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2013 Vol 11 # 1


Quantum-chemical justification of the Wachtershauser’s evolutionary emergence hypothesis of the complementary DNA base pairs

O.Î. Brovarets’

Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Zabolotnoho Str., 03680, Kyiv, Ukraine

Research and Educational Center «State Key Laboratory of Molecular and Cell Biology»
150, Zabolotnoho Str., 03680, Kyiv, Ukraine

Institute of High Technologies, Taras Shevchenko National University of Kyiv
2g, Hlushkova Ave, 03022, Kyiv, Ukraine

Summary. The quantum-chemical evidence to support the evolutionary origin hypothesis of the complementary DNA base pairs was obtained for the first time. It was shown that hydrogen-bonded base pairs – the evolutionary precursors of the Watson-Crick DNA base pairs – are, on the one hand, isomorphiń and isoelectronic structures, and, on the other hand, they are isomorphic and isoelectronic with the Watson-Crick base pairs. Moreover, all four base pairs have similar dynamical properties, and the evolutionary analogues of the Watson-Crick base pairs can acquire all four configurations characteristic for the Watson-Crick DNA base pairs.

Keywords: molecular evolution; hypothesis of the DNA base pairs emergence; isomorphity; isoelectronity; quantum-chemical calculations.

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Zinc and zinc nanoparticles: biological role and application in biomedicine

Ę.˛. Bogutska1, Yu.P. Sklyarov2, Yu.˛. Prylutskyy1

1 Taras Shevchenko National University of Kyiv
Volodymyrska Str., 64, 01601, Kyiv

2 O. Bogomolets National Medical University
T. Shevchenko Avenue, 13, 01601, Kyiv

Summary. Due to nanodimension of functional components of living cells, the application of nanotechnologies in biomedical purposes is an important problem for today. One of the most promising directions is to use zinc nanoparticles for molecular diagnostics, target delivery of drugs, developing new pharmaceutical preparations. The paper presents the data on biological properties of zinc and its compounds, their location in the organism and role in important biological processes, which show the ways of possible practical applications of zinc nanoparticles in biomedicine. Particular attention is paid to the role of ion’s zinc in muscle functioning.

Keywords: zinc, zinc nanoparticles, functional properties, biomedical applications.

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Structure of alkyl radicals upon alkylation by thiotepa

T.P. Voloshchuk, V.I. Adonin, I.I. Vorobiova, A.I. Potopalsky

Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
150, Zabolotnogo Str., Kyiv, 03680, Ukraine

Summary. Aim. To determine conditions for reactions of alkylation by thiotepa (as exemplified by adenine) to obtain most efficient antitumoral drugs and identify their construction. For this two monofunctional analogs of thiotepa, ethyleneimine and monoaziridindiethylphosphate were used. Methods. Reversed-phase HPLC, acid hydrolysis, UV-spectroscopy, paper and thin-layer chromatography. Results. At one and the same site of alkylation can be generated up to 4 products with differing degree of thiotepa aziridine cycle opening and, accordingly, various antitumoral activities. In the alkylation by thiotepa depending on conditions four different alkyl radicals can be formed. Conclusions. Reactions of alkylating by thiotepa should be carried out in neutral and alkalescent media.

Keywords: alkylation, thiotepa, DNA, nucleic acids bases.

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Spectrophotometry of the supramolecular complexes of ivy and licorice triterpene glycosides with laevomycetin (chloramphenicol)

L.A. Yakovishin, E.N. Korzh, A.D. Degtyar, A.V. Klimenko

Sevastopol National Technical University
University Str., 33, Sevastopol, 99053, Ukraine

Summary. Using a method of spectrophotometry, the complexation of laevomycetin (chloramphenicol) with triterpene glycosides α-hederin (hederagenin 3-O-α-L-rhamnopyranosyl-(12)-O-α-L-arabinopyranoside), hederasaponin C (hederagenin 3-O-α-L-rhamnopyranosyl-(12)-O-α-L-arabinopyranosyl-28-Î-α-L-rhamnopyranosyl-(14)-Î-β-D-glucopyranosyl-(16)-Î-β-D-glucopyranoside) and glycyram (monoammonium glycyrrhizinate) in aqueous solutions at pH 7,2 was investigated. Glycosides form complexes with laevomycetin in the 1:1 molar proportion. The stability constants were determined equal to 4,24·104 Ě-1 for laevomycetin–α-hederin complex, 2,15·104 Ě-1 for laevomycetin–hederasaponin C complex and 8,57·104 Ě-1 for laevomycetin–glycyram complex. The glycyram–laevomycetin complex is more stable.

Keywords: triterpene glycosides, glycyrrhizic acid, glycyram, α-hederin, hederasaponin C, laevomycetin, molecular complex, spectrophotometry.

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Molecular dynamics of proteins: classic force fields and reliability of trajectories

O.Yu. Nyporko

Institute of High Technologies, Taras Shevchenko National University of Kyiv
2g, Hlushkova Ave, Kyiv, 03022, Ukraine

Summary. Methods of computational molecular dynamics (MD) allow to distinguish and estimate the nuances of proteins structure/behavior that can't be detected by instrumental methods, in particular, to identify correlated movements of the remote parts of the protein and distant effects of amino acid substitutions. To check the reliability of these methodological approaches the molecular dynamics of a set of water-soluble globular proteins was computed using classical protein-validated force fields. Low-energy molecular ensembles calculated from MD data were compared to the appropriate ensembles derived from NMR spectroscopy data. The high degree of correlation ensembles' structures and of mobility of corresponding amino acid residues indicates the reliability of used force fields and relevance of MD results to instrumental NMR data.

Keywords: protein spatial structure, proteins behavior, molecular dynamics, molecular ensembles, NMR spectroscopy, force fields.

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N-arilamides  of  triazinobenzotiazine-carboxylic acids – inhibitors of RNA synthesis
as antimicrobial and antiviral agents

Î.V. Vasylchenko1,2, D.B. Starosyla2, O.A. Tarasov3, M.O. Platonov1, S.L. Rybalko2, O.M. Deriabin3, L.G. Palchykovska1

1 Institute of Molecular Biology and Genetics NAS of Ukraine
150, Zabolotnoho Str., Kyiv, 03680, Ukraine

2 State Institution «The L.V. Gromashevsky Institute of epidemiology and infectious diseases of AMS of Ukraine»
5, Amosova Str., Kyiv, 03038, Ukraine   

3 The Institute of veterinary medicine NAAS of Ukraine
30, Donetska Str., Kyiv, 03151, Ukraine

Summary. Biological activity of the newly synthesized 6-methyl-triazinobenzotiazine-6-(TBT-6)- and triazinobenzotiazine-8-(TBT-8-)-carboxylic acids N-arilamides was investigated for the first time. Compounds 4, 5, 6, 12 and 13 appeared to be an effective inhibitors of RNA synthesis and had IC50 value in the range from 4,9 to 15,9 µM. Row of compounds, namely 1, 4, 6, 9, 10, 12 showed significant antimicrobial activities against both Gramm-positive and Gramm-negative bacteria in the MIC value interval from 0,97 to 1,56 µM.  The base acids 1 and 9 showed plural character of activity against both types of bacteria. N-Arilamides 4, 5, 6, 12 and 13 demonstrated pronounced activity against Bovine viral diarrhea with the value of EC50 from 1,54 to 30 µĚ. Compound 5 proved to be the most effective with EC50 equals 1,54 µM and SI>80. It is important that substances 4, 6, 12, 13 revealed rather effective antimicrobial and antiviral activity. According to the result obtained, assumption can be made that, at least in the case of  N-arilamides of TBT acids 4, 5, 6, 12 and 13 their probable targets in bacteria and viruses are  RNA synthesizing complexes.

Keywords: N-arylamides of TBT-6 and TBT-8-carboxylic acids, inhibitors of RNA synthesis, antimicrobial and antiviral agents.

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A new approach to 2,4,5-trisubstituted thiazoles from β-dicarbonylic compounds, arylglyoxals and thioamides

L.L. Zamigajlo1, A.O. Vinnyk2, O.V. Turov3 , N.M. Kolos2

1 State Scientific Institution «Institute for Single Crystals» of the NASU
60, Lenina av., Kharkov, 61001, Ukraine

2 Organic Chemistry Department, V.N. Karazin Kharkov National University
4, Svobody sq., Kharkov, 61077, Ukraine

3 NMR laboratory, T.G. Shevchenko Kyiv National University
64, Vladimirskaya str., 01601, Ukraine

Summary. A rapid and efficient one-pot three-component synthesis of 2-R-4-arylthiazoles containing a 4-hydroxycoumarin or dimedone fragment in the 5th position from β-dicarbonylic compounds, arylglyoxals and thioamides has been developed. 2-Amino-4,5-disubstituted thiazole derivatives were obtained by the reaction of bis-adducts based on CH-acids and arylglyoxals with thioureas.

Keywords: β-dicarbonylic compounds, thiazole, one-pot synthesis, thioamide, thiohydantoin.

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In silico validation of methods for estimation of drugs lipophilicity/solubility

M.V. Protopopov1, A.Yu. Nyporko1, V.G. Bdzhola2, S.Ŕ. Starosila1,
S.M. Yarmoluk
2

1 Taras Shevchenko Kyiv National University
60, Volodymirska Str., Kyiv, 01601, Ukraine

2 Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Zabolotnoho Str., Kyiv, 03680, Ukraine

Summary. Accuracy evaluation of LogP and LogS is crucial for drugs development. With the aim to determine the most exact techniques of these parameters estimation general methods have been validated. We had reviewed literature data about principles of operation of these methods, calculated the correlation coefficient between experimental and predicted values of LogP/LogS and respective calculation errors. The most valid methods were XLOG2, JCEM and OCHEM with its correlation coefficients 0.93952, 0.91122 and 0.90215 respectively. Despite the largest one XLOGP2 has the lowest error (MAE=0.44695, RMSE=0.8382). According to our calculation, the most appropriate methods for LogP values estimation were XLOGP2 and JCHEM.

Keywords: LogĐ, LogS, lipophilicity, Lipinski’s rule of five, ADME/Tox.

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