Peptide-Based Drug Design

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138 Hilpert et al. Table 2 (Continued) Descriptor Ref. symbols a (number) Explanation log P Hydration potential or free energy of transfer from vapor phase to water logD Salt chromotography dG Partition coefficient for amino acids in octanol/water — Partition coefficient for acetylamide derivatives ofamino acids in octanol/water dG = RTln f; f = fraction buried/accessible amino acids HPLC retention times for nine combinations of three different pH and three eluent mixtures (9 descriptors) Lejon et al., 2001 (3) a Lejon et al., 2004 Jenssen et al., z1 First principal component of Hellberg et al., 2005 1987, related to hydrophilicity z2 Second principal component of Hellberg et al., 1987, related to bulk z3 Second principal component of Hellberg et al., 1987, related to electronic properties Frecer et al., 2004 (3) Qm Total charge AI � o/w Amphipathicity Lipophilicity index Frecer, 2006 (25) Q Total charge L Overall lipophilicity P, N Lipophilicity of polar and nonpolar faces Sp,Sn Surface area of polar and nonpolar faces Mw, MwP,MwN Molecular mass of polar and nonpolar faces CSL, CHL ,CAR Count of small lipophilic, highly lipophilic and aromatic residues forming the nonpolar face total number of hydrogen bond donor and acceptor centers
Cationic Antimicrobial <strong>Peptide</strong>s 139 Ostberg and Kaznessis, 2005 Hilpert et al.,2006 HBdon, HBacc Number of hydrogen bond donors and acceptors RotBon Total number of rotatable bonds P/L, P/N, L/N, A-phipathicity descriptors based on other Q/L, Q/N, SP/SN, MwP/MwN,,Q/CSL, Q/CHL and Q/CAR (18) descriptors MWEI Molecular weight CHRG Formal charge SASA Solvent accessible surface area FOSA Hydrophobic component of SASA NESA Negative component of SASA POSA Positive component of SASA EELE Electrostatic portion of potential energy ESOL Energy change of solvation in water EVDW Van der Waals portion of potential energy FLEX KierFlex; flexibility of the peptide DIPO Dipole moment of peptide PMOI Principle moment of inertia HBAC Number of hydrogen bond acceptors HBDN Number of hydrogen bond donors MVOL Molecular volume DENS Density of the peptide GLOB Globularity of peptide LOGP Octanol/water partition coefficient (51) D1, D2, D3 Distance between the first and second arginines, the second and third, and the third and fourth, measured as number of residues Dmax,Davg Maximum and average distance between any two consecutive arginines ASA H Water accessible surface are of all hydrophobic atmons S3x, S4x, S5x Hydrophobicity using Eisenberg scale over 3, 4, or 5 residues, for each residue position (x varies from 1 to 12, the length of the peptides) S3max, S3min, Hydrophobicity maximum and minimum values S4max, S4min, S5max, S5min using Eisenberg scale Maximal stretch of hydrophobic residues (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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Page 98 and 99: 6 NMR in Peptide Drug Development J
Page 100 and 101: NMR of Peptides 89 usually require
Page 102 and 103: NMR of Peptides 91 limiting the siz
Page 104 and 105: NMR of Peptides 93 and STD NMR expe
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 154 and 155: 144 Hilpert et al. Table 3 Summary
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
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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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