The preparation of new phosphorus-centered functional groups for modified oligonucleotides and other natural phosphates

Efforts to develop synthetic methodologies allowing the preparation of alpha,alpha- difluorophosphonothioates, alpha,alpha-difluorophosphonodithioates, alpha,alpha-difluorophosphono- trithioates, and alpha,alpha-difluorophosphinates are reviewed in the light of applications in the field of modified oligonucleotides and cyclitol phosphates. Two successful approaches have been developed, based either on the addition of phosphorus-centered radicals onto gem-difluoroalkenes or on a process involving the addition of lithiodifluorophosphono- thioates 91 onto a ketone and the subsequent deoxygenation reaction of the adduct. The radical route successfully developed a practical route to alpha,alpha-difluoro-H-phosphinates which proved to be useful intermediates to a variety of phosphate isosters. The ionic route led to the first preparation of phosphonodifluoromethyl analogues of nucleoside- 3'-phosphates.     

Voltammetric detection of guanosine and adenosine using a carbon paste electrode modified with 1-ethyl-3-methylimidazolium ethylsulfate

A novel kind of carbon paste electrode (CPE) was prepared by mixing graphite powder, liquid paraffin and the ionic liquid 1-ethyl-3-methylimidazolium ethylsulfate. The resulting electrode was used for the simultaneous determination of guanosine and adenosine by differential pulse voltammetry. Compared to a conventional CPE, the oxidation peak currents are largely increased, and the oxidation peak potentials are negatively shifted. The electrochemical responses to guanosine and adenosine were investigated. Under optimized conditions, the calibration curves are linear in the concentration range from 1.0?×?10^-6?mol?L^-1 to 1.6?×?10^-4?mol?L^-1 for guanosine, and from 1.0?×?10^-6?mol?L^-1 to 2.7?×?10^-4?mol?L^-1 for adenosine at pH 3.5. Substances potentially interfering in the biological matrix do no interfere. The method was successfully applied to detect adenosine and guanosine in human urine without sample treatments.

Solventless protocol for efficient bis-N-boc protection of adenosine, cytidine, and guanosine derivatives

A solvent-free reaction employing a simple low-energy ball mill apparatus converts the amino groups of adenosine, 2-deoxyadenosine, cytidine, 2-deoxycytidine, guanosine, and 2-deoxyguanosine as well as some of their ribosyl O-protected derivatives to the corresponding bis-N-Boc carbamates. In the case of guanosine compounds, the carbonyl group of the base moiety was also blocked as its O-Boc enol carbonate. A variation of this approach using transient in situ O-silylation permitted the preparation of bis-N-Boc nucleosides in which the sugar hydroxyls were unprotected. The ball mill reactions were rapid, convenient, and very high-yielding except in the case of the guanosine compounds. This highly efficient method protects the amino groups of these nucleosides with a base stable and acid labile group suitable for further synthetic manipulation.     

Electrochemical determination of melamine using oligonucleotides modified gold electrodes

A novel and simple electrochemical method for determination of melamine is developed based on oligonucleotides film modified gold electrodes. The electrochemical probe of ferricyanide was used to investigate the interactions between oligonucleotides and melamine. Results of cyclic voltammetries, differential pulse stripping voltammetries, electrochemical impedance spectrometry and atomic force microscope, proved that melamine might interact with oligonucleotides mainly through electrostatic and hydrogen-bonding interactions. The interactions between oligonucleotides and melamine lead to the increase in the peak currents of ferricyanide, which could be used for electrochemical sensing of melamine. The redox peak currents of ferricyanide were linear with the concentration of melamine in the range from 3.9 × 10⁻⁸ to 3.3 × 10⁻⁶ M with a linear coefficiency of 0.990. The detection limit was 9.6 × 10⁻⁹ M. The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of melamine. Particularly, the proposed method was applied successfully to the determination of melamine in milk products, and the recovery was 95%.     

Synthesis, physicochemical and biochemical studies of 1',2'-oxetane constrained adenosine and guanosine modified oligonucleotides, and their comparison with those of the corresponding cytidine and thymidine analogues

We have earlier reported the synthesis and antisense properties of the conformationally constrained oxetane-C and -T containing oligonucleotides, which have shown effective down-regulation of the proto-oncogene c-myb mRNA in the K562 human leukemia cells. Here we report on the straightforward syntheses of the oxetane-A and oxetane-G nucleosides as well as their incorporations into antisense oligonucleotides (AONs), and compare their structural and antisense properties with those of the T and C modified AONs (including the thermostability and RNase H recruitment capability of the AON/RNA hybrid duplex by Michaelis-Menten kinetic analyses, their resistance in the human serum, as well as in the presence of exo and endonucleases).     

Synthesis and biological activities of 4-phenyl-5-pyridyl-1,3-thiazole derivatives as selective adenosine A3 antagonists

To investigate the potency of an adenosine A3 receptor (A3AR) antagonist as an anti-asthmatic drug, a novel series of 4-phenyl-5-pyridyl-1,3-thiazole derivatives was synthesized and evaluated in human adenosine A1, A2A and A3 receptor and rat adenosine A3 receptor binding assays. From investigation of the SAR study, compound 7af was identified as a highly potent human and rat A3AR antagonist. This compound inhibited IB-MECA-induced plasma protein extravasation in the skin of rats and showed good oral absorption. Also, compound 7af significantly inhibited antigen-induced hyper-responsiveness to acetylcholine in actively sensitized Brown Norway rats. These results show that 4-phenyl-5-pyridyl-1,3-thiazole derivatives are potential candidates to enable the evaluation of A3AR antagonists. Further evaluation of this class of compounds may afford a novel anti-inflammatory agent such as an anti-asthmatic drug.     

Protection of the amino group of adenosine and guanosine derivatives by elaboration into a 2,5-dimethylpyrrole moiety

[reaction: see text] Protection of the amino group of adenine and guanine nucleosides was effected by heating the substrates in 2,5-hexanedione. The resulting 2,5-dimethylpyrrole adducts were stable toward bases but were hydrolyzed with TFA/H(2)O to regenerate the amino function.     

Monitoring G-quadruplex structures and G-quadruplex-ligand complex using 2-aminopurine modified oligonucleotides

The fluorescent base 2-aminopurine (2Ap) was incorporated into the human telomeric DNA sequence d[AGGG(TTAGGG)₃]. The substitution of 2Ap for A in the TTA loops did not affect the G-quadruplex stability. Interestingly, a significant change in the fluorescence intensity of 2Ap between the G-quadruplex and duplex was observed. Therefore, we demonstrated that 2Ap can be used to monitor the duplex to quadruplex conformational change in the human telomeric DNA sequence. This mechanism is explained by the difference in the base stacking in the TTA loop region. Moreover, these probes distinguished between the basket-type and propeller-type G-quadruplexes. We also demonstrated the detection of the telomerase inhibitor agent, such as TMPyP4, using a 2Ap modified telomeric DNA. The formation of the G-quadruplex-ligand complex was observed by the fluorescence titration of TMPyP4.     

烯丙基作为保护基在修饰寡核苷酸合成中的应用

研究了烯丙基作为核苷糖环羟基保护基在寡核苷酸及其类似物的合成中应用的可能性。烯丙基保护基可用PdCl2在温和条件下脱除,适合应用于对碱不稳定的寡核苷酸的合成。应用烯丙基保护基成功地合成了三胸苷二碳酸酯和二胸苷亚硫酸酯。     

In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors

There is a great demand for the discovery of new therapeutic molecules that combine the high specificity and affinity of biologic drugs with the bioavailability and lower cost of small molecules. Small, natural-product-like peptides hold great promise in bridging this gap; however, access to libraries of these compounds has been a limitation. Since ribosomal peptides may be subjected to in vitro selection techniques, the generation of extremely large libraries (>10(13)) of highly modified macrocyclic peptides may provide a powerful alternative for the generation and selection of new useful bioactive molecules. Moreover, the incorporation of many non-proteinogenic amino acids into ribosomal peptides in conjunction with macrocyclization should enhance the drug-like features of these libraries. Here we show that mRNA-display, a technique that allows the in vitro selection of peptides, can be applied to the evolution of macrocyclic peptides that contain a majority of unnatural amino acids. We describe the isolation and characterization of two such unnatural cyclic peptides that bind the protease thrombin with low nanomolar affinity, and we show that the unnatural residues in these peptides are essential for the observed high-affinity binding. We demonstrate that the selected peptides are tight-binding inhibitors of thrombin, with K(i)(app) values in the low nanomolar range. The ability to evolve highly modified macrocyclic peptides in the laboratory is the first crucial step toward the facile generation of useful molecular reagents and therapeutic lead molecules that combine the advantageous features of biologics with those of small-molecule drugs.     

Remote substituents influence both the thermodynamics and kinetics of zinc binding to tris-pyridyl methanol derivatives

[reaction: see text] Three families of tris-pyridyl methanol ligands were synthesized. An analysis of the Zn(2+) binding properties of the ligands revealed that both steric and electronic properties of the pyridine substituents, as well as the nature of the group on the tertiary alcohol oxygen, control the thermodynamics and kinetics of complex formation.     

Synthesis of f luorescein-labeled oligonucleotides bearing a tag in position 2′ of modified adenosine and arabinoadenosine

Oligonucleotide conjugates containing fluorescein residues in the sugar-phosphate back-bone were synthesized by the standard solid-phase phosphoramidite method using phosphor-amidites of 9-[2-deoxy-5-O-(4,4′-dimethoxytrityl)-2-methoxalylamino-β-D-ribofuranosyl]-and 9-[2-deoxy-5-O-(4,4′-dimethoxytrityl)-2-methoxalylamino-β-D-arabinofuranosyl]-N ⁶-benzoyladenine. The relative efficiency of the oligonucleotide synthesis with modified phosphoramidites was estimated. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1618–1624, September, 2006.     

Voltammetric determination of adenosine and guanosine using fullerene-C60-modified glassy carbon electrode

A fullerene-C₆₀-modified glassy carbon electrode (GCE) is used for the simultaneous determination of adenosine and guanosine by differential pulse voltammetry. Compared to a bare glassy carbon electrode, the modified electrode exhibits an apparent shift of the oxidation potentials in the cathodic direction and a marked enhancement in the voltammetric peak current response for both the biomolecules. Linear calibration curves are obtained over the concentration range 0.5 μM-1.0 mM in 0.1 M phosphate buffer solution at pH 7.2 with a detection limit of 3.02 × 10⁻⁷ M and 1.45 × 10⁻⁷ M for individual determination of adenosine and guanosine, respectively. The interference studies showed that the fullerene-C₆₀-modified glassy carbon electrode exhibited excellent selectivity in the presence of hypoxanthine, xanthine, uric acid and ascorbic acid. The proposed procedure was successfully applied to detect adenosine and guanosine in human blood plasma and urine, without any preliminary pre-treatment.     

Synthesis and RNA binding selectivity of oligonucleotides modified with five-atom thioacetamido nucleic acid backbone structures

Convenient chemical synthesis and incorporation of dithymidine and thymidine-cytidine dimer blocks connected with a five-atom amide linker N3'-CO-CH2-S-CH2 into oligonucleotides (ONs) are reported. The UV-Tm experiments for binding affinities of these mixed backbone ONs with complementary DNA and RNA sequences revealed important results such as significantly higher RNA-binding selectivity as compared with complementary DNA. NMR studies of the dimer blocks suggested a marginal increase in the N-type sugar conformations over that of the native DNA.     

Synthesis of prolonged-release drugs for osteoplasty that are based on chemically modified calcium phosphates

In order to use hydroxyapatite and other biocompatible calcium phosphates as carriers for local prolonged-release drug, it is necessary to have an active component capable of retaining the preparation deposited onto the carrier surface for a long time (at least, for a few days). The grafting of the layer of active functional groups onto the carrier surface is employed to affect kinetic adsorption-desorption characteristics of calcium phosphates. The method of chemical modification of biocompatible calcium phosphates that uses B(OC₄H₉)₃, SiCl₄, POCl₃, PCl₅, and SnCl₄ is developed. The effect of the modification of calcium phosphate’s surface on the kinetics of hydrolytic desorption of octadecylamine and tetraethylenepentamine modeling the hydrophobic and hydrophilic drugs, respectively, as well as gentamicin, an antibiotic that is widely used in clinical practice to prevent and cure inflammation processes upon the damage of bony tissue, is studied. It is shown that the rate of desorption of these substances from calcium phosphates into the aqueous phase is significantly retarded when the carrier surface is preliminarily modified. By means of ESR and IR Fourier spectroscopy, the interaction of octadecylamine and tetraethylenepentamine with calcium phosphate’s surface is investigated. A conclusion about the existence of two mechanisms of adsorption of amines on modified calcium phosphates is drawn. The procedure for the preparation of biocompatible calcium phosphates with hemisorbed gentamicin is developed.