Biochemistry (Moscow)最新文献

{"title":"Dual-Reporter SARS-CoV-2 Replicon for Screening Viral Polymerase Inhibitors.","authors":"Sergey P Korolev, Aleksandra A Shulepova, Andrey N Anisenko, Simon O Galkin, Liudmila A Alexandrova, Maxim V Jasko, Elena S Matyugina, Mikhail S Novikov, Anastasiya L Khandazhinskaya, Sergey N Kochetkov, Marina B Gottikh","doi":"10.1134/S0006297924110166","DOIUrl":"https://doi.org/10.1134/S0006297924110166","url":null,"abstract":"<p><p>To design a safe cellular system for testing inhibitors targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2, a genetic construct was engineered containing viral cDNA with two blocks of reporter genes while the genes encoding structural S, E, and M proteins were absent. The first reporter block, consisting of Renilla luciferase and green fluorescent protein (Rluc-GFP), was located upstream of the SARS-CoV-2 5'-UTR. Meanwhile, the second block represented by firefly luciferase and red fluorescent protein (Fluc-RFP) was positioned downstream of the transcription regulatory sequence (TRS-N). While the first block of reporter genes can be transcribed by both viral RdRp and cellular polymerases, the second block can only be transcribed by the viral polymerase according to the <i>Coronaviridae</i> discontinuous transcription mechanism. This allowed us to accurately assess effectiveness of the viral RdRp inhibition. To facilitate the search for nucleoside RdRp inhibitors the cell line was obtained expressing herpes simplex virus thymidine kinase, which provides the first stage of nucleoside phosphorylation. When screening the ability of a number of compounds to inhibit catalytic activity of the SARS-CoV-2 RdRp, we discovered antiviral activity of 2'-amino-2'-deoxyadenosine and adenosine-N1-oxide, which exceeded activity of molnupiravir, a therapeutic agent used in the treatment of COVID-19.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"2037-2050"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prenatal Hypoxia Predisposes to Impaired Expression of the <i>chrna4</i> and <i>chrna7</i> Genes in Adult Rats without Affecting Acetylcholine Metabolism during Embryonic Development.","authors":"Oleg V Vetrovoy, Sofiia S Potapova, Viktor A Stratilov, Ekaterina I Tyulkova","doi":"10.1134/S0006297924110099","DOIUrl":"https://doi.org/10.1134/S0006297924110099","url":null,"abstract":"<p><p>Previous studies have shown that the combined effect of fetal hypoxia and maternal stress hormones predetermines tendency to nicotine addiction in adulthood. This study in rats aimed to investigate the effect of prenatal severe hypoxia (PSH) on acetylcholine metabolism in the developing brain, as well as on expression of acetylcholine receptors <i>chrna4</i> and <i>chrna7</i> in both the developing brain and adult brain structures following nicotine consumption. In the developing brain of PSH rats, no changes were found in the activity of choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) or disturbances in the acetylcholine levels. However, decreased <i>chrna4</i> expression was detected on the day 15 of pregnancy, while elevation in the <i>chrna7</i> expression was observed on the days 15 and 16 of embryogenesis. In adulthood, the consequences of PSH were manifested as decreased expression of <i>chrna4</i> in the medial prefrontal cortex (PFC), nucleus accumbens (NAacc), and hypothalamus (HT), decreased expression of <i>chrna7</i> in the PFC and hippocampus (HPC). Whereas, nicotine consumption did not decrease the expression levels of <i>chrna4</i> and <i>chrna7</i> compared to the control group in the adult PSH rats. Thus, prenatal hypoxia predisposes to impaired expression of the <i>chrna4</i> and <i>chrna7</i> genes in adult rats without affecting acetylcholine metabolism during embryonic development.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"1950-1960"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LncRNA Genes of the SNHG Family: Co-methylation and Common Functions in Ovarian Cancer.","authors":"Eleonora A Braga, Elena A Filippova, Leonid A Uroshlev, Svetlana S Lukina, Irina V Pronina, Tatyana P Kazubskaya, Dmitry N Kushlinskiy, Vitaliy I Loginov, Marina V Fridman, Alexey M Burdennyy, Nikolay E Kushlinskii","doi":"10.1134/S0006297924110178","DOIUrl":"https://doi.org/10.1134/S0006297924110178","url":null,"abstract":"<p><p>Genes of the small nucleolar RNA host gene (SNHG) family may participate in oncogenesis through the regulatory functions of encoded long non-coding RNAs (lncRNAs) and by influencing formation of small nucleolar RNAs and ribosome biogenesis. The aim of this work was to evaluate changes in the methylation levels and extent of co-methylation of the SNHG family lncRNA genes (<i>SNHG1</i>, <i>GAS5/SNHG2</i>, <i>SNHG6</i>, <i>SNHG12</i>, <i>SNHG17</i>) in clinical samples of ovarian cancer (OC) as an indication for the similarity of their roles in oncogenesis. Analysis of a representative set of 122 OC samples by quantitative methylation-specific PCR showed a statistically significant (<i>p</i> &lt; 0.01-0.0001) increase in the methylation level of all five studied lncRNA genes. There was also a correlation between the increased methylation levels of <i>GAS5</i>, <i>SNHG6</i>, and <i>SNHG12</i> and OC progression (clinical stage, tumor size, and metastasis), indicating possible functional significance of hypermethylation of these genes. For four genes (<i>SNHG1</i>, <i>GAS5</i>, <i>SNHG6</i>, and <i>SNHG12</i>), a statistically significant pairwise positive correlation of methylation levels (co-methylation) was observed (<i>r</i>_s &gt; 0.35; <i>p</i> ≤ 0.001), which was in agreement with the GEPIA 2.0 data (426 OC samples) showing co-expression of these genes (<i>r</i>_s &gt; 0.5; <i>p</i> &lt; 0.001). The correlation between the expression levels of <i>GAS5</i> and <i>SNHG6</i> was confirmed by RT-qPCR (<i>r</i>_s = 0.46; <i>p</i> = 0.007). Bioinformatics analysis predicted miRNAs common for the <i>SNHG1</i>, <i>GAS5</i>, <i>SNHG6</i>, and <i>SNHG12</i> lncRNA and potentially capable of interacting with one or more of these lncRNAs via competing endogenous RNA mechanism, as well as mRNAs, whose expression might be affected by the studied lncRNAs. We also investigated a possible involvement of genes for these mRNAs in oncogenesis-related processes, such as RNA processing and splicing and epithelial-mesenchymal transition. As a result of this work, four SNHG family lncRNAs with coregulation and joint putative biological functions in the pathogenesis of OC were identified.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"2051-2068"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Intricated <i>pas de deux</i> of Addicted Brain and Body Is Orchestrated by Stress and Neuroplasticity.","authors":"Natalia V Gulyaeva, Danil I Peregud","doi":"10.1134/S0006297924110014","DOIUrl":"https://doi.org/10.1134/S0006297924110014","url":null,"abstract":"<p><p>Dependence on psychoactive substances is a phenomenon that is based on the alterations of common molecular and cellular mechanisms, structures and neuronal networks underlying normal brain functioning and realizing stress response, reinforcement and aversion, learning and memory. As a result, aberrant neuroplasticity states associated with somatic changes are formed, which determine the pathogenesis and symptoms of dependence and at the same time can be considered as targets for the development of therapies for such addictions. An integrative scheme of stress and neuroplastic changes participation in the formation of the vicious circle of substance use disorders based on a holistic approach is presented. This special issue of the journal focuses on the molecular mechanisms of psychoactive substance use disorders.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"1863-1867"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142793934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"(Strept)avidin Binds Glycoconjugates.","authors":"Nadezhda V Shilova, Svetlana M Polyakova, Alexey Yu Nokel, Alexander D Lipatnikov, Elena A Gordeeva, Marina V Lavrenteva, Nicolai V Bovin","doi":"10.1134/S0006297924110142","DOIUrl":"https://doi.org/10.1134/S0006297924110142","url":null,"abstract":"<p><p>Fluorescently labeled and conjugated (strept)avidins are widely used for imaging biotinylated molecules in immunological assays and histochemistry. We showed that besides biotin, these proteins bind glycans, including fragments of mammalian glycoproteins and glycolipids, in particular, ABO blood group antigens, oligolactosamines, and 6-<i>O</i>-sulfated oligosaccharides. This interaction is inhibited in a dose-dependent manner by micromolar concentrations of polymeric, but not monomeric, glycan conjugates (i.e., requires polyvalence). Taking into account the cluster organization of cell glycans (glycoproteins and glycolipids), the ability of (strept)avidins to bind glycans might be a source of errors in the analysis of carbohydrate-containing samples, which can be prevented by avoiding a large excess of (strept)avidin in analytical systems.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"2023-2027"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142793917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purmorphamine Alters Anxiety-Like Behavior and Expression of Hedgehog Cascade Components in Rat Brain after Alcohol Withdrawal.","authors":"Danil I Peregud, Nataliya I Shirobokova, Aleksei A Kvichansky, Mikhail Yu Stepanichev, Natalia V Gulyaeva","doi":"10.1134/S0006297924110087","DOIUrl":"https://doi.org/10.1134/S0006297924110087","url":null,"abstract":"<p><p>Disturbances in the Hedgehog (Hh) signaling play an important role in dysmorphogenesis of bone tissue and central nervous system during prenatal alcohol exposure, which underlies development of fetal alcohol syndrome. The involvement of Hh proteins in the mechanisms of alcohol intake in adults remains obscure. We investigated the role of the Hh cascade in voluntary ethanol drinking and development of anxiety-like behavior (ALB) during early abstinence and assessed changes in the expression of Hh pathway components in different brain regions of male Wistar rats in a model of voluntary alcohol drinking using the intermittent access to 20% ethanol in a two-bottle choice procedure. Purmorphamine (Hh cascade activator and Smoothened receptor agonist) was administered intraperitoneally at a dose of 5 mg/kg body weight prior to 16-20 sessions of alcohol access. Purmorphamine had no effect on the ethanol preference; however, rats exposed to ethanol and receiving purmorphamine demonstrated changes in the ALB during the early abstinence period. Alcohol drinking affected the content of the Sonic hedgehog (Shh) and Patched mRNAs only in the amygdala. In rats exposed to ethanol and receiving purmorphamine, the level of Shh mRNA in the amygdala correlated negatively with the time spent in the open arms of the elevated plus maze. Therefore, we demonstrated for the first time that alterations in the Hh cascade induced by administration of purmorphamine did not affect alcohol preference in voluntary alcohol drinking. It was suggested that Hh cascade is involved in the development of anxiety after alcohol withdrawal through specific changes in the Hh cascade components in the amygdala.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"1938-1949"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vimentin and Desmin Intermediate Filaments Maintain Mitochondrial Membrane Potential.","authors":"Alexander A Dayal, Olga I Parfenteva, Wang Huiying, Anton S Shakhov, Irina B Alieva, Alexander A Minin","doi":"10.1134/S0006297924110154","DOIUrl":"https://doi.org/10.1134/S0006297924110154","url":null,"abstract":"<p><p>Intermediate filaments (IFs) represented by a diverse range of proteins, are one of the three main cytoskeleton components in different types of animal cells. IFs provide mechanical strength to cells and help position the nucleus and organelles in the cell. Desmin is an IF protein typical of muscle cells, while vimentin, which has a similar structure, is expressed in many mesenchymal cells. Both proteins are synthesized during myogenesis and regeneration of damaged muscle tissue and form a mixed IF network. Both desmin and vimentin regulate mitochondrial activity, including mitochondrial localization and maintenance of mitochondrial membrane potential, in the corresponding cells, but the role of mixed IFs in the control of mitochondrial functions remains unclear. To investigate how a simultaneous presence of these proteins affects mitochondrial membrane potential, we used BHK21 cells expressing both vimentin and desmin IFs. Expression of vimentin or desmin individually or both proteins simultaneously was suppressed using gene knockout and/or RNA interference. It was found that disruption of biosynthesis of either vimentin or desmin did not affect the mitochondrial membrane potential, which remained unchanged compared to cells expressing both proteins. Simultaneous abolishment of both proteins resulted in a 20% reduction in the mitochondrial membrane potential, indicating that both vimentin and desmin play an equally important role in its maintenance.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"2028-2036"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of the Circulating Tumor Markers: Perspectives of a Multimodal Liquid Biopsy.","authors":"Ekaterina S Kuligina, Grigoriy A Yanus, Evgeny N Imyanitov","doi":"10.1134/S0006297924110129","DOIUrl":"10.1134/S0006297924110129","url":null,"abstract":"<p><p>Over the past decade, liquid biopsy (LB) has become a routine diagnostic test essential for the treatment of malignant tumors of various localizations. Its capabilities include early diagnosis, molecular genotyping, prognosis, prediction, and monitoring of tumor response. Typically, liquid biopsy involves the extraction of a single type of tumor-derived molecules or cellular elements from blood and subsequent molecular analysis. These elements may include circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), circulating tumor RNA (ctRNA), or contents of extracellular vesicles (exosomes). Despite the technical sophistication of molecular analysis methods for circulating biomarkers, this diagnostic approach has limited relevance. In a significant proportion of cancer patients (ranging from 10 to 50%, depending on the tumor type), none of these analytes can be detected and analyzed, even in the presence of large, progressing neoplastic foci in the body. It seems reasonable to suggest that heterogeneous fractions of the circulating tumor-specific biomarkers complement each other, thus simultaneous analysis of several fractions will not only increase sensitivity of the method but also more accurately characterize and predict the clinical situation. This review examines the possibilities and advantages of applying a combined multiparametric approach to liquid biopsy, which involves testing multiple circulating analytes in a single blood sample.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 11","pages":"1985-1997"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A New Approach for Studying Poly(ADP-Ribose) Polymerase Inhibitors Using Permeabilized Adherent Cells","authors":"Stanislav I. Shram,&nbsp;Tatyana A. Shcherbakova,&nbsp;Tatyana V. Abramova,&nbsp;Maria S. Smirnovskaya,&nbsp;Anastasia I. Balandina,&nbsp;Andrey V. Kulikov,&nbsp;Vytas K. Švedas,&nbsp;Vladimir N. Silnikov,&nbsp;Nikolay F. Myasoedov,&nbsp;Dmitry K. Nilov","doi":"10.1134/S0006297924090086","DOIUrl":"10.1134/S0006297924090086","url":null,"abstract":"<p>Poly(ADP-ribose) polymerase (PARP) inhibitors have been proposed as pharmacological agents in the treatment of various diseases. Recently, factors and mechanisms responsible for regulating PARP catalytic activity have been identified, some of which can significantly influence the effectiveness of inhibitors of this enzyme. In this regard, it is important to develop new models and methods that would reflect the cellular context in which PARP functions. We proposed to use digitonin-permeabilized adherent cells to study poly(ADP-ribosyl)ation reaction (PARylation) in order to maintain the nuclear localization of PARP and to control the concentrations of its substrate (NAD⁺) and tested compounds in the cell. A specific feature of the approach is that before permeabilization, cellular PARP is converted to the DNA-bound state under conditions preventing premature initiation of the PARylation reaction. Experiments were carried out in rat H9c2 cardiomyoblasts. The activity of PARP in permeabilized cells was analyzed by measuring the immunofluorescence of the reaction product poly(ADP-ribose). The method was verified in the studies of PARP inhibition by the classic inhibitor 3-aminobenzamide and a number of new 7-methylguanine derivatives. One of them, 7,8-dimethylguanine, was found to be a stronger inhibitor compared to 7-methylguanine, due to a formation of additional hydrophobic contact with the protein. The proposed approach opens up new prospects for studying the mechanisms of PARP activity regulation in cells and can be used in high-throughput screening of PARP inhibitors.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 9","pages":"1619 - 1630"},"PeriodicalIF":2.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142410811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to: Pharmacological Doses of Thiamine Benefit Patients with the Charcot–Marie–Tooth Neuropathy by Changing Thiamine Diphosphate Levels and Affecting Regulation of Thiamine-Dependent Enzymes","authors":"Artem V. Artiukhov,&nbsp;Olga N. Solovjeva,&nbsp;Natalia V. Balashova,&nbsp;Olga P. Sidorova,&nbsp;Anastasia V. Graf,&nbsp;Victoria I. Bunik","doi":"10.1134/S0006297924090116","DOIUrl":"10.1134/S0006297924090116","url":null,"abstract":"","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"89 9","pages":"1657 - 1657"},"PeriodicalIF":2.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142410812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}