Recent advances in target characterization and identification by photoaffinity probes

Molecules

Volumn 18, Issue 9, 2013, Pages 10425-10451

  Sumranjit, Jitapa ^a,b   Chung, Sang J ^c  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^c Dongguk University   (South Korea)

Author keywords

Affinity chromatography; Bioorthogonal ligation; Chemical proteomics; Click chemistry; Photo crosslinking; Photoaffinity labeling; Protein target identification; Two step labeling

Indexed keywords

AZIDE; BENZOPHENONE DERIVATIVE; CROSS LINKING REAGENT; DIAZONIUM COMPOUND; PROPOFOL; PROTEIN; PYRIMIDINONE DERIVATIVE; PYRONE DERIVATIVE; PHOTOAFFINITY LABELING;

ANIMAL; CHEMISTRY; CLICK CHEMISTRY; HUMAN; METABOLISM; PHOTOAFFINITY LABELING; REVIEW; STAINING;

ANIMALS; AZIDES; BENZOPHENONES; CLICK CHEMISTRY; CROSS-LINKING REAGENTS; DIAZONIUM COMPOUNDS; HUMANS; PHOTOAFFINITY LABELS; PROPOFOL; PROTEINS; PYRIMIDINONES; PYRONES; STAINING AND LABELING;

EID: 84885126826     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules180910425     Document Type: Article

References (53)

1. Dubinsky, L.; Krom, B.P.; Meijler, M.M. Diazirine based photoaffinity labeling. Bioorg. Med. Chem. 2012, 20, 554-570.
2. Leslie, B.J.; Hergenrother, P.J. Identification of the cellular targets of bioactive small organic molecules using affinity reagents. Chem. Soc. Rev. 2008, 37, 1347-1360.
3. Mizuhara, T.; Oishi, S.; Ohno, H.; Shimura, K.; Matsuoka, M.; Fujii, N. Design and synthesis of biotin- or alkyne-conjugated photoaffinity probes for studying the target molecules of PD 404182. Bioorg. Med. Chem. 2013, 21, 2079-2087.
4. Lapinsky, D.J. Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bioorg. Med. Chem. 2012, 20, 6237-6247.
5. Das, J. Aliphatic diazirines as photoaffinity probes for proteins: Recent developments. Chem. Rev. 2011, 111, 4405-4444.
6. Vodovozova, E.L. Photoaffinity labeling and its application in structural biology. Biochemistry-Moscow 2007, 72, 1-20. (Pubitemid 46219182)
7. Hilbold, B.; Perrault, M.; Ehret, C.; Niu, S.L.; Frisch, B.; Pécheur, E.I.; Bourel-Bonnet, L. Benzophenone-containing fatty acids and their related photosensitive fluorescent new probes: Design, physico-chemical properties and preliminary functional investigations. Bioorg. Med. Chem. 2011, 19, 7464-7473.
8. Qvit, N.; Monderer-Rothkoff, G.; Ido, A.; Shalev, D.E.; Amster-Choder, O.; Gilon, C. Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates. Biopolymers 2008, 90, 526-536.
9. Leyva, E.; de Loera, D.; Leyva, S. Photochemistry of 7-azide-1-ethyl-3- carboxylate-6,8-difluoroquinolone: A novel reagent for photoaffinity labeling. Tetrahedron Lett. 2008, 49, 6759-6761.
10. Peng, Q.; Xia, Y.; Qu, F.; Wu, X.; Campese, D.; Peng, L. Synthesis of a photoactivatable phospholipidic probe containing tetrafluorophenylazide. Tetrahedron Lett. 2005, 46, 5893-5897. (Pubitemid 41073437)
11. Kumar, N.S.; Young, R.N. Design and synthesis of an all-in-one 3-(1,1-difluoroprop-2-ynyl)-3Hdiazirin-3-yl functional group for photo-affinity labeling. Bioorg. Med. Chem. 2009, 17, 5388-5395.
12. Platz, M.S. Comparison of phenylcarbene and phenylnitrene. Acc. Chem. Res. 1995, 28, 487-492.
13. Lim, R.K.V.; Lin, Q. Bioorthogonal chemistry: Recent progress and future directions. Chem. Commun. 2010, 46, 1589-1600.
14. 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.; Overkleeft, H.S. Bioorthogonal chemistry: Applications in activity-based protein profiling. Acc. Chem. Res. 2011, 44, 718-729.
15. Schneider, D.; Schneider, T.; Rösner, D.; Scheffner, M.; Marx, A. Improving bioorthogonal protein ubiquitylation by click reaction. Bioorg. Med. Chem. 2013, 21, 3430-3435.
16. Zeng, D.; Zeglis, B.M.; Lewis, J.S.; Anderson, C.J. The growing impact of bioorthogonal click chemistry on the development of radiopharmaceuticals. J. Nucl. Med. 2013, 54, 829-832.
17. Shieh, P.; Hangauer, M.J.; Bertozzi, C.R. Fluorogenic azidofluoresceins for biological imaging. J. Am. Chem. Soc. 2012, 134, 17428-17431.
18. Herner, A.; Nikic, I.; Kallay, M.; Lemke, E.A.; Kele, P. A new family of bioorthogonally applicable fluorogenic labels. Org. Biomol. Chem. 2013, 11, 3297-3306.
19. Crump, C.J.; Am Ende, C.W.; Eric Ballard, T.; Pozdnyakov, N.; Pettersson, M.; Chau, D.M.; Bales, K.R.; Li, Y.M.; Johnson, D.S. Development of clickable active site-directed photoaffinity probes for γ-secretase. Bioorg. Med. Chem. Lett. 2012, 22, 2997-3000.
20. Crump, C.J.; Johnson, D.S.; Li, Y.M. Development and mechanism of γ-secretase modulators for Alzheimer's disease. Biochem. 2013, 52, 3197-3216.
21. Fuwa, H.; Takahashi, Y.; Konno, Y.; Watanabe, N.; Miyashita, H.; Sasaki, M.; Natsugaril, H.; Kan, T.; Fukuyama, T.; Tomita, T.; et al. Divergent synthesis of multifunctional molecular probes to elucidate the enzyme specificity of dipeptidic γ-secretase inhibitors. ACS Chem. Biol. 2007, 2, 408-418. (Pubitemid 350001562)
22. Crump, C.J.; Fish, B.A.; Castro, S.V.; Chau, D.M.; Gertsik, N.; Ahn, K.; Stiff, C.; Pozdnyakov, N.; Bales, K.R.; Johnson, D.S.; et al. Piperidine acetic acid based γ-secretase modulators directly bind to presenilin-1. ACS Chem. Neurosci. 2011, 2, 705-710.
23. Rowland, M.M.; Bostic, H.E.;Gong, D.; Speers, A.E.; Lucas, N.; Cho, W.; Cravatt, B.F.; Best, M.D. Phosphatidylinositol 3,4,5-trisphosphate activity probes for the labeling and proteomic characterization of protein binding partners. Biochemistry 2011, 50, 11143-11161.
24. Ge, J.; Cheng, X.; Tan, L.P.; Yao, S.Q. Ugi reaction-assisted rapid assembly of affinity-based probes against potential protein tyrosine phosphatases. Chem. Commun. 2012, 48, 4453-4455.
25. Zhang, Z.Y. Protein tyrosine phosphatases: Structure and function, substrate specificity, and inhibitor development. Annu. Rev. Pharmacol. Toxicol. 2002, 42, 209-234.
26. Li, L.; Tang, W.; Zhao, Z. Synthesis and application of prenyl-derived photoaffinity probes. Chin. J. Chem. 2009, 27, 1391-1396.
27. Cisar, J.S.; Cravatt, B.F. Fully functionalized small-molecule probes for integrated phenotypic screening and target identification. J. Am. Chem. Soc. 2012, 134, 10385-10388.
28. Park, J.; Oh, S.; Park, S.B. Discovery and target identification of an antiproliferative agent in live cells using fluorescence difference in two-dimensional gel electrophoresis. Angew. Chem. Int. Ed. 2012, 51, 5447-5451.
29. Neelarapu, R.; Holzle, D.L.; Velaparthi, S.; Bai, H.; Brunsteiner, M.; Blond, S.Y.; Petukhov, P.A. Design, synthesis, docking, and biological evaluation of novel diazide-containing isoxazole- and pyrazole-based histone deacetylase probes. J. Med. Chem. 2011, 54, 4350-4364.
30. Colca, J.R.; McDonald, W.G.; Waldon, D.J.; Thomasco, L.M.; Gadwood, R.C.; Lund, E.T.; Cavey, G.S.; Mathews, W.R.; Adams, L.D.; Cecil, E.T.; et al. Cross-linking in the living cell locates the site of action of oxazolidinone antibiotics. J. Biol. Chem. 2003, 278, 21972-21979. (Pubitemid 36792605)
31. Colca, J.R.; McDonald, W.G.; Waldon, D.J.; Leone, J.W.; Lull, J.M.; Bannow, C.A.; Lund, E.T.; Mathews, W.R. Identification of a novel mitochondrial protein ("mitoNEET") cross-linked specifically by a thiazolidinedione photoprobe. Am. J. Physiol. Endocrinol. Metable 2004, 286, E252-E260. (Pubitemid 38140317)
32. Colca, J.R.; McDonald, W.G.; Cavey, G.S.; Cole, S.L.; Holewa, D.D.; Brightwell-Conrad, A.S.; Wolfe, C.L.; Wheeler, J.S.; Coulter, K.R.; Kilkuskie, P.M.; et al. Identification of a mitochondrialtarget of thiazolidinedione insulin sensitizers (mTOT)-relationship to newly identifiedmitochondrial pyruvate carrier proteins. PLoS One 2013, 8, e61551.
33. Gandy, M.N.; Debowski, A.W.; Stubbs, K.A. A general method for affinity-based proteomic profiling of exo-α-glycosidases. Chem. Commun. 2011, 47, 5037-5039.
34. Addy, P.S.; Saha, B.; Pradeep Singh, N.D.; Das, A.K.; Bush, J.T.; Lejeune, C.; Schofield, C.J.;Basak, A. 1,3,5-Trisubstituted benzenes as fluorescent photoaffinity probes for human carbonic anhydrase II capture. Chem. Commun. 2013, 49, 1930-1932.
35. Punescu, E.; Louise, L.; Jean, L.; Romieu, A.; Renard, P.Y. A versatile access to new halogenated 7-azidocoumarins for photoaffinity labeling: Synthesis and photophysical properties. Dyes Pigm. 2011, 91, 427-434.
36. Murai, Y.; Masuda, K.; Ogasawara, Y.; Wang, L.; Hashidoko, Y.; Hatanaka, Y.; Iwata, S.; Kobayashi, T.; Hashimoto, M. Synthesis of photoreactive 2-phenethylamine derivatives-synthesis of adenosine derivatives enabling functional analysis of adenosine receptors by photoaffinity labeling. Eur. J. Org. Chem. 2013, 2013, 2428-2433.
37. Murai, Y.; Masuda, K.; Sakihama, Y.; Hashidoko, Y.; Hatanaka, Y.; Hashimoto, M. Comprehensive synthesis of photoreactive (3-trifluoromethyl) diazirinyl indole derivatives from 5- and 6-trifluoroacetylindoles for photoaffinity labeling. J. Org. Chem. 2012, 77, 8581-8587.
38. Ma, J.; Yin, W.; Zhou, H.; Liao, X.; Cook, J.M. General approach to the total synthesis of 9-methoxy-substituted indole alkaloids: synthesis of mitragynine, as well as 9-methoxygeissoschizol and 9-Methoxy-Nb- methylgeissoschizol. J. Org. Chem. 2008, 74, 264-273.
39. Baran, P.S.; Hafensteiner, B.D.; Ambhaikar, N.B.; Guerrero, C.A.; Gallagher, J.D. Enantioselective total synthesis of avrainvillamide and the stephacidins. J. Am. Chem. Soc. 2006, 128, 8678-8693.
40. Eto, H.; Eguchi, C.; Kagawa, T. Production of L-Tryptophan from γ-glutamaldehydic acid. Bull. Chem. Soc. Jpn. 1989, 62, 961-963.
41. Wartmann, T.; Lindel, T. L-phototryptophan. Eur. J. Org. Chem. 2013, 9, 1649-1652.
42. Rennhack, A.; Jumpertz, T.; Ness, J.; Baches, S.; Pietrzik, C.U.; Weggen, S.; Bulic, B. Synthesis of a potent photoreactive acidic γ-secretase modulator for target identification in cells. Bioorg. Med. Chem. 2012, 20, 6523-6532.
43. Li, P.; Zhang, Y.; Wang, L. Iron-catalyzed ligand-free three-component coupling reactions of aldehydes, terminal alkynes, and amines. Chem. Eur. J. 2009, 15, 2045-2049.
44. Zhang, Y.; Li, P.; Wang, M.; Wang, L. Indium-catalyzed highly efficient three-component coupling of aldehyde, alkyne, and amine via C-H bond activation. J. Org. Chem. 2009, 74, 4364-4367.
45. Wei, C.; Li, C.-J. A highly efficient three-component coupling of aldehyde, alkyne, and amines via Ca-H activation catalyzed by gold in water. J. Am. Chem. Soc. 2003, 125, 9584-9585. (Pubitemid 36975910)
46. Jayakar, S.S.; Dailey, W.P.; Eckenhoff, R.G.; Cohen, J.B. Identification of propofol binding sites in a nicotinic acetylcholine receptor with a photoreactive propofol analog. J. Biol. Chem. 2013, 288, 6178-6189.
47. White, B.H.; Howard, S.; Cohen, S.G.; Cohen, J.B. The hydrophobic photoreagent 3-(trifluoromethyl)-3-m-([125I]iodophenyl)diazirine is a novel noncompetitive antagonist of the nicotinic acetylcholine receptor. J. Biol. Chem. 1991, 266, 21595-21607.
48. White, B.H.; Cohen, J.B. Agonist-induced changes in the structure of the acetylcholine receptor M2 regions revealed by photoincorporation of an uncharged nicotinic noncompetitive antagonist. J. Biol. Chem. 1992, 267, 15770-15783.
49. Arevalo, E.; Chiara, D.C.; Forman, S.A.; Cohen, J.B.; Miller, K.W. Gating-enhanced accessibility of hydrophobic sites within the transmembrane region of the nicotinic acetylcholine receptor's δ-subunit: A time-resolved photolabeling study. J. Biol. Chem. 2005, 280, 13631-13640. (Pubitemid 40517257)
50. Hamouda, A.K.; Chiara, D.C.; Blanton, M.P.; Cohen, J.B. Probing the structure of the affinity-purified and lipid-reconstituted Torpedo nicotinic acetylcholine receptor. Biochemistry 2008, 47, 12787-12794.
51. Kita, M.; Hirayama, Y.; Yamagishi, K.; Yoneda, K.; Fujisawa, R.; Kigoshi, H. Interactions of theantitumor macrolide aplyronine a with actin and actin-related proteins established by its versatile photoaffinity derivatives. J. Am. Chem. Soc. 2012, 134, 20314-20317.
52. Battenberg, O.A.; Nodwell, M.B.; Sieber, S.A. Evaluation of α-pyrones and pyrimidones as photoaffinity probes for affinity-based protein profiling. J. Org. Chem. 2011, 76, 6075-6087.
53. Wang, R.E.; Hunt, C.R.; Chen, J.; Taylor, J.S. Biotinylated quercetin as an intrinsic photoaffinity proteomics probe for the identification of quercetin target proteins. Bioorg. Med. Chem. 2011, 19, 4710-4720.