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Cell-Based Proteome Profiling Using an Affinity-Based Probe (AfBP) Derived from 3-Deazaneplanocin A ()

Authors

  • Dr. Eric K. W. Tam,

    1. Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)
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    • These authors contributed equally to this work.

  • Dr. Zhengqiu Li,

    1. Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 (Singapore), Fax: (+65) 6779-1691
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    • These authors contributed equally to this work.

  • Yi Ling Goh,

    1. Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)
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  • Xiamin Cheng,

    1. Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 (Singapore), Fax: (+65) 6779-1691
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  • Sze Yue Wong,

    1. Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)
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  • Dr. Sridhar Santhanakrishnan,

    1. Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)
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  • Prof. Dr. Christina L. L. Chai,

    Corresponding author
    1. Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)
    2. Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
    • Christina L. L. Chai, Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)

      Shao Q. Yao, Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 (Singapore), Fax: (+65) 6779-1691

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  • Prof. Dr. Shao Q. Yao

    Corresponding author
    1. Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 (Singapore), Fax: (+65) 6779-1691
    • Christina L. L. Chai, Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665 (Singapore)

      Shao Q. Yao, Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 (Singapore), Fax: (+65) 6779-1691

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Abstract

3-Deazaneplanocin A (), a global histone methylation inhibitor, has attracted significant interest in epigenetic research in recent years. The molecular mechanism of action and the cellular off-targets of , however, are still not well-understood. Our aim was to develop novel -derived small-molecule probes suitable to be used in live mammalian cells for identification of potential cellular targets of under physiologically relevant settings. In the current study, we have successfully designed, synthesized, and tested one such probe, called . is a ‘clickable’ affinity-based probe (AfBP) derived from with minimal structural modifications. The probe was found to be highly cell-permeable, and possessed similar anti-apoptotic activities as in MCF-7 mammalian cells. Two additional control probes were made as negative labeling/pull-down probes in order to minimize false identification of background proteins due to unavoidable, intrinsic nonspecific photo-crosslinking reactions. All three probes were subsequently used for in-situ proteome profiling in live mammalian cells, followed by large-scale pull-down/LC-MS/MS analysis for identification of potential cellular protein targets that might interact with in native cellular environments. Our LC-MS/MS results revealed some highly enriched proteins that had not been reported as potential targets. These proteins might constitute unknown cellular off-targets of . Though further validation experiments are needed in order to unequivocally confirm these off-targets, our findings shed new light on the future use of as a validated chemical probe for epigenetic research and as a potential drug candidate for cancer therapy.

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