Organic Chemistry in Living Cells: Profiling of Functional Biomolecules


I propose the development of novel chemistry-based functional proteomics and metabolomics methodologies and their implementation in the areas of immunology (with the emphasis on antigen processing and presentation) and glycobiology (with the emphasis on glycolipid processing and metabolism). Key to the proposal is the design of molecular probes that will modify subsets of biomolecules and that will enable enrichment, purification and identification of the modified biomolecules from complex biological material. Ideally, application of the probes should be possible within the context of living cells. In the context of antigen presentation, probes that will report on protease activities involved in the generation of antigenic peptides from MHC class I- and II pathways will be evaluated. At the same time, synthetic antigenic peptides and proteins, equipped with a latent ligation handle, will be administered to various antigen presenting cells, including dendritic cell types and macrophages. With these tools, proteolytic activities can be directly correlated to the efficiency and mechanism of antigen trafficking, processing and presentation.



  • P.P. Geurink(2010): Synthetic tools to illuminate matrix metalloproteinase and proteasome activities  October 6, 2010
  • W.A. van der Linden(2011): Towards subunit specific proteasome inhibitors , LEIDEN  December 22, 2011

Scientific article

  • M. Ayturan, M. Reich, C. Driessen, M. Kraus, R. Weissert, H.S. Overkleeft, N. Fissolo(2008): Dual inhibition of proteasomal and lysosomal proteolysis ameliorates autoimmune central nervous system inflammation European Journal of Immunology pp. 2401 - 2411
  • A.F. Kisselev, M. Sae-Heng, W.A. van der Linden, G.A. van der Marel, H.S. Overkleeft, L.I. Willems, M. Verdoes, U. Hillaert, B.I. Florea, D.V. Filippov(2008): Azido-BODIPY acid reveals quantitative Staudinger-Bertozzi ligation in two-step activity-based proteasome profiling ChemBioChem pp. 1735 - 1738
  • H. Ovaa, H.S. Overkleeft, H. Muller, C. Driessen, E. Malenke, M. Kraus, E. Koscielniak, J.T. Hartmann, T. Ruckrich, J. Gogel(2008): Ritonavir induces endoplasmic reticulum stress and sensitizes sarcoma cells toward bortezomib-induced apoptosis Molecular Cancer Therapy pp. 1940 - 1948
  • H. Kalbacher, E. Tolosa, T. Kessler, H.S. Overkleeft, S. Schempp, A. Beck, M. Reich, G. Jahn, C. Driessen(2008): Human cytomegalovirus infection interferes with major histocompatibility complex type II maturation and endocytic proteases in dendritic cells at multiple levels Journal of General Virology pp. 2427 - 2436
  • G.A. van der Marel, H.A.M. Kerstjens, N. Abello, A.J.M. van Oosterhout, D.S. Postma, P.P. Geurink, J. Lugtenburg, H.S. Overkleeft, R. Bischoff, M. van der Toorn(2008): Poly(ethylene glycol)-based stable isotope labeling reagents for the quantitative analysis of low molecular weight metabolites by LC-MS Analytical Chemistry pp. 9171 - 9180
  • H.S. Overkleeft, T. Ruckrich, M. Kraus, H. Ovaa, M. Verdoes, A. Beck, C. Driessen, J. Gogel, H. Kalbacher(2009): Characterization of the ubiquitin-proteasome system in bortezomib-adapted cells Leukemia pp. 1098 - 1105
  • M.D. Witte, D. Horst, H.S. Overkleeft, E. Wiertz, G.A. van der Marel(2009): Synthesis and biological evaluation of a chitobiose-based peptide N-glycanase inhibitor library Journal of Organic Chemistry pp. 605 - 616
  • S.H.L. Verhelst, M. Kaiser, H.S. Overkleeft, F. Kaschani, R.A.L. van der Hoorn, Z.M. Wang, M. Bogyo, P.F. van Swieten, C.S. Wong, M. Verdoes(2009): Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click chemistry' Plant Journal pp. 373 - 385
  • G.A. van der Marel, C. Driessen, J. Kuiper, S. Van Calenbergh, M. Verdoes, H.S. Overkleeft, K.L.L. Habets, A. Saragliadis, B.I. Florea, U. Hillaert, F. Ossendorp(2009): Receptor-mediated targeting of cathepsins in professional antigen presenting cells Angewandte Chemie - International Edition pp. 1629 - 1632
  • G.A. van der Marel, H.S. Overkleeft, M.D. Witte, B.I. Florea, O. Adeyanju, M. Verdoes(2009): O-GlcNAc peptide epoxyketones are recognized by mammalian proteasomes Journal of the American Chemical Society pp. 12064
  • H.S. Overkleeft, B.I. Florea, G.A. van der Marel, M. Verdoes(2009): Chemical tools to study the proteasome European Journal of Organic Chemistry pp. 3301 - 3313
  • R. Huber, M. Groll, R. Dudler, C. Driessen, J. Clerc, H.S. Overkleeft, M. Kraus, A.S. Bachmann, B.I. Florea, M. Kaiser(2009): Syringolin A selectively labels the 20S proteasome in murine EL4 and wildtype and bortezomib adapted leukemic cells ChemBioChem pp. 2546
  • E. Spalburg, A.W. Tuin, R.H. Mars-Groenendijk, M. Overhand, G.M. Grotenbreg, A.J. de Neeling, H.S. Overkleeft, G.A. van der Marel, D. Noort(2009): Activity-based protein profiling reveals broad reactivity of the nerve agent Sarin Chemical Research in Toxicology pp. 683 - 689
  • P. Brundin, R. Smith, J.J. Lucas, M. Diaz-Hernandez, J.Y. Li, N.P. Dantuma, B.I. Florea, C.J. Maynard, H.S. Overkleeft, C. Bottcher, Z. Ortega(2009): Accumulation of ubiquitin conjugates in a polyglutamine disease model occurs without global ubiquitin/proteasome system impairment Proceedings of the National Academy of Sciences of the USA pp. 13986 - 13991
  • J. Verasdonck, M.D. Witte, N. Li, H.S. Overkleeft, C.-L. Kuo, B.I. Florea, P.P. Geurink, G.A. van der Marel(2010): A cleavable linker based on the levulinoyl ester for activity-based protein profiling Angew. Chem. Int. Ed. pp. 6802
  • G.A. van der Marel, B.I. Florea, W.A. van der Linden, C. Oskam, H.S. Overkleeft, P.P. Geurink(2010): Proteasome selectivity towards Michael acceptor containing oligopeptide-based inhibitors Org. Biomol. Chem. pp. 1885
  • B.I. Florea, M.P. Spaans, P.P. Geurink, S.L. Downey, H.S. Overkleeft, A.F. Kisselev, G.A. van der Marel, N. Liu, A.M.C.H. van den Nieuwendijk(2010): Incorporation of fluorinated phenylalanine generates highly specific inhibitor for proteasome's chymotrypsin-like sites J. Med. Chem. pp. 2319
  • W.A. van der Linden, B.I. Florea, B.A. Duivenvoorden, G.A. van der Marel, H.S. Overkleeft, A.F. Kisselev, M. Verdoes, L.I. Willems(2010): A panel of subunit-selective activity-based proteasome probes Org. Biomol. Chem. pp. 2719
  • K.H. Richau, J. Misas-Villamil, T. Colby, H.S. Overkleeft, J. Schmidt, I. Kolodziejek, T. Shindo, R.A.L. van der Hoorn, M. Verdoes, C. Gu(2010): Proteasome activity profiling: a simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities Plant J. pp. 160
  • M. Altun, M.J. Edelmann, B. Ulfhake, A.L. Goldberg, B.M. Kessler, R. Piccirillo, H.C. Beschke, H.S. Overkleeft(2010): Muscle wasting in aged, sarcopenic rats is associated with enhanced activity of the ubiquitin-proteasome pathway J. Biol. Chem. pp. 39597
  • F.A. Ossendorp, W.A. van der Linden, H. den Dulk, M. Verdoes, K. Sasaki, P.A. van Veelen, H. van den Elst, H.S. Overkleeft, T. Hofmann, K. Tanaka, A.F. Kisselev, A. de Ru, N. Li, J. Brouwer, S. Murata, B.I. Florea, P.P. Geurink(2010): Acitivity-based profiling reveals reactivity of the murine thymoproteasome-specific subunit beta5t Chem. Biol. pp. 795
  • P.P. Geurink, M.D.P. Risseeuw, A.F. Kisselev, M.J. Voges, A.E.M. Blom, A.A. Pletnev, B.I. Florea, M. Screen, S.L. Downey, M. Verdoes, A.E.M. Blom, H.S. Overkleeft, W.A. van der Linden, M. Britton(2010): The nature of pharmacophore influences active site specificity of proteasome inhibitors J. Biol. Chem. pp. 40125
  • H.S. Overkleeft, B.M. Kessler, P.P. Geurink, G.A. van der Marel, B.I. Florea(2010): Probing the proteasome cavity in three steps: bio-orthogonal photo-reactive suicide substrates Chem. Comm. pp. 9052
  • H.S. Overkleeft, B.I. Florea, M. Verdoes, G.A. van der Marel, L.I. Willems(2010): Two-step labeling of endogenous enzymatic activities by Diels-Alder ligation ChemBioChem pp. 1769


Project number


Main applicant

Prof. dr. H.S. Overkleeft

Affiliated with

Universiteit Leiden, Faculteit der Wiskunde en Natuurwetenschappen, Leiden Institute of Chemistry

Team members

Mw. V.D. Bock, Dr. B. Florea, Dr. P.P. Geurink MSc, Dr. T. Hofmann-Seitz, Dhr. W.F.J. Hogendorf MSc, Dr. W.A. van der Linden


01/07/2004 to 17/12/2012