Design and Synthesis of Triazole-Linked xylo-Nucleoside Dimers

Three triazole-linked nonionic xylo-nucleoside dimers T^L-t-T^xL, T^L-t-A^BzxL and T^L-t-C^BzxL have been synthesized for the first time by Cu(I) catalyzed azide-alkyne [3 + 2] cycloaddition reaction (CuAAC) of 1-(3′-azido-3′-deoxy-2′-O,4′-C-methylene-β-D-ribo-furanosyl)thymine with different alkynes, i.e., 1-(5′-deoxy-5′-C-ethynyl-2′-O,4′-C-methylene-β-D-xylofuranosyl)thymine, 9-(5′-deoxy-5′-C-ethynyl-2′-O,4′-C-methylene-β-D-xylo-furanosyl)-N6-benzoyladenine and 1-(5′-deoxy-5′-C-ethynyl-2′-O,4′-C-methylene-β-D-xylofuranosyl)-N4-benzoylcytosine in 90%–92% yields. Among the two Cu(I) reagents, CuSO₄.5H₂O-sodium ascorbate in THF:^tBuOH:H₂O (1:1:1) and CuBr.SMe₂ in THF used for cycloaddition (click) reaction, the former one was found to be better yielding than the latter one.     

Synthesis of 3′-Fluoro-3′-deoxy-N6-cyclopentyladenosine

Abstract

Starting from 9-(β-D-xylofuranosyl)-6-chloropurine, the title compound was prepared in four steps. Reaction with cyclopentylamine followed by treatment of the 2′-O,5′-O-ditritylated material with diethylaminosulfur trifluoride (DAST), yielded after deprotection the desired compound.     

Stereocontrolled Synthesis of Pyridazine,Pyrazine, and Triazine 2′-DEOXY-β-Nucleosides by Means of Intramolecular Glycosylation

Abstract

The stereocontrolled synthesis of 2′-deoxynucleoside analogs was explored by intramolecular glycosylation of pyridazine, pyrazines and triazines. These heterocycles were temporarily connected to the 5-O position in 1-thioglycoside via ethereal linkage.     

Synthesis and anti-HIV evaluation of new 2′,3′- dideoxy-3′-thiacytidine prodrugs

Abstract

A series of anti-HIV prodrugs possessing various polyaminated side arms have been developed. The incorporation of a N-Boc protected monoamine or diamine side arm into the backbone of the 2′,3′-dideoxy-3′-thiacytidine 1 (BCH-189) provided an increase in antiviral potency, which could be several orders magnitude greater than the parent drug (1) depending on the cell culture systems used (MT-4 or MDMs). Twenty six 2′,3′-dideoxy-3′-thiacytidine prodrugs which differ from each other by the length, the nature of the 5′-O function and the 5′-O or /and N-4 position on the nucleoside moiety were synthesized. Among this new series of prodrugs, several congeners (12c and 12a) were found to inhibit HIV-1 replication in cell culture with 50% effective concentrations ECso of 10 and 50 nM respectively, in MT-4 cells. Compound 12c was found more active on infected MDMs cells with 50% effective concentration of 0.01 nM. The synthesis and the antiviral properties of these compounds are discussed.     

Determination of the Group Electronegativity of CF3 Group in 3′-O-CF3-Thymidine by 1-NMR

Abstract

The interplay of enthalpy of the gauche effect (ΔH°_GE) of the [X3′-C3′-C4′-O4′] fragment in various 3′-substituted (X) 2′,3′-dideoxythymidine derivatives 1–7 and the inherent anomeric effect drives the two-state North ? South equilibrium in the constituent sugar moiety. The group electronegativity of 3′-OCF₃ substituent in Marriott's, Inamoto's and Mullay's scales has been determined from simple calibration graphs correlating the group electronegativity of various 3′-substituents (X) in 2′,3′-dideoxythymidine derivatives 1–7 with the experimental strength (ΔH°_GE) of the [X3′-C3′-C4′-O4′] gauche effect. ΔH°_GE has been experimentally determined from pseudorotational analyses of temperature-dependent ³J_HH coupling constants, and can be used as an unambiguous tool for direct experimental estimation of the group electronegativity of a specific substituent covalently attached to 3′-carbon of 2′,3′-dideoxythymidine, which can be compared, in turn, with the theoretical estimation carried out according to Marriott's or Inamoto's procedure. Inconsistency found between theoretical values in Marriott's and Inamoto's scales, on the one hand, and between our experimental estimate and the theoretical value in Marriott's scale, on the other, have been solved by refining the electronegativity scale using our experimental data for 1–7.     

Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of CAc Derivatives

Abstract

We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dC^bz has been eliminated by the use of dC^Ac phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dC^Ac hydrogen phosphonate and DMT ribo C^Ac-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.     

Oxidative Cyclization of 2′,3′-O-Isopropylidene-Adenosines into 5′-O,8-Cycloadenosines with Lead Tetraacetate: Remarkable Effect of N6-Substituents on the Oxidation

Abstract

Oxidation of 2′,3′-O-isopropylideneadenosines (1) with lead tetraacetate (LTA) in dry benzene resulted in the formation of the corresponding 5′-O,8-cyclo-2′,3′-O-isopropylideneadenosines (2), which has a new methodological implication for the chemical modification of adenosines. The occurrence of the oxidative cyclization was remarkably affected by the nature of N⁶-substituents: N⁶-benzoyl substitution prominently accelerated the oxidative cyclization in comparison with none and dimethyl substitutions. In the oxidation of N⁶,N⁶-dimethyladenosine (1d), an intriguing oxidative demethylation was observed.     

Synthesis and Absolute Configuration of Pyriculol

A total synthesis of optically active pyriculol is described. The Wittig reaction between an aldehyde 19 and a triphenylphosphonium ylide 12 gave an intermediate 20. Successive treatment of 20 with p-toluenesulfonic acid, active manganese dioxide, and potassium carbonate gave (3′R,4′S)-pyriculol (23), which was identical with natural pyriculol (1) in all respects. From this synthesis, the absolute stereochemistry of pyriculol (1) was determined to be 2-[(3′R,4′S)-3′,4′-dihydroxy- (1′E,5′E)-1′,5′-heptadienyl]-6-hydroxybenzaldehyde     

Structural and Conformational Studies on Deoxyguanosyl-3′,5′-Deoxyadenosine Monophosphate and Its Ethyl Phosphotriester Analogs - Left-Handed Dimers

Abstract

The mode of base-base stacking, the handedness and the sugar(dGpA)phosphate backbone conformation of deoxyguanosyl 3′-5′ deoxyadenosine and its diastereomeric ethyl phosphotriester analogs were studied by ¹H NMR, UV and CD spectroscopy. The results indicate the three dimers are left-handed, while the sugar phosphate backbone is comprised predominantly of C_2′-endo, gg (C_4′-C_5′) and g′g′ (C_5′-O) conformers. The two bases are extensively stacked and interact about 90° along the dyad axes. The extent of base overlap in dGpA is slightly greater than in either ethyl phosphotriester analog. The absolute configurations of the two ethyl phosphotriester diastereoisomers of dGpA can be assigned by one-dimensional and two-dimensional ¹H NMR nuclear Overhauser enhancement experiments.     

The Synthesis of Dimethyl Esters of dl-O,O′-Dimethylfukiic Acid and dl-O,O′-Dimethylepifukiic Acid

The synthesis of dimethyl esters of dl-O,O′-dimethylfukiic acid (11) and dl-O,O′-dimethylepifukiic acid (12) are described.     

Synthesis and Antiherpetic Activities of Several Acyclic Analogues Of Guanosine

Abstract

Several acyclic analogues of guanosine, 2′-deoxy-2′, 3′-secoguanosine(3), 3′-deoxy-2′, 3′-secoguanosine (4), and 2′-, 3′-dideoxy-2′-, 3′-secoguanosine were synthesized from guanosine. In addition, the 3′-, 5′-cyclic phosphate (21) and 3′-, 5′-cyclic methylphosphonates (22a, b) of 3 were also prepared. At concentrations up to 300 μM none of these compounds had significant antiherpetic activity in antiviral assays in vitro.     

New Classes of Fluorinated L-Nucleosides; Synthesis and Antiviral Activity

Abstract

The synthesis of 3′-fluorinated apionucleosides 7 and 2′-fluoro-2′, 3′-unsaturated L-nucleosides 8 via common synthon, 2-fluoro-butenolide 2, has been described. Among the newly synthesized nucleosides, L-2′-F-d4C, L-2′-F-d4FC and L-2′-F-d4A exhibit significant anti-HIV and anti-HBV activities.     

A Short High Yielding Synthesis of the Potent Anti-VZV Carbocyclic Nucleoside Analogue Carba-BVDU

Abstract

A short high yielding synthesis of the potent anti-varicella-zoster virus (VZV) carbocyclic nucleoside analogue carba-BVDU 1 starting from aminodiol 2 is described. Reaction of 2 with acyl carbamate 3 and subsequent ring closure under acidic conditions afforded 5-ethyl-2′-deoxy-4′a-carbauridine 5. In situ acetylation of 5 afforded 3′,5′-di-O-acetyl-5-ethyl-2′-deoxy-4′a-carbauridine 6 in 78% overall yield from 2. Radical bromination of 6 with either bromine or NBS and subsequent treatment with triethylamine gave an efficient conversion to 3′,5′-di-O-acetyl-5-(E)-(2-bromovinyl)-2′-deoxy-4′a-carbauridine 7. Deacetylation of 7 afforded 1 in an overall 45–53% yield from 2.     

Crystal Structure of 1-(2′,3′,5′-Tri -O-Acetyl-β-D-ribofuranosyl)-3-acetoxy-2-pyridone: An Antitumour Agent

Abstract

1–C3′, 3′, 5′–Tri—O—acetyl— β—D—ribof uranosyll)—3—acetoxy —2—pyridone,crystallised in space group P2 with z=2 and cell parameters a=12. 446(2), b=10. 415(2), c=7. 600(2) A, β=03. 3O(4). The structure was solved by direct methods and refined by full—matrix least—squares to a final R value of 0·251 for 1847 observed reflections. The sugar—pucker is found to be ³ECC3′ endo) with P = 17.7° and x_CN=170. 2(2)° in the range. The C4′-C5′ conformation is gauche minus. Because of the absence of H—bond donor atoms. the crystal structure is stabilised by a network of C-H—-O close contacts. No base stacking is observed.     

Synthesis and NMR Spectra of Some New Carbohydrate Modified Uridine Phosphoramidites

Abstract

The one step reaction of 2′- and 3′-keto derivatives of uridine with bromodifluoromethyl[tris(dimethylamino)]phosphonium bromide and zinc gives the corresponding 2′- and 3′-difluoromethylene nucleosides in good yield. Desilylation and phosphitylation of the resultant 2′- or 3′-hydroxyls provides the target 2′- and 3′-phosphoramidites 7 and 8 for use in oligonucleotide synthesis¹.     

Improved Synthesis of 2′-Amino-LNA

Abstract

2′-Amino-LNA phosphoramidite (10) was synthesised by means of a new strategy, which is convergent with the synthesis of 2′-oxy-LNA up until a late stage intermediate (1).     

Studies Towards Synthesis of Dinucleoside Arylphosphonates with Metal Complexing Properties

Abstract

An efficient and stereospecific synthesis of dinucleoside 4′-(2,2′:6′,2″-terpyridyl)phosphonate 2 and 5-(2,2′-bipyridyl)phosphonate 3 via a palladium(0) cross coupling strategy has been developed.     

Synthesis of an Alanyl Adenosine Analog

Abstract

The synthetic route towards a 3′-alanyl-3′-amino-3′-deoxyadenosine derivative is described which allows the automated synthesis of 3′-aminoacylated RNA strands.     

An Inverse Approach in Oligodeoxyribonucleotide Synthesis

Abstract

We synthesized 3′-O-dimethoxytrityl-5′O-phosphoramidites and 5′-O-succinates which can be used as monomeric building blocks for the built up of oligodeoxyribonucleotides in the alternative 5′-3′ direction. With this inverse strategy oligonucleotide 3′-conjugates as well as 3′-3′ and 5′-5′ internucleotidic linkages can be easily formed.     

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.