Polynucleotides. LII1 Synthesis and properties of poly(2′-deoxy-2′-fluoroadenylic acid)

2′-Deoxy-2′-fluoroadenosine was chemically transformed to its 5′-diphosphate and polymerized with polynucleotide phosphorylase to give poly(2′-deoxy-2′-fluoroadenylic acid) [poly(Af)]. Polymerization proceeded smoothly as in the case of poly(A) and the yield of the polymerization was 55%. The UV absorption spectra of poly(Af) closely resembled those of poly(A) and the hypochromicity was 32% at pH 7.0. The CD profile at 25° and neutrality showed similar pattern to that of other poly(2′-deoxy-2′-halogenoadenylic acids) with somewhat larger [θ] values both in the positive and negative maxima. Acid titration of poly(Af) showed a transition point at pH 5.2 and the Tm of the acid form was 37° which was significantly lower than that of poly(A), but similar to that of poly(2′-azido-2′-deoxyadenylic acid). Poly(Af) formed 1:1 and 1:2 complexes with poly-(U) having Tm of 49° and 62° at 0.04M and 0.15M Na⁺ concentration, respectively. Poly(Af) also formed a 1:2 complex with poly(I) and its Tm was 36° at 0.05M Na⁺ concentration. These data showed that poly(Af) has rather similar properties to those of poly(A), but not to poly(dA).     

Synthesis and carbonic anhydrase inhibitory properties of amino acid – coumarin/quinolinone conjugates incorporating glycine,alanine and phenylalanine moieties

N-Protected amino acids (Gly, Ala and Phe) were reacted with amino substituted coumarin and quinolinone derivatives, leading to the corresponding N-protected amino acid–coumarin/quinolinone conjugates. The carbonic anhydrase (CA, EC 4.2.1.1) inhibitory activity of the new compounds was assessed against various human (h) isoforms, such as hCA I, hCA II, hCA IV and hCA XII. The quinolinone conjugates were inactive as enzyme inhibitors, whereas the coumarins were ineffective hCA I/II inhibitors (K_Is?>?50?μM) but were submicromolar hCA IV and XII inhibitors, with inhibition constants ranging between 92?nM and 1.19?μM for hCA IV, and between 0.11 and 0.79?μM for hCA XII. These coumarin derivatives, as many others reported earlier, thus show an interesting selective inhibitory profile for the membrane-bound over the cytosolic CA isoforms.     

Synthesis and biophysical properties of 5′-thio-2′,4′-BNA/LNA oligonucleotide

Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5′-thio or phosphorothiolate-modified nucleotides, in which the 5′-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5′-thio-2′,4′-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5′-thio-2′,4′-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated.     

Synthesis,Cytostatic Activity and Inhibition of Ribonucleotide Reductase by 5′-Phosphoramidates and 5′-Diphosphates,of 2′-O-Allyl-arabinofuranosyl Nucleosides

Abstract

The diphosphates of a series of 2′-O-allyl-1-β-D-arabinofuranosyl derivatives, previously obtained by us, have been prepared and tested for their inhibitory activity in an in vitro assay using R1 and R2 subunits of the purified recombinant mouse ribonucleotide reductase (RNR). 2′-O-Allyl-araU diphosphate proved to be inhibitory, with an IC₅₀ of 100 μM. The 5′-phosphoramidate pronucleotide of 2′-O-allyl-araU was also prepared and tested for inhibition of tumor cell proliferation.     

Synthesis and fluorescent properties of 5-(1-pyrenylethynyl)-2′-deoxyuridine-containing oligodeoxynucleotides

Novel reagents for the fluorescent labeling of oligo- and polynucleotides have been prepared: 5-(1-pyrenylethynyl)-2′-deoxyuridine 3′-phosphoramidite and a solid support carrying this nucleoside. Oligo-nucleotides containing one or several modified units have been synthesized, and the fluorescence of these probes has been shown to change upon hybridization with the complementary sequence. Fluorescent Nucleosides. III. The previous communications, see [1, 2]. Prefix “d” in the oligodeoxynucleotide designations is omitted.     

On the kinetics of the enzyme-catalyzed hydrolysis of axial chiral alkyl allenecarboxylates: preparation of optically active R-(−)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid and its optically pure S-(+)-methylester

Pig liver esterase (PLE) was used for the preparation of optically active alkyl allenecarboxylates with axial chirality. Free and immobilized enzymes were used as biocatalysts for the kinetic resolution of racemic ester substrates. Whereas the biotransformations using the free biocatalyst resulted in moderately to high enantiomeric ratios, the immobilization significantly decreased the E-value. The reaction conditions were optimized with respect to the enantiomeric ratio and scaled up. The enantiomeric ratio (E-value) was thereby enhanced by a factor of four to E=60. Under optimized conditions (free enzyme, addition of acetone as a cosolvent and Triton X-100 as an emulgator) in a preparative scale biotransformation, 282 mg of optically pure S-(+)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid methylester (96% ee, 82% yield) and 257 mg of R-(−)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid (83% ee, 80% yield) could be synthesized from the racemic substrate.     

Effective syntheses of 2′,4′-BNANC monomers bearing adenine,guanine, thymine,and 5-methylcytosine,and the properties of oligonucleotides fully modified with 2′,4′-BNANC

We efficiently synthesized 2′-O,4′-C-aminomethylene-bridged nucleic acid (2′,4′-BNA^NC) monomers bearing the four nucleobases, guanine, adenine, thymine, and 5-methylcytosine and incorporated these monomers into oligonucleotides. Initially, we carried out the transglycosylation reaction on several 2′-O-substituted 5-methyluridines to evaluate the effects of 2′-substitutions on this reaction. Under the optimized conditions, purine nucleobases were successfully introduced, and 2′,4′-BNA^NC monomers bearing adenine or guanine were obtained over several steps. In addition, the improved synthesis of the 2′,4′-BNA^NC monomers bearing thymine or 5-methylcytosine was also achieved. The obtained 2′,4′-BNA^NC monomers were subsequently incorporated into oligonucleotides and the duplex-forming abilities of the modified oligonucleotides were investigated. Duplexes containing 2′,4′-BNA^NC monomers in both or either strands were found to possess excellent thermal stabilities.     

The amino acid conjugate formed by the interaction of the anion transport inhibitor 4,4′-diisothiocy ano-2,2′- stilbenedisulfonic acid (DIDS) with band 3 protein from human red blood cell membranes

The specific anion transport inhibitor 4,4′-diisothiocyano-2,2′-stilbenedisulfonic acid (DIDS) and its reduced analog (H₂DIDS), when irreversibly bound to band 3 protein of the red blood cell membrane, form amino acid conjugates through interaction with the ?-amino group of a particular lysine residue. The specific residue is located in a transmembrane segment of band 3 protein and appears to be a close neighbor of the transport site.     

Synthesis of 8-Bromo- and 8-Azido-2′-deoxyadenosine-5′-O-(1-thiotriphosphate)

Abstract

Treatment of 3′-O-methoxyacetylated 8-bromo-2′-deoxyadenosine (5), with a twofold excess of salicyl phosphorochloridite (6), and subsequent reaction with bis(tri-n-butylammonium) pyrophosphate and oxidation with sulfur followed by removal of the protecting group gives predominantly 8-bromo-2′-deoxyadenosine-5′-O-(1-thiotriphosphate) (7), and minor amounts of the corresponding brominated monothiophosphate. Alternatively, the photoreactive dATP analog 8-azido-2′-deoxyadenosine-5′-O-(1-thiotriphosphate) (11), is obtained by phosphorylation of unprotected 8-azido-2′-deoxyadenosine (9) with a 1.8 molar equivalent excess of thiophosphoryl chloride and bis(tri-n-butylammonium) pyrophosphate. A protection of the nucleobase 6-amino group is not required. The photoaffinity labeling reagent 11, was characterized by ³¹P-NMR and ion-spray mass spectroscopy and its photolysis upon long wavelength UV irradiation was studied. Both α-thioderivatives of 2′-deoxyadenosine triphosphates can be incorporated into plasmid DNA by T7 DNA polymerase. Thus, they can be used for interference studies of protein binding and for cross-linking with amino acids in protein-nucleic acid-complexes.     

Synthesis and Properties of mRNA 5′-Cap Analogues with 7-Methylguanine Replaced by Benzimidazole or 3-Methylbenzimidazole

Abstract

Several new analogues of the mRNA 5′-cap structure, m⁷G(5′)Pn(5′)N, with n = 2–4, have been synthesized in which the m⁷G component is replaced by 1-(β-D-ribofuranosyl)benzimidazole (RBz) or 3-methyl-RBz. The latter, like m⁷G, has a positively charged imidazole ring and is likewise fluorescent. All compounds have been characterized by various physico-chemical and enzymatic criteria, and by ¹H and ³¹P NMR spectroscopy.     

Synthesis and Binding Properties of a Homopyrimidine 2′,5′-Linked Xylose Nucleic Acid (2′,5′-XNA)

Abstract

The synthesis and hybridization properties of pyrimidine 2′,5′-RNA and 2′,5′-Xylose Nucleic Acid (2′,5′-XNA) are described.     

Nucleosides. Part 3.1 Synthesis of 2-N-Substituted 1-β-D-Arabinofuranosylisocytosine Derivatives by The Reaction of 2′,5′-Dichloro-2′,5′-Dideoxyuridine with Amines

Abstract

Reaction of 2′,5′-dichloro-2′,5′-dideoxyuridine (1) with ammonia and benzylamine afforded the corresponding 2-N-substituted 1-(5-chloro-5-deoxy-β-D-arabinofuranosyl)-isocytosine derivatives (2 and 10). Reaction of 1 with ammonia, methylamine, cyclohexylamine, and benzylamine followed by treatment with methanolic sodium methoxide gave the corresponding 2-N-substituted 1-(2,5-anhydro-β-D-arabino-furanosyl)isocytosine derivatives (6, 11, and 12).     

Synthesis and Properties of Some (2′-5′) Linked Dinucleoside Monophosphates Modified with 3′-Difluoromethylene Groups

Abstract

The title dimers were prepared to investigate conditions required for the synthesis of 3′-difluoromethylene modified oligonucleotides on solid support. As a result a new synthetic cycle was developed that enabled the solid phase synthesis of the modified oligonucleotides.     

5′-O-Aliphatic and amino acid ester prodrugs of (−)-β-d-(2R,4R)-dioxolane-thymine (DOT): Synthesis,anti-HIV activity,cytotoxicity and stability studies

A series of (?)-β-d-(2R,4R)-dioxolane-thymine-5′-O-aliphatic acid esters as well as amino acid esters were synthesized as prodrugs of (?)-β-d-(2R,4R)-dioxolane-thymine (DOT). The compounds were evaluated for anti-HIV activity against HIV-1_LAI in human peripheral blood mononuclear (PBM) cells as well as for their cytotoxicity in PBM, CEM and Vero cells. Improved anti-HIV potency in vitro was observed for the compound 2–4 (5′-O-aliphatic acid esters) without increase in cytotoxicity in comparison to the parent drug. Chemical and enzymatic hydrolysis of the prodrugs was also studied, in which the prodrugs exhibited good chemical stability with the half-lives from 3 h to 54 h at pH 2.0 and 7.4 phosphate buffer. However, the prodrugs were relatively labile to porcine esterase with the half-lives from 12.3 to 48.0 min.     

Nucleosides. 145. Synthesis of 2,5′-Anhydro-2-Thiouridine and its Conversion to 3′-O-Acetyl-2,2′-Anhydro-5′-Chloro-5′-Deoxy-2-Thiouridine. Studies Directed Toward the Synthesis of 2′-Deoxy-2′-Substituted arabino Nucleosides (7)

Abstract

In an attempt to introduce a substituent at C-2′ in the “up” arabino configuration directly by nucleophilic displacement reaction of a preformed pyrimidine ribonucleoside, we synthesized 2,5′-anhydro-5′-deoxy-2-thiouridine (6) in three steps from uridine. Compound 6 was converted into the 3′-O-acetyl derivative 7. Upon treatment of 7 with triflyl chloride in methylene chloride in the presence of triethylamine and p-dimethylaminopyridine, 2,2′-anhydro-1-(3-O-acetyl-5-chloro-2,5-dideoxy-β-D-arabinofuranosyl)-2-thiouracil (9) was obtained as the only isolable product. Obviously, the intermediate 3′-O-acetyl-2,5′-anhydro-2′-O-triflyl-2-thiouridine (8) was attacked by the chloride nucleophile at C-5′ first giving the 2′-O-triflyl-2-thiouridine intermediate from which 9 was formed by intramolecular nucleopilic reaction.     

Synthesis of 2′-Deoxy[5′-13C]Ribonucleotides and HMQC-Noesy NMR Study of the Dickerson's Dodecamer with 13C-Labeling at the 5′ Positions

Abstract

In addition to the synthesis of 2′-deoxy[5′-¹³C]ribonucleosides (6) via the D-[5-¹³C]ribose derivative (4), the construction of the corresponding dodecanucleotide with the Dickerson's sequence and its HMQC-NOESY NMR analysis are described.     

Synthesis of 2′-O-(thymin-1-yl)methyluridine and its incorporation into secondary nucleic acid structures

A double-headed nucleoside wherein an additional thymine is attached to the 2′-O-position of uridine via a methylene linker is prepared and incorporated into oligonucleotides. With single incorporations of the modified nucleotide monomer, these oligonucleotides form duplexes with the complementary DNA sequences which are thermally less stable as compared to the unmodified duplexes. However, stabilization of bulged duplexes or three way junctions is observed. A cross-strand interaction between two additional thymines is also seen in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif, however, much weaker than obtained with the corresponding analogue with the methylene linker directly attached to the 2′-C-position. This demonstrates that the ability to act as a compressed dinucleotide is unique for the latter and due to its perfect preorganization of the additional base in the duplex core.     

Interaction of tritium-labeled H2DIDS (4,4′-diisothiocyano-1,2,diphenyl ethane-2,2′disulfonic acid) with the ehrlich mouse ascites tumor cell

Summary The experiments reported in this paper were undertaken to explore the interaction of tritiated H₂DIDS (4,4-diisothiocyano-1,2,diphenyl ethane-2,2-disulfonic acid) with Ehrlich ascites tumor cells. Addition of (³H)H₂DIDS to tumor cell suspension at 21°C, pH 7.3, resulted in: (i) rapid reversible binding which increased with time and (ii) inhibition of sulfate transport. Tightly bound H₂DIDS, i.e., reagent not removed by cell washing, also increased with time. Binding of 0.02 nmol H₂DIDS/mg dry mass or less did not affect sulfate transport, but, at greater than 0.02 nmol and up to 0.15 nmol the relationship between tight binding and inhibition of transport is linear. The fact that H₂DIDS could bind to the cell and yet not affect anion transport suggests that binding sites exist unrelated to those concerned with the regulation of anion permeability. Support for this is the observation that H₂DIDS is spontaneously released from cells even after extensive washings by a temperature-sensitive process. The most important source of released H₂DIDS is the cell surface coat which labels rapidly (within 1 min) and is then spontaneously released into the medium. A second source is derived from H₂DIDS that slowly entered the cells. Consequently, at least four modes of interaction exist between H₂DIDS and ascites tumor cells. These include both reversible and irreversible binding to membrane components which regulate anion permeability, irreversible binding to cell surface proteins or glycocalyx, and finally incorporation of H₂DIDS into the intracellular phase.     

Synthesis and Anti-Retroviral Activity of O,O′-BIS(3′-Azido-2′,3′-Dideoxythymidin-5′-yl) Phosphoramidate Derivatives

Abstract

A simple and efficient protocol for the preparation of various symmetrical dinucleoside phosphoramidates derived from AZT, is presented. It consists of the phosphonylation of AZT with phosphonic acid in the presence of DCC to produce the symmetrical H-phosphonate diester, followed by its oxidative conversion to various phosphoramidate analogues. The synthesized compounds were evaluated for their anti-HIV activity in different cell cultures.