Peptide-Based Drug Design

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144 Hilpert et al. Table 3 Summary of Results of QSAR Studies on Antimicrobial Activity Number of Predicted to descriptors (set Accuracy of observed Ref. Models size) a Data description Methodb Data size predictionsc correlation(R2 ) d nd LOO 20 Plot of predicted to observed MICs shows good correlation 12 Lactoferricin from bovine (LFB) Principal component analysis (PCA) Strom et al., 2001 (73) Lactoferricin from murine (LFM) 18 derivatives of LFM that varied at up to 4 positions. Projections to latent structures (PLS) nd 20 Good correlation visible in plot Single training set 12 Lactoferricin from bovine (LFB) Lactoferricin from murine (LFM), plus 18 derivatives of LFM that varied at up to 4 positions (same data as Strom et al., 2001) Projections to latent structures (PLS) Lejon et al., 2001 (71) 0.957 (E. coli) 0.924 (S. aureus) 11 Prediction of 2 peptides E. coli and S. aureus outside training set was poor 15 LFB derivatives Single training set Projections to latent structures (PLS) Lejon et al., 2004 (72)
Cationic Antimicrobial <strong>Peptide</strong>s 145 0.966 (E. coli) 0.905 (S. aureus) 23 Prediction of 2 peptides E.coli and S. aureus outside training set was poor 50 Prediction of 1 peptide for S. aureus was good 39 LFB derivatives Single training set Projections to latent structures (PLS) 0.79 (E. coli) 0.75 (S. aureus) Single training set 7 — 0.8989 (HSV-1) 0.8276 (HSV-2) Single training set 42 LFB, LFM, LFC (goat), LFH (human) derivatives 75 Lactoferricin derivatives PCA on all descriptors and biological response Projections to latent structures Jenssen et al., 2005 (74) LOO 7 — 0.98 3 Cyclic peptides similar to protegrin Multivariate linear regression Frecer et al., 2004 (76) 2 (25) Potegrin 1 derivatives LOO 97 — 0.604 55 — 0.69 5 (18) Protegrin 1 derivatives Single training set Frecer, Mulitple linear 2006 regression chosen (77) using genetic function approximation (GFA) allowing up to 5 descriptors in the final models Ostberg Multiple linear regression and using the most Kaznessis, statistically significant 2005 combinations of (78) descriptors (Continued)
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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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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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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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Page 106 and 107: NMR of Peptides 95 The basis of the
Page 108 and 109: NMR of Peptides 97 Fig. 5. Overlay
Page 110 and 111: NMR of Peptides 99 Fig. 7. Schemati
Page 112 and 113: NMR of Peptides 101 4.4.2. Saturati
Page 114 and 115: NMR of Peptides 103 4.6. Diffusion
Page 116 and 117: NMR of Peptides 105 Fig. 13. Propos
Page 118 and 119: NMR of Peptides 107 protein prevent
Page 120 and 121: NMR of Peptides 109 6. Wuthrich, K.
Page 122 and 123: NMR of Peptides 111 45. Morris, K.
Page 124 and 125: NMR of Peptides 113 78. Aumailley,
Page 126 and 127: 116 Copps et al. Fig. 1. Potential
Page 128 and 129: 118 Copps et al. Fig. 2. Flowchart
Page 130 and 131: 120 Copps et al. 10. In accordance
Page 132 and 133: 122 Copps et al. Fig. 3. DSSP for g
Page 134 and 135: 124 Copps et al. ingly with the sam
Page 136 and 137: 126 Copps et al. 19. Essman, U., Pe
Page 138 and 139: 128 Hilpert et al. Key Words: Scree
Page 140 and 141: 130 Hilpert et al. Table 1 (Continu
Page 142 and 143: 132 Hilpert et al. different natura
Page 144 and 145: 134 Hilpert et al. wt A C D E F …
Page 146 and 147: 136 Hilpert et al. methods primaril
Page 158 and 159: 148 Hilpert et al. of substituting
Page 160 and 161: 150 Hilpert et al. in models that c
Page 162 and 163: 152 Hilpert et al. than control. Gi
Page 164 and 165: 154 Hilpert et al. Table 4 Accuracy
Page 166 and 167: 156 Hilpert et al. 25. Pini, A., Gi
Page 168 and 169: 158 Hilpert et al. 55. Giacometti,
Page 170 and 171: 9 Investigating the Mode of Action
Page 172 and 173: Proline-Rich Antimicrobial Peptides
Page 186 and 187: 10 Serum Stability of Peptides Håv
Page 188 and 189: Serum Stability of Peptides 179 2.
Page 192 and 193: Serum Stability of Peptides 183 �
Page 196 and 197: 11 Preparation of Glycosylated Amin
Page 198 and 199: Glycosylated Amino Acid Synthesis 1
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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
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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.,
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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
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Index 303 solid phase, 180, 214 sul
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