Development of bioorthogonal reactions and their applications in bioconjugation

Molecules

Volumn 20, Issue 2, 2015, Pages 3190-3205

  Zheng, Mengmeng ^a   Zheng, Li ^a   Zhang, Peiyuan ^a   Li, Jinbo ^a   Zhang, Yan ^a  

^a NANJING UNIVERSITY   (China)

Author keywords

Bioconjugation strategies; Biomolecules; Bioorthogonal reactions; Chemical probes

Indexed keywords

BIOMATERIAL; LIPID; NUCLEIC ACID; PROTEIN;

ANIMAL; CHEMISTRY; HUMAN;

ANIMALS; BIOCOMPATIBLE MATERIALS; HUMANS; LIPIDS; NUCLEIC ACIDS; PROTEINS;

EID: 84928922781     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules20023190     Document Type: Review

References (82)

1. Kalia, J.; Raines, R.T. Advances in bioconjugation. Curr. Org. Chem. 2010, 14, 138-147.
2. Patterson, D.M.; Nazarova, L.A.; Prescher, J.A. Finding the right (bioorthogonal) chemistry. ACS Chem. Biol. 2014, 9, 592-605.
3. Ramil, C.P.; Lin, Q. Bioorthogonal chemistry: Strategies and recent developments. Chem. Commun. 2013, 49, 11007-11022.
4. Shieh, P.; Bertozzi, C.R. Design strategies for bioorthogonal smart probes. Org. Biomol. Chem. 2014, 12, 9307-9320.
5. Debets, M.F.; van Hest, J.C.; Rutjes, F.P. Bioorthogonal labelling of biomolecules: New functional handles and ligation methods. Org. Biomol. Chem. 2013, 11, 6439-6455.
6. Staudinger, H.; Meyer, J. Uber neue organische phosphorverbindeugen iii. Phosphinmethylenederivate und phosphinimine. Helv. Chim. Acta 1919, 2, 635-646.
7. Saxon, E.; Bertozzi, C.R. Cell surface engineering by a modified staudinger reaction. Science 2000, 287, 2007-2010.
8. Kiick, K.L.; Saxon, E.; Tirrell, D.A.; Bertozzi, C.R. Incorporation of azides into recombinant proteins for chemoselective modification by the staudinger ligation. Proc. Natl. Acad. Sci. USA 2002, 99, 19-24.
9. Prescher, J.A.; Dube, D.H.; Bertozzi, C.R. Chemical remodelling of cell surfaces in living animals. Nature 2004, 430, 873-877.
10. Michael, A. Ueber die einwirkung von diazobenzolimid auf acetylendicarbonsauremethylester. J. Prakt. Chem. 1893, 48, 94-95.
11. Huisgen, R. 1,3-dipolar cycloadditions past and future. Angew. Chem. Int. Ed. 1963, 2, 565-632.
12. Rostovtsev, V.V.; Green, L.G.; Fokin, V.V.; Sharpless, K.B. A stepwise huisgen cycloaddition process: Copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew. Chem. Int. Ed. 2002, 41, 2596-2599.
13. Tornoe, 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.
14. Sletten, E.M.; Bertozzi, C.R. From mechanism to mouse: A tale of two bioorthogonal reactions. Acc. Chem. Res. 2011, 44, 666-676.
15. McKay, C.S.; Finn, M.G. Click chemistry in complex mixtures: Bioorthogonal bioconjugation. Chem. Biol. 2014, 21, 1075-1101.
16. Hong, V.; Steinmetz, N.F.; Manchester, M.; Finn, M.G. Labeling live cells by copper-catalyzed alkyne - Azide click chemistry. Bioconjugate Chem. 2010, 21, 1912-1916.
17. Soriano Del Amo, D.; Wang, W.; Jiang, H.; Besanceney, C.; Yan, A.C.; Levy, M.; Liu, Y.; Marlow, F.L.; Wu, P. Biocompatible copper(I) catalysts for in vivo imaging of glycans. J. Am. Chem. Soc. 2010, 132, 16893-16899.
18. 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.
19. Baskin, J.M.; Prescher, J.A.; Laughlin, S.T.; Agard, N.J.; Chang, P.V.; Miller, I.A.; Lo, A.; Codelli, J.A.; Bertozzi, C.R. Copper-free click chemistry for dynamic in vivo imaging. Proc. Natl. Acad. Sci. USA 2007, 104, 16793-16797.
20. 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.
21. Codelli, J.A.; Baskin, J.M.; Agard, N.J.; Bertozzi, C.R. Second-generation difluorinated cyclooctynes for copper-free click chemistry. J. Am. Chem. Soc. 2008, 130, 11486-11493.
22. Debets, M.F.; van Berkel, S.S.; Schoffelen, S.; Rutjes, F.P.; van Hest, J.C.; van Delft, F.L. Aza-dibenzocyclooctynes for fast and efficient enzyme PEGylation via copper-free (3+2) cycloaddition. Chem. Commun. 2010, 46, 97-99.
23. Dommerholt, J.; Schmidt, S.; Temming, R.; Hendriks, L.J.; Rujtes, F.P.; van Hest, J.C.; Lefeber, D.J.; Friedl, P.; van Delft, F.L. Readily accessbile bicyclononynes for bioorthogonal labeling and three-dimensional imaging of living cells. Angew. Chem. Int. Ed. 2010, 49, 9422-9425.
24. Balcar, J.; Chrisam, G.; Huber, F.X.; Sauer, J. Reaktivität von stickstoff-heterocyclen genenüber cyclooctin als dienophil. Tetrahedron Lett. 1983, 24, 1481-1484.
25. Thalhammer, F.; Wallfahrer, U.; Sauer, J. Reaktivität einfacher offenkettiger und cyclischer dienophile bei diels-alder-reaktionen mit inversem elektronenbedarf. Tetrahedron Lett. 1990, 31, 6851-6854.
26. Sauer, J.; Heldmann, D.K.; Hetzenegger, J.; Krauthan, J.; Sichert, H.; Schuster, J. 1,2,4,5-tetrazine: Synthesis and reactivity in [4+2] cycloadditions. Eur. J. Org. Chem. 1998, 1998, 2885-2896.
27. Blackman, M.L.; Royzen, M.; Fox, J.M. Tetrazine ligation: Fast bioconjugation based on inverse-electron-demand diels-alder reactivity. J. Am. Chem. Soc. 2008, 130, 13518-13519.
28. Devaraj, N.K.; Weissleder, R.; Hilderbrand, S.A. Tetrazine-based cycloadditions: Application to pretargeted live cell imaging. Bioconjugate Chem. 2008, 19, 2297-2299.
29. Devaraj, 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.
30. Patterson, D.M.; Nazarova, L.A.; Xie, B.; Kamber, D.N.; Prescher, J.A. Functionalized cyclopropenes as bioorthogonal chemical reporters. J. Am. Chem. Soc. 2012, 134, 18638-18643.
31. Yang, J.; Seckute, J.; Cole, C.M.; Devaraj, N.K. Live-cell imaging of cyclopropene tags with fluorogenic tetrazine cycloadditions. Angew. Chem. Int. Ed. 2012, 51, 7476-7479.
32. Lang, K.; Davis, L.; Torres-Kolbus, J.; Chou, C.; Deiters, A.; Chin, J.W. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nat. Chem. 2012, 4, 298-304.
33. Clovis, J.S.; Eckell, A.; Huisgen, R.; Sustmann, R. 1.3-dipolare cycloadditionen, xxv. Der nachweis des freien diphenylnitrilimins als zwischenstufe bei cycloadditionen. Chem. Ber. 1967, 100, 60-70.
34. Wang, Y.; Vera, C.I.; Lin, Q. Convenient synthesis of highly functionalized pyrazolines via mild, photoactivated 1,3-dipolar cycloaddition. Org. Lett. 2007, 9, 4155-4158.
35. Song, W.; Wang, Y.; Qu, J.; Lin, Q. Selective functionalization of a genetically encoded alkene-containing protein via "photoclick chemistry" in bacterial cells. J. Am. Chem. Soc. 2008, 130, 9654-9655.
36. Song, W.; Wang, Y.; Qu, J.; Madden, M.M.; Lin, Q. A photoinducible 1,3-dipolar cycloaddition reaction for rapid, selective modification of tetrazole-containing proteins. Angew. Chem. Int. Ed. 2008, 47, 2832-2835.
37. Wang, J.; Zhang, W.; Song, W.; Wang, Y.; Yu, Z.; Li, J.; Wu, M.; Wang, L.; Zang, J.; Lin, Q. A biosynthetic route to photoclick chemistry on proteins. J. Am. Chem. Soc. 2010, 132, 14812-14818.
38. Yu, Z.; Pan, Y.; Wang, Z.; Wang, J.; Lin, Q. Genetically encoded cyclopropene directs rapid, photoclick-chemistry-mediated protein labeling in mammalian cells. Angew. Chem. Int. Ed. 2012, 51, 10600-10604.
39. An, P.; Yu, Z.; Lin, Q. Design of oligothiophene-based tetrazoles for laser-triggered photoclick chemistry in living cells. Chem. Commun. 2013, 49, 9920-9922.
40. Yu, Z.; Ohulchanskyy, T.Y.; An, P.; Prasad, P.N.; Lin, Q. Fluorogenic, two-photon-triggered photoclick chemistry in live mammalian cells. J. Am. Chem. Soc. 2013, 135, 16766-16769.
41. Li, Z.; Hao, P.; Li, L.; Tan, C.Y.; Cheng, X.; Chen, G.Y.; Sze, S.K.; Shen, H.M.; Yao, S.Q. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angew. Chem. Int. Ed. 2013, 52, 8551-8556.
42. Li, Z.; Wang, D.; Li, L.; Pan, S.; Na, Z.; Tan, C.Y.; Yao, S.Q. "Minimalist" cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. J. Am. Chem. Soc. 2014, 136, 9990-9998.
43. Yu, Z.; Ho, L.Y.; Lin, Q. Rapid, photoactivatable turn-on fluorescent probes based on an intramolecular photoclick reaction. J. Am. Chem. Soc. 2011, 133, 11912-11915.
44. Wang, Y.; Song, W.; Hu, W.J.; Lin, Q. Fast alkene functionalization in vivo by photoclick chemistry: Homo lifting of nitrile imine dipoles. Angew. Chem. Int. Ed. 2009, 48, 5330-5333.
45. Seitchik, J.L.; Peeler, J.C.; Taylor, M.T.; Blackman, M.L.; Rhoads, T.W.; Cooley, R.B.; Refakis, C.; Fox, J.M.; Mehl, R.A. Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with trans-cyclooctenes. J. Am. Chem. Soc. 2012, 134, 2898-2901.
46. Lin, S.; Zhang, Z.; Xu, H.; Li, L.; Chen, S.; Li, J.; Hao, Z.; Chen, P.R. Site-specific incorporation of photo-cross-linker and bioorthogonal amino acids into enteric bacterial pathogens. J. Am. Chem. Soc. 2011, 133, 20581-20587.
47. Lin, S.; Yan, H.; Li, L.; Yang, M.; Peng, B.; Chen, S.; Li, W.; Chen, P.R. Site-specific engineering of chemical functionalities on the surface of live hepatitis D virus. Angew. Chem. Int. Ed. 2013, 52, 13970-13974.
48. Yang, M.; Jalloh, A.S.; Wei, W.; Zhao, J.; Wu, P.; Chen, P.R. Biocompatible click chemistry enabled compartment-specific ph measurement inside E. coli. Nat. Commun. 2014, 5, 4981.
49. Li, J.; Jia, S.; Chen, P.R. Diels-alder reaction-triggered bioorthogonal protein decaging in living cells. Nat. Chem. Biol. 2014, 10, 1003-1005.
50. Xie, R.; Hong, S.; Chen, X. Cell-selective metabolic labeling of biomolecules with bioorthogonal functionalities. Curr. Opin. Chem. Biol. 2013, 17, 747-752.
51. Haltiwanger, R.S.; Lowe, J.B. Role of glycosylation in development. Annu. Rev. Biochem. 2004, 73, 491-537.
52. Laughlin, S.T.; Bertozzi, C.R. Imaging the glycome. Proc. Natl. Acad. Sci. USA 2009, 106, 12-17.
53. Laughlin, S.T.; Baskin, J.M.; Amacher, S.L.; Bertozzi, C.R. In vivo imaging of membrane-associated glycans in developing zebrafish. Science 2008, 320, 664-667.
54. Chang, P.V.; Dube, D.H.; Sletten, E.M.; Bertozzi, C.R. A strategy for the selective imaging of glycans using caged metabolic precursors. J. Am. Chem. Soc. 2010, 132, 9516-9518, doi:10.1021/ja101080y.
55. Xie, R.; Hong, S.; Feng, L.; Rong, J.; Chen, X. Cell-selective metabolic glycan labeling based on ligand-targeted liposomes. J. Am. Chem. Soc. 2012, 134, 9914-9917.
56. Rong, J.; Han, J.; Dong, L.; Tan, Y.; Yang, H.; Feng, L.; Wang, Q.W.; Meng, R.; Zhao, J.; Wang, S.Q.; et al. Glycan imaging in intact rat hearts and glycoproteomic analysis reveal the upregulation of sialylation during cardiac hypertrophy. J. Am. Chem. Soc. 2014, 136, 17468-17476.
57. Qu, D.; Wang, G.; Wang, Z.; Zhou, L.; Chi, W.; Cong, S.; Ren, X.; Liang, P.; Zhang, B. 5-ethynyl-2′-deoxycytidine as a new agent for DNA labeling: Detection of proliferating cells. Anal. Biochem. 2011, 417, 112-121.
58. Taylor, J.H.; Woods, P.S.; Hughes, W.L. The organization and duplication of chromosomes as revealed by autoradiographic studies using tritium-labeled thymidinee. Proc. Natl. Acad. Sci. USA 1957, 43, 122-128.
59. Gratzner, H.G. Monoclonal antibody to 5-bromo- and 5-iododeoxyuridine: A new reagent for detection of DNA replication. Science 1982, 218, 474-475.
60. Salic, A.; Mitchison, T.J. A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc. Natl. Acad. Sci. USA 2008, 105, 2415-2420.
61. Cinquin, O.; Crittenden, S.L.; Morgan, D.E.; Kimble, J. Progression from a stem cell-like state to early differentiation in the C. elegans germ line. Proc. Natl. Acad. Sci. USA 2010, 107, 2048-2053.
62. Neef, A.B.; Luedtke, N.W. Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides. Proc. Natl. Acad. Sci. USA 2011, 108, 20404-20409.
63. Rieder, U.; Luedtke, N.W. Alkene-tetrazine ligation for imaging cellular DNA. Angew. Chem. Int. Ed. 2014, 53, 9168-9172.
64. Arndt, S.; Wagenknecht, H.A. "Photoclick" postsynthetic modification of DNA. Angew. Chem. Int. Ed. 2014, 53, 14580-14582.
65. Song, C.X.; Szulwach, K.E.; Fu, Y.; Dai, Q.; Yi, C.; Li, X.; Li, Y.; Chen, C.H.; Zhang, W.; Jian, X.; et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2011, 29, 68-72.
66. Maier, O.; Oberle, V.; Hoekstra, D. Fluorescent lipid probes: Some properties and applications (a review). Chem. Phys. Lipids 2002, 116, 3-18.
67. Jao, C.Y.; Roth, M.; Welti, R.; Salic, A. Metabolic labeling and direct imaging of choline phospholipids in vivo. Proc. Natl. Acad. Sci. USA 2009, 106, 15332-15337.
68. Neef, A.B.; Schultz, C. Selective fluorescence labeling of lipids in living cells. Angew. Chem. Int. Ed. 2009, 48, 1498-1500.
69. Gubbens, J.; Ruijter, E.; de Fays, L.E.; Damen, J.M.; de Kruijff, B.; Slijper, M.; Rijkers, D.T.; Liskamp, R.M.; de Kroon, A.I. Photocrosslinking and click chemistry enable the specific detection of proteins interacting with phospholipids at the membrane interface. Chem. Biol. 2009, 16, 3-14.
70. Tully, S.E.; Cravatt, B.F. Activity-based probes that target functional subclasses of phospholipases in proteomes. J. Am. Chem. Soc. 2010, 132, 3264-3265.
71. Hang, H.C.; Geutjes, E.J.; Grotenbreg, G.; Pollington, A.M.; Bijlmakers, M.J.; Ploegh, H.L. Chemical probes for the rapid detection of fatty-acylated proteins in mammalian cells. J. Am. Chem. Soc. 2007, 129, 2744-2745.
72. Charron, G.; Zhang, M.M.; Yount, J.S.; Wilson, J.; Raghavan, A.S.; Shamir, E.; Hang, H.C. Robust fluorescent detection of protein fatty-acylation with chemical reporters. J. Am. Chem. Soc. 2009, 131, 4967-4975.
73. Yang, Y.Y.; Ascano, J.M.; Hang, H.C. Bioorthogonal chemical reporters for monitoring protein acetylation. J. Am. Chem. Soc. 2010, 132, 3640-3641.
74. Rangan, K.J.; Yang, Y.Y.; Charron, G.; Hang, H.C. Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters. J. Am. Chem. Soc. 2010, 132, 10628-10629.
75. Li, J.; Lin, S.; Wang, J.; Jia, S.; Yang, M.; Hao, Z.; Zhang, X.; Chen, P.R. Ligand-free palladium-mediated site-specific protein labeling inside gram-negative bacterial pathogens. J. Am. Chem. Soc. 2013, 135, 7330-7338.
76. Li, N.; Lim, R.K.; Edwardraja, S.; Lin, Q. Copper-free sonogashira cross-coupling for functionalization of alkyne-encoded proteins in aqueous medium and in bacterial cells. J. Am. Chem. Soc. 2011, 133, 15316-15319.
77. Li, Q.; Dong, T.; Liu, X.; Lei, X. A bioorthogonal ligation enabled by click cycloaddition of o-quinolinone quinone methide and vinyl thioether. J. Am. Chem. Soc. 2013, 135, 4996-4999.
78. Li, C.; Dong, T.; Li, Q.; Lei, X. Probing the anticancer mechanism of (-)-ainsliatrimer a through diverted total synthesis and bioorthogonal ligation. Angew. Chem. Int. Ed. 2014, 53, 12111-12115.
79. Sletten, E.M.; Bertozzi, C.R. A bioorthogonal quadricyclane ligation. J. Am. Chem. Soc. 2011, 133, 17570-17573.
80. Ning, X.; Temming, R.P.; Dommerholt, J.; Guo, J.; Ania, D.B.; Debets, M.F.; Wolfert, M.A.; Boons, G.J.; van Delft, F.L. Protein modification by strain-promoted alkyne-nitrone cycloaddition. Angew. Chem. Int. Ed. 2010, 49, 3065-3068.
81. Tang, W.; Becker, M.L. "Click" reactions: A versatile toolbox for the synthesis of peptide-conjugates. Chem. Soc. Rev. 2014, 43, 7013-7039.
82. Kolodych, S.; Rasolofonjatovo, E.; Chaumontet, M.; Nevers, M.C.; Creminon, C.; Taran, F. Discovery of chemoselective and biocompatible reactions using a high-throughput immunoassay screening. Angew. Chem. Int. Ed. 2013, 52, 12056-12060.