 Modified Nucleosides: in Biochemistry, Biotechnology and Medicine
ISBN: 978-3-527-31820-9
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684 pages
September 2008
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List of Contributors.
PART I: BIOCHEMISTRY AND BIOPHYSICS.
1. Investigations on Fluorine-Labeled Ribonucleic Acids by 19F NMR Spectroscopy (Christoph Kreutz and Ronald Micura).
1.1 Introduction.
1.2 19NMR Spectroscopy of Nucleic Acids.
1.3 Conclusions.
References.
2. 8-Oxo-7,8-Dihydro-2Î Deoxyguanosine: A Major DNA Oxidation Product (Jean Cadet and Paolo Di Mascio).
2.1 Introduction.
2.2 Formation of 8-Oxo-7,8-Dihydroguanine.
2.3 Raeactivity of 8-Oxo-7,8-Dihydro-2Î -Deoxyguanosine.
2.4 Formation of 8-Oxo-7,8-Dihydro-2Î -Deoxyguanosine in Cellular DNA.
2.5 Synthesis of 8-OxodGuo and Insertion into Oligonucleotides.
2.6 Conclusions.
References.
3. Modified DNA Bases: Probing Base-Pair Recognition by Polymerases (Eric T. Kool).
3.1 Introduction.
3.2 Basic Principles and Methods in Replication.
3.3 Alternative Hydrogen-Bonding Schemes.
3.4 Non-Polar Nucleoside Isosteres.
3.5 Non-Polar Steric Probes.
3.6 Minor Groove Hydrogen Bonds in Polymerases.
3.7 Other Non-Polar Bases and Pairs.
3.8 Replication of Designed Bases in Living Cells.
3.9 Conclusions and Future Prospects.
References.
4. 2Î -Deoxyribose-Modified Nucleoside Triphosphates and their Recognition by DNA Polymerases (Karl-Heinz Jung and Andreas Marx).
4.1 Introduction.
4.2 Modified Nucleotides as Alternative Building Blocks to Natural Acids.
4.3 DNA Polymerase Selectivity: 4Î -C-Modified Nucleotides.
4.4 Concluding Remarks.
References.
5. Pyrimidine Dimers: UV-Induced DNA Damage (Shigenori Iwai).
5.1 Introduction.
5.2 Formation of Pyrimidine Dimers.
5.3 Chemical Synthesis of Oligonucleotides Containing Pyrimidine Dimers.
5.4 Structure and Mutagenesis of Pyrimidine Dimer-Containing DNA.
5.5 Repair of Pyrimidine Dimers in Cells.
5.6 Bypass of Pyrimidine Dimers by DNA Polymerases.
References.
6. Locked Nucleic Acids: Properties, Applications, and Perspectives (Paul Nielsen and Jesper Wengel).
6.1 Introduction.
6.2 LNA in Higher-Affinity Hybridization: Designing Sequences.
6.3 Structural Studies.
6.4 Analogues of LNA and their Structural Impact.
6.5 LNA as Potential Therapeutics.
6.6 LNA-Probes.
6.7 Concluding Remarks.
References.
7. Synthesis and Properties of Oligonucleotides Incorporating Modified Nucleobases Capable of Watson-Crick-Type Base-Pair Formation (Mitsuo Sekine, Akio Ohkubo, Itaru Okamoto and Kohji Seio).
7.1 Introduction.
7.2 Natural, Enzyme-Assisted Sophisticated Devices for Maintaining Correct Base Recognition of Canonical Nucleobases.
7.3 Synthesis and Properties of Oligodeoxynucleotides Incorporating 4-N-Acylated Cytosine Derivatives.
7.4 Base-Recognition Ability of 4-N-Alkoxycarbonylcytosine Derivatives.
7.5 Synthesis and Properties of Oligonucleotides Incorporating 4-N-Carbamoylcytosine Derivatives.
7.6 2-Thiouracil as an Improved Nucleobase in Place of Thymine.
7.7 Modified Adenine Bases Capable of Recognizing the Thymine Base.
7.8 Design of Modified Guanine Bases Capable of Recognizing Cytosine.
7.9 Conclusions.
References.
8. The Properties of 4Î -Thionucleosides (Masataka Yokoyama.
8.1 Introduction.
8.2 Synthesis of 4Î -Thionucleosides.
8.3 Synthesis of Isothionucleosides.
8.4 Synthesis of L-Thionucleosides.
8.5 Synthesis of Thioxonucleosides.
8.6 Synthesis of Miscellaneous Thionucelosides.
8.7 Biological Activity of Thionucleosides.
8.8 Conclusions.
References.
9. S-Adenosyl-L-methionine and Related Compounds (Christian Dalhoff and Elmar Weinhold).
9.1 Introduction.
9.2 The Biochemistry of AdoMet.
9.3 The Chemistry and Biochemistry of Modified AdoMet.
9.4 AdoMet as a Pharmaceutical.
9.5 Concluding Remarks.
References.
PART II: BIOTECHNOLOGY.
10. 5-Substituted Nucleosides in Biochemistry and Biotechnology (Mohammad Ahmadian and Donald E. Bergstrom).
10.1 Introduction.
10.2 Synthesis.
10.3 Incorporation of C-5 Substituted Pyrimidine Nucleotides into Nucleic Acids through Modified Nucleotide 5Î -Triphosphates.
10.4 C-5 Substituents that Stabilize DNA Duplexes.
10.6 Conclusions.
References.
11. Universal Base Analogues and their Applications to Biotechnology (Kathleen Too and David Loakes).
11.1 Introduction.
11.2 General Methods of Synthesis.
11.3 Properties of Universal Bases.
11.4 Structure, Stacking, and Stabilization.
11.5 Hydrogen-Bonding Universal Base Analogues.
11.6 Applications of Universal Base Analogues.
11.7 Triphosphate Derivatives.
11.8 Therapeutic Applications.
References.
PART 111: MEDICNAL CHEMISTRY.
12. The Properties of Locked Methanocarba Nucleosides in Biochemistry, Biotechnology, and Medicinal Chemistry (Victor E. Marquez).
12.1 Introduction.
12.2 Structural Representation.
12.3 Synthesis of Locked Nucleosides.
12.4 Synthesis of Oligodeoxynucleotides (ODNS) Containing Locked Nucleosides.
12.5 Molecular Targets, Ligand Properties, and Binding Modes.
12.6 Concluding Remarks.
References.
13. Synthesis, Chemical Properties and Biological Activities of Cyclic Bis(3Î -5Î )diguanylic Acid (c-di-GMP) and its Analogues (Mamoru Hyodo and Yoshihiro Hayakawa)
13.1 Introduction.
13.2 Synthesis of c-di-GMP and its Analogues.
13.3 Chemical Properties of c-di-GMP and its Analogues.
13.4 Bioactivities of c-di-GMP and its Analogues.
13.5 Conclusions.
References.
14. Siderophore Biosynthesis Inhibitors (Courtney C. Aldrich and Ravindranadh V. Somu).
14.1 Introduction.
14.2 Synthesis, Physio-Chemical Properties, Metabolism, Mechanism of Action, and Biological Activity.
14.3 Background of Siderophores: Molecular Target and Rationale for Inhibitor Design.
14.4 Ligand Properties/Binding Mode.
14.5 Conclusions.
References.
15. Synthesis and Biological Activity of Selected Carbocyclic Nucleosides (Adam Mieczkowski and Luigi A. Agrofoglio).
15.1 Introduction.
15.2 A-5021, Synguanol, and Cyclopropane Derivatives.
15.3 Lobucavir and Cyclodutane Nucleoside Derivatives.
15.4 Carbovir and 2Î ,3Î -Unsaturated Nucleoside Derivatives.
15.5 Locked Nucleosides.
15.6 Conclusions.
References.
16. 4Î -C-Ethynyl-2Î -Deoxynucleosides (Hiroshi Ohrui).
16.1 Introduction.
16.2 Murine Toxicity of Purine 4Î EdNs.
16.3 4Î EdA Derivatives Stable to Adenosine Deaminase, and their Biological Properties.
16.4 4Î -C-Ethynylnucleosides without 3Î -OH.
17. Modified Nucleosides as Selective Modulators of Adenosine Receptors for Therapeutic Use (Kenneth A. Jacobson, Bhalchandra V. Joshi, Ben Wang, Athena Klutz, Yoonkyung Kim, Andrfei A. Ivanov, Artem Melman, and Zhan-Guo Gao.
17.1 Introduction.
17.2 Molecular Targets and Binding Modes.
17.3 AR Agonists as Clinical Candidates.
17.4 Summary.
References.
18. The Design of Foodesine HCI and Other Purine Nucleoside Phosphorylase Inhibitors (Philip E. Morris and Vivekanand P. Kamath).
18.1 Introduction.
18.2 Purine Nucleoside Phosphorylase Enzyme Structure.
18.3 First-Generation PNP Inhibitors: Substrate Analogues.
18.4 Second-Generation PNP Inhibitors: Transition-State Inhibitors.
18.5 Third-Generation PNP Inhibitors: Transition-State Inhibitors.
19. Formycins and their Analogues: Purine Nucleoside Phosphorylase Inhibitors and their Potential Application in Immunosuppression and Cancer (Agnieszka Bzowska).
19.1 Introduction.
19.2 Chemical Structure of Formycins and their Analogues.
19.3 Spectral Properties of Formycins.
19.4 Sources of Formycins.
19.5 The Biological Activity of Formycins: A Brief Summary.
19.6 Formycins and Analogues as Purine Nucleoside Phosphorylase Inhibitors.
19.7 Formycins as Inhibitors of Parasitic PNPs and Hydrolases.
19.8 Actual and Potential Applications of Formycins.
References.
20. 1-(3-C-Aethynyl-β-D-ribo-pentofuranosyl)cytosine (ECyd) (Akira Matsuda).
20.1 Introduction.
20.2 Synthesis of ECyd and its Analogues.
20.3 Cytotoxic Activity and Structure-Activity Relationships of ECyd Analogues In Vitro, and In Vitro Antitumor Activity.
20.4 Structural Features of ECyd and 4Î -Thio-ECyd.
20.5 Metabolism and Mechanism of Action.
20.6 An Apoptotic Pathway Involving the Action of ECyd.
20.7 Combination of ECyd with Low-Dose X-Irradiation.
20.8 ECyd is Effective against Gemcitabine-Resistant Human Pancreatic Cancer Cells.
20.9 Conclusions.
References.
21. Syntheses and Biological Activity of Neplanocin and Analogues (Dilip K. Tosh, Hea Ok Kim, Shantanu Pal, Jeong A. Lee, and Lak Shin Jeong).
21.1 Introduction.
21.2 New Methodologies in the Synthesis of Neplanocin A.
21.3 Modifications on Neplanocin A and Aristeromycin.
21.4 Conclusions.
References.
22. Clitocine and Its Analogues (Hyunik Shin and Changhee Min).
22.1 Clitocine: Isolation, Synthesis, and Biological Activity.
22.2 Clitocine Analogues.
References.
PART IV: ANTITUMORALS AND ANTIVIRALS.
23. Capecitabine Preclinical Studies: From Discovery to Translational Research (Hideo Ishitsuka and Nobuo Shimma).
23.1 Introduction.
23.2 Drug Design and Discovery of Capecitabine.
23.3 Preclinical Studies.
23.4 Translational Research for Optimizing Capecitabine Efficacy.
23.5 Conclusions.
References.
24. Tenofovir and Adefovir as Antiviral Agents (Tomas Cihlar, William E Delaney IV, and Richard Mackman).
24.1 Introduction.
24.2 Synthesis.
24.3 Mechanism of Action.
24.4 Activity in Animal Models.
24.5 Clinical Experience.
24.6 Drug Resistance.
24.7 Novel Antiviral Nucleotides and Nucleotide Prodrugs.
24.8 Conclusions.
References.
25. Clofarabine: From Design to Approval (John A. Secrist III, Jaideep V. Thottassery, and William B. Parker).
25.1 Introduction.
25.2 Clofarabine: The Background.
25.3 The Beginnings.
25.4 The Next Generation of Compounds.
25.5 Mechanism of Action of Clofarabine.
25.6 Clofarabine to the Clinic.
25.7 Summary and Comments.
References.
Index.
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