Biochimie最新文献

{"title":"Human prostacyclin and thromboxane synthases: Molecular interactions, regulation, and pharmacology","authors":"Pavel V. Ershov,&nbsp;Evgeniy O. Yablokov,&nbsp;Yuri V. Mezentsev,&nbsp;Alexis S. Ivanov","doi":"10.1016/j.biochi.2025.04.003","DOIUrl":"10.1016/j.biochi.2025.04.003","url":null,"abstract":"<div><div>Prostanoids are lipid mediators of the human body that are involved in the inflammation and platelet aggregation. Prostacyclin is a vasodilator and inhibitor of platelet aggregation, and a product of the enzymatic reaction catalyzed by prostacyclin synthase (PTGIS). Thromboxane is a vasoconstrictor and synthesized by thromboxane synthase (TBXAS1). An imbalance of prostanoids can accompany cardio-/cerebrovascular diseases and cancers. PTGIS and TBXAS1 are clinically relevant membrane-bound enzymes of the multigene family of cytochromes P450 (CYPs), also known as CYP8A1 and CYP5A1, respectively. Particular studies of these functional antagonists will contribute to the elucidation of pathogenic mechanisms. The purpose of this work was to analyze the literature landscape over a period of 2020–2024 in the field of biological, pharmacogenomic, and pharmacological features of PTGIS and TBXAS1 as well as to explore the potential of their regulation at the post-transcriptional and post-translational levels using systems biological analysis. The review discusses recent findings on the novel aspects of both synthases established in gene knockout and overexpression experiments, current preclinical pharmacology, and potential ways of gene expression regulation. Identification of protein-protein interactions and post-translational modifications appear to be the main options for modulating PTGIS and TBXAS1 activity. The microsomal CYPs are known to form complexes with each other and direct interactions of CYP2E1 with both synthases can probably lead to modulation of their activity. Progress in the preclinical development of low molecular weight compounds as inhibitors of TBXAS1 is more prospective than PTGIS that is applied as gene therapy biologicals for <em>in vivo</em> production of prostacyclin due to its noticeable anticancer and vasodilator effects.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 76-88"},"PeriodicalIF":3.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic changes associated with continuous long term in vitro expansion of bone marrow-derived mesenchymal stem cells","authors":"Vitali V. Maldonado ,&nbsp;Hanna Jensen ,&nbsp;C. Lowry Barnes ,&nbsp;Rebekah M. Samsonraj","doi":"10.1016/j.biochi.2025.04.002","DOIUrl":"10.1016/j.biochi.2025.04.002","url":null,"abstract":"<div><div>In vitro expansion of mesenchymal stem cells is necessary to obtain a higher cell number for clinical applications. However, long-term expansion can produce significant phenotypic changes on these cells, decreasing their therapeutic utility. Therefore, understanding the phenotypic changes that long-term expansion triggers in mesenchymal stem cells will allow for better and more consistent cell therapy results. Here, we evaluate the phenotypic changes caused by continuous passaging through colony forming unit-fibroblast assay, senescence beta-galactosidase staining, morphology examination, secretome analysis, surface marker expression, protein quantification, osteogenic and adipogenic differentiation, and CD4⁺ T lymphocyte immunosuppressive potential. Long-term in vitro culture decreases mesenchymal stem cell osteogenic potential and self-renewal, increases cell size, and senescence, but does not consistently affect adipogenic differentiation. Surface marker expression remains similar for positive and negative markers, while secretory phenotype shifts with decreased p14ARF, MMP-3, p21 Waf1/Cip1,ENA-78, GCP-2, GROα, IL-3, IL-7, IL-8, RANTES, TNFβ, and VEGF-A expression, and increased p53, p16 INK4a, MCP-1, and SDF-1 expression. Immunomodulatory potential remains unchanged. These findings can help better understand the phenotypic changes that mesenchymal stem cells undergo while expanded in vitro.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 62-75"},"PeriodicalIF":3.3,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143848046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Divergent ferroptotic pathways in breast cancer cells: IGFBP6-regulated mitochondrial lipid peroxidation under erastin and omega-3 DHA treatment","authors":"Mariia Silkina ,&nbsp;Alexandra Razumovskaya ,&nbsp;Timur Kulagin ,&nbsp;Artem Fatkulin ,&nbsp;Karina Klycheva ,&nbsp;Darya Olkhovik ,&nbsp;Darya Averinskaya ,&nbsp;Oksana Kolodeeva ,&nbsp;Olga Kolodeeva ,&nbsp;Alexander Tonevitsky ,&nbsp;Sergey Nikulin","doi":"10.1016/j.biochi.2025.03.010","DOIUrl":"10.1016/j.biochi.2025.03.010","url":null,"abstract":"<div><div>Breast cancer remains a major challenge and new therapeutic approaches are needed for its treatment. Ferroptosis is considered a promising alternative cell death mechanism to eliminate resistant cancer cells. In previous works, we identified that lower <em>IGFBP6</em> gene expression in tumor tissue corresponds to a worse prognosis for breast cancer patients and, at the same, time makes them more sensitive to ferroptosis. In this study, we further investigated the mechanism of ferroptosis induction in <em>IGFBP6</em> knockdown and control MDA-MB-231 breast cancer cells by the canonical ferroptosis inducer erastin and omega-3 docosahexaenoic acid (DHA). Our results indicate that there is a significant overlap between the mechanisms of action of both of these molecules, as they regulate the same subset of genes, and their action can be inhibited by canonical ferroptosis inhibitors. On the other hand, we also observed significant differences between the effects of erastin and DHA. The most notable of these are the additional activation of apoptosis-related genes by DHA and its minor peroxidation of mitochondrial lipid membranes. Interestingly, our kinetic analysis of ferroptosis induction showed that <em>IGFBP6</em> knockdown cells began to die earlier and could hardly be rescued from erastin-induced ferroptosis by mitochondrial antioxidant SkQ1, in contrast to control cells. Overall, our data suggest that the action of DHA is less dependent on mitochondrial membrane peroxidation during ferroptosis induction, and this molecule can be a promising candidate for the treatment of breast cancer, especially in the case of reduced <em>IGFBP6</em> gene expression in cancer cells.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 48-61"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing amplification efficiency and reducing molecular diagnostic reaction time through rational design of T4 gp32 Variants in recombinase polymerase amplification","authors":"Lin Zhang ,&nbsp;Lvping Wu ,&nbsp;Yiwei Guo ,&nbsp;Enjie Wang ,&nbsp;Jiaxing Zhang ,&nbsp;Shengping You ,&nbsp;Rongxin Su ,&nbsp;Wei Qi","doi":"10.1016/j.biochi.2025.03.008","DOIUrl":"10.1016/j.biochi.2025.03.008","url":null,"abstract":"<div><div>Recombinase polymerase amplification (RPA) is a prominent isothermal nucleic acid amplification method widely applied in molecular diagnostics. The stability and functionality of the single-stranded DNA-binding protein T4 gene 32 (gp32) crucial for pre-synaptic filament formation and D-loop stabilization, play a key role in determining RPA efficiency. In this study, V62C/T80C and Y186R mutants with improved performance were screened by rational disulfide bond construction and virtual saturation mutagenesis, respectively. The structural changes in V62C/T80C and the altered ssDNA-binding capacity in Y186R both contribute to RPA amplification by enhancing the formation of UvsX-ssDNA presynaptic filaments and stabilizing the D-loop structure during homologous recombination, respectively. The two mutants each demonstrated unique advantages in the RPA process. V62C/T80C significantly accelerates the amplification process, reducing the RPA reaction time by 47 %, while Y186R showed a 123 % increase in efficiency across the entire amplification cycle. Totally, this study applied a rational strategy on gp32 optimization, shortening RPA reaction times, enhancing the RPA reaction efficiency, and advancing its application in clinical and point-of-care diagnostics.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 1-9"},"PeriodicalIF":3.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular and biochemical approaches of the trypanothione system in Leishmania spp.: A key player in parasite resistance to antimonial therapy","authors":"Geovane Dias-Lopes ,&nbsp;Sara Maria Xavier Cruz ,&nbsp;Bernardo Acácio Santini Pereira ,&nbsp;Anabel Zabala-Peñafiel ,&nbsp;Carlos Roberto Alves","doi":"10.1016/j.biochi.2025.03.007","DOIUrl":"10.1016/j.biochi.2025.03.007","url":null,"abstract":"<div><div>The trypanothione system is a crucial antioxidant defense mechanism in <em>Leishmania</em> spp. The enzymes involved, including trypanothione reductase (TR), trypanothione synthetase (TS), tryparedoxin (TXN) and tryparedoxin peroxidase (TXNPx) are essential for maintaining the redox balance. This system plays a fundamental role in the biology of <em>Leishmania</em> spp., contributing to parasite resistance against metalloid-based treatments, such as trivalent antimony (Sb³⁺). The mechanisms underlying this resistance, particularly those linked to the functionality of the trypanothione system, have garnered increasing interest. This review prioritizes studies conducted with clinical isolates of <em>Leishmania</em> spp. that evaluated gene expression, protein abundance, and enzyme activity to determine how variations in trypanothione-related mechanisms influence their clinical outcomes. Additionally, complementary strategy involving different protocols to determine intracellular non-protein thiols have further enrich the information into these studies. Notably, the evidence gathered here highlights that studies have focused on only four <em>Leishmania</em> spp. with just one belonging to the <em>Viannia</em> subgenus. Several approaches have been used to determine TR and TXNPx enzyme activity in parasite lysates, supporting their use as tools for studying resistant phenotypes. Additionally, the assessment of TR, TXNPx and TS activities has been applied in kinetic studies for screening of inhibitor compounds. The functional insights presented herein may aid in elucidating the basis of parasite resistance and guide the development of more effective therapeutic strategies against leishmaniasis in its different clinical forms.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 40-47"},"PeriodicalIF":3.3,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glutathionylation and metabolic dysfunction-associated steatotic liver disease","authors":"Zhe Jiang ,&nbsp;Lin Chen ,&nbsp;Xiaobing Dou","doi":"10.1016/j.biochi.2025.03.006","DOIUrl":"10.1016/j.biochi.2025.03.006","url":null,"abstract":"","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leishmania (Viannia) braziliensis Thor strain and subpopulations Thor03, Thor10, and Thor22 have differences in the surface membrane proteases activity profile","authors":"Fatemeh Farshchi ,&nbsp;Geovane Dias-Lopes ,&nbsp;Luzia Monteiro de Castro Cortes ,&nbsp;Léa Cysne-Finkelstein ,&nbsp;Franklin Souza-Silva ,&nbsp;Carlos Roberto Alves","doi":"10.1016/j.biochi.2025.03.005","DOIUrl":"10.1016/j.biochi.2025.03.005","url":null,"abstract":"<div><div>The <em>Leishmania (Viannia) braziliensis</em> Thor strain is composed of subpopulations with distinct biological features, as differences of the virulence profile <em>in vitro</em> and <em>in vivo</em> in murine model. As the surface of these parasites is the first contact with the host, this study assesses comparative approaches of surface membrane proteases of promastigotes and axenic amastigotes of <em>L. (V.) braziliensis</em> Thor strain and Thor03, Thor10, and Thor22 subpopulations, accessing differential profiles among these parasites. Here is explored the phospholipase C (PLC) property as a pivotal tool to selectively recover surface proteases of these parasites. The treatment of parasites with PLC yielded protein fractions with metalloprotease, cysteine protease, and serine protease activities, which were detectable by gelatin-SDS-PAGE and fluorogenic substrates and specific inhibitors, showing distinct profiles from both promastigotes and axenic amastigotes of the Thor strain, Thor03, Thor10, and Thor22 subpopulations. Data of protease activity quantitative in solution show metalloprotease as the highest activity, followed by cysteine protease and serine protease onto the surface of promastigotes and axenic amastigotes. The biological significance of these findings points to the potential of the Thor strain, helped by respective subpopulations, to adapt to hosts, as well as reinforcing the importance of this class of enzyme in the first hours of infection.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico activity and effect of synthetic chalcones on Candida albicans and Candida tropicalis biofilms","authors":"Antonia Thassya Lucas dos Santos ,&nbsp;Maria Audilene de Freitas ,&nbsp;Maria Lucilene Queiroz da Silva ,&nbsp;Francildo dos Santos Silva ,&nbsp;Andressa Guilhermino dos Santos ,&nbsp;Aparecida Vitória Silva Menêses ,&nbsp;Naiza Saraiva Farias ,&nbsp;Joara Nályda Pereira Carneiro ,&nbsp;Victor Juno Alencar Fonseca ,&nbsp;Hélcio Silva dos Santos ,&nbsp;Francisco Rogenio da Silva Mendes ,&nbsp;Jacilene Silva ,&nbsp;Márcia Machado Marinho ,&nbsp;Emmanuel Silva Marinho ,&nbsp;Henrique Douglas Melo Coutinho ,&nbsp;Maria Flaviana Bezerra Morais-Braga","doi":"10.1016/j.biochi.2025.03.004","DOIUrl":"10.1016/j.biochi.2025.03.004","url":null,"abstract":"<div><div>Biofilm formation is considered one of the most important virulence factors for <em>Candida</em> species, which presents an extracellular matrix of polymeric substances that limits the passage of antifungals, leading to fungal resistance. Therefore, the present study investigated the biofilm eradication effect of synthetic chalcones against <em>Candida albicans</em> and <em>Candida tropicalis</em>. Molecular docking studies were conducted to verify the mechanism of action of chalcones on <em>Candida</em> species proteins. The biofilm eradication effect was determined using crystal violet methodology to quantify biomass and Thiazolyl blue tetrazolium bromide (MTT) to verify the influence on metabolic activity. A molecular docking study was also carried out with <em>Candida</em> proteins using the Protein Data Bank repository (<span><span>https://www.rcsb.org/</span><svg><path></path></svg></span>) and Autodocktools™ software. The results showed that (1E,4E)-1,5-diphenylpenta-1,4-dien-3-one (DB-Acetone), (1E,3E,6E,8E)-1,9-diphenylnona-1,3,6,8-tetraen-5-one (DB-CNM), and (1E,4E)-1,5-bis(4-methoxyphenyl)penta-1,4-dien-3-one (DB-Anisal) were able to eradicate the biomass of <em>C. albicans</em> CA INCQS 40006 (ATCC 10231), while fluconazole only reduced the biomass at the three tested concentrations (IC₅₀, IC₅₀ × 10, and IC₅₀ × 20) against <em>C. tropicalis</em> CT INCQS 40042 (ATCC 13803). Both chalcones and fluconazole successfully reduced metabolic activity across all tested strains. The molecular docking study concluded that DB-Acetone, DB-Anisal, and DB-CNM exhibited significant affinity energy values toward the binding sites of <em>C. albicans</em> and <em>C. tropicalis</em>. It is concluded that the synthetic chalcones showed promising results in inhibiting <em>Candida</em> spp. biofilm, demonstrating efficacy in reducing biomass as well as metabolic activity.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"234 ","pages":"Pages 29-39"},"PeriodicalIF":3.3,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cloning, Expression, Characterization and in silico studies of l-asparaginase from Vibrio sp. (GBPx3)","authors":"Sareh sadat Mousavi Natanzi ,&nbsp;Sedigheh Asad ,&nbsp;Hossein Mahboudi ,&nbsp;Solat Eslami","doi":"10.1016/j.biochi.2025.03.003","DOIUrl":"10.1016/j.biochi.2025.03.003","url":null,"abstract":"<div><div><span>l</span>-asparaginase is a critical therapeutic enzyme for treating acute lymphoblastic leukemia (ALL), a common childhood malignancy. In this study, the <span>l</span>-asparaginase coding sequence from halophilic <em>Vibrio</em> sp. (GBPx3) was cloned, expressed in <em>Escherichia coli</em>, and characterized. The enzyme exhibited a molecular weight of 39.2 kDa and demonstrated a <em>K</em>_<em>m</em> of 4.517 mM, <em>k</em>_<em>cat</em> of 2.88 1/s, and <em>V</em>_<em>max</em> of 0.1055 μmol/min, reflecting high specificity for <span>l</span>-asparagine and minimal activity (0.4 %) toward <span>l</span>-glutamine. Optimal activity was observed at physiological conditions (37 °C, pH 7.5 and 125–150 mM NaCl), consistent with human serum osmolality. The half-life of the enzyme was 2.64 h in human serum at 37 °C that is longer than the half-life reported for <em>E. coli</em> <span>l</span>-asparaginase. Additionally, the enzyme had no toxic impact on human umbilical vein endothelial cells (HUVEC) and human erythrocytes. The recombinant <span>l</span>-asparaginase was predicted to be 29.3 % helix, 35.6 % turns, and 35.1 % random by circular dichroism spectroscopy. AlphaFold predicted a 3D structure with promising validation scores. The molecular docking study showed that Thr14, Ser60, Thr91, and Asp92 are putative active site residues, with a negative binding energy of −4.5 kJ/mol for the substrate-enzyme interaction. The enzyme's low immunogenicity, high serum stability, and reduced glutaminase activity highlight its potential as a safer therapeutic alternative. Future experiments and protein engineering studies are needed to explore enzyme's <em>in vivo</em> efficacy and improve its clinical effectiveness.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"233 ","pages":"Pages 122-131"},"PeriodicalIF":3.3,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inside front cover-EDB","authors":"","doi":"10.1016/S0300-9084(25)00047-1","DOIUrl":"10.1016/S0300-9084(25)00047-1","url":null,"abstract":"","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"231 ","pages":"Page IFC"},"PeriodicalIF":3.3,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143591894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}