Chemistry of Nucleosides and Nucleotides: Volume 1

400 Pages·1988·16.97 MB·English

by  Tohru Ueda (auth.)

Chemistry qf
Nuc leos ides
and Nucleotides
Volume 1
of
Chemistry
Nucleosides
and Nucleotides
Volume 1
Edited by
Leroy B. Townsend
Uniumity of Michigan
Ann Arbo" Michigan
Plenum Press • New York and London
Library of Congress Cataloging in Publication Data
Chemistry ofnucleosides and nucleotides 1 edited by Leroy B. Townsend.
p. em.
Includes bibliographical references and indexes.
ISBN-13: 978-1-4612-8283-9 e-ISBN-13: 978-1-4613-0995-6
DOl: 10.1007/978-1-4613-0995-6
I. Nucleotides. 2. Nucleosides. I. Townsend, Leroy B.
QD436.N85C47 1988 88·22359
547.7'9-dc19 CIP
This limited facsimile edition has been issued
for the purpose of keeping this title available
to the scientific community.
10987 6 54 3
© 1988 Plenum Press, New York
A Division of Plenum Publishing Corporation
233 Spring Street, New York, N.Y. 10013
All rights reserved
No part of this book may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, electronic, mechanical, photocopying, microfilming,
recording, or othenvise, without written permission from the Publisher
Contributors
Mono lkehara, Faculty of Pharmaceutical Sciences, Osaka University, Osaka,
Japan 565
Rich B. Meyer, Jr., MicroProbe Corporation, Bothell, Washington 98021
Eiko Ohtsuka, Faculty of Pharmaceutical Sciences, Osaka University, Osaka,
Japan 565
Roland K. Robins, Nucleic Acid Research Institute, Costa Mesa, California
92626
Prem C. Srivastava, Nuclear Medicine Group, Health and Safety Research
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
Toshiki Tanaka, Faculty of Pharmaceutical Sciences, Osaka University, Osaka,
Japan 565
Tohru Ueda, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo
060, Japan
Seiichi Uesugi, Faculty of Pharmaceutical Sciences, Osaka University, Osaka,
Japan 565
v
Preface
The present volume is the first of a projected four-volume treatise. This volume
contains the following chapters: "Synthesis and Reaction of Pyrimidine
Nucleosides," "Synthesis and Properties of Purine Nucleosides and Nucleotides,"
and "Synthesis and Properties of Oligonucleotides."
These three chapters were selected for inclusion in Volume I because the
areas have provided the basis and impetus for the initiation and development of
the other areas of research, which will be described in subsequent volumes. Each
chapter is rather comprehensive in nature and should provide a ready reference
source for not only the novice but also the experienced investigator or researcher.
The chapters have been prepared by authors with considerable experience in each
particular area of research, and this has resulted in a lucid presentation of each
well-defined area.
These volumes were designed with medicinal chemists, medicinal organic
chemists, organic chemists, carbohydrate chemists, physical chemists, and
biological chemists in mind. However, because of the tremendous recent interest
in this research area owing to the biological and chemotherapeutic evaluation of
nucleosides and nucleotides as anticancer, antiviral, and antiparasitic agents, these
volumes should also be valuable additions to the libraries of virologists,
biochemical pharmacologists, oncologists, and pharmacologists.
We would like to thank the authors for their enthusiasm and help in making
these volumes available to the scientific community.
Leroy B. Townsend
Ann Arbor
vii
Contents
Chapter 1
Synthesis and Reaction of Pyrimidine Nucleosides
Tohru Ueda
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . I
2. Synthesis of Pyrimidine Nucleosides ............................... 2
2.1. The Vorbriiggen Method ................................... 2
2.2. The Mercuri Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.3. Ring Closure of N-Substituted Ribosylamines .................. 6
3. Reaction of Pyrimidine Nucleosides in the Heterocyclic Moiety ........ 8
3.1. Protonation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2. Alkylation and Related Reactions ........................... 9
3.3. N-Oxidation and N-Amination ............................. 12
3.4. Nitration ................................................ 13
3.5. Hydroxymethylation and Related Reactions .................. 14
3.6. Halogenation .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 16
3.7. Mercuration, Metallation, and Related Reactions .............. 23
3.8. Nucleophilic Additions ..................................... 27
3.9. Reactions of 5-Halogenopyrimidine Nucleosides with
Nucleophiles and Related Reactions .......................... 33
3.10. Substitution at C-4 and C-2 and Related Reactions ............. 41
3.11. Oxidations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 46
3.12. Reductions ..... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 48
4. Synthesis and Reactions of Cyclonucleosides ........................ 49
4.1. Synthesis of Cyclonucleosides ................................ 50
4.2. Reaction of Cyclonucleosides '" . . . . . . . . . . . . . . . . . . . . . . . . . . .. 59
4.3. Cyclonucleosides Bridged by Sulfur and Nitrogen .............. 67
4.4. Cyclonucleosides Bridged by Carbon ......................... 71
5. Reactions of Pyrimidine Nucleosides in the Sugar Moiety............. 74
5.1. Alkylation of Sugar Hydroxyl Groups. . . . . . . . . . . . . . . . . . . . . . . .. 74
5.2. Conversion of Sugar Hydroxyls to Halogeno Groups ............ 76
5.3. Conversion of 5' and (3')-Hydroxyl Groups to Other
Functional Groups ........................................ 79
Contents
5.4. Epoxides of Pyrimidine N ucleosides . . . . . . . . . . . . . . . . . . . . . . . . . .. 81
5.5. Introduction of Double Bonds in the Sugar Moiety. . . . . . . . . . . . .. 83
5.6. Oxidation of the Sugar Moiety .............................. 88
6. Reactions Involving Cleavage of Glycosyl Bond and
Anomerization ................................................ 93
7. References 95
Chapter 2
Synthesis and Properties of Purine Nucleosides
and Nucleotides
Prern C. Srivastava, Roland K. Robins, and Rich B. Meyer, Jr.
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 113
2. Synthesis of Purine Nucleosides and Nucleotides ..................... 114
2.1. Direct Glycosylation of Purines .............................. 114
2.2. Synthesis of Purine Nucleosides and Nucleotides from Imidazole
and Pyrimidine Nucleosides and Nucleotides .................. 148
2.3. Phosphorylation of Purine Nucleosides ........................ 158
2.4. Synthesis of Purine Nucleoside Cyclic Phosphates ............... 162
3. Reactions of Purine N ucleosides and N ucleotides .................... 166
3.1. Reactions of the Carbohydrate Portion.of Purine
Nucleosides and Nucleotides ................................ 166
3.2. Reactions of the Purine Ring of Purine
Nucleosides and Nucleotides ................................ 197
3.3. Interaction of the Sugar and the Purine Ring: Purine Cyclo-
nucleosides ............................................... 249
3.4. Hydrolysis of the Glycosyl Bond: Stabilities and Mechanism 264
4. References .................................................... 267
Chapter 3
Synthesis and Properties of Oligonucleotides
Morio Ikehara, Eiko Ohtsuka, Seiichi Uesugi, and Toshiki Tanaka
I. Introduction ................................................. 283
2. Protecting Groups and Phosphorylation Methods ................... 285
2.1. Protecting Groups for Bases ................................. 286
2.2. Protecting Groups for Sugar Hydroxyl Groups ................. 287
2.3. Protecting Groups for Phosphates and Phosphorylating Reagents .. 292
2.4. Condensing Reagents ...................................... 294
3. Synthesis of Oligonucleotides by the Phosphotriester Method .......... 297
3.1. Synthesis ofOligo(deoxyribonucleotides) in Solution ............ 297
3.2. Synthesis ofOligo(deoxyribonucleotides) on Polymer Supports ... 301
3.3. Synthesis ofOligo(ribonucleotides) in Solution ................. 305
3.4. Synthesis ofOligo(ribonucleosides) on Polymer Supports ........ 309
4. Phosphite Method .............................................. 310
4.1. Synthesis ofOligo(deoxyribonucleotides) in Solution ............ 310
Contents xi
4.2. Synthesis ofOligo(deoxyribonucleotides) on Polymer Supports ... 314
4.3. Synthesis ofOligo(ribonucleotides) in Solution ................. 316
4.4. Synthesis ofOligo(ribonucleotides) on Polymer Support ......... 317
4.5. Synthesis of Modified N ucleotides ............................ 318
5. Purification and Characterization of Oligonucleotides ................ 320
5.1. Isolation of Oligonucleotides ................................ 320
5.2. Identification of Oligonucleotides ............................ 321
6. Joining Reactions and Other Usage of Synthetic Oligonucleotides 324
6.1. Synthesis of Genes by Joining of Deoxyoligonucleotides
with DNA Ligase ......................................... 324
6.2. Use of Oligonucleotides as Probes or Primers for
Sequencing DNA ......................................... 328
6.3. Use of Deoxyoligonucleotides on Site-Directed Mutagenesis 329
6.4. Joining of Ribo-oligonucleotides with RNA Ligase .............. 330
7. Structure and Properties of Oligonucleotides ....................... 331
7.1. Crystal Structure of Oligonucleotides ......................... 331
7.2. Conformation of Oligonucleotides in Solution .................. 337
7.3. Interaction of Oligonucleotides with Drugs .................... 344
7.4. Reactions of Oligonucleotides with Drugs ..................... 348
8. References .................................................... 353
Index ........................................................... 369
Chapter 1
Synthesis and Reaction of
Pyrimidine Nucleosides
Tohru Ueda
1. Introduction
Nucleic acids playa fundamental role in the transformation of genetic infor
mation. DNAs carry the genetic information and these are replicated during cell
division. The genetic information, the sequence of four nucleobases, adenine (A),
guanine (G), cytosine (C), and thymine (T) of the DNA strands, are transcribed
to RNAs (messenger RNA, mRNA). These are then translated to furnish specific
proteins coded by the mRNA, on the system called polysome, which consists of
various ribosomal RNAs, proteins and transfer RNAs (tRNA) carrying specific
amino acids to be connected in a specific sequence.
Throughout these transformations, the complementary hydrogen bond for
mation between A-T (U) and G-C is the essential chemical event. Therefore, for
the study of genetic control, the chemistry of nucleosides becomes very important.
In addition, nucleosides in the form of phosphate esters, such as ATP and other
nucleoside polyphosphates, play an essential role in the energy transfer and
regulation of metabolic systems.
A large number of new pyrimidine and purine nucleosides have been syn
thesized and tested for their biological activities. It is reasonable to expect that the
nucleoside analogues will exhibit various activities through the interactions at
many enzymatic pathways of synthesis and metabolism of nucIeosides, nucIeotides,
DNA, and RNA. Thus, the nucIeosides are major candidates for chemothera
peutic agents, especially for virus and cancer.
This chapter deals with the synthesis of pyrimidine nucIeosides (Section 2)
and reactions of preformed nucleosides (Sections 3-5). Excellent books and
reviews related to the present subjects are available. (\-10)
To"rv Ued .. • Facuhy of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan.
2 Toh.... Ueda
2. Synthesis of Pyrimidine Nucleosides
A nucleoside was originally designated as the N-ribosyl (or 2-deoxyribosyl)
derivative of pyrimidines and purines and exists in nature as the constituent of
nucleic acids and as nucleoside antibiotics. Some nucleosides are found as
naturally occurring substances. The C-nucleosides are the subject of another
chapter.
The usual ribonucleosides and 2'-deoxyribonucleosides are now commercially
available and there is no need to elaborate on their synthesis. However, for the
synthesis of pyrimidine nucleosides modified at either the sugar and base
moieties-as is often found in the nucleoside antibiotics-the N-glycosylation
proced ure is efficien t.
Recent progress on the synthetic studies of pyrimidine nucleosides has
provided a general method, the Vorbruggen procedure. Therefore, this section is
devoted primarily to this method with very brief discussions of the previous
procedures of pyrimidine nucleoside synthesis.
2.1. The Vorbrrlggen Method
The usual pyrimidine bases, cytosine (1) and uracil [or thymine, (2), are
more than ambident nucleophiles to be glycosyhlted. Therefore, the first practical
synthetic procedure was the Hilbert-Johnson reaction. (1/) This procedure used a
2,4-dialkoxypyrimidine (3) for the base, which was then condensed with a protec
ted sugar halide (4) to afford the nucleoside (5). In structure (3), nitrogen-l is the
most nucleophilic and usually the first to be alkylated. From compound (5), the
cytosine nucleoside (6) and uracil nucleoside (7) were prepared by ammonolysis
and hydrolysis, respectively. While the 2,4-dialkoxypyrimidine cannot be
prepared directly from the parent base, for example, from uracil, the trimethyl
silylation procedure does afford the 2,4-bis-O-trimethylsilylated derivative.
Thus, treatment of (1) or (2) with excess of hexamethyldisilazane (HMDS)
and chlorotrimethylsilane gives 2,4-bistrimethylsilykytosine (8) and 2,4-bistri
methylsilyluracil (9), respectively. These derivatives are soluble in most organic
solvents. A condensation of these silylated bases with the protected ribosyl halides
gives the sugar-protected nucleosides and constitutes a modified silyl-Hilbert
Johnson reaction. (12) The major problem in these condensations is the use of
generally unstable protected sugar halides. Vorbriiggen and co-workers have
overcome this problem by using a stable acyl sugar and certain Lewis acids for
an activation of the sugar portion in the condensation with the silyl base. For
example, the treatment of bistrimethylsilylated 5-substituted uracils (10) with
I-O-acetyl-2,3,5-tri-O-benzoyl-o-ribose (11) and stannic chloride in an inert
solvent such as 1,2-dichloroethane or acetonitrile at room temperature afforded
the benzoylated nucleosides (12) in high yields.(I3) This method is adaptable for
the synthesis of 6-azauridine, 2-thiocytidine, and 2-thio-5-butyluridine. 6-Methyl
uridine,(I4) 5-azacytidine, (15) 2- and 4-pyridone, and 2-pyrimidinone ribosides(l6)
were prepared in a similar manner. The disaccharide nucleosides were also
prepared by this method. (17)