Sequence-dependent binding of dipeptides by an artificial receptor in water

Chemistry - A European Journal

Volumn 12, Issue 36, 2006, Pages 9186-9195

  Schmuck, Carsten ^a   Rupprecht, Daniel ^a   Wienand, Wolfgang ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Artificial receptors; Guanidinium cations; Molecular recognition; Peptides; Supramolecular chemistry

Indexed keywords

COMPLEXATION; FLUORESCENCE; HYDROPHOBICITY; POSITIVE IONS; SUPRAMOLECULAR CHEMISTRY; SYNTHESIS (CHEMICAL);

ARTIFICIAL RECEPTORS; GUANIDINIUM CATIONS; MOLECULAR RECOGNITION; PEPTIDES;

AMINO ACIDS;

DIPEPTIDE; WATER;

ARTICLE; BINDING SITE; CHEMISTRY; HYDROGEN BOND; MASS SPECTROMETRY; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; SPECTROFLUOROMETRY; ULTRAVIOLET SPECTROPHOTOMETRY;

BINDING SITES; DIPEPTIDES; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; PROTEIN BINDING; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; WATER;

EID: 33845787150     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200600573     Document Type: Article

References (85)

1. For review articles on artificial peptide receptors see: a) M. W. Peczuh, A. D. Hamilton, Chem. Rev. 2000, 100, 2479-2494;
2. b) H.-J. Schneider, Adv. Supramol. Chem. 2000, 7, 185-216;
3. c) H.-J. Schneider, Angew. Chem. 1993, 105, 890-892;
4. Angew. Chem. Int. Ed. Engl. 1993, 32, 848-850;
5. d) T. H. Webb, C. S. Wilcox, Chem. Soc. Rev. 1993, 22, 383-395.
6. Two recent examples for the application of artificial peptide receptors can be found in: a) X. Salvatella, M. Martinell, M. Gairí, M. G. Mateu, M. Feliz, A. D. Hamilton, J. de Mendoza, E. Giralt, Angew. Chem. 2004, 116, 198-200;
7. Angew. Chem. Int. Ed. 2004, 43, 196-198;
8. b) P. Breccia, M. vanGool, R. Peréz-Fernandez, S. Martín-Santamaria, F. Gago, P. Prados, J. de Mendoza, J. Am. Chem. Soc. 2003, 125, 8270-8284.
9. For examples of peptide recognition in polar solvents see: a) C. Schmuck, M. Heil, Chem. Eur. J. 2006, 12, 1339-1348;
10. b) C. Schmuck, M. Heil, J. Scheiber, K. Baumann, Angew. Chem. 2005, 117, 7374-7379;
11. Angew. Chem. Int. Ed. 2005, 44, 7208-7212;
12. c) M. Kruppa, C. Mandl, S. Miltschitzky, B. König, J. Am. Chem. Soc. 2005, 127, 3362-3365;
13. d) P. Krattinger, H. Wennemers, Synlett 2005, 706-708;
14. e) C. Schmuck, M. Heil, ChemBioChem 2003, 4, 1232-1238;
15. f) A. T. Wright, E. V. Anslyn. Org. Lett. 2004, 6, 1341-1344;
16. g) T. Mizutani, K. Wada, S. Kitagawa, Chem. Commun. 2002, 1626-1627;
17. h) S. Rensing, T. Schrader, Org. Lett. 2002, 4, 2161-2164;
18. i) M. Sirish, H.-J. Schneider, Chem. Commun. 1999, 907-908;
19. j) M. Davies, M. Bonnat, F. Guillier, J. D. Kilburn, M. Bradley, J. Org. Chem. 1998, 63, 8696-8703;
20. k) R. Breslow, Z. Yang, R. Ching, G. Trojandt, F. Odobel, J. Am. Chem. Soc. 1998, 120, 3536-3537.
21. For review articles on the use of combinatorial receptor libraries in supramolecular studies see: a) N. Srinivasan, J. D. Kilburn, Curr. Opin. Chem. Biol. 2004, 8, 305-310;
22. b) B. Linton, A. D. Hamilton. Curr. Opin. Chem. Biol. 1999, 3, 307-312;
23. c) Y. R. DeMiguel. J. M. K. Sanders, Curr. Opin. Chem. Biol. 1998, 2, 417-421;
24. d) W. C. Still. Acc. Chem. Res. 1996, 29, 155-163.
25. C. Schmuck, L. Geiger, J. Am. Chem. Soc. 2004, 126, 8898-8899.
26. For another interesting approach to sequence-specific peptide recognition by designed receptors see: a) M. Wehner, D. Janssen, G. Schäfer, T. Schrader, Eur. J. Org. Chem. 2006, 138-153;
27. b) M. Wehner. T. Schrader, Angew. Chem. 2002, 114, 1827-1831;
28. Angew. Chem. Int. Ed. 2002, 47, 1751-1754.
29. For reviews on hydrophobic interactions see: a) B. Widom, P. Bhimalapuram, K. Koga, Phys. Chem. Chem. Phys. 2003. 5, 3085-3093;
30. b) L. R. Pratt, A. Pohorille. Chem. Rev. 2002, 102, 2671-2691;
31. c) N. T. Southall, K. A. Dill, A. D. J. Haymet, J. Phys. Chem. B 2002. 106, 521-533.
32. a) R. D. Süssmuth, ChemBioChem 2002, 3, 295-298;
33. b) K. C. Nicolaou, C. N. C. Boddy, S. Bräse, N. Winssinger, Angew. Chem. 1999, 111, 2230-2287;
34. Angew. Chem. Int. Ed. 1999, 38, 2096-2152;
35. c) D. H. Williams, B. Bardsley, Angew. Chem. 1999, 111, 1264-1286;
36. Angew. Chem. Int. Ed. 1999, 38, 1173-1193;
37. d) C. T. Walsh, S. L. Fisher, I.-S. Park, M. Prahalad, Z. Wu, Chem. Biol. 1996, 3, 21-28.
38. Cyclodextrins and calixarenes are also often used as hydrophobic pockets in supramolecular receptors but these are too large to allow discrimination between different alkyl groups such as methyl and isopropyl.
39. a) P. J. Loll, J. Kaplan, B. S. Selinsky, P. H. Axelsen, J. Med. Chem. 1999, 42, 4714-4719;
40. b) D. H. Williams, M. S. Westwell, Chem. Soc. Rev. 1998, 27, 57-64.
41. For selected examples of other artificial receptors that bind D-Ala-D-Ala, but mostly only in organic and not in aqueous solvents, see; a) J. Shepherd, T. Gale, K. B. Jensen, J. D. Kilburn, Chem. Eur. J. 2006, 12, 713-720;
42. b) C. Chamorro, R. M. J. Liskamp, Tetrahedron 2004, 60, 11145-11157;
43. c) K. A. Ahrendt, J. A. Olsen, M. Wakao, J. Trias, J. A. Ellman, Bioorg. Med. Chem. Lett. 2003, 13, 1683-1686;
44. d) A. Casnati, F. Sansone, R. Ungaro, Acc. Chem. Res. 2003, 36, 246-254;
45. e) G. Chiosis, I. G. Boneca, Science 2001, 293, 1484-1486;
46. f) R. Xuo, G. Greiveldinger, L. E. Marenus, A. Cooper, J. A. Ellman, J. Am. Chem. Soc. 1999, 121, 4898-4899.
47. Carboxylate-binding pockets more closely related to the natural antibiotic have also been used in the past, but these are synthetically much more challenging without providing any improvement in terms of affinity; see for example: a) H. T. ten Brink, D. T. S. Rijkers, R. M. J. Liskamp, J. Org. Chem. 2006, 71, 1817-1824;
48. b) R. J. Pieters, Tetrahedron Lett. 2000, 41, 7541-7545;
49. c) N. Pant, A. Hamilton, J. Am. Chem. Soc. 1988, 110, 2002-2003.
50. a) C. Schmuck, L. Geiger, Curr. Org. Chem. 2003, 7, 1485-1502;
51. b) C. Schmuck, Chem. Eur. J. 2000, 6, 709-718.
52. For recent reviews on carboxylate binding by artificial receptors see: a) K. A. Schug, W. Lindner, Chem. Rev. 2005, 105, 67-113;
53. b) M. D. Best, S. L. Tobey, E. V. Anslyn, Coord. Chem. Rev. 2003, 240, 3-15;
54. c) P. A. Gale, Coord. Chem. Rev. 2003, 240, 191-221;
55. d) R. J. Fitzmaurice, G. M. Kyne, D. Douheret, J. D. Kilburn, J. Chem. Soc. Perkin Trans. 1 2002, 841-864;
56. e) T. S. Snowden, E. V. Anslyn, Curr. Opin. Chem. Biol. 1999, 3, 740-746;
57. f) P. D. Beer, P. Schmitt, Curr. Opin. Chem. Biol. 1997, 1, 475-482;
58. g) A. Bianchi, K. Bowman-James, E. Garcia-España, Supramolecular Chemistry of Anions, Wiley-VCH, New York, 1997;
59. h) F. P. Schmidtchen. M. Berger, Chem. Rev. 1997, 97, 1609-1646;
60. i) C. Seel, A. Galán, J. de Mendoza, Top. Curr. Chem. 1995, 175, 101-132.
61. a) A. Collet, J.-P. Dutata, B. Lozach, J. Canceill, Top. Curr. Chem. 1993, 165, 103-129;
62. b) A. Collet, Tetrahedron 1987, 43, 5725-5759.
63. The more readily available cyclotriveratrylenes (= symmetrically tris-substituted cyclotribenzylenes) have already been used in supramolecular chemistry but mostly only as rigid scaffolds to attach other binding groups and not as binding pockets in themselves. For some examples see: a) C. J. Sumby, J. Fisher, T. J. Prioir, M. J. Hardie, Chem. Eur. J. 2006, 12, 2945-2959:
64. b) S. Zhang, L. Echegoyen, J. Am. Chem. Soc. 2005, 127, 2006-2011; see also ref. [9b].
65. A related receptor derived from simple phenylalanine instead of this unnatural cyclotribenzylene amino acid had already been studied in the past but failed to show efficient and selective dipeptide binding in aqueous solvents: C. Schmuck, W. Wienand, unpublished results.
66. C. Schmuck, W. Wienand. Synthesis 2002, 655-663.
67. S. Gair, R. F. W. Jackson, Curr. Org. Chem. 1998, 2, 527-550.
68. For the iodocyclotribenzylene 3 we did not observe any coalescence due to ring flip in the NMR up to a temperature of 120 °C. For data on the conformational behavior of cyclotriveratrylenes and the unsubstituted parent hydrocarbon see also: T. Sato, K. Uno, J. Chem. Soc. Perkin Trans. 1 1973, 895-900.
69. T. Schmuck, W. Wienand. J. Am. Chem. Soc. 2003, 125, 452-459.
70. a) K. Hirose, J. Inclusion Phenom. Macrocyclic Chem. 2001, 39, 193-209;
71. b) K. A. Connors, Binding Constants, Wiley, New York, 1987.
72. -3 M.
73. For the equations and procedures used for data analysis see: C. Schmuck, M. Schwegmann, Org. Biomol. Chem. 2006, 4, 836-838.
74. P. McCarthy, Anal. Chem. 1978, 50, 2165-2165.
75. To avoid detection of the Raman band of water the spectra were recorded with use of synchronous wavelength screening with a Δλ of 20 nm between excitation and emission.
76. Titrations were carried out in a pH range from 5.77 to 6.29 to ensure that the acyl guanidine is fully protonated while the dipeptide is still deprotonated. In this range we did not observe any variation in the association constant K as a function of pH for different titrations with the same substrate.
77. N. M. Sangeetha, U. Maitra, Chem. Soc. Rev. 2005, 34, 821-836.
78. Other solvents such as methanol, in which the receptor is more readily soluble, are not reasonable here as they would drastically reduce the importance of hydrophobic interactions between the cyclotribenzylene moiety and the dipeptide, thereby destroying any substrate selectivity.
79. For similar conclusions in different systems see: a) C. Schmuck, U. Machon, Chem. Eur. J. 2005, 11, 1109-1118;
80. b) S.-Y. Chang, H. S. Kim, K.-J. Chang, K.-S. Jeong, Org. Lett. 2004, 6, 181-184;
81. c) G. M. Kyne, M. E. Light, M. B. Hursthouse, J. de Mendoza, J. D. Kilburn. J. Chem. Soc. Perkin Trans. 1 2001, 1258-1263;
82. d) K. Kavallieratos, C. M. Bertao, R. H. Crabtree, J. Org. Chem. 1999, 64, 1675-1683.
83. a) B. M. Crowley, D. L. Boger, J. Am. Chem. Soc. 2006, 128, 2885-2892;
84. b) C. C. McComas, B. M. Crowley, D. L. Boger, J. Am. Chem. Soc. 2003, 125, 9314-9315.
85. F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, W. C. Still, J. Comput. Chem. 1990, 11, 440-467.