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2009 Vol VII #2


Photolabile protecting groups

O.D. Fedoryak

Institute of Bioorganic and Petroleum Chemistry, NAS of Ukraine
1 Murmanska Str., Kyiv, 02660, Ukraine


Summary: Photolabile protecting groups have been known to the chemical community for a long time. They differ conceptually from the classical protecting groups used in organic synthesis because they do not require addition of a cleaving reagent. This is a major advantage, allowing chemists to perform reactions with high selectivity at very mild reaction conditions. The possibility of breaking bonds only by illumination seems to be very appealing not only to classical organic synthesis but also to the solid-phase organic synthesis. Photolabile protecting groups have become important also in combinatorial chemistry and cell biology. Photoremovable protecting groups for controlling and manipulating cell physiology are valuable because of their ability to inactivate or "cage" a physiologically active messenger and then release or "uncage" it with a flash of light. This is an excellent way to achieve temporal control over messenger release and examine the fast kinetics or spatial heterogeneity of biochemical responses in cell or tissue culture.
To be useful in biological experiments, a caging group must undergo photolysis rapidly, in high yield, and at wavelengths that are not detrimental to the biological system. It should not interfere with the methods used to measure the response of the system, and the postphotolysis remains of the caging group must not interact with the physiological processes under study. The caged compound should exhibit good water solubility and hydrolytic stability in the dark. A summary of the major families of photolabile protecting groups with some of their advantages, drawbacks and applications is given in the review.

Keywords:
photolabile protecting groups, photolysis, caged compounds.

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Synthesis of vicinal 2-aryl(hetaryl)-2-[aryl(hetaryl)-sulfonyl]-ethanamines

O.V. Rudnichenko, I.M. Fesun, M.O. Chekanov, A.R. Synyugin, M.I. Vlasenko, D.I. Inshin, S.M. Yarmoluk

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

Summary: As a part of study on the synthesis of sulfur-containing compounds of pharmacological interest, 2-aryl(hetaryl)-2-[aryl(hetaryl)-sulfonyl]-nitroethanes were prepared by the reaction of aryl- and hetarylaldehydes with nitromethane in the condition of Henry condensation, and the subsequent addition of a sulfinic acids. There are row of a new 2-aryl(hetaryl)-2-[aryl(hetaryl)-sulfonyl]-nitroethanes was synthesized, which was easily reducted in a 2-aryl(hetaryl)-2-[aryl(hetaryl)-sulfonyl]-ethanamines.
Keywords:
antipsychotics, Henry condensation, hetarylaldehydes, vic-aminosulfones, reduction.

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Physicochemical mechanism of the wobble DNA base pairs Gu·Thy and Ade·Cyt transition into the mismatched base pairs Gua*·Thy and Ade·Cyt* formed by the mutagenic tautomers

O.O. Brovarets'1,2, D.M. Hovorun2

1Taras Shevchenko National University of Kyiv
2 Glushkova Ave., Kyiv, 03187, Ukraine

2Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine

Summary: For the first time the new physicochemical mechanism has been proposed and grounded in order to underastand the origin of the spontaneous transitions. It is based on the tautomerization, induced by the interaction of the DNA-polymerase recognition center with the canonic nucleotide bases, of the pyrimidine bases in wobble base pairs Gu·Thy and Ade·Cyt which transition into the pairs Gua*·Thy and Ade·Cyt* accordingly.

Keywords:
spontaneous transitions, wobble DNA base pairs, recognition center of DNA-polymerase, intermolecular hydrogen bonds, analysis of the electron density topology, DFT.

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The new physicochemical mechanism of the mutagenic action of 5-bromouracil

O.O. Brovarets'1,2, D.M. Hovorun2

1Taras Shevchenko National University of Kyiv
2 Glushkova Ave., Kyiv, 03187, Ukraine

2Institute of Molecular Biology and Genetics, NAS of Ukraine
150 Zabolotny Str., Kyiv, 03143, Ukraine

Abstract: For the first time the universal molecular mechanism of 5BrUra mutagenic action which lead to the kinetic and based on that fact that barrier of the reaction 5BrUra·Gua→5BrUra·Gua* is substantially smaller, than ana-logous one for reaction Thy·Gua→Thy·Gua* which induces spontaneous transition.

Keywords: 5-bromouracil, spontaneous transitions, incorporation mistakes, replication mistakes, mutagenic me-chanism, intermolecular hydrogen bonds, analysis of the electron density topology, DFT.

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Application of UHV-AFM for investigation of structure of plant viruses and their interaction with Si (1 1 1) surface

V.L. Karbivskiy, T.A. Korniyuk

Institute of Metal Physics, NAS of Ukraine
Bulvar Akademika Vernadskogo, 36, Kyiv, 03680, Ukraine

Abstract: In this research we applied ultrahigh-vacuum atomic force microscopy (UHV-AFM) for investigation of tobacco mosaic virus (TMV) and alfalfa mosaic virus (AMV) interaction with Si (1 1 1) surface. Changes of virion conformation and different degree of order on the investigated surface were determined. It was demonstrated that adsorption of TMV virions is accompanied with formation of predominantly single-layer ordered films while AMV adsorption is accompanied with formation of unordered accumulations of the virions and more abrupt change of the height of viral particles. It was determined that the change of virions' height depended on the quantity of negatively-charged amino acid residues on the outer surface of capsid.

Keywords: UHV-AFM, plant viruses, capsid, Si (1 1 1), conformation.

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Calculation of structure and spectra of the glycine radical with dehydrogenated carboxyl group

B.F. Minaev, O.A. Lut, G.V. Baryshnikov, V.A. Minaeva

Bogdan Khmelnytskyi Cherkasy National University
81 Shevchenko blvd., Cherkasy, 18031, Ukraine

Abstract: A new type of glycine radical with the dehydrogenated carboxyl group (so far unknown) has been detected by electrochemical methods on Pt electrode and studied by quantum chemical methods in gas phase, solvents and on the surfaces of metal clusters. The structure, conformational behavior, electron paramagnetic resonance (EPR) and infra-red (IR) spectra of this glycine radical in two isomeric forms and a number of other well-known carbon-cenetered and nitrogen-cenetered glycine radicals have been studied by density functional theory (DFT) with linear response (LR) and quadratic response (QR) technique. Spin catalysis of oxidative decarboxylation of glycine on platinum and copper surfaces and some other magnetic phenomena in decay of amino acids are discussed.

Keywords: glycine radical, triplet state of dyes, carboxyl group, asymmetric vibrations.

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Synthesis of carboxyalkyl derivatives of 3-furylcoumarins for the fluorescent labeling of biomolecules

Ia.B. Kuziv1, V.V. Ishchenko2, V.P. Khilya2, I.Ya. Dubey1

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

2Department of Chemistry, Taras Shevchenko National University
64 Volodymyrska Str., Kyiv, 01033, Ukraine

Abstract:Synthesis and spectral properties of a series of fluorescent reagents based on 7-substituted 3-furylcoumarins with intense blue emission that can be covalently linked to oligonucleotides and other biomolecules via carboxyalkyl linker group are described.

Keywords: fluorescent probes, coumarins, covalent labeling, conjugates.

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Influence of the cell signaling systems modulators on enzymatic hydrolysis of phospholipids in langmuir monolayer films

A.M. Lyakhov, V.V. Prokopenko, S.Ye. Mogilevich

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

Abstract:The actions of two groups of bioregulators, which have opposite effect to adenylate cyclase and phosphoinositide cellular signaling systems, on enzymatic hydrolysis of the synthetic distearoylphosphatidylcholine of Langmuir monolayer films by phospholipase A2, were studied. It was found, that bioregulators, which activate adenylate cyclase and(or) inhibit phosphoinositide signaling systems of the cell, in the 10-4 М concentration, significantly reduce enzymatic cleavage of phospholipids (most strongly – isoprenaline, yohimbine, nifedipine). For physiologically active substances, which inhibit adenylate cyclase and(or) activate phosphoinositide signaling systems, of authentic influence on current of fermentative reaction is not revealed.

Keywords: phospholipase A2, phosphoinositide and adenylate cyclase signaling systems, Langmuir monolayer films, distearoylphosphatidylcholine, physiologically active substances.

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Search for FGFR1 inhibitors among oxindole derivatives

A.A. Gryshchenko, V.G. Bdzhola, O.V. Borovikov, O.P. Kukharenko, L.V. Pletnyova, S.M. Yarmoluk

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

Abstract:Protein kinase FGFR1 plays a key role in oncogenic transformation and oncovasculogenesis. Inhibitors of this kinase can be used as anticancer drugs. Protein kinase FGFR1 inhibitors searching were performed among oxindole derivatives. 9 compounds from 920 oxindole derivatives have been chosen using virtual screening. The most active compound was 2-Hydroxy-benzoic acid (2-oxo-1,2-dihydro-indol-3-ylidene)-hydrazide (IC50 1.25 μM). Structure-activity relationship of tested compounds was investigated and optimization strategies were proposed.

Keywords: protein kinase FGFR1, oxindole, docking.

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Synthesis and antioxidant activity evaluation of ethyl 4-(5-cyano 4-oxo-6-phenylamino-3,4-dihydro-2H-[1,3]thiazin-2-yl)-1-phenyl-1H-pyrazole-3-carboxylates

М.А. Potopnyk, N.E. Bodnar, M.D. Obushak, V.S. Matiychuk

Ivan Franko National University of Lviv
Kyryla and Mefodia Str., Lviv, 79005, Ukraine

Abstract:New ethyl 4-(5-cyano 4-oxo-6-arylamino-3,4-dihydro-2H-[1,3]thiazin-2-yl)-1-phenyl-1H-pyrazole-3- carboxylates were prepared from 2-cyano-3-mercapto-3-phenylamino-acrylamide and ethyl 4-formyl-1-phenyl-1H-pyrazole-3-carboxylate. Their antioxidant properties were evaluated by methods of scavenging effect on 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals. The results show that the ethyl 4-[5-cyano-6-(naphthalen-1-ylamino)-4-oxo-3,4-dihydro-2H-[1,3]thiazin-2-yl]-1-phenyl-1H-pyrazole-3-carboxylate have the best activity.

Keywords: antioxidants, 1,3-thiazine, pyrazole, DPPH.

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Synthesis of 3-(aminomethyl)- and 3-(2-aminoethyl)-quinolin-2-ones

M.O. Chekanov, А.R. Synyugin, S.S. Lukashov, S.M. Yarmoluk

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

Abstract:For the first time, it has been found and described series of 3-(aminomethyl)- and 3-(2-aminoethyl)-quinolin-2-ones.

Keywords: 2-quinolones, 2-chloroquinolines.

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