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Integrated Thermal Proteome Profiling and Affinity Ultrafiltration Mass Spectrometry (iTPAUMS): A Novel Paradigm for Elucidating the Mechanism of Action of Natural Products

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    Integrated Thermal Proteome Profiling and Affinity Ultrafiltration Mass Spectrometry (iTPAUMS): A Novel Paradigm for Elucidating the Mechanism of Action of Natural Products
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    • Hengyuan Yu
      Hengyuan Yu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      More by Hengyuan Yu
    • Yang Chen
      Yang Chen
      Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Xihu University School of Medicine, Hangzhou 310006, China
      More by Yang Chen
    • Yichen Wang
      Yichen Wang
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      More by Yichen Wang
    • Weiliang Fu
      Weiliang Fu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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    • Rui Xu
      Rui Xu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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    • Jie Liu
      Jie Liu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      Shandong C.P. Freda Pharmaceutical Co., Ltd., Jinan 250104, China
      Engineering Research Center for Medicines of Orthopedic Pain of Shandong Province, Jinan 250104, China
      More by Jie Liu
    • Yong Chen
      Yong Chen
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
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    • Xuesong Liu
      Xuesong Liu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
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    • Yongjiang Wu*
      Yongjiang Wu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      *Email: [email protected]
      More by Yongjiang Wu
      Orcidhttps://orcid.org/0000-0003-0246-9067
    • Tengfei Xu*
      Tengfei Xu
      College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
      Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
      *Email: [email protected]
      More by Tengfei Xu
      Orcidhttps://orcid.org/0000-0002-3212-568X
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    Analytical Chemistry

    Cite this: Anal. Chem. 2024, 96, 40, 15980–15990
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    https://doi.org/10.1021/acs.analchem.4c03398
    Published September 10, 2024
    Copyright © 2024 American Chemical Society
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    Abstract

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    Natural products (NPs) are foundational to drug discovery, offering a rich repertoire of molecular diversity with multifaceted modes of action against a broad array of targets. Despite their potential, deconvoluting the intricate mechanism of action (MoA) of NPs, characterized by their multicomponent, multitarget, and multilevel interactions, remains a formidable challenge. Here, we introduce an innovative pipeline called integrated thermal proteome profiling and affinity ultrafiltration mass spectrometry (iTPAUMS). This approach combines the high-throughput capacity of thermal proteome profiling (TPP) with the specificity of affinity ultrafiltration mass spectrometry (AUMS), creating a powerful toolkit for elucidating complex MoAs of NPs. Significantly, our investigation represents a pioneering application of TPP to delineate the target group of NPs mixtures and overcome the long-standing obstacle of mapping specific component-target interactions through AUMS. Our findings demonstrate the utility of iTPAUMS in constructing a comprehensive component-target atlas, providing a robust analytical foundation for unraveling the intricate pharmacological landscapes of NPs and advancing drug discovery.

    Copyright © 2024 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.4c03398.

    • Additional experimental details, materials and methods, including cell cultures and cell viability assay, colony-formation assay, molecular dynamics and Western blotting (PDF)

    • Search results of TPP (XLSX)

    • Proteins hits of TPP (XLSX)

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    Analytical Chemistry

    Cite this: Anal. Chem. 2024, 96, 40, 15980–15990
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.analchem.4c03398
    Published September 10, 2024
    Copyright © 2024 American Chemical Society
    Request reuse permissions

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