Peptide-Based Drug Design

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Proline-Rich Antimicrobial Peptides 175 6. Gennaro, R., Zanetti, M., Benincasa, M., Podda, E. and Miani, M. (2002) Pro-rich antimicrobial peptides from animals: structure, biological functions and mechanism of action. Curr. Pharm. Des. 8, 763–778. 7. Otvos, L., Jr. (2002) The short proline-rich antibacterial peptide family. Cell Mol. Life Sci. 59, 1138–1150. 8. Podda, E., Benincasa, M., Pacor, S., Micali, F., Mattiuzzo, M., Gennaro, R. and Scocchi, M. (2006) Dual mode of action of Bac7, a proline-rich antibacterial peptide. Biochim. Biophys. Acta 1760, 1732–1740. 9. Cudic, M. and Otvos, L., Jr. (2002) Intracellular targets of antibacterial peptides. Curr. Drug Targets 3, 101–106. 10. Otvos, L., Jr., Rogers, M. E., Consolvo, P. J., Condie, B. A., Lovas, S., Bulet, P. and Blaszczyk-Thurin, M. (2000) Interaction between heat shock proteins and antimicrobial peptides. Biochemistry 39, 14150–14159. 11. Kragol, G., Lovas, S., Varadi, G., Condie, B. A., Hoffmann, R. and Otvos, L., Jr. (2001) The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding. Biochemistry 40, 3016–3026. 12. Boman, H. G., Agerberth, B. and Boman, A. (1993) Mechanisms of action on Escherichia coli of cecropin P1 and PR-39, two antibacterial peptides from pig intestine. Infect. Immun. 61, 2978–2984. 13. Shi, Y., Cromie, M. J., Hsu, F. F., Turk, J. and Groisman, E. A. (2004) PhoPregulated Salmonella resistance to the antimicrobial peptides magainin 2 and polymyxin B. Mol. Microbiol. 53, 229–241. 14. Mattiuzzo, M., Bandiera, A., Gennaro, R., Benincasa, M., Pacor, S., Antcheva, N. and Scocchi, M. (2007) Role of the Escherichia coli SbmA in the antimicrobial activity of proline-rich peptides. Mol. Microbiol. 66, 151–163. 15. Tossi, A., Scocchi, M., Zanetti, M., Gennaro, R., Storici, P. and Romeo, D. (1997) An approach combining rapid cDNA amplification and chemical synthesis for the identification of novel, cathelicidin-derived, antimicrobial peptides. Methods Mol. Biol. 78, 133–150. 16. Miller, J. H. (1992) A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Volume 1. Cold Spring Harbor Laboratory Press, New York. 17. Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, New York 18. Chen, W. P. and Kuo, T. T. (1993) A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res. 21, 2260. 19. Dower, W. J., Miller, J. F. and Ragsdale, C. W. (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16, 6127–6145. 20. Benincasa, M., Scocchi, M., Podda, E., Skerlavaj, B., Dolzani, L. and Gennaro, R. (2004) Antimicrobial activity of Bac7 fragments against drug-resistant clinical isolates. Peptides 25, 2055–2061. 21. Lavina, M., Pugsley, A. P. and Moreno, F. (1986) Identification, mapping, cloning and characterization of a gene (sbmA) required for microcin B17 action on Escherichia coli K12. J. Gen. Microbiol. 132, 1685–1693.
176 Scocchi et al. 22. Salomon, R. A. and Farias, R. N. (1995) The peptide antibiotic microcin 25 is imported through the TonB pathway and the SbmA protein. J. Bacteriol. 177, 3323–3325. 23. Yorgey, P., Lee, J., Kordel, J., Vivas, E., Warner, P., Jebaratnam, D. and Kolter, R. (1994) Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor. Proc. Natl. Acad. Sci. U S A 91, 4519–4523. 24. Locher, K. P., Lee, A. T. and Rees, D. C. (2002) The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296, 1091–1098. 25. de Cristobal, R. E., Solbiati, J. O., Zenoff, A. M., Vincent, P. A., Salomon, R. A., Yuzenkova, J., Severinov, K. and Farias, R. N. (2006) Microcin J25 uptake: His5 of the MccJ25 lariat ring is involved in interaction with the inner membrane MccJ25 transporter protein SbmA. J. Bacteriol. 188, 3324–3328. 26. Meacham, K. J., Zhang, L., Foxman, B., Bauer, R. J. and Marrs, C. F. (2003) Evaluation of genotyping large numbers of Escherichia coli isolates by enterobacterial repetitive intergenic consensus-PCR. J. Clin. Microbiol. 41, 5224–5226.
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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
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
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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
Page 198 and 199: Glycosylated Amino Acid Synthesis 1
Page 218 and 219: 12 Synthesis of O-Phosphopeptides o
Page 220 and 221: Solid-Phase Synthesis of O-Phosphop
Page 232 and 233: 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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