A peptide dendrimer enzyme model with a single catalytic site at the core

Journal of the American Chemical Society

Volumn 129, Issue 43, 2007, Pages 13238-13246

  Javor, Sacha ^a   Delort, Estelle ^a   Darbre, Tamis ^a   Reymond, Jean Louis ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACYLOXYPYRENE; FLUOROGENIC; FUNCTIONAL SCREENING;

CATALYSIS; DENDRIMERS; ENZYMES; ESTERS; NUCLEAR MAGNETIC RESONANCE;

PEPTIDES;

ARGININE; AROMATIC AMINO ACID; DENDRIMER; ENZYME; ESTER; ESTERASE; FLUOROGENIC 1 ACYLOXYPYRENE 3,6,8 TRISULFONATE DERIVATIVE; HISTIDINE DERIVATIVE; PEPTIDE; PROTEIN; PYRENE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CATALYST; CHEMICAL BINDING; COMBINATORIAL LIBRARY; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; HYDROLYSIS; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE; PH; PROTEIN CONFORMATION; PROTEIN DENATURATION;

AMINO ACID SEQUENCE; CATALYTIC DOMAIN; DATABASES, PROTEIN; DENDRIMERS; DIFFUSION; ESTERASES; HYDROGEN-ION CONCENTRATION; KINETICS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES;

EID: 35848953420     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja074115f     Document Type: Article

References (86)

1. Toscano, M. D.; Woycechowsky, K. J.; Hilvert, D. Angew. Chem., Int. Ed. 2007, 46, 3212-3236.
2. (a) Lerner, R. A.; Benkovic, S. J.; Schultz, P. G. Science 1991, 252, 659-667.
3. (b) Schultz, P. G.; Lerner, R. A. Acc. Chem. Res. 1993, 26, 391-395.
4. (c) Schultz, P. G.; Lerner, R. A. Science 1995, 269, 1835-1842.
5. (d) MacBeath, G.; Hilvert, D. Chem. Biol. 1996, 3, 433-445.
6. (e) Thomas, N. R. Nat. Prod. Rep. 1996, 13, 479-511.
7. (f) Stevenson, J. D.; Thomas, N. R. Nat. Prod. Rep. 2000, 17, 535-537.
8. (g) Keinan, E., Ed. Catalytic Antibodies; Wiley-VCH: Weinheim, 2005.
9. (a) Reetz, M. T. Angew. Chem., Int. Ed. 2001, 40, 284-310.
10. (b) Bloom, J. D.; Meyer, M. M.; Meinhold, P.; Otey, C. R.; MacMillan, D.; Arnold, F. H. Curr. Opin. Struct. Biol. 2005, 15, 447-452.
11. (a) Bolon, D. N.; Voigt, C. A.; Mayo, S. L. Curr. Opin. Chem. Biol. 2002, 6, 125-129.
12. (b) Kuhlman, B.; Baker, D. Curr. Opin. Struct. Biol. 2004, 14, 89-95.
13. (c) Dwyer, M. A.; Hellinga, H. W. Curr. Opin. Struct. Biol. 2004, 14, 495-504.
14. (d) Moffet, D. A.; Hecht, M. H. Chem. Rev. 2001, 101, 3191-3203.
15. Berkessel, A. Curr. Opin. Chem. Biol. 2003, 7, 409-419.
16. (a) Qi, D.; Tann, C.-M.; Haring, D.; Distefano, M. D. Chem. Rev. 2001, 101, 3081-3112.
17. (b) Andersson, L. K.; Caspersson, M.; Baltzer, L. Chem. Eur. J. 2002, 8, 3687-3689.
18. (a) van de Velde, F.; Arends, I. W.; Sheldon, R. A. J. Inorg. Biochem. 2000, 80, 81-89.
19. (b) Wahler, D.; Reymond, J.-L. Can. J. Chem. 2002, 80, 665-670.
20. Thomas, C. M.; Ward, T. R. Chem. Soc. Rev. 2005, 34, 337-346.
21. Hult, K.; Berglund, P. Curr. Opin. Biotechnol. 2003, 14, 395-400.
22. (a) Kirby, A. J. Angew. Chem., Int. Ed. 1996, 35, 706-724.
23. (b) Woggon, W.-D. Acc. Chem. Res. 2005, 38, 127-136.
24. (c) Motherwell, W. B.; Bingham, M. J.; Six, Y. Tetrahedron 2001, 57, 4663-4686.
25. (d) Breslow, R.; Zhang, X.; Huang, Y. J. Am. Chem. Soc. 1997, 119, 4535-4536.
26. (e) Breslow, R.; Huang, Y.; Zhang, X.; Yang, J. Proc. Natl. Acad. Sci. U.S.A., 1997, 94, 11156-11158.
27. (a) Newkome, G. R.; Moorefield, C. N.; Vögtle, F. Dendritic Molecules: Concepts, Synthesis, Applications; VCH: Weinheim, 2001.
28. (b) Tomalia, D. A.; Dvornic, P. R. Nature 1994, 372, 617-618.
29. (c) Smith, D. K.; Diederich, F. Top. Curr. Chem. 2000, 210, 183-227.
30. (d) Helms, B.; Fréchet, J. M. J. Adv. Synth. Catal. 2006, 348, 1125-1148.
31. (e) Smith, D. K.; Diederich, F. Chem. Eur. J. 1998, 4, 1353-1361.
32. (f) Liang, C.; Fréchet, J. M. J. Prog. Polym. Sci. 2005, 30, 385-402.
33. Grayson, S. M.; Fréchet, J. M. J. Chem. Rev. 2001, 101, 3819-3868.
34. (g) Lee, C. C.; Mackay, J. A.; Fréchet, J. M. J.; Szoka, F. C. Nat. Biotechnol. 2005, 23, 1517-1526.
35. Reviews on catalysis with dendrimers: (a) Oosterom, G. E.; Reek, J. N.; Kamer, P. C.; van Leeuwen, P. W. Angew. Chem., Int. Ed. 2001, 40, 1828-1849.
36. (b) Twyman, L. J.; King, A. S.; Martin, I. K. Chem. Soc. Rev. 2002, 31, 69-82.
37. (c) Kofoed, J.; Reymond, J.-L. Curr. Opin. Chem. Biol. 2005, 9, 656-664.
38. (d) Astruc, D.; Heuze, K.; Gatard, S.; Mery, D.; Nlate, S.; Plault, L. Adv. Synth. Catal. 2005, 347, 329-338.
39. (e) Helms, B.; Fréchet, J. M. J. Adv. Synth. Catal. 2006, 348, 1125-1148.
40. Recent reports: (f) Wang, Z.-J.; Deng, G.-J.; Yong, L.; He, Y.-M.; Tang, W.-J.; Fan, Q.-H. Org. Lett. 2007, 9, 1243-1246.
41. (g) Ouali, A.; Laurent, R.; Caminade, A. M.; Majoral, J.-P.; Taillefer, M. J. Am. Chem. Soc. 2006, 128, 15990-15991.
42. (h) van de Coevering, R.; Alfers, A. P.; Meeldiijk, J. D.; Martinez-Viviente, E.; Pregosin, P. S.; Klein, Gebbink, R. J. M.; van Koten, G. J. Am. Chem. Soc. 2006, 128, 12700-12713.
43. (i) Abu-Reziq, R.; Alper, H.; Wang, D.; Post, M. L. J. Am. Chem. Soc. 2006, 128, 5279-5282.
44. For early examples of catalytic polymers with imidazole groups: (a) Overberger, C. G.; Salamone, J. C. Acc. Chem. Res. 1969, 2, 217-224.
45. (b) Overberger, C. G.; Mitra, S. Pure Appl. Chem. 1979, 51, 1391-1404.
46. For other examples and reviews: (c) Suh, J. Acc. Chem. Res. 2003, 36, 562-570.
47. (d) Benaglia, M. Puglisi.; Cozzi, F. Chem. Rev. 2003, 103, 3401-3429.
48. (e) Bosman, A. W.; Vestberg, R.; Heumann, A.; Fréchet, J. M. J.; Hawker, C. J. J. Am. Chem. Soc. 2003, 123, 5908-5917.
49. (a) Crespo, L.; Sanclimens, G.; Pons, M.; Giralt, E.; Royo, M.; Albericio, F. Chem. Rev. 2005, 1663-1681.
50. (b) Sadler, K.; Tam, J. P. Rev. Mol. Biotechnol. 2002, 90, 195-229.
51. (c) Darbre, T.; Reymond, J.-L. Acc. Chem. Res. 2006, 39, 925-934.
52. (a) Esposito, A.; Delort, E.; Lagnoux, D.; Djojo, F.; Reymond, J.-L. Angew. Chem., Int. Ed. 2003, 42, 1381-1383.
53. (b) Lagnoux, D.; Delort, E.; Douat-Casassus, C.; Esposito, A.; Reymond, J.-L. Chem. Eur. J. 2004, 10, 1215-1226.
54. (c) Douat-Casassus, C.; Darbre, T.; Reymond, J.-L. J. Am. Chem. Soc. 2004, 126, 7817-7826.
55. (d) Clouet, A.; Darbre, T.; Reymond, J.-L. Adv. Synth. Catal. 2004, 346, 1195-1204.
56. (a) Delort, E.; Darbre, T.; Reymond, J.-L. J. Am. Chem. Soc. 2004, 126, 15642-15643.
57. (b) Delort, E.; Nguyen-Trung, N.-Q.; Darbre, T.; Reymond, J.-L. J. Org. Chem. 2006, 71, 4468-4480.
58. Kofoed, J.; Darbre, T.; Reymond, J.-L. Org. Biomol. Chem. 2006, 3268-3281.
59. (a) Warshel, A.; Florian, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5950-5955.
60. (b) Bruice, T. C. Chem. Rev. 2006, 106, 3119-3139.
61. (c) Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-1202.
62. Liu, L.; Breslow, R. J. Am. Chem. Soc. 2003, 125, 12110-12111.
63. Hecht, S.; Fréchet, J. M. J. J. Am. Chem. Soc. 2001, 123, 6959-6960.
64. Liang, C. O.; Helms, B.; Craig, J.; Frechet, J. M. J. Chem. Commun. 2003, 2524-2525
65. Piotti, M. E.; Rivera, F., Jr.; Bond, R.; Hawker, C. J.; Fréchet, J. M. J. J. Am. Chem. Soc. 1999, 121, 9471-9472.
66. (a) Clouet, A.; Darbre, T.; Reymond, J.-L. Angew. Chem., Int. Ed. 2004, 43, 4612-4615.
67. (b) Clouet, A.; Darbre, T.; Reymond, J.-L. Biopolymers 2006, 84, 114-123.
68. (a) Kolomiets, E.; Johansson, E. M. V.; Renaudet, O.; Darbre, T.; Reymond, J.-L. Org. Lett. 2007, 9, 1465-1468.
69. (b) Johansson, E. M. V.; Kolomiets, E.; Rosenau, F.; Jäger, K.-E.; Darbre, T.; Reymond, J.-L. New J. Chem. 2007, 31, 1291-1299.
70. Schug, K. A.; Lindner, W. Chem. Rev. 2005, 105, 67-113.
71. Clark, D. D.; Boyd, J. M.; Ensign, S. A. Biochemistry 2004, 43, 6763-6771.
72. Hotta, K.; Wilson, I. A.; Hilvert, D. Biochemistry 2002, 41, 772-779.
73. (a) Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
74. (b) Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
75. DeLano, W. L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA. http://www.pymol.org.
76. Cohen, Y.; Avram, L.; Frish, L. Angew. Chem., Int. Ed. 2005, 44, 520-554.
77. Wilkins, D. K.; Grimshaw, S. B.; Receveur, V.; Dobson, C. M.; Jones, J. A.; Smith, L. J. Biochemistry 1999, 38, 16424-16431.
78. (a) Newkome, G. R.; Young, J. K.; Baker, G. R.; Potter, R. L.; Audoly, L.; Cooper, D.; Weis, C. D.; Morris, K.; Johnson, C. S., Jr., Macromolecules 1993, 26, 2394-2396.
79. (b) Young, J. K.; Baker, G. R.; Newkome, G. R.; Morris, K. F.; Johnson, C. S., Jr. Macromolecules 1994, 27, 3464-3471.
80. (c) Ihre, H.; Hult, A.; Söderlind, E. J. Am. Chem. Soc. 1996, 118, 6388-6395.
81. (d) Hecht, S.; Vladimirov, N.; Fréchet, J. M. J. J. Am. Chem. Soc. 2001, 123, 18-25.
82. (e) Jeong, S. W.; O'Brien, D. F.; Orädd, G.; Lindblom, G. Langmuir 2002, 18, 1073-1076.
83. (f) Fritzinger, B.; Scheler, U. Macromol. Chem. Phys. 2005, 206, 1288-1291.
84. (g) Wong, S.; Appelhans, D.; Voit, B.; Scheler, U. Macromolecules 2001, 34, 678-680.
85. (h) Ong, W.; Grindstaff, J.; Sobransingh, D.; Toba, R.; Quintela, J. M.; Peinador, C.; Kaifer, A. E. J. Am. Chem. Soc. 2005, 127, 3353-3361.
86. Addition of hydroxypyrene-trisulfonates to solutions of RG3 and RMG3 lead to precipitation precluding the determination of hydrodynamic radii for the dendrimer-substrate complexes. Precipitation was also observed upon attempted microcalorimetric measurements with these dendrimers.