Russian Journal of Bioorganic Chemistry最新文献

Objective: The development of controllable gene editing systems based on the CRISPR/Cas technology is a problem of immediate interest in modern molecular biology and genetic engineering. An interesting solution of this problem is modification of guide RNA by introduction of photocleavable linkers. Methods: We developed an approach to the synthesis of cyclic photocleavable guide crRNA for the CRISPR/Cas9 system with a photolinker based on 1-(2-nitrophenyl)-1,2-ethanediol (PL). In cyclic form, such guide RNA is not functional. Upon irradiation by UV-light, such guide RNA is linearized and CRISPR/Cas9 system is activated. Two chemical methods for the cyclization of RNA were tested: Michael reaction (thiol-maleimide condensation) and Cu-catalyzed azide-alkyne cycloaddition (CuAAC, click-chemistry reaction). For this purpose, 5′,3′-modified RNA containing reactive groups were prepared. Results and Discussion: The advantages of the CuAAC reaction for cyclic RNA preparation was demonstrated. Efficiency of cyclic RNA depends on their secondary structure and on the ability of reactive groups to move closer. A series of photocleavable and control non-cleavable cyclic crRNA was obtained. It was shown that cyclic crRNAs guide Cas9 nuclease for plasmid cleavage less efficiently, but linearization of photocleavable cyclic crRNA increases the extent of plasmid cleavage. Conclusions: The developed approach allows to synthesize cyclic photocleavable RNA that can be used for spatiotemporal activation of guide RNA for gene editing. Photoregulation of gene editing will allow minimizing the off-target effects.

Objective: The biochip method allows microscale multiparametric analysis of macromolecular samples using a matrix of immobilized molecular probes. Selection of materials for biochip fabrication, functionalization of the carrier surface, and the method of immobilization of molecular probes are the key tasks of biochip technology. Methods: Methods of obtaining polymer coating from polyvinyl acetate on the surface of polyethylene terephthalate polymer substrates and subsequent production of brush polymers by photoinduced radical copolymerization of acrylate monomers have been studied. Cell matrices with numerous reactive chemical groups for subsequent immobilization of proteins were formed by photolithography method. Methods of activation of carboxyl groups on brush polymers attached to the surface of polyethylene terephthalate were tested. Immobilization of model protein streptavidin labeled with fluorescent dye Su3 was performed to test the method of activation of carboxyl groups. Results and Discussion: A variant of the immunofluorescence assay in a biological microarray format was tested on the model “streptavidin–biotinylated immunoglobulin.” Conclusions: Streptavidin immobilized in brush polymer cells retains functionality and spatial accessibility for binding to biotinylated immunoglobulin and subsequent manifestation by antibodies fluorescently labeled with Cy5 dye, which opens prospects for the use of biological microarrays with brush polymer cells on polyethylene terephthalate substrates for immunofluorescence analysis of various protein targets.

Coumarins are the natural products which are characterized as 1,2-benzopyrones. The discovery of coumarins is done with enlarged chemical space through many synthetic course of action. They are found in many plants such as cinnamon, tonka beans, and sweet clover. Cassia cinnamon has the highest amount of coumarin whereas Ceylon cinnamon has the lowest. Many biological activities and applications of coumarins are attributed to their capacity to engage in non-covalent interactions with numerous enzymes and receptors found in living organisms. Some of the pharmacological properties are anticancer, anticoagulant, antifungal, antiviral, antitubercular, antioxidant, anti-inflammatory, antidiabetic, antibacteria, antihypertensive, antihyperglycemic, anticonvulsant, antiparasitic, antineurodegenerative, etc. A review has been carried out based on various pharmacological activities containing Coumarin derivatives to rationalize the activities based on the structural variations. Coumarin derivatives have been attracting increasing interest for their usefulness and excellent contribution in the prevention, curing, and treatment of the diseases, growth modulation, cell growth and regulation of immune response.

Objective: To screen the synthesized analogues for their in vitro DPPH free radical scavenging activity. Due to their high efficacy and inexpensiveness compared to natural antioxidants, synthetic antioxidants are frequently used. The current work is primarily concerned with investigating the free radical scavenging activity of derivatives of thiobarbituric acid, based on the findings of the literature review. Methods: A series of N,N-diethylthiobarbiturates (I–XVII) were synthesized, and screened for their DPPH radical scavenging activity. Results and discussion: Limited structure-activity relationship has been established on the basis of different substituents and their varying positions. These synthetic compounds showed varying degree of inhibition in the range of IC₅₀ values 20.28 ± 0.15 to 286.19 ± 0.16 μM. Limited structure-activity relationship was revealed that hydroxyl containing compounds (V) (IC₅₀ = 20.28 ± 0.15 μM), (IV) (IC₅₀ = 22.89 ± 0.19 μM), and (I) (IC₅₀ = 26.34 ± 0.03 μM) showed comparable free radical scavenging activities with standard quercetin (IC₅₀ = 16.96 ± 0.14 μM). Conclusions: The study indicates that N,N-diethylthiobarbiturate derivatives have the potential to be synthetic antioxidants since they have strong DPPH radical scavenging action. Additionally, molecules with hydroxyl substituting demonstrate efficacy that is comparable to that of the natural antioxidant quercetin.

Objective: To synthesize bis-Schiff bases bearing thiobarbituric acid and to screen their anti-urease inhibitory potential. Methods: In this study, 1,3-dimethylbarbituric acid derivatives were synthesized by a four-step process. Using K₂CO₃, 2,4-dihydroxy benzaldehyde and chloro ethyl acetate were esterified in DMF in the first step under reflux condition. The reaction was then carried out by combining the esterified aldehyde with 1,3-dimethylbarbituric acid at room temperature for about an 1 h. Hydrazine hydrate was then mixed with compound (II) in ethanol solvent with acetic acid acting as catalyst. Finally, substituted aromatic aldehydes were treated with bis-hydrazide (III) using ethanol and acetic acid as a catalyst. Results: The newly synthesized compounds were screened for their urease inhibition (in vitro). Four analogs, including (IIIj) (IC₅₀ = 15.22 ± 0.49 μM), (IIIg) (IC₅₀ = 16.05 ± 0.16 μM), (IIIa) (IC₅₀ = 16.29 ± 0.73 μM), and (IIIb) (IC₅₀ = 21.17 ± 0.21 μM) were found most powerful inhibitors than standard thiourea (IC₅₀ = 22.80 ± 2.20 μM). The urease inhibition was also seen in compound (IIIi), (IIIc), (IIIh), (IIIe), (IIId), and (IIIf) however it was less from standard. The structure stability and chemical reactivity of the compounds were checked by density functional theory (DFT) method. Furthermore, the molecular docking simulation was performed to check the protein (urease) and ligand interactions and binding affinities by using AutoDock Vina. Conclusions: The synthesized derivatives attributed temendous potential against urease enzyme. Compound (IIIj) was found as the most potent anti-urease agent. Additional research including taxicological and in vivo is necessary to know the safety, effectivness and mechanism of action of these potent molecules.

Objective: The main objective of this work is to synthesize thiobarbituric acid based bis-Schiff base derivatives and to evaluate their ability to inhibit urease enzyme and DPPH free radical scavenging potential. Methods: Thiobarbituric acid derived bis-Schiff bases (IIIa–IIIi) were synthesized by treating 2,4-dihydroxybenzaldehyde and the starting moiety 1,3-diethyl-2-thiobarbituric acid in ethanol through refluxed followed by treating chloro ethyl acetate in DMF solvent. Subsequently, hydrazine hydrate was added to compound (II), yielding bis-hydrazide in better yield, which was further reacted via refluxed with benzaldehydes in ethanol, catalyzed by acetic acid to yield compounds (IIIa–IIIi) in excellent yields. Results: The resulting compounds were tested to inhibit urease enzyme and DPPH free radical scavenging activity. Among the series, compound (IIId) (IC₅₀ = 16.11 ± 0.92 µM), (IIIc) (IC₅₀ = 19.11 ± 0.55 µM), and (IIIf) (IC₅₀ = 21.01 ± 1.42 µM) were found as promising lead urease inhibitors, stronger than the standard thiourea (IC₅₀ = 21.15 ± 0.32 µM). Moreover, compound (IIIa) (IC₅₀ = 40.21 ± 0.12 µM) was found as the excellent antioxidant agent comparing it with the standard ascorbic acid. Molecular docking study was performed to analyze the most potent compounds against urease enzyme. The results also shows that all compounds had good ADME properties there was no violation found in compounds ranges all are under druglikness criteria. Additional research combining in vivo, toxicological, and computational analyses can offer thorough understandings of the effectiveness, safety, and fundamental mechanisms of action of these potentially beneficial antioxidant substances. Conclusions: These compounds showed tremendous potential as DPPH free radical scavengers and urease enzyme inhibitors. Compound (IIId) demonstrated the greatest suppression of urease enzyme activity, however compound (IIIa) displayed superior antioxidant effects. Additional research, incorporating in vivo, toxicological, and computational examinations, is necessary to thoroughly assess the effectiveness, safety, and fundamental mechanisms of action of these intriguing antioxidant molecules.

Gelatins are formed during processing of animal connective tissues (primarily collagens) and, from a biochemical point of view, are polypeptide products. In the case of the commercial gelatins the majority, on 52.5%, is made from the bovine skin and bones, on 46.0%—from porcine skin, and only 1.5%—from other animal tissues. At the beginning of the 21st century, the bulk of commercial gelatins are used in food industry, about a third in the medical sector, and only about 6% in technical or other industrial applications. Currently, trends toward a healthy lifestyle have intensified, which, along with the religious and cultural traditions of many countries, encourages scientists to look for gelatin sources not related to mammals but close to them in physicochemical and functional characteristics. Therefore, recently a tendency has emerged for a decline in the huge production of gelatins from mammals (cattle and pigs), although not significant compared with the relative increase in the production of gelatins from by-products and waste from industrial poultry farming. Moreover, over the past decades, global poultry meat production has increased by more than a third. It was shown that bovine and porcine skin gelatins have optimal amino acid (AA) compositions for their applications. Of course, the AA compositions of porcine and bovine gelatins obtained under different technological conditions may vary significantly. However, in general, these differences are not critical and, therefore, sometimes gelatins are obtained from mixed animal waste. Recently, in Russia, a composition of protein ingredients from porcine and bovine skin hydrolysates with the addition of dried blood plasma has been developed, which had a much better AA composition than traditional gelatins, and this suggested increased biological and nutritional values of the developed product. In addition, various authors found that some specific peptides improved a number of parameters and biological properties of gelatins from mixed animal waste. Thus, new compositions with an optimal AA composition and improved nutritional and functional properties are being actively developed on the basis of known gelatins. The present review provides a detailed description of the main studies on the AA composition of gelatins and its relationship with the key biochemical and technological indicators of gelatin-based materials.

Objective: ATP-dependent Lon proteases are key players in the quality control system of cellular proteins. The Lon family includes three main subfamilies (A, B, and C), whose representatives are common in bacteria, eukaryotes, and archaea. Recently, enzymes that potentially form a new “hybrid” subfamily LonBA have been discovered in bacteria of the Bacilli and Clostridia classes. This study aims to characterize the structure of LonBA proteases and elucidate their features by comparison with classical LonA and LonB proteases. Methods: Bioinformatics analysis methods and approaches were used to comparatively characterize Lon proteases of different subfamilies. Results and Discussion: Analysis of sequences of the common pool of Firmiqutes’ Lons showed that they contain both classical LonA and “hybrid” LonBA proteases. The ATPase component of the latters is similar to the ATPase fragment of LonB proteases, while the catalytic P domain is similar to the P domain of LonA proteases. Degrees of similarity of different structural fragments of LonBAs were estimated. Groups of short and long LonBA proteases were identified. Sources of short-LonBAs are both bacilli and clostridia, but long ones—only clostridia. Conclusions: The new subfamily of LonBA proteases was shown to consist of two communities of enzymes that differ in the structure of their N-terminal fragments and protease domains.

Objective: The β-pore-forming toxins hemolysin II (HlyII) and cytotoxin K2 (CytK2) are important pathogenic factors of the opportunistic bacterium Bacillus cereus and are secreted as monomers that can oligomerize in the presence of a target cell to form transmembrane channels. Analysis of the nucleotide sequence of HlyII and CytK2 suggests the possibility of truncated forms of these proteins that was confirmed by immunochemical, and chromatography-mass spectroscopic analyzes. Methods: HlyII and CytK2 were expressed in recombinant strains of E. coli BL21(DE3) carrying plasmids pET29 which produced the intracellular proteins HlyII and CytK2 from B. cereus ATCC14579^T. In the case of HlyII, fractions containing soluble intracellular proteins, periplasmic proteins, and cellular debris were obtained and analyzed using monoclonal antibodies. The truncated protein forms HlyII and CytK2 were analyzed by chromatography-mass spectrometry analysis. Results and Discussion: Analysis of the primary amino acid sequences of HlyII and CytK2 revealed the presence of potential internal translation initiation sites within the sequence. The presence of the truncated forms of HlyII was confirmed by immunochemical analysis using monoclonal antibodies and by chromatography-mass spectrometry. During expression of the CytK2 protein in E. coli cells, a protein fragment was identified and excised from a polyacrylamide gel, the identity of which with the CytK2 protein was confirmed by chromatography-mass spectrometry analysis. Conclusions: The results obtained confirm the general concept that the bacterial genome is capable of encoding a wider range of proteins than the number of genes it contains. The opportunistic bacterium B. cereus is often the cause of nosocomial infections, one of its key virulent factors are hemolysin II and cytotoxin K2. Using monoclonal antibodies and mass spectrometric analysis it has been shown that these hemolytic enzymes are capable of forming shortened forms.