


Vol 50, No 6 (2024)
Articles
Member of the international editorial board of the journal "Bioorganic Chemistry" Academician Shavkat Ismailovich Salikhov (on the 80th anniversary of his birth)



Porphyrins as polyfunctional ligands for binding to DNA. Prospects for application
Abstract
The study of the interaction of nucleic acids with ligands is relevant not only from a scientific point of view, but also has high potential practical significance. Complexes of nucleic acids with ligands affect the biochemical functions of the most important carrier of genetic information, which opens up opportunities for treating genetic diseases and controlling the aging of both cells and the organism as a whole. Among the huge variety of potential ligands, porphyrins and related compounds occupy a special place, due to their ability to generate reactive oxygen species under irradiation with light. The photocatalytic properties of porphyrins can be used in the creation of molecular tools for genetic engineering and the treatment of viral and bacterial infections at the genetic level. Modification of porphyrin compounds allows targeting of the ligand to a specific biological target. The review summarizes the literature data describing the processes of complexation of nucleic acids with aromatic ligands, mainly with porphyrins. The influence of the structure of macroheterocyclic compounds on the features of interaction with nucleic acids is analyzed. Promising directions for further research are outlined.



Blood erythrocytes – a biological model for evaluating antioxidant activity of chemical compounds
Abstract
This review presents an analysis of literature, including our own work, on various aspects of using RBC as an in vitro model in the comprehensive evaluation of antioxidant activity of a wide range of natural and synthetic compounds, their mixtures, and plant extracts. The existing practice of using human, laboratory, and domestic animal red blood cells is examined. The characteristics of the most commonly used initiators of oxidative stress in such studies, 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH) and H2O2, as well as the mechanisms underlying the development of the hemolytic process are discussed. A critical analysis of methodological approaches to assessing the level of hemolysis is provided. The review further discusses the evaluation of erythrocyte survival under oxidative stress conditions and the ability of the tested compounds to act as membrane protectors. The text considers the criteria for a comprehensive assessment of erythrocytes, facilitating the study of cellular and molecular mechanisms underlying antioxidant activity of a wide range of substances on a model of oxidative hemolysis of erythrocytes. Traditional methods include assessment of the intensity of membrane lipid peroxidation (LPO) processes through measurement of concentration of products that react with 2-thiobarbituric acid, a s well assessment of relative content of oxidized forms of hemoglobin in erythrocytes. The use of modern fluorescent methods is another promising approach. In particular, the fluorescence of heme degradation products, the decrease in intensity of which can indicate the presence of antioxidant activity in the compounds under investigation, is a sensitive marker of oxidative stress in erythrocytes. Another prominent fluorescent method is the assessment of the level of oxidative stress by measuring the intracellular concentration of ROS in erythrocytes. Analysis of our own and literature data allows us to recommend the method of oxidative hemolysis of erythrocytes as the method to screen newly developed compounds in order to select the most interesting candidates for further in-depth studies. It is appropriate for establishing the structure-activity relationship and developing a strategy for the targeted synthesis of new biologically active compounds combining high hemocompatibility and antioxidant activity, promising for biomedical applications.



Covalent epidermal growth factor receptor (EGFR) inhibitors in targeted therapy of drug-resistant non-small cell lung cancer
Abstract
Non-small cell lung cancer (NSCLC) is the main subtype of lung cancer and is a common cause of cancer-related mortality worldwide. Mutations in the epidermal growth factor receptor (EGFR) gene play a leading role in the pathogenesis of NSCLC, causing its pathological activity. The first generation of EGFR inhibitors, acting reversibly, effectively block the effects of EGFR with activating mutations by benefiting from competition with adenosine triphosphate for binding to the kinase. However, after several months of treatment, a secondary T790M mutation often occurs, causing resistance to subsequent therapy with these drugs. Effective inhibition of EGFR with the T790M mutation was possible due to second-generation inhibitors acting via a covalent mechanism. However, the second generation of covalent inhibitors has received limited use in therapy due to insufficient selectivity for EGFR T790M and a narrow therapeutic window. The discovery of covalent pyrimidine-based inhibitors has led to the emergence of a number of effective and safer third-generation drugs for the treatment of NSCLC with the EGFR T790M mutation. This review contains a brief description of first- and second-generation EGFR inhibitors and a detailed discussion of the main stages in the development of third-generation inhibitors. The main emphasis is placed on the identified “structure–activity” patterns. Data are provided on inhibitors that have received the status of approved drugs for the treatment of NSCLC. Promising directions for the development of novel EGFR inhibitors are indicated.



Vitamin В12 in drug delivery systems
Abstract
Vitamin B12 is a vital biologically active compound for human and is involved in a wide range of metabolic processes. The widespread vitamin B12 deficiency and vitamin’s low penetrating ability into cells determine the urgency of delivery systems development for the design of formulations with improved biopharmaceutical properties. This work provides a brief discussion of the main chemical and biochemical properties of the vitamin B12, as well as considers oral, injectable and transdermal multicomponent dosage forms of vitamin B12 that are aimed at solving the issue. Moreover, the literature analysis of the prospects of using vitamin B12 as an auxiliary component for both passive and active delivery of other drug molecules, for example, peptide nucleic acids and antitumor drugs, is presented. The review describes in detail the types of proposed delivery systems for biologically active compounds, in which vitamin B12 is one of the components.



Synthesis and cytotoxic activity evaluation of maleopimaric and dihydroquinopimaric esters and amides
Abstract
The new 1-, 1,4- and 1,4,20-diethoxyphosphoryl-containing esters were synthesized as a result of interaction of dihydroquinopimaric acid methyl ester hydroxyl derivatives with diethylchlorophosphite, A study of the cytotoxic activity in vitro on 60 cell lines of nine different human tumors of methyl ester of dihydroquinopimaric acid with diethoxyphosphoryl, furan and indole fragments, as well as diterpene amides with linear, heterocyclic and aromatic amines residues showed that diethoxyphosphoryl and benzylamine substituents are of key importance for the manifestation of the cytotoxic effect. Diethoxyphosphoryl derivatives (XIX) and (XVII), and benzylamide (IX) showed cytotoxic activity against one, seven and four cell lines of breast cancer, leukemia, non-small cell lung cancer, melanoma and prostate cancer, respectively. The greatest activity was demonstrated by maleopimaric acid benzylamide (XIII), which effectively inhibited the growth of 19 cell lines of eight cancer types and had a significant cytotoxic effect against all studied leukemia cell lines.



Adaptation of a protocol for the automated solid-phase phosphoramidite synthesis of oligodeoxyribonucleotides for the preparation of their N-unsubstituted phosphoramidate analogues (P-NH2)
Abstract
A new approach to the automated synthesis of N-unsubstituted phosphoramidate oligodeoxyribonucleotides (P-NH2) based on an optimized solid-phase phosphoramidite protocol using the Staudinger reaction has been proposed. The rapid and efficient oxidation of model P(III)-containing phosphite triethers by the organic azide (9H-fluoren-9-yl)methylcarbonylazide (FmocN3) to the corresponding phosphamides –(OPO(OR)(NFmoc))–, where R is a residue of nucleoside or alkyl nature, has been demonstrated. Removal of the alkaline-labile fluorenyl group from the modified internucleoside linkage allows the production of electroneutral, under physiological conditions of pH ~7, N-unsubstituted phosphoramidate (–(OPO(O)(NH2))– or (P-NH2)) residues in the oligonucleotide chain instead of the classical negatively charged phosphodiester (–(OPO(O)(O)(O¯))–) or (P-O)) residues. In optimizing the synthetic protocol, it has been demonstrated that to improve the efficiency of P-NH2-oligonucleotide synthesis, it is necessary to include an additional Fmoc-group cleavage step in the automatic synthesis protocol after each oxidation step of the growing oligomer chain via the Staudinger reaction. An almost complete absence of dependence of the P-NH2-oligonucleotide yield on both the localization of the P-NH2-strand in the chain and the type of dinucleotide fragment being modified was shown. A set of mono- and bis-modified octadeoxyribonucleotides was obtained, and a detailed study of the thermal stability of complementary DNA/DNA complexes under different buffer conditions was performed. It was shown that under high ionic strength conditions (1 M NaCl, pH 7.2), the introduction of a single P-NH2 strand reduced the thermostability of the DNA complex by an average of 1.3°C. When the ionic strength of the solution decreases, the destabilizing effect of the P-NH2-modification decreases significantly, which further confirms the electroneutral status of the introduced phosphoramidate linkage. Thus, we have developed a protocol for the preparation of partially modified oligonucleotide derivatives bearing uncharged but isostructured to native P-O-strands – phosphoramidate residues P-NH2.



Structural analysis of LZTFL1 protein by the principal component analysis method (PCA-seq)
Abstract
The single-nucleotide mutation rs17713054G>A in the promoter region of LZTFL1 (leucine zipper transcription factor like 1) gene is a factor in the severe course of coronavirus infection COVID-19. Computer statistical analysis of the gene by principal component analysis (PCA-seq) revealed the presence of a high correlation between the first principal component of the translated amino acid sequence and eleven amino acid indices of the AAindex database, characterizing the physicochemical and biochemical properties of the protein. The indices BEGF750102, CHOP780209, PALJ810110, GEIM800107, QIAN880121, LEVM780102, PRAM900103 are associated with β-folding parameters. The LZTFL1 protein is part of the Bardet-Biedl Syndrome (BBS) protein complexes that regulate intracellular transport in the ciliated epithelium of the lungs. It is assumed that the presence of β-sheet elements in the structure of the LZTFL1 protein plays an important role in ACE2 receptor-mediated endocytosis, stimulating the rate of angiotensin-converting enzyme 2 recycling and accelerating the delivery of adherented coronavirus SARS-CoV-2 virions into the cell during the initiation of severe acute respiratory syndrome COVID-19.



Inhibition of dipeptidylpeptidase-IV by 2-S-cyanopyrrolidine inhibitors of prolyl endopeptidase
Abstract
Many regulatory neuropeptides contain a large amount of proline residues. The unique proline peptide bond conformation protects these peptides from enzymatic degradation; therefore enzymes cleaving the proline peptide bonds in neuropeptides are of particular interest. The abnormal activity of serine peptidases that cleave peptides at the carboxyl group of proline residues prolyl endopeptidase (PEP) and dipeptidyl peptidase IV (DPP-IV) were observed in patients with anxiety disorders. PEP is involved in the maturation and degradation of neuropeptides and peptide hormones, it also is associated with the regulation of blood pressure and various disorders of the central nervous system. DPP-IV is involved in many physiological processes, in particular in glucose homeostasis in type II diabetes and immunity. When studying the metabolism of the N-acyl derivative of the aminoacyl-2-cyanopyrrolidine PEP inhibitor a decreasing in the activity of DPP-IV at the initial time was detected. This was an unexpected effect observed for inhibitors of the general formula X-Y-2-S-cyanopyrrolidine, where X represents the N-protective group and Y represents the amino acid (any besides glycine and proline). Molecular dynamics simulations of inhibitor complexes with proteases revealed the possibility of PEP inhibitors binding in the DPP-IV active site with hydrogen bonds and hydrophobic interactions that allow linkage of the nitrile group with the catalytic serine residue in the DPP-IV active site. The present study opens the prospect of creating new pharmacologically active ligands of PEP and DPP-IV.



New cationic carbohydrate-containing amphiphiles and liposomes based on them for effective delivery of short nucleic acids into eukaryotic cells
Abstract
New cationic amphiphiles containing lactose or D-mannose residues were synthesized and cationic liposomes with 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) were obtained. The cytotoxicity and transfection activity of new carbohydrate-containing amphiphiles and cationic liposomes against HEK 293, BHK and BHK IR-780 cells were studied. It has been shown that cationic amphiphiles effectively deliver only short fluorescein-labeled oligodeoxyribonucleotide into eukaryotic cells, while cationic liposomes formed by lactose containing amphiphile and DOPE effectively mediate the transport of short oligonucleotide and small interfering RNA and were non-toxic to cells. The resulting cationic amphiphiles can be used for intracellular delivering of nucleic acids both individually and part of cationic liposomes.



The adjuvant effect of benzo(a)pyrene on specific IgE production is linked with the accumulation of germinal center B cells within the spleen and extrafollicular b-cells ativation within the lungs
Abstract
Despite a large number of works focused on the search for the mechanisms of formation of IgE-producing B cells, the question of the relative contribution of germinal centers and extrafollicular foci B cells in this process still remains controversial. Of particular interest is the study of the mechanisms of stimulation of the allergic immune response under the influence of air pollutants. The aim of the work was to study the connection between the adjuvant effect of benzo(a)pyrene (BaP) on the production of specific IgE in a novel low-dose allergy model with changes in the subpopulation composition of B-cells in the tissue of the immunization site and secondary lymphoid organs. Antigen without any stimuli was administrated to one group of BALB/c mice for 9 weeks in a low (0.3 μg) dose. BaP was administrated to another group of mice along with antigens at a dose of 4 ng. B-cell subpopulations were analyzed by flow cytometry. BaP significantly stimulated the production of allergen-specific IgG1 at early (3 weeks) time point, and allergen-specific IgE at late (9 weeks) time point. The aeropollutant increased the content of CD19+CD38–CD95+B220+ germinal center B-cells with the phenotype and their precursors (CD19+CD38+CD95+B220+) with the phenotype in the spleen at early and late time points, but not in the lungs or regional lymph nodes. Under its influence, the content of CD19+CD38–CD95+B220– and CD19+CD38+CD95+B220+ extrafollicular plasmablasts in the spleen at an early time point and in lung tissue at a later time point also increases. In the spleen, BaP increased the content of CD138+CD19–B220+ and CD138+CD19–B220– mature plasma cells, and in regional lymph nodes the content of CD138+CD19+B220– immature plasma cells at a later time point. The adjuvant effect of BaP on the production of specific IgE was largely associated with stimulation of the formation of germinal centers in the spleen and with extrafollicular activation of B cells in lung tissue.



Pyridine derivatives of 3,4-dihydroquinoxalin-2-one and 3,4-dihydro-2H-1,4-benzoxazin-2-one acute toxicity evaluation
Abstract
An acute toxicity test was conducted on derivatives of bis(3,4-dihydroquinoxalin-2-one) and bis(3,4-dihydro-2H-1,4-benzoxazin-2-one) synthesized based on 3,5-diacetyl-2,6-dimethylpyridine by single intraperitoneal injection in guinea pigs. It was found that according to K.K. Sidorov’s classification, one of the pyridine derivatives, bis(3,4-dihydroquinoxalin-2-one), exhibited low toxicity, as evidenced by the absence of lethal outcomes when administered to animals in the range of 100 to 400 µg/kg. However, it was accompanied by signs of neurological disorders regardless of the compound dose, which disappeared within a day. When guinea pigs were inoculated with another pyridine derivative, bis(3,4-dihydro-2H-1,4-benzoxazin-2-one), more pronounced and prolonged intoxication symptoms were observed, including convulsive movements of the hind limbs, decreased mobility, and delayed reaction to stimuli, leading to the death of 33% of subjects at a dose of 100 mg/kg, 66% at a dose of 200 mg/kg, and 100% of animals at a dose of 400 mg/kg. Analysis of hematological and biochemical studies conducted on the 15th day after the administration of the test compounds showed no significant deviations from normal physiological values, despite some individual parameters showing differences compared to the control group. Thus, the acute toxicity parameters of the studied compounds were not the same and were more pronounced in the pyridine derivative bis(3,4-dihydro-2H-1,4-benzoxazin-2-one); however, both compounds can be recommended for subsequent study of antibacterial and antiviral activity in guinea pigs.



Non-agglomerated oligonucleotide-containing nanocomposites based on titanium dioxide nanoparticles
Abstract
Stability and monodispersity are important properties of nanoparticles and nanocomposites that ensure the reliability of their application in biological systems and the reproducibility of results. The preparation of non-agglomerated oligonucleotide-containing nanocomposites based on anatase titanium dioxide nanoparticles (Ans~ODN) is the aim of this work. The immobilization of oligodeoxynucleotides on TiO2 nanoparticles has been studied by the dynamic light scattering and transmission electron microscopy. The antiviral activity of the synthesized samples has been performed on VERO cells infected with herpes simplex virus of the first type. The effect of NaCl on the agglomeration of nanoparticles and nanocomposites in aqueous solutions has been studied. The presence of NaCl leads to agglomeration of nanoparticles and nanocomposites. It has been shown that nanocomposites are formed in an aqueous solution in the absence of NaCl. A comparison of the biological activity of nanocomposites prepared in water and saline solution has been carried out with an example of inhibition of replication of the herpes simplex virus of the first type in the cell culture. The studied nanocomposite, regardless of the preparation method (in water or 0.9% NaCl), inhibited virus replication by 4.5 orders of magnitude when used 1 day after preparation. After 10 days of storage, the activity of the sample prepared in saline solution was two orders of magnitude lower than that of the active sample prepared in water. We have developed the method for the preparation of non-agglomerated oligonucleotide-containing nanocomposites based on anatase nanoparticles and demonstrated their potential use for the study of their biological activity. Unlike nanocomposites prepared in the presence of salt, which lose their efficacy during storage, nanocomposites that are not prone to agglomeration can be obtained in water for future use.



Expression of extracellular fragment of murine PD-L1 and production of antibodies to PD-L1
Abstract
A number of molecules expressed on mammalian cells are involved in the formation of autotolerance. These primarily include CTLA-4/B7 and PD1-PD-L1 signaling pathways. Blockers of these signaling pathways, called checkpoint inhibitors (CPIs) of immunity, are used in the clinic for the treatment of various forms of cancer. Antibodies to CTLA-4 cause systemic toxicity and are approved only for some tumors. Antibodies against PD1 or PD-L1 have been successfully used for the treatment of various forms of cancer and are characterized by low toxicity. However, the response to therapy using CPIs is not always observed. The development of more effective approaches to cancer therapy based on PD1/PD-L1 inhibitors requires additional research. The aim of this work was to express the extracellular part of the murine PD-L1 protein (exPD-L1) and obtain antibodies to PD-L1. The mouse exPD-L1 protein was obtained and characterized in the bacterial expression system. exPD-L1 protein was used to immunize mice in order to produce anti-PD-L1 antibodies. Using hybridomic technology, 5 clones expressing antibodies to exPD-L1 were obtained. Antibodies of the B12 clone were developed in the ascitic fluid of BALB/c mice and purified by affinity chromatography. The ELISA method for purified antibodies showed specific binding to the exPD-L1 protein and the commercial protein of the extracellular part of murine PD-L1. Experiments using flow cytometry and confocal microscopy have shown that the antibodies obtained bind the intracellular form of the PD-L1 protein, unlike commercial antibodies binding the membrane form.


