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Volume 44, Nº 5 (2018)

Review Article

The Role of Intercellular Communication in Cancer Progression

Shender V., Arapidi G., Pavlyukov M., Shnaider P., Anufrieva K., Stepanov G., Govorun V.

Resumo

Although understanding of the molecular biology of cancer has advanced and medicine has an impressive arsenal of chemotherapeutic drugs, the problem of tumor resistance to individual drugs and drug combinations has not yet been resolved. Known mechanisms of cancer chemoresistance do not explain the reason for such a phenomenon as “apoptosis-induced proliferation,” where cells dying under the effect of the therapy secrete some signaling molecules into the extracellular medium to promote proliferation, survival, and acquisition of a more aggressive phenotype of neighboring cancer cells. The nature of this unexpected phenomenon is only now beginning to be partially clarified, but the nature of such signaling between apoptotic cancer cells and their neighboring cells remains largely unknown. For this reason, in this review we discuss currently known types of intercellular communication of tumor cells, give specific examples of important secreted molecules involved in signaling between cancer cells, and describe possible cell interactions contributing to the progress of cancer outgrowth.

Russian Journal of Bioorganic Chemistry. 2018;44(5):473-480
pages 473-480 views

Article

Mass Spectrometric Amino Acid Sequencing of Short and Mid-Sized Peptides in a ESI-O-TOF System as an Alternative to MS/MS: I. Selective Fragmentation of Peptides with y-Ion Formation

Nazimov I., Bublyaev R.

Resumo

The possibility of mass spectrometric sequencing of peptides without the need for the conventional MS/MS analysis has been demonstrated experimentally. The peptide hydrolysate was fractionated by reversephase chromatography on a microbore column. The eluate fraction was injected into the mass spectrometer via an electrospray ion source that directly coupled a liquid chromatography instrument to a time-of-flight mass spectrometer (HPLC-MS). Fragmentation of the peptides eluted from the column was performed in the mass spectrometer interface by varying the voltage difference between the mass spectrometer nozzle and skimmer. A restricted set of intensive peaks of y-ions, which corresponded to sequential cleavage of all amino acids from the peptide, was obtained. The ratios of the y-ion peak intensities to the background were (5−100)/1. The presence of Lys and Arg in the peptides provided for a substantial increase of informative peak intensity in the mass spectra. The mass spectra of short peptides (up to 10 residues) were processed manually, whereas the Proteos hardware and software system was used to process the fragmentation results for a long N-terminal peptide of the human hemoglobin α-chain.

Russian Journal of Bioorganic Chemistry. 2018;44(5):481-491
pages 481-491 views

Synthetic Antimicrobial Peptides: I. Antimicrobial Activity of Amphiphilic and Nonamphiphilic Cationic Peptides

Amirkhanov N., Tikunova N., Pyshnyi D.

Resumo

Comparative antimicrobial properties of three artificial cationic synthetic antimicrobial peptides (SAMP): (RAhaR)4AhaβA (where R is Arg, Aha is 6-aminohexanoic acid, βA is beta-alanine), (KFF)3K and R9F2 with various amphiphilic properties have been studied relative to pathogenic strains of microorganisms: Gram-negative bacteria Pseudomonas aeruginosa, Escherichia coli, Proteus mirabilis, and Salmonella enterica, Gram-positive bacteria Staphylococcus aureus, and pathogenic yeast fungus Candida albicans. The selectivity index (SI) values of the peptide preparations were calculated as the ratio of the 50% cytotoxic concentration (TC50) towards eukaryotic host cells to the MIC50 values of the testing antimicrobial peptides. The studied SAMPs appeared to be the most active against the pathogenic yeast fungus C. albicans and the bacterial strains St. aureus and P. aeruginosa. The SI values in these cases exceed 40. Some assumed molecular interactions of the studied SAMPs on the microbial cells have been considered, and possible pathways to increase their antimicrobial activity have been suggested. The proposed SAMPs can serve as a basis for the design and synthesis of new promising synthetic antimicrobial agents.

Russian Journal of Bioorganic Chemistry. 2018;44(5):492-503
pages 492-503 views

Three-Dimensional Structure of Recombinant Adenine Phosphoribosyltransferase from Thermophilic Bacterial Strain Thermus thermophilus HB27

Esipov R., Timofeev V., Sinitsyna E., Tuzova E., Esipova L., Kostromina M., Kuranova I., Miroshnikov A.

Resumo

Adenine phosphoribosyltransferase (APRT) from a thermophilic bacterial strain Thermus thermophilus НВ27 (TthHB27APRT) belongs to the family of type I phosphoribosyltransferases and catalyzes the magnesium-dependent transfer of 5'-phosphoribosyl group from 5'-phosphoribosylpyrophosphate to N9 adenine nitrogen with formation of adenosine-5'-monophosphate and pyrophosphate. The crystals of the recombinant enzyme suitable for X-ray study were grown in a capillary using the counter-diffusion technique. Crystals with unit-cell parameters α = 69.860 Å, b = 82.160 Å, c = 91.390 Å, α = 90.00°, β = 102.58°, and γ = 90.00° belong to the space group Р21 and contain six enzyme monomers in the asymmetric unit. The set of X-ray data from grown crystals was collected on a Spring-8 synchrotron radiation facility (Japan) and three-dimensional structure of the enzyme was solved at 2.7-Å resolution by molecular replacement method using the BALBES software. The polypeptide fold in the enzyme monomer and the structure of biologically active dimer were described. Based on the comparison with structures of homologous APRTs from a thermophilic strain ThtHB8 and Homo sapiens, positions of active site and a number of functionally important amino acids were located.

Russian Journal of Bioorganic Chemistry. 2018;44(5):504-510
pages 504-510 views

Prediction of the Ligands of the CYP9e Subfamily of Ant Cytochrome P450 with the ChEBI Ontologies of Chemical and Biological Characteristics

Konorov E., Belenikin M.

Resumo

Cytochromes P450 are involved in the metabolism of various endogenous and exogenous compounds, and their role in the detoxification of xenobiotics has been extensively studied. CYP9e, one of the subfamilies of cytochromes P450, whose functions have been poorly studied, is amplified in the black garden ant Lasius niger. We have performed molecular modeling of 23 proteins of this family belonging to L. niger and other ant species, as well as molecular docking and virtual screening of suspected ligands. The substances used as ligands have been annotated with ChEBI ontologies to predict the chemical and biological properties of molecules forming complexes with CYP9e of ants. It has been shown that, among the ligands forming energetically favorable complexes, ChEBI ontologies of mycotoxins, phytotoxins, steroids, glycosides and terpenoids are overrepresented. Nevertheless, it has been demonstrated that in carrying out a large number of inaccurate simulations, the results of function predictions can be correlated with molecular docking and the evolutionary history of a protein family.

Russian Journal of Bioorganic Chemistry. 2018;44(5):511-517
pages 511-517 views

Effect of the Deletion of the (173–280) Fragment of the Inserted α-Helical Domain on the Functional Properties of АТР-Dependent Lon Protease from E. coli

Kudzhaev A., Dubovtseva E., Serova O., Andrianova A., Rotanova T.

Resumo

The effect of the coiled-coil (CC) region of the α-helical inserted domain of Escherichia coli Lon protease (Ec-Lon) on the functional activity of the enzyme has been characterized. A recombinant form des-CC(G5)-Lon in which the deleted CC fragment is replaced by a pentaglycine peptide has been obtained and investigated. It has been shown that the CC region is involved in the recognition of the nucleotide nature by the enzyme and the interaction of the enzyme with the protein substrate. It has been also established that the CC region is necessary for the formation and functioning of the ATPase and peptidase active centers, the occurrence of allosteric interactions between them, and for the implementation of proteolysis by a unique processive mechanism.

Russian Journal of Bioorganic Chemistry. 2018;44(5):518-527
pages 518-527 views

Properties of Bioconjugates of Streptokinase with Anionic Polyamidoamine Dendrimers of Various Generations

Aisina R., Mukhametova L., Gershkovich K., Ivanova E., Zakharyan E., Karakhanov E.

Resumo

Covalent conjugates of streptokinase (SK) with polyamidoamine (PAMAM) dendrimers G1.5, G2.5, and G3.5 (SK–G1.5, SK–G2.5, and SK–G3.5) with the protein–polymer molar ratios of (1: 1), (1: 5), and (1: 10) were obtained and their properties were studied as compared to the properties of free SK. It was shown that the initial rates of formation of the modified Pm. SK complex, activation of plasminogen, and lysis of the plasma clot under the action of SK–dendrimer conjugates decreased with increasing number of bound dendrimers (from 1 to 10) and increased with increasing dendrimer generation (from G1.5 up to G3.5). Conjugates SK–G3.5 (1: 1) and (1: 5) were the most active compared to other conjugates. It was found that the catalytic efficiency of plasminogen activation (kPg/KPg) by conjugates SK–G3.5 (1: 1) (0.15 μM–1 min–1) and SK–G3.5 (1: 5) (0.12 μM–1 min–1) was comparable to the efficiency of free SK (0.18 μM–1 min–1). Probably, small in size, soft, and easily deformable dendrimers G1.5 and G2.5 are able to penetrate into the internal shielded cavities of the native SK molecule and there modify amino groups that are important for the effective formation of the Pm · SK complex. By contrast, the larger and more rigid molecule of dendrimer G3.5 modifies, mainly, exposed lysine residues in the SK molecule, without affecting the latent internal lysines. Conjugates SK–G3.5 (1: 1) and (1: 5), which had the maximum activator activity, retained up to 85% of thrombolytic activity compared to the activity of free SK. In addition, due to modification of the exposed lysines—most sensitive to proteolysis in the SK molecule—with dendrimer G3.5, which has the highest density of negative charge on its surface, SK–G3.5 (1: 1) and (1: 5) conjugates were more stable in plasma and caused less exhaustion of plasma levels of plasminogen, α2-antiplasmin, and fibrinogen than free SK in vitro. Thus, thrombolytic activity of the SK–dendrimer conjugates depends on the degree of modification of the amino groups of SK, size, stiffness, and density of the negative charge on the surface of the PAMAM dendrimer. Conjugates SK–G3.5 (1: 1) and (1: 5) are potential candidates for the development of a new thrombolytic agent.

Russian Journal of Bioorganic Chemistry. 2018;44(5):528-537
pages 528-537 views

Synthesis and Antiproliferative Activity of Conjugates of Anthracycline Antibiotics with Sesquiterpene Lactones of the Elecampane

Semakov A., Anikina L., Afanasyeva S., Pukhov S., Klochkov S.

Resumo

The daunorubicin and doxorubicin anthracycline antibiotics were modified with the Inula helenium L. sesquiterpene lactones (alantolactone, isoalantolactone, and alloalantolactone) and with their epoxy derivatives. Antiproliferative properties of these conjugates were studied on tumor and normal cell lines. The daunorubicin conjugates with the sesquiterpene lactones (isoalantolactone, allantolactone, and alloalantolactone) and with their epoxy derivatives were found to exhibit the higher activity against human tumor cell lines than the corresponding doxorubicin conjugates. The daunorubicin conjugate with epoxyisoalantolactone proved to be the most effective compound, because it was more cytotoxic than daunorubicin towards a number of cell lines, including those daunorubicin-resistant, and did not affect normal human cells.

Russian Journal of Bioorganic Chemistry. 2018;44(5):538-546
pages 538-546 views

Synthesis and Biological Activity of Nitrilic Derivatives of the Methyl Ester of Maleopimaric Acid

Tret’yakova E., Salimova E., Parfenova L.

Resumo

An effective method of a modification of the anhydride ring of the maleopimaric acid methyl ester by means of the cyanoethylation reaction was developed. A primary screening of a cytotoxic activity in vitro demonstrated an ability of the cyanoethyl derivative of the maleopimaric acid methyl ester to induce the death of the PC-3 cells of prostate cancer.

Russian Journal of Bioorganic Chemistry. 2018;44(5):547-552
pages 547-552 views

Amino Derivatives of Natural Epoxyalantolactone: Synthesis and Cytotoxicity toward Tumor Cells

Pukhov S., Afanasyeva S., Anikina L., Semakov A., Dubrovskaya E., Klochkov S.

Resumo

Reactions of natural epoxyalantolactone with primary and secondary amines, which lead to hydrated benzo[g]furo[4,3,2-cd]indolones and eudesmane-type amino derivatives, respectively, have been studied. Epoxyalantolactone conjugates have been synthesized with the involvement of pharmacophoric amines, and their cytotoxic activity toward some tumor cell lines has been tested. The involvement of the signaling pathway of protein p53 in the death of tumor cells, the contribution of oxidative stress, and the induction of apoptosis have been investigated in experiments in vitro.

Russian Journal of Bioorganic Chemistry. 2018;44(5):553-561
pages 553-561 views

Synthesis of Unsymmetrical Polymethine Cyanine Fluorescent Dyes for Nucleic Acid Analysis by Real-Time PCR

Natyrov A., Vlasova N., Matvienko I., Volkov E., Bayramov V., Kurochkin V., Alexeev J.

Resumo

The synthesis of unsymmetrical polymethine cyanine derivatives of f luorescent dyes is described, and their potential as a component of hybridization probes for the real-time PCR technique is first demonstrated.

Russian Journal of Bioorganic Chemistry. 2018;44(5):562-571
pages 562-571 views

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