Peptide-Based Drug Design

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Contents Preface............................................................ v Contributors....................................................... ix 1. Peptide-BasedDrugDesign:HereandNow..................... Laszlo Otvos, Jr. 1 2. Strategies for the Discovery, Isolation, and Characterization of Natural Bioactive Peptides from the Immune System ofInvertebrates.............................................. Philippe Bulet 9 3. Sequence Analysis of Antimicrobial Peptides by Tandem Mass Spectrometry................................................ Christin Stegemann and Ralf Hoffmann 31 4. The Spot Technique: Synthesis and Screening of Peptide MacroarraysonCelluloseMembranes....................... Dirk F.H. Winkler and William D. Campbell 47 5. Analysis of A� Interactions Using ProteinChip Technology . . . . . . Eleni Giannakis, Lin-Wai Hung, Keyla Perez Camacaro, David P. Smith, Kevin J. Barnham, and John D. Wade 71 6. NMR in Peptide Drug Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . Jan-Christoph Westermann and David J. Craik 87 7. Molecular Dynamics Simulations of Peptides . . . . . . . . . . . . . . . . . . . 115 Jeffrey Copps, Richard F. Murphy, and Sandor Lovas 8. Short Linear Cationic Antimicrobial Peptides: Screening, Optimizing,andPrediction.................................. 127 Kai Hilpert, Christopher D. Fjell, and Artem Cherkasov 9. Investigating the Mode of Action of Proline-Rich Antimicrobial Peptides Using a Genetic Approach: A Tool to Identify New Bacterial Targets Amenable to the Design of NovelAntibiotics............................................161 Marco Scocchi, Maura Mattiuzzo, Monica Benincasa, Nikolinka Antcheva, Alessandro Tossi, and Renato Gennaro 10. Serum Stability of Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 Håvard Jenssen and Stein Ivar Aspmo vii
viii Contents 11. Preparation of Glycosylated Amino Acids Suitable for Fmoc Solid-PhaseAssembly....................................... 187 Mare Cudic and Gayle D. Burstein 12. Synthesis of O-Phosphopeptides on Solid Phase . . . . . . . . . . . . . . . . . 209 David Singer and Ralf Hoffmann 13. Peptidomimetics: Fmoc Solid-Phase Pseudopeptide Synthesis. . . . 223 Predrag Cudic and Maciej Stawikowski 14. Synthesis of Toll-Like Receptor-2 Targeting Lipopeptides as Self-Adjuvanting Vaccines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247 Brendon Y. Chua, Weiguang Zeng, and David C. Jackson 15. Synthesis of a Multivalent, Multiepitope Vaccine Construct . . . . . . 263 Laszlo Otvos, Jr. 16. Cysteine-Containing Fusion Tag for Site-Specific Conjugation of Therapeutic and Imaging Agents to Targeting Proteins . . . . . . 275 Marina V. Backer, Zoia Levashova, Richard Levenson, Francis G. Blankenberg, and Joseph M. Backer Index..............................................................295
Page 2 and 3: Peptide-Based Drug Design
Page 4 and 5: METHODS IN MOLECULAR BIOLOGY TM Pep
Page 6 and 7: Preface Natural products chemistry
Page 10 and 11: Contributors Nikolinka Antcheva •
Page 12 and 13: Contributors xi Alessandro Tossi
Page 14 and 15: 2 Otvos advance of computer power a
Page 16 and 17: 4 Otvos see derivatives active in b
Page 18 and 19: 6 Otvos was designed based on ligan
Page 20 and 21: 8 Otvos 27. Borghouts, C., Kunz, C.
Page 22 and 23: 10 Bulet Key Words: Invertebrate im
Page 24 and 25: 12 Bulet 6. 5 �L or higher volume
Page 26 and 27: 14 Bulet 2.5.2.1. MALDI-TOF-MS 1. M
Page 28 and 29: 16 Bulet 7. Small-volume low-protei
Page 30 and 31: 18 Bulet 3. Centrifuge between 8000
Page 32 and 33: 20 Bulet internal diameter). Increa
Page 34 and 35: 22 Bulet interest. As no instrument
Page 36 and 37: 24 Bulet 3. Incubate the plates in
Page 38 and 39: 26 Bulet bioactive peptides from th
Page 40 and 41: 28 Bulet 21. Chernysh, S., Kim, S.I
Page 42 and 43: 3 Sequence Analysis of Antimicrobia
Page 44 and 45: Sequence Analysis of Antimicrobial
Page 58 and 59:
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)
Page 70 and 71:
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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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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144 Hilpert et al. Table 3 Summary
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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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10 Serum Stability of Peptides Håv
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Serum Stability of Peptides 179 2.
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Serum Stability of Peptides 183 �
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11 Preparation of Glycosylated Amin
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Glycosylated Amino Acid Synthesis 1
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12 Synthesis of O-Phosphopeptides o
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Solid-Phase Synthesis of O-Phosphop
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13 Peptidomimetics: Fmoc Solid-Phas
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Peptidomimetics 225 O O R S N H Pep
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Peptidomimetics 227 not without its
Page 238 and 239:
Peptidomimetics 229 Oxidation step:
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Peptidomimetics 231 of peptidosulfo
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Peptidomimetics 233 8. Allow the re
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Peptidomimetics 235 3.3.2. Solid-Ph
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Peptidomimetics 237 On the other ha
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Peptidomimetics 239 nitrogen (73).
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Peptidomimetics 241 3. Cover the re
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Peptidomimetics 243 efficient synth
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Peptidomimetics 245 55. Alsina, J.,
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14 Synthesis of Toll-Like Receptor-
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Lipopeptides 249 2. Materials 2.1.
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Lipopeptides 251 Fig. 1. Structural
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Lipopeptides 253 8. To enable lipid
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Lipopeptides 255 Representative res
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Lipopeptides 257 Fig. 2. Immunogeni
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Lipopeptides 259 8. A large plastic
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Lipopeptides 261 26. Nardin, E.H.,
Page 272 and 273:
264 Otvos response, synthetic pepti
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266 Otvos Fig. 3. Schematic present
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268 Otvos 3. Methods The main goal
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270 Otvos 3.2.3. Purification and Q
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272 Otvos 6. Meyer, D., and Torres,
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16 Cysteine-Containing Fusion Tag f
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Targeted Therapeutic and Imaging Ag
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Index A A� peptides aggregation a
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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
Page 310:
Index 303 solid phase, 180, 214 sul
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