Pharmaceutical Aspects of Oligonucleotides

Book Cover......Page 1
Title......Page 5
Copyright......Page 6
Contents......Page 7
Contributors......Page 13
Preface......Page 15
PART ONE General Features......Page 17
1.1 Introduction......Page 18
1.2 Cell Proliferation Arrest through Release of Deoxynucleosides......Page 19
1.3 Extracellular Aptameric Effects of Phosphorothioate Oligodeoxynucleotide Analogues......Page 21
1.4 Aptameric Effects of G-quartet Oligonucleotides and Analogues......Page 22
1.5 Immune Stimulation by Oligodeoxynucleotides Containing CpG Motifs......Page 26
1.7 Antisense Inhibition of Gene Expression by Steric Block......Page 27
1.8 Antisense Inhibition of Gene Expression through Ribonuclease H-mediated Destruction of Target mRNA......Page 29
1.9 Oligonucleotides in Vivo......Page 36
Acknowledgements......Page 37
References......Page 38
PART TWO Chemical Aspects......Page 48
2.1 Introduction......Page 49
2.2 Design of Oligonucleotides......Page 53
2.2.2 Degree of Modification......Page 54
2.3 Oligonucleotide Modifications: Synthesis and Properties......Page 56
2.3.1 Unmodified Oligonucleotides having 3′5′-Phosphodiester Linkages......Page 57
2.3.1.1 Chemical synthesis......Page 58
2.3.1.2 Enzymatic synthesis and ligation......Page 60
2.3.2 Oligonucleotides with 2′5\'-Linkages and 3\'3\'-/ 5\'5\'-Inversions......Page 61
2.3.3.1 Phosphorothioates......Page 62
2.3.3.2 Alkylphosphonates and arylphosphonates......Page 63
2.3.3.3 Other modifications on phosphorus......Page 64
2.3.4 Oligonucleotides Containing Dephospho Linkages......Page 65
2.3.5 Modification of the Sugar Moiety......Page 66
2.3.5.2 2′-Modified oligonucleotides......Page 67
2.3.5.4 Other sugar-modified analogues......Page 68
2.3.6 Peptide Nucleic Acids......Page 69
2.3.7.1 Universal bases and abasic sites......Page 71
2.3.8.2 3′-end conjugates......Page 72
2.3.8.4 Types of conjugate......Page 73
2.4.1 UV Spectroscopy of Oligonucleotides......Page 75
2.41.2 Melting curves of DNA......Page 76
2.4.2 Analysis of Oligonucleotides by High-Performance Liquid Chromatography......Page 77
2.4.2.2 Anion-exchange HPLC......Page 78
2.4.3 Electrophoretic Techniques......Page 79
2.4.3.2 Capillary Gel Electrophoresis (CGE)......Page 80
2.4.4.1 Electrospray Ionization Mass Spectrometry (ESI-MS)......Page 81
2.4.4.2 Matrix-Assisted Laser Desorption Ionization (MALDI)......Page 82
2.4.5 NMR of Oligonucleotides......Page 83
References......Page 84
3.1 Introduction......Page 96
3.2.1 Structure......Page 97
3.2.3 Dimers′ Stability in Biological Media......Page 98
3.3.2 Pro-oligonucleotides′ Stability in Biological Media......Page 100
3.3.4 Conclusion......Page 102
3.4.2 Automated Synthesis on Solid Support......Page 103
3.4.2.2 Phosphoramidite building blocks......Page 104
3.4.3 Fully SATE Pro-oligonucleotides......Page 105
3.4.5 Stability of Pro-oligonucleotides of Second Generation in Biological Media......Page 108
3.4.6 Preliminary Data of Pro-oligos′ Cell Uptake......Page 109
3.5 Conclusion......Page 110
References......Page 112
4.1 Introduction......Page 116
4.2 Antisense......Page 117
4.5 Antigene......Page 119
4.7 Pharmacology......Page 121
Acknowledgement......Page 122
References......Page 123
PART THREE Delivery......Page 126
5.1 Delivery Vehicles for the Improved Uptake of Nucleic Acids: a Survey......Page 127
5.2 The Potential of Peptides for Nucleic Acids Delivery......Page 129
5.3 Strategies for the Coupling of Peptides to Oligonucleotides......Page 130
5.4 Poly (L-lysine)-based Delivery Systems......Page 132
5.5 Conjugation to Fusogenic Peptides Allowing Membrane Fusion or Membrane Translocation......Page 133
5.5.3 Antennapaedia Peptide......Page 134
5.5.4 Tat Basic Domain......Page 136
5.6 Conclusions......Page 138
References......Page 140
6.1 Introduction......Page 145
6.2.1 Rationale of Using Nanoparticles for the Delivery of ONs......Page 146
6.2.2 Preparation of Nanoparticles by Polymerization of a Monomer......Page 148
6.2.3 Nanoparticles Obtained from Preformed Polymers......Page 150
6.2.4 Association of ONs to Nanoparticles......Page 152
6.3 In Vitro Stability of ONs Adsorbed onto Nanoparticles......Page 154
6.4 Cell Interactions with ON Loaded Nanoparticles......Page 155
6.6 In Vivo Studies with Oligonucleotide Nanoparticles......Page 156
6.7 Microparticles......Page 157
References......Page 158
7.1 Introduction......Page 164
7.2 Anionic Liposomes......Page 165
7.3 Cationic Liposomes......Page 168
7.3.1 Intracellular delivery and Distribution......Page 169
7.3.2 Pharmacological Efficacy in Vitro......Page 172
7.3.3 Pharmacological Efficacy in Vivo......Page 174
7.4 pH-sensitive Liposomes......Page 175
7.5 Immunoliposomes and Other Molecularly Targeted Liposomes......Page 179
7.6 Fusogenic Liposomes and Proteoliposomes......Page 181
7.7 Conclusions......Page 183
References......Page 184
8.2 Comb-type Polycations as a Stabilizer for DNA Duplex and Triplex......Page 192
NA Carrier .........Page 205
References......Page 212
PART FOUR Biopharmaceutics......Page 219
9.1 Introduction......Page 220
9.2 Oligonucleotide-Binding Proteins on the Cell Surface......Page 222
9.3 Intracellular Compartmentalization......Page 224
9.4 Oligonucleotide Delivery Reagents—Practical Considerations......Page 226
9.5.1 Oligonucleotides......Page 227
9.5.2 Delivery......Page 228
9.5.3 Controls......Page 229
References......Page 230
10.1 Overview of Cellular Uptake of Antisense Oligonucleotides......Page 233
10.2.1 Interactions of Oligonucleotides with the Lipid Bilayer......Page 235
10.2.2 Oligonucleotide Receptors and Transporter Proteins......Page 236
10.3 Mechanisms of Enhancement of Oligonucleotide Permeation across Membranes......Page 238
References......Page 241
11.1 Introduction......Page 246
11.2 Pharmacokinetics......Page 247
11.2.1 Analytical Chemistry......Page 248
11.4 Cellular Pharmacokinetics......Page 249
11.5 Preclinical Pharmacokinetics......Page 251
11.6 Clinical Pharmacokinetics......Page 255
11.7 Conclusions......Page 256
References......Page 257
PART FIVE Pharmacological Activity......Page 262
12.1 Novel Approaches for Anticancer Therapy......Page 263
12.2.1 Bcl-2......Page 265
12.2.2 C-myb......Page 266
12.2.3 raf Kinase......Page 267
12.2.4 Protein Kinase C-α......Page 269
12.2.5 Protein Kinase A......Page 270
12.3.1 Discovery of ras Antisense Inhibitors......Page 271
12.3.2 Specificity of ras Antisense Inhibitors......Page 272
12.3.3 Cellular Responses Resulting from Inhibition of ras Gene Expression......Page 275
12.3.4 Antitumour Activity of ras Antisense Oligonucleotides in Animal Models......Page 277
12.4 Conclusions and Future Prospects......Page 279
References......Page 280
13.1 Introduction......Page 284
13.2 ICAM-1, a Case Study......Page 285
13.2.1.1 Proof of mechanism......Page 289
13.2.1.2 Human xenografts......Page 291
13.2.13 Rodent allografts......Page 292
13.2.1.4 Renal ischaemia......Page 293
73.2.7.5 Colitis......Page 294
13.2.3 Clinical Studies with ISIS 2302......Page 295
13.2.4 Second- and Third-generation Chemistry......Page 296
13.3.1 Other Endothelial-Leukocyte Adhesion Molecules......Page 297
13.3.2 Interleukin 1 Receptor......Page 298
13.3.3 NF-κB......Page 299
13.3.5 Nitric Oxide Synthetase......Page 300
13.4 Regulation of Immune Response by Non-antisense Mechanisms......Page 301
References......Page 302
14.1 Introduction......Page 309
14.2 Design of Antisense Oligonucleotides for Antiparasite Use......Page 310
14.3 Antiparasite Effects of Antisense Oligonucleotides......Page 313
14.3.1 Antisense Oligonucleotides against Plasmodium......Page 314
14.3.2 Antisense Oligonucleotides against Trypanosomatids......Page 316
14.3.3 Other Parasites......Page 320
14.4 RNA Structures are Valid Targets for Regulatory Oligonucleotides......Page 321
14.5 Conclusion......Page 326
References......Page 327
Index......Page 334