Practical Synthesis of AZT and AZDU from Xylose: Efficient Deoxygenation via Nucleoside 2′-Xanthates

Abstract

An efficient deoxygenation procedure for nucleoside 2′-xanthates has been developed and applied to the total synthesis of AZT and AZDU from xylose.     

Diastereomeric Process Control in the Synthesis of 2′-O-(2-Methoxyethyl) Oligoribonucleotide Phosphorothioates as Antisense Drugs

Abstract

Coupling of 2′-O-methoxyethylsubstituted nucleoside phosphoramidites to 5′-hydroxyl group of a nucleoside or nucleotide on solid support is under stereochemical process control and is independent of scale, concentration, synthesizer, ratio of amidite diastereomers, solid support etc. However, activators and phosphate protecting groups do play a role in influencing the ratio of phosphorothioate diesters obtained by sulfurization of phosphite triesters.     

Synthesis and Evaluation of Novel 6′,6′-Difluoro 5′-Deoxycarbocyclic Phosphonic Acid Nucleosides as Antiviral Agents

The authors describe highly efficient synthetic routes for the preparation of novel 6′,6′-difluoro 5′-deoxycarbocyclic phosphonic acid nucleosides from 1,4-dihydroxy-2-butene. The discovery that the 6′-fluorinated carbocyclic nucleoside (2, EC₅₀ = 0.16 μM) is a potent anti-HSV-1 agent led to the syntheses and biological evaluations of 6′-modified 5′-deoxyversions of carbocyclic phosphonate nucleosides. The synthesized nucleoside analogues 15, 18, 22, and 25 were tested for anti-HIV activity and for cytotoxicity. However, none of them showed significant anti-HIV-1 activity or cytotoxicity at concentrations up to 100 μM.     

Synthesis of Novel 3′-Hydroxymethyl 5′-Deoxythreosyl Phosphonic Acid Nucleoside Analogues as Potent Antiviral Agents

A very efficient synthetic route to novel 3′-hydroxymethyl 5′-deoxythreosyl phosphonic acid nucleosides was described. The discovery of threosyl phosphonate nucleoside (PMDTA, EC₅₀ = 2.53 μM) as a potent antihuman immunodeficiency virus (anti-HIV) agent has led to the synthesis and biological evaluation of 3′-modified 5′-deoxy versions of the threosyl phosphonate nucleosides. 3′-Hydroxymethyl 5 ′-deoxythreosyl phosphonic acid nucleoside analogues 15, 19, 24, and 28 were synthesized from 1,3-dihydroxyacetone and tested for anti-HIV activity as well as cytotoxicity. The adenine analogue 19 exhibits moderate in vitro anti-HIV-1 activity (EC₅₀ = 10.2 μM).     

Preparation of Nucleoside H-Phosphonoselenoate Monoesters Via the Phosphinate Approach

An efficient entry to nucleoside 3′-H-phosphonoselenoate monoesters via phosphinate intermediates was developed. It involves a reaction of suitably protected nucleosides with triethylammonium phosphinate in the presence of pivaloyl chloride, followed by selenization of the intermediate nucleoside phosphinates with triphenylphosphine selenide, to produce the corresponding nucleoside H-phosphonoselenoates in 86–92% yields.     

Synthesis of a New Hydroxyamino Linked Thymidine Dimer via a Radical C-C Bond Formation

Abstract

An efficient synthesis of a thymidine nucleoside dimer [T-3′-β-O-N(CH₃)-CH₂-5′-T] has been accomplished via an intermolecular radical coupling reaction. The novel dimer contains an achiral and neutral backbone linkage which may have potential application in constructing backbone modified antisense oligonucleosides.     

A simple and efficient synthesis of nucleotides containing 5′-S- or 3′-S-phosphorothioate linkage.

Abstract

A new efficient synthesis procedure leading to the nucleotide containing 5′-S or 3′-S-phosphorothioate linkage will be presented. The tittle compounds were prepared in the reaction anhydronucleoside with nucleoside phosphorodithioates. The second way is based on phosphitylation reaction using the nucleosidylphosphorofluoridites.     

Synthesis of High Quality Phosphorothioate Oligonucleotides as Antisense Drugs. Use of I-Linker in the Elimination of 3′-Terminal Phosphorothioate Monoesters

Abstract

Detritylation of a 5′-O-DMT-2′-deoxyadenosine moiety attached to solid support under acidic condition leads to depurination during oligonucleotide synthesis. Deprotection followed by reversed phase HPLC purification leads to desired oligonucleotide contaminated with significant levels of 3′-terminal phosphorothiaote (3′-TPT) monoester (n?1)-mer. However, it is demonstrated that attachment of dA nucleoside through its exocyclic amino group to solid support leads to substantial reduction of 3′-TPT formation thereby improving the quality of oligonucleotide synthesized.     

A Convenient High Yield Synthesis of N4-Isobutyryl-2′-O-Methylcytidine and Its Monomer Units For Incorporation into Oligonucleotides

Abstract

We designed an efficient three step procedure for the synthesis of N⁴-isobutyryl-2′-O-methylcytidine. This protected nucleoside was then used to prepare a methylphosphonamidite monomer for incorporation into oligonucleotides. Transamination at the C⁴ position of cytidine using ethylenediamine, which has been reported for the N⁴-benzoyl cytidine, was not observed with N⁴-isobutyryl protected 2′-O-methylcytidine.     

Synthesis and Hybridization Properties of Oligodeoxynucleotides Containing 3′-Deoxy-3′-C-methyleneuridine

Abstract

3′-Deoxy-3′-C-methyleneuridine nucleoside 1 ¹ has been incorporated into oligodeoxynucleotides. Relative to the unmodified references, oligomers containing nucleoside 1 displayed reduced binding affinities towards complementary DNA and RNA with a tendency towards RNA-selective hybridization.     

A Rapid Method for the Functionalisation of Polymer Supports for Solid Phase Oligonucleotide Synthesis

Abstract

A rapid method is described for the covalent anchoring of appropriately protected 2′-deoxyribonucleoside-3′-O-succinates to LCAA-CPG, widely used support for solid phase oligonucleotide synthesis. The method involves the reaction of nucleoside-3′-O-succinates with aminoalkyl functions of the support in the presence of improved and commercially available condensing reagent, TBTU or TPP-DTNP to generate fully functionalised polymer supports with excellent nucleoside loadings.     

The Behaviour of 2′-Deoxy-2′-Fluorouridine Incorporated into Oligonucleotides by the Phosphoramidite Approach

Abstract

2′-Deoxy-2′-fluorouridine has been chemically incorporated into an oligodeoxynucleotide of the structure 5′ACGGAX 3′ (X=U(2′-F)) using the phosphoramidite method and the behaviour of the product has been studied. 5′-O-Monomethoxytrityl-2′-deoxy-2′-fluorouridine was fixed on silica gel at the 3′-end and the chain elongated on a DNA-synthesizer using nucleoside methoxyphosphoramidites. After alkaline work-up two products were observed. One was found to be the desired fluoro containing hexamer, whereas the other corresponds to an araU-hexamer (X=arabino-furanosyluridine). The latter compound is supposed to be a product of alkaline hydrolysis of the C-2′-F-bond. The oligomers containing 2′-fluoro- and ara-U at their 3′-end were chemically sequenced by a solid phase method on CCS-paper which confirmed the right primary structure.     

Pyrimidine Nucleotidases/Phosphotransferases from Human Erythrocyte

Abstract

Two cytoplasmic pyrimidine 5′-nucleotidase have been purified from human erythrocytes to homogeneity and partially characterized. The two enzymes, indicated as PN-I and PN-II, preferentially hydrolyse pyrimidine 5′-monophosphates and 3′-monophosphates, respectively. The kinetic analysis demonstrate that pyrimidine 5′-nucleotidases, in the presence of suitable nucleoside substrates, can operate as phosphotransferases by transferring phosphate to various nucleoside acceptors, including nucleoside analogues known as important drugs widely used in chemotherapy.     

Novel Synthesis of 4′C-Aryl-Branched Acyclic Nucleoside Using [3,3]-Sigmatropic Rearrangement

Abstract

A very efficient synthetic route for preparing a novel 4′-C-aryl branched-1′,2′-seco-2′,3′-dideoxy-2′,3′-didehydro-nucleoside is described. Mesylate 7 was successfully synthesized via a Horner-Wadsworth-Emmons reaction and a [3,3]-sigmatropic rearrangement, with which an adenine base was coupled by nucleophilic substitution conditions (K₂CO₃, 18-Crown-6, DMF) to give the target nucleoside 9.     

Synthesis and Evaluation of Novel Oligodeoxynucleotides Containing 3′-C-(3-Benzoyloxypropyl)thymidine and Bicyclo Nucleoside Derivatives

Abstract

The stereoselective synthesis of 3′-C-Allyluridine derivative 2 has been accomplished. This nucleoside was used as a key synthon for the synthesis of oligodeoxynucleotides containing 3′-C-(3-benzoyloxypropyl)thymidine (X) or bicyclo nucleoside (Y+Z) monomers. Preliminary thermal experiments are reported.     

3′-AZIDO-3′-DEOXY-5′-O-ISONICOTINOYLTHYMIDINE,A NEW PRODRUG OF ZIDOVUDINE. SYNTHESIS,SOLID STATE CHARACTERIZATION AND ANTI HIV-1 ACTIVITY

ABSTRACT

Synthesis, solid state characterization and anti HIV-1 activity of 3′-azido-3′-deoxy-5′-O-isonicotinoylthymidine (2), a new prodrug of zidovudine (AZT, 1), are described. Two solid forms of 2 prepared by crystallization from ethyl acetate-petroleum ether (form α) and from a melt sample of form α (amorphous form) were characterized by X-ray diffractometry, infrared spectroscopy, differential scanning calorimetry (DSC) and thermogravimetry (TGA) techniques. The novel nucleoside exhibited antiviral activity against standard and resistant strain panels of HIV-1 as well as cytotoxicity similar to that of AZT.     

Synthesis and Structural Analysis of Oxadiazole Carboxamide Deoxyribonucleoside Analogs

Two novel C-linked oxadiazole carboxamide nucleosides 5-(2′-deoxy-3′,5′-β-D-erythro-pentofuranosyl)-1,2,4-oxadiazole-5-carboxamide (1) and 5-(2′-deoxy-3′,5′-β-D-erythro-pentofuranosyl)-1,2,4-oxadiazole-3-carboxamide (2) were successfully synthesized and characterized by X-ray crystallography. The crystallographic analysis shows that both unnatural nucleoside analogs 1 and 2 adapt the C2′-endo (“south”) conformation. The orientation of the oxadiazole carboxamide nucleobase moiety was determined as anti (conformer A) and high anti (conformer B) in the case of the nucleoside analog 1 whereas the syn conformation is adapted by the unnatural nucleoside 2. Furthermore, nucleoside analogs 1 and 2 were converted with high efficiency to corresponding nucleoside triphosphates through the combination chemo-enzymatic approach. Oxadiazole carboxamide deoxyribonucleoside analogs represent valuable tools to study DNA polymerase recognition, fidelity of nucleotide incorporation, and extension.

     

5′-Hydrogenphosphonates and 5′-Methylphosphonates of Sugar Modified Pyrimidine Nucleosides as Potential Anti-HIV-1 Agents.1

Abstract

A number of nucleoside 5′-hydrogerphosphonates and nucleoside 5′-methylphosphonates were prepared, to study their ability to inhibit replication of HIV-1. Two compounds, the 5′-hydrogenphosphonate of 3′-azido-3′-deoxythymidine (AZT-HP, IVc) and of 3′-deoxy-3′-fluorothymidine (FLT-HP, IVa), exhibit potent anti-HIV-1 activity with selectivity indices similar to or better than those of their parent nucleosides.     

New Nucleoside Analogues for the Recognition of Pyrimidine-Purine Inversion Sites

Abstract

A new nucleoside designed to enhance triplex stability has been synthesised in 15 steps starting from sugar 2. This pathway contains the sugar derivative 9 which is a useful intermediate for the introduction of other natural and unnatural bases into the 2′-aminoethoxy nucleoside containing scaffold.     

Kinetic Properties of Adenine Nucleotide Analogues Against Purified 5-Phosphoribosyl-1-pyrophosphate Synthetases from E. coli,Rat Liver and Human Erythrocytes

Abstract

The nucleoside analogue 2′,3′-dideoxyadenosine (ddA), the phosphonate isostere of 2′,3′-dideoxy-2′,3′-didehydro-adenosine (d4A) 5′-monophosphate (d4API), and the acyclic nucleoside phosphonates PMEoA, PMEA, FPMPA and PMPA are potent and selective antiretroviral agents. We found that these compounds are recognized as substrates by the PRPP synthetases from E. coli, rat liver and human erythrocytes, as their monophosphate and triphosphate form in the reverse and forward reaction, respectively. In particular, ddA-5′-monophosphate (ddAMP) and ddA-5′-triphosphate proved to be excellent substrates for the enzymes. D4API was a relatively good substrate of the rat liver and human erythrocyte PRPP synthetases. The acyclic nucleoside phosphonates were rather poor substrates, as evident from their low V_max values. None of the PRPP synthetases are found to act stereospecifically: they recognized both the S- and R-enantiomers of FPMPA and PMPA in a comparably efficient manner. Our data indicate that PRPP synthetase may recognize a much broader range of adenine nucleotide analogues than previously thought.