2024
$4.1MGenomics approaches to elucidating pathways to antibiotic resistance in Neisseria gonorrhoeaeR01AI132606 · NIAID · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI Yonatan H Grad · 2017 to 2026
$3.8MIdentification and analysis of compensatory mutations that support the evolution of antibiotic resistance in Neisseria gonorrhoeaeR01AI153521 · NIAID · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI GRAD, YONATAN H, JERSE, ANN E. · 2020 to 2024
$3.7MHarnessing machine learning to develop new antibiotics for Neisseria gonorrhoeaeK08AI182474 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI Melis N. Anahtar · 2024 to 2026
$590kPhysical Biology and Deep Learning for Antibiotic Resistance and DiscoveryK25AI168451 · NIAID · BROAD INSTITUTE, INC. · PI Felix Wong · 2023 to 2026
$486kNIAID NIH HHS 75N93021C00002NIAID NIH HHS K08 AI182474NIAID NIH HHS K25 AI168451NIAID NIH HHS R01 AI132606NIAID NIH HHS R01 AI146194NIAID NIH HHS R01 AI153521NIGMS NIH HHS T32 GM144273
Abstract
The antimicrobial resistance crisis necessitates structurally distinct antibiotics. While deep learning approaches can identify antibacterial compounds from existing libraries, structural novelty remains limited. Here, we developed a generative artificial intelligence framework for designing de novo antibiotics through two approaches: a fragment-based method to comprehensively screen >10
Indexed as
Anti-Bacterial AgentsDeep LearningDrug DesignAnimalsFemaleGonorrheaHumansMethicillin-Resistant Staphylococcus aureusMiceMicrobial Sensitivity TestsNeisseria gonorrhoeaeStaphylococcal InfectionsStaphylococcus aureusAnti-Bacterial Agentsantibioticsbacterial infectionde novo designdrug discoveryfragmentsgenerative artificial intelligencegraph neural networksmachine learningNeisseria gonorrhoeaeStaphylococcus aureus
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