Interdisciplinary and application-oriented, this ready reference focuses on methods and processes with a high practical aspect, covering new trends in drug delivery, in-vivo analysis, structure formation and much more.
Of great interest to chemists and life scientists in academia and industry.
Table of Contents
Foreword by Dr Hamaguchi xiii
Foreword by Dr Noyori xv
Preface xvii
1 Control of DNA Packaging by Block Catiomers for Systemic Gene Delivery System 1
Kensuke Osada
1.1 Introduction 1
1.2 Packaging of pDNA by Block Catiomers 2
1.2.1 Rod-Shaped Packaging of pDNA 3
1.2.2 Rod Shape or Globular Shape 5
1.3 PolyplexMicelles as a Systemic Gene Delivery System 6
1.3.1 Stable Encapsulation of pDNAWithin Polyplex Micelles for Systemic Delivery 6
1.3.2 PolyplexMicelles for Efficient Cellular Entry 9
1.3.3 PolyplexMicelles for Safe Endosome Escape 11
1.3.4 PolyplexMicelles for Nuclear Translocation 13
1.3.5 PolyplexMicelles for Efficient Transcription 13
1.4 Design Criteria of Block Catiomers Toward Systemic Gene Therapy 14
1.5 Rod Shape or Toroid Shape 17
1.6 Summary 18
References 18
2 Manipulation of Molecular Architecture with DNA 25
Akinori Kuzuya
2.1 Introduction 25
2.2 Molecular Structure of DNA 25
2.3 Immobile DNA Junctions 26
2.4 Topologically Unique DNA Molecules 28
2.5 DNA Tiles and Their Assemblies 28
2.6 DNA Origami 30
2.7 DNA Origami as a Molecular Peg Board 32
2.8 Molecular Machines Made of DNA Origami 33
2.9 DNA Origami Pinching Devices 33
2.10 Novel Design Principles 35
2.11 DNA-PAINT: An Application of DNA Devices 36
2.12 Prospects 36
References 36
3 Chemical Assembly Lines for Skeletally Diverse Indole Alkaloids 43
Hiroki Oguri
3.1 Introduction 43
3.2 Macmillan’s Collective Total Synthesis by Means of Organocascade Catalysis 45
3.3 Systematic Synthesis of Indole Alkaloids Employing Cyclopentene Intermediates by the Zhu Group 52
3.4 Biogenetically Inspired Synthesis Employing a Multipotent Intermediate by the Oguri Group 58
References 68
4 Molecular Technology for Injured Brain Regeneration 71
Itsuki Ajioka
4.1 Introduction 71
4.2 Biology of Angiogenesis 71
4.3 Angiogenesis for Injured Brain Regeneration 73
4.4 Molecular Technology to Promote Angiogenesis 74
4.5 Biology of Cell Cycle 75
4.6 Biology of Neurogenesis 77
4.7 Molecular Technology to Promote Neuron Regeneration 78
4.8 Conclusion 80
References 80
5 Engineering the Ribosomal Translation Systemto Introduce Non-proteinogenic Amino Acids into Peptides 87
Takayuki Katoh
5.1 Introduction 87
5.2 Decoding the Genetic Code 88
5.3 Aminoacylation of tRNA by Aminoacyl-tRNA Synthetases 90
5.4 Methods for Preparing Noncanonical Aminoacyl-tRNAs 91
5.4.1 Ligation of Aminoacyl-pdCpA Dinucleotide with tRNA Lacking the 3′-Terminal CA 91
5.4.2 Post-aminoacylationModification of Aminoacyl-tRNA 93
5.4.3 Misacylation of Non-proteinogenic Amino Acids by ARSs 94
5.4.4 Flexizyme, an Aminoacylation Ribozyme 94
5.5 Methods for Assigning Non-proteinogenic Amino Acids to the Genetic Code 95
5.5.1 The Nonsense Codon Method 96
5.5.2 Genetic Code Reprogramming 97
5.5.3 The Four-base Codon Method 98
5.5.4 The Nonstandard Base Method 100
5.6 Limitation of the Incorporation of Noncanonical Amino Acids: Substrate Scope 101
5.7 Improvement of the Substrate Tolerance of Ribosomal Translation 103
5.8 Ribosomally Synthesized Noncanonical Peptides as Drug Discovery Platforms 104
5.9 Summary and Outlook 105
References 106
6 Development of Functional Nanoparticles and Their Systems Capable of Accumulating to Tumors 113
Satoru Karasawa
6.1 Introduction 113
6.2 Accumulation Based on Aberrant Morphology and Size 114
6.3 Accumulation Based on Aberrant pH Microenvironment 117
6.4 Accumulation Based on Temperature of Tumor Microenvironment 124
6.5 Perspective 129
References 129
7 Glycan Molecular Technology for Highly Selective In Vivo Recognition 131
Katsunori Tanaka
7.1 Molecular Technology for Chemical Glycan Conjugation 133
7.1.1 Conjugation to Lysine 133
7.1.2 Conjugation to Cysteine 133
7.1.3 Bioorthogonal Conjugation 136
7.1.4 Enzymatic Glycosylation 136
7.2 In Vivo Kinetic Studies of Monosaccharide-Modified Proteins 137
7.2.1 Dissection-Based Kinetic and Biodistribution Studies: Effects of Protein Modification by Galactose, Mannose, and Fucose 137
7.2.2 Noninvasive Imaging of In Vivo Kinetic and Organ-Specific Accumulation of Monosaccharide-Modified Proteins 138
7.3 In Vivo Kinetic Studies of Oligosaccharide-Modified Proteins 139
7.3.1 In Vivo Kinetics of Proteins Modified by a Few Molecules of N-glycans 139
7.3.2 In Vivo Kinetics of Proteins Modified by Many N-glycans: Homogeneous N-glycoalbumins 141
7.3.3 In Vivo Kinetics of Proteins Modified by Many N-glycans: Heterogeneous N-glycoalbumins 145
7.3.4 Tumor Targeting by N-glycoalbumins 148
7.3.5 Glycan Molecular Technology on Live Cells: Tumor Targeting by N-glycan-Engineered Lymphocytes 148
7.4 Glycan Molecular Technology Adapted as Metal Carriers: In Vivo Metal-Catalyzed Reactions within Live Animals 150
7.5 Concluding Remarks 153
Acknowledgments 155
References 155
8 Molecular Technology Toward Expansion of Nucleic Acid Functionality 165
Michiko Kimoto and Kiyohiko Kawai
8.1 Introduction 165
8.2 Molecular Technologies that Enable Genetic Alphabet Expansion 168
8.2.1 Nucleotide Modification 168
8.2.2 Unnatural Base Pairs (UBPs) asThird Base Pairs Toward Expansion of Nucleic Acid Functionality 168
8.2.3 High-Affinity DNA Aptamer Generation Using the Expanded Genetic Alphabet 169
8.3 Molecular Technologies that Enable Fluorescence Blinking Control 171
8.3.1 Single Molecule Detection Based on Blinking Observations 171
8.3.2 Blinking Kinetics 172
8.3.3 Control of Fluorescence Blinking by DNA Structure 174
8.3.3.1 Triplet Blinking 174
8.3.3.2 Redox Blinking 175
8.3.3.3 Isomerization Blinking 176
8.4 Conclusions 178
Acknowledgments 178
References 178
9 Molecular Technology for Membrane Functionalization 183
MichioMurakoshi and TakahiroMuraoka
9.1 Introduction 183
9.2 Synthetic Approach for Membrane Functionalization 185
9.2.1 Formation of Multipass Transmembrane Structure 185
9.2.2 Formation of Supramolecular Ion Channels 187
9.2.3 Demonstration of Ligand-Gated Ion Transportation 187
9.2.4 Light-Triggered Membrane Budding 190
9.3 Semi-biological Approach for Membrane Functionalization 191
9.3.1 Mechanical Analysis of the Transmembrane Structure of Membrane Proteins 191
9.3.2 Development of the Nanobiodevice Using a Membrane Protein Expressing in the Inner Ear 193
9.3.3 Improvement of Protein Performance by Genetic Engineering 198
References 199
10 Molecular Technology for Degradable Synthetic Hydrogels for Biomaterials 203
Hiroharu Ajiro and Takamasa Sakai
Scope of the Chapter 203
10.1 Degradation Behavior of Hydrogels 203
10.2 Polylactide Copolymer 205
10.3 Trimethylene Carbonate Derivatives 207
10.4 Polyurethane 211
References 213
11 Molecular Technology for Epigenetics Toward Drug Discovery 219
Takayoshi Suzuki
11.1 Introduction 219
11.2 Epigenetics 219
11.3 Isozyme-Selective Histone Deacetylase (HDAC) Inhibitors 221
11.3.1 Identification of HDAC3-Selective Inhibitors by Click Chemistry Approach 221
11.3.2 Identification of HDAC8-Selective Inhibitors by Click Chemistry Approach and Structure-Based Drug Design 224
11.3.3 Identification of HDAC6-Insensitive Inhibitors Using C-H Activation Reaction 224
11.3.4 Identification of HDAC6-Selective Inhibitors by Substrate-Based Drug Design 228
11.3.5 Identification of SIRT1-Selective Inhibitors by Target-Guided Synthesis 228
11.3.6 Identification of SIRT2-Selective Inhibitors by Structure-Based Drug Design and Click Chemistry Approach 232
11.4 Histone Lysine Demethylase (KDM) Inhibitors 234
11.4.1 Identification of KDM4C Inhibitors by Structure-Based Drug Design 235
11.4.2 Identification of KDM5A Inhibitors by Structure-Based Drug Design 237
11.4.3 Identification of KDM7B Inhibitors by Structure-Based Drug Design 238
11.4.4 Identification of LSD1 Inhibitors by Target-Guided Synthesis 239
11.4.5 Small-Molecule-Based Drug Delivery System Using LSD1 and its Inhibitor 250
11.5 Summary 253
References 254
12 Molecular Technology for Highly Efficient Gene Silencing: DNA/RNA Heteroduplex Oligonucleotides 257
Kotaro Yoshioka, Kazutaka Nishina, Tetsuya Nagata, and Takanori Yokota
12.1 Introduction 257
12.2 Therapeutic Oligonucleotides 257
12.2.1 siRNA 257
12.2.2 ASO 258
12.3 Chemical Modifications ofTherapeutic Oligonucleotide 259
12.3.1 Modifications of Internucleotide Linkage 259
12.3.2 Modifications of Sugar Moiety 260
12.4 Ligand Conjugation for DDS 261
12.4.1 Development of Ligand Molecules for Therapeutic Oligonucleotides 261
12.4.2 Vitamin E for Ligand Molecule 261
12.4.3 siRNA Conjugated with Tocopherol 261
12.4.4 ASO Conjugated with Tocopherol 261
12.5 DNA/RNA Heteroduplex Oligonucleotide 262
12.5.1 Basic Concept of Heteroduplex Oligonucleotide 262
12.5.2 HDO Conjugated with Tocopherol (Toc-HDO) 264
12.5.2.1 Design of Toc-HDO 264
12.5.2.2 Potency of Toc-HDO 264
12.5.2.3 Adverse Effect of Toc-HDO 266
12.5.2.4 Mechanism of Toc-HDO 268
12.6 Future Prospects 269
References 269
13 Molecular Technology for Highly Sensitive Biomolecular Analysis: Hyperpolarized NMR/MRI Probes 273
Shinsuke Sando and Hiroshi Nonaka
13.1 Hyperpolarization 273
13.2 Requirements for HP Molecular Imaging Probes 275
13.3 HP 13C Molecular Probes for Analysis of Enzymatic Activity 277
13.3.1 [1-13C]Pyruvate 277
13.3.2 HP 13C Probes for Analysis of Glycolysis and Tricarboxylic Acid Cycle 278
13.3.3 γ-Glutamyl-[1-13C]glycine: HP 13C Probe for Analysis of γ-glutamyl Transpeptidase 278
13.3.4 [1-13C]Alanine-NH2: HP 13C Probes for Analysis of Aminopeptidase N 282
13.4 HP 13C Molecular Probes for Analysis of the Chemical Environment 283
13.4.1 [1-13C]Bicarbonate 283
13.4.2 [1-13C]Ascorbate and Dehydroascorbate 283
13.4.3 [13C]Benzoylformic Acid for Sensing H2O2 284
13.4.4 [13C,D3]-p-Anisidine for Sensing of HOCl 284
13.4.5 [13C,D]EDTA for Sensing of Metal Ions 285
13.5 HP 15N Molecular Probes 286
13.6 A Strategy for Designing HP Molecular Probes 287
13.6.1 Scaffold Structure for Design of 15NHP Probes: [15N,D9]TMPA 288
13.6.1.1 [15N,D14]TMPA 291
13.6.2 Scaffold Structure for Designing 13CHyperpolarized Probes 292
13.7 Conclusion 294
References 294
14 Molecular Technologies in Life Innovation: Novel Molecular Technologies for Labeling and Functional Control of Proteins Under Live Cell Conditions 297
Itaru Hamachi, Shigeki Kiyonaka, Tomonori Tamura, and Ryou Kubota
14.1 General Introduction 297
14.2 Ligand-Directed Chemistry for Neurotransmitter Receptor Proteins Under Live Cell Condition and its Application 300
14.3 Affinity-Guided DMAP Reaction for Analysis of Live Cell Surface Proteins 308
14.4 Coordination Chemistry-Based Chemogenetic Approach to Switch the Activity of Glutamate Receptors in Live Cells 312
14.5 Concluding Remarks 320
References 321
15 Molecular Technologies for Pseudo-natural Peptide Synthesis and Discovery of Bioactive Compounds Against Undruggable Targets 329
Joseph M. Rogers and Hiroaki Suga
15.1 Introduction 329
15.2 Peptides Could Target Undruggable Targets 330
15.2.1 Druggable Proteins 330
15.2.2 Undruggable Proteins 332
15.2.3 Natural Peptides as Drugs 333
15.2.4 Modification to Peptides can ImproveTheir Drug-Like Characteristics 334
15.2.4.1 Macrocyclization 334
15.2.4.2 Amino Acids with Unnatural Side Chains 335
15.2.4.3 Backbone Modifications Including N-Methylation 335
15.2.4.4 Cyclosporin - A Membrane-Permeable Anomaly 336
15.2.4.5 Membrane Permeability Cannot be Calculated from Amino Acid Content 336
15.2.5 Cyclosporin -The Inspiration for the Cyclic Peptide Approach to Undruggable Targets 337
15.3 Molecular Technologies to Discover Functional Peptides 337
15.3.1 Ribosomal Synthesis of Peptides 337
15.3.2 Natural Peptide Synthesis is an Efficient Method to Generate Huge Libraries 339
15.3.3 Selection Methods 340
15.3.3.1 Intracellular Peptide Selection 340
15.3.3.2 Phage Display 341
15.3.3.3 A Cell-Free Display, mRNA Display 345
15.3.4 Other Methods of Selection 347
15.4 Molecular Technology for Pseudo-natural Peptide Synthesis and Its Use in Peptide Drug Discovery 347
15.4.1 The Need for Pseudo-natural Synthesis -The Limitations of SPPS 348
15.4.2 Intein Cyclization and SICLOPPS 348
15.4.3 Post-translationModification 351
15.4.4 Genetic Code Expansion 352
15.4.5 Replacing Amino Acids in Translation 354
15.4.6 Genetic Code Reprogramming 355
15.4.6.1 Flexizymes 355
15.4.6.2 RaPID System 356
15.5 Conclusion 361
Acknowledgment 361
References 362
Index 371
