N,N′-linked oligoureas as foldamers: Chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

Journal of the American Chemical Society

Volumn 127, Issue 7, 2005, Pages 2156-2164

  Violette, Aude ^a   Averlant Petit, Marie Christine ^c   Semetey, Vincent ^a,e   Hemmerlin, Christine ^c   Casimir, Richard ^a,f   Graft, Roland ^d   Marraud, Michel ^c   Briand, Jean Paul ^a   Rognan, Didier ^b   Guichard, Gilles ^a  

^a INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b CNRS   (France)

^c LAB DE CHIM PHYS MACROMOLECULAIRE   (France)

^d Institut de Chimie   (France)

^e HARVARD UNIVERSITY   (United States)

^f INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSTATICS; HYDROGEN BONDS; ISOMERIZATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; POLYPEPTIDES; SOLVENTS;

CHEMICAL SHIFTS; ELECTROSTATIC INTERACTION; FOLDAMERS; HELICAL STRUCTURE;

ENZYMES;

ALKYL GROUP; C PEPTIDE; ISOCYANIC ACID DERIVATIVE; METHANOL; OLIGOMER; PEPTIDE; PYRIDINE; SOLVENT; UREA DERIVATIVE; BIOMIMETIC MATERIAL; DRUG DERIVATIVE; UREA;

ACYLATION; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; CHIRALITY; CIRCULAR DICHROISM; CONFORMATION; HYDROGEN BOND; ISOMERIZATION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEAR MAGNETIC RESONANCE; OPTICAL ROTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; CHEMICAL STRUCTURE; CHEMISTRY; SYNTHESIS; THERMODYNAMICS;

BIOMIMETIC MATERIALS; CIRCULAR DICHROISM; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; SOLVENTS; THERMODYNAMICS; UREA;

EID: 13944267446     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja044392b     Document Type: Article

References (82)

1. For a review, see: Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. Rev. 2001, 101, 3893-4011.
2. Patch, J. A.; Barron, A. E. Curr. Opin. Chem. Biol. 2002, 6, 872-877.
3. Selected examples: (a) Patch, J. A.; Barron, A. E. J. Am. Chem. Soc. 2003, 125, 12092-12093.
4. (b) Arvidsson, P. I.; Ryder, N. S.; Weiss, H. M.; Gross, G.; Kretz, O.; Woessner, R.; Seebach, D. ChemBioChem 2003, 4, 1345-1347.
5. (c) Wu, C. W.; Seurynck, S. L.; Lee, K. Y.; Barron, A. E. Chem. Biol. 2003, 10, 1057-1063.
6. (d) Porter, E. A.; Weisblum, B.; Gellman, S. H. J. Am. Chem. Soc. 2002, 124, 7324-7330.
7. (e) Umezawa, N.; Gelman, M. A.; Haigis, M. C., Raines, R. T.; Gellman, S. H. J. Am. Chem. Soc. 2002, 124, 368-369.
8. (f) Rueping, M.; Mahajan, Y.; Sauer, M.; Seebach, D. ChemBioChem 2002, 3, 257-259.
9. Gellman, S. H. Acc. Chem. Res. 1998, 31, 173-180.
10. (b) Appella, D. H.; Christianson, L. A.; Karle, I. L.; Powell, D. R.; Gellman, S. H. J. Am. Chem. Soc. 1996, 118, 13071-13072.
11. For reviews, see: (a) Guichard, G. β-Peptides, γ-Peptides and Isosteric Backbones: New Scaffolds with Controlled Shapes for mimicking protein secondary structure elements. In Pseudopeptides in Drug Development: Nielsen, P. E., Ed.; Wiley-VCH Verlag: Weinheim, Germany, 2004; pp 33-120.
12. (b) Seebach, D.; Beck, A. K.; Bierbaum, D. J. Chem. Biodiv. 2004, 1, 1111-1239.
13. Lelais, G.; Seebach, D. Biopolymers 2004, 76, 206-243.
14. Hue, I. Eur. J. Org. Chem. 2004, 17-29.
15. (e) Seebach, D.; Kimmerlin, T.; Sebesta, R.; Campo, M. A.; Beck, A. K. Tetrahedron 2004, 60, 7455-7460.
16. (f) Cheng, R. P. Curr. Opin. Struct. Biol. 2004, 14, 512-520.
17. (g) Cheng, R. P.; Gellman, S. H.; DeGrado, W. F. Chem. Rev. 2001, 101, 3219-3232.
18. (h) Seebach, D.; Matthews. J. L. Chem Commun. 1997, 2015-2022.
19. (a) Seebach, D.; Overhand, M.; Kühnle, F. N. M.; Martinoni, B.; Oberer, L.; Hommel, U.; Widmer, H. Helv. Chim. Acta 1996, 79, 913-941.
20. (b) Appella, D. H.; Christianson, L. A.; Klein, D. A.; Powell, D. R.; Huang, X.; Barchi, J. J., Jr.; Gellman, S. H. Nature 1997, 387, 381-384.
21. Seebach, D.; Gademann, K.; Schreiber, J. V.; Matthews, J. L.; Hintermann, T.; Jaun, B.; Oberer, L.; Hommel, U.; Widmer, H. Helv. Chim. Acta 1997, 80, 2033-2038.
22. Claridge, T. D. W.; Goodman, J. M.; Moreno, A.; Angus, D.; Barker, S. F.; Taillefumier, C.; Watterson, M. P.; Fleet, G. W. J. Tetrahedron Lett. 2001, 42, 4251-4255.
23. (e) Gademann, K.; Häne, A.; Rueping, M.; Jaun, B.; Seebach, D. Angew. Chem., Int. Ed. 2003, 42, 1534-1537.
24. (a) Hintermann, T.; Gademann, K.; Jaun, B.; Seebach, D. Helv. Chim. Acta 1998, 81, 983-1002.
25. (b) Hanessian, S.; Luo, X.; Schaum, R.; Michnick, S. J. Am. Chem. Soc. 1998, 120, 8569-8570.
26. (c) Hanessian, S.; Luo, X.; Schaum, R. Tetrahedron Lett. 1999, 40, 4925-4929.
27. (d) Seebach, D.; Brenner, M.; Rueping, M.; Schweizer, B.; Jaun, B. Chem. Commun. 2001, 207-208.
28. (d) Seebach, D.; Brenner, M.; Rueping, M.; Jaun, B. Chem.-Eur. J. 2002, 8, 573-584.
29. Hagihara, M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber, S. L. J. Am. Chem. Soc. 1992, 114, 6568-6570.
30. (a) Cho, C. Y.; Moran, E. J.; Cherry, S. R.; Stephans, J. C.; Fodor, S. P. A.; Adams, C. L.; Sundaram, A.; Jacobs, J. W.; Schultz, P. G. Science 1993, 261, 1303-1305.
31. (b) Cho, C. Y.; Youngquist, R. S.; Paikoff, S. J.; Beresini, M. H.; Herbert, A. R.; Berleau, L. T.; Liu, C. W.; Wemmer, D. E.; Keough, T.; Schultz, P. G. J. Am. Chem. Soc. 1998, 120, 7706-7718.
32. (a) Burgess, K.; Linthicum, D. S.; Shin, H. Angew. Chem., Int. Ed. Engl. 1995, 34, 907-908.
33. (b) Burgess, K.; Ibarzo, J.; Linthicum, D. S.; Russell, D. H.; Shin, H.; Shitangkoon, A.; Totani, R.; Zhang, A. J. J. Am. Chem. Soc. 1997, 119, 1556-1564.
34. Semetey, V.; Didierjean, C.; Briand, J.-P.; Aubry, A.; Guichard, G. Angew. Chem. 2002, 115, 1975-1978; Angew. Chem., Int. Ed. 2002. 41, 1895-1898.
35. Semetey, V.; Didierjean, C.; Briand, J.-P.; Aubry, A.; Guichard, G. Angew. Chem. 2002, 115, 1975-1978; Angew. Chem., Int. Ed. 2002. 41, 1895-1898.
36. Lin, P.; Ganesan, A. Bioorg. Med. Chem. Lett. 1998, 8, 511-514.
37. Yang, D.; Zhang, Y.-H.; Zhu, N.-Y. J. Am. Chem. Soc. 2002, 124, 9966-9967.
38. (a) Semetey, V.; Rognan, D.; Hemmerlin, C.; Graff, R.; Briand, J.-P.; Marraud, M.; Guichard, C. Angew. Chem. 2002, 115, 1973-1l975; Angew. Chem., Int. Ed. 2002, 41, 1893-1895.
39. (a) Semetey, V.; Rognan, D.; Hemmerlin, C.; Graff, R.; Briand, J.-P.; Marraud, M.; Guichard, C. Angew. Chem. 2002, 115, 1973-1l975; Angew. Chem., Int. Ed. 2002, 41, 1893-1895.
40. (b) Hemmerlin, C.; Marraud, M.; Rognan, D.; Graff, R.; Semetey, V.; Briand, J. -P.; Guichard, G. Helv. Chim. Acta 2002, 85, 3692-3711.
41. (a) Kirshenbaum, K.; Barron, A. E.; Goldsmith, R. A.; Armand, P.; Bradley, E. K.; Truong, K. T. V.; Dill, K. A.; Cohen, F. E.; Zuckermann, R. N. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 4305-4308.
42. (b) Wu, C. W.; Sanborn, T. J.; Zuckermann, R. N.; Barron, A. E. J. Am. Chem. Soc. 2001, 123, 2958-2963.
43. McReynolds, K. D.; Gervay-Hague, J. Tetrahedron: Asymmetry 2000, 11, 337-362.
44. 14 helix might thus not be unique, and unambiguous structural assignment cannot be derived simply from CD measurements. Glattli, A.; Daura, X.; Seebach, D.; van Gunsteren, W. F. J. Am. Chem. Soc. 2002, 124, 12972-12978.
45. (a) Kim, J. M.; Bi, Y.; Paikoff, S.; Schultz, P. G. Tetrahedron Lett. 1996, 37, 5305-5308.
46. (b) Boeijen, A.; Liskamp, R. M. J. Eur. J. Org. Chem. 1999, 2127-2135.
47. (c) Guichard, G.; Semetey, V.; Didierjean, C.; Aubry, A.; Briand, J.-P.; Rodriguez, M. J. Org. Chem. 1999, 64, 8702-8705.
48. ( d) Guichard, G.; Semetey, V.; Rodriguez, M.; Briand, J.-P. Tetrahedron Lett. 2000, 41, 1553-1557.
49. Rink, H. Tetrahedron Lett. 1987, 37, 3787-3790.
50. Fairman, R.; Shoemaker, K. R.; York, E. J.; Stewart, J.; Baldwin, R. L. Proteins: Struct., Funct., Genet. 1989, 5, 1-7.
51. Sreerama, N.; Woody, R. W. Circular Dichroism of Peptides and proteins. In Circular Dichroism: Principles and Applications. 2nd ed.; Berova, N., Nakanishi, K., Woody, R. W., Eds.; John Wiley & Sons: New York, 2000; pp 601-620.
52. (a) Grammaticakis, P. Bull. Soc. Chim. Fr. 1968, 1057-1070.
53. (b) Boldea, A.; Drugarin, C.; Mracec, M.; Simon, Z. Rev. Roum. Chim. 1976, 21, 1345-1353.
54. (a) Hosoya, H.; Tanaka, J.; Nagakura, S. Bull. Chem. Soc. Jpn. 1960, 33, 850-860.
55. (b) Janssen, M. J. Recl. Trav. Chim. Pays-Bas 1960, 79, 454-463.
56. Rang, K.; Sandström, J.; Svensson, C. Can. J. Chem. 1998, 76, 811-820.
57. b, respectively (Supporting Information).
58. (a) Manning, M. C.; Woody, R. W. Biochemistry 1989, 28, 8609-8613.
59. (b) Cooper, T. M.; Woody. R. W. Biopolymers 1990, 30, 657-676.
60. (c) Woody, R. W. Eur. Biophys. J. 1994, 23, 253-262. Sreerama, N.; Manning, M. C.; Powers, M. E.; Zhang, J.-X.; Goldenberg, D. P.; Woody, R. W. Biochemistry 1999, 38, 10814-10822. Woody, A. Y.; Woody, R. W. Biopolymers 2003, 72, 500-513.
61. (c) Woody, R. W. Eur. Biophys. J. 1994, 23, 253-262. Sreerama, N.; Manning, M. C.; Powers, M. E.; Zhang, J.-X.; Goldenberg, D. P.; Woody, R. W. Biochemistry 1999, 38, 10814-10822. Woody, A. Y.; Woody, R. W. Biopolymers 2003, 72, 500-513.
62. (c) Woody, R. W. Eur. Biophys. J. 1994, 23, 253-262. Sreerama, N.; Manning, M. C.; Powers, M. E.; Zhang, J.-X.; Goldenberg, D. P.; Woody, R. W. Biochemistry 1999, 38, 10814-10822. Woody, A. Y.; Woody, R. W. Biopolymers 2003, 72, 500-513.
63. (a) Bhattacharjee, S.; Toth, G.; Lovas, S.; Hirst, J. D. J. Phys. Chem. B 2003, 107, 8682-8688.
64. (b) Andrew, C. D.; Bhattacharjee, S.; Kokkoni, N.; Hirst, J. D.; Jones, G. R.; Doig, A. J. J. Am. Chem. Soc. 2002, 124, 12706-12714.
65. The nomenclature used for the description of backbone and side-chain protons is shown in Figure SI (Supporting Information).
66. 0 was changed from 300 to 600 MHz.
67. 2.
68. A better dispersion of NH proton resonance was achieved at this temperature compared to 293 K, thus facilitating the interpretation of NOE connectivities.
69. (a) Stilbs, P. Acta Chem. Scand. 1971, 25, 2635-2642.
70. (b) Stilbs, P.; Forsén, S. J. Phys. Chem. 1971, 75, 1901-1902.
71. (c) Filleux-Blanchard, M. L.; Durand, A. Org. Magn. Reson. 1971, 3, 187-191.
72. (d) Filleux-Blanchard, M. L.; Durand, A. Bull. Soc. Chim. Fr. 1972, 12, 4710-4715.
73. (e) Martin, M. L.; Filleux-Blanchard, M. L.; Martin, G. J.; Webb, G. A. Org. Magn. Reson. 1980, 13, 396-402.
74. (f) Haushalter, K. A.; Lau, J.; Roberts, J. D. J. Am. Chem. Soc. 1996, 118, 8891-8896.
75. Semetey, V.; Hemmerlin, C.; Didierjean, C.; Schaffner, A.-P.; Giner, A. G.; Aubry, A.; Briand, J.-P.; Marraud, M.; Guichard, G. Org. Lett. 2001, 3, 3843-3846.
76. (a) Jimenez Blanco, J. L.; Benito, J. M.; Mellet, C. O.; Garcia Fernandez, J. M. Org. Lett. 1999, 1, 1217-1220.
77. (b) Ortiz Mellet, C.; Moreno Marin, A.; Jimenez Blanco, J. L.; Garcia Fernandez, J. M.; Fuentes, J. Tetrahedron: Asymmetry 1994, 5, 2325-2334.
78. (a) Hirota, N.; Mizuno, K.; Goto, Y. J. Mol. Biol. 1998, 27, 365-78.
79. (b) Hirota, N.; Mizuno, K.; Goto, Y. Protein Sci. 1997, 6, 416-421.
80. Gademann, K.; Jaun, B.; Seebach, D.; Perozzo, R.; Scapozza, L.; Folkers, G. Helv. Chim. Acta 1999, 82, 1-11.
81. (a) Seebach, D.; Schreiber. J. V.; Abele, S.; Daura, X.; van Gunsteren, W. F. Helv. Chim. Acta 2000, 83, 34-57.
82. (b) Raguse, T. L.; Lai, J. R.; Gellman, S. H. Helv. Chim. Acta 2002, 85, 4154-4164.