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Vol 43, No 2 (2017)

Article

The genome nucleotide sequence of herpes simplex virus 1 strain L2

Skoblov M.Y., Lavrov A.V., Bragin A.G., Zubtsov D.A., Andronova V.L., Galegov G.A., Skoblov Y.S.

Abstract

The genome nucleotide sequence of the reference strain of herpes simplex virus type 1 was obtained using the technique of full size sequencing. For the virus genome structure determination, 402444 reads with an average length of 202 bp were performed, which corresponded to the 542-fold genome coverage. The data were collected to 52 contigs with N50-4518 and the total contig length of 120929 bp. The sequence obtained was deposited into the GenBank database.

Russian Journal of Bioorganic Chemistry. 2017;43(2):140-142
pages 140-142 views

Modular lentiviral vector system for chimeric antigen receptor design optimization

Kulemzin S.V., Chikaev N.A., Volkova O.Y., Kuznetsova V.V., Taranin A.V., Gorchakov A.A.

Abstract

The article reports the development of a collection of lentiviral vector constructs enabling time-efficient production and testing of different variants of chimeric antigen receptors (CAR). These artificial surface proteins make it possible to redirect the activity of immune cytotoxic T-cells towards cancer cells. Chimeric antigen receptors usually encompass four functional modules, namely, antigen recognition, flexible linker, transmembrane, and signal modules. The use of modules with different properties allows modulating the affinity and specificity of CAR interaction with target antigens, as well as intensity and quality of activation signaling, which determines the cytotoxic properties of CAR T-cells, as well as their proliferation rate and time of persistence in the organism. The proposed vector system make it possible to easily test various combinations of CAR modules while its being open to distribution allows the direct comparison of the results obtained by different scientific groups.

Russian Journal of Bioorganic Chemistry. 2017;43(2):107-114
pages 107-114 views

Circular RNAs of human blood cells, plasma, and plasma subfractions

Savelyeva A.V., Bariakin D.N., Kuligina E.V., Morozov V.V., Richter V.A., Semenov D.V.

Abstract

Circular RNAs (circRNAs) are a novel class of regulatory noncoding RNAs with the closed structure of a phosphate–ribose chain. Here, we searched for the characteristic sequences of exon–exon junctions of circular RNAs in high-throughput sequencing data of RNA from human blood cells, plasma, and plasma subfractions. Eighty-eight characteristic junctions of circular RNAs’ exons were identified, eight of which are related to fragments of previously unannotated novel circular human transcripts. The set of 88 circular RNAs identified in human blood was enriched with transcripts of genes encoding transcription factors and proteins involved in biogenesis and transport of membrane vesicles. RT-PCR analysis of circular RNA content in human blood plasma subfractions revealed full-length circular transcripts mostly in fractions of blood plasma membrane particles, such as microvesicles and exosomes. Our results and previously published data suggest that extracellular circular RNAs may be regulators of fundamental cellular processes. The results can be used for the development of novel methods of low invasive diagnostics of human diseases.

Russian Journal of Bioorganic Chemistry. 2017;43(2):115-125
pages 115-125 views

Proteome analysis of circulating exosomes in health and breast cancer

Tamkovich S.N., Bakakina Y.S., Tutanov O.S., Somov A.K., Kirushina N.A., Dubovskaya L.V., Volotovski I.D., Laktionov P.P.

Abstract

Microvesicles were isolated from blood plasma and total blood of healthy females and breast cancer patients by filtration and ultracentrifugation. According to flow cytometry, different subpopulations of exosomes were represented in blood of healthy donors and cancer patients at different levels with median fluorescence intensity (MFI) values in both groups arranged in the following order: CD24/СD9 > СD9/СD81 > CD9/CD63 = CD24/CD63. Concentration of exosomes in blood plasma of healthy females estimated by nanoparticle tracking analysis (NTA) did not exceed (3.71 ± 1.15) × 107 particles/mL of blood and did not differ from that in plasma of breast cancer patients, which averaged (3.99 ± 1.03) × 107 particles/mL of blood. Concentration of total exosomes in blood (including exosomes from plasma and blood cell surface-bound exosomes) did not depend on the presence/absence of a tumor; the values were (7.66 ± 0.7) × 107 particles/mL of healthy blood and (9.4 ± 1.24) × 107 particles/mL of blood from cancer patients. Comparative analysis of exosomes using 2-D electrophoresis with subsequent analysis of 2-D proteomic maps revealed proteins missing in blood or differentially expressed in healthy females and breast cancer women. The data presented provide the possibility for identification of exosomal proteomic markers and isolation of tumor-specific exosomes, which contributes to the development of breast cancer diagnostics.

Russian Journal of Bioorganic Chemistry. 2017;43(2):126-134
pages 126-134 views

Oligonucleotide inhibitors of HIV-1 integrase efficiently inhibit HIV-1 reverse transcriptase

Korolev S.P., Zatsepin T.S., Gottikh M.B.

Abstract

The impact of conjugates of 11-mer 2′-О-methyl oligoribonucleotides with eosin and 6-carboxy-4,7,2′,4′,5′,7′-hexachlorofluorescein on the functioning of HIV-1 reverse transcriptase (RT) was studied. These compounds were shown to inhibit the activity of RT RNase H domain. The inhibition efficiency was higher for eosin conjugates and did not depend on the oligonucleotide primary structure. The eosin conjugates were also found to block the RT polymerase activity including the mutant proteins resistant to nonnucleoside inhibitors. Since the conjugates are efficient inhibitors of HIV-1 integrase, we can assume that they belong to a new class of HIV-1 dual acting inhibitors, potentially capable of blocking several initial stages of the viral replication cycle.

Russian Journal of Bioorganic Chemistry. 2017;43(2):135-139
pages 135-139 views

DNA sequence-specific ligands: XVI. Series of the DBP(n) fluorescent dimeric bisbenzimidazoles with 1,4-piperazine-containing linkers

Koval V.S., Ivanov A.A., Salyanov V.I., Stomakhin A.A., Oleinikov V.A., Zhuze A.L.

Abstract

A novel series of the DBP(n) fluorescent symmetric dimeric bisbenzimidazoles in which the bisbenzimidazole fragments were attached to an oligomeric linker with the 1,4-piperazine residue in its center were prepared. The DBP(n) molecules were distinguished by the number of methylene groups n (where n = 1, 2, 3, 4) in the linker. The DBP(n) synthesis was based on a condensation of the monomeric bisbenzimidazole (MB) with 1,4-piperazinedialkylcarbonic acids. The ability of the DBP(n) dimeric bisbenzimidazoles to form complexes with the double-stranded DNA was demonstrated by a complex of physicochemical methods, including spectroscopy in the visual UV-area, circular dichroism (CD), and fluorescence. The DBP(1–4) molecules were localized in the DNA minor groove by the CD method with the use of cholesteric liquid-crystalline dispersions (CLCD) of the double-stranded DNA. The DBP(n) dimeric bisbenzimidazoles were easily soluble in water, penetrated through cellular and nuclear membranes, and stained DNA in living cells distinct from the previously synthesized DB(n) series.

Russian Journal of Bioorganic Chemistry. 2017;43(2):143-149
pages 143-149 views

A synthetic fragment 60–70 of the receptor for advanced glycation end products exhibits a therapeutic effect in an animal model of Alzheimer’s disease

Koroev D.O., Volpina O.M., Volkova T.D., Kamynina A.V., Filatova M.P., Balasanyants S.M., Samokhin A.N., Bobkova N.V.

Abstract

Six synthetic peptides overlapping a fragment 60–76 of the receptor for advanced glycation end products (RAGE) were studied on a protective effect on spatial memory of animals in the experimental model of Alzheimer’s disease. It was shown that only a peptide corresponding to the fragment 60–70 of RAGE exhibits a therapeutic activity. Intranasal administration of this peptide into bulbectomized mice, which develop neurodegenerative features of the Alzheimer type, completely protects animal memory. Thus, it was found that the N-terminal region (60–70) within the peptide sequence 60–76 of RAGE is responsible for the revealed protective effect. The synthetic peptide RAGE-(60–70) could be the basis for the development of a new drug for the treatment of Alzheimer’s disease.

Russian Journal of Bioorganic Chemistry. 2017;43(2):150-154
pages 150-154 views

Polyamidoamine dendrimers with different surface charge as carriers in anticancer drug delivery

Yabbarov N.G., Nikolskaya E.D., Zhunina O.A., Kondrasheva I.G., Zamulaeva I.A., Severin E.S.

Abstract

Second-generation (G2) polyamidoamine (PAMAM) dendrimers are branched polymers containing 16 surface primary amine groups. Due to their structural properties, these polymers can be used as universal carriers in various drug delivery systems. Amine-terminated PAMAM dendrimers are characterized by a high positive surface charge, leading to effective but nonspecific interactions with negatively charged cell plasmatic membranes. To reduce the nonspecific internalization of PAMAM dendrimers, their primary amine groups are often modified by acetic or succinic anhydrides, polyethylene glycol derivatives and other compounds. In this work, the role of primary amine groups, which are localized on the surface of doxorubicin-conjugated (Dox) dendrimers, was studied with regard to their intracellular distribution and internalization rates using SKOV3 human ovarian adenocarcinoma cells. It was demonstrated that all Dox-labeled G2-derivatives containing different numbers of acetamide groups synthesized in this work show high rates of cellular uptake at 37°С. As expected, the conjugate carrying the maximum number of primary amine groups demonstrated the highest rates of binding and endocytosis. At the same time, the G2-Dox conjugate containing the maximum number of acetamide groups showed colocalization with LAMP2, a marker of lysosomes and late endosomes, as well as the highest level of cytotoxic activity against SKOV3 cells. We conclude that second-generation PAMAM dendrimers are characterized by varied pathways of internalization and intracellular distribution due to the number of primary amine groups on their surface and, as a consequence, a different surface charge.

Russian Journal of Bioorganic Chemistry. 2017;43(2):155-162
pages 155-162 views

Synthesis and pharmacological activity of 3-phenoxybenzoic acid derivatives

Spasov A.A., Popov Y.V., Lobasenko V.S., Korchagina T.K., Vassiliev P.M., Kuznetsova V.A., Brigadirova A.A., Rashchenko A.I., Babkov D.A., Kochetkov A.N., Kovaleva A.I., Efremova O.S.

Abstract

New esters of N-benzoyl-3-phenoxyphenylcarboxamide acid and N-benzoyl-N′-4-bromophenyl-3-phenoxybenzamidine were synthesized. Some of the synthesized compounds were shown to inhibit the activity of dipeptidyl peptidase-4 and nonenzymatic glycosylation of proteins and manifested antiplatelet and antioxidant properties. The compounds tested did not display the antagonistic effect toward angiotensin II type 1 receptor, did not influence the activity of glycogen phosphorylase and had very little ability to break cross-links of the glycated proteins. The derivatives with the biological activity of two types were found, which can serve as basic molecules in the search for new drug products.

Russian Journal of Bioorganic Chemistry. 2017;43(2):163-169
pages 163-169 views

Synthesis and antimicrobial and toxic properties of novel 1,3-bis(alkyl)-6-methyluracil derivatives containing 1,2,3- and 1,2,4-triazolium fragments

Voloshina A.D., Semenov V.E., Strobykina A.S., Kulik N.V., Krylova E.S., Zobov V.V., Reznik V.S.

Abstract

The antimicrobial activity and cytotoxicity of novel 1,3-bis(alkyl)-6-methyluracil derivatives containing 1,2,3- and 1,2,4-triazolium fragments in alkyl chains have been studied. The compounds have been tested for the antimicrobial activity toward some gram-positive and gram-negative bacteria and fungal cultures. The cytotoxic action has been estimated toward mammalian cells. It has been found that the basic structural factor that affects the antimicrobial activity is the nature of alkyl radicals at triazole fragments.

Russian Journal of Bioorganic Chemistry. 2017;43(2):170-176
pages 170-176 views

Synthesis of functionalized benzo[f]2H-chromenes and evaluation of their antimicrobial activities

Chanu I.H., Devi L.R., Khumanthem N., Singh N.I., Kumar D., Singh O.M.

Abstract

Knoevenagel cyclocondensations of α-hydroxy naphthaldehyde with β-oxodithioesters and ketene dithioacetals yielded 2H-benzo[f]chromene-2-thiones and 2H-benzo[f]chromen-2-ones, respectively, in high yields. The newly synthesized compounds were evaluated for antifungal and antibacterial activities. Among them, compounds (2-furyl)(3-thioxo-3H-benzo[f]chromen-2-yl)methanone and phenyl(3-oxo-3H-benzo[f]chromen-2-yl)methanone exhibited excellent antifungal activity against tested fungi Curvularia lunata and Fusarium moniliforme. The highest antibacterial activity against the tested bacteria Escherichia coli and Staphylococcus aureus was observed for (4-chlorophenyl)(3-oxo-3H-benzo[f]chromen-2-yl)methanone. The results of antimicrobial screening demonstrate that (2-furyl)(3-thioxo-3H-benzo[f]chromen-2-yl)methanone, phenyl(3-oxo-3H-benzo[f]chromen-2-yl)methanone, and (4-chlorophenyl)(3-oxo-3H-benzo[f]chromen-2-yl)methanone are promising as antimicrobial drugs.

Russian Journal of Bioorganic Chemistry. 2017;43(2):177-185
pages 177-185 views

Synthesis of thiazole-based substituted piperidinone oximes: Profiling of antioxidant and antimicrobial activity

Naik N., Harini S.T., Kumar H.V., Rangaswamy J.

Abstract

The synthesis of novel thiazole-based piperidinone oximes and screening of their antioxidant and antimicrobial activity are described. The obtained results revealed that the electronic effects of active substituents at C-4 terminals of phenyl rings on either side of piperidinone skeleton, as well as at 2-hydrazinyl thiazole, played a major role in development of antioxidant and antimicrobial activity. Antioxidant activity seems to be based also on radical dissipating ability of the thiazole ring. The nucleophilic character of sulfur in thiazole and lipophilic nature of piperidinone skeleton substantially influenced the observed antimicrobial activity of thiazole-based piperidinone oximes. Among the synthesized compounds, 2,6-bis(4-hydroxy-3-methoxyphenyl)-1-methylpiperidin-4-one O-(2-(2-(4-hydroxy-3-methoxybenzylidene)hydrazinyl)thiazol-4-yl) oxime exhibited excellent antioxidant activity whereas compound 2,6-bis(4-chloro phenyl)-1-methylpiperidin-4-one O-(2-(2-(4-nitrobenzylidene)hydrazinyl)thiazol-4-yl)oxime emerged as an outstanding antimicrobial agent.

Russian Journal of Bioorganic Chemistry. 2017;43(2):186-196
pages 186-196 views

Synthesis of coumarin appended pyrazolyl-1,3,4-oxadiazoles and pyrazolyl-1,3,4-thiadiazoles: Evaluation of their in vitro antimicrobial and antioxidant activities and molecular docking studies

Renuka N., Vivek H.K., Pavithra G., Ajay Kumar K.

Abstract

A series of semicarbazones, thiocarbazones, 1,3,4-oxadiazoles, and 1,3,4-thiadiazoles bearing coumarin and pyrazole moiety have been synthesized. The new synthesized compounds were screened in vitro for their antimicrobial and antioxidant activities. Preliminary studies showed that among the synthesized new compounds, chloro-substituted thiosemicarbazone showed excellent activities against all tested organisms; at the same time, methyl substituted thiosemicarbazone showed greater activity against E. coli. Chloro-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole demonstrated greater DPPH and hydroxyl radical scavenging abilities. Molecular docking studies indicate that 1,3,4-oxadiazoles and 1,3,4-thiadiazoles manifest better interaction with CAT (catalase) and GPx (glutathione peroxidase) than that with SOD (superoxide dismutase). Studies on the antimicrobial and antioxidant activities of the synthesized compounds compared with those of their starting compounds are discussed.

Russian Journal of Bioorganic Chemistry. 2017;43(2):197-210
pages 197-210 views

A synthesis of tritium-labeled juvenile hormone and radiometric analysis of the enzymatic hydrolysis level

Romanova I.V., Alekseev A.A., Richter V.A., Gruntenko N.E., Agafontsev A.M., Karpova E.K.

Abstract

A method of insect juvenile hormone III (JH-III) labeling by thermally activated tritium was developed. Purification of the labeled compound was performed on a TLC silica gel plate using a system of hexane-ethyl acetate 2: 1. The molar radioactivity of [3H]JH-III was 2.2 Ci mmol–1. It was shown that tritium-labeled juvenile hormone can be used in the radiometric method for quantitative measurement of the activity of specific enzymes that hydrolyze juvenile hormone.

Russian Journal of Bioorganic Chemistry. 2017;43(2):211-215
pages 211-215 views

Review Article

Self-organization of a chromatin fibril into topologically-associated domains

Razin S.V., Gavrilov A.A., Kos P., Ulianov S.V.

Abstract

A number of recent experimental approaches demonstrated that a three-dimensional organization of the eukaryotic genome play an important role in the regulation of its activity. One of the most important results was a discovery of the genome separation into relatively independent topologically-associated domains (TADs). They restricted the action area of regulatory elements, i.e., they simultaneously were regulatory domains of the genome. In this connection, an understanding of the molecular mechanism of the TAD formation has become a very topical problem. Here, we review and discuss our recent data which demonstrated that the TAD formation was directed by simple physical laws and was based on establishing multiple internucleosomal contacts.

Russian Journal of Bioorganic Chemistry. 2017;43(2):99-106
pages 99-106 views

Letter to the Editor

The secreted protein Noggin4 is an activator of the Wnt/PCP-signaling pathway

Bayramov A.V., Eroshkin F.M., Martynova N.Y., Orlov E.E., Borodulin A.V., Zaraisky A.G.

Abstract

The protein Noggin4 of the African clawed frog Xenopus laevis has been shown to act as a modulator of the “noncanonical” Wnt/PCP-signaling pathway that plays an important role in the regulation of cell motility. Induction of disturbances in the expression of Noggin4 led to the activation of Wnt/PCP-pathway and the related anomalies of early embryonic development. The Noggin4 protein can bind the Wnt11 protein that normally contributes to the activation of the Wnt/PCP-pathway and of enhancing the activator effect of this protein in luciferase assays. Thus, Noggin4 can be used as a tool for specific experimental regulation of the activity of the Wnt/PCP pathway.

Russian Journal of Bioorganic Chemistry. 2017;43(2):216-219
pages 216-219 views

Green fluorescent protein with tryptophan-based chromophore stable at low pH

Gorbachev D.A., Sarkisyan K.S., Mishin A.S., Lukyanov K.A.

Abstract

Using directed (substitution T203Y) and subsequent random mutagenesis of the monomeric cyan fluorescent protein mTurquoise2, we obtained a protein with a tryptophan-based chromophore that fluoresces in the green region of the spectrum (excitation maximum 482 nm, emission maximum 519 nm). Fluorescence of the new protein is highly stable in a wide range of pH (pKa 4.9), more stable than all monomeric green fluorescent proteins with a tyrosine-based chromophore.

Russian Journal of Bioorganic Chemistry. 2017;43(2):220-222
pages 220-222 views

Synthetic analogue of Fridericia luciferin with improved spectral properties

Osipova Z.M.

Abstract

New bioluminescent analogue of Fridericia luciferin was synthesized for the first time. Bioluminescence emission maximum of the compound demonstrates a 50-nm bathochromic shift compared to the luciferin. The obtained analogue may find use in the novel in vivo bioimaging applications.

Russian Journal of Bioorganic Chemistry. 2017;43(2):223-225
pages 223-225 views

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