Bioorganometallic chemistry. 13. Regioselective reduction of NAD(+) models, 1-benzylnicotinamde triflate and beta-nicotinamide ribose-5'-methyl phosphate, with in situ generated [CpRh(Bpy)H](+): structure-activity relationships, kinetics, and mechanistic aspects in the formation of the 1,4-NADH derivatives

Cofactor regeneration; i.e., regiospecific conversion of NAD(+) to 1,4-NADH, has been extensively studied and is a crucial component in the eventual use of 1,4-NADH in a variety of bioorganic synthesis processes involving the formation of chiral organic compounds. We have studied the reduction of a model NAD(+) compound, 1-benzylnicotinamide triflate, 1a, using [CpRh(bpy)(H(2)O)](2+), 2 (Cp = eta(5)-C(5)Me(5), bpy = 2,2'-bipyridyl), as the catalyst precursor and sodium formate (HCO(2)Na) as the hydride source in 1:1 H(2)O/THF and have found exclusive 1-benzyl-1,4-dihydronicotinamide regioselectivity, as was observed previously for natural NAD(+) that provided 1,4-NADH (see: Steckhan et al. Organometallics 1991, 10, 1568). Moreover, a variety of 3-substituted derivatives of 1-benzylpyridinium triflate, in addition to the -C(O)NH(2) group (1a), were also studied to ascertain that this 3-functionality (e.g., -C(O)NHCH(3), -C(S)NH(2), -C(O)CH(3), -C(O)OCH(3), and -CN, 1b,d-g) coordinates to a [CpRh(bpy)H](+) complex to direct the concerted, regioselective transfer of the hydride group from the rhodium to the 4-ring position of the NAD(+) model; all coordinating 3-substituents had relative rates in the 0.9-1.3 range with substrate 1a set to 1.0. If in fact the 3-substituent presented a steric effect [-C(O)NH(CH(2)CH(3))(2), 1c] or was a nonbinding group (-CH(3), 1h; -H, 1i), no catalytic hydride transfer was observed even with the more electrophilic 2 and 6 ring positions being readily available, which further implicated the crucial coordination of the NAD(+) model to the CpRh metal ion center. We also found that the 1-benzyl substituent on the nitrogen atom exerted a substantial electron-withdrawing effect, in comparison to the electron-donating 1-methyl substituent, and favorably affected the rate of the regioselective reduction (rate enhancement of 1-benzyl/1-methyl = 2.0). The kinetics of the regioselective reduction of 1a were studied to show that the initial rate of reduction, r(i), is affected by the concentrations of the substrate, 1a, precatalyst, 2, and the hydride source, HCO(2)Na, in 1:1 H(2)O/THF: d[1-benzyl-1,4-dihydronicotnamide]/dt = k(cat)[1a][2][HCO(2)Na]. Furthermore, we wish to demonstrate that a previously synthesized aqueous NAD(+) model, beta-nicotinamide ribose-5'-methyl phosphate, 3, shows a similar regioselectivity for the 1,4-NADH analogue, while the initial rate (r(i)) for the regioselective reduction of 3 and NAD(+) itself was found to be comparable in water but faster by a factor of approximately 3 in comparison to 1a in 1:1 H(2)O/THF; the solvent, THF, appeared to inhibit the rate of reduction in 1a by presumably competing with the substrate 1a for the CpRh metal ion center. However, in H(2)O, the initial kinetic rate for substrate 3 was not affected by its concentration and implies that, in H(2)O, [CpRh(bpy)H](+) formation is rate determining. We assume that binding of 3 and NAD(+) to the CpRh metal ion center is also a pertinent step for 1,4-dihydro product formation, the experimental rate expression in H(2)O being d[1,4-dihydro-beta-nicotinamide ribose-5'-methyl phosphate]/dt = k(cat)[2][HCO(2)Na]. What we have discovered, for the first time, is evidence that the regioselective reduction of NAD(+) to 1,4-NADH by [CpRh(bpy)H](+) is a consequence of the amide's ability to coordinate to the CpRh metal center, thereby constricting the kinetically favorable six-membered ring transition state for plausible concerted hydride transfer/insertion to C4 to regioselectively provide the 1,4-NADH derivative; [CpRh(bpy)H](+) can be categorized as a biomimetic enzymatic hydride via its ability to bind and regioselectively transfer hydride to C4, exclusively. Clearly, the pyrophosphate and adenosine groups associated with the structure of NAD(+) are not essential in the rate of hydride transfer to C4, with NAD(+) model 3 having a similar initial rate (r(i)) of reduction as NAD(+) itself in water. Finally, a catalytic cycle will be proposed to account for our overall observations.

Synthesis of cyclopentenyl carbocyclic nucleosides as potential antiviral agents against orthopoxviruses and SARS

A practical and convenient methodology for the synthesis of chiral cyclopentenol derivative (+)-12a has been developed as the key intermediate that was utilized for the synthesis of biologically active carbocyclic nucleosides. The selective protection of allylic hydroxyl group followed by the ring-closing metathesis (RCM) reaction with Grubbs catalysts provided (+)-12a on a 10 g scale with 52% overall yield from D-ribose (4). The key intermediate (+)-12a was utilized for the synthesis of unnatural five-membered ring heterocyclic carbocyclic nucleosides. The newly synthesized 1,2,3-triazole analogue (17c) exhibited potent antiviral activity (EC(50) 0.4 microM) against vaccinia virus and moderate activities (EC(50) 39 microM) against cowpox virus and severe acute respiratory syndrome coronavirus (SARSCoV) (EC(50) 47 microM). The 1,2,4-triazole analogue (17a) also exhibited moderate antiviral activity (EC(50) 21 microM) against SARSCoV.

Do arsenosugars pose a risk to human health? The comparative toxicities of a trivalent and pentavalent arsenosugar

Seafood frequently contains high concentrations of arsenic (approximately 10-100 mg/kg dry weight). In marine algae (seaweed), this arsenic occurs predominantly as ribose derivatives known collectively as arsenosugars. Although it is clear that arsenosugars are not acutely toxic, there is a possibility of arsenosugars having slight chronic toxicity. In general, trivalent arsenicals are more toxic than their pentavalent counterparts, so in this work we examine the hypothesis that trivalent arsenosugars might be significantly more toxic than pentavalent arsenosugars in vitro. We compared the in vitro toxicity of (R)-2,3-dihydroxypropyl-5-deoxy-5-dimethylarsinoyl-beta-D-riboside, a pentavalent arsenosugar, to that of its trivalent counterpart, (R)-2,3-dihydroxypropyl-5-deoxy-5-dimethylarsino-beta-D-riboside. The trivalent arsenosugar nicked plasmid DNA, whereas the pentavalent arsenosugar did not. The trivalent arsenosugar was more cytotoxic (IC50 = 200 microM, 48 h exposure) than its pentavalent counterpart (IC50 > 6000 microM, 48 h exposure) in normal human epidermal keratinocytes in vitro as determined via the neutral red uptake assay. However, both the trivalent and the pentavalent arsenosugars were significantly less toxic than MMA(III), DMA(III), and arsenate. Neither the pentavalent arsenosugar nor the trivalent arsenosugar were mutagenic in Salmonella TA104. The trivalent arsenosugar was readily formed by reaction of the pentavalent arsenosugar with thiol compounds, including, cysteine, glutathione, and dithioerythritol. This work suggests that the reduction of pentavalent arsenosugars to trivalent arsenosugars in biology might have environmental consequences, especially because seaweed consumption is a significant environmental source for human exposure to arsenicals.

Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers

Biological polymers such as nucleic acids and proteins are ubiquitous in living systems, but their ability to address problems beyond those found in nature is constrained by factors such as chemical or biological instability, limited building-block functionality, bioavailability, and immunogenicity. In principle, sequence-defined synthetic polymers based on nonbiological monomers and backbones might overcome these constraints; however, identifying the sequence of a synthetic polymer that possesses a specific desired functional property remains a major challenge. Molecular evolution can rapidly generate functional polymers but requires a means of translating amplifiable templates such as nucleic acids into the polymer being evolved. This review covers recent advances in the enzymatic and nonenzymatic templated polymerization of nonnatural polymers and their potential applications in the directed evolution of sequence-defined synthetic polymers.

A novel thrombin binding aptamer containing a G-LNA residue

In this work, we report the solution structure, thermodynamic studies, and the pharmacological properties of a new modified thrombin binding aptamer (TBA) containing a G-LNA residue, namely d(5'-GGTTGGTGTGGTTGg-3'), where upper case and lower case letters represent DNA and LNA residues, respectively. NMR and CD spectroscopy, as well as molecular dynamics and mechanic calculations, has been used to characterize the three-dimensional structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT, and TT loops. d(5'-GGTTGGTGTGGTTGg-3') is characterized by the same folding of TBA, being two strands parallel to each other and two strands oriented in opposite manner. This led to a syn-anti-syn-anti and anti-syn-anti-syn arrangements of the Gs in the two tetrads. d(5'-GGTTGGTGTGGTTGg-3') possesses an anticoagulant activity, even if decreased with respect to the TBA.

Synthesis of Spirocyclic C-Arylribosides via Cyclotrimerization

[reaction: see text] Spirocyclic C-arylribosides were synthesized from the known gamma-ribonolactone derivative. Lithium acetylide addition followed by glycosylation with 3-(trimethylsilyl)propargyl alcohol converted the ribonolactone to silylated diynes. After desilylation or iodination, subsequent ruthenium-catalyzed cycloaddition of resultant diynes with alkynes or chloroacetonitrile gave spirocyclic C-arylribosides.

Studies on the lead-catalyzed synthesis of aldopentoses

The object of this work was to find an efficient means of synthesizing ribose in a manner that could be considered prebiotic. The starting point for synthesis was an aqueous solution of formaldehyde. Heretofore the most frequently used catalyst for this purpose has been calcium hydroxide. Unfortunately this system produces a wide array of products in addition to ribose which constitutes 1% or less of the final product. Attempts were made to find more mild conditions under which the formaldehyde could be reacted. Magnesium hydroxide suspensions were used for this purpose. Formaldehyde does not yield any sugars when incubated in magnesium hydroxide suspensions alone. However, if the magnesium hydroxide suspension was supplemented with doubly charged lead salts and catalytic amounts of any intermediate in the prebiotic pentose pathway, aldopentoses accounted for 30 per cent or more of the final product. The presence of lead in the incubation mixture also accelerated a number of other reactions including the interconversion of the four common aldopentoses, ribose, arabinose, lyxose and xylose.

Single-stranded microRNA mimics

miRNAs are ∼22-nt RNAs that bind to the Argonaute family of proteins and have important regulatory roles in plants and animals. Here, we show that miRNAs exhibit targeting activity in cells when delivered as single strands that are 5'-phosphorylated and that contain 2'-fluoro ribose modifications. Length preferences, chemical modification sensitivity, and genome-wide seed-based targeting all suggest that this activity is Ago-based. Activity could be enhanced by annealing of segmented passenger strands containing non-nucleic acid spacers. Furthermore, screening of randomly generated sequences identified pyrimidine rich 3' cassette sequences that increased single strand activity. These results provide an initial step in the development of single-stranded miRNA mimics for therapeutic use.

Novel synthesis of L-ribose from D-mannono-1,4-lactone

[reaction: see text] D-Mannono-1,4-lactone was efficiently converted into L-ribose in eight steps. A key step of this synthesis is the cyclization of a gamma-hydroxyalkoxamate under Mitsunobu conditions. It is noteworthy that the O-alkylation product was obtained in 94% yield and that none of the N-alkylation product was detected in this cyclization.

Synthesis, conformational analysis, and biological activity of C-thioribonucleosides related to tiazofurin

The syntheses of furanthiofurin [5beta-D-(4'-thioribofuranosyl)furan-3-carboxamide, 1] and thiophenthiofurin [5beta-D-(4'-thioribofuranosyl)thiophene-3-carboxamide, 2], two C-thioribonucleoside analogues of tiazofurin, are described. Direct trifluoroacetic acid-catalyzed C-glycosylation of ethyl furan-3-carboxylate with 1-O-acetyl-2,3,5-tri-O-benzyl-4-thio-D-ribofuranose gave 2- and 5-glycosylated regioisomers, as a mixture of alpha and beta anomers. Ethyl 5-(2,3,5-tri-O-benzyl)-beta-D-(4'-thioribofuranosyl)furan-3-carboxylate (6beta) was debenzylated and then converted into the corresponding amide (furanthiofurin) by reaction with ammonium hydroxide. A similar C-glycosylation of ethyl thiophene-3-carboxylate with 1,2,3,5-tetra-O-acetyl-4-thio-D-ribofuranose catalyzed by stannic chloride afforded an anomeric mixture of 2- and 5-glycosylated regioisomers. Deacetylation of ethyl 5-(2,3,5-tri-O-acetyl)-beta-D-(4'-thioribofuranosyl)thiophene-3-carboxylate (13beta) with methanolic ammonia and treatment of the ethyl ester with ammonium hydroxide gave thiophenthiofurin. The glycosylation site and anomeric configuration were established by (1)H NMR spectroscopy. Thiophenthiofurin was found to be cytotoxic in vitro toward human myelogenous leukemia K562, albeit 39-fold less than thiophenfurin, while furanthiofurin proved to be inactive. K562 cells incubated with thiophenthiofurin resulted in inhibition of inosine 5'-monophosphate dehydrogenase (IMPDH) and an increase in IMP pools with a concurrent decrease in GTP levels. From computational studies it was deduced that, among the C-nucleoside analogues of tiazofurin, activity requires an electrophilic sulfur adjacent to the C-glycosidic bond and an energetically favorable conformer around chi = 0 degrees. Among these, the more constrained (least flexible) compounds (tiazofurin and thiophenfurin) are more active than the less constrained thiophenthiofurin. Those compounds which contain a nucleophilic oxygen in place of the thiazole or thiophene (oxazofurin, furanfurin, and furanthiofurin) show the least activity.

Chiral Induction in a Ribose-Decorated Metallostar through Intrinsic and Interionic Diastereomeric Interactions

A ribose-functionalized bpy ligand has been prepared and shown to give modest diastereomeric excesses of Lambda-[FeL(3)](2+) complexes; interconversion of Delta and Lambda cations is relatively fast, and in CHCl(3), the favored complexes with Delta- or Lambda-TRISPHAT counterions are homochiral, (Delta(+)Delta(-)) or (Lambda(+)Lambda(-)). In the case of the Delta-TRISPHAT salt, a single diastereomer is observed (de > or = 96%).

A practical synthesis of L-ribose

L-Ribose was synthesized by a simple four-step method with overall yield of 76.3% from a protected L-arabinose derivative, which is a compatible intermediate for the synthesis of L-deoxyribose. The key step of this strategy is the Swern oxidation and subsequent stereoselective reduction accompanied by inversion of the 2-hydroxy group of protected L-arabinose.

Synthesis and antiviral evaluation of certain novel pyrazinoic acid C-nucleosides

Pyrazine (1,4-diazine) C-nucleosides constitute a rare class of nucleic acid analogues that has only recently been reported in the literature. As part of our ongoing investigation into the synthesis and reactivity of these compounds, we have developed an electrophilic esterification of a lithiated pyrazine C-nucleoside (1) to give, following deprotection, the versatile intermediate ethyl 3,5-dichloro-6-(beta-d-ribofuranosyl)pyrazine-2-carboxylate (4). This intermediate was subjected to a variety of reaction conditions to generate a series of pyrazinoic acid C-nucleosides. These compounds, along with 3, 5-dichloro-2-(beta-d-ribofuranosyl)pyrazine (2) and 4, were evaluated for antiviral activity and cytotoxicity. No significant activity was observed for compounds 2 and 5-9, but 4 was active against two herpes viruses and cytotoxic in the micromolar range.

Efficient Synthesis of Methyl 3,5-Di-O-benzyl-α-d-ribofuranoside and Application to the Synthesis of 2‘-C-β-Alkoxymethyluridines

Methyl 3,5-di-O-arylmethyl-alpha-D-ribofuranosides have been used extensively as synthons to construct 2'-C-branched ribonucleosides. Herein, we describe efficient access to methyl 3,5-di-O-arylmethyl-alpha-D-ribofuranosides (aryl: 2-ClC(6)H(4), 3-ClC(6)H(4), 4-ClC(6)H(4), 4-BrC(6)H(4), 2,4-Cl(2)C(6)H(3), Ph) in 72-82% yields from methyl D-ribofuranoside. We also demonstrate efficient access to the versatile precursor methyl 3,5-di-O-benzyl-alpha-D-ribofuranoside (3f) and the synthesis of 2'-C-beta-methoxymethyl- and 2'-C-beta-ethoxymethyluridine in six steps from 3f with overall yields of 18% and 32%, respectively.

Sugar synthesis from a gas-phase formose reaction

Prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas-phase conditions were studied in the absence of any known catalyst. The ion-molecule reaction products, diose and triose, were sought by mass spectrometry, and relevant masses were observed. Ab initio calculations were used to evaluate protic formose mechanism possibilities. A bilateral theoretical and experimental effort yielded a physical model for glycoaldehyde generation whereby a hydronium cation can mediate formaldehyde dimerization followed by covalent bond formation leading to diose and water. These results advance the possibility that ion-molecule reactions between formaldehyde (CH(2)O) and H(3)O(+) lead to formose reaction products and inform us about potential sugar formation processes in interstellar space.

Effect of a chemical modification on the hydrated adenosine intermediate produced by adenosine deaminase and a model reaction for a potential mechanism of action of 5-aminoimidazole ribonucleotide carboxylase

Using the hydrated adenosine intermediate (6R)-6-amino-1, 6-dihydro-6-hydroxy-9-(beta-D-ribofuranosyl)purine (2) produced by adenosine deaminase (ADA, EC 3.5.4.4) as a starting point, the active site probe and inhibitor platform 5-(formylamino)imidazole riboside (FAIRs, 4) was designed by removal of the-C6(OH)(NH2)-molecular fragment of 2 generated by the early events of the enzyme-catalyzed hydrolysis. FAIRs was synthesized directly from the sodium salt of 5-amino-1-(beta-D-ribofuranosyl)imidazole-4-carboxylic acid (CAIR) along a reaction sequence involving a tandem N-formylation/decarboxylation that may have a mechanistic connection to the Escherichia coli purE-catalyzed constitutional isomerization of N5-CAIR to CAIR. The physical and spectral properties of FAIRs were elucidated, its X-ray crystal and NMR solution structures were determined, and its interaction with ADA was investigated. Crystalline FAIRs exists solely as the Z-formamide rotamer and exhibits many of the same intramolecular hydrogen bonding events known to contribute to the association of Ado to ADA. In water and various organic solvents, however, FAIRs exists as NMR-distinct, slowly interconverting Z and E rotamers. This truncated enzymatic tetrahedral intermediate analog was determined to be a competitive inhibitor of ADA with an apparent Ki binding constant of 40 microM, a value quite close to that (33 microM) of the natural substrate's K(m). The actual species selected for binding by ADA, though, is likely the minor hydroxyimino prototropic form of Z-FAIRs possessing a far lower true Ki value. As the structural features of FAIRs appear well-suited to support its use as a template for constructing active site probes of both ADA and AIR carboxylases, a variety of carbohydrate-protected versions of FAIRs suitable for facile aglycon elaborations were synthesized. The N3-alkylation, N3-borane complexation, and C4-iodination of some of these were investigated in order to assess physicochemical properties that may assist in the elucidation of mechanisms for the AIR carboxylases. The survey of these properties taken together with a reasonable mechanism for the model CAIRs-->FAIRs synthetic transformation is interpreted to support a mechanism for the purE-catalyzed N5-CAIR-->CAIR biosynthetic one that involves a carboxylative sp3-rehybridization of the imidazole C4 atom rather than one possessing a dipole-stabilized C4 sp2 carbanionic intermediate.

O-Aryl α,β-d-ribofuranosides: synthesis & highly efficient biocatalytic separation of anomers and evaluation of their Src kinase inhibitory activity

A series of peracetylated O-aryl α,β-d-ribofuranosides have been synthesized and an efficient biocatalytic methodology has been developed for the separation of their anomers which was otherwise almost impossible by column chromatographic or other techniques. The incubation of 2,3,5-tri-O-acetyl-1-O-aryl-α,β-d-ribofuranoside with Lipozyme® TL IM immobilized on silica led to the selective deacetylation of only one acetoxy group, viz the C-5'-O-acetoxy group of the α-anomer over the other acetoxy groups derived from the two secondary hydroxyl groups present in the molecule and also over three acetoxy groups (derived from one primary and two secondary hydroxyls of the β-anomer). This methodology led to the easy synthesis of both, α- and β-anomers of O-aryl d-ribofuranosides. All the arylribofuranosides were screened for inhibition of Src kinase. 1-O-(3-Methoxyphenyl)-β-d-ribofuranoside exhibited the highest activity for inhibition of Src kinase (IC(50)=95.0μM).

Elaboration ofd-(−)-Ribose into a Tricyclic, Natural Product-like Scaffold

The construction of natural product-like, tricyclic compounds is reported. Starting from a D-(-)-ribose-derived dihydrofurane, the tricyclic scaffold is prepared via an intramolecular hetero-Diels-Alder reaction. The reaction proceeds with very high diastereoselectivity through an endo transition state, as established on the basis of X-ray structural analysis of the products. Further modification and derivatization of the obtained products is described.

A convenient preparation of 1,2,3-tri-O-acetyl-beta-D-ribofuranose by enzymatic regioselective 5-O-deacetylation of the peracetylated ribofuranose

The lipase from Candida rugosa (Sigma) was used to catalyze the regioselective deacetylation at the 5-position of 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose on a preparative scale. Enzymatic deacetylation provides a convenient one-step preparation of 1,2,3-tri-O-acetyl-beta-D-ribofuranose.

The synthesis of D-ribofuranosyl derivatives of methyl propiolate and a study of the activating influence of the ester group in cycloaddition reactions

2,3,5-Tri-O-benzyl-D-ribofuranosyl bromide (17) has been converted into methyl 3-(2,3,5-tri-O-benzyl-beta-D-ribofuranosyl) propiolate (8) and its alpha anomer 10 in 21 and 42% yields, respectively, by reaction with the silver salt of methyl propiolate. Attempts to prepare 8 from (beta-D-ribofuranosyl)ethyne (1) by standard methods were unsuccessful. The reactions of the esters 8 and 10 and the ethyne 1 with several 1,3-dipoles have been examined. With diazomethane, 8 and 10 gave the pyrazole esters 20 and 28, respectively, whereast the ethyne 1 reacted more slowly to give a mixture of 23 (37%) and 26 (31%). The ester 10 was converted into the triazoles 32 (51%) and 36 (34%) by reaction with benzyl azide. Treatment of the ester 10 with phenylhydrazine gave the pyrazolone 38 in 71% yield. A number of the products of dipolar addition have been converted into new D-ribofuranosyl-pyrazoles and -triazoles by hydrogenolysis.