Ilona Kammerl Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Germany
1 protocol

Silke Meiners Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Germany
1 protocol

Hermen Overkleeft Department of Bio-organic Synthesis, Leiden University, The Netherlands
1 protocol

Oliver Vosyka Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Germany
1 protocol

Bogdan I. Florea
  • Department of Bio-organic Synthesis, Leiden University, The Netherlands
  • 1 Author merit

Education

Ph.D in Bio-Pharmaceutical Sciences, Department of Drug delivery technology, Leiden University, The Netherlands, 2003

Current Position

Lecturer, Department of Bio-organic synthesis, Leiden Institute for Chemistry, Leiden University, The Netherlands

Publications

  1. Soriano, G. P., Overkleeft, H. S. and Florea, B. I. (2017). Two-Step Activity-Based Protein Profiling with the Proteasome System as Model of Study. Methods Mol Biol 1491: 205-215.
  2. Soriano, G. P., Besse, L., Li, N., Kraus, M., Besse, A., Meeuwenoord, N., Bader, J., Everts, B., den Dulk, H., Overkleeft, H. S., Florea, B. I. and Driessen, C. (2016). Proteasome inhibitor-adapted myeloma cells are largely independent from proteasome activity and show complex proteomic changes, in particular in redox and energy metabolism. Leukemia 30(11): 2198-2207.
  3. de Bruin, G., Xin, B. T., Florea, B. I. and Overkleeft, H. S. (2016). Proteasome Subunit Selective Activity-Based Probes Report on Proteasome Core Particle Composition in a Native Polyacrylamide Gel Electrophoresis Fluorescence-Resonance Energy Transfer Assay. J Am Chem Soc 138(31): 9874-9880.
  4. Xin, B. T., de Bruin, G., Huber, E. M., Besse, A., Florea, B. I., Filippov, D. V., van der Marel, G. A., Kisselev, A. F., van der Stelt, M., Driessen, C., Groll, M. and Overkleeft, H. S. (2016). Structure-Based Design of beta5c Selective Inhibitors of Human Constitutive Proteasomes. J Med Chem 59(15): 7177-7187.
  5. de Bruin, G., Xin, B. T., Kraus, M., van der Stelt, M., van der Marel, G. A., Kisselev, A. F., Driessen, C., Florea, B. I. and Overkleeft, H. S. (2016). A Set of Activity-Based Probes to Visualize Human (Immuno)proteasome Activities. Angew Chem Int Ed Engl 55(13): 4199-4203.
  6. de Bruin, G., Mock, E. D., Hoogendoorn, S., van den Nieuwendijk, A. M., Mazurek, J., van der Marel, G. A., Florea, B. I., Overkleeft, H. S. (2016). Enantioselective synthesis of adamantylalanine and carboranylalanine and their incorporation into the proteasome inhibitor bortezomib. Chem Commun (Camb) 52(21): 4064-4067.
  7. Paniagua Soriano, G., De Bruin, G., Overkleeft, H. S. and Florea, B. I. (2014). Toward understanding induction of oxidative stress and apoptosis by proteasome inhibitors. Antioxid Redox Signal 21(17): 2419-2443.
  8. Li, N., Kuo, C. L., Paniagua, G., van den Elst, H., Verdoes, M., Willems, L. I., van der Linden, W. A., Ruben, M., van Genderen, E., Gubbens, J., van Wezel, G. P., Overkleeft, H. S. and Florea, B. I. (2013). Relative quantification of proteasome activity by activity-based protein profiling and LC-MS/MS. Nat Protoc 8(6): 1155-1168.
  9. Willems, L. I., Li, N., Florea, B. I., Ruben, M., van der Marel, G. A. and Overkleeft, H. S. (2012). Triple bioorthogonal ligation strategy for simultaneous labeling of multiple enzymatic activities. Angew Chem Int Ed Engl 51(18): 4431-4434.
  10. Li, N., Overkleeft, H. S. and Florea, B. I. (2012). Activity-based protein profiling: an enabling technology in chemical biology research. Curr Opin Chem Biol 16(1-2): 227-233.
  11. van der Linden, W. A., Li, N., Hoogendoorn, S., Ruben, M., Verdoes, M., Guo, J., Boons, G. J., van der Marel, G. A., Florea, B. I. and Overkleeft, H. S. (2012). Two-step bioorthogonal activity-based proteasome profiling using copper-free click reagents: a comparative study. Bioorg Med Chem 20(2): 662-666.
  12. van der Linden, W. A., Willems, L. I., Shabaneh, T. B., Li, N., Ruben, M., Florea, B. I., van der Marel, G. A., Kaiser, M., Kisselev, A. F. and Overkleeft, H. S. (2012). Discovery of a potent and highly beta1 specific proteasome inhibitor from a focused library of urea-containing peptide vinyl sulfones and peptide epoxyketones. Org Biomol Chem 10(1): 181-194.
  13. Willems, L. I., van der Linden, W. A., Li, N., Li, K. Y., Liu, N., Hoogendoorn, S., van der Marel, G. A., Florea, B. I. and Overkleeft, H. S. (2011). Bioorthogonal chemistry: applications in activity-based protein profiling. Acc Chem Res 44(9): 718-729.
  14. Hoogendoorn, S., Habets, K. L., Passemard, S., Kuiper, J., van der Marel, G. A., Florea, B. I. and Overkleeft, H. S. (2011). Targeted pH-dependent fluorescent activity-based cathepsin probes. Chem Commun (Camb) 47(33): 9363-9365.
  15. Geurink, P. P., Florea, B. I., Van der Marel, G. A., Kessler, B. M. and Overkleeft, H. S. (2010). Probing the proteasome cavity in three steps: bio-orthogonal photo-reactive suicide substrates. Chem Commun (Camb) 46(47): 9052-9054.
  16. Risseeuw, M. D., Florea, B. I., van der Marel, G. A., Overkleeft, H. S. and Overhand, M. (2010). Sugar amino acid based peptide epoxyketones as potential proteasome inhibitors. Bioorg Chem 38(5): 202-209.
  17. Geurink, P. P., Florea, B. I., Li, N., Witte, M. D., Verasdonck, J., Kuo, C. L., van der Marel, G. A. and Overkleeft, H. S. (2010). A cleavable linker based on the levulinoyl ester for activity-based protein profiling. Angew Chem Int Ed Engl 49(38): 6802-6805.
  18. Florea, B. I., Verdoes, M., Li, N., van der Linden, W. A., Geurink, P. P., van den Elst, H., Hofmann, T., de Ru, A., van Veelen, P. A., Tanaka, K., Sasaki, K., Murata, S., den Dulk, H., Brouwer, J., Ossendorp, F. A., Kisselev, A. F. and Overkleeft, H. S. (2010). Activity-based profiling reveals reactivity of the murine thymoproteasome-specific subunit beta5t. Chem Biol 17(8): 795-801.
  19. Willems, L. I., Verdoes, M., Florea, B. I., van der Marel, G. A. and Overkleeft, H. S. (2010). Two-step labeling of endogenous enzymatic activities by Diels-Alder ligation. Chembiochem 11(12): 1769-1781.
  20. Verdoes, M., Willems, L. I., van der Linden, W. A., Duivenvoorden, B. A., van der Marel, G. A., Florea, B. I., Kisselev, A. F. and Overkleeft, H. S. (2010). A panel of subunit-selective activity-based proteasome probes. Org Biomol Chem 8(12): 2719-2727.
  21. van der Linden, W. A., Geurink, P. P., Oskam, C., van der Marel, G. A., Florea, B. I. and Overkleeft, H. S. (2010). Proteasome selectivity towards Michael acceptor containing oligopeptide-based inhibitors. Org Biomol Chem 8(8): 1885-1893.
  22. Geurink, P. P., Liu, N., Spaans, M. P., Downey, S. L., van den Nieuwendijk, A. M., van der Marel, G. A., Kisselev, A. F., Florea, B. I. and Overkleeft, H. S. (2010). Incorporation of fluorinated phenylalanine generates highly specific inhibitor of proteasome's chymotrypsin-like sites. J Med Chem 53(5): 2319-2323.
  23. Witte, M. D., Florea, B. I., Verdoes, M., Adeyanju, O., Van der Marel, G. A. and Overkleeft, H. S. (2009). O-GlcNAc peptide epoxyketones are recognized by mammalian proteasomes. J Am Chem Soc 131(34): 12064-12065.
  24. Hillaert, U., Verdoes, M., Florea, B. I., Saragliadis, A., Habets, K. L., Kuiper, J., Van Calenbergh, S., Ossendorp, F., van der Marel, G. A., Driessen, C. and Overkleeft, H. S. (2009). Receptor-mediated targeting of cathepsins in professional antigen presenting cells. Angew Chem Int Ed Engl 48(9): 1629-1632.
  25. Verdoes, M., Florea, B. I., Hillaert, U., Willems, L. I., van der Linden, W. A., Sae-Heng, M., Filippov, D. V., Kisselev, A. F., van der Marel, G. A. and Overkleeft, H. S. (2008). Azido-BODIPY acid reveals quantitative Staudinger-Bertozzi ligation in two-step activity-based proteasome profiling. Chembiochem 9(11): 1735-1738.
  26. Verdoes, M., Hillaert, U., Florea, B. I., Sae-Heng, M., Risseeuw, M. D., Filippov, D. V., van der Marel, G. A. and Overkleeft, H. S. (2007). Acetylene functionalized BODIPY dyes and their application in the synthesis of activity based proteasome probes. Bioorg Med Chem Lett 17(22): 6169-6171.
  27. Verdoes, M., Florea, B. I., van der Linden, W. A., Renou, D., van den Nieuwendijk, A. M., van der Marel, G. A. and Overkleeft, H. S. (2007). Mixing of peptides and electrophilic traps gives rise to potent, broad-spectrum proteasome inhibitors. Org Biomol Chem 5(9): 1416-1426.
  28. Verdoes, M., Florea, B. I., Menendez-Benito, V., Maynard, C. J., Witte, M. D., van der Linden, W. A., van den Nieuwendijk, A. M., Hofmann, T., Berkers, C. R., van Leeuwen, F. W., Groothuis, T. A., Leeuwenburgh, M. A., Ovaa, H., Neefjes, J. J., Filippov, D. V., van der Marel, G. A., Dantuma, N. P. and Overkleeft, H. S. (2006). A fluorescent broad-spectrum proteasome inhibitor for labeling proteasomes in vitro and in vivo. Chem Biol 13(11): 1217-1226.
1 Protocol published
Activity-based Pull-down of Proteolytic Standard and Immunoproteasome Subunits
Activity-based probes (ABP) are small organic molecules that irreversibly bind to the active center of a specific enzyme family and may be coupled to a fluorophore or an affinity tag (Li et al., 2013). Here, we describe a method to ...
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