Biomedical Chemistry: Research and Methods

Journal Information
EISSN : 2618-7531
Current Publisher: Institute of Biochemistry (10.18097)
Total articles ≅ 86
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N.S. Ionov, P.V. Pogodin, V.V. Poroikov
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00140

Abstract:
The D3Targets-2019-nCoV web service predicting the interaction of chemical compounds with SARS-CoV-2 virus proteins and human proteins involved in the pathogenesis of COVID-19 by structural similarity and molecular docking was evaluated. The quality of the prediction was assessed as a balanced accuracy, which was calculated based on the results of the prediction for the structures of chemical compounds from the test set we compiled. The test set consisted of 35 active and 59 inactive molecules, including compounds with the experimetnaly confirmed absence of activity against the selected targets and compounds active against SARS-CoV-2 targets, not presented in the CoViLigands database. The authors of the analyzed web service did not indicate the thresholds for the values of the similarity score and the docking scoring function, using which it would be possible to reliably divide the compounds into active and inactive with respect to target proteins. Therefore, we assessed the balanced accuracy of the predictive methods D3Targets-2019-nCoV at various thresholds for cutting off active substances from inactive ones. Using our test set it was found that the highest value of balanced accuracy (0.59) was achieved when choosing active molecules based on the results of 2D similarity assessment (cutoff threshold was 46%). Assessment of 3D similarity did not allow achieving balanced accuracy values exceeding 0.5. It is shown that using the 2Dх3D integral similarity assessment recommended by the authors, the maximum value of the balanced accuracy 0.57 was achieved at a threshold of 31%. The calculated balanced accuracy for molecular docking results does not exceed 0.51. On the case study for the tideglusib, it was shown that the values of the scoring function for two target proteins, the activity against which was confirmed in the experiment (3CLpro and GSK3B), do not differ significantly from the values of the scoring function for the remaining 44 targets were not confirmed.
V.V. Shapovalova, S.P. Radko, K.G. Ptitsyn, G.S. Krasnov, K.V. Nakhod, O.S Konash, M.A. Vinogradina, E.A. Ponomarenko, D.S. Druzhilovskiy, A.V. Lisitsa
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00131

Abstract:
Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the "Oxford nanopore".
A.A. Yakovlev, T.A. Druzhkova, A.B. Guekht, N.V. Gulyaeva
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00143

Abstract:
Blood exosomes and microvesicles, collectively known as small extracellular vesicles (sEV), are vesicles about 100-150 nm in size. Small EV are involved in various aspects of signaling in the body; in addition, they can serve as markers of various pathologies. For biochemical studies, vesicle solubilization is often required. We tested the ability of various detergents to dissolve membranes of the sEV. Small EV were isolated from the blood serum of healthy volunteers by gel filtration on Sepharose CL-2B and tried to solubilize them using the anionic detergent DOC (sodium deoxycholate), non-ionic detergent Brij 35 (polyoxyethyleneglycol dodecyl ether), zwitterionic detergent CHAPS (3 - [(3-chloramidopropyl) dimethylammonio] -1-propanesulfonate), and cationic detergent CTAB (cetyl trimethylammonium bromide). The concentration of sEV in the solution was determined by dynamic light scattering. We find DOC is the most effective for sEV solubilization.
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

Abstract:
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

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

Abstract:
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.
V.S. Skvortsov, D.S. Druzhilovskiy, A.V. Veselovsky
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00124

Abstract:
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
Victoria 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

Abstract:
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

Abstract:
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.
O.A. Buneeva, L.N. Aksenova, A.E. Medvedev
Biomedical Chemistry: Research and Methods, Volume 3; doi:10.18097/bmcrm00115

Abstract:
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
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