Bioorthogonal chemistry: Applications in activity-based protein profiling

Accounts of Chemical Research

Volumn 44, Issue 9, 2011, Pages 718-729

  Willems, Lianne I ^a   Van Der Linden, Wouter A ^a   Li, Nan ^a   Li, Kah Yee ^a   Liu, Nora ^a   Hoogendoorn, Sascha ^a   Van Der Marel, Gijs A ^a   Florea, Bogdan I ^a   Overkleeft, Herman S ^a  

^a NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYNE; AZIDE; BIOTIN; FLUORESCENT DYE; PHOSPHINE; PHOSPHINE DERIVATIVE; PROTEASOME; PROTEIN;

ARTICLE; CHEMISTRY; CLICK CHEMISTRY; METABOLISM;

ALKYNES; AZIDES; BIOTIN; CLICK CHEMISTRY; FLUORESCENT DYES; PHOSPHINES; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEINS;

EID: 80053005611     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar200125k     Document Type: Article

References (45)

1. Mahal, L. K.; Yarema, K. J.; Bertozzi, C. R. Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis Science 1997, 276, 1125-1128 (Pubitemid 27218123)
2. Saxon, E.; Bertozzi, C. R. Cell surface engineering by a modified Staudinger reaction Science 2000, 287, 2007-2010 (Pubitemid 30158675)
3. Huisgen, R. 1,3-Dipolar cycloaddition - introduction, survey, mechanism. In 1,3- Dipolar Cycloaddition Chemistry; Padwa, A., Ed.; Wiley-Interscience: New York, 1984; Vol. 1, pp 1-176.
4. Tornøe, C. W.; Christensen, C.; Meldal, M. Peptidotriazoles on solid phase: [1,2,3]- triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides J. Org. Chem. 2002, 67, 3057-3064 (Pubitemid 34457265)
5. Wang, Q.; Chan, T. R.; Hilgraf, R.; Fokin, V. V.; Sharpless, K. B.; Finn, M. G. Bioconjugation by copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition J. Am. Chem. Soc. 2003, 125, 3192-3193 (Pubitemid 36512443)
6. Agard, N. J.; Prescher, J. A.; Bertozzi, C. R. A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems J. Am. Chem. Soc. 2004, 126, 15046-15047 (Pubitemid 39557262)
7. 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.; Overkleeft, H. S. Azido-bodipy-acid reveals quantitative Staudinger-Bertozzi ligation in two-step activity-based proteasome profiling ChemBioChem 2008, 9, 1735-1738
8. Agard, N. J.; Baskin, J. M.; Prescher, J. A.; Lo, A.; Bertozzi, C. R. A comparative study of bioorthogonal reactions with azides ACS Chem. Biol. 2006, 1, 644-648
9. Debets, M. F.; Van der Doelen, C. W. J.; Rutjes, F. P. J. T.; Van Delft, F. L. Azide: a unique dipole for metal-free bioorthogonal ligations ChemBioChem 2010, 11, 1168-1184 and references cited therein
10. 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.; Overkleeft, H. S. Two-step bioorthogonal activity-based proteasome profiling using copper-free click reagents: A comparative study. Bioorg. Med. Chem. 2011, DOI: 10.1016/j.bmc.2011.06.037.
11. Ning, X.; Guo, J.; Wolfert, M. A.; Boons, G. J. Visualizing metabolically labeled glycoconjugates of living cells by copper-free and fast Huisgen cycloadditions Angew. Chem., Int. Ed. 2008, 47, 2253-2255
12. Berry, A. F.; Heal, W. P.; Tarafder, A. K.; Tolmachova, T.; Baron, R. A.; Seabra, M. C.; Tate, E. W. Rapid multilabel detection of geranylgeranylated proteins by using bioorthogonal ligation chemistry ChemBioChem 2010, 11, 771-773
13. Devaray, N. K.; Weissleder, R.; Hilderbrand, S. A. Tetrazine-based cycloadditions: application to pretargeted live cell imaging Bioconjugate Chem. 2008, 19, 2297-2299
14. Devaray, N. K.; Upadhyay, R.; Haun, J. B.; Hilderbrand, S. A.; Weissleder, R. Fast and sensitive pretargeted labeling of cancer cells through a tetrazine/ trans -cyclooctene cycloaddition Angew. Chem., Int. Ed. 2009, 48, 7013-7016
15. Devaray, N. K.; Hilderbrand, S.; Upadhyay, R.; Mazitschek, R.; Weissleder, R. Bioorthogonal turn-on probes for imaging small molecules inside living cells Angew. Chem., Int. Ed. 2010, 49, 2869-2872
16. Willems, L. I.; Verdoes, M.; Florea, B. I.; Van der Marel, G. A.; Overkleeft, H. S. Two- step labeling of endogenous enzymatic activities by Diels-Alder ligation ChemBioChem 2010, 11, 1769-1781
17. Zhang, M. M.; Tsou, L. K.; Charron, G.; Raghavan, A. S.; Hang, H. C. Tandem fluorescence imaging of dynamic S-acylation and protein turnover Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 8627-8632
18. Heal, W. P.; Jovanovic, B.; Bessin, S.; Wright, M. H.; Magee, A. I.; Tate, E. W. Bioorthogonal chemical tagging of protein cholesterylation in living cells Chem. Commun. 2011, 47, 4081-4083
19. Evans, M. J.; Cravatt, B. F. Mechanism-based profiling of enzyme families Chem. Rev. 2006, 106, 3279-3301 (Pubitemid 44376936)
20. Rizvi, S. A.; Courson, D. S.; Keller, V. A.; Rock, R. S.; Kozmin, S. A. The dual mode of action of bistramide A entails severing of filamentous actin and covalent protein modification Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 4088-4092 (Pubitemid 351754339)
21. Liu, Y.; Patricelli, M. P.; Cravatt, B. F. Activity-based protein profiling: the serine hydrolases Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14694-14699 (Pubitemid 30019702)
22. Greenbaum, D.; Medzihradszky, K. F.; Burlingame, A.; Bogyo, M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools Chem. Biol. 2000, 7, 569-581
23. Speers, A. E.; Adam, G. C.; Cravatt, B. F. Activity-based protein profiling in vivo using a copper(I)-catalyzed azid-alkyne [3 + 2] cycloaddition J. Am. Chem. Soc. 2003, 125, 4686-4687 (Pubitemid 36505343)
24. Ovaa, H.; Van Swieten, P. F.; Kessler, B. M.; Leeuwenburgh, M. A.; Fiebiger, E.; Van den Nieuwendijk, A. M. C. H.; Galardy, P. J.; Van der Marel, G. A.; Ploegh, H. L.; Overkleeft, H. S. Chemistry in living cells: detection of active proteasomes by a two- step labeling strategy Angew. Chem., Int. Ed. 2003, 42, 3626-3630
25. Witte, M. D.; Florea, B. I.; Verdoes, M.; Adeyanju, O.; Van der Marel, G. A.; Overkleeft, H. S. O-GlcNAc peptide epoxyketones are recognized by mammalian proteasomes J. Am. Chem. Soc. 2009, 131, 12064-12065
26. Berkers, C. R.; Verdoes, M.; Lichtman, E.; Fiebiger, E.; Kessler, B. M.; Anderson, K. C.; Ploegh, H. L.; Ovaa, H.; Galardy, P. J. Activity probe for in vivo profiling of the specificity of the proteasome inhibitor bortezomib Nat. Methods 2005, 2, 357-362 (Pubitemid 41130981)
27. Britton, M.; Lucas, M. M.; Downey, S. L.; Screen, M.; Pletnev, A. A.; Verdoes, M.; Tokhunts, R. A.; Amir, O.; Goddard, A. L.; Pelphrey, P. M.; Wright, D. L.; Overkleeft, H. S.; Kisselev, A. F. Selective inhibitor of proteasome's caspase-like sites sensitizes cells to specific inhibition of chymotrypsin-like sites Chem. Biol. 2009, 16, 1278-1289
28. Verdoes, M.; Willems, L. I.; Van der Linden, W. A.; Duivenvoorden, B. A.; Van der Marel, G. A.; Florea, B. I.; Kisselev, A. F.; Overkleeft, H. S. A panel of subunit- selective activity-based proteasome probes Org. Biomol. Chem. 2010, 8, 2719-2727
29. Chan, E. W. S.; Chattopadhaya, S.; Panicker, R. C.; Huang, X.; Yao, S. Q. Developing photoactive affinity probes for proteomics profiling: hydroxamate-based probes for metalloproteases J. Am. Chem. Soc. 2004, 126, 14435-14446 (Pubitemid 39463627)
30. Hagenstein, M. C.; Mussgnug, J. H.; Lotte, K.; Plessow, R.; Bockhinke, A.; Kruse, O.; Sewald, N. Affinity-based tagging of protein families with reversible inhibitors: a concept for functional proteomics Angew. Chem., Int. Ed. 2003, 42, 5635-5638 (Pubitemid 37509375)
31. Vocadlo, D. J.; Davies, G. J.; Laine, R.; Withers, S. G. Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate Nature 2001, 412, 835-838 (Pubitemid 32801467)
32. Vocadlo, D. J.; Bertozzi, C. R. A strategy for functional proteomic analysis of glycosidase activity from cell lysates Angew. Chem., Int. Ed. 2004, 43, 5338-5342 (Pubitemid 39433912)
33. Stubbs, K.; Scaffidi., A.; Debowski, A. W.; Mark, B. L.; Stick, R. V.; Vocadlo, D. J. Synthesis and use of mechanism-based protein profiling probes for retaining beta-D- glucosaminidases facilitate identification of Pseudomonas aeruginosa NagZ J. Am. Chem. Soc. 2008, 130, 327-335
34. Witte, M. D.; Walvoort, M. T. C.; Li, K.-Y; Kallemeijn, W. W.; Donker-Koopman, W. E.; Boot, R. G.; Aerts, J. M. F. G.; Codée, J. D. C.; Van der Marel, G. A.; Overkleeft, H. S. Activity-based profiling of retaining β-glucosidases: a comparative study. ChemBioChem 2011, in press.
35. Witte, M. D.; Kallemeijn, W. W.; Aten, J.; Li, K.-Y; Strijland, A.; Donker-Koopman, W. E.; Van den Nieuwendijk, A. M. C. H.; Bleijlevens, B.; Kramer, G.; Florea, B. I.; Hooibrink, B.; Hollak, C. E. M.; Ottenhoff, R.; Boot, R. G.; Van der Marel, G. A.; Overkleeft, H. S.; Aerts, J. M. F. G. Ultrasensitive in situ visualization of active glucocerebrosidase molecules Nat. Chem. Biol. 2010, 6, 907-913
36. Gandy, M. N.; Debowski, A. W.; Stubbs, K. A. A general method for affinity-based proteomic profiling of exo-alpha-glycosidases Chem. Commun. 2011, 47, 5037-5039
37. Gartner, C. A.; Elias, J. E.; Bakalarski, C. E.; Gygi, S. P. Catch-and-release reagents for quantitative proteomics analyses J. Proteome Res. 2007, 6, 1482-1491 (Pubitemid 46724046)
38. Verhelst, S. H. L.; Fonovic, M.; Bogyo, M. A mild chemically cleavable linker system for functional proteomics applications Angew. Chem., Int. Ed. 2007, 46, 1284-1286 (Pubitemid 46981376)
39. Dirksen, A.; Yegneswaran, S.; Dawson, P. E. Bisaryl hydrazones as exchangeable biocompatible linkers Angew. Chem., Int. Ed. 2010, 49, 2023-2027
40. Speers, A. E.; Cravatt, B. F. A tandem orthogonal proteolysis strategy for high-content chemical proteomics J. Am. Chem. Soc. 2005, 127, 10018-10019 (Pubitemid 40995443)
41. For more examples, see: Yang, Y. Y.; Grammel, M.; Raghavan, A. S.; Charron, G.; Hang, H. C. Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics Chem. Biol. 2010, 17, 1212-1222 and references cited therein
42. See also Szychowski, J.; Mahdavi, A; Hodas, J. J.; Bagert, J. D.; Ngo, J. T.; Landgraf, P.; Dieterich, D. C.; Schuman, E. M.; Tirrell, D. A. Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition J. Am. Chem. Soc. 2010, 132, 18351-18360
43. Geurink, P. P.; Florea, B. I.; Li, N.; Witte, M. D.; Verasdonck, J.; Kuo, C. L.; Van der Marel, G. A.; Overkleeft., H. S. A cleavable linker based on the levulinoyl ester for activity-based protein profiling Angew. Chem., Int. Ed. 2010, 38, 6802-6905
44. Geurink, P. P.; Florea, B. I.; Van der Marel, G. A.; Kessler, B. M.; Overkleeft, H. S. Probing the proteasome cavity in three steps: bioorthogonal photo-reactive suicide substrates Chem. Commun. 2010, 47, 9052
45. Weerapana, E.; Wang, C.; Simon, G. M.; Richter, F.; Khare, S.; Dillon, M. B. D.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. Quantitative reactivity profiling predicts functional cysteines in proteomes Nature 2010, 468, 790-795