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Vol 49, No 5 (2023)

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Condensates of SARS-CoV-2 Nucleoprotein on Viral RNA and Their Small Molecule Modulators

Svetlova J.I., Pavlova I.I., Aralov A.V., Varizhuk A.M.


Several types of biopolymers undergo liquid-liquid phase separation (form condensates) in aqueous solutions, and this phenomenon has been characterized in detail for proteins with intrinsically disordered regions. One example of such proteins is the nucleocapsid (N) protein of the severe acute respiratory syndrome coronavirus 2. In this review, we analyzed available data on N-protein separation in the presence of viral RNA. Particular attention was paid to transient contacts within the condensates and the N-protein/RNA fragments that form these contacts. We also discussed the presumed role of the condensates in the SARS-CoV-2 life cycle and summarized their influence on the host protective machinery. Finally, we commented on the possibility of regulating the viral condensates using synthetic or native small molecules (phase separation modulators), which can provide a new option in the design of antiviral agents.

Bioorganičeskaâ himiâ. 2023;49(5):443-454
pages 443-454 views

C60 Fullerene Amino Acid Derivatives: Synthesis and Biomedical Applications

Yamskova O.V., Kurilov D.V., Volkov V.A., Voronkov M.V., Zavarzin I.V.


Water-soluble forms of fullerene C60 possess unique physicochemical and biological properties, making them promising candidates for the development of various drugs in the fields of medicine and veterinary science. Of particular interest are studies on the synthesis and characterization of C60 fullerene derivatives with biogenic additives such as amino acids and peptides. This review focuses on different approaches to the synthesis of amino acid derivatives of fullerene C60 and their promising biomedical applications.

Bioorganičeskaâ himiâ. 2023;49(5):455-487
pages 455-487 views

Dynamics of Storage Lipids during the Recovery of Partially Bleached Coral Sinularia heterospiculata

Sikorskaya T.V., Solodiy D.D., Maskin E.V.


Global warming is causing the loss of coral symbionts and their bleaching. Researches of coral recovery are very important for the conservation of coral reefs. The lipidomic approach can provide detailed information about the processes that take place in the coral during bleaching and recovery. Using supercritical fluid chromatography in combination with mass-spectrometry, the dynamics of the main classes of storage lipids triacylglycerols (TG) and monoalkyldiacylglycerols (MADAG) during the recovery of the octocoral Sinularia heterospiculata after heat stress (32°C). It was shown that MADAG plays an important role in the energy balance of S. heterospiculata after heat stress. Under stress, the coral S. heterospiculata primarily consumed saturated MADAG molecular species. Changes in the profile of TG molecular species occurred only on the 16th day of the experiment. Probable, the stressed octocoral S. heterospiculata changes its energy strategy during recovery; therefore, the qualitative composition of reserve lipids is rearranged during the recovery period.

Bioorganičeskaâ himiâ. 2023;49(5):488-493
pages 488-493 views

A New Complex of the Glucose Phosphate Isomerase Ribozyme with the Enzyme Hexokinase in Yeast

Solovjeva O.N.


The existence of a previously unknown ribozyme with the catalytic function of glucose phosphate isomerase was shown. It catalyzes the interconversion of glucose 6-phosphate and fructose 6-phosphate. This ribozyme was found in baker’s yeast Saccharomyces cerevisiae and was isolated as a complex with the enzyme hexokinase. The complex was easily isolated on an immunoaffinity column with antibodies to hexokinase. The ribozyme consists of 41–42 nucleotides and has a molecular weight of about 14.15–14.5 kDa. Km and Vmax are accordingly 0.14 ± 0.02 mM and 14.0 ± 1.3 U/mg for glucose 6-phosphate and 0.2 ± 0.03 mM and 15.4 ± 1.4 U/mg for fructose 6-phosphate. These kinetic characteristics are approximately the same in the complex and for the free ribozyme. Hexokinase within the complex retains its catalytic activity.

Bioorganičeskaâ himiâ. 2023;49(5):494-501
pages 494-501 views

Research of the Protein Profile and Allergenic Properties of the Tropomyosin and Other Allergenic Components in the Composition of Water-Salt Extract of Giant Tiger Shrimp (Penaeus monodon)

Berzhets V.M., Alatortseva G.I., Nesterenko L.N., Khlgatian S.V., Petrova S.Y., Petrova N.S., Vasilyeva A.V., Pishulina L.A., Emelyanova O.Y.


Despite the success in identifying new crustacean allergens other than tropomyosin, many potential allergens remain unidentified. At present there are no diagnostic and treatment crustaceans allergens on the Russian market, including tropomyosin of invertebrates. The aim of the research was to explore allergenic properties of tropomyosin and other proteins in water-salt extract from tiger shrimp (Penaeus monodon). Raw and boiled meat of giant tiger shrimp was used to prepare allergenic extracts. To identify the specific activity of experimental allergens, sera from patients allergic to crustaceans with an established degree of activity (class 3) were used. The levels of specific IgE were from 3.5 to 17.5 IU/mL. ELISA was performed with the allergen samples. Polyacrylamide gel electrophoresis of raw and boiled shrimp allergen preparations was followed by Western blotting with the most allergen-specific serum. It has been shown that the extracts from raw and boiled shrimp have allergenic activity (bind IgE). The heat treatment of shrimp had no effect on allergenic activity except for one sample, where a strong reaction with the antigens was found. It is proved that the selected extraction conditions make it possible to reveal the multifractional nature of the protein profile of raw and boiled shrimp extracts. In Western blotting experiments the raw shrimp extract showed a weak reaction; tropomyosin was not detected. At the same time five protein fractions were identified in the boiled shrimp samples which reacted with IgE antibodies of a patient with crustaceans’ allergy. The data obtained will allow us expanding the knowledge about crustacean allergy and continueing our research to determine the optimal conditions for cleaning shrimp allergens.

Bioorganičeskaâ himiâ. 2023;49(5):502-508
pages 502-508 views

Synthetic Transformations of Higher Terpenoids. 42. Synthesis of New 18-Nor-4-(Carboxyethyl)Isopimara-7,15-Diene Derivatives and Study of Their Cytotoxicity on MCF7, U-87 MG and DU 145 Cancer Cell Lines

Gromova M.A., Kharitonov Y.V., Rybalova Т.V., Larionov V.А., Golubeva T.S., Shults E.E.


(E)-16-Aryl-substituted derivatives of tricyclic diterpenoids were synthesized by cross-coupling of isopimaric acid derivatives with substituted iodorenes catalyzed by palladium acetate in the presence of silver carbonate. Condensation of (E)-18-nor-4-(carboxyethyl)-16-(2-carboxyethyl)isopimar-7,15-diene dichloride with propargylamine hydrochloride leads to the corresponding dialkine, which readily reacts with diazide in the Cu(I) catalyzed cycloaddition (CuAAC) reaction, with the formation of macroheterocyclic compound containing a pimaran type tricyclic diterpenoid core and 1,2,3-triazole rings in the linker chain. Reaction of in situ prepared (E)-18-nor-16-azido-4-(carboxyethyl)isopimar-7,15-diene acid chloride with propargylamine hydrochloride or an alkynyl-substituted derivative of the protected Gly-Gly dipeptide leads to the corresponding azidoalkynes. The intramolecular CuAAC reaction of azidodipeptidylalkine afforded a macroheterocyclic derivative containing a dipeptide and triazole moiety in the linker chain. The obtained compounds showed higher (compared with the isopimaric acid) cytotoxicity on tumor cells MCF-7 and were less toxic to non-cancer cells than the reference drug doxorubicin. The GI50 value of the most active compound is 6.3 μM, selectivity index >15) (MTT test). The synthesized derivatives of the tricyclic diterpenoid isopimaric acid can be used to develop new antitumor agents.

Bioorganičeskaâ himiâ. 2023;49(5):509-522
pages 509-522 views

Induction of the Antioxidant Activity by Selenium Compounds in the Aspergillus niger Mycelium

Poluboyarinov P.A., Kuznetsova A.V., Moiseeva I.Y., Mikulyak N.I., Kaplun A.P.


Investigation of the antioxidant activity (AOA) induction by selenium compounds (Na2SeO3, diacetophenonyl selenide (DAPS-25), L-selenocystine) in various organisms is interesting as a protection from stress induced cell membranes damages. A comparative analysis of the antioxidant activity of 23 amino acids was performed by coulometric titration with electrogenerated bromine and iodine. The activity decreases in the order: cystine > tryptophan > selenocystine > tyrosine > 3,3'-dimethyl-L-selenocystine > methionine. Only amino acids with sulfhydryl and selenol groups as more active reductants can interact with the electrogenerated iodine: cysteine > selenocysteine > threo-3-methyl-L-selenocysteine. Probably the correction of the antioxidant status at the amino acids level is based on the sulfhydryl and selenol groups in radicals. In case they are not enough, cystine, selenocystin, tryptophan, tyrosine, and methionine will act as scavenger-reductants. It was found that selenium compounds dose-dependently induce the total antioxidant activity of the A. niger mycelium and affect indicators of the antioxidant status (amino acid composition and catalase activity), which in turn stimulates the biomass accumulation. DAPS-25 and sodium selenite treatment at the high doses (0.025 mg Se/L) caused the greatest effect on the total AOA induction (3.4–5.5 times). Lower concentrations (0.0025–0.00025 mg Se/L) had a lesser effect (25.8–41.7%). Activity in samples with L-selenocystin increased by 1.6–43.3%. It is noted that the iodine antioxidant activity in the mycelium was generally lower than the bromine one.

Bioorganičeskaâ himiâ. 2023;49(5):523-536
pages 523-536 views


Biological Microarray for Detection of Somatic Mutations in the Genes of Isocitrate Dehydrogenase 1 and 2

Varachev V.O., Guskov D.A., Shekhtman A.P., Rogozhin D.V., Polyakov S.A., Chudinov A.V., Zasedatelev A.S., Nasedkina T.V.


Mutations in isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) genes are important diagnostic and prognostic markers in a number of tumors (chondroid tumors, brain tumors, leukemia). To determine mutations in the IDH1/2 genes the method of allele-specific hybridization on a biological microarray was developed, which makes it possible to determine the presence of a mutation in a tumor sample (chondroid tumors and glioblastoma) and the variant of nucleotide substitution. When comparing IDH1/2 mutation detection methods using a biological microarray and DNA melting analysis with a TaqMan probe, full coincidence of results was obtained, with the biochip method making it possible to determine the type of nucleotide substitution without an additional sequencing step.

Bioorganičeskaâ himiâ. 2023;49(5):537-542
pages 537-542 views

Species-Level Identification of SARS-CoV-2 by E Gene Conservative Locus

Lapa S.A., Shingareva A.A., Faizuloev E.B., Ammour Y.I., Shershov V.E., Chudinov A.V.


The appearance of mutations in the genes encoding the surface proteins of the new type of coronavirus SARS-CoV-2, when it circulates in the host population, makes it difficult to use monoclonal antibodies for its species identification. In such cases, the choice of conservative genetic targets allows identification by molecular biological methods. In this work, previously developed primers specific to the E gene fragment were tested to detect a new type of coronavirus on six isolates belonging to different genetic variants (the original Wuhan strain, delta and omicron). The choice of a conservative site of the E gene encoding the small transmembrane protein E as a target for reverse transcription with subsequent amplification (RT-PCR) made it possible to detect coronavirus regardless of its subtypes characterized by antigenic heterogeneity in N- and S‑proteins. The possibility of species-level identification of COVID-19 pathogen circulating in Russia is shown, both in the total reaction volume (in a single test tube) and on biological microarrays.

Bioorganičeskaâ himiâ. 2023;49(5):543-547
pages 543-547 views

Alternative Chromophore Binding Sites in Non-Covalent Fluorescent Complexes of Bacterial Lipocalin

Goryacheva E.A., Artemyev I.V., Arhipova S.F., Rossohin A.V., Gilvanov A.R., Pletnev V.Z., Pletnevа N.V.


The three-dimensional structure of DiB3, a fluorescent non-covalent complex of a genetically engineered variant of the bacterial protein lipocalin Blc with a synthetic GFP-like chromophore M739, was determined by the calculation method of molecular mechanics. Compared to the crystal structure of the related DiB1 complex, an alternative binding site for the M739 chromophore was found in the structure of the DiB3 complex.

Bioorganičeskaâ himiâ. 2023;49(5):548-552
pages 548-552 views

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