An Alternative Route for Preparation of α-Methylphosphonyl-β, γ-Diphosphates of Thymidine Derivatives

Abstract

An alternative “one pot” synthesis of α-methylphosphonyl-β, γ-diphosphates of thymidine and 3′-azidothymidine is proposed. p-Toluene-sulphonic acid was used as desililating agent for triphosphate analogues.     

Improved Targeting of the Flanks of a DNA Stem Using α-Oligodeoxynucleotides.-The Enhanced Effect of an Intercalator

Abstract

2′-Deoxy-5′-0-(4,4′-dimethoxytrityl)-5-methyl-N ⁴-(1-pyrenylmethyl)-α-cytidine (5) was prepared by reaction of 1-pyrenylmethylamine with an appropriate protected 4-(l,2,4-triazolyl)-α-thymidine derivative 3 which was synthesized from 5-O-DMT protected α-thymidine 1. Aminolysis of 3 afforded 3′-O-acetyl-2′-deoxy-5′-O-(4,4′-dimethoxytrityl)-5-methyl-α-cytidine (8). Benzoylation of 8 and removal of acetyl afforded N ⁴-benzoyl-2-deoxy-5–0-(4,4′-dimethoxytrityl)-5-methyl-α-cytidine (10). The amidites of compounds 5and 10 were prepared and used in α-oligonucleotide synthesis. DNA three-way junction (TWJ) is stabilized when an α-ODN is used for targeting the dangling flanks of the stem in a DNA hairpin. Further stabilization of the TWJ is observed when 5 is inserted into the α-ODN at the junction region.

     

8-Aza-1-deazapurine Nucleosides as Antiviral Agents

Abstract

2′,3′-Dideoxy-8-aza-1-deazaadenosine (21) and its α-anomer (20) were synthesized via glycosylation of 7-chloro-3H-1,2,3-triazolo[4,5-b]pyridi-ne with 2,3-dideoxy-5-O-[(1, 1)-dimethylethyl)diphenylsilyl]-D-glycero-o-pen-tofuranosyl chloride. The reaction gave a mixture of α- and β-anomers of N³-, N⁴- and N¹-glycosylated regioisorners (12–15). The α- and β-anomers of the N⁴-glycosylated isomer 26 and 27 were also synthesized through the glycosylation of 8-aza-1-deazaadenine with 1-acetoxy-2,3-dideoxy-5-O-f(1,1-di-methylethyl)dimethylsilyl]-D-glycero-pentouranose. These dideoxynucleo-sides and a series of previously synthesized 8-aza-1-deazapurine nucleosidcs were tested for activity against several DNA and RNA viruses, HIV-1 included. The α- and β-anomers of 7-chloro-3-(2-deoxy-D-erythro-pentofuranosyl)-3H-1,2,3-triazolo[4,5-b]pyridine (3a and 4) showed activities against Sb-1 and Coxs viruses. The α- and β-anomers of 2′,3′-dideoxy-8-aza-1-deazaadenosine (20 and 21) were found active as inhibitors of adenosine deaminase.     

Synthesis of Novel Alkyl Triphosphates and Their Substrate Properties Toward Terminal Deoxynucleotidyltransferase

Novel triphosphate derivatives bearing bulky or small groups at α-position attached to the triphosphate residue through linkers of different structures and lengths were synthesized and studied as substrates toward terminal deoxynucleotidyltransferase. The substrate efficacy depends on the structure of substituents, linker length, and nature of metal activator. The replacement of hydrophobic groups by small substituents decreased the substrate efficacy by about 20 times in respect to hydrophobic residues. The dependence on metal activator is the following: Co²⁺ > Mn²⁺ >> Mg²⁺. The model of interaction of alkyl triphosphates with linkers of different lengths bearing TdT active site is presented.     

Asymmetric Synthesis of α-Methylglutamic Acid and α-Methylornithine by a Chiral Isocyano Amide Reagent

An efficient approach to the asymmetric syntheses of α-methylglutamic acid and α-methylornithine is described. Two chiral reagents, (2′S)-N-(2′-methoxymethylpyrrolidine)-2-isocyanopropionamide 4 and (2′S)-N-(2′-hydroxymethylpyrrolidine)-2-isocyanopropionamide 5, were employed for the asymmetric induction. α-Methylglutamic acid 7 was synthesized by the asymmetric Michael-addition of methyl acrylate to 4 and 5 as the key step. The optical yield of 7 was 10~45% (R-form). α-Methylornithine 12 was also synthesized by the reaction of 4 with acrylonitrile as the key step. The optical yield of 12 was 31.7% (R-form).     

Nucleotides. LXXIV Synthesis of a-D-Arabino-oligonucleotides

The 5 α-D-arabinofuranosylnucleosides α-araU (15), α-araT (18), α-araC (22), α-araA (25), and α-araG (28) have been synthesized by the modified silyl-method. The amino groups at the nucleobases and the 2′-hydroxy group at the sugar moiety were protected by the 2-(4-nitro-phenyl) ethoxycarbonyl (npeoc) group (37-40) and the amide function in α-araG was additionally blocked by the 2-(4-nitrophenyl)ethyl group (63) to improve solubility in organic solvents. Mono-and dimethoxytritylation of the 5′-OH group was performed in the usual manner to give 41-48, 64, and 65 in high yields and further substitution of the 3′-OH group led to the monomeric building blocks 66-75 as well as the 3′-O-succinoyl derivatives 76-85 functioning as starting units in solid-support oligonucleotide synthesis. A large number of oligo-α-arabinonucleotides have been prepared on modified CPG-material applying the npeoc/npe strategy as a very efficient synthetic tool for highly purified, homogenous oligomers. Hybridizations between α-arabinonucleotide strands revealed in analogy to earlier findings an antiparallel orientation whereas the combination of an oligo-α-D-arabinonucleotide with a complementary oligo-2′-deoxy-β-D-ribofuranosylnucleotide showed base-pairing only if a parallel polarity was present. The advantages in oligo-α-arabinonucleotide synthesis were furthermore demonstrated by the synthesis of the tα-ANA ^his a structural analog of the natural tRNA ^his of the phage T5.     

Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli

Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-Å-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP + Ca^2 +) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the α1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the α- and β-phosphates of the substrate, weakening the P_α-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.     

Synthesis of blockwise alkylated (1→4) linked trisaccharides as surfactants: influence of configuration of anomeric position on their surface activities

New carbohydrate-based surfactants consisting of hydrophilic cellobiosyl and hydrophobic glucosyl residues, methyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranosyl-(1→4)-2,3,6-tri-O-methyl-α-d-glucopyranoside 1 (GβGαMα, G: glucopyranosyl residue, α and β: α-(1→4)- and β-(1→4) glycosidic bonds, M: methyl group), 2 (G_βG_βM_α), 3 (G_βG_αM_β), 4 (G_βG_βM_β), 5 (G_βG_αE_α, E: ethyl group), 6 (G_βG_βE_α), 7 (G_βG_αE_β), 8 (G_βG_βE_β) and eight α-and β-glycoside mixtures (a mixture of 1 and 2: 1/2 = 62/38 (9), 32/68 (10); a mixture of 3 and 4: 3/4 = 69/31 (11), 32/68 (12); a mixture of 5 and 6: 5/6 = 62/38 (13), 33/67 (14); a mixture of 7 and 8: 7/8 = 59/41 (15), 29/71 (16)) were synthesized via combined methods consisting of acid-catalyzed alcoholysis of cellulose ethers and glycosylation of phenyl thio-cellobioside derivatives. Their surface activities in aqueous solution depended on their chemical structures: α- or β-(1→4) linkage between hydrophilic cellobiosyl and hydrophobic glucosyl blocks, methyl or ethyl groups of hydrophobic glucosyl block, and α- or β-linked ether group at the C-1 of hydrophobic glucosyl block. The mixing effect of α- and β-glycosides on surface activities was also investigated. As a result, ethyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranosyl-(1→4)-2,3,6-tri-O-ethyl-β-d-glucopyranoside 7 (G_βG_αE_β) had the highest surface activity, and its critical micellar concentration (CMC) and γ_CMC (surface tension at CMC) values of compound 7 were 0.5 mM (ca. 0.03 wt %) and 34.5 mN/m, respectively. The surface tensions of α- and β-glycoside mixtures except for compounds 9 and 10 were almost equal to those of pure compounds. The syntheses of the mixtures of α- and β-glycosides without purification process are easier than those of pure compounds. Thus, the mixtures should be more practical compounds for industrial use as a surfactant.     

Chemoenzymic Synthesis of Pα-Methyl Deoxynucleoside Triphosphates

Abstract

5′-O-(methylphosphonyl)-N-(phenylacetyl)-2 ′-deoxycytidine, deoxyadenosine and deoxyguanosine were pyrophosphorylated and the resulting N-protected P α-methyl nucleoside triphosphates were deblocked by treatment with penicillin amidase at pH 7.8, 25°C to give P α-methyl nucleoside triphosphates.     

Pyrimidine-fused heterocycle derivatives as a novel class of inhibitors for α-glucosidase

The needs for diverse inhibitors of α-glucosidase (α-Gls) encouraged us to synthesize five different poly-hydroxy functionalized pyrimidine-fused heterocyclic (PHPFH) molecules, having either aliphatic or aromatic side chains (C₁–C₅) and their inhibitory activities were examined spectroscopically against yeast and mouse intestinal α-Gls. The results revealed that aromatic substitution of the synthetic compounds has significant impact on their inhibitory properties. Moreover C₃ with the substituted moiety as 4-(4-aminophenylsulfonyl) phenyl (4-APSP) revealed strong inhibitory activity with non-competitive and competitive inhibition modes against yeast and mouse α-Gls, respectively. Furthermore, in the presence of increasing concentration of C₃, both Trp and 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence intensities of yeast α-Gls were gradually decreased, suggesting that C₃ binding induced significant structural alteration which was accompanied with the reduction of hydrophobic surfaces. Also, the interaction between yeast α-Gls and C₃ was proved to be spontaneous and driven mainly by hydrophobic forces. Overall, this study suggests that aromatic substitution on pyrimidine-fused heterocyclic (PFH) scaffold may represent a novel class of promising inhibitors of α-Gls.     

Different Mechanisms of Inhibition of DNA Synthesis by (E)-5-(2-Bromovinyl)-2′-deoxyuridine in Cells Transfected with Gene for Thymidine Kinase of Herpes Simplex Virus Type 1 and in Cells Infected with the Virus

Abstract

The effect of (E)-5-(2-bromovinyl)-2′-deoxyuridine (BVDU) on deoxyribonucleoside 5′-triphosphate pools was studied in cells transfected with gene for thymidine kinase of herpes simplex virus type 1 and cells infected with the virus. When infected cells were treated with BVDU, the triphosphate form of the nucleoside analog was detected. When transfected cells were treated with BVDU, the triphosphate form was not detected and the pattern of changes in the pools was the same as after 5-fluoro-2′-deoxyuridine treatment. BVDU seems to inhibit DNA synthesis differently in the two cell lines and nucleotide metabolism in the transfected cells was not the same as in the infected cells.     

New quinoxalinone inhibitors targeting secreted phospholipase A2 and α-glucosidase

Elevated blood glucose and increased activities of secreted phospholipase A2 (sPLA2) are strongly linked to coronary heart disease. In this report, our goal was to develop small heterocyclic compound that inhibit sPLA2. The title compounds were also tested against α-glucosidase and α-amylase. This array of enzymes was selected due to their implication in blood glucose regulation and diabetic cardiovascular complications. Therefore, two distinct series of quinoxalinone derivatives were synthesised; 3-[N′-(substituted-benzylidene)-hydrazino]-1H-quinoxalin-2-ones 3a–f and 1-(substituted-phenyl)-5H-[1,2,4]triazolo[4,3-a]quinoxalin-4-ones 4a–f. Four compounds showed promising enzyme inhibitory effect, compounds 3f and 4b–d potently inhibited the catalytic activities of all of the studied proinflammatory sPLA2. Compound 3e inhibited α-glucosidase (IC₅₀?=?9.99?±?0.18 µM); which is comparable to quercetin (IC₅₀?=?9.93?±?0.66 µM), a known inhibitor of this enzyme. Unfortunately, all compounds showed weak activity against α-amylase (IC₅₀?>?200 µM). Structure-based molecular modelling tools were utilised to rationalise the SAR compared to co-crystal structures with sPLA2-GX as well as α-glucosidase. This report introduces novel compounds with dual activities on biochemically unrelated enzymes mutually involved in diabetes and its complications.     

Kinetics and regioselectivity of three GH62 α-L-arabinofuranosidases from plant pathogenic fungi

BackgoundXylan is the second most abundant plant cell wall polysaccharide after cellulose with α-L-arabinofuranose (L-Araf) as one of the major side substituents. Capacity to degrade xylan is characteristic of many plant pathogens; and corresponding enzymes that debranch arabinoxylan provide tools to tailor xylan functionality or permit its full hydrolysis.MethodThree GH62_2 family α-arabinofuranosidases (Abfs) from plant pathogenic fungi, NhaAbf62A from Nectria haematococca, SreAbf62A from Sporisorium reilianum and GzeAbf62A from Gibberella zeae, were recombinantly produced in Escherichia coli. Their biochemical properties and substrate specificities were characterized in detail. Particularly with ¹H NMR, the regioselectivity and debranching preference of the three Abfs were directly compared.ResultsThe activities of selected Abfs towards arabinoxylan were all optimal at pH 6.5. Their preferred substrates were wheat arabinoxylan, followed by soluble oat spelt xylan. The Abfs displayed selectivity towards either α-(1 → 2) or α-(1 → 3)-L- Araf mono-substituents in arabinoxylan. Specifically, SreAbf62A and GzeAbf62A removed m-α-(1 → 3)-L-Araf and m-α-(1 → 2)-L-Araf substituents with a similar rates, whereas NhaAbf62A released m-α-(1 → 3)-L-Araf 1.9 times faster than m-α-(1 → 2)-L-Araf.Major conclusionsBuilding upon the known selectivity of GH62 family α-arabinofuranosidases towards L-Araf mono-substituents in xylans, the current study uncovers enzyme-dependent preferences towards m-α-(1 → 3)-L-Araf and m-α-(1 → 2)-L-Araf substitutions. Comparative sequence-structure analyses of Abfs identified an arginine residue in the xylose binding +2R subsite that was correlated to the observed enzyme-dependent L-Araf debranching preferences.General significanceThis study expands the limited pool of characterized GH62 Abfs particularly those from plant pathogenic fungi, and provides biochemical details and methodology to evaluate regioselectivity within this glycoside hydrolase family.     

Fatty acid synthesis by isolated chromoplasts from the daffodil. Energy sources and distribution patterns of the acids

1. Fatty acid synthesis in isolated intact chromoplasts from [1-¹⁴C]acetate was made possible by using ATP, ADP (via adenylate kinase), and, with decreasing efficiency, UTP, CTP, and GTP as energy sources. 2. The glycolytic path from dihydroxyacetone phosphate to acetyl-CoA operates within the chromoplasts. The glycolytic intermediates, especially 2-phosphoglycerate and phosphoenolpyruvate, served as very effective energy donors for fatty acid synthesis by phosphorylating the endogenous adenine nucleotide pool. 3. In the presence of exogenous ATP or ADP, appreciable amounts of in vitro formed fatty acids were found as acyl-CoA and subsequent products, mainly phosphatidylcholine. When other energy sources were used most of the acids formed were in the free form, and to a minor extent, in the phosphatidic acid and diacylglycerol fractions. Similar results have recently been reported for spinach chloroplasts (Kleinig and Liedvogel 1979, FEBS Lett.101, 339–342).Abbreviations ATP adenosine triphosphate - ADP adenosine diphosphate - UTP uridine triphosphate - CTP cytidine triphosphate - GTP gnanosine triphosphate     

Characteristics of Transglucosylation of Honeybee α-Glucosidase I

Transglucosylation of an α-glucosidase (I) from honeybee was investigated. The honeybee α- glucosidase catalyzed the predominant formation of α-1,4-glucosidic linkage from sucrose, phenyl α-glucoside, or maltose. The major product from sucrose was 4^G-a-glucosyl-sucrose (erlose), which differs from the report by Huber and Thompson that 3^F-a-glucosyl-sucrose (melezitose) is mainly synthesized from sucrose by the transglucosylation of the same α-glucosidase: Biochemistry, 12, m 4011 (1973). Melezitose was not detected as the transglucosylation product of this enzyme.     

Synthesis and Antimicrobial Activity of Chiral cis-Cycloheximide Isomers

Such (+)- and (?)-cis-cycloheximide isomers as isocyclohcximide (1a, 1b), α-epiisocycloheximide (2a, 2b) and neocycloheximide (3a, 3b) were synthesized by aldol condensation of (?)-(2R, 4R)- and (+)-(2S, 4S)-cis-2,4-dimethyl-1-cyclohexanone (5a, 5b). obtained by microbial resolution, with 4-(2-oxoethyl)-2,6-piperidinedione (7). The absolute configuration of the (?)-cis-ketone 5a was confirmed by chemical correlation with natural (2S, 4S, 6S, αR)-cycloheximide (4). The newly synthesized isomer, (?)-α-epiisocycloheximide (2b), showed strong antimicrobial activity against S. cerevisiae andP. oryzae close to that of natural cycloheximide (4).     

Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design

Topoisomerases (Topos) are very important protein targets for drug design in cancer treatment. Human Topo type IIα (hTopo IIα) has been widely studied experimentally and theoretically. Here, we performed protein rigid/flexible side-chain docking to study a set of thirty-nine 3-substituted-2,6-piperazindiones (labelled 1a, (R)-[(2–20)a] and (S)-[(2–20)b]) derived from α-amino acids. To explain the ligand–protein complexes at the electronic level [using the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) energies], density functional theory calculations were carried out. Finally, to show adenosine triphosphate (ATP) binding-site constituents, the Q-SiteFinder program was used. The docking results showed that all of the test compounds bind to the ATP-binding site on hTopo IIα. Recognition is mediated by the formation of several hydrogen bond acceptors or donators. This site was the largest (631 Å³) according to the Q-SiteFinder program. When using the protein rigid docking protocol, compound 13a derived from (R)-Lys showed the highest affinity. However, when a flexible side-chain docking protocol was used, the compound with the highest affinity was 16a, derived from (R)-Trp. Frontier molecular orbital studies showed that the HOMO of the ligand interacts with the LUMO located at side-chain residues from the protein-binding site. The HOMO of the binding site interacts with the LUMO of the ligand. We conclude that some ligand properties including the hindrance effect, hydrogen bonds, π–π interactions and stereogenic centres are important for the ligand to be recognised by the ATP-binding site of hTopo IIα.     

Dinucleoside Polyphosphate NAD Analogs as Potential NMN Adenylyltransferase Inhibitors. Synthesis and Biological Evaluation

Abstract

Two dinucleoside polyphosphate NAD analogs, P¹-(adenosine-5′)-P³-(nicotinamide riboside-5′)triphosphate (Np₃A, 1) and P¹-(adenosine-5′)-P⁴-(nicotinamide riboside-5′)tetraphosphate (Np₄A, 2), were synthesized and tested as inhibitors of both microbial and human recombinant NMN adenylyltransferase. Compounds 1 and 2 proved to be selective inhibitors of microbial enzymes.