Biomedical Chemistry: Research and Methods

Journal Information
EISSN : 2618-7531
Current Publisher: Institute of Biochemistry (10.18097)
Total articles ≅ 83

Latest articles in this journal

M.S. Denisov, Ya.A. Beloglazova
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00127

The discovery and investigations of new therapeutic agents with anticoronaviral activity is extremely important due to the COVID-19 pandemic caused by the SARS-CoV-2 virus. Currently, there are no anti-COVID-19 drugs, characterized by efficacy which has been proved in correspondence with criteria of evidence-based medicine. However, there are some anti SARS-CoV-2 drugs, acting on the other Coronaviridae family member causing SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). Consequently, a wide range of organic substances of synthetic and natural origin were studied for the anticoronaviral activity. The review summarizes and systematizes the literature data on the anti-coronavirus activity of triterpenoids. The structural features of triterpenoids, which are important for the mechanisms of anticoronaviral activity, are discussed. The structures of the most active compounds are presented. The material is classified by approaches to study the anticoronaviral activity of individual substances or plants extracts. Recommendations for the further research of triterpenoids anticoronaviral activity are given.
D.D. Zhdanov, N.S. Novachly, M.V. Pokrovskaya, S.S. Aleksandrova, T.A. Kabardokov, N.N. Sokolov
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00128

The aim of this work was to identify genes whose mRNAs were subjected to alternative splicing by apoptotic endonuclease EndoG in CD4+ T lymphocytes from healthy humans, mice, and rats. In order to induce EndoG, lymphocytes were transfected with an EndoG-containing plasmid, or a control pGFP plasmid, or were incubated with cisplatin. Efficiency of transfection, number of cells with DNA damages and the level of EndoG expression have been monitored. Total cell mRNA has been sequenced and the changes in proportion of splice variants of genes were analyzed. The changes in the proportion of 28 mRNA splice variants have been identified in human and murine lymphocytes in both transfected with EndoG gene or incubated with cisplatin. Thus, EndoG can be considered as a potent modulator of alternative splicing of mRNA of identified genes.
I. Mamatova, I. Askarov, M. Mamarakhmonov
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00125

Peach is a medicinal plant which has many traditional applications uses against various diseases. In this study we have evaluated differences in tannins and flavonoids in the composition of flowers and peach leaves and their antioxidant properties. Antibacterial activity of the peach flower and leaf extract was investigated using Mycobacterium tuberculosis and E. coli by the disk diffusion method. Total fractions of flavonoids and tannins were obtained using ethanol and aqueous extraction, respectively. The antioxidant activity was evaluated using the adrenaline autooxidation test. The results have shown that the peach flower extract contains many flavonoids, tannins that probably account for better antimicrobial effects as compared with the peach leaf extract. This shows perspectives for the use of peach flowers for the treatment of many diseases, especially for tuberculosis, and other diseases associated with overproduction of free radicals.
V. V. Shumyantseva, L.E. Agafonova, T.V. Bulko, A.V. Kuzikov, R.A. Masamrekh
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00119

The electrochemical method of analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules is considered. Materials and complex systems for modifying electrodes as well as methods for producing modified electrodes to increase the sensitivity of recording the flow of electrochemical reactions on the surface of the electrodes are described. Methods of electrode modifications based on synthetic lipid-like didodecyldimethylammonium bromide, gold and silver nanoparticles, one-dimensional nanoparticles based on lead compounds, titan oxide nanoparticles, dispersions of carbon nanotubes in organic solvents, in polymers with different chemical structure are considered. It is shown that the appropriate functionalization of the working electrode surface makes it possible to increase the sensitivity of the electrochemical biosensor system and decrease the limit of detection. The results are presented in the form of an algorithm applicable for selection the beneficial type of modified electrode for the corresponding electrochemical reaction and biosample analysis.
Natalia Shushkova, S.E. Novikova, T.E. Farafonova, V.G. Zgoda
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00118

The conditioned media in which the tumor cells are cultured represents a model object for studying of secretome and proteomic composition of exosomes. This pool of proteins is of particular interest in terms of the search for potential markers of malignant diseases. The efficiency of the isolation of exosomes and secretome from the cell culture media largely determines the success of their analysis by the mass spectrometric method. In this paper, we have applied various approaches to isolate secretome and exosomes originated from Caco-2 colorectal adenocarcinoma cells. The combination of ultrafiltration and centrifugation provided a deep proteomic analysis of the secretome and exosomes obtained from the one initial volume of conditioned medium without the addition of fetal bovine serum. Applying tandem mass spectrometric analysis we have identified 436 secreted proteins. In exosomes, the characteristic proteins ALIX, CD63, syntenin, lactadherin (MFGE8) were identified. Using targeted mass spectrometry, the exosome markers CD82, CD9 and HSPA8 were determined at the levels of 0.08 ± 0.03 fmol/μg, 0.13 ± 0.03 fmol/μg and 2.6 ± 0.02 fmol/μg of total protein, respectively. Among the secreted proteins, there were many markers associated with tumor progression and metastasis, such as DAG1, PODXL, LRRN4, TGFBI, IL6ST, DSC1, DSG1, and NPC2.
V.S. Skvortsov, D.S. Druzhilovskiy, A.V. Veselovsky
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00124

Pneumonia caused by the COVID-19 virus has led to quick search of drugs that would able to block the spread of this virus. A standard way of drug development is a long process. One approach that can significantly accelerate drug development is drug reposition. In this study a virtual screening of the database of approved drugs has been used for search inhibitors against 3СLpro COVID-19, the main protease of COVID-19. Molecular docking, simulation of molecular dynamics and binding energy estimation by MM-GBSA method allowed to select several compounds for further experimental testing. The most promising drugs are the HIV protease inhibitor Indinavir, the inhibitor of protease hepatitis C Telaprevir, the antiulcer drug Dalargin, and the ErB receptor tyrosine kinase inhibitor Neratinib
O.A. Buneeva, L.N. Aksenova, A.E. Medvedev
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00115

The increase in enzyme inhibition developed during prolonged incubation of an enzyme preparation with a chemical substance may be associated with both the non-covalent and also with covalent enzyme-inhibitor complex formation. The latter case involves catalytic conversion of a mechanism-based irreversible inhibitor (a poor substrate) into a reactive species forming covalent adduct(s) with the enzyme and thus irreversibly inactivating the enzyme molecule. Using a simple approach, based on comparison of enzyme inhibition after preincubation with a potential inhibitor at 4ºC or 37ºC we have analyzed inhibition of monoamine oxidase A (MAO A) by known MAO inhibitors pargyline and pirlindole (pyrazidol). MAO A inhibitory activity of pirlindole (reversible tight binding inhibitor of MAO A) assayed after mitochondrial wash was basically the same for the incubation at both 4ºC and 37ºC. In contrast to pirlindole, the effect of pargyline (mechanism based irreversible MAO inhibitor) strongly depended on the temperature of the incubation medium. At 37ºC the residual activity MAO A in the mitochondrial fraction after washing was significantly lower than in the mitochondrial samples incubated with pargyline at 4ºC. Results of this study suggest that using analysis of both time- and temperature-dependence of inhibition it is possible to discriminate mechanism-based irreversible inhibition and reversible tight binding inhibition of target enzym
V. V. Shumyantseva, T.V. Bulko, P.I. Koroleva
Biomedical Chemistry: Research and Methods, Volume 2; doi:10.18097/bmcrm00110

Modern methods of analysis of drugs for their quantitative assessment are considered. Particular attention is paid to the electrochemical methods of drug registration, based on the reaction of electrooxidation of molecules. Systems and materials for modifying electrodes are described, as well as methods for producing modified electrodes for electrochemical reactions on the surface of electrodes. The authors present data on the electroanalysis of acetaminophen, diclofenac, ibuprofen, omeprazole, using electrodes modified with carbon nanomaterials based on carbon nanotubes and graphene. It was shown that electroanalytical methods allow the registration of therapeutic drugs in a wide range of detectable concentrations (0.1 μМ - 10 mM), which can be used to work with biological fluids (plasma, blood, urine), to conduct drug monitoring and study drug-drug interactions.
P.A. Bobrovsky, A.K. Larin, N.F. Polina, V.N. Lazarev
Biomedical Chemistry: Research and Methods, Volume 2; doi:10.18097/bmcrm00113

Human peptidoglycan recognition proteins (PGLYRPs) are the components of innate immunity that exhibit antibacterial activity. In this study a cell line secreting recombinant PGLYRP1 into a culture medium was obtained. Transcriptional profiling of cell lines expressing PGLYRP1 was performed at different stages of C. trachomatis infection. Differential gene expression was studied using the whole transcriptome profiling method on the HumanHT-12 v4 Expression BeadChip microchip using the Illumina Direct Hybridization Whole-Gene Expression Assay protocol. Sample clustering followed by bioinformatics analysis revealed about 100 differentially expressed genes in response to infection with C. trachomatis. PGLYRP1- expressing cells infected with C. trachomatis had a similar transcriptional profile as non-infected cells.
V.S. Skvortsov, N.N. Alekseychuk, Yu.V. Miroshnichenko, A.V. Rybina
Biomedical Chemistry: Research and Methods, Volume 2; doi:10.18097/bmcrm00100

The possibility of prediction of selected ion fraction in the total peptide fraction obtained during mass spectrometry with positive ionization by electrospray was investigated on the basis of the amino acid sequence. The data obtained in the MS / MS experiment [Ramus et al., 2015] using the standardized UPS1 kit (48 highly purified human proteins) and deposited in ProteomeXchange (identifier PXD001819) were used as the initial data set. For each of the identified peptides belonging to one of the proteins of the UPS kit, a list of detected ions of different charge was formed. The sum of the peak intensities detected for the primary ion was used as a measure of quantity. Since the ratio of the peptide fractions of ions with different charges does not depend on the concentration in the experimental sample, the total sample was assembled by combining the data obtained for different dilutions of UPS1. A set of equations of prediction of the fraction of 1+, 2+, and 3+ ions has been constructed. This computational analysis has shown applicability of the proposed for prediction of the ion fraction of the peptide with selected charge in mass spectrometry with positive electrospray ionization.
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