The mechanism of the chemical synthesis of oligonucleotides and its synthetic consequences.

The data obtained mainly by pulsed NMR spectroscopy on phosphorus nuclei on the mechanism of the internucleotide phosphodiester (PDE) group formation are summarised. With arylsulphonyl chloride as condensing reagent monomeric nucleotide derivative B (nucleoside metaphosphate or its pyridinium adduct) is the highly reactive intermediate. In the presence of PDE groups in nucleoside or nucleotide component the significantly less reactive derivatives with trisubstituted pyrophosphoryl residues are formed both with arylsulphonyl chloride and dicyclohexylcarbodiimide (DCC). The reactive B form of nucleotide component may be obtained using greater excess of arylsulphonyl chloride with simultaneous convertion of PDE groups to tetrasubstituted pyrophosphates amenable to side reactions. The convertion of PDE groups to easily hydrolysable dicyclohexylurea derivatives by reaction with DCC is proposed to reversible blocking of PDE groups of nucleoside component. The B type derivatives of mononucleotides or oligonucleotides with blocked PDE groups seems to be the best nucleotide components.     

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.     

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.     

Acetylation and cleavage of purine nucleosides. Synthesis of 6-azauridine, 5-fluorouridine, and 5-methyluridine.

Inosine (I) when acetylated with acetic anhydride in the presence of acetyl chloride in acetic acid solution (the so called "acid acetylation"), affords an acetylated nucleoside III (75%) along with cleavage products of the nucleoside (hypoxanthine, 19%). The reaction of I with acetyl chloride (7 days) results in the formation of hypoxanthine (95%) and triacetylribofuranosyl chloride (IV) isolated in the form of tetraacetylribofuranose (47%). The acetylated purine nucleoside affords a similar result by reaction with acetyl chloride or acetyl bromide. 2'-Deoxyuridine gives a diacetyl derivative (80%) by reaction with acetyl bromide. On treatment with acetyl bromide, the nucleoside bond of purine nucleosides is quantitatively cleavaged (4 h, 20 degrees C) with the formation of tri-O-acetyl-D-ribofuranosyl bromide (X). The halogenose X affords pure beta-anomers, namely, 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose (75%), the triacetyl derivatives of 5-methyluridine (XVIIa; 75%, referred to guanosine), 6-azauridine (XVIII; 71%), and 5-fluorouridine (XIXa; 75%).     

The reactions of mercurated pyrimidine nucleotides with thiols and with hydrogen sulfide.

In the presence of thiols, 5-mercuripyrimidine nucleotides are quantitatively converted to 5-thiomercuri derivatives, but these compounds are unstable and decompose at a rate dependent on the nature of the thiol. The decomposition involves three different reactions and proceeds via a symmetrical mercury derivative of the nucleotide. The end product is the unmodified nucleotide. Similar reactions occur in the presence of hydrogen sulfide. Since mercurated nucleoside triphosphates are substrates for RNA- and DNA polymerase only in the form of thiomercuri derivatives, this implies that when DNA is replicated or transcribed in vitro with a mercurated substrate, the latter is rapidly demercurated to the unmodified substrate which is incorporated as well. Hence the product of the in vitro synthesis can only be partially mercurated in any one pyrimidine. Also, formation of cross-links in the resulting polymer is possible.     

Synthesis,intramolecular migrations and enzymic hydrolysis of partially pivaloylated methyl alpha-D-mannopyranosides

A series of methyl O-pivaloyl-alpha-D-mannopyranosides was synthesized using pivaloyl chloride in pyridine. The 3,6-di-O-pivaloyl derivative 6 undergoes intramolecular transesterification in neutral conditions (buffer, pH 7.2) to give its 2,6-di-O-pivaloyl analogue 5. The course of this migration was followed using 14C-labelled 6. As opposed to 6 compound 5 was shown to be a good substrate for esterases present in rabbit serum. Thus, regioselective enzymic hydrolysis led to the preferential cleavage of the 2-OPiv group to yield a mixture of 2- and 6-O-monopivalates in a ratio of 1:2.6.     

Stereochemistry of Internucleotide Bond Formation by the H-Phosphonate Method. 5. The Role of Brønsted and H-Bonding Base Catalysis in Ribonucleoside H-Phosphonate Condensation—Chemical and Stereochemical Consequences

Efficiency and stereoselectivity of condensations of ribonucleoside 3′-H-phosphonates with ethanol promoted by pivaloyl chloride were investigated as a function of tertiary amines used. Side reactions leading to an increased demand for the condensing agent were identified as derived from an attack of the pivalate anion at carbonyl centers of reactive pivaloyl derivatives. The conditions that secured quantitative yields of H-phosphonate diester condensations were assessed. Several tertiary amines promoted condensations with stereoselectivity higher than that observed for pyridine derivatives. A correlation between diastereoselectivity of the product formation and Brønsted and H-bonding basicities of the amine used was found.     

Properties of 2-hydroxylaminoimidazoles and their implications for the biological effects of 2-nitroimidazoles

In aqueous solution, in the presence of ammonium chloride, N1-substituted 2-nitroimidazoles are readily reduced to the corresponding hydroxylamines. In air, under neutral conditions, analogous to the reactions of aromatic hydroxylamines, 2-hydroxylaminoimidazoles are converted to the azoxy derivatives via a base-catalyzed condensation reaction between the hydroxylamine and its oxidation product, the nitroso derivative. In nitrogen, rearrangement to form the 2-amino-4(5)hydroxyimidazole derivative followed by addition of water across the C4-C5 double bond to yield isomers of a 4,5-dihydro-4,5-dihydroxy derivative appears to be a major reaction. 2-hydroxylaminoimidazoles undergo a complex series of reactions with glutathione. The initial reaction is the formation of a labile conjugate involving an N-S-linkage. Subsequently in the presence of excess GSH, under neutral conditions, two stable conjugates identified as 2-amino-4-S-glutathionyl- and 2-amino-5-S-glutathionyl imidazoles are formed. Nucleophilic attack by GSH on the imidazole ring of a nitrenium ion is postulated as the initial step in the formation of the stable GSH conjugates as well as the 2-amino-4,5-dihydro dihydroxy derivative. The results provide a molecular mechanism for many of the biological effects of N1-substituted 2-nitroimidazoles in hypoxic mammalian cells.     

Defining the involvement of HOCl or Cl2 as enzyme-generated intermediates in chloroperoxidase-catalyzed reactions.

Peroxidatic substrates, catechol (CAT) and 2,4,6-trimethylphenol (TMP) were used as probes of thechloride dependent reactions catalyzed by chloroperoxidase (CPO). TMP is consumed only in the presence of chloride. TMP is a competitive inhibitor versus CAT, but CAT is a noncompetitive inhibitor versus TMP in chloride-dependent CPO-catalyzed peroxidation reactions. The ratio of TMP versus CAT consumed by the chloride-dependent CPO reaction in direct competition studies increases as the chloride concentration is increased from 1.0 to 400 mM. Ratios of non-enzymatic HOCl reactions under conditions otherwise similar to those of the CPO reactions are relatively insensitive to changes in chloride concentration and are experimentally indistinguishable from the values attained by the enzyme system at high chloride concentrations. Comparison of enzymatic ratios with those of the HOCl reactions indicate that the proportion of the enzymatic reaction involving a freely dissociable, enzyme-generated, oxidized halogen species varies from 10% at low chloride concentrations to essentially 100% at high chloride concentrations. All data are consistent with a mechanism in which chloride competes with CAT for binding to both CPO compound I and the CPO chlorinating intermediate (EOCl). Chloride binding to CPO compound I leads to the formation of EOCl and initiates the CPO chloride-dependent pathway. When CAT binds to either compound I or EOCl, it is directly oxidized to product. When chloride binds to EOCl, it either induces release of HOCl or reacts with EOCl to produce Cl2, which is released from the enzyme. TMP and CAT compete for reaction with the free oxidized halogen species. This is the first direct evidence for kinetically significant involvement of a free oxidized halogen species as an intermediate in any CPO-catalyzed reaction.     

Studies on ferrochelatase: The effects of thiols and other factors on the determination of activity

1. Haems are unstable under aerobic conditions in the presence of thiols, which are used to activate the ferrochelatase enzyme; catalase inhibits this degradation of haem. In addition, thiols interfere with the determination of protohaem as its pyridine haemochromogen derivative. 2. Three ferrochelatase assays are described that minimize interference by these two reactions. Two of these assays involve measurement of porphyrin utilization, one spectrophotometrically and the second spectrofluorimetrically. The third assay measures haem formation by a pyridine haemochromogen technique. Results obtained with these three methods were in close agreement at a GSH concentration of 4mm. 3. The stimulatory effect of GSH on ferrochelatase has been confirmed. The spectrum of the haem formed is dependent on GSH concentration; at high GSH concentrations (20mm) the haem is in the reduced state, but at low concentration (4mm) the spectrum of the product resembles that of an oxidized haemoprotein such as ferrihaemoglobin. 4. The inhibitory effect of oxygen on ferrochelatase activity has been confirmed by spectrophotometric assay of porphyrin disappearance.     

A model study directed towards the preparation of nucleopeptides via H-phosphonate intermediates.

The monofunctional phosphitylating reagents bis-(N,N-diethylamino)chlorophosphine and salicylchlorophosphine have been applied for the preparation of H-phosphonates of the amino acids serine, threonine and tyrosine. Experimental evidence showed that the latter reagent was less effective for the synthesis of a tyrosine H-phosphonate. The amino acids (peptide) H-phosphonates of serine or threonine proved to be suitable starting compounds for the formation of a phosphate diester bond with the 5'-OH of a d-nucleoside derivative using pivaloyl chloride as the activating reagent.     

5′-Phosphonates of Ribonucleosides and 2′-Deoxyribonucleosides: Synthesis and Antiviral Activity

Abstract

5′-Phosphonates of natural 2′-deoxynucleosides and ribonucleosides were synthesized by condensation of 3′-O-acylated 2′-deoxynucleosides or 2′,3′-substituted (2′,3′-O-isopropylidene, 2′,3′-O-methoxymethylene or 2′,3′-O-ethoxymethylene) ribonucleosides. As condensing agents, either N,N′-dicyclohexylcarbodiimide or 2,4,6-triisopropylbenzenesulphonyl chloride were used. Nucleoside 5′-ethoxycarbonylphosphonates were converted into corresponding nucleoside 5′-aminocarbonylphosphonates by action of ammonia in methanol or aqueous ammonia. 5′-Hydrogenphosphonothioates of thymidine and 3′-deoxythymidine were obtained by reaction of phosphinic acid in the presence of pivaloyl chloride with 3′-O-acetylthymidine or 3′-deoxythymidine, respectively, followed by addition of powedered sulfur. 5′-O-methylenephosphonates of thymidine and 2′-deoxyadenosine were prepared by intramolecular reaction of corresponding 3′-O-iodomethylphosphonates under basic conditions. All compounds were tested for inhibition of several viruses, including HSV-2 and CMV, but showed no activity. A few compounds insignificantly inhibited HIV-1 reproduction. Thymidine 5′-hydrogenphosphonate neutralized anti-HIV action of 3′-azido-3′-deoxythymidine (AZT) and it indirectly showed that even some nucleoside 5′-phosphonates could be partly hydrolyzed in cell culture to corresponding nucleosides.

5′-Phosphonates of modified 2′-deoxynucleosides in which one group in a phosphate residue is substituted for hydrogen, alkyl or other groups, have shown to be potent biologically     

Quantitative correlations relating the interaction of Zn(II)-tetraphenylporphine and horseradish peroxidase with amines

Reactions of nucleophilic substitution and enzymatic processes involving metalloporphirins (MP) are considered in terms of coordination of zinc(II)tetraphenylporphine (Zn-TPhP) with corresponding ligands/nucleophiles/substrates/bases. Linear correlations are performed between kinetic parameters of the Zn-TPhP coordination processes in chloroform (stability constants) and reactions of nucleophilic substitution both in aqueous and organic solvents involving pyridines, pyridine N-oxides, anilines, primary amines, as well as in reactions of oxidation of anilines with horseradish peroxidase in aqueous media (rate constants). Thermodynamic parameters of the complex formation and nucleophilic substitution linearly correlate with each other in the case of pyridines, anilines, and primary amines.     

5-substituted arabinofuranosyluracil nucleosides: synthesis and antiviral properties

A number of 5-alkyl (ethyl, propyl, isopropyl, butyl) analogues of araU, their alpha-anomers and N3-isomers have been synthesized by a number of different procedures, based on the catalytic condensation of the appropriate 5-alkyl-2,4-bis-(trimethylsilyloxy)-pyrimidine with 2,3,5-tri-O-benzyl-alpha-D-arabinofuranosyl chloride. The resulting protected nucleosides were deblocked by a new procedure based on the use of BF3 X Et2O in C2H5SH. The chloromercuri derivative of araU, on reaction with allyl chloride in the presence of Li2PdCl4, gave the 5-allyl derivative, which was catalytically reduced to the corresponding 5-propyl analogue. The antiviral activities of these compounds have been evaluated. 5-Allyl-araU showed moderate specific activity (MIC 20 micrograms/ml) against herpes simplex type 1 virus in PRK cell cultures. Structure-activity relationships are discussed for the 5-alkyl deoxy- and arabino- uracil nucleoside series.     

Comparative mutagenicity of halogenated pyridines in the Salmonella typhimurium/mammalian microsome test

The Salmonella/microsome assay with strains TA97, TA98, TA100 and TA102 was used to examine the potential mutagenicity and structure-activity of 16 mono- and di-halogenated pyridines. The chemical reactivity of the halopyridines suggests that nucleophilic displacement of halogens can occur with halogens at positions 2, 4 and 6 being displaced in addition-elimination reactions. 2-Chloropyridine gave a positive result with rat-liver metabolic activation, and 2-fluoropyridine gave equivocal results under these conditions. Mutagenic responses were also obtained with 2-chloromethyl pyridine and 3-chloromethyl pyridine, in both the presence and absence of rat-liver S9. These results suggest that the halogenated pyridines, especially with halogens at the 2-position, and singly on a methyl substituent, have mutagenic activity in the Salmonella assay.     

Glutaraldehyde fixation chemistry: oxygen-consuming reactions

In tissue fixed with glutaraldehyde, dissolved O2 is rapidly consumed by two processes: residual respiration and glutaraldehyde-induced chemical uptake. The nature of the chemistry which consumes O2 during tissue fixation was investigated by studying model reactions of glutaraldehyde with amines and with homogenized tissue suspensions. The addition of glutaraldehyde to solutions of most primary amines and ammonia stimulated rapid O2 consumption. The reaction of glutaraldehyde with primary amines (e.g., 25 mM ethanolamine, glycine, or methylamine) consumed 50% of the dissolved O2 in 15 to 20 s at 37 degrees C. The initial rate of O2 uptake followed second-order kinetics with respect to the primary amine concentration. The total amount of O2 consumed was sufficient to account for the stoichiometric conversion of the primary amines to pyridines. These data are consistent with the synthesis of pyridine derivatives from glutaraldehyde-amine precursors in which the last step is an irreversible oxidation of dihydropyridines to pyridines. The addition of glutaraldehyde to homogenized muscle suspensions, in which respiration was chemically inhibited, significantly increased the rate of O2 uptake. Thus, in tissue O2 is rapidly depleted both by respiration and the chemical demands of the glutaraldehyde-amine reactions during the cross-linking process. Since these experiments were done under conditions commonly used for tissue fixation, hypoxia should be assumed to exist in biological preparations fixed with glutaraldehyde.     

Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions.

Our review of the metabolic pathways of pyridines and aza-arenes showed that biodegradation of heterocyclic aromatic compounds occurs under both aerobic and anaerobic conditions. Depending upon the environmental conditions, different types of bacteria, fungi, and enzymes are involved in the degradation process of these compounds. Our review indicated that different organisms are using different pathways to biotransform a substrate. Our review also showed that the transformation rate of the pyridine derivatives is dependent on the substituents. For example, pyridine carboxylic acids have the highest transformation rate followed by mono-hydroxypyridines, methylpyridines, aminopyridines, and halogenated pyridines. Through the isolation of metabolites, it was possible to demonstrate the mineralization pathway of various heterocyclic aromatic compounds. By using 14C-labeled substrates, it was possible to show that ring fission of a specific heterocyclic compound occurs at a specific position of the ring. Furthermore, many researchers have been able to isolate and characterize the microorganisms or even the enzymes involved in the transformation of these compounds or their derivatives. In studies involving 18O labeling as well as the use of cofactors and coenzymes, it was possible to prove that specific enzymes (e.g., mono- or dioxygenases) are involved in a particular degradation step. By using H2 18O, it could be shown that in certain transformation reactions, the oxygen was derived from water and that therefore these reactions might also occur under anaerobic conditions.     

Copper generated reactive oxygen leads to formation of lysine-DNA adducts

This work describes the addition of a lysine derivative to guanine base in a nucleoside, an oligonucleotide, and to a large DNA that occurs via oxidation by copper generated reactive oxygen species. Nucleophiles present during oxidation leads to the formation of adducts. In this work, 2′-deoxyguanosine is oxidized by copper generated reactive oxygen species in the presence of a lysine derivative, Nα-acetyl-lysine methyl ester. Under these conditions the guanidinohydantoin-lysine adduct is observed in a relative yield of 27% when compared to other guanine oxidation products. MS² strongly supports that lysine is added to the 5-position during the formation of guanidinohydantoin-lysine. A fourteen-nucleotide DNA duplex was oxidized under similar conditions. Digestion showed formation of the same guanidinohydantoin-lysine nucleoside. The reaction was then examined on a 392-nucleotide DNA substrate. Oxidation in the presence of the lysine ester showed adduct formation as stops in a primer extension assay. Adducts predominately formed at a 5′-GGG at position 415. Six of the seven sites that showed reaction greater than 3-fold above background were guanine sites. We conclude from this study that copper can catalyze the formation of DNA-protein adducts and may form in cells with elevated copper and oxidative stress.     

Conversion of Nucleoside H-Phosphonate Monoesters to the Corresponding H-Phosphonothioates. 31P NMR Studies

Abstract

³¹P NMR Studies on the conversion of nucleoside H-phosphonate monoesters into the corresponding H-phosphonothioates revealed that the key intermediate, the nucleoside trimethylsilyl pivaloyl phosphite 3, may undergo under the reaction conditions at least two parallel transformations to, most likely, the nucleoside trimethylsilyl chlorophosphite 6 and the monosilylated nucleoside H-phosphonate 5.