Building better bioorthogonal reactions

Current Opinion in Chemical Biology

Volumn 21, Issue , 2014, Pages 103-111

  Shih, Hui Wen ^a   Kamber, David N ^a   Prescher, Jennifer A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE; ALKENE; ALKYNE; AZIDE; FUNCTIONAL GROUP; KETONE; REAGENT; TETRAZINE DERIVATIVE; BIOMATERIAL; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS;

BIOCOMPATIBILITY; BIOORTHOGONAL REACTION; CHEMICAL ENGINEERING; CHEMICAL REACTION; CHEMICAL STRUCTURE; COMPUTER MODEL; HUMAN; IN VIVO STUDY; NONHUMAN; ORGANIC CHEMISTRY; PHOTOACTIVATION; REVIEW; BIOCHEMISTRY; CHEMISTRY; ENGINEERING; METABOLISM; PROCEDURES;

BIOCHEMISTRY; BIOCOMPATIBLE MATERIALS; ENGINEERING; HUMANS; INDICATORS AND REAGENTS;

EID: 84905233480     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.07.002     Document Type: Review

References (73)

1. Ramil C.P., Lin Q. Bioorthogonal chemistry: strategies and recent developments. Chem Commun 2013, 49:11007-11102.
2. Patterson D.M., Nazarova L.A., Prescher J.A. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014, 9:592-605.
3. Grammel M., Hang H.C. Chemical reporters for biological discovery. Nat Chem Biol 2013, 9:475-484.
4. Welsch M.E., Snyder S.A., Stockwell B.R. Privileged scaffolds for library design and drug discovery. Curr Opin Chem Biol 2010, 14:347-361.
5. Bianco A., Townsley F.M., Greiss S., Lang K., Chin J.W. Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol 2012, 8:748-750.
6. Debets M.F., van der Doelen C.W., Rutjes F.P., van Delft F.L. Azide: a unique dipole for metal-free bioorthogonal ligations. ChemBioChem 2010, 11:1168-1184.
7. van Berkel S.S., van Eldijk M.B., van Hest J.C.M. Staudinger ligation as a method for bioconjugation. Angew Chem Int Ed 2011, 50:8806-8827.
8. Worrell B.T., Malik J.A., Fokin V.V. Direct evidence of a dinuclear copper intermediate in Cu(I)-catalyzed azide-alkyne cycloadditions. Science 2013, 340:457-460.
9. Kennedy D.C., McKay C.S., Legault M.C., Danielson D.C., Blake J.A., Pegoraro A.F., Stolow A., Mester Z., Pezacki J.P. Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions. J Am Chem Soc 2011, 133:17993-18001.
10. Uttamapinant C., Tangpeerachaikul A., Grecian S., Clarke S., Singh U., Slade P., Gee K.R., Ting A.Y. Fast, cell-compatible click chemistry with copper-chelating azides for biomolecular labeling. Angew Chem Int Ed 2012, 51:5852-5856.
11. Rudolf G.C., Sieber S.A. Copper-assisted click reactions for activity-based proteomics: fine-tuned ligands and refined conditions extend the scope of application. ChemBioChem 2013, 14:2447-2455.
12. Jiang H., Zheng T., Lopez-Aguilar A., Feng L., Kopp F., Marlow F.L., Wu P. Monitoring dynamic glycosylation in vivo using supersensitive click chemistry. Bioconjug Chem 2014, 25:698-706.
13. Lin W., Du Y., Zhu Y., Chen X. A cis-membrane FRET-based method for protein-specific imaging of cell-surface glycans. J Am Chem Soc 2014, 136:679-687.
14. Jewett J.C., Bertozzi C.R. Cu-free click cycloaddition reactions in chemical biology. Chem Soc Rev 2010, 39:1272-1279.
15. Tra V.N., Dube D.H. Glycans in pathogenic bacteria-potential for targeted covalent therapeutics and imaging agents. Chem Commun 2014, 50:4659-4673.
16. Hinz F.I., Dieterich D.C., Tirrell D.A., Schuman E.M. Non-canonical amino acid labeling in vivo to visualize and affinity purify newly synthesized proteins in larval zebrafish. ACS Chem Neurosci 2012, 3:40-49.
17. Siegrist M.S., Whiteside S., Jewett J.C., Aditham A., Cava F., Bertozzi C.R. D-amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem Biol 2013, 8:500-505.
18. Liechti G.W., Kuru E., Hall E., Kalinda A., Brun Y.V., VanNieuwenhze M., Maurelli A.T. A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis. Nature 2014, 506:507-510.
19. Bateman L.A., Zaro B.W., Chuh K.N., Pratt M.R. N-propargyloxycarbamate monosaccharides as metabolic chemical reporters of carbohydrate salvage pathways and protein glycosylation. Chem Commun 2013, 49:4328-4330.
20. Ekkebus R., van Kasteren S.I., Kulathu Y., Scholten A., Berlin I., Geurink P.P., de Jong A., Goerdayal S., Neefjes J., Heck A.J., Komander D., et al. On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc 2013, 135:2867-2870.
21. Agarwal P., van der Weijden J., Sletten E.M., Rabuka D., Bertozzi C.R. A Pictet-Spengler ligation for protein chemical modification. Proc Natl Acad Sci USA 2013, 110:46-51.
22. Devaraj N.K., Weissleder R. Biomedical applications of tetrazine cycloadditions. Acc Chem Res 2011, 44:816-827.
23. Selvaraj R., Fox J.M. Trans-cyclooctene-a stable, voracious dienophile for bioorthogonal labeling. Curr Opin Chem Biol 2013, 17:753-760.
24. Rossin R., van den Bosch S.M., Ten Hoeve W., Carvelli M., Versteegen R.M., Lub J., Robillard M.S. Highly reactive trans-cyclooctene tags with improved stability for Diels-Alder chemistry in living systems. Bioconjug Chem 2013, 24:1210-1217.
25. Zeglis B.M., Sevak K.K., Reiner T., Mohindra P., Carlin S.D., Zanzonico P., Weissleder R., Lewis J.S. A pretargeted PET imaging strategy based on bioorthogonal Diels-Alder click chemistry. J Nucl Med 2013, 54:1389-1396.
26. Lee S., Koo H., Na J.H., Han S.J., Min H.S., Lee S.J., Kim S.H., Yun S.H., Jeong S.Y., Kwon I.C., Choi K., et al. Chemical tumor-targeting of nanoparticles based on metabolic glycoengineering and click chemistry. ACS Nano 2014, 8:2048-2063.
27. van den Bosch S.M., Rossin R., Renart Verkerk P., Ten Hoeve W., Janssen H.M., Lub J., Robillard M.S. Evaluation of strained alkynes for Cu-free click reaction in live mice. Nucl Med Biol 2013, 40:415-423.
28. Debets M.F., van Berkel S.S., Dommerholt J., Dirks A.T., Rutjes F.P., van Delft F.L. Bioconjugation with strained alkenes and alkynes. Acc Chem Res 2011, 44:805-815.
29. Taylor M.T., Blackman M.L., Dmitrenko O., Fox J.M. Design and synthesis of highly reactive dienophiles for the tetrazine-trans-cyclooctene ligation. J Am Chem Soc 2011, 133:9646-9649.
30. 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.
31. Borrmann A., Milles S., Plass T., Dommerholt J., Verkade J.M., Wiessler M., Schultz C., van Hest J.C., van Delft F.L., Lemke E.A. Genetic encoding of a bicyclo[6.1.0]nonyne-charged amino acid enables fast cellular protein imaging by metal-free ligation. ChemBioChem 2012, 13:2094-2099.
32. Lang K., Davis L., Wallace S., Mahesh M., Cox D.J., Blackman M.L., Fox J.M., Chin J.W. Genetic encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions. J Am Chem Soc 2012, 134:10317-10320.
33. Yu Z., Lin Q. Design of spiro[2.3]hex-1-ene, a genetically encodable double-strained alkene for superfast photoclick chemistry. J Am Chem Soc 2014, 136:4153-4156.
34. Karver M.R., Weissleder R., Hilderbrand S.A. Synthesis and evaluation of a series of 1,2,4,5-tetrazines for bioorthogonal conjugation. Bioconjug Chem 2011, 22:2263-2270.
35. 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.
36. 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.
37. Sanders B.C., Friscourt F., Ledin P.A., Mbua N.E., Arumugam S., Guo J., Boltje T.J., Popik V.V., Boons G.J. Metal-free sequential [3+2]-dipolar cycloadditions using cyclooctynes and 1,3-dipoles of different reactivity. J Am Chem Soc 2011, 133:949-957.
38. McGrath N.A., Raines R.T. Diazo compounds as highly tunable reactants in 1,3-dipolar cycloaddition reactions with cycloalkynes. Chem Sci 2012, 3:3237-3240.
39. Chou H.H., Raines R.T. Conversion of azides into diazo compounds in water. J Am Chem Soc 2013, 135:14936-14939.
40. 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.
41. Chen S.J., Ren J., Wang Z.W. A highly regioselective tandem 1,3-dipolar cycloaddition of cyclopropene 1,1-diesters and nitrile oxides: synthesis of highly functionalized isoxazoles. Tetrahedron 2009, 65:9146-9151.
42. 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.
43. 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.
44. Lin Y.A., Boutureira O., Lercher L., Bhushan B., Paton R.S., Davis B.G. Rapid cross-metathesis for reversible protein modifications via chemical access to Se-allyl-selenocysteine in proteins. J Am Chem Soc 2013, 135:12156-12159.
45. Lercher L., McGouran J.F., Kessler B.M., Schofield C.J., Davis B.G. DNA modification under mild conditions by Suzuki-Miyaura cross-coupling for the generation of functional probes. Angew Chem Int Ed 2013, 52:10553-10558.
46. Yusop R.M., Unciti-Broceta A., Johansson E.M., Sanchez-Martin R.M., Bradley M. Palladium-mediated intracellular chemistry. Nat Chem 2011, 3:239-243.
47. Chankeshwara S.V., Indrigo E., Bradley M. Palladium mediated chemistry in living cells. Curr Opin Chem Biol 2014, 21:128-135.
48. Crisalli P., Kool E.T. Water-soluble organocatalysts for hydrazone and oxime formation. J Org Chem 2013, 78:1184-1189.
49. Wendeler M., Grinberg L., Wang X., Dawson P.E., Baca M. Enhanced catalysis of oxime-based bioconjugations by substituted anilines. Bioconjug Chem 2013, 25:93-101.
50. Arumugam S., Popik V.V. Sequential 'click'-'photo-click' cross-linker for catalyst-free ligation of azide-tagged substrates. J Org Chem 2014, 79:2702-2708.
51. Poloukhtine A.A., Mbua N.E., Wolfert M.A., Boons G.J., Popik V.V. Selective labeling of living cells by a photo-triggered click reaction. J Am Chem Soc 2009, 131:15769-15776.
52. Ramil C.P., Lin Q. Photoclick chemistry: A fluorogenic light-triggered in vivo ligation reaction. Curr Opin Chem Biol 2014, 21:89-95.
53. 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.
54. Lee Y.J., Wu B., Raymond J.E., Zeng Y., Fang X.Q., Wooley K.L., Liu W.R.S. A genetically encoded acrylamide functionality. ACS Chem Biol 2013, 8:1664-1670.
55. 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.
56. Minto R.E., Blacklock B.J. Biosynthesis and function of polyacetylenes and allied natural products. Prog Lipid Res 2008, 47:233-306.
57. Wainman Y.A., Neves A.A., Stairs S., Stockmann H., Ireland-Zecchini H., Brindle K.M., Leeper F.J. Dual-sugar imaging using isonitrile and azido-based click chemistries. Org Biomol Chem 2013, 11:7297-7300.
58. Matsuura M., Saikawa Y., Inui K., Nakae K., Igarashi M., Hashimoto K., Nakata M. Identification of the toxic trigger in mushroom poisoning. Nat Chem Biol 2009, 5:465-467.
59. Nguyen D.P., Elliott T., Holt M., Muir T.W., Chin J.W. Genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation. J Am Chem Soc 2011, 133:11418-11421.
60. Newman D.J., Cragg G.M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 2012, 75:311-335.
61. Wallace S., Chin J.W. Strain-promoted sydnone bicyclo-[6.1.0]-nonyne cycloaddition. Chem Sci 2014, 5:1742-1744.
62. 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.
63. Kamber D.N., Nazarova L.A., Liang Y., Lopez S.A., Patterson D.M., Shih H.W., Houk K.N., Prescher J.A. Isomeric cyclopropenes exhibit unique bioorthogonal reactivities. J Am Chem Soc 2013, 135:13680-13683.
64. Liang Y., Mackey J.L., Lopez S.A., Liu F., Houk K.N. Control and design of mutual orthogonality in bioorthogonal cycloadditions. J Am Chem Soc 2012, 134:17904-17907.
65. Gold B., Dudley G.B., Alabugin I.V. Moderating strain without sacrificing reactivity: design of fast and tunable noncatalyzed alkyne-azide cycloadditions via stereoelectronically controlled transition state stabilization. J Am Chem Soc 2013, 135:1558-1569.
66. Willems L.I., Li N., Florea B.I., Ruben M., van der Marel G.A., Overkleeft H.S. Triple bioorthogonal ligation strategy for simultaneous labeling of multiple enzymatic activities. Angew Chem Int Ed 2012, 51:4431-4434.
67. Hudak J.E., Barfield R.M., de Hart G.W., Grob P., Nogales E., Bertozzi C.R., Rabuka D. Synthesis of heterobifunctional protein fusions using copper-free click chemistry and the aldehyde tag. Angew Chem Int Ed 2012, 51:4161-4165.
68. Chang P.V., Prescher J.A., Hangauer M.J., Bertozzi C.R. Imaging cell surface glycans with bioorthogonal chemical reporters. J Am Chem Soc 2007, 129:8400-8401.
69. Nikic I., Plass T., Schraidt O., Szymanski J., Briggs J.A., Schultz C., Lemke E.A. Minimal tags for rapid dual-color live-cell labeling and super-resolution microscopy. Angew Chem Int Ed 2014, 53:2245-2249.
70. Neves A.A., Stockmann H., Wainman Y.A., Kuo J.C., Fawcett S., Leeper F.J., Brindle K.M. Imaging cell surface glycosylation in vivo using 'double click' chemistry. Bioconjug Chem 2013, 24:934-941.
71. Karver M.R., Weissleder R., Hilderbrand S.A. Bioorthogonal reaction pairs enable simultaneous, selective, multi-target imaging. Angew Chem Int Ed 2012, 51:920-922.
72. Sachdeva A., Wang K., Elliott T., Chin J.W. Concerted, rapid, quantitative, and site-specific dual labeling of proteins. J Am Chem Soc 2014, 136:7785-7788.
73. Cole C.M., Yang J., Seckute J., Devaraj N.K. Fluorescent live-cell imaging of metabolically incorporated unnatural cyclopropene-mannosamine derivatives. ChemBioChem 2013, 14:205-208.