The structure characterization of dinucleoside and nucleoside glucopyranosides lipophilic phosphotriesters by fast-atom bombardment tandem mass spectrometry

Rules for the gas-phase fragmentation mechanism of the negative ions of lipophilic phosphotriester molecules of biological interest have been established by fast-atom bombardment mass spectrometry/mass spectrometry. The mass-analyzed ion kinetic energy spectra of the [M ? H]^? of dinucleoside (1–4) and nucleoside glucopyranoside (5–9) phosphotriesters show that in the absence of charges on the phosphate bridge, the availability of acidic protons on the 5′-end nucleobase drives a preferred reaction path which leads to 5′-O-nucleotide or 6-O-glucopyranoside monophosphate anions.     

Synthesis of tetradialdose phosphonate nucleosides as mimics of l-nucleotides

Structurally modified nucleoside analogues are a major source of therapeutic agents and building blocks for incorporation into synthetic oligonucleotides able to interfere with information transfer or other biological functions. This work describes the synthesis of non-natural l-nucleoside phosphonate mimics containing two anomeric centers. Such compounds feature either a di- or monohydroxy tetradialdose sugar as the glycone unit, while adenine is present as nucleobase. By judicious use of protecting groups at the 2- and 3-position of commercial 1-O-acetyl-2,3,5-tri-O-benzoyl-β-d-ribofuranose, both the phosphonate and nucleobase moieties were stereoselectively introduced to provide a dihydroxylated compound with cis-configured substituents as the sole reaction product. Subsequent selective deprotection and deoxygenation at the 3′-position occurred smoothly to afford the corresponding 4′-monohydroxy tetradialdose containing analogue.     

Nucleotides. Part XLV. Synthesis of new (2′–5′)adenylate trimers,containing 5′-amino-5′-deoxyadenosine residues at the 5′-end of the oligoadenylate chain,and of its analogues,carrying a 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus

The 5′-amino-5′-deoxy-2′,3′-O-isopropylideneadenosine ( 4 ) was obtained in pure form from 2′,3′-O-isopropylideneadenosine ( 1 ), without isolation of intermediates 2 and 3 . The 2-(4-nitrophenyl)ethoxycarbonyl group was used for protection of the NH₂ functions of 4 (→7) . The selective introduction of the palmitoyl (= hexadecanoyl) group into the 5′-N-position of 4 was achieved by its treatment with palmitoyl chloride in MeCN in the presence of Et₃N (→ 5 ). The 3′-O-silyl derivatives 11 and 14 were isolated by column chromatography after treatment of the 2′,3′-O-deprotected compounds 8 and 9 , respectively, with (tert-butyl)dimethylsilyl chloride and 1H-imidazole in pyridine. The corresponding phosphoramidites 16 and 17 were synthesized from nucleosides 11 and 14 , respectively, and (cyanoethoxy)bis(diisopropylamino)phosphane in CH₂Cl₂. The trimeric (2′–5′)-linked adenylates 25 and 26 having the 5′-amino-5′-deoxyadenosine and 5′-deoxy-5′-(palmitoylamino)adenosine residue, respectively, at the 5′-end were prepared by the phosphoramidite method. Similarly, the corresponding 5′-amino derivatives 27 and 28 carrying the 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus, were obtained. The newly synthesized compounds were characterized by physical means. The synthesized trimers 25–28 were 3-, 15-, 25-, and 34-fold, respectively, more stable towards phosphodiesterase from Crotalus durissus than the trimer (2′–5′)ApApA.     

Nucleosides. 130. Synthesis of 2′-Deoxy-2′-substituted- and 5′-Deoxy-5′-substituted-ψ-uridine Derivatives. Crystalline and Molecular Structure of 2′-Chloro-2′-deoxy-1,3-dimethyl-ψ-uridine. Studies Directed Toward the Synthesis of 2′-Deoxy-2′-substituted-arabino-Nucleosides. 1

A method was developed to prepare 5′-deoxy-5′-substituted-ψ-uridine derivatives 4 from 3′,5′-O-(1, 1, 3, 3-tetraisopropyldisiloxanyl)-1,3-dimethyl-ψ-uridine 1 via a silyl rearrangement reaction. Nucleophilic displacement of the mesyloxy function of 2′-O-mesyl-1,3-dimethyl-ψ-uridine 7 afforded products with the 2′-substituent in the “down” ribo configuration 8 . X-Ray crystallographic analysis of the 2′-chloro derivative 8a firmly established the molecular structure of 8 and provided evidence for neighboring group participation of the 4-carbonyl function of 7 during the nucleophilic reactions. Treatment of 1,3-dimethyl-ψ-uridine 11 with α-acetoxyisobutyryl chloride afforded a mixture from which two 2′-chloro-2′-deoxy-C-nucleosides were obtained. The major product (33% yield) was identical with 8 . The minor product (7% yield) was consequently assigned the arabino nucleoside 14 . This is the first direct introduction of a 2′-substituent in the “up” configuration in a preformed pyrimidine nucleoside.     

Dipyrido[3,2-a:2′,3′-c]phenazine-Tethered Oligo-DNA: Synthesis and Thermal Stability of Their DNA⋅DNA and DNA⋅RNA Duplexes and DNA⋅DNA⋅DNA Triplexes

Dipyrido[3,2-a:2′,3′-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA (ODN) at a site without nucleobase, either at the 5′- or 3′-end or at a internucleotide position, via linkers of 7, 12, or 18 atoms lengths. These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites: Glycerol, serving as artificial nucleoside without nucleobase, was modified to amines 10 , 23 , and 24 , which were suitable for the subsequent key reaction with dppz-carboxylic acid 3 (Schemes 2 and 3). The products of these reactions (see 5 – 7 ) were then transformed to the standard phosphoramidite derivatives (see 27 , 29 , and 30 ) or used for loading on a CPG support (see 28 , 31 , and 32 ). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis. The 9-mer ODN-dppz conjugates 35 – 43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11 ( 60 ) or R11 ( 61 )), while the 18-mer ODN-dppz conjugates 48 – 56 were tested for their ability to form stable triplexes with a DNA target duplex D24⋅D24 ( 62 ) (see Tables 1 and 2). The presence of the conjugated dppz derivative increases the stability of DNA⋅DNA and DNA⋅RNA duplexes, typically by a ΔT_m of 7.3 – 10.9° and 4.5 – 7.4°, respectively, when the dppz is tethered at the 5′- or 3′-terminal (Table 2). The dppz derivatives also stabilize triplexes when attached to the 5′- or 3′-end, with a ΔT_m varying from 3.8 – 11.1° (Table 3). The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA⋅DNA duplexes (ΔT_m=0.5 to 4.2°) and DNA⋅RNA duplexes (ΔT_m=−1.5 to 0.9°), while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all. Different types of modifications in the middle of the 18-mer ODN, in general, do not lead to any triplex formation, except when the dppz derivative is tethered to the ODN through a 12-atom-long linker (Entry 9 in Table 3).     

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-butyldiphenylsilyl)-3′-azido-3′-deoxyadenosine and 3′-azido-3′-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3′-azido-3′-deoxy-2′-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6–41.2 kcal/mol and have low energy barriers of 10.4–13.5 kcal/mol. Reduction of the azido group occurred to give 3′-amino-3′-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl)thymidine with 2,2′-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N₂O-saturated aqueous solutions of AZT and cysteine produced 3′-amino-3′-deoxythymidine and thymine most likely by both radical and ionic processes.     

An effective and convenient synthesis of cordycepin from adenosine

Cordycepin is a purine nucleoside analog with potent and diverse biological activities. Herein, we designed two methods to synthesize cordycepin. One method mainly converted the 3′-OH group into an iodide group and further dehalogenation to yield the final product. Although this method presented a short synthetic procedure, the synthesis had a low overall yield, resulting in only 13.5% overall yield. To improve the overall yield of cordycepin, another synthetic route was studied, which consisted of four individual steps: (1) 5′-OH protection (2) esterification (3) -O-tosyl (-OTs) group removal (4) deprotection. The key step in the synthetic method involved the conversion of 5′-O-triphenylmethyladenosine to 3′-O-tosyl-5′-O-triphenylmethyladenosine, using LiAlH₄ as reducing agent. The main advantages of this route were an acceptable total product yield and the commercial availability of all starting materials. The optimal reaction conditions for each step of the route were identified. The overall yield of cordycepin obtained from adenosine as the starting material was 36%.     

Synthesis of porphyrinyl-nucleosides

Several porphyrinyl-nucleosides were prepared in the reaction of the OH group of one, two or four meso-p-hydroxyphenyl substituents of porphyrin with 5′-O-tosylates of 2′,3′-O-isopropylidene-adenosine or -uridine, or 5′-O-tosylthymidine; the remaining porphyrin meso-substituents were p-tolyl, p-hydroxyphenyl or 4-pyridyl. The following porphyrinyl-nucleosides were obtained with 8–17% yield: meso-di(p-tolyl)di(p-phenylene-5′-O-2′,3′-O-isopropylidene-adenosine) (or -uridine)porphyrins 1,2 , the respective meso-tetranucleosideporphyrins 3,4 -meso-mono(p-phenylene-5′-O-thymidine)porphyrins 5–7 , meso-di(p-tolyl)di(p-phenylene-5′-O-thymidine)porphyrins 8,9 and the meso-di(p-hydroxyphenyl)di(p-phenylene-5′-O-thymidine)porphyrins 10. Other compounds prepared belonged to the series: meso(4-pyridyl)_4?n(p-phenylene-5′-O-2′,3′-O-isopropylideneuridine)_nporphyrin, n = 1, 2 or 4, 11–13. N-Methylation gave the water soluble iodide salts: (N-methyl-4-pyridinium)4_4?n(p-phenylene-5′-O-2′,3′-isopropylideneuridine)_nporphyrins, n = 1, 2 or 4, 14–16. The ms fab showed in most cases stepwise detachment of the CH₂(5′)-nucleoside fragments. The porphyrins meso disubstituted by thymidine represent a convenient substrate for the build-up of both nucleoside units into the oligo/polynucleotide chains.     

Studies on the Michael addition of naphthoquinones to sugar nitro olefins: first synthesis of polyhydroxylated hexahydro-11H-benzo[a]carbazole-5,6-diones and hexahydro-11bH-benzo[b]carbazole-6,11-diones

A strategy for the synthesis of the novel (6bR,7R,8S,9S,10S,10aR)-8-(benzyloxy)-7,9,10-trihydroxy-6b,7,8,9,10,10a-hexahydro-11H-benzo[a]carbazole-5,6-dione is reported. The key steps were the Michael addition of 2-hydroxy-1,4-naphthoquinone to 1-nitrocyclohexene or 3-O-benzyl-5,6-dideoxy-1,2-O-isopropylidene-6-nitro-α-d-xylo-hex-5-enefuranose and the diastereoselective intramolecular Henry reaction of 3-O-benzyl-5,6-dideoxy-5-C-(3′-hydroxy-1′,4′-naphthoquinon-2′-yl)-1,2-O-isopropylidene-6-nitro-α-d-glucofuranose to give the key (1S,2S,3S,4R,5R,6R)-3-(benzyloxy)-1,2,4-trihydroxy-5-(3′-hydroxy-1′,4′-naphthoquinon-2′-yl)-6-nitrocyclohexane. When 2-hydroxy-1,4-naphthoquinone was replaced by (1,4-dimethoxynaphthalen-2-yl)lithium, the novel (1R,2S,3S,4R,4aS,11bS)-2-(benzyloxy)-1,3,4-trihydroxy-1,2,3,4,4a,5-hexahydro-11bH-benzo[b]carbazole-6,11-dione was obtained.     

LC–DAD–ESI-MS–MS Separation and Chemical Characterization of the Inflammatory Fraction of the Roots of Euphorbia kansui

In China the roots of Euphorbia kansui T.N. Liou ex T.P. Wang, known as ‘kansui’, have been used for centuries as a herbal remedy for edema, ascites, and asthma. Kansui, has inflammatory and tumor-promoting toxicity, and other side-effects, however, which have seriously restricted its clinical application. In the work discussed in this paper a simple and rapid LC–DAD–ESI-MS–MS method has been established for separation and characterization of the main compounds in the toxic fraction of E. kansui roots. Twelve diterpene derivatives were identified in the inflammatory fraction of kansui: kansuinine C, kansuinine B, kansuinine A, kansuinine D, 5-O-benzoyl-20-deoxyingenol, kansuinine E, kansuiphorin C, 3-O-benzoyl-20-deoxyingenol, 3-O-(2′E,4′Z-decadienoyl)-5-O-acetylingenol, 3-O-(2′E,4′Z-decadienoyl)-20-deoxyingenol, 20-O-(2′E, 4′E-decadienoyl)ingenol, and 3-O-(2′E,4′Z-decadienoyl)-20-O-acetylingenol. The inflammatory fraction was separated on a C₁₈ reversed-phase column with a mobile phase gradient. The proposed method is a scientific and technical platform enabling the herbal medicine industry to perform quality control and ensure the safety of preparations that contain this class of poisonous diterpenoids.     

Synthesis of 5-Methyluridine and Its 5′-Mercapto-, 2-Amino-, and 4′,5′-Unsaturated Analogues

The stereospecific cis-hydroxylation of 1-(2,3-dideoxy-β-D -glyceropent-2-enofuranosyl)thymine (1) into 1-β-D -ribofuranosylthymine (2) by osmium tetroxide is described. Treatment of 2′,3′-O, O-isopropylidene-5-methyl-2,5′-anhydrouridine (8) with hydrogen sulfide or methanolic ammonia afforded 5′-deoxy-2′,3′-O, O-isopropylidene-5′-mercapto-5-methyluridine (9) and 2′,3′-O, O-isopropylidene-5-methyl-isocytidine (10) , respectively. The action of ethanolic potassium hydroxide on 5′-deoxy-5′-iodo-2′,3′-O, O-isopropylidene-5-methyluridine (7) gave rise to the corresponding 1-(5-deoxy-β-D -erythropent-4-enofuranosyl)5-methyluracil (13) and 2-O-ethyl-5-methyluridine (14) . The hydrogenation of 2 and its 2′,3′-O, O-isopropylidene derivative 4 over 5% Rh/Al₂O₃ as catalyst generated diastereoisomers of the corresponding 5-methyl-5,6-dihydrouridine ( 17 and 18 ).     

Dinucleotides containing two allyl groups by combinations of allyl phosphotriesters, 5-allyl-, 2′-O-allyl- and 2′-arabino-O-allyl uridine derivatives as substrates for ring-closing metathesis

Five different dinucleotides, each containing two allyl groups in various positions, were prepared and studied as substrates for ring-closing metathesis reactions. These dinucleotides were designed from appropriate nucleoside building blocks combining four different positions for the allyl group; the allyl phosphotriester linkage, 5-allyl-2′-deoxyuridine, and ribo- as well as arabino-configured 2′-O-allyluridine. Thus, convenient procedures for these building blocks were developed. From the dinucleotides, two new cyclic nucleotide structures were obtained; one connecting two adjacent nucleobase moieties and the other forming an unsaturated four-carbon linkage between the phosphate moiety and the adjacent pyrimidine nucleobase. The latter cyclic dinucleotide was also prepared with a saturated four-carbon linkage using a tandem ring-closing metathesis-hydrogenation procedure. This compound was found to be significantly more stable towards a nucleophilic ring-opening than its unsaturated counterpart.     

Acetyl derivatives of nucleoside 5′-triphosphates,I

Acetyl derivatives of nucleoside 5′-phosphates and nucleoside 5′-triphosphates (both ribo and deoxyribo series) were prepared by accomplishing partial (O-) and full (N, O-) acetylation of the basic compounds with acetic anhydride in pyridine medium.     

A synthesis of 3′-α-fluoro-2′,3′-dideoxyadenosine via a bromine rearrangement during fluorination with MOST reagent

A facile method for the synthesis of 3′-α-fluoro-2′,3′-dideoxyadenosine 6 has been developed. Fluorination of 5′-O-acetyl-3′-β-bromo-3′-deoxyadenosine 3 with MOST gave 2′-β-bromo-3′-α-fluoro-2′,3′-dideoxyadenosine 4 via a rearrangement of the 3′-β-bromine to the 2′-β position during 3′-α fluorination. The 2′-β bromine was reduced by radical reduction and then the 5′-O-acetyl group was removed to afford 3′-α-fluoro-2′,3′-dideoxyadenosine 6 in good yield. A possible mechanism for the rearrangement is discussed.     

Synthesis of 5′-halo-2′,3′-lyxo-epoxy and 2′,3′-unsaturated thieno[3,2-d]pyrimidine nucleosides

A series of thieno[3,2-d]pyrimidine-2,4-dione nucleosides modified in the carbohydrate moiety has been synthesized. In the first part, synthetic routes are described for the replacement of 5′-hydroxyl group in preformed 1-(β-D-ribofuranosyl)thieno[3,2-d]pyrimidine-2,4-dione I by fluoro, iodo or chloro atoms. Reduction of the 5′-iodo substituent of VI was then carried out catalytically using palladium on carbon as catalyst to give the expected 5′-deoxy derivative VIII. The lyxo-epoxide derivative XII was then synthesized by sequential treatment of the 5′-deoxy-5′-chloro derivative X with methanesulfonyl chloride and with sodium hydroxide. In the second part, most of attention has been devoted to apply different methods reported in the literature that allow access to 2′,3′-olefinic derivatives from the corresponding 2′,3′-dihydroxy precursor. The 5′-O-silyl protected bisxanthate XIV either on reduction with tri-n-butyltin hydride or by reductive elimination of the haloacetate XVI afforded the free 2′,3′-olefin nucleoside after removal of the 5′-protecting group. However none of the compounds in this series exhibited significant antiviral activity against HIV at the doses tested.     

Synthesis of mono-, di- and trisulfated Lewis x trisaccharides

3′-Sulfated and 3′,6′-disulfated Lewis x trisaccharides have been prepared through selective sulfation of methyl 2-acetamido-6-O-benzyl-2-deoxy-4-O-β-D-galactopyranosyl-3-O-(2,3,4-tri-O-benzyl-α-L-fucopyranosyl)-β-D-glucopyranoside, followed by catalytic hydrogenolysis. In a similar manner, 3′,6-disulfated and 3′,6,6′-trisulfated Lewis x trisaccharides have been selectively obtained from methyl 2-acetamido-2-deoxy-4-O-β-D-galactopyranosyl-3-O-(2,3,4-tri-O-benzyl-α-L-fucopyranosyl)-β-D-glucopyranoside.     

Probing of PSE acetal protection for nucleoside chemistry

The use of phenylsulfonylethylidene (PSE) acetal as a new 3′,5′-bridged protecting group in nucleoside chemistry is reported. The PSE acetal demonstrates to be compatible with Lewis acids used in standard glycosylation reactions. In addition, a selective 2′-O-deacylation from a 3′,5′-O-(phenylsulfonyl)-2′-O-acetyl nucleoside can be achieved, giving access to subsequent chemical modifications in 2′ position. However, the PSE acetal cleavage surprisingly appeared to be purine/pyrimidine base dependent.     

4-Oxa(thia)-9-oxa-2-azabicyclo[4.2.1]nonane-3-on(thion) derivatives

The synthesis of 7,8-dihydroxy-2-(2-methoxycarbonylethyl)-4,9-dioxa-2-azabicyclo[4.2.1]nonane- 3-thione ( 16 ) and of its parents 9-oxa-4-thia-3-thione 17 , and 9-oxa-4-thia-3-one 18 is described. The conversion of 5′-deoxy-5′-iodo-2′,3′-O, O-isopropylidene-5,6-dihydrouridin ( 1 ) into the 2-O-methyl-5,6-dihydrouridine 5 , the 5′-O-acetyl-5,6-dihydrouridine 4 , and into the N-(5-O-acetyl-2,3-O, O-isopropylidene-β-D -ribofuranosyl)-N-(2-methoxycarbonyl thyl)-urea ( 6 ) invoked 2′,3′-O, O-isopropylidene-2,5′-anhydro-5,6-dihydrouridine ( 2 ) as the common intermediate.     

Regioselective Transformations of 2′,3′-Seconucleosides into Anhydro Structures and Chiral Crown Ethers

Intramolecular cyclisation of properly protected and activated derivatives of 2′,3′-secouridine ( = 1-{2-hydroxy-1-[2-hydroxy-1-(hydroxymethyl)ethoxy]-ethyl}uracil; 1 ) provided access to the 2,2′-, 2,3′-, 2,5′-, 2′,5′-, 3′,5′-, and 2′,3′-anhydro-2′,3′-secouridines 5, 16, 17, 26, 28 , and 31 , respectively (Schemes 1–3). Reaction of 2′,5′-anhydro-3′-O-(methylsulfonyl)- ( 25 ) and 2′,3′-anhydro-5′-O-(methylsulfonyl)-2′,3′-secouridine ( 32 ) with CH₂CI₂ in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene generated the N(3)-methylene-bridged bis-uridine structure 37 and 36 , respectively (Scheme 3). Novel chiral 18-crown-6 ethers 40 and 44 , containing a hydroxymethyl and a uracil-1-yl or adenin-9-yl as the pendant groups in a 1,3-cis relationship, were synthesized from 5′-O-(triphenylmethyl)-2′,3′-secouridine ( 2 ) and 5′-O,N⁶-bis(triphenylmethyl)-2′,3′-secoadenosine ( 41 ) on reaction with 3,6,9-trioxaundecane-1,11-diyl bis(4-toluenesulfonate) and detritylation of the thus obtained (triphenylmethoxy) methylcompound 39 and 43 , respectively (Scheme 4).     

Über Pterinchemie. 85. Mitteilung. Polyacetylierte 5,6,7,8-Tetrahydro-D- und -L-neopterine. Ein besonderer Fall von N(5)-Alkylierung des 5,6,7,8-Tetrahydroneopterin-Gerüstes

Polyacetylated 5,6,7,8-Tetrahydro-D - and L -neopterins. A Special Case of N(5)-Alkylation of 5,6,7,8-Tetrahydroneopterins Improved conditions are reported for the preparation of the earlier described (6R)- and (6S)-1′-O,2′-O,3′-O,2-N,5-pentaacetyl-5,6,7,8-tetrahydro-L -neopterins, one of which could be obtained as pure crystals. Its structure, determined by X-ray-diffraction analysis, corresponds to the (6R)-enantiomer. The method has also been used to make the corresponding D -diastereoisomers. Further acetylation of (6RS)-1′-O,2′-O,3′-O,2-N-tetraacetyl-5,6,7,8-tetrahydro-D -neopterin under drastic conditions yields a mixture of several polyacetylated D -neopterin derivatives and a polyacetylated ethyl-tetrahydro-D -neopterin which was isolated in crystalline form and established by X-ray-diffraction analysis to be (6R)-1′-O,2′-O,3′-O,4-O,2-N,2-N,8-heptaacetyl-5-ethyl-5,6,7,8-tetrahydro-D -neopterin.