AI-recognized mitochondrial phenotype enables identification of drug targets


Revealing a drug’s mechanism of action (MOA) is costly and time-consuming. In this study, we used deep learning to extract temporal mitochondrial phenotypic features after exposure to drugs with known MOAs using re-identification algorithms. The trained model could then predict the MOAs of unidentified substances, facilitating phenotypic screening-based drug discovery and repurposing.

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Fig. 1: Deep learning predicts drug MOA via temporal mitochondrial phenotype.

References

  1. Chandrasekaran, S. N. et al. Image-based profiling for drug discovery: due for a machine-learning upgrade? Nat. Rev. Drug Discov. 20, 145–159 (2021). A review article that describes in detail the application of image-based profiling to the field of drug discovery through machine learning methods.

    Article 

    Google Scholar 

  2. Way, G. P. et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Syst. 13, 911–923.e9 (2022). This paper reports that morphology and gene expression are complementary profiling assays, each with its own advantages and disadvantages.

    Article 

    Google Scholar 

  3. Spinelli, H. M. The multifaceted contributions of mitochondria to cellular metabolism. Nat. Cell Biol. 20, 745–754 (2018). A review article that presents multifaceted roles of mitochondria in cell metabolism.

    Article 

    Google Scholar 

  4. Eisner, P. M. et al. Mitochondrial dynamics in adaptive and maladaptive cellular stress responses. Nat. Cell Biol. 20, 755–765 (2018). A review article that presents the role of mitochondrial dynamics in adaptive and non-adaptive cellular stress responses.

    Article 

    Google Scholar 

Download references

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This is a summary of: Yu, M. et al. Deep learning large-scale drug discovery and repurposing. Nat. Comput. Sci. https://doi.org/10.1038/s43588-024-00679-4 (2024).

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AI-recognized mitochondrial phenotype enables identification of drug targets.
Nat Comput Sci (2024). https://doi.org/10.1038/s43588-024-00682-9

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  • Published: 22 August 2024

  • DOI: https://doi.org/10.1038/s43588-024-00682-9


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