Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems
Open accessAbstract
Chemical modification of proteins provides powerful tools to realize a broad range of exciting biological applications, including the development of new classes of biopharmaceuticals and functional studies of individual proteins in complex biological systems. Numerous strategies for linking desired chemical probes with target proteins have been developed in the last two decades, with most exploiting genetic protein engineering and/or bio-orthogonal chemistry that utilizes unnatural amino acids incorporated into proteins. Modification of native proteins in test tubes and biological contexts by site-specific and target-selective approaches remains challenging because appropriate organic chemistry to carry out such modifications is currently limited. Nonetheless, a variety of promising strategies have appeared recently that address this grand challenge in chemical biology. These new chemistries yield native protein-based well-defined bioconjugations, specific labeling of endogenous proteins in various biological crude milieus, and the establishment of chemical proteomics as a new research area in protein science. In this Perspective, we focus on recent remarkable progress in chemistry for native protein modification. We survey chemical characteristics of the methods and describe briefly these advanced applications to address unsolved biological issues. Current limitations and future directions of this research field are also discussed.
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In 2021, Hamachi et al. developed a small molecule covalent inhibitor (compound 76) based on NASA reaction group that prevents HDM2-p53 interaction.
“In 2021, Hamachi et al. developed a small molecule covalent inhibitor, compound (76), based on the N-acyl-N-alkyl sulfonamide (NASA) reaction group, which can prevent the interaction between HDM2 and p53.”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [221]
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Miki, T., Awa, M., Nishikawa, Y., Kiyonaka, S., Wakabayashi, M., Ishihama, Y., & Hamachi, I. (2016) · Nature Methods · doi:10.1038/nmeth.3998 · Cited by 70 · see citing works
Self-citationAffinity-Guided Oxime Chemistry for Selective Protein Acylation in Live Tissue Systems
Tamura, T., Song, Z., Amaike, K., et al. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b07339 · Cited by 69 · see citing works
Self-citationYasueda, Y., Tamura, T., Fujisawa, A., Kuwata, K., Tsukiji, S., Kiyonaka, S., & Hamachi, I. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b02254 · Cited by 67 · see citing works
Self-citationAnalysis of Cell-Surface Receptor Dynamics through Covalent Labeling by Catalyst-Tethered Antibody
Hayashi, T., Yasueda, Y., Tamura, T., Takaoka, Y., & Hamachi, I. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b02867 · Cited by 66 · see citing works
Self-citationHayashi, T., Sun, Y., Tamura, T., Kuwata, K., Song, Z., Takaoka, Y., & Hamachi, I. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4043214 · Cited by 59 · see citing works
Self-citationChemical Profiling of the Endoplasmic Reticulum Proteome Using Designer Labeling Reagents
Fujisawa, A., Tamura, T., Yasueda, Y., Kuwata, K., & Hamachi, I. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b08606 · Cited by 59 · see citing works
Self-citationLive‐Cell Protein Sulfonylation Based on Proximity‐drivenN‐Sulfonyl Pyridone Chemistry
Matsuo, K., Nishikawa, Y., Masuda, M., & Hamachi, I. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201707972 · Cited by 58 · see citing works
Self-citationQuantitative comparison of protein dynamics in live cells and in vitro by in-cell 19F-NMR
Takaoka, Y., Kioi, Y., Morito, A., et al. (2013) · Chemical Communications · doi:10.1039/c3cc39205h · Cited by 56 · see citing works
A Naturally Encoded Dipeptide Handle for Bioorthogonal Chan–Lam Coupling
Ohata, J., Zeng, Y., Segatori, L., et al. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201800828 · Cited by 52 · see citing works
Matsuo, K., Kioi, Y., Yasui, R., et al. (2013) · Chemical Science · doi:10.1039/c3sc50560j · Cited by 47 · see citing works
Amaike, K., Tamura, T., & Hamachi, I. (2017) · Chemical Communications · doi:10.1039/c7cc07177a · Cited by 46 · see citing works
Self-citationTakaoka, Y., Sun, Y., Tsukiji, S., & Hamachi, I. (2010) · Chemical Science · doi:10.1039/c0sc00513d · Cited by 45 · see citing works
Self-citationOrganelle‐Specific Activity‐Based Protein Profiling in Living Cells
Wiedner, S. D., Anderson, L. N., Sadler, N., Chrisler, W., Kodali, V., Smith, R. D., & Wright, A. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201309135 · Cited by 42 · see citing works
Synthetic Chromatin Acylation by an Artificial Catalyst System
Ishiguro, T., Amamoto, Y., Tanabe, K., Liu, J., Kajino, H., Fujimura, A., Aoi, Y., Osakabe, A., Horikoshi, N., Kurumizaka, H., et al. (2017) · Chem · doi:10.1016/j.chempr.2017.04.002 · Cited by 38 · see citing works
Molecular recognition in protein modification with rhodium metallopeptides
Ball, Z. T. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.12.017 · Cited by 35 · see citing works
A Vinylogous Photocleavage Strategy Allows Direct Photocaging of Backbone Amide Structure
Mangubat-Medina, A. E., Martin, S. C., Hanaya, K., & Ball, Z. T. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b04893 · Cited by 34 · see citing works
In Situ Construction of Protein-Based Semisynthetic Biosensors
Ueda, T., Tamura, T., & Hamachi, I. (2018) · ACS Sensors · doi:10.1021/acssensors.7b00894 · Cited by 30 · see citing works
Self-citationNucleus-selective Chemical Proteomics Using Hoechst-tagged Reactive Molecules
Yasueda, Y., Tamura, T., & Hamachi, I. (2015) · Chemistry Letters · doi:10.1246/cl.151083 · Cited by 22 · see citing works
Self-citationTakaoka, Y., Uchinomiya, S., Kobayashi, D., Endo, M., Hayashi, T., Fukuyama, Y., Hayasaka, H., Miyasaka, M., Ueda, T., Shimada, I., et al. (2018) · Chem · doi:10.1016/j.chempr.2018.03.021 · Cited by 19 · see citing works
Self-citationLive cell off-target identification of lapatinib using ligand-directed tosyl chemistry
Yamaura, K., Kuwata, K., Tamura, T., et al. (2014) · Chemical Communications · doi:10.1039/c4cc05885b · Cited by 18 · see citing works
Self-citationIn Situ Protein Labeling in Complex Environments
Tamura, T., Shigemitsu, H., & Hamachi, I. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12553-3 · Cited by 2 · see citing works
Self-citation
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Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials
Xie, X., Yu, T., Li, X., Zhang, N., Foster, L. J., Peng, C., Huang, W., & He, G. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01589-z · Cited by 396 · see citing works
Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation
Zhang, T., Hatcher, J. M., Teng, M., Gray, N. S., & Kostic, M. (2019) · Cell Chemical Biology · doi:10.1016/j.chembiol.2019.09.012 · Cited by 178 · see citing works
Qin, X., Wang, R., Xu, H., Tu, L., Chen, H., Li, H., Liu, N., Wang, J., Li, S., Yin, F., et al. (2022) · Autophagy · doi:10.1080/15548627.2021.2022360 · Cited by 55 · see citing works
- Authors
- Tamura, T., & Hamachi, I.
- Affiliations
- Kyoto University (JP)
- Corresponding author
- Hamachi, Itaru
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-12-28
- Volume
- 141
- Issue
- 7
- Pages
- 2782-2799
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2908038781
- Cited by
- 339
- References
- 119
- Citations by year
- 2026: 25 · 2025: 40 · 2024: 58 · 2023: 46 · 2022: 48 · 2021: 56 · 2020: 46 · 2019: 20
- FWCI
- 12.49
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of the American Chemical Society (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Funders
- Japan Society for the Promotion of Science (17H06348)
- Exploratory Research for Advanced Technology (JPMJER1802)
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- covalent protein labeling, bioconjugation, chemoproteomics, bioorthogonal chemistry, unnatural amino acids, site-specific protein modification, biopharmaceuticals, chemical biology
- MeSH terms
- Animals, Cysteine, Humans, Lysine, Methionine, Proteins, Molecular Probes, Proteome, Amino Acids, Aromatic
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