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Discovery of senolytics using machine learning

Author

Listed:
  • Vanessa Smer-Barreto

    (University of Edinburgh)

  • Andrea Quintanilla

    (CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22)

  • Richard J. R. Elliott

    (University of Edinburgh)

  • John C. Dawson

    (University of Edinburgh)

  • Jiugeng Sun

    (University of Edinburgh)

  • Víctor M. Campa

    (CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22)

  • Álvaro Lorente-Macías

    (University of Edinburgh)

  • Asier Unciti-Broceta

    (University of Edinburgh)

  • Neil O. Carragher

    (University of Edinburgh)

  • Juan Carlos Acosta

    (University of Edinburgh
    CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22)

  • Diego A. Oyarzún

    (University of Edinburgh
    University of Edinburgh, Max Born Crescent
    The Alan Turing Institute)

Abstract

Cellular senescence is a stress response involved in ageing and diverse disease processes including cancer, type-2 diabetes, osteoarthritis and viral infection. Despite growing interest in targeted elimination of senescent cells, only few senolytics are known due to the lack of well-characterised molecular targets. Here, we report the discovery of three senolytics using cost-effective machine learning algorithms trained solely on published data. We computationally screened various chemical libraries and validated the senolytic action of ginkgetin, periplocin and oleandrin in human cell lines under various modalities of senescence. The compounds have potency comparable to known senolytics, and we show that oleandrin has improved potency over its target as compared to best-in-class alternatives. Our approach led to several hundred-fold reduction in drug screening costs and demonstrates that artificial intelligence can take maximum advantage of small and heterogeneous drug screening data, paving the way for new open science approaches to early-stage drug discovery.

Suggested Citation

  • Vanessa Smer-Barreto & Andrea Quintanilla & Richard J. R. Elliott & John C. Dawson & Jiugeng Sun & Víctor M. Campa & Álvaro Lorente-Macías & Asier Unciti-Broceta & Neil O. Carragher & Juan Carlos Acos, 2023. "Discovery of senolytics using machine learning," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39120-1
    DOI: 10.1038/s41467-023-39120-1
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    References listed on IDEAS

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    1. Reut Yosef & Noam Pilpel & Ronit Tokarsky-Amiel & Anat Biran & Yossi Ovadya & Snir Cohen & Ezra Vadai & Liat Dassa & Elisheva Shahar & Reba Condiotti & Ittai Ben-Porath & Valery Krizhanovsky, 2016. "Directed elimination of senescent cells by inhibition of BCL-W and BCL-XL," Nature Communications, Nature, vol. 7(1), pages 1-11, September.
    2. Dai Kusumoto & Tomohisa Seki & Hiromune Sawada & Akira Kunitomi & Toshiomi Katsuki & Mai Kimura & Shogo Ito & Jin Komuro & Hisayuki Hashimoto & Keiichi Fukuda & Shinsuke Yuasa, 2021. "Anti-senescent drug screening by deep learning-based morphology senescence scoring," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Frank von Delft & Mark Calmiano & John Chodera & Ed Griffen & Alpha Lee & Nir London & Tatiana Matviuk & Ben Perry & Matt Robinson & Annette von Delft, 2021. "A white-knuckle ride of open COVID drug discovery," Nature, Nature, vol. 594(7863), pages 330-332, June.
    4. Heike Fuhrmann-Stroissnigg & Yuan Yuan Ling & Jing Zhao & Sara J. McGowan & Yi Zhu & Robert W. Brooks & Diego Grassi & Siobhan Q. Gregg & Jennifer L. Stripay & Akaitz Dorronsoro & Lana Corbo & Priscil, 2017. "Identification of HSP90 inhibitors as a novel class of senolytics," Nature Communications, Nature, vol. 8(1), pages 1-14, December.
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