Abstract
Over the years, the proteasome has been extensively investigated due to its crucial roles in many important signaling pathways and its implications in diseases. Two proteasome inhibitors—bortezomib and carfilzomib—have received FDA approval for the treatment of multiple myeloma, thereby validating the proteasome as a chemotherapeutic target. As a result, further research efforts have been focused on dissecting the complex biology of the proteasome to gain the insight required for developing next-generation proteasome inhibitors. It is clear that chemical probes have made significant contributions to these efforts, mostly by functioning as inhibitors that selectively block the catalytic activity of proteasomes. Analogues of these inhibitors are now providing additional tools for visualization of catalytically active proteasome subunits, several of which allow real-time monitoring of proteasome activity in living cells as well as in in vivo settings. These imaging probes will provide powerful tools for assessing the efficacy of proteasome inhibitors in clinical settings. In this review, we will focus on the recent efforts towards developing imaging probes of proteasomes, including the latest developments in immunoproteasome-selective imaging probes.
Similar content being viewed by others
References
Konstantinova, I. M., Tsimokha, A. S., & Mittenberg, A. G. (2008). Role of proteasomes in cellular regulation. International Review of Cell and Molecular Biology, 267, 59–124.
Marques, A. J., Palanimurugan, R., Matias, A. C., Ramos, P. C., & Dohmen, R. J. (2009). Catalytic mechanism and assembly of the proteasome. Chemical Reviews, 109, 1509–1536.
Navon, A., & Ciechanover, A. (2009). The 26 S proteasome: From basic mechanisms to drug targeting. Journal of Biological Chemistry, 284, 33713–33718.
Griffin, B. A., Adams, S. R., & Tsien, R. Y. (1998). Specific covalent labeling of recombinant protein molecules inside live cells. Science, 281, 269–272.
Hallermalm, K., Seki, K., Wei, C., Castelli, C., Rivoltini, L., Kiessling, R., et al. (2001). Tumor necrosis factor-alpha induces coordinated changes in major histocompatibility class I presentation pathway, resulting in increased stability of class I complexes at the cell surface. Blood, 98, 1108–1115.
Murata, S., Sasaki, K., Kishimoto, T., Niwa, S., Hayashi, H., Takahama, Y., et al. (2007). Regulation of CD8+ T cell development by thymus-specific proteasomes. Science, 316, 1349–1353.
De, M., Jayarapu, K., Elenich, L., Monaco, J. J., Colbert, R. A., & Griffin, T. A. (2003). Beta 2 subunit propeptides influence cooperative proteasome assembly. Journal of Biological Chemistry, 278, 6153–6159.
Murata, S., Yashiroda, H., & Tanaka, K. (2009). Molecular mechanisms of proteasome assembly. Nature Reviews Molecular Cell Biology, 10, 104–115.
Yewdell, J. W. (2005). Immunoproteasomes: Regulating the regulator. Proceedings of the National Academy of Sciences of the United States of America, 102, 9089–9090.
Groettrup, M., Kirk, C. J., & Basler, M. (2010). Proteasomes in immune cells: More than peptide producers? Nature Reviews Immunology, 10, 73–78.
Rockwell, C. E., Monaco, J. J., & Qureshi, N. (2012). A critical role for the inducible proteasomal subunits LMP7 and MECL1 in cytokine production by activated murine splenocytes. Pharmacology, 89, 117–126.
Seifert, U., Bialy, L. P., Ebstein, F., Bech-Otschir, D., Voigt, A., Schroter, F., et al. (2010). Immunoproteasomes preserve protein homeostasis upon interferon-induced oxidative stress. Cell, 142, 613–624.
Angeles, A., Fung, G., & Luo, H. (2012). Immune and non-immune functions of the immunoproteasome. Frontiers in Bioscience, 17, 1904–1916.
Diaz-Hernandez, M., Hernandez, F., Martin-Aparicio, E., Gomez-Ramos, P., Moran, M. A., Castano, J. G., et al. (2003). Neuronal induction of the immunoproteasome in Huntington’s disease. Journal of Neuroscience, 23, 11653–11661.
Mishto, M., Bellavista, E., Santoro, A., Stolzing, A., Ligorio, C., Nacmias, B., et al. (2006). Immunoproteasome and LMP2 polymorphism in aged and Alzheimer’s disease brains. Neurobiology of Aging, 27, 54–66.
Fitzpatrick, L. R., Khare, V., Small, J. S., & Koltun, W. A. (2006). Dextran sulfate sodium-induced colitis is associated with enhanced low molecular mass polypeptide 2 (LMP2) expression and is attenuated in LMP2 knockout mice. Digestive Diseases and Sciences, 51, 1269–1276.
Kuhn, D. J., Hunsucker, S. A., Chen, Q., Voorhees, P. M., Orlowski, M., & Orlowski, R. Z. (2009). Targeted inhibition of the immunoproteasome is a potent strategy against models of multiple myeloma that overcomes resistance to conventional drugs and nonspecific proteasome inhibitors. Blood, 113, 4667–4676.
Kuhn, D. J., & Orlowski, R. Z. (2012). The immunoproteasome as a target in hematologic malignancies. Seminars in Hematology, 49, 258–262.
Muchamuel, T., Basler, M., Aujay, M. A., Suzuki, E., Kalim, K. W., Lauer, C., et al. (2009). A selective inhibitor of the immunoproteasome subunit LMP7 blocks cytokine production and attenuates progression of experimental arthritis. Nature Medicine, 15, 781–787.
Ho, Y. K., Bargagna-Mohan, P., Wehenkel, M., Mohan, R., & Kim, K. B. (2007). LMP2-specific inhibitors: chemical genetic tools for proteasome biology. Chemistry & Biology, 14, 419–430.
Parlati, F., Lee, S. J., Aujay, M., Suzuki, E., Levitsky, K., Lorens, J. B., et al. (2009). Carfilzomib can induce tumor cell death through selective inhibition of the chymotrypsin-like activity of the proteasome. Blood, 114, 3439–3447.
Singh, A. V., Bandi, M., Aujay, M. A., Kirk, C. J., Hark, D. E., Raje, N., et al. (2011). PR-924, a selective inhibitor of the immunoproteasome subunit LMP-7, blocks multiple myeloma cell growth both in vitro and in vivo. British Journal of Haematology, 152, 155–163.
Lee, W., & Kim, K. B. (2011). The immunoproteasome: An emerging therapeutic target. Current Topics in Medicinal Chemistry, 11, 2923–2930.
Bogyo, M., McMaster, J. S., Gaczynska, M., Tortorella, D., Goldberg, A. L., & Ploegh, H. (1997). Covalent modification of the active site threonine of proteasomal beta subunits and the Escherichia coli homolog HslV by a new class of inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 94, 6629–6634.
Bogyo, M., Shin, S., McMaster, J. S., & Ploegh, H. L. (1998). Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. Chemistry & Biology, 5, 307–320.
Nazif, T., & Bogyo, M. (2001). Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 98, 2967–2972.
Kessler, B. M., Tortorella, D., Altun, M., Kisselev, A. F., Fiebiger, E., Hekking, B. G., et al. (2001). Extended peptide-based inhibitors efficiently target the proteasome and reveal overlapping specificities of the catalytic beta-subunits. Chemistry & Biology, 8, 913–929.
Gu, C., Kolodziejek, I., Misas-Villamil, J., Shindo, T., Colby, T., Verdoes, M., et al. (2010). Proteasome activity profiling: A simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities. Plant Journal, 62, 160–170.
Kraus, M., Ruckrich, T., Reich, M., Gogel, J., Beck, A., Kammer, W., et al. (2007). Activity patterns of proteasome subunits reflect bortezomib sensitivity of hematologic malignancies and are variable in primary human leukemia cells. Leukemia, 21, 84–92.
Mirabella, A. C., Pletnev, A. A., Downey, S. L., Florea, B. I., Shabaneh, T. B., Britton, M., et al. (2011). Specific cell-permeable inhibitor of proteasome trypsin-like sites selectively sensitizes myeloma cells to bortezomib and carfilzomib. Chemistry & Biology, 18, 608–618.
Berkers, C. R., Verdoes, M., Lichtman, E., Fiebiger, E., Kessler, B. M., Anderson, K. C., et al. (2005). Activity probe for in vivo profiling of the specificity of proteasome inhibitor bortezomib. Nature Methods, 2, 357–362.
Chauhan, D., Catley, L., Li, G., Podar, K., Hideshima, T., Velankar, M., et al. (2005). A novel orally active proteasome inhibitor induces apoptosis in multiple myeloma cells with mechanisms distinct from Bortezomib. Cancer Cell, 8, 407–419.
Crawford, L. J., Walker, B., Ovaa, H., Chauhan, D., Anderson, K. C., Morris, T. C., et al. (2006). Comparative selectivity and specificity of the proteasome inhibitors BzLLLCOCHO, PS-341, and MG-132. Cancer Research, 66, 6379–6386.
Kristiansen, M., Deriziotis, P., Dimcheff, D. E., Jackson, G. S., Ovaa, H., Naumann, H., et al. (2007). Disease-associated prion protein oligomers inhibit the 26S proteasome. Molecular Cell, 26, 175–188.
Crawford, L. J., Windrum, P., Magill, L., Melo, J. V., McCallum, L., McMullin, M. F., et al. (2009). Proteasome proteolytic profile is linked to Bcr-Abl expression. Experimental Hematology, 37, 357–366.
Verdoes, M., Florea, B. I., Menendez-Benito, V., Maynard, C. J., Witte, M. D., van der Linden, W. A., et al. (2006). A fluorescent broad-spectrum proteasome inhibitor for labeling proteasomes in vitro and in vivo. Chemistry & Biology, 13, 1217–1226.
Verdoes, M., Berkers, C. R., Florea, B. I., van Swieten, P. F., Overkleeft, H. S., & Ovaa, H. (2006). Chemical proteomics profiling of proteasome activity. Methods in Molecular Biology, 328, 51–69.
Verdoes, M., Hillaert, U., Florea, B. I., Sae-Heng, M., Risseeuw, M. D., Filippov, D. V., et al. (2007). Acetylene functionalized BODIPY dyes and their application in the synthesis of activity based proteasome probes. Bioorganic & Medicinal Chemistry Letters, 17, 6169–6171.
Verdoes, M., Willems, L. I., van der Linden, W. A., Duivenvoorden, B. A., van der Marel, G. A., Florea, B. I., et al. (2010). A panel of subunit-selective activity-based proteasome probes. Organic & Biomolecular Chemistry, 8, 2719–2727.
Screen, M., Britton, M., Downey, S. L., Verdoes, M., Voges, M. J., Blom, A. E., et al. (2010). Nature of pharmacophore influences active site specificity of proteasome inhibitors. The Journal of biological chemistry, 285, 40125–40134.
Ruckrich, T., Kraus, M., Gogel, J., Beck, A., Ovaa, H., Verdoes, M., et al. (2009). Characterization of the ubiquitin–proteasome system in bortezomib-adapted cells. Leukemia, 23, 1098–1105.
Berkers, C. R., van Leeuwen, F. W., Groothuis, T. A., Peperzak, V., van Tilburg, E. W., Borst, J., et al. (2007). Profiling proteasome activity in tissue with fluorescent probes. Molecular Pharmaceutics, 4, 739–748.
Berkers, C. R., Leestemaker, Y., Schuurman, K. G., Ruggeri, B., Jones-Bolin, S., Williams, M., et al. (2012). Probing the specificity and activity profiles of the proteasome inhibitors bortezomib and delanzomib. Molecular Pharmaceutics, 9, 1126–1135.
de Jong, A., Schuurman, K. G., Rodenko, B., Ovaa, H., & Berkers, C. R. (2012). Fluorescence-based proteasome activity profiling. Methods in Molecular Biology, 803, 183–204.
Clerc, J., Groll, M., Illich, D. J., Bachmann, A. S., Huber, R., Schellenberg, B., et al. (2009). Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition. Proceedings of the National Academy of Sciences of the United States of America, 106, 6507–6512.
Clerc, J., Florea, B. I., Kraus, M., Groll, M., Huber, R., Bachmann, A. S., et al. (2009). Syringolin A selectively labels the 20 S proteasome in murine EL4 and wild-type and bortezomib-adapted leukaemic cell lines. ChemBioChem, 10, 2638–2643.
Kolodziejek, I., Misas-Villamil, J. C., Kaschani, F., Clerc, J., Gu, C., Krahn, D., et al. (2011). Proteasome activity imaging and profiling characterizes bacterial effector syringolin A. Plant Physiology, 155, 477–489.
Meng, L., Mohan, R., Kwok, B. H., Elofsson, M., Sin, N., & Crews, C. M. (1999). Epoxomicin, a potent and selective proteasome inhibitor, exhibits in vivo antiinflammatory activity. Proceedings of the National Academy of Sciences of the United States of America, 96, 10403–10408.
Florea, B. I., Verdoes, M., Li, N., van der Linden, W. A., Geurink, P. P., van den Elst, H., et al. (2010). Activity-based profiling reveals reactivity of the murine thymoproteasome-specific subunit beta5t. Chemistry & Biology, 17, 795–801.
Groll, M., Schellenberg, B., Bachmann, A. S., Archer, C. R., Huber, R., Powell, T. K., et al. (2008). A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism. Nature, 452, 755–758.
Ovaa, H., van Swieten, P. F., Kessler, B. M., Leeuwenburgh, M. A., Fiebiger, E., van den Nieuwendijk, A. M., et al. (2003). Chemistry in living cells: Detection of active proteasomes by a two-step labeling strategy. Angewandte Chemie (International ed. in English), 42, 3626–3629.
Verdoes, M., Florea, B. I., Hillaert, U., Willems, L. I., van der Linden, W. A., Sae-Heng, M., et al. (2008). Azido-BODIPY acid reveals quantitative Staudinger–Bertozzi ligation in two-step activity-based proteasome profiling. ChemBioChem, 9, 1735–1738.
Kaschani, F., Verhelst, S. H., van Swieten, P. F., Verdoes, M., Wong, C. S., Wang, Z., et al. (2009). Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using ‘click chemistry’. Plant Journal, 57, 373–385.
van Swieten, P. F., Samuel, E., Hernandez, R. O., van den Nieuwendijk, A. M., Leeuwenburgh, M. A., van der Marel, G. A., et al. (2007). A cell-permeable inhibitor and activity-based probe for the caspase-like activity of the proteasome. Bioorganic & Medicinal Chemistry Letters, 17, 3402–3405.
Britton, M., Lucas, M. M., Downey, S. L., Screen, M., Pletnev, A. A., Verdoes, M., et al. (2009). Selective inhibitor of proteasome’s caspase-like sites sensitizes cells to specific inhibition of chymotrypsin-like sites. Chemistry & Biology, 16, 1278–1289.
Willems, L. I., Li, N., Florea, B. I., Ruben, M., van der Marel, G. A., & Overkleeft, H. S. (2012). Triple bioorthogonal ligation strategy for simultaneous labeling of multiple enzymatic activities. Angewandte Chemie (International ed. in English), 51, 4431–4434.
Carmony, K. C., Lee, D. M., Wu, Y., Lee, N. R., Wehenkel, M., Lee, J., et al. (2012). A bright approach to the immunoproteasome: Development of LMP2/beta1i-specific imaging probes. Bioorganic & Medicinal Chemistry, 20, 607–613.
Lei, B., Abdul Hameed, M. D., Hamza, A., Wehenkel, M., Muzyka, J. L., Yao, X. J., et al. (2010). Molecular basis of the selectivity of the immunoproteasome catalytic subunit LMP2-specific inhibitor revealed by molecular modeling and dynamics simulations. The Journal of Physical Chemistry B, 114, 12333–12339.
Wehenkel, M., Ban, J. O., Ho, Y. K., Carmony, K. C., Hong, J. T., & Kim, K. B. (2012). A selective inhibitor of the immunoproteasome subunit LMP2 induces apoptosis in PC-3 cells and suppresses tumour growth in nude mice. British Journal of Cancer, 107, 53–62.
Sharma, L. K., Lee, N. R., Jang, E. R., Lei, B., Zhan, C. G., Lee, W., et al. (2012). Activity-based near-infrared fluorescent probe for LMP7: A chemical proteomics tool for the immunoproteasome in living cells. ChemBioChem, 13, 1899–1903.
Willems, L. I., Li, N., Florea, B. I., Ruben, M., van der Marel, G. A., & Overkleeft, H. S. (2012). Triple bioorthogonal ligation strategy for simultaneous labeling of multiple enzymatic activities. Angewandte Chemie International Edition, 51, 4431–4434.
Acknowledgments
We gratefully acknowledge the National Institutes of Health for their financial support (R01 CA128903).
Conflict of interest
All authors declare that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Carmony, K.C., Kim, K.B. Activity-Based Imaging Probes of the Proteasome. Cell Biochem Biophys 67, 91–101 (2013). https://doi.org/10.1007/s12013-013-9626-4
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12013-013-9626-4