Peptide and Protein Design for Biopharmaceutical Applications

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ISBN: 9780470319611 | 0470319615
Cover: Hardcover
Copyright: 11/9/2009

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Peptides serve as effective drugs in the clinic today, with researchers developing new methods to create ls"tailor-maders" peptides and proteins with improved pharmacological properties. This one-volume reference includes real-life case studies and contributions from international experts, and provides a comprehensive overview of the experimental and computational methods for peptide and protein design, with an emphasis on specific applications for therapeutics and biomedical research. Design of Peptides and Proteins for Biopharmaceutical Applications is essential for scientists in peptide and protein drug design, biomedicine, biochemistry, biophysics, molecular modeling, synthetic organic chemistry, and medicinal/pharmaceutical chemistry.

List of Contributors	p. ix
Preface	p. xi
Introduction	p. 1
Computational Approaches in Peptide and Protein Design: An Overview	p. 5
Introduction	p. 5
Basics and Tools	p. 6
The Importance of Computational Approaches	p. 6
Tools and Procedures: Force Fields and Sampling	p. 9
Computational Study of Cyclopentapeptide Inhibitors of CXCR4	p. 31
The 3D Pharmacophore Model for FC131	p. 32
A 3D Model of the TM Region of CXCR4	p. 36
Docking of FC131 to CXCR4	p. 39
Acknowledgements	p. 42
References	p. 42
Aspects of Peptidomimetics	p. 49
Introduction	p. 49
Modified Peptides	p. 51
Pseudopeptides	p. 65
Secondary Structure Mimics (Excluding Turn Mimics)	p. 75
ß-strand Mimetics	p. 75
Helix Mimetics	p. 87
Examples of Peptidomimetics	p. 92
Conclusion	p. 104
References	p. 105
Design of Cyclic Peptides	p. 133
Introduction	p. 133
Pharmaceutical Research Today	p. 133
General Advantages of Cyclic Peptide Structures	p. 134
Examples of Cyclic Peptides of Medicinal Interest	p. 135
General Considerations	p. 137
Peptide Cyclization	p. 138
Possibilities of Peptide Cyclization	p. 138
Synthesis of Cyclic Peptides	p. 139
Chemical Modifications of Cyclic Peptides	p. 141
Concluding Remarks	p. 146
Conformation and Dynamics of Cyclic Peptides	p. 146
Reductions in Conformational Space	p. 146
Conformational Arrangements in Cyclic Structures	p. 148
Flexibility of Cyclized Scaffolds	p. 151
Experimental Structure Characterization	p. 152
Concepts in the Rational Design of Cyclic Peptides	p. 154
The Influence of Amino Acid Composition	p. 154
The Dunitz-Waser Concept	p. 155
The Spatial Screening Technique	p. 156
General Strategy for Finding Active Hits	p. 157
Examples of Cyclic Peptides as Drug Candidates	p. 159
Cilengitide as Integrin Inhibitor	p. 159
CXCR4 Antagonists	p. 163
Sandostatin and the Veber-Hirschmann Peptide as Examples of Rational Design	p. 164
Conclusion	p. 166
References	p. 166
Carbohydrates in Peptide and Protein Design	p. 177
Introduction	p. 177
Configurational and Conformational Properties of Carbohydrates	p. 178
Carbohydrates in Peptidomimetics	p. 181
Glycopeptides	p. 183
Carbohydrates as Scaffolds in the Design of Nonpeptide Peptidomimetics	p. 185
Sugar Amino Acids	p. 187
Cyclodextrin-Peptide Conjugates	p. 193
Carboproteins: Protein Models on Carbohydrate Templates	p. 198
Conclusion	p. 199
References	p. 200
De Novo Design of Proteins	p. 207
Introduction	p. 207
Secondary Structure Elements	p. 208
The ¿-helix	p. 208
The ß-sheet	p. 214
Loops, Turns and Templates	p. 214
Assembling a Specified Tertiary Structure from Secondary Structural Elements	p. 215
Computational Methods	p. 215
Coiled Coils	p. 216
¿-helical Bundles	p. 220
Fluorous Interactions	p. 225
Additional Topics	p. 228
Proteins on Templates	p. 229
Foldamers	p. 234
Biopharmaceutical Applications of De Novo Design	p. 236
¿-helical Structures in Biopharmaceutical Applications	p. 236
Foldamers in Biopharmaceutical Applications	p. 238
References	p. 238
Design of Insulin Variants for Improved Treatment of Diabetes	p. 249
Introduction	p. 249
Diabetes Management and the Need for Insulin Engineering	p. 251
Insulin Structure	p. 256
Prolonged-acting Insulin Solids	p. 258
Prolonged-acting Insulin Solutions	p. 259
Fast-acting Insulins	p. 265
Glucose-sensitive Insulin Preparations	p. 267
Alternative Insulin Delivery	p. 271
Insulin Mimetics	p. 272
Pushing the Limits of Insulin Engineering	p. 273
Conclusion	p. 274
References	p. 275
Index	p. 287
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