High-throughput sequence determination of cyclic peptide library members by partial Edman degradation/mass spectrometry

Journal of the American Chemical Society

Volumn 128, Issue 39, 2006, Pages 13000-13009

  Joo, Sang Hoon ^a   Xiao, Qing ^a   Ling, Yun ^a   Gopishetty, Bhaskar ^a   Pei, Dehua ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC PEPTIDE; CYCLIC PEPTIDE LIBRARY MEMBERS; EDMAN DEGRADATION; THROUGHPUT SEQUENCE DETERMINATION;

BIOMEDICAL ENGINEERING; DEGRADATION; DRUG PRODUCTS; LEAD COMPOUNDS; MASS SPECTROMETRY; MOLECULAR DYNAMICS; THROUGHPUT;

PROTEINS;

CYCLOPEPTIDE; DRUG ANALOG; PEPTIDE LIBRARY; POLYPEPTIDE ANTIBIOTIC AGENT; STREPTAVIDIN; TYROCIDINE;

AMINO ACID SEQUENCE; ANTIBACTERIAL ACTIVITY; ARTICLE; BACTERIAL CELL; CONTROLLED STUDY; DRUG PROTEIN BINDING; HIGH THROUGHPUT SCREENING; MASS SPECTROMETRY; MEDICAL RESEARCH; MOLECULAR PROBE; NONHUMAN; PARTIAL EDMAN DEGRADATION MASS SPECTROMETRY; PEPTIDE SYNTHESIS; SEQUENCE ANALYSIS;

ANTI-INFECTIVE AGENTS; COMBINATORIAL CHEMISTRY TECHNIQUES; OLIGOPEPTIDES; PEPTIDE LIBRARY; PEPTIDES, CYCLIC; SEQUENCE ANALYSIS, PROTEIN; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; STREPTAVIDIN; TYROCIDINE;

EID: 33749532845     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja063722k     Document Type: Article

References (43)

1. Reviewed by: Hamada, Y.; Shioiri, T. Chem. Rev. 2005, 105, 4441-4482.
2. For examples see: (a) Fernandez-Lopez, S.; Kim, H.-S.; Choi, E. C.; Delgado, M.; Granja, J. R.; Khasanov, A.; Kraehenbuehl, K.; Long, G.; Weinberger, D. A.; Wilcoxen, K. M.; Ghadiri, M. R. Nature 2001, 412, 452-456.
3. (b) Kohli, R. M.; Walsh, C. T.; Burkart, M. D. Nature 2002, 418, 658-661.
4. (c) Qin, C.; Bu, X.; Zhong, X.; Ng, N. L. J.; Guo, Z. J. Comb. Chem. 2004, 6, 398-406.
5. (d) Dartois, V.; Sanchez-Quesada, J.; Cabezas, E.; Chi, E.; Dubbelde, C.; Dunn, C.; Granja, J.; Gritzen, C.; Weinberger, D.; Ghadiri, M. R.; Parr, T. R. Jr. Antimicrob. Agents Chemother. 2005, 49, 3302-3310.
6. For examples see: (a) McBride, J. D.; Freeman, H. N.; Domingo, G. J.; Leatherbarrow, R. J. J. Mol. Biol. 1996, 259, 819-827.
7. (b) Eichler, J.; Lucka, A. W.; Pinilla, C.; Houghten, R. A. Mol. Diversity. 1996, 1, 233-240.
8. (c) March, D. R.; Abbenante, G.; Bergman, D. A.; Brinkworth, R. I.; Wickramasinghe, W.; Begun, J.; Martin, J. L.; Fairlie, D. P. J. Am. Chem. Soc. 1996, 118, 3375-3382.
9. (d) Bratkovic, T.; Lunder, M.; Popovic, T.; Kreft, S.; Turk, B.; Strukelj, B.; Urleb, U. Biochem. Biophys. Res. Commun. 2005, 332, 897-903.
10. For examples see: (a) Spatola, A. F.; Crozet, Y.; deWit, D.; Yanagisawa, M. J. Med. Chem. 1996, 39, 3842-3846.
11. (b) Zang, X.; Yu, Z.; Chu, Y.-H. Bioorg. Med. Chem. Lett. 1998, 8, 2327-2332.
12. (c) Leduc, A.-M.; Trent. J. O.; Wittliff, J. L.; Bramlett, K. S.; Briggs, S. L.; Chirgadze, N. Y.; Wang, Y.; Burris, T. P.; Spatola, A. F. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 11273-11278.
13. (d) Sakamoto, K.; Yuji, Y.; Hashiguchi, S.; Sugimura, K. Pep. Sci. 2003, 39, 279-280.
14. (e) Tavassoli, A.; Benkovic, S. J. Angew. Chem., Int. Ed. 2005, 44, 2760-2763.
15. Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.; Kazmierski, W. M.; Knapp, R. J. Nature 1991, 354, 82-84.
16. (b) Houghten, R. A.; Pinilla, C.; Blondelle, S. E.; Appel, J. R.; Dooley, C. T.; Cuervo, J. H. Nature 1991, 354, 84-86.
17. (c) Furka, A.; Sebestyen, F.; Asgedom, M.; Dibo, G. Int. J. Peptide Protein Res. 1991, 37, 487-493.
18. Eckert, K.; Schwarz, H.; Tomer, K. B.; Gross, M. L. J. Am. Chem. Soc. 1985, 107, 6765-6769.
19. (b) Schilling, B.; Wang, W.; McMurray, J. S.; Medzihradszky, K. F. Rapid Commun. Mass Spectrom. 1999, 13, 2174-2179.
20. (c) Ngoka, L. C. M.; Gross, M. L. J. Am. Soc. Mass Spectrom. 1999, 10, 732-746.
21. (d) Siegel, M. M.; Huang, J.; Lin, B.; Tsao, R.; Edmonds, C. G. Bio. Mass Spectrom. 1994, 23, 186-204.
22. (e) Redman, J. E.; Wilcoxen, K. M.; Ghadiri, M. R. J. Comb. Chem. 2003, 5, 33-40.
23. Wang, P.; Arabaci, G.; Pei, D. J. Comb. Chem. 2001, 3, 251-254.
24. (b) Sweeney, M. C.; Pei, D. J. Comb. Chem. 2003, 5, 218-222.
25. Each random position contained 20 amino acids: A, D, E, F, G, H, I, K, L, N, P, Q, R, S, T, V, W, Y, and (S)-2-aminobutyric acid (C) and norleucine (M) as cysteine and methionine replacements, respectively.
26. Yu. Z.; Chu, Y.-H. Bioorg. Med. Chem. Lett. 1997, 7, 95-98.
27. Liu, R.; Marik, J.; Lam, K. S. J. Am. Chem. Soc. 2002, 124, 7678-7680.
28. See reviews: (a) Lambert, J. N.; Mitchell, J. P.; Roberts, K. D. J. Chem. Soc., Perkins Trans. 2001, 1, 471-484.
29. (b) Li, P.; Roller, P. P.; Xu, J. Curr. Org. Chem. 2002, 6, 411-440.
30. (c) Davies, J. S. J. Pep. Sci. 2003, 9, 471-501.
31. 2 resin of low loading capacity gave the best results among the resins tested so far.
32. Vagner, J.; Barany, G.; Lam, K. S.; Krchnak, V.; Sepetov, N. F.; Ostrem, J. A.; Strop, P.; Lebl, M. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8194-8199.
33. (a) Devlin, J. J.; Panganiban, L. C.; Devlin, P. E. Science 1990, 249, 404-406.
34. (b) Giebel, L. B.; Cass, R. T.; Milligan, D. L.; Young, D. C.; Arze, R., Johnson, C. R. Biochemistry 1995, 34, 15430-15435.
35. Prenner, E. J.; Lewis, R. N. A. H.; McElhaney, R. N. Biochim. Biophys. Acta 1999, 1462, 201-221.
36. Hancock, R. E. W. Lancet 1997, 349, 418-422.
37. Danders, W.; Marahiel, M. A.; Krause, M.; Kosui, N.; Kato, T.; Izumiya, N.; Kleinkauf, H. Antimicrob. Agents Chemother. 1982, 22, 785-790.
38. Lin, H., Walsh, C. T. J. Am. Chem. Soc. 2004, 126, 13998-14003.
39. (a) Bu, X.; Wu, X.; Xie, G.; Guo, Z. Org. Lett. 2002, 4, 2893-2895.
40. (b) Qin, C.; Zhong, X.; Bu, X.; Ng, N. L. J.; Guo, Z. J. Med. Chem. 2003, 46, 4830-4833.
41. Ohlmeyer, M. H. J.; Swanson, R. N.; Dillard, L. W.; Reader, J. C.; Asouline, G.; Kobayashi, R.; Wigler, M.; Still, W. C. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 10922-10926.
42. Thakkar, A.; Wavreille, A.-S.; Pei, D. Anal. Chem. 2006, 78, 5935-5939.
43. Hu, X.; Nguyen, K. T.; Jiang, V. C.; Lofland, D.; Moser, H. E.; Pei, D. J. Med. Chem. 2004, 47, 4941-4949.