Structure-activity relationships of 2'-deoxy-2',2'-difluoro-L-erythro-pentofuranosyl nucleosides

Following the recent discoveries that some L-nucleosides are more or equal potent than their D-counterparts, we synthesized 2'-deoxy-2',2'-difluoro-L-erythro-pentofuranosyl nucleosides as potential antiviral agents. The target compounds were synthesized via the key intermediates 7a or 7b from L-gulono gamma-lactone. Compound 2 was oxidatively cleaved and coupled with ethyl bromodifluoroacetate in the presence of activated zinc under Reformatsky conditions to obtain a diasteomeric mixture of 4(R) and 4(S), in a 4:1 ratio. The major 4(R) isomer was cyclized and treated appropriately to obtain the mesylate 8a or 8b, which was condensed with various silyl-protected pyrimidines. Condensation of the alcohol 7a or 7b with 6-chloropurine under Mitsunobu conditions afforded the 6-chlorpurine analogs 53a or 53b and 54a or 54b. Further treatment of the compounds 53a, 54a and 53b, 54b afforded the inosine and adenine derivatives 57-60, respectively. The condensation of 2-amino-6-chloropurine with compound 8a and subsequent treatment with 2-mercaptoethanol/sodium methoxide afforded the guanine analogs 63 and 64. All of the synthesized nucleosides 31-52, 57-60, 63, and 64 were evaluated for antiviral activity and for cellular toxicity. Adenine derivative 57 showed a moderate activity against HIV-1 in PBM cells (3.4 microM). None of the other compounds showed any significant activities against HIV-1, HBV, HSV-1, HSV-2, and toxicity in Vero, CEM, and PBM cell lines up to 100 microM. The X-ray structure of the 5-iodocytosine analog showed a 2'-exo/3'-endo conformation for the carbohydrate moiety, which is different from those of the biologically active compounds (-)-FTC and L-FMAU.     

Gamma irradiation of 2'-deoxyadenosine in oxygen-free aqueous solutions: identification and conformational features of formamidopyrimidine nucleoside derivatives

The two major radiation-induced decomposition products of 2'-deoxyadenosine in oxygen-free aqueous solution have been isolated by reverse-phase HPLC. The 1H and 13C NMR features of the two modified nucleosides obtained in DMSO-d6 are indicative of a similar formamidopyrimidine structure for the base residue (the ring-opened form of a C-8 hydroxylated purine). Interestingly, the sugar moiety exhibits a pyranose configuration, the two nucleosides being a pair of alpha and beta anomers. One-bond and long-range 1H-13C 2D NMR experiments have allowed the complete assignment of the carbon atoms. Confirmation of the base structure was obtained by 1H-15N scalar-correlated 2D NMR experiments. Attempts were made to characterize the expected furanose form of the initially generated formamidopyrimidine derivative. In this respect, isomerization reaction of the sugar moiety of the latter compound takes place rapidly after gamma-irradiation as inferred from 1H NMR analysis. The conformational study of the sugar moiety of the two pyranose anomers was inferred from detailed 600.13 MHz 1H NMR analysis in D2O. The alpha anomer exhibits a predominant 1C4 conformation whereas the beta anomer adopts preferentially a 4C1 conformation. In addition, the dynamic study of the restricted rotation of the formamido bond has revealed a 1/5 ratio in favor of the s-cis rotamer for both nucleosides. The energy barrier at coalescence was determined to be delta G# = 75.5 kJ.mol-1 (Tc = 370 K).     

Nucleosides. 116. 1-(beta-D-Xylofuranosyl)-5-fluorocytosines with a leaving group on the 3' position. Potential double-barreled masked precursors of anticancer nucleosides

Syntheses of five pairs of cytosine and 5-fluorocytosinexylofuranosyl nucleosides in which the 3'-hydroxyl group is replaced by Cl, Br, OMs, or OTs are described. Those xylosyl nucleosides with a good leaving group at the 3' position exhibit good inhibitory activity against L5178Y and P815 mouse leukemic cells in vitro at rather low concentrations, and like that of ara-C this cytotoxicity is reversed by 2'-deoxycytidine but not by thymidine. Xylosylcytosines are not active against ara-C resistant lines of L5178Y and P815 cells; however, the corresponding 5-fluorocytosine analogues exhibit significant cytotoxicity against these ara-C resistant leukemic cell lines, and this activity is reversed by thmidine but not by deoxycytidine. These data support the "double-barreled" masked precursor hypothesis in that xylosyl-5-fluorocytosines substituted at the 3' position by a good leaving group exhibit activity akin to that of ara-C in the ara-C sensitive lines, while these nucleosides act as 5-fluoropyrimidines in the ara-C resistant lines.     

How accurate is parent rating of hearing for children with otitis media?

L-Enantiomers of 4'-thioarabinofuranosyl pyrimidine nucleosides were synthesized from D-xylose. Methyl 2,3,5-tri-O-benzyl-D-xylofuranoside 6 was converted to the corresponding xylitol 7, which was treated with MsCl and then Na2S to give 1,4-anhydro-L-4-thioarabitol 8. As previously reported, Pummerer rearrangement of 8 followed by glycosylation with a silylated thymine and N4-acetylcytosine derivative and deprotection gave the corresponding alpha- and beta-L-4'-thioarabinofuranosyl pyrimidine nucleosides.     

Biological activity and phosphorylation of 2'-azido-2'-deoxyuridine and 2'-azido-2'-deoxycytidine

2'-Azido-2'-deoxyuridine and 2'-azido-2'-deoxycytidine were evaluated for their inhibitory activity against ribonucleotide reductase and for subsequent cell growth inhibition. Their mono- and di-phosphates were synthesized and their inhibitory activities against the reductase were also determined in a permeabilized cell system, along with the two nucleosides. The results of the present study identify the first phosphorylation step involved in the conversion of the two azidonucleosides to the corresponding diphosphates to be rate-limiting in the overall activation.     

Nucleosides. 102. Synthesis of some 3'-deoxy-3'-substituted arabinofuranosylpyrimidine nucleosides

The synthesis of some 3'-deoxy-3'-substituted arabinofuranosylcytosine (4a-d) and uracil (7a-d, 8a-d, X =Br, I, N3, SCN) nucleosides was accomplished by treatment of the requisite 2',3'-anhydrolyxofuranosylpyrimidine nucleoside (5,6a,b) with the appropriate ammonium salt in refluxing ethanol. Cleavage of the oxirane ring provided the desired 3'-deoxy-3'-substituted pyrimidine nucleosides (4a-d, 7a-d, and 8a-d). In vitro screening of compounds 4a-d, and 7a-d, with L5178Y cells in culture showed no significant inhibitory properties.     

Mechanism of hydroxylamine mutagenesis. Crystal structure and conformation of 1,5-dimethyl-N4-hydroxycytosine

The crystal structure of the title compound, which is a formal analogue of 5-methyl-N4-hydroxycytosine nucleosides, has been determined by X-ray diffraction. The space group is P2(1)/c with a = 7.368 (2), b = 12.096 (3), c = 9.192 (4) A, beta = 113.94 (3) degrees. Three-dimensional intensity data were collected with a four-circle diffractometer, and the structure was refined by block-diagonal least-squares to R = 0.053. The compound is in the imino form, and the exocyclic N4-OH is located essentially in the plane of the pyrimidine ring, and syn to the ring (N(3). There is an intramolecular hydrogen bond involving the N(3)-H as donor and O(4) as acceptor, viz. N(3)-H(31)----O(4)-H. With this conformation, which probably prevails also in solution, the compound would be unable to participate in normal Watson-Crick base pairing. It is shown that a similar situation may prevail for N4-hydroxycytosine nucleosides. The implications with regard to the molecular mechanism of hydroxylamine mutagenesis, with particular reference to the T-even bacteriophages, are discussed. Analogous considerations are applied to an examination of the possible behaviour of hydroxylamine-modified adenine nucleosides.     

7-Deazapurine 2'-deoxyribofuranosides are noncleavable competitive inhibitors of Escherichia coli purine nucleoside phosphorylase (PNP)

A series of 7-deazapurine 2'-deoxyribofuranosides were synthesized according to already known procedures and their substrate and inhibitor properties with purified E. coli purine nucleoside phosphorylase were examined. In agreement with previous findings, substrate activity was not detected for any of the compounds tested. Most of the nucleosides showed weak inhibition in the preliminary screening, i.e. at a concentration of about 100 microM. However some combinations of 6-chloro, 6-amino or 6-methoxy substituents with bulky hydrophobic groups at position 7 of the base and/or chloro, amino, methoxy or methylthio group at position 2 markedly enhanced affinity of such modified nucleosides for the E. coli enzyme. The most potent inhibition was observed for two nucleosides: 6-chloro- and 2-amino-6-chloro-7-deazapurine 2'-deoxyribofuranosides that show inhibition constants Ki = 2.4 and 2.3 microM, respectively. Several other compounds were also found to be good inhibitors, with inhibition constants in the range 5-50 microM. In all instances the inhibition was competitive vs. the nucleoside substrate 7-methylguanosine. Inhibition constants for 7-deazapurine nucleosides are in general several-fold lower than those observed for their purine counterparts. Therefore 7-deaza modification together with substitutions at positions 2, 6 and 7 of the base is a very promising approach to obtain competitive noncleavable inhibitors of E. coli PNP that may bind to the enzyme with inhibition constants in the microM range.     

Molecular mechanics studies on the conformations of 2',3'-dideoxy-2',3'-didehydroguanine nucleoside, D4G

Conformational energy calculations have been presented on guanine nucleoside in which the furanose ring is replaced by 2',3'-dideoxy-2',3'-didehydrofuran using molecular mechanics and conformational analysis. Conformational energies have been evaluated using the MM2 and AMBER94 force field parameters at two different dielectric constants. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (chi) and C4'-C5' (gamma) bonds torsions. In general, the chi-gamma interrelationships differ from the corresponding plots for unmodified nucleosides and nucleotides, reported previously. Consistency of the calculated preferred conformations with the x-ray data is sensitive to the force field employed.     

Serine 318 is essential for the pyrimidine selectivity of the N2 Na+-nucleoside transporter

Molecular cloning has isolated two subtypes of Na+-nucleoside transporters; one is pyrimidine-selective (N2), and the other is purine-selective (N1). Using chimeric rat N2/N1 transporters, we previously demonstrated that transmembrane domains (TM) 8 and 9 are the major sites for substrate binding and discrimination. Interestingly, when TM8 of N2 was replaced by that of N1, the resulting chimera, T8, lost the pyrimidine selectivity of N2 and accepted both purine and pyrimidine nucleosides. Five residues differ between rat N2 and N1 in TM8. To identify the critical residues responsible for transport selectivity, the five residues in N2 were systematically changed to their equivalents in N1. Replacing the serine residue at position 318 to its equivalent N1 residue, glycine, caused N2 to lose its selectivity for pyrimidine nucleosides and accept purine nucleosides as substrates. In contrast, replacing the other four residues did not change the pyrimidine selectivity of N2. Furthermore, when glycine 318 in chimera T8 was changed back to serine, the chimeric transporter regained pyrimidine selectivity. These observations suggest that serine 318 is located in the nucleoside permeation pathway and is responsible for the substrate selectivity of N2. An adjacent residue, glutamine 319, was found to be important in modulating the apparent affinity for nucleosides.     

Quantitative analysis of similarities and differences in neurotoxicities caused by adenosine and 2'-deoxyadenosine in sympathetic neurons

These experiments characterize the nucleoside transport and quantify the neurotoxicity of adenosine and 2'-deoxyadenosine (dAdo) in chick sympathetic neurons. We show that [3H]adenosine transport was sensitive to low temperature, specific inhibitors of nucleoside transport, and an excess concentration of adenosine. However, many of these treatments had a marginal effect on [3H]dAdo transport. Total retention of [3H]dAdo over short and long periods was approximately 10 times less than that of [3H]adenosine. These data suggest that adenosine and dAdo enter sympathetic neurons by different routes. Uptake of (3H]norepinephrine ([3H]NE) decreased in neurons damaged by nucleosides and increased to control levels when neurons were protected by various agents against adenosine or dAdo toxicity. These results indicate that [3H]NE uptake serves as a quantitative index of toxicity by the nucleosides. Using this approach we demonstrate that phosphorylation of both nucleosides is essential for their lethal action. For example, iodotubercidin prevented nucleoside-induced neuronal death, but the effect was much more pronounced in the case of dAdo toxicity (IC50 of 0.83 +/- 0.4 vs. 30 +/- 1.6 nM). Another kinase inhibitor, 5'-amino 5'-deoxyadenosine, was effective in protecting neurons against dAdo but had no effect against adenosine toxicity. These results suggest that specific kinases are associated with the phosphorylation of adenosine and dAdo in sympathetic neurons to produce toxic metabolic products. Finally, neurons were susceptible to dAdo toxicity from the time of plating to 4 weeks in culture but were resistant to adenosine toxicity 8 h after plating. In conclusion, our results highlight major differences in the mechanism of neurotoxicity by adenosine and dAdo and provide insights for identification of biochemical pathways leading to neuronal death.     

Studies on the synthesis of oligonucleotides containing photoreactive nucleosides: 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine

Oligonucleotides containing the photoreactive nucleosides 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine have been prepared using protected 2-fluoro-2'-deoxyinosine and 8-bromo-2'-deoxyadenosine phosphoramidites. After the assembly of the oligonucleotides, the nucleoside derivatives are converted to the corresponding azido derivatives by treatment with lithium azide in dry DMF. Deprotection of oligonucleotides carrying these azidonucleosides is performed with concentrated ammonia at room temperature.     

Synthesis and biological properties of the four optical isomers of 5-o-carboranyl-2',3'-didehydro-2',3'-dideoxyuridine

The four isomers of the 5-o-carboranyl-2',3'-didehydro-2',3'-dideoxyuridine (d4CU) were synthesized and their antiviral activity and cytotoxicity in normal and cancer human cells determined. Coupling of silylated 5-o-carboranyluracil with the protected D/L 2,3-dideoxy-2-phenylselenenylribosylacetates provided after oxidative elimination and deprotection, the desired compounds. The presence of the electron deficient 5-o-carboranyl moiety on uracil influenced the yield of the various isomers. In general, the compounds demonstrated weak anti-human immunodeficiency virus activity in primary human lymphocytes. No marked difference in the biological profile was noted for the various optical isomers, suggesting that the high lipophilicity of these nucleosides imparted by the carboranyl moiety overrides stereochemical considerations in the 2',3'-didehydro-2',3'-dideoxyaglycon moiety.     

Studies on base-boronated oligonucleotides. 2 (1). Incompatibility of DMT and cyanoborane groups during oligonucleotide synthesis

The cyanoborane (-BH2CN) nucleosides and nucleotides are a new class of compounds that mimic natural and synthetic congeners in many ways and exhibit interesting biochemical and biophysical properties. The B-N bond is isoelectronic with the C-N+ bond of N7-alkylated 2'-nucleosides, as well as the C-C bond of naturally occurring 7-alkyl-7-deazanucleosides. These compounds differ from normal guanosine in that they are incapable of hydrogen bonding at the 7-position. The syntheses of N7-cyanoborane 2'-deoxyguanosine, N2-(dimethylaminomethylene)-N7-cyanoborane 5'-(dimethoxytrityl)-2'-deoxyguanosine (3), and N2-isobutyryl-N7-cyanoborane 5'-(dimethoxytrityl)-2'-deoxyguanosine (9) are described. Removal of the dimethoxytrityl (DMT) group from 3 or 9 is accompanied by significant loss of the cyanoborane moiety. Additionally, dimethoxytritylation of a cyanoboronated nucleoside leads to partial deboronation, thus limiting use of the commercially available 5'-DMT nucleosides as viable precursors in base-boronated oligonucleotide synthesis. The incompatibility of the cyanoborane moiety under DMT removal/addition conditions necessitated the search for an alternative method of protecting the 5'-hydroxyl of the nucleoside. This paper addresses the possible cause of deboronation and describes the synthesis of N7-cyanoboronated nucleosides by a method that avoids transient protection of the sugar hydroxyls.     

Serological characterization of Actinobacillus pleuropneumoniae biotype 1 strains antigenically related to both serotypes 2 and 7

Free radical formation in nucleosides and nucleotides containing cytosine as base was studied after X-irradiation at 77 K of samples prepared in frozen aqueous BeF2 glasses and in frozen aqueous solutions by means of electron spin resonance (ESR) spectroscopy. By comparison with radical patterns from the cytosine base and from 1-CH3-cytosine, by using specifically base-deuterated nucleosides and by comparison between the 2'-deoxy- and the ribonucleotide it could be demonstrated that a radical at the C1'-position of the sugar was formed in nucleosides and nucleotides in both matrices. Quantitative analysis showed that in the BeF2 glass an initial population of about 10% of substrate located species due to this radical was present at 77 K and developed to about 25% after decay of the .OH (.OD) radicals at about 140 K. This was taken as proof that at least part of these radicals were formed from .OH radicals. In frozen aqueous solutions about 20% of C1' located sugar radicals were found to be present at 77 K, the population remaining roughly constant with increasing temperature to 140 K. The mechanistic findings of these unexpected results are discussed in terms of mobile .OH radicals and/or hole transfer in the glass and in the glassy regions of the frozen aqueous solutions.     

DNA vaccines for bacterial infections

The uptake and transportation of purine and pyrimidine based nucleosides by trophozoites of axenically grown Entamoeba histolytica (HMI-IMSS) were studied. The trophozoites transported adenosine and its analog tubercidin (1 microM) at a significant rate but poor transportation was observed in case of uridine (about 10% relative rate), inosine (3%), thymidine (2%) and formycin B (1%). The Km for adenosine was 160 +/- 42 microM. Unlabeled nucleosides (100 microM) inhibited adenosine and tubercidin transport. Adenosine related compounds 5'-deoxyadenosine and nebularin inhibited adenosine and tubercidine transport by 50% or more. However, inosine related compounds guanosine, 3'-deoxyinosine and formycin B were less inhibitory. The pyrimidine nucleosides uridine, thymidine and cytidine were poorly inhibitory. 6-[(4 nitrobenzyl)-mercapto] purine ribonucleoside, an inhibitor of mammalian nucleoside transporter, inhibited adenosine or tubercidin transport in E. histolytica variably between 0-30% at 10 microM, but dilazep, a known inhibitor, was inactive upto 10 microM. Increase in temperature from 22 degrees C to 33 degrees C enhanced the rate of transport of adenosine 4.5 fold, tubercidin 7.3 fold and of inosine 4 fold. These findings along with the structure activity figures suggested that transport was mediated and not passive.     

Synthesis and biological activity of certain 4'-thio-D-arabinofuranosylpurine nucleosides

A series of 4'-thio-D-arabinofuranosylpurine nucleosides was prepared and evaluated as potential anticancer agents. The details of a convenient and high-yielding synthesis of the carbohydrate precursor 1-O-acetyl-2,3,5-tri-O-benzyl-4-thio-D-arabinofuranose (6) are presented. Proof of structure and configuration at all chiral centers of the nucleosides was obtained through an X-ray crystal structure of 9alpha as well as through NOE experiments on 9beta and 9alpha. All six target compounds were evaluated in a series of human cancer cell lines in culture. Two target compounds, beta anomers with diaminopurine (12) and guanine (16) as the bases, had significant cytotoxicity. One of these compounds (12) was selected for animal studies but was found to have no selectivity at the maximum tolerated dose in the murine colon 36 tumor model.     

Location of the carbohydrate groups of ovomucoid

The aims of this investigation were to establish the optimum reaction conditions for silylation of nucleotides with bis(trimethylsilyl)trifluoroacetamide (BSTFA) and to investigate the chromatographic properties of the following nucleosides: adenosine, guanosine, cytidine, thymine, inosine, xanthosine, and uridine. Closed tube silylations were performed with a 1000 molar excess of BSTFA at 25, 75, 120, 150, and 175 degrees for 15, 30, 60, 120 and 240 min. The optimal time and temperature for derivatization were found to be 150 degrees and 15 min. Using these reaction conditions, samples were then silylated with 50, 100, 200, 500, and 1000 molar excess of BSTFA; a molar excess of 225 was best. The stability of the nucleoside derivatives on standing at room temperature for 1-7 days was investigated. Quantitative gas-liquid chromatography of trimethylsilyl (TMS) nucleosides can be performed if samples are analyzed within 48 h, after which time the relative weight response for the nucleosides decreased somewhat. Chromatographic column studies were made using various liquid phases and supports. With methylsiloxanes as the liquid phase, Supelcoport as support was found to be superior. Resolution of TMS guanosine from TMS cytidine was attempted at different column lengths using 3% (w/w) SE-30 on Supelcoport, different loadings (%, w/w) of SE-30 on Supelcoport, and different polarity liquid phases, 4% (w/w) OV-11 or 3% (w/w) OV-17 or 4% (w/w) Dexsil-300 on Supelcoport. A complete separation of the six ribonucleosides including guanosine and cytidine was obtained with 1 m x 4 mm I.D. glass columns of 4% (w/w) OV-11 and 3% (w/w) OV-17 on 100-120 mesh Supelcoport. It was observed that with 2'-deoxycytidine, one obtains the TMS cytosine peak (retention temperature 150 degrees) plus another peak with a retention temperature of 120 degrees, under all derivatization conditions with BSTFA and bis(trimethylsilyl)-acetamide. Similar formation of bases from other 2'-deoxyribonucleosides occurred when the molar excess of BSTFA was greater than 500. The minimal detectable amounts obtained for all the nucleosides ranged from 5 to 10 ng injected with a signal-to-noise ratio of 3. The relative standard deviations for all nucleosides and deoxynucleosides ranged from 1.2 to 4.8% on different methylsiloxanes on Supelcoport columns.     

Polymerization of nucleotide analogues I: reaction of nucleoside 5'-phosphorimidazolides with 2'-amino-2'-deoxyuridine

2'-Amino-2'-deoxyuridine reacts efficiently with nucleoside 5'-phosphorimidazolides in aqueous solution. The dinucleoside monophosphate analogues were obtained in yields exceeding 80% under conditions in which little reaction occurs with the natural nucleosides. In a similar way, the 5'-phosphorimidazolide of 2'-amino-2'-deoxyuridine undergoes self-condensation in aqueous solution to give a complex mixture of oligomers. The phosphoramidate bond in the dinucleoside monophosphate analogues is stable for several days at room temperature and pH 7. The mechanisms of their hydrolysis under acidic and alkaline conditions are described.     

New nucleoside conjugates with phospholipids: synthesis of anti-HIV activity of rac-1-hexadecyl-2-acyl-sn-glycero-3-phosphonucleosides

New nucleoside-phospholipid conjugates were synthesized based on 1,2-disubstituted glycerides and nucleosides. These contain rac-1-hexadecyl-2-palmitoyl(or 2-methylcarbamoyl)-sn-glycero-3-phosphate as the phospholipid component and 2',3'-didehydro-3'-deoxythymidine, 1-(Z-5-hydroxypentene-2-yl)thymine, or 2',3'-isopropylideneuridine as a nucleoside component. The conjugates were synthesized by three different ways: from rac-1-hexadecyl-2-acyl-sn-glycero-3-phospodichlorides, -3-phosphatidic acids, or -3-H-phosphonates. When subjected to mild alkaline hydrolysis, conjugates containing a 2-palmitoyl group formed conjugates with the lysophospholipid component that had not yet been described. All the conjugates obtained were amorphous compounds stable at room temperature. Their hemolytic and anti-HIV activities were determined. Some conjugates were found to completely inhibit in vitro HIV-1 reproduction in lower doses than the corresponding nucleosides.