Synthesis of the first double-functionalized dinucleotide mRNA cap analogue for its specific labeling

The modification of various important nucleotide-based molecules (such as nucleotides, RNA, DNA, oligonucleotides) with fluorophores, affinity tags and reactive moieties is of enormous utility for studying their localization, structure and dynamics, as well as diverse biological functions involving their interacting partners. Herein, we report chemical methodology in which the dinucleotide mRNA cap analogue is doubly modified within its second nucleotide. The prepared dinucleotide contains an alkyne at the N2-position of guanine, and levulinic acid within the ribose moiety. Such modifications may be further used for specific labeling of the cap, for instance with a fluorophore that will allow the molecule to be tracked inside the cell and an attachment cell-penetrating peptide that will help to deliver it to the area of interest. Exemplar molecules were attached in order to demonstrate the utility of the newly synthesized cap analogue.     

Synthesis of functionalized acenaphthenes and a new class of homooxacalixarenes

The 5,6-dialkoxyethers of acenaphthene have been synthesized for the first time via modified Ullmann reaction conditions. Further modifications of the 5,6-dimethoxyacenaphthene allowed the synthesis of the first acenaphthene analogue of the octahomotetraoxacalixarenes. The X-ray structure of this new macrocycle and its complexation study with C(60) are reported.     

Synthesis of cyclic adenosine 5'-diphosphate ribose analogues: a C2'endo/syn "southern" ribose conformation underlies activity at the sea urchin cADPR receptor

Novel 8-substituted base and sugar-modified analogues of the Ca(2+) mobilizing second messenger cyclic adenosine 5'-diphosphate ribose (cADPR) were synthesized using a chemoenzymatic approach and evaluated for activity in sea urchin egg homogenate (SUH) and in Jurkat T-lymphocytes; conformational analysis investigated by (1)H NMR spectroscopy revealed that a C2'endo/syn conformation of the "southern" ribose is crucial for agonist or antagonist activity at the SUH-, but not at the T cell-cADPR receptor.     

S-adenosylhomocysteine analogues with the carbon-5' and sulfur atoms replaced by a vinyl unit

Cross-metathesis of suitably protected 5'-deoxy-5'-methyleneadenosines with racemic and chiral N-Boc-protected six-carbon amino acids bearing a terminal double bond in the presence of the Hoveyda-Grubbs catalyst gave adenosylhomocysteine analogues with the C5'-C6' double bond. Bromination with pyridinium tribromide and dehydrobromination with DBU followed by standard deprotections yielded the 5'-(bromo)vinyl analogue. [structure: see text]     

A versatile strategy for the synthesis of functionalized 2,2'-bi- and 2,2':6',2' '-terpyridines via their 1,2,4-triazine analogues

A general synthetic route for the synthesis of functionalized bi- and terpyridines is reported. Functionalized 1,2,4-triazene 4-oxides 7 and 8-obtained from the reaction of hydrazones 1 with pyridine aldehydes and followed by oxidation-are functionalized by introduction of a cyano group via nucleophilic aromatic substitution. The thus-obtained 5-cyano-1,2,4-triazines 9 and 10 undergo facile inverse-electron-demand Diels-Alder reactions with enamines and alkenes to yield functionalized bi- and terpyridines, respectively. The substituent at position 6 of the 1,2,4-triazene 4-oxides must be aromatic or heteroaromatic in order to allow their facile synthesis, but other substituents and reagents may vary. Each step of the synthetic route allows diversification, which makes the approach particularly useful for the facile synthesis of a large variety of functionalized bi- and terpyridines.     

Quantitative FT-IRRAS spectroscopic studies of the interaction of avidin with biotin on functionalized quartz surfaces

The interaction of avidin with biotin was studied on functionalized quartz surfaces terminated with 3-aminopropyltrimethoxysilane (3-APTMS), 2,2'-(ethylenedioxy)bis(ethylenediamine) (DADOO), and fourth-generation amine-terminated polyamidoamine (G4-NH2 PAMAM) dendrimers with the use of Fourier transform infrared reflection-absorption spectroscopy (FT-IRRAS). In particular, the molecular recognition ability of these surfaces was quantified through FT-IRRAS in combination with the use of an alkyne dicobalt hexacarbonyl probe coupled with avidin. The degree of nonspecific adsorption of avidin was determined by exposure of the amine-terminated and/or biotinylated surfaces to solutions of biotin-saturated avidin. The results indicate that the biotinylated 3-APTMS layer exhibits a very low specific binding capacity for avidin (on the order of 0.15 pmol of avidin/cm2) and substantial nonspecific adsorption. Both the binding capacity and the specificity were greatly improved when the 3-APTMS layer on quartz was modified through serial chemisorption of glutaraldehyde (GA), DADOO, and/or G4-NH2 PAMAM dendrimer layers. Among these layers, the biotinylated G4-NH2 PAMAM dendrimer layer exhibited the highest capacity for avidin binding (2.02 pmol of avidin/cm2) with a specificity of approximately 90%. This effect can be attributed to the efficient packing/ordering of the binding dendrimer layer, leading to a more dense and better organized layer of biotin headgroups on the subsequent biotinylated surface.     

Synthesis of nucleoside dimers bridged on ribose with a butadiynyl group

[reaction: see text] The nucleoside dimer linked by a butadiynediyl group at C-3'beta may serve as a building block for the preparation of backbone-modified oligonucleotides for DNA repair or mutation in functional genomics. We prepared this type of dimer by an Eglington or Sonogashira coupling reaction. The unsymmetrical dimer was synthesized by coupling the acetylene with the bromoacetylene. Only marginal cytotoxicity was detected for one of the dimers.     

A new class of DNA quadruplexes formed by oligodeoxyribonucleotides containing a 3'-3' or 5'-5' inversion of polarity site

Unprecedented DNA quadruplex structures containing a 3'-3' or 5'-5' inversion of polarity site in the G-tract are presented; the quadruplexes are characterized by different elements of symmetry and glycosidic angle conformations.     

Synthesis of phosphatidylcholine analogues derived from glyceric acid: a new class of biologically active phospholipid compounds

Synthesis of a new class of phosphatidylcholine analogues derived from glyceric acid is reported for spectroscopic studies of phospholipases and the conformation of phospholipid side-chains in biological membranes, using fluorescence resonance energy transfer (FRET) techniques.     

Synthesis of nucleoside 3',5'-cyclic boranophosphorothioate,a new type of cyclic nucleotide

The first examples of a borane-containing doubly P-modified chiral cyclic nucleoside monophosphate (cNMP), e.g., thymidine and 5-fluoro-2'-deoxyuridine 3',5'-cyclic boranophosphorothioates, have been synthesized; these cNMP analogues with increased lipophilicity could be potential anticancer prodrugs and useful probes for mechanistic studies.     

Synthesis and conformational studies of peptido-squaramide foldable modules: a new class of turn-mimetic compounds

The β-turn unit is one of the most important secondary structure elements in proteins. The access to new conformationally controlled foldable modules can afford compounds with interesting bioactivities. Here, we describe a new family of peptido-squaramide foldable modules based on the considerable potential of the squaramide unit as a hydrogen bond donor and acceptor as well as the low rotational barrier of the C-N bond. The conformational analysis by NMR of these modules in chloroform and acetonitrile solution shows that a disecondary squaramide with the 4-aminobutyric acid in one of its substituents can mimic the β-turn structure driven by the formation of an intramolecular hydrogen bonded ten-membered ring. This structure, although flexible, has been successfully combined with dipeptide chains to induce the formation of a hairpin-like structure driven by the formation of several cross-strand intramolecular hydrogen bonds.     

Synthesis and in vitro evaluation of botryllazine B analogues as a new class of inhibitor against human aldose reductase

Botryllazine B analogues of diverse substitution patterns have been prepared, and their in vitro inhibitory activities against recombinant human aldose reductase (h-ALR2) evaluated. Among the 15 compounds tested, 6-(4-aminophenyl)-2-(4-hydroxyphenyl)carbonylpyrazine (7b) proved to be the most potent inhibitor, with IC₅₀=0.91 μM. Kinetic analyses of 7b and botryllazine B (1) revealed that these inhibitors exhibit an unprecedented mixed-type inhibition on h-ALR2 with respect to the substrate d,l-glyceraldehyde, in the presence of NADPH at inhibitor concentrations near the IC₅₀ values.     

Solid-phase synthesis of a new diphosphate 5-aminoimidazole-4-carboxamide riboside (AICAR) derivative and studies toward cyclic AICAR diphosphate ribose

The solid-phase synthesis of the first example of a new diphosphate AICAR derivative is reported. The new substance is characterized by the presence of a 5'-phosphate group while a second phosphate moiety is installed on a 5-hydroxypentyl chain attached to the 4-N-position of AICAR. Cyclization of the diphosphate derivative by pyrophosphate bond formation allowed for the formation of a novel AICAR-based cyclic ADP-ribose (cADPR) mimic.     

Development of a new test method for measurement of tack and studies on tack between cap and base compounds

A new test method has been developed to measure the autohesive tack between cap and base compounds at higher temperatures of contact. This method is a modification of the 180° peel test by incorporating a separator or a perforated sheet at the interface. This gives reproducible results and simulates the coextrusion process at a relatively higher temperature of contact.

The effects of reinforcing filler, oil, contact temperature, contact area, contact time and peel rate on tack are reported here.     

Synthesis and PKC binding of a new class of a-ring diversifiable bryostatin analogues utilizing a double asymmetric hydrogenation and cross-coupling strategy

The design, asymmetric synthesis, and biological evaluation of a new class of bryostatin analogues based on a pseudosymmetric spacer domain are described. An aryl bromide diversification site is incorporated allowing access to systematically varied analogues. The new analogues all exhibit potent, nanomolar affinity to PKC.     

Synthesis of new vitamin D3 analogues with a decalin-type CD-ring

Vitamin D analogues, characterized by a decalin CD-ring fragment are described.     

A new concept for the preparation of beta-L- and beta-D-2',3'-dideoxynucleoside analogues

[reaction: see text] A new method for the synthesis of 2',3'-dideoxynucleoside analogues has been developed. An electrochemical activation of 2-substituted furans is followed by the coupling with a pyrimidine or purine base. This gives planar furyl nucleosides as key intermediates, which are hydrogenated cis-selectively to give the corresponding beta-2',3'-dideoxynucleosides as racemic mixtures. An enzymatic kinetic resolution gives rise to beta-D- and beta-L-configured derivatives in high optical purity. This is exemplified by the synthesis of beta-D- and beta-L-3'-deoxythymidine.     

Synthesis and evaluation of thiosemicarbazones functionalized with furyl moieties as new chemosensors for anion recognition

A family of heterocyclic thiosemicarbazone dyes ( and ) containing furyl groups was synthesized in good yields, characterized and their response in acetonitrile in the presence of selected anions was studied. Acetonitrile solutions of and showed absorption bands in the 335-396 nm range which are modulated by the electron donor or acceptor strength of the heterocyclic systems appended to the thiosemicarbazone moiety. Fluoride, chloride, bromide, iodide, dihydrogen phosphate, hydrogen sulphate, nitrate, acetate and cyanide anions were used in recognition studies. From these anions, only sensing features were seen for fluoride, cyanide, acetate and dihydrogen phosphate. Two clearly different chromo-fluorogenic behaviours were observed: (i) a small shift of the absorption band due to the coordination of the anions with the thiourea protons and (ii) the appearance of a new red shifted band due to deprotonation. For the latter effect, a change in the colour of solution from pale yellow to purple was observed. Fluorescence studies were also in agreement with the different effects observed in the UV/Vis titrations. In this case, hydrogen bonding interactions were visible through the enhancement of the emission band, whereas deprotonation induced the appearance of a new red-shifted emission. Logarithms of stability constants for the two processes (complex formation + deprotonation) for receptors in the presence of fluoride and acetate anions were determined from spectrophotometric titrations using the HypSpec V1.1.18 program. Semi-empirical calculations to evaluate the hydrogen-donating ability of the receptors and a prospective electrochemical characterization of compound in the presence of fluoride were also performed.