The reaction of activated RNA species with aqueous fluoride ion: a convenient synthesis of nucleotide 5′-phosphorofluoridates and a note on the mechanism

The chemistry of 5′-phosphorimidazolides of ribonucleosides is extended to include their reaction with alkali metal fluorides in aqueous solution. High yields of 5′-phosphorofluoridates are formed, especially with potassium fluoride, but no detectable oligomerization products were formed. A combination of HPLC, mass spectrometry, synthesis, kinetics, and NMR confirms the identities of the products. Judicious control of pH leads to higher yields in shorter reaction times. This new methodology contrasts favorably with other synthetic routes involving non-aqueous chemistry or aqueous chemistry with a nucleotide triphosphate.     

Simultaneous measurement of trace monoadenosine and diadenosine monophosphate in biomimicking prebiotic synthesis using high-performance liquid chromatography with ultraviolet detection and electrospray ionization mass spectrometry characterization

The method for simultaneous separation and determination of trace monoadenosine and diadenosine monophosphate (i.e. 2′-AMP, 3′-AMP, 5′-AMP and 3′-5′ ApA) in biomimicking prebiotic synthesis was developed using high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection and electrospray ionization mass spectrometry (ESI-MS) identification. The separation was performed on a Supelco C₁₈ column with a gradient elution (solvent A: 10 mM NH₄Ac aqueous solution; solvent B: MeOH). The flow rate was set at 1.0 ml/min. The quantitative determination was achieved by HPLC with UV detection at 260 nm. The linearity ranged from 0.5 to 100 μg/ml for each nucleotide. The limits of detection (LODs) for the four nucleotides were less than 0.30 μg/ml. The recovery ranged from 95.2 to 100.7%. The intra-day relative standard deviations (RSDs) of the retention times were between 0.7 and 1.1%. Both full-scan ESI-MS and -MS² for the four nucleotides under both positive and negative polarity were carried out and the possible cleavage pathways of them were depicted. The specific ions, [AMP + H]⁺ at m/z 348 and [ApA + H]⁺ at m/z 597, were chosen to characterize the four nucleotides in biomimicking prebiotic synthesis between N-(O,O-diisopropyl) phosphoryl amino acid (Dipp-aa) and adenosine. Using the proposed HPLC/UV/ESI-MS method, the concentration of 2′-AMP, 3′-AMP, 5′-AMP and 3′-5′ ApA in the biomimicking prebiotic synthesis samples were determined.     

Use of a solid-supported coupling reagent for a selective phosphitylation of the primary alcohol of N-isobutyryl-2′-deoxy or 2′-O-methyl guanosine

We have developed a 5′-regioselective phosphitylation of 3′,5′-OH-guanosine derivatives thanks to a solid-supported coupling reagent with either a standard or a bulky phosphine. A 5′-phosphitylation up to a 95% selectivity was obtained with a quantitative conversion of starting nucleoside. After oxidation into thionophosphotriester or phosphotriester by means of solid-supported oxidizers, the 5′-phosphorylated N²-i-Bu-2′-OMe guanosines were isolated in good yields (70-80%).     

2′,2′-Ligation demonstrates the thermal dependence of DNA-directed positional control

An oligodeoxynucleotide (ODN) containing a 2′-aminoalkylmercaptouridine was ligated chemically with another ODN containing a 2′-carboxyalkylmercaptouridine to produce a 2′,2′-amide linked conjugate. Templation by a DNA hairpin resulted in ligation yields of >95%. At room temperature, similar yields were obtained for amide ligations between pendent nucleotides located adjacent to each other or separated by three nucleotides. However, at 4 °C, ligation was vastly favored for the case where the pendent amine and carboxylate were attached to adjacent residues (i.e., at the 3′- and 5′-terminus of the two ODNs). No reaction was observed to occur either at 4 °C or at room temperature between pendent nucleotides separated by nine nucleotides. Denaturing gel electrophoresis, MALDI-TOF MS, and full nuclease digestion coupled with LC-MS were used to characterize the reaction products.     

Ion-pair high-performance liquid chromatography with diode array detection coupled to dual electrospray atmospheric pressure chemical ionization time-of-flight mass spectrometry for the determination of nucleotides in baby foods

A liquid chromatography with diode array detection coupled to dual electrospray atmospheric pressure chemical ionization time-of-flight mass spectrometry (HPLC/ESI-APCI-TOF-MS) method is described for the rapid determination of five monophosphate nucleotides (cytidine 5′-monophosphate, uridine 5′-monophosphate, adenosine 5′-monophosphate, inosine 5′-monophosphate and guanosine 5′-monophosphate) in baby foods. The method is based on the deproteinisation of foods and direct analysis of nucleotides by ion-pair HPLC using isocratic elution with a mobile phase of 5% (v/v) methanol and 95% (v/v) 0.1 M formate buffer (pH 5.5) containing 0.01 M N,N-dimethylhexylamine (DMHA) at a flow-rate of 0.7 mL min⁻¹. The HPLC was hyphenated with two different detection systems, photodiode-array (DAD) and ESI-APCI-TOF-MS in negative mode. The method was validated for linearity, detection and quantitation limits, selectivity, accuracy and precision. The recoveries obtained for spiked samples were satisfactory for all the analytes. The method was successfully applied to the analysis of nucleotides in different baby and/or functional food samples, as cereals, purees and dairy products. A study was also carried out on the stability of nucleotides in acidified dairy infant food with pasteurized yoghourt and follow-on formulae samples stored at room temperature and at 30 °C.     

Regioselective Suzuki coupling on pyridinium N-(3,5-dibromoheteroar-2-yl)aminides

A regioselective Suzuki-Miyaura cross-coupling reaction on 3′,5′-dibromo pyridinium N-(2′-azinyl)aminides is reported. A series of 3′-aryl(or heteroaryl)-5′-bromo-pyridinium N-(2′-pirazinyl)aminides were obtained in good yields. Two isomeric 3′,5′-diaryl pyridinium N-(2′-azinyl)aminides were also prepared.     

Friedel-Crafts acylation of W(CO)5-complexes of azaferrocenes

Blocking of the lone pair of electrons on the nitrogen in azaferrocene by co-ordination to the W(CO)₅ moiety enables Friedel-Crafts acylation of this heteroferrocene. W(CO)₅-complexes of azaferrocene and 2,5-dimethylazaferrocene react with acetyl- and propionyl chloride or acetic anhydride in the presence of aluminium chloride in dichloromethane at r.t. to give W(CO)₅-complexes of 1′-acylazaferrocenes in 10-50% isolated yields. The low yields presumably result from instability of the products in the reaction medium. The X-ray structure of the complex of 1′-acetylazaferrocene has been determined.     

Silica-bonded S-sulfonic acid: an efficient and recyclable solid acid catalyst for the synthesis of 4,4′-(arylmethylene)bis(1H-pyrazol-5-ols)

Silica-bonded S-sulfonic acid (SBSSA) is employed as a recyclable catalyst for the condensation reaction of aromatic aldehydes with 3-methyl-l-phenyl-5-pyrazolone. This condensation reaction was performed in ethanol under refluxing conditions giving 4,4′-alkylmethylene-bis(3-methyl-5-pyrazolones) in 75-90% yields.     

From oxides of internal perfluoroolefins to fluorocontaining camphor thiazolinylhydrazones

The reaction of oxides of internal trans- and cis-perfluoroolefins with (1S, 4S)- or racemic camphor thiosemicarbazone leads to the formation of trans- and cis-isomers of (1S, 4S)- or racemic camphor 5′-fluoro-4′-hydroxy-4′,5′-di(perfluoroalkyl)-1′,3′-thiazolinyl-2′-hydrazones, respectively. Unsymmetrical dodecafluoro-2,3-epoxyhexane yields a mixture of regioisomeric hydrazones. The molecular structure of the trans-isomer of (1S, 4S)-camphor 5′-fluoro-4′-hydroxy-4′,5′-bis(trifluoromethyl)-1′,3′-thiazolinyl-2′-hydrazone has been established by X-ray crystallography. The quite rare example of cocrystallization of two diastereomers of the latter in homochiral crystal (sp. group P2₁) has been revealed.     

A highly sensitive enzyme immunoassay for evaluation of 2′-deoxycytidine plasma level as a prognostic marker for breast cancer chemotherapy

A highly sensitive competitive enzyme immunoassay (EIA) has been developed and validated for the determination of the plasma level of 2′-deoxycytidine (dCyd), the potential prognostic marker for breast cancer chemotherapy. This assay employed a monoclonal antibody that recognizes dCyd with a high specificity, and 5′-succinyl-dCyd (5′sdCyd) conjugate of bovine serum albumin (5′sdCyd-BSA) immobilized onto microplate wells as a solid phase. The assay involved a competitive binding reaction between dCyd, in plasma sample, and the immobilized 5′sdCyd-BSA for the binding sites of the anti-dCyd antibody. The bound antibody was quantified with horseradish peroxidase-labeled anti-immunoglobulin second antibody and 3,3′,5,5′-tetramethylbenzidine as a peroxidase substrate. The concentration of dCyd in the sample was quantified by its ability to inhibit the binding of the antibody to the immobilized 5′sdCyd-BSA and subsequently the color formation in the assay. The assay limit of detection was 8 nM and the effective working range at relative standard deviations (R.S.D.s) of ≤10% was 20-800 nM. No cross-reactivity from the structurally related nucleobases, nucleosides, and nucleotides was observed in the proposed assay. Mean analytical recovery of added dCyd was 98-100 ± 3.2-8.2%. The precision of the assay was satisfactory; R.S.D. was 3.4-4.2 and 4.3-8.9% for intra- and inter-assay precision, respectively. The proposed EIA was compared favorably with HPLC method in its ability to accurately measure dCyd spiked into plasma samples. The analytical procedure is convenient, and one can analyze 200 samples per working day, facilitating the processing of large-number batch of samples. The proposed EIA is expected to contribute in further evaluation of dCyd as a prognostic marker for breast cancer chemotherapy and elucidation of the role of dCyd in various biological and biochemical systems.     

A facile and effective synthesis of lamivudine 5′-diphosphate

We report on the first solution synthesis of lamivudine 5′-diphosphate in both high yield and purity. Efficient synthesis of lamivudine 5′-monophosphate was obtained through lamivudine H-phosphonate oxidation by (−)-(8,8-dichlorocamphorylsulfonyl)oxaziridine.Diphosphorylation was performed by nucleophilic substitution of the phosphorimidazolate derivative of lamivudine. HPLC coupled with UV or MS detection was found to be an invaluable tool for the follow-up of phosphorylation reactions.     

Multi-component, 1,3-dipolar cycloaddition reactions for the chemo-, regio- and stereoselective synthesis of novel hybrid spiroheterocycles in ionic liquid

A library of novel 1-methyl-4-arylpyrrolo-(spiro[2.2′]indan-1′,3′-dione)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones and 1-methyl-4-arylpyrrolo-(spiro[2.11′]-11H-indeno[1,2-b]quinoxaline)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones have been synthesized via 1,3-dipolar azomethine ylide cycloaddition in the ionic liquid, 1-butyl-3-methylimidazolium bromide ([BMIm]Br), in excellent yields.     

Efficient synthesis of 3-cyanovinylcarbazole-1′-β-deoxyriboside-5′-triphosphate: a reversible photo-cross-linking probe

We describe an efficient synthesis of 3-cyanovinylcarbazole-1′-β-deoxyriboside-5′-triphosphate containing light-responsive artificial nucleobase 3-cyanovinylcarbazole, which can be used as a reversible photo-cross-linking probe with nucleic acid compounds for various biological applications. A three-step synthesis of 3-cyanovinylcarbazole-1′-β-deoxyriboside starting from 3-cyanovinylcarbazole, followed by ‘one-pot, three-step’ procedure is presented to accomplish the title compound 3-cyanovinylcarbazole-1′-β-deoxyriboside-5′-triphosphate in good yields.     

Novel four-component route to the synthesis of spiro[indoline-3,4′-pyridine]-3′-carboxylate derivatives

An effective route to spiro[indoline-3,4′-pyridine]-3′-carboxylate derivatives is described. This involves reaction of isatin, 1-phenyl-2-(1,1,1-triphenyl-λ⁵-phosphanylidene)-1-ethanone, and benzylamine derivatives or aliphatic amines in the presence of alkyl acetoacetate (1,3-dicarbonyl compounds) in dry methanol under reflux conditions. The reactive 1:1 enaminone, which is obtained from the addition of the amine to 1,3-dicarbonyl compound, adds to the α,β-unsaturated ketone, which is formed from the reaction of isatin and 1-phenyl-2-(1,1,1-triphenyl-λ⁵-phosphanylidene)-1-ethanone, to produce the alkyl 1′-benzyl-2′-methyl-2-oxo-6′-phenyl-1′H-spiro[indoline-3,4′-pyridine]-3′-carboxylate derivatives in excellent yields.     

Synthesis of triaryls: hydroxy and amine dinaphthyl and diphenanthryl aryls by one-pot electron-transfer nucleophilic substitution reactions

A new one-pot synthetic route to achieve the preparation of hydroxy and amine binaphthyl and biphenanthryl aryls is here reported. This approach involves the reaction of 1,4-bromoiodobenzene, 4,4′-diiodobiphenyl, and 1,4- and 1,5-diiodonaphthalene with the anions of 2-naphthylamine, 2-naphthol, and 9-phenanthrylamine under irradiation in liquid ammonia. The reactions proceed to afford triaryl derivatives in moderate to good yields (∼45% of 1,4-phenylene- and 1,4-naphthylene-1,1′-dinaphthalen-2-ols as well as 1,4-phenylene-1,1′-dinaphthalen-2-amine and 10,10′-diphenanthren-9-amine). Lower yields (27%) of polyaryl derivatives are obtained by reaction of 4,4′-diiodobiphenyl with anions of 2-naphthol and 9-phenanthrylamine.     

The Thorpe-Ziegler-type reaction of 3-cyanopyridine-2(1H)-thiones with Biginelli 6-bromomethyl-3,4-dihydropyrimidin-2(1H)-ones: cascade assembling of tetra- and pentacyclic heterocyclic scaffolds

3-Cyanopyridine-2(1H)-thiones have been shown to react with Biginelli-type ethyl 4-aryl-6-(bromomethyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates upon heating in DMF giving rise to ethyl 4-aryl-6-{[(3-cyanopyridin-2-yl)thio]methyl}-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates. The latter upon treatment with an excess of NaH or t-BuOK in boiling DMF undergo a tandem Thorpe-Ziegler-type heterocyclization to give pyrido[3″,2″:4′,5′]thieno[2′,3′:5,6]pyrido[4,3-d]pyrimidine derivatives in good yields. Selected compounds were tested for antibacterial and antifungal activity.     

Facile synthesis of acetylene-substituted terthiophenes

A modified Horner-Emmons condensation reaction has been employed for the synthesis of acetylene-substituted terthiophenes in excellent yields. Conjugating 3′-aryl substituents to terthiophene using an ethyne rather than an ethene linker results in enhanced planarity of the resulting molecule as established by X-ray structural analysis of (2,2′:5′,2″-terthiophen-3′-yl)-4?-pyridylethyne.     

Synthesis of new fluorescent 2-(2′,2″-bithienyl)-1,3-benzothiazoles

Bithienyl-1,3-benzothiazole derivatives were synthesised by reacting various 5-formyl-5′-alkoxy- or 5-formyl-5′-N,N-dialkylamino-2,2′-bithiophenes with ortho-aminobenzenethiol in good to excellent yields. Evaluation of the fluorescence properties of these compounds was carried out. They show strong fluorescence in the 450-600 nm region, as well as high quantum yields and large Stokes’ shifts.     

A simple one-pot synthesis of functionalised 6-(indol-3-yl)-2,2′-bipyridine derivatives via multi-component reaction under neat condition

A series of 4-aryl-6-(1H-indol-3-yl)-2,2-bipyridine-5-carbonitrile derivatives were synthesized via a one-pot multi-component reaction of aromatic aldehydes, 3-(cyanoacetyl)indole and 2-acetyl pyridine in ammonium acetate by conventional heating and microwave irradiation under solvent-free condition. Also a series of 6,6′-di(1H-indol-3-yl)-4,4′-diaryl-2,2′-bipyridine-5,5′-dicarbonitrile derivatives were synthesized using cinnamils, 3-(cyanoacetyl)indole and ammonium acetate. The methodology affords high yields of product at short reaction time.     

Scalable synthesis of substituted 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH): useful for the preparation of crystalline 5′-O-DMPx-protected nucleosides

A convenient single-step synthesis of several 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH) analogs has been accomplished using a Friedel-Crafts reaction. Treatment of various DMPx-OH with unprotected 2′-O-methoxyethyl-ribonucleosides (MOE) in the presence of B(C₆F₅)_3, as a Lewis Acid catalyst, furnished 5′-O-protected derivatives of 2′-MOE-ribonucleosides in good yields. The deprotection of the DMPx groups was accomplished by acid hydrolysis under very mild conditions. Among the five DMPx analogs synthesized, the 2,7-dimethyl-9-(4-nitrophenyl)xanthene-9-yl group furnished crystalline products enabling non-chromatographic isolation of 5′-O-protetced nucleosides.