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  1. No Access

    Article

    Discovery of a structural class of antibiotics with explainable deep learning

    The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance crisis1–9. Deep learning approaches have aided in exploring chemical spaces1,10–15; these t...

    Felix Wong, Erica J. Zheng, Jacqueline A. Valeri, Nina M. Donghia… in Nature (2024)

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    Article

    Discovering small-molecule senolytics with deep neural networks

    The accumulation of senescent cells is associated with aging, inflammation and cellular dysfunction. Senolytic drugs can alleviate age-related comorbidities by selectively killing senescent cells. Here we scre...

    Felix Wong, Satotaka Omori, Nina M. Donghia, Erica J. Zheng… in Nature Aging (2023)

  3. Article

    Open Access

    Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies

    Antibiotic tolerance, or the ability of bacteria to survive antibiotic treatment in the absence of genetic resistance, has been linked to chronic and recurrent infections. Tolerant cells are often characterize...

    Erica J. Zheng, Ian W. Andrews, Alexandra T. Grote… in Nature Communications (2022)

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    Article

    Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate

    Growth rate and metabolic state of bacteria have been separately shown to affect antibiotic efficacy1–3. However, the two are interrelated as bacterial growth inherently imposes a metabolic burden4; thus, determi...

    Allison J. Lopatkin, Jonathan M. Stokes, Erica J. Zheng… in Nature Microbiology (2019)