Peptide-Based Drug Design

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Index 301 peptidosulfonamide, disadvantage of, 227 schematic representation of, 225 Peptidosulfonamides assembly of, methods for, 226 peptidomimetics, disadvantage of, 227 synthesis of, 223–225 solid-phase, 230 Peptoids assembly of, methods for, 226 peptide-peptoid hybrid synthesis and, 238 polymer class represented by, 238 sequencing of, 240 synthesis of, 223 methods for, 239 Peptomers assembly of, methods for, 226 sequencing of, 240 synthesis of, 224 Pharmacokinetics, 182 Phosphoamino acids direct incorporation of derivatives of Fmoc, 211 partially protected, 211 Phosphonopeptides assembly of, methods for, 226 synthesis of, 223 Phosphopeptides as cocrystallized, 217 disease-specific changes influenced by, 209 methods for synthesis by Fmoc chemistry of, 214 MS and, 216, 219 O-, solid phase synthesis of, 209–217 synthesis of, 214 synthetic, analysis of, 216 Phosphorylation global, 215 of hydroxyl groups, 209 of partially protected peptides, 212 Phosphothreonine, 214 Phosphotyrosine, 214 Photo-induced cross-linking of unmodified proteins (PICUP) assays, method, 74 PICUP assays. See Photo-induced cross-linking of unmodified proteins assays Plasmids, 171, 277–279 See Projections to latent structures Polypeptides, 276–277 Polypropylene rod, peptides bound to, 57 Principal component analysis (PCA), 136 Projections to latent structures (PLS), 136 Proline-rich antimicrobial peptides (PRPs) biological membranes as crossed by, 162 characteristics of, 161–162 E. coli mutants resistant to, 165–166, 169 genomic DNA libraries and, 166 mode of action of, 161–171 molecular interactions of, methods for identifying, 165–173 resistance, 163–164, 167–169, 171 characterization of, 164 resistant mutant clones, 164–165 characterization of, 167 resistant mutant clones’ degree of resistance, 167 ProteinChip technology arrays, 73–74, 76–80 A� capture and quantitation using antibody-coated arrays of, 76–80 A� interactions analysis using, 71–83 method of, 73 Proteins. See also Amyloid precursor protein; Glycoproteins; Major histocompatibility complex proteins AP-labeled, 50, 63 biotin labeling of samples of, 50, 63–64 chemical shifts for, 95 chemiluminescence and, 50 Cys-tagged, 276–285 site-specific conjugation to, 279–280 drugs in human disease treatment, 10 expression, 285–286 fusion Cys-tag for site-specific modification of targeting, 276–277 glycosylation of, 189 HRP-labeled, 50, 63 imaging/therapeutic agents coupled to, 276–277 M2, 263 mammalian, 209 modifications via novel Cys-tag of, 276 native, 264 producing, 263 peptide interactions with, 47 protein conjugation, 285, 289–290 purification, 285–287 site-specifically biotinylated Cys-tagged, 282–283 staining and, 63 targeted, 162 targeted into liposomes, lipidation for insertion of, 286 therapeutics, 185 transport, 162 use of Cys-tagged, 280–282 PRPs. See Proline-rich antimicrobial peptides
302 Index Purification of immune-defense peptides, 13, 18–20 of natural bioactive peptides, 18–20 peptides, 13, 18–20, 270 protein, 285–287 Purity control, 13 Q QSAR. See Quantitative structure-activity relationships Quantitative structure-activity relationships (QSAR) AMPs’ activity predicted by, 135–154 antibacterial peptides modeled by, 135–136, 150–154 descriptors, 135, 148–149 used for AMPs studies, 137–143, 150–151 essential assumption of, 135 inductive analysis of, 127 inductive descriptors, 149–154 of lactoferricin derivatives, 136, 147, 149 limitations of current studies with, 148–149 peptides’ activities and, 151 peptides as modeled by, 127 of protegrin analogues, 147–148 of scrambled bactenecin-derived peptides, 148 in screening program, 135 studies of AMPs, 137–146 R Radiolabeled tracers, 280–281, 290 REMD. See Replica Exchange Molecular Dynamics Replica Exchange Molecular Dynamics (REMD) MD simulation and, 120–121 parallel computing required by, 124 simulation methods for, 121 RMSD. See Root-mean-square deviation RNA hairpin, bound peptides, 106–107 Rocking shaker, 51 Root-mean-square deviation (RMSD), analysis, 122 S Saccharide, 191 Saturation transfer difference (STD), NMR, 100–101 Self-adjusting lipopeptides immunogenicity of, 247 Th1-/Th2- type immune responses induced by, 247 TLR-2 used for targeting/signaling by, 247 Sequencing. See also Edman sequencing amino acid, 21, 134 gene, 72 of peptides, 13, 31–46 of peptoids, 240 of peptomers, 240 SOM230, 5 Spectroscopy. See also Circular dichoism spectroscopy Spot synthesis on cellulose, 47–64 for screening peptides, 133 manual, 51 outline of, 51–52 of peptide array, 53–55 of peptide macroarrays on cellulose membranes, 47–64 of peptides, 47–64 screening techniques and, 48–49 substitution analysis performed by, 133–135 STD. See Saturation transfer difference Substitution analysis, 57 example of, 58 by Spot synthesis, 57 Sulfonilchloride methodology, 229 synthesis, 228 Synthesis. See also Spot synthesis by biological process, 132 of depsipeptides, 223, 236 ¥ Fmoc-based phosphopeptide, 210 of glycopeptides, 187, 189, 191 of glycoproteins, 187, 189 of glycosides, 193, 195, 200, 205 glycosylamine, 200 glycosylated amino acids, 187–198 of immunocontraceptive lipopeptide vaccine, 247 of lipopeptides, 249–254 manual peptide, 250 of multiepitope vaccine construct, 263–267 of N-glycosylated amino acids, 199 of O-glycosylated amino acids, 193 of oligoureas, 223, 233 peptide drug manufacturing and chemical, 4 peptide-peptoid hybrid, 238 of peptides, 47, 132, 167–168, 178 methods for, 179 peptides’ multiple solid phase, 214 of peptidosulfonamides, 223–226 of peptoids, 223 methods for, 239 of peptomers, 224 of phosphonopeptides, 223, 230 of phosphopeptides, 214
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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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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
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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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Page 310: Index 303 solid phase, 180, 214 sul
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