S. A. Shilova, T. V. Rakitina, V. O. Popov, E. Yu. Bezsudnova
{"title":"Prospects of Application of D-amino Acid Transaminase from Aminobacterium colombiense for (R)-selective Amination of α‑Keto Acids","authors":"S. A. Shilova, T. V. Rakitina, V. O. Popov, E. Yu. Bezsudnova","doi":"10.3103/S0027131423010054","DOIUrl":"10.3103/S0027131423010054","url":null,"abstract":"<p>D-amino acid transaminase from <i>Aminobacterium colombiense</i> was applied for (<i>R</i>)-selective amination of 2-oxobutyrate, 2-oxovalerate and 2-oxo-4-phenylbutyrate to produce non-natural D-amino acids—D-homoalanine, D-norvaline and D-homophenylalanine. To increase the product yield of D-amino acids, a one-pot three-enzyme system was developed. The system included transaminase from <i>A. colombiense</i>, (<i>R</i>)-2-hydroxyglutarate dehydrogenase and glucose dehydrogenase and effectively shifted the equilibrium of transamination reaction toward the products. The system functioned at both neutral and slightly alkaline pH. We found that at high substrate concentrations (500 mM) transaminase from <i>A. colombiense</i> was inhibited by the products accumulated in the system. The optimization of operational conditions of the three‑enzyme system led to the following yields of the target products: 435 mM D-homoalanine, 320 mM D-norvaline and 47.5 mM D-homophenylalanine; the enantiomeric excess of the produced D-amino acids exceeded 99.5%.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"78 1","pages":"10 - 19"},"PeriodicalIF":0.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4915650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. A. Filippova, I. P. Andreeva, G. V. Presnova, M. M. Ulyashova, M. Yu. Rubtsova
{"title":"Lateral Flow Hybridization Assay to Determine Transcripts of TEM-Type Beta-Lactamase Genes in Bacteria Resistant to Antibiotics","authors":"A. A. Filippova, I. P. Andreeva, G. V. Presnova, M. M. Ulyashova, M. Yu. Rubtsova","doi":"10.3103/S0027131423010030","DOIUrl":"10.3103/S0027131423010030","url":null,"abstract":"<p>A technique for lateral flow hybridization analysis of specific bacterial beta-lactamase mRNAs, including the preparation of a biotinylated target DNA and its analysis on a test strip with immobilized oligonucleotide probes, is developed. When the target DNA and probe structures are complementary, DNA duplexes are formed in the test zone of the strip, which interact with the conjugate of streptavidin and gold nanoparticles. The technique is used to determine the transcripts of the genes encoding TEM-type beta-lactamases isolated from the culture of <i>E. coli</i> producing the corresponding recombinant beta-lactamase. It is shown that single-stranded 330 bp target DNA is determined most effectively in lateral flow analysis.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"78 1","pages":"28 - 34"},"PeriodicalIF":0.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4923310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. S. Iurchenko, A. A. Loginova, E. P. Sergeev, E. V. Pometun, V. I. Tishkov, S. S. Savin, A. A. Pometun
{"title":"Engineering the Active Site of Formate Dehydrogenase from Staphylococcus aureus: Introduction of the Additional Loop and Histigine Residues to the Structure","authors":"T. S. Iurchenko, A. A. Loginova, E. P. Sergeev, E. V. Pometun, V. I. Tishkov, S. S. Savin, A. A. Pometun","doi":"10.3103/S0027131423010078","DOIUrl":"10.3103/S0027131423010078","url":null,"abstract":"<p>NAD<sup>+</sup>-dependent formate dehydrogenase (EC 1.2.1.2, FDH) from pathogenic bacterium <i>Staphylococcus aureus</i> (SauFDH) differs significantly from other FDHs both in terms of primary structure and catalytic properties. A distinctive feature of SauFDH is the highest (about 2.5–3 times) specific activity compared to other formate dehydrogenases. At the same time, SauFDH has high Michaelis constants for both substrates. Based on the analysis of three-dimensional structures and the alignment of amino acid sequences, replacements promising in terms of changing catalytic parameters were selected. The replacement of I220H resulted in an increase in <span>(K_{{text{M}}}^{{{text{NA}}{{{text{D}}}^{{text{ + }}}}}})</span>; the value of <i>k</i><sub>cat</sub> has not changed. When T250H is replaced, an increase in <span>(K_{{text{M}}}^{{{text{NA}}{{{text{D}}}^{{text{ + }}}}}})</span> is observed, <i>k</i><sub>cat</sub> decreases from 20 to 13 s<sup>–1</sup>. The replacement of K368H led to a slight increase in <span>(K_{{text{M}}}^{{{text{NA}}{{{text{D}}}^{{text{ + }}}}}})</span>, <i>k</i><sub>cat</sub> decreased from 20 to 6 s<sup>–1</sup>. The introduction of TGA and AGA additional inserts in α-helix at the C-terminus of the enzyme led to an increase in <span>(K_{{text{M}}}^{{{text{NA}}{{{text{D}}}^{{text{ + }}}}}})</span> and <span>(K_{{text{M}}}^{{{text{HCO}}{{{text{O}}}^{ - }}}})</span>. A bigger effect was observed for <span>(K_{{text{M}}}^{{{text{NA}}{{{text{D}}}^{{text{ + }}}}}})</span>—the difference was more than 10 times. For mutant SauFDH with insertions <i>k</i><sub>cat</sub> significantly reduced to 4 s<sup>–1</sup>. Similar results were observed for mutants with multipoint replacements. Thus, the C-terminal sequence has been shown to play an important role in the catalysis of SauFDH.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"78 1","pages":"42 - 53"},"PeriodicalIF":0.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4917521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Yu. Mikhailova, U. A. Budanova, Yu. L. Sebyakin
{"title":"Modeling the Interaction of Low Molecular Weight Targeting Ligands and Synthesis of Lipotripeptides with Potential Inhibitory Ability Against Integrin αVβ3","authors":"A. Yu. Mikhailova, U. A. Budanova, Yu. L. Sebyakin","doi":"10.3103/S0027131423020050","DOIUrl":"10.3103/S0027131423020050","url":null,"abstract":"<p>Low molecular weight RGD peptides and RGD mimetics are widely studied as ligands targeting the corresponding receptor in the diagnosis and therapy of cancer, as well as in the field of bone tissue regeneration. Some of them are undergoing preclinical trials. The aim of this study is to select the optimal variants of the ligand structure based on an aliphatic RGD mimetic. By methods of molecular modeling (blind docking and active site docking), the most advantageous constructions for the formation of a stable complex with the integrin α<sub>V</sub>β<sub>3</sub> are determined. A scheme is developed and two lipotripeptides Gnd-GABA-Gly-Asp(C<sub>16</sub>)<sub>2</sub> and Gnd-β-Ala-Gly-Asp(C<sub>16</sub>)<sub>2</sub> with the potential ability to inhibit this receptor on the surface of tumor tissues are synthesized.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"78 2","pages":"55 - 62"},"PeriodicalIF":0.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4924778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biligand Complexes of Cholesterol and Thiocholesterol with Silver Nanoclusters: Experimental Data and DFT-Modeling","authors":"Ya. A. Gromova, A. Yu. Ermilov, T. I. Shabatina","doi":"10.3103/S0027131422070069","DOIUrl":"10.3103/S0027131422070069","url":null,"abstract":"<p>TEM experimental data for “Silver–Cholesterol” (Ag–Ch) and “Silver–Thiocholesterol” (Ag–TCh<b>)</b> systems showed the formation of silver nanoclusters of (6.0 ± 0.5) nm and (2.0 ± 0.5) nm in size correspondingly. Supramolecular organization of the systems due to donor-acceptor or electrostatic interactions with cholesteric ligands led to the formation of elongated helix aggregates with plasmonic absorbtion in visible and near-IR spectral regions. Using the DFT /B3LYP5 method the structures of biligand complexes of Ag<sub>13</sub> silver cluster with cholesteric ligands Ch and TCh were modeled and compared with the structure of monoligand complexes. O- and S-containing ligands were coordinated by vertices on different sides of the Ag<sub>13</sub> icosahedron. The energies of model reactions of the formation of monoligand and biligand complexes are compared. A tendency of the Ag<sub>13</sub> metal cluster to attach more ligands was found out. It can be assumed that the system retains the tendency of further aggregation with the attaching of the additional ligand molecules.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S65 - S71"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4974830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. I. Vernaya, A. S. Shumilkin, D. L. Karlova, A. S. Shevchenko, A. A. Makeeva, A. V. Shabatin, A. M. Semenov, T. I. Shabatina, M. Ya. Melnikov
{"title":"Cryoformation and Properties of Dioxidine/Gelatin Systems","authors":"O. I. Vernaya, A. S. Shumilkin, D. L. Karlova, A. S. Shevchenko, A. A. Makeeva, A. V. Shabatin, A. M. Semenov, T. I. Shabatina, M. Ya. Melnikov","doi":"10.3103/S0027131422070124","DOIUrl":"10.3103/S0027131422070124","url":null,"abstract":"<p>Cryoforming of gelatin systems with the antibacterial drug dioxidine is carried out. The study considers the effect of systems’ synthesis conditions (gelatin concentration in the precursor solution) on their structural characteristics, antibacterial activity, and drug release time. The composition and structure of the dioxidine/gelatin and dioxidine/hydrolyzed collagen systems are characterized by SEM, IR, and UV spectroscopy. The disk diffusion method is used to determine the antibacterial activity of the obtained systems against <i>E. coli</i> and <i>S. aureus</i>.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S7 - S12"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4976406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification and Authentication of Cow Milk Powder Using a Smartphone and Chemometric Analysis","authors":"V. G. Amelin, Z. A. Ch. Shogah, D. S. Bolshakov","doi":"10.3103/S0027131422070033","DOIUrl":"10.3103/S0027131422070033","url":null,"abstract":"<p>The possibility of identifying and authenticating cow milk powder by the method of chemical colorimetry of the fluorescence of samples using a smartphone camera and chemometric analysis is shown. A fundamental test device for direct colorimetric analysis of milk powder is proposed, excluding the stage of sample preparation. Fluorescence excitation is carried out with a portable source of monochromatic UV radiation (λ = 365 nm). The colorimetric parameters of milk powder fluorescence in RGB space are recorded using a smartphone camera. We use chemometric processing of the calculated analytical signal, which makes it possible to reduce the analysis time and visualize the studied data. The data array of the fluorescence colorimetric parameters (RGB) are evaluated by principal component analysis (PCA) and hierarchical clustering analysis (HCA) using the XLSTAT software.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S36 - S41"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4976579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Possible Reason for the Predomination of Vanadium in the Microelement Composition of Sulfurous Oils","authors":"G. V. Lisichkin","doi":"10.3103/S0027131422070094","DOIUrl":"10.3103/S0027131422070094","url":null,"abstract":"<p>In accordance with the abiogenic hypothesis of the origin of oil, deposits formed as a result of degassing of the Earth, in particular, due to the interaction of mantle methane and its polycondensation products with elemental sulfur, are thermodynamically open systems. In open systems, self-organization processes are realized and a progressive evolution of the catalyst of the basic reaction occurs, accompanied by an increase in its activity and accumulation in the system. The predominance of vanadium in the trace element composition of sour oils may be due to its catalytic activity in the basic reaction of the formation of C–S bonds.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S42 - S45"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4974829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Synthesis, Biological and Acidic Properties of Some New 2-Ethoxy-4-[(3-alkyl-4,5-dihydro-1H-1,2,4-triazol-5-one-4-yl)-azomethine]-phenyl 2-Methylbenzoate Derivatives","authors":"Haydar Yüksek, Bahar Bankoğlu-Yola, Sevda Manap, Özlem Gürsoy-Kol","doi":"10.3103/S0027131422070070","DOIUrl":"10.3103/S0027131422070070","url":null,"abstract":"<p>The synthesis of 2-ethoxy-4-[(3-alkyl-4,5-dihydro-1<i>H</i>-1,2,4-triazol-5-one-4-yl)-azomethine]-phenyl 2-methylbenzoates (<b>4</b>) from the reactions of 3-alkyl-4-amino-4,5-dihydro-1<i>H</i>-1,2,4-triazol-5-ones (<b>2</b>) with 3-ethoxy-4-(2-methylbenzoxy)-benzaldehyde (<b>3</b>) is described. The acetylation reactions of compounds <b>4</b> were investigated, and <b>5</b> type <i>N</i>-acetyl derivatives were obtained and the newly synthesized compounds were fully characterized. Also, in vitro antibacterial activities of the fourteen new compounds were screened against six bacteria such as <i>Escherichia coli</i>, <i>Pseudomonas aeruginosa</i>, <i>Staphylococcus aureus</i>, <i>Bacillus subtilis</i>, <i>Bacillus cereus</i> and <i>Klebsiella pneumonia</i> according to agar well diffusion method. In addition, the newly synthesized 14 novel compounds were tested for their antioxidant activities using three different methods. Furthermore, to investigate the effects of solvents and molecular structure upon acidity, the compounds <b>4</b> were titrated potentiometrically with tetrabutylammonium hydroxide in four non-aqueous solvents (isopropyl alcohol, <i>tert</i>-butyl alcohol, <i>N</i>,<i>N</i>-dimethylformamide and acetone).</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S55 - S64"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4974266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. I. Vernaya, A. S. Shumilkin, A. V. Shabatin, T. I. Shabatina, M. Ya. Melnikov
{"title":"Synthesis of Iron Oxide Nanoparticles by Thermal Decomposition of Cryochemically Modified Precursors","authors":"O. I. Vernaya, A. S. Shumilkin, A. V. Shabatin, T. I. Shabatina, M. Ya. Melnikov","doi":"10.3103/S0027131422070112","DOIUrl":"10.3103/S0027131422070112","url":null,"abstract":"<p>Highly dispersed powders of superparamagnetic iron oxides of various morphologies are obtained by the thermal decomposition of formate and ammonium citrate of iron(III), subjected to cryochemical treatment by the spray cryogenic drying method. The composition and structure of the obtained particles and cryo-modified precursor salts are characterized by the following physicochemical methods: X-ray diffraction analysis, thermoanalytical methods (TG, DSC), IR spectroscopy, scanning electron microscopy, and the chromatographic method for determining the specific surface by the thermal desorption of argon.</p>","PeriodicalId":709,"journal":{"name":"Moscow University Chemistry Bulletin","volume":"77 1","pages":"S1 - S6"},"PeriodicalIF":0.7,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4974267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}