Chemical approaches to the synthesis of peptides and proteins

Cover......Page 1
Half Title......Page 2
Series Page......Page 3
Title Page......Page 4
Copyright Page......Page 5
About the Authors......Page 6
Preface......Page 8
Table of Contents......Page 10
Chapter 1: Introduction......Page 18
 1.1 Amino Acids and Peptide and Protein Structure......Page 20
 1.2 Amino Acid Activation and Coupling......Page 21
  1.2.1 Acid Azides, Acid Halides, and Anhydrides......Page 23
  1.2.3 Coupling Reagents......Page 24
 1.3 Protection Schemes for Peptide Synthesis......Page 25
  1.3.1 Nα Protection......Page 27
  1.3.3 Protection of the C-Terminus......Page 28
  1.4.1 Synthesis in Solution......Page 29
  1.4.2 Solid-Phase Peptide Synthesis......Page 30
  1.4.3 SPPS vs. Synthesis in Solution......Page 32
 References......Page 33
 2.1 The Solid Support......Page 36
  2.1.2 Polyamide......Page 37
 2.2 Protection Schemes......Page 38
  2.2.1 Nα Protection......Page 39
  2.2.2 Side Chain Protection of Individual Amino Acids......Page 40
   2.2.2.1 Lysine and Ornithine......Page 41
   2.2.2.2 Arginine......Page 43
   2.2.2.3 Histidine......Page 45
   2.2.2.4 Tryptophan......Page 48
   2.2.2.5 Asparagine and Glutamine......Page 49
   2.2.2.6 Aspartic and Glutamic Acids......Page 50
   2.2.2.7 Serine and Threonine......Page 52
   2.2.2.8 Tyrosine......Page 53
   2.2.2.9 Methionine......Page 54
   2.2.2.10 Cysteine......Page 56
 2.3 Attachment of the First Amino Acid to the Solid Support......Page 58
  2.3.1 Peptide Acids......Page 59
  2.3.2 Peptide Amides......Page 62
  2.3.3 Side Chain and Backbone Amide Anchoring......Page 63
   2.4.1.1 Carbodiimides......Page 65
   2.4.1.2 Phosphonium and Uronium Reagents......Page 70
   2.4.1.3 Preformed Active Esters......Page 72
   2.4.1.4 Preformed Anhydrides......Page 73
   2.4.1.5 Amino Acid Halides......Page 75
    2.4.2.1.1 Formation of Diketopiperazines......Page 76
    2.4.2.1.2 Formation of Aspartimides......Page 78
    2.4.2.1.3 Formation of Pyroglutamic Acid......Page 80
    2.4.2.2.1 Deletion Peptides and Truncated Sequences......Page 81
    2.4.2.2.2 Difficult Sequences......Page 82
  2.4.3 On-Resin Monitoring of SPPS......Page 84
   2.4.3.2 The Ninhydrin Test......Page 85
   2.4.3.3 Amino Acid Analysis......Page 86
   2.4.3.4 Solid-Phase Edman Degradation......Page 87
   2.5.1.1 Liquid Hydrogen Fluoride......Page 88
   2.5.2.1 Alkylation......Page 89
   2.5.2.2 Undesired Cyclization Reactions......Page 90
   2.5.2.3 Other Side Reactions During Acidolytic Cleavage......Page 91
  2.6.1 Bovine Pancreatic Ribonuclease A......Page 92
  2.6.2 Human Immunodeficiency Virus Protease......Page 94
  2.6.3 Ubiquitin......Page 96
  2.6.4 ß-Amyloid Protein......Page 97
 References......Page 99
 3.1 Strategic Considerations......Page 112
 3.2 Protection Schemes......Page 113
  3.2.1 Na Protection......Page 114
  3.2.3 Protection of the C-Terminus......Page 116
    3.2.3.1.1 Benzyl and Substituted Benzyl Esters......Page 117
    3.2.3.1.2 Phenacyl Esters......Page 118
    3.2.3.1.4 Methyl and Substituted Methyl Esters......Page 119
    3.2.3.1.6 Phenyl Esters......Page 120
   3.2.3.2 Hydrazides......Page 121
  3.3.1 Amino Acid Coupling......Page 122
    3.3.1.2.1 Mixed Carboxylic Acid Anhydrides......Page 123
    3.3.1.2.2 Mixed Carbonic Acid Anhydrides......Page 124
    3.3.1.2.3 N-Carboxyanhydrides and Urethane N-Protected Carboxyanhydrides......Page 125
    3.3.1.2.4 Mixed Anhydrides with Acids Derived from Phosphorus......Page 126
   3.3.1.3 Active Esters......Page 127
   3.3.1.4 Carbodiimides......Page 128
   3.3.1.5 Phosphonium and Uronium Reagents......Page 129
   3.3.1.6 Acyl Halides......Page 130
   3.3.2.1 Racemization and Epimerization in Peptide Synthesis......Page 131
    3.3.2.1.1 Direct Enolization......Page 132
    3.3.2.1.2 Formation and Epimerization of 5(4H)-Oxazolones......Page 133
    3.3.2.2.1 Glycine and Proline as C-Terminal Amino Acids......Page 136
    3.3.2.2.2 Coupling Methods that Proceed with Minimal Racemization......Page 137
  3.3.3 Side Reactions during Chain Elongation......Page 138
 3,4 Final Removal of Protecting Groups......Page 139
  3.5.1 Use of Picolyl Ester-Protecting Groups......Page 140
   3.5.2.1 Repetitive Mixed Anhydride Approach......Page 141
  3.5.3 Liquid-Phase Peptide Synthesis......Page 142
  3.6.1 Porcine Gastrin I......Page 143
  3.6.3 Bovine Pancreatic Ribonuclease A......Page 144
 References......Page 147
Chapter 4: Convergent Approaches to the Synthesis of Large Peptides and Proteins......Page 156
 4.1 Convergent Solid-Phase Peptide Synthesis......Page 157
   4.1.1.1 Acidolytic Cleavage of Protected Peptides from the Solid Support......Page 158
    4.1.1.1.1 Highly Acid-Labile Handles and Resins......Page 159
    4.1.1.1.2 The Wang Resin......Page 160
    4.1.1.2.1 The Kaiser Oxime Resin......Page 161
    4.1.1.2.2 Cleavage of the Peptide–Resin Anchorage by a ß-Elimination Reaction......Page 162
    4.1.1.3.1 Nitrobenzyl Resins......Page 163
    4.1.1.3.2 Phenacyl Resins......Page 164
  4.1.2 Purification of Protected Peptide Segments......Page 165
    4.1.2.1.1 Structural Modification......Page 166
    4.1.2.1.2 Use of Special Solvents or Additives to Enhance Solubility......Page 167
    4.1.2.2.2 Reversed-Phase High-Performance Liquid Chromatography......Page 168
   4.1.3.1 The Solid Support......Page 170
   4.1.3.3 Incorporation of the First Segment......Page 171
   4.1.3.5 Side Reactions......Page 172
   4.1.4.1 Rat Atrial Natriuretic Factor......Page 173
   4.1.4.2 Prothymosin α......Page 174
   4.1.4.3  ß-amyloid Protein......Page 175
   4.1.4.4 The 3-repeat Region of Human Tau-2......Page 177
   4.1.4.5 The N-Terminal Repeat Region of γ-zein......Page 179
  4.2.1 Lipophilic Segment-Coupling Strategy......Page 181
 4.3 Coupling of Minimally Protected Peptides in Aqueous Solution......Page 182
  4.3.1 Activation of C-Terminal Thiocarboxyl or Thioester Groups......Page 183
    4.3.1.1.1 Bovine [Cys(Cam)14,17]-Apocytochrome C......Page 187
    4.3.1.1.2 α-Inhibin-92......Page 189
    4.3.1.1.3 DNA-Binding Protein of Bacillus174 stearothermophilus......Page 191
 4.4 Chemical Ligation of Peptide Segments......Page 192
   4.4.1.1 Chemical Ligation by Thioester or Thioether Formation......Page 193
   4.4.1.2 Chemical Ligation by Hydrazone or Oxime Formation......Page 198
  4.4.2 Segment Coupling by Prior Chemical Ligation......Page 201
   4.4.2.1 Template-Assisted Coupling......Page 203
   4.4.2.2 Native Chemical Ligation......Page 207
   4.4.2.3 Domain Ligation......Page 208
   4.4.3.1 Multiple Antigenic Peptides......Page 212
   4.4.3.2 Template-Assembled Synthetic Proteins......Page 214
 References......Page 217
Chapter 5: Formation of Disulfide Bridges......Page 226
  5.1.2 Intermolecular Disulfide Bridges......Page 227
 5.2 Protection of Cysteine in Peptide Synthesis......Page 228
  5.3.1 From Precursors with Free Sulfhydryl Groups......Page 231
  5.3.2 From Precursors with Protected Sulfhydryl Groups......Page 234
   5.3.3.1 Selective Activation of Cysteine Residues In Situ......Page 236
   5.3.3.2 Selective Activation that Gives a Stable, Isolable Intermediate......Page 237
   5.3.3.3 Use of the S-3-Nitro-2-Pyridinesulfenyl Group......Page 239
  5.4.1 Intramolecular Disulfide Bridges......Page 240
   5.4.2.1 Preparation of Parallel and Antiparallel Homodimers Linked by Two Disulfide Bridges......Page 244
   5.4.2.2 Insulin and Related Peptides......Page 245
 References......Page 248
Chapter 6: Peptide Libraries......Page 254
  6.1.1 Peptide Synthesis on Polyethylene Pins......Page 255
  6.1.2 Peptide Synthesis in Tea Bags......Page 259
  6.1.3 Peptide Synthesis on Special Solid Supports......Page 260
  6.1.4 Light-Directed, Spatially Addressable Parallel Peptide Synthesis......Page 261
 6.2 Peptide Library Techniques......Page 263
  6.2.1 Synthesis of Peptide Libraries by Coupling Mixtures of Amino Acids......Page 264
  6.2.2 Synthesis of Peptide Libraries by the Split-and-Combine Method......Page 265
  6.2.3 Peptide Library Deconvolution......Page 266
   6.2.3.1 The Dual-defined Method......Page 267
   6.2.3.2 The Positional Scanning Method......Page 268
   6.2.3.3 The Bogus Coin Method......Page 269
  6.2.4 One-Bead/One-Peptide Libraries......Page 270
   6.2.4.1 Screening of One-Bead/One-Peptide Libraries in Solution......Page 272
   6.2.4.2 Encoded Combinatorial Peptide Synthesis......Page 274
    6.2.4.2.1 Library Encoding with Oligonucleotides......Page 275
    6.2.4.2.2 Library Encoding with Peptides......Page 276
    6.2.4.2.3 Library Encoding with Aryl Halide Tags......Page 277
  6.2.5 Quality Control......Page 278
   6.2.5.3 Other Techniques......Page 279
   6.2.6.1 Screening Libraries of Immobilized Peptides......Page 280
   6.2.6.2 Screening of Peptide Libraries in Solution......Page 281
  6.3.1 An All D-Amino Acid Opioid Peptide......Page 282
  6.3.2 Novel Ligands for the SH3 Domain of Phosphatidylinositol 3-Kinase......Page 283
  6.3.3 Sequence-Selective Peptide Binding with a Peptido-Steroidal Receptor......Page 284
 References......Page 285
Index......Page 288