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2006 Vol IV #2


Novel reagents for oligonucleotide labeling with imidazophenazine

I.Ya. Dubey, D.M. Fedoryak1

Institute of Molecular Biology and Genetics, NAS of Ukraine,
150 Zabolotny Str., Kyiv, 03143, Ukraine

1Institute of Bioorganic and Petroleum Chemistry, NAS of Ukraine, 1 Murmanska Str., Kyiv, 02094, Ukraine


Summary: The synthesis of new reagents for the modification of oligonucleotides with intercalating agent imidazo[4,5-b]phenazine is described. Imidazophenazine derivatives 5 and 8 were prepared by heterocycle alkylation with protected bromoalkyl reagents, ethyl 3-bromopropionate and 4-bromobutylacetate in the presence of potassium carbonate and iodide, followed by deprotection and, in the case of 8, phosphorylation. Ñarboxyalkyl reagent 5 can be used for the post-synthetic oligonucleotide modification via aminoalkyl linker group, whereas H-phosphonate reagent 8 will be useful for the direct solid phase synthesis of 5’-modified oligonucleotides.

Keywords: imidazophenazine, oligonucleotides, intercalators, modification, conjugates.


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This article is sponsored by Otava, Ltd.

Synthesis and spectral studies styrylcyanines based on 4-oxo-4,6,7,8-tetrahydropyrrolo[1,2-a]thieno[2,3-d]pyrimidinium and 5-oxo-1,2,3,5-tetrahydropyrrolo[2,1-b]quinazolinium

A.O. Balanda, K.D. Volkova, V.B. Kovalska, V.P. Tokar1, S.M. Yarmoluk

Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny str., Kyiv, 03143, Ukraine

1Taras Shevchenko National University
6 Acad. Glushkova ave., Kyiv, 03147, Ukraine

Abstract: A series of novel styrylcyanine dyes based on 4-oxo-4,6,7,8-tetrahydropyrrolo[1,2-a]thieno[2,3-d]pyrimidinium and
5-oxo-1,2,3,5-tetrahydropyrrolo[2,1-b]quinazolinium. Spectral-luminescent properties of obtained dyes in unbound state and in presence of nucleic acids and BSA (bovine serum albumin) were evaluated. p-dimethylaminostyryls based on 4-oxo-4,6,7,8-tetrahydropyrrolo[1,2-a]thieno[2,3-d]pyrimidinium appeared to selectively interact with RNA and thus could be used as RNA-specific fluorescent probes. Besides, for these dyes large values of two-photon absorption cross-sections were admitted in RNA presence.

Keywords: styrylcyanine dyes, nucleic acids detection, two-photon excitation.


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Chlorosulfonic acid catalyzed highly efficient solvent-free synthesis of 3,4-dihydropyrimidin-2(1H)-ones and thiones

S.A. Kotharkar, R.R. Nagawade1, D.B. Shinde

Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431004, (M.S.), India

1Wockhardt Research Centre, Chikalthana, Aurangabad, 431210, (M.S.), India


Summary: Chlorosulfonic acid (ClSO3H) is used as an alternative to conventional acid catalyst in the Biginelli reaction of aldehydes, 1,3-dicarbonyl compounds and urea or thiourea. This method gives the desired dihydropyrimidines in higher yields under solvent-free conditions in shorter time.

Keywords: ClSO3H catalyst, Biginelli reaction.

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Influence of the triterpene glycosides and their complexes on mollusks

L.A. Yakovishin, V.A. Ertahova, E.A. Bazyura

Sevastopol National Technical University
Streletskaya balka, Studgorodok, Sevastopol, 99053, Ukraine


Summary: Ñomparative study of molluscicidal activity of triterpene glycosides of hederagenin and glycyrrhetic acid, and their complexes with cholesterol, glycine, L-alanine and L-valine on Planorbis corneus, Planorbis corneus var. rubra and Melanoides tuberculata has been performed. It is shown that hederagenin monodesmosidic glycosides possess higher toxicity as compared to its bidesmosidic glycoside and glycyrrhinic acid. For high activity of glycosides, the presence of free carboxyl group at C-17 position of the aglycone part is necessary. The addition of cholesterol to the glycosides reduces their molluscicidal activity. The complexes of hederagenin 3-O-α-L-rhamnopyranosyl-(1->2)-O-α-L-arabinopyranoside with glycine and L-alanine revealed high toxicity. The glycoside complex with L-valine is not active on Planorbis corneus, Planorbis corneus var. rubra, and Melanoides tuberculata.

Keywords: triterpene glycosides, molluscicidal activity, complex, Planorbis corneus, Planorbis corneus var. rubra, Melanoides tuberculata.

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Study of Ukrain composition using HPLC and UV-spectroscopy methods

T.P. Voloshchuk, Yu.V. Patskovsky, L.A. Zayika

Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine


Summary: The composition of an antitumor and immunomodulatory preparation Ukrain was investigated using HPLC and UV spectroscopy methods. The preparation was found to contain not only already known Chelidonium majus L. alkaloids (about 10), but also some substances with non-identified structure. The amount of these substances can be estimated as around 40 %. They are not alkylated alkaloids, because sulfur and phosphorus are not detected in preparation, and they also cannot be attributed to any of the known celandine alkaloids according to their UV-spectra. In composition of Ukrain there are no substances proper to the formula declared for it containing three molecules of chelidonine per one molecule of thiotepa (N,N’,N’’-triethylenethiophosphoramide).

Keywords: Ukrain, Chelidonium majus, alkaloid, thiotepa, celandine.

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Syntesis and antimicrobial evaluation of novel 2-substituted-3-mercapto-1,4-naphthoquinones

M.V. Stasevych, V.G. Chervetsova, M.Yu. Plotnikov, M.O. Platonov, S.I. Sabat, R.Ya. Musyanovych, V.P. Novikov

Institute of Chemistry and Chemical Technology, National University «Lviv Polytechnic», 12 Bandera Str., Lviv, 79013, Ukraine


Summary: A series of 2-substituted-3-mercapto-1,4-naphthoquinones were synthesized and evaluated for their antimicrobial activities. The detailed synthetic protocol, spectroscopic and antimicrobial data are reported. 2-Morpholino-3-mercapto-1,4-naphthoquinone and 2-piperydyno-3-mercapto-1,4-naphthoquinone showed greater antibacterial activity than well known antibiotic oxacillin. The quantum-chemistry calculations were carried out using semi-empirical PM3 method to study the molecular geometry and electronic structure of obtained thiols. Biological activity prediction using computer program PASS C&T was performed, made and indicated the necessity of further investigation of new synthesized compounds.

Keywords: thiol, naphthoquinone, antimicrobial activity, PASS C&T.

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This article is sponsored by Otava, Ltd.

Synthesis of 4-substituted 1-arylhexahydrothieno[3,4-b]pyrazin-2(1H)-one 6,6-dioxides

P.V. Shaitanov, Yu.V. Bezugly, V.M. Sapelkin, S.M. Yarmoluk

Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine


Summary: An effective method of synthesis of 4-substituted 1-arylhexahydrothieno[3,4-b]pyrazin-2(1H)-one 6,6-dioxidesis on the basis of 3-arylamino-2,3-dihydrothieno 1,1-dioxides is proposed. The biological activity of new bicycle sulfones has been predicted using PASS software.

Keywords: 2-ketopiperazine, thiolene, 3-arylamino-2,3-dihidrothieno 1,1-dioxide, chloracetamide 3-arylamino 2,3-dihydrothieno 1,1-dioxide, hexahydrothieno[3,4-b]pyrazin-2(1H)-one 6,6-dioxides, PASS-prognosis, intramolecular cyclization.


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This article is sponsored by Otava, Ltd.

Application of distribution function of rotation and translation degrees of freedom for CK2 inhibitors Ki estimation

O.Ya. Yakovenko, A.G. Golub, V.G. Bdzhola, S.M. Yarmoluk

Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine


Summary: The method of estimating dissociation constants from distribution functions of rigid body translation and rotation degrees of freedom has been developed. Two ways of Ki estimations have been proposed. The first approach, arbitrary model (AM), is derived directly from statistical physics equations. The results show significant overestimation of binding free energy. The second one, quasy-arbitrary model (QM), was derived from assumption about non-symmetrical shape of bound ligand configuration space. The correct ranking of ligands with the similar binding mode was obtained for common distribution theory equations, but the QM Ki estimation method was found to be more appropriate than AM method. The predictive results of method were tested with a set of mainly rigid CK2 inhibitors with resolved crystal structures.

Keywords: distribution function, configuration space, rotation-translation, freedom degree, free energy, Ki estimation.

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Ñomprehensive conformational analyses of 2’-deoxythymidine by quantum-chemical density functional method

R.O. Zhurakivsky, D.M. Hovorun1

Taras Shevchenko National University
2 Glushkova Ave., Kyiv, 03127, Ukraine

1Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine


Summary: For the first time the comprehensive conformational analyses of 2’-deoxythymidine has been performed by means of quantum-chemical density functional method on MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) theory level. Main geometric, energetical and polar characteristics are provided for all of its 92 stable conformers as well as conformational equilibrium at normal conditions.

Keywords: nucleosides, conformational analysis, density functional theory, 2’-deoxythymidine.

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