Peptidomimetics 245 55. Alsina, J., Scott, W. L., and O’Donell, M. J., (2005) Solid-phase synthesis of α-substituted proline hydantoins and analogs. Tetrahedron Lett. 46, 3131–3135. 56. Nefzi, A., Giulianotti, M., Truong, L., Rattan, S., Ostresh, J. M., and Houghten, R. A., (2002) Solid-phase synthesis of linear ureas tethered to hydantoins and thiohydantoins. J. Comb. Chem. 4, 175–178. 57. Shemyakin, M. M., Shchukina, L. A., Vinogradova, E. I., Ravidel, G. A., and Ovchinnikov, Y. A. (1966) Mutual replaceability of amide and ester groups in biologically active peptide and depsipeptides. Experimentia 22, 535–536. 58. Bramson, H. N., Thomas, N. E., and Kaiser, E. T. (1985) The use of N-methylated peptides and depsipeptides to probe the binding of heptapeptide substrates to cAMPdependent protein kinase. J. Biol. Chem. 260, 15452–15457. 59. Arad, O., and Goodman, M., (1990) Depsipeptide analogues of elastin repeating sequences: synthesis. Biopolymers 29, 1633–1649. 60. Coombs, G. S., Rao, M. S., Olson, A. J., Dawson, P. E., and Madison, E. L. (1999) Revisiting catalysis by chymotrypsin family serine proteases using peptide substrates and inhibitors with unnatural main chains. J. Biol. Chem. 274, 24074–24079. 61. Davidson, B. S. (1993) Ascidians: producers of amino acid-derived metabolites. Chem. Rev. 93, 1771–1791. 62. Fusetani, N., and Matsunaga, S. (1993) Bioactive sponge peptides. Chem. Rev. 93, 1793–1806. 63. Woo, A. J., Strohl, W. R., and Priestley, N. D. (1999) Nonactin biosynthesis: the product of nonS catalyzes the formation of the furan ring of nonactic acid. Antimicrob. Agents Chemother. 43, 1662–1668. 64. Stawikowski, M., and Cudic, P. (2006) Depsipeptide synthesis, in <strong>Peptide</strong> Characterization and Application Protocols (Fields, G. B., ed.), Humana Press, Totowa, NJ, pp. 321–339. 65. Kuisle, O., Lolo, M., Quinoa, E., and Riguera, R. (1999) Solid phase synthesis of depsides and depsipeptides. Tetrahedron 55, 14807–14812. 66. Kuisle, O., Quinoa, E., and Riguera, R., (1999) A general methodology for automated solid-phase synthesis of depsides and depsipeptides. Preparation of a valinomycin analogue. J. Org Chem. 64, 8063–8075. 67. Marder, O., and Albericio, F. (2003) Industrial application of coupling reagents in peptides. Chim. Oggi 6, 35–40. 68. Berry J. D., Digiovanna V. C., Metrick S. S., and Murugan R. (2001) Catalysis by 4-dialkylaminopyridines. Arkivoc i, 201–226. 69. Stawikowski, M., and Cudic, P. (2006) A novel strategy for the solid-phase synthesis of cyclic lipodepsipeptides. Tetrahedron Lett. 47, 8587–8590. 70. Park, B.-D., and Lee, Y.-S. (2000) The effect of PEG groups on swelling properties of PEG-grafted-polystyrene resins in various solvents. React. Funct. Polymers 44, 41–46. 71. Hudson, D. (1988) Methodological implications of simultaneous solid-phase peptide synthesis. 1. Comparison of different coupling procedures. J. Org. Chem. 53, 617–624.
246 Cudic and Stawikowski 72. Podlech J. (2001) Carbodiimides, in Synthesis of <strong>Peptide</strong>s and Peptidomimetics,4th ed. (Goodman, M., Felix, A., Moroder, L., and Toniolo, C., eds.), Thieme, Stuttgart, pp. 517–533. 73. Patch, J. A., Kirshenbaum, K., Seurynck, S., Zuckermann, R., and Barron, A. E. (2004) Versatile oligo (N-substituted) glycines: the many roles of peptoids in drug discovery, in Pseudo-<strong>Peptide</strong>s in <strong>Drug</strong> Development (Neilsen, P. E., ed.), Wiley- VCH, Weinheim, pp. 1–31. 74. Kwon, Y. U., and Kodadek, T. (2007) Quantitative evaluation of the relative cell permeability of peptoids and peptides. J. Am. Chem. Soc. 129, 1508–1509. 75. Schröder, T., Schmitz, K., Niemeier, N., et al. (2007) Solid-phase synthesis, bioconjugation, and toxicology of novel cationic oligopeptoids for cellular drug delivery. Bioconjugate Chem. ASAP Article; DOI: 10.1021/bc0602073. 76. Miller, S. M., Simmon, R. J., Ng, S., Zuckermann, R. N., Kerr, J. M., and Moos, W. H. (1995) Comparison of the proteolytic susceptibilities of homologous L-amino acid, D-amino acid, and N-substituted glycine peptide and peptoid oligomers. <strong>Drug</strong> Dev. Res. 35, 20–32. 77. Stawikowski, M., Stawikowska, R., Jaskiewicz, A., Zablotna, E., and Rolka, K. (2005) Examples of peptide-peptoid hybrid serine protease inhibitors based on the trypsin inhibitor SFTI-1 with complete protease resistance at the P1-P1’ reactive site. Chembiochem. 6, 1057–1061. 78. Simon, R. J., Kania, R. S., Zuckermann, R. N., et al. (1992) Peptoids: a modular approach to drug discovery. Proc. Natl. Acad. Sci. USA 89, 9367–9371. 79. Kruijtzer, J. A. W., Hofmeyer, L. J. F., Heerma, W., Versluis, C., and Liskamp, R. M., J. (1998) Solid-phase syntheses of peptoids using Fmoc-protected N-substituted glycines: the synthesis of (retro)peptoids of Leu-enkephalin and substance P. Chem.Eur.J. 4, 1570–1580. 80. Uno, T., Beausoleil, E., Goldsmith, R. A., Levine, B.H., and Zuckermann, R. N. (1999) New submonomers for poly N-substituted glycines (peptoids). Tetrahedron Lett. 40, 1475–1478. 81. Zuckermann, R. N., Kerr, J.M., Kent, S. B. H., and Moos, W. H. (1992) Efficient method for the preparation of peptoids oligo(N-substituted glycines) by submonomer solid-phase synthesis. J. Am. Chem. Soc. 114, 10646–10647. 82. Ostergaard, S., and Holm, A. (1997) Peptomers: a versatile approach for the preparation of diverse combinatorial peptidomimetic bead libraries. Mol. Diver. 3, 17–27. 83. Boeijen, A., and Liskamp, R. M. J. (1998) Sequencing of peptoid peptidomimetics by Edman degradation. Tetrahedron Lett. 39, 3589–3592. 84. Greene, W. T., and Wuts, G. M. P. (1999) Protective Groups in Organic Synthesis, 3rd ed., John Wiley & Sons, Inc., New York, p. 198. 85. Bernatowicz, M. S., Daniels, S. B., and Koster, H. (1989) A comparison of acid labile linkage agents for the synthesis of peptide C-terminal amides. Tetrahedron Lett. 30, 4645–4648.
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Peptide-Based Drug Design
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METHODS IN MOLECULAR BIOLOGY TM Pep
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Preface Natural products chemistry
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Contents Preface...................
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Contributors Nikolinka Antcheva •
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Contributors xi Alessandro Tossi
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2 Otvos advance of computer power a
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4 Otvos see derivatives active in b
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6 Otvos was designed based on ligan
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8 Otvos 27. Borghouts, C., Kunz, C.
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10 Bulet Key Words: Invertebrate im
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12 Bulet 6. 5 �L or higher volume
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14 Bulet 2.5.2.1. MALDI-TOF-MS 1. M
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16 Bulet 7. Small-volume low-protei
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18 Bulet 3. Centrifuge between 8000
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20 Bulet internal diameter). Increa
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22 Bulet interest. As no instrument
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24 Bulet 3. Incubate the plates in
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26 Bulet bioactive peptides from th
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28 Bulet 21. Chernysh, S., Kim, S.I
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3 Sequence Analysis of Antimicrobia
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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Sequence Analysis of Antimicrobial
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4 The Spot Technique: Synthesis and
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The Spot Technique 49 3. For amine
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The Spot Technique 51 2. Biotinylat
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The Spot Technique 53 the solutions
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The Spot Technique 55 solution. Ens
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The Spot Technique 57 (see Fig. 3)
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The Spot Technique 59 Fig. 5. Princ
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The Spot Technique 61 library, the
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The Spot Technique 63 7. Regenerati
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The Spot Technique 65 following rul
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The Spot Technique 67 20. Atherton,
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The Spot Technique 69 50. Bolger, G
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5 Analysis of A� Interactions Usi
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Analysis of Aβ Interactions 73 are
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Analysis of Aβ Interactions 75 Ana
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Analysis of Aβ Interactions 77 3.
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Analysis of Aβ Interactions 79 4.
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Analysis of Aβ Interactions 81 5.
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Analysis of Aβ Interactions 83 2.
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Analysis of Aβ Interactions 85 9.
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6 NMR in Peptide Drug Development J
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NMR of Peptides 89 usually require
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NMR of Peptides 91 limiting the siz
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NMR of Peptides 93 and STD NMR expe
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NMR of Peptides 95 The basis of the
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NMR of Peptides 97 Fig. 5. Overlay
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NMR of Peptides 99 Fig. 7. Schemati
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NMR of Peptides 101 4.4.2. Saturati
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NMR of Peptides 103 4.6. Diffusion
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NMR of Peptides 105 Fig. 13. Propos
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NMR of Peptides 107 protein prevent
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NMR of Peptides 109 6. Wuthrich, K.
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NMR of Peptides 111 45. Morris, K.
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NMR of Peptides 113 78. Aumailley,
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116 Copps et al. Fig. 1. Potential
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118 Copps et al. Fig. 2. Flowchart
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120 Copps et al. 10. In accordance
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122 Copps et al. Fig. 3. DSSP for g
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124 Copps et al. ingly with the sam
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126 Copps et al. 19. Essman, U., Pe
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128 Hilpert et al. Key Words: Scree
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130 Hilpert et al. Table 1 (Continu
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132 Hilpert et al. different natura
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134 Hilpert et al. wt A C D E F …
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136 Hilpert et al. methods primaril
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138 Hilpert et al. Table 2 (Continu
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140 Hilpert et al. Table 2 (Continu
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142 Hilpert et al. Table 2 (Continu
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144 Hilpert et al. Table 3 Summary
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146 Hilpert et al. Table 3 (Continu
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148 Hilpert et al. of substituting
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150 Hilpert et al. in models that c
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152 Hilpert et al. than control. Gi
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154 Hilpert et al. Table 4 Accuracy
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156 Hilpert et al. 25. Pini, A., Gi
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158 Hilpert et al. 55. Giacometti,
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9 Investigating the Mode of Action
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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10 Serum Stability of Peptides Håv
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Serum Stability of Peptides 179 2.
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Serum Stability of Peptides 181 9.
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Serum Stability of Peptides 183 �
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Serum Stability of Peptides 185 13.
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11 Preparation of Glycosylated Amin
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Index 297 phosphopeptides influenci
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Index 299 for genetically synthetic
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Index 301 peptidosulfonamide, disad
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Index 303 solid phase, 180, 214 sul