Peptide-Based Drug Design

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Contributors Nikolinka Antcheva • Department of Life Sciences, University of Trieste, Trieste, Italy Stein Ivar Aspmo • Recovery Development, Novozymes AS, Bagsvaerd, Denmark Joseph M. Backer • SibTech, Inc., Brookfield, CT Marina V. Backer • SibTech, Inc., Brookfield, CT Kevin J. Barnham • Department of Pathology, University of Melbourne, Victoria, Australia, and The Mental Health Research Institute of Victoria, Parkville, Victoria, Australia Monica Benincasa • Department of Life Sciences, University of Trieste, Trieste, Italy Francis G. Blankenberg • Department of Pediatrics & Division of Nuclear Medicine/Department of Radiology & MIPS (Molecular Imaging Program at Stanford,) Stanford University, Stanford, CA Philippe Bulet • TIMC-IMAG, UMR5525 UFF CNRS, Archamps, France Gayle D. Burstein • Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL Keyla Perez Camacaro • Department of Pathology, University of Melbourne, Victoria, Australia William D. Campbell • Biomime Solutions, Inc., Surrey, British Columbia, Canada Artem Cherkasov • Division of Infectious Diseases, Faculty of Medicine, University of British Columbia Vancouver, British Columbia, Canada Brendon Y. Chua • Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia Jeffrey Copps • Department of Biomedical Sciences, Creighton University, Omaha, NE David J. Craik Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia Mare Cudic • Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL Predrag Cudic • Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL Christopher D. Fjell • Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada ix
x Contributors Renato Gennaro • Department of Life Sciences, University of Trieste, Trieste, Italy Eleni Giannakis • Howard Florey Institute, University of Melbourne, Parkville, Victoria, Australia; and Bio-Rad Laboratories, Hercules, CA Kai Hilpert • Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada Ralf Hoffmann • Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany Lin-Wai Hung • Howard Florey Institute and Department of Pathology, University of Melbourne, Parkville, Victoria, Australia David C. Jackson • Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia HÅvard Jenssen Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada Zoia Levashova • Department of Pediatrics & Division of Nuclear Medicine/Department of Radiology & MIPS (Molecular Imaging Program at Stanford), Stanford University, Stanford, CA Richard Levenson • Biomedical Systems, CRI, Inc., Woburn, MA SÁndor Lovas • Department of Biomedical Sciences, Creighton University, Omaha, NE Maura Mattiuzzo • Department of Life Sciences, University of Trieste, Trieste, Italy Richard F. Murphy • Department of Biomedical Sciences, Creighton University, Omaha, NE Laszlo Otvos, Jr. • Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA Marco Scocchi • Department of Life Sciences, University of Trieste, Trieste, Italy David Singer • Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany David P. Smith • Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; and Mental Health Research Institute of Victoria, Parkville, Victoria, Australia Maciej Stawikowski • Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL Christin Stegemann • Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
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 8 and 9: Contents Preface...................
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)
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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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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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Peptide-Based Drug Design

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