Biomolecules

23 pages, 3304 KB

Open AccessArticle

Fingolimod Improves Anxiety-like Behavior and Modulates Sphingosine-1-Phosphate Receptors Gene Expression in a Diabetic Mouse Model

by Przemysław Leonard Wencel, Kamilla Blecharz-Klin, Agnieszka Piechal, Justyna Pyrzanowska, Dagmara Mirowska-Guzel and Robert Piotr Strosznajder

Biomolecules 2025, 15(11), 1485; https://doi.org/10.3390/biom15111485 (registering DOI) - 22 Oct 2025

Abstract

Background: Type 2 diabetes mellitus (T2DM) is a rapidly expanding worldwide health issue associated with impairments in memory and executive functions. The bioactive sphingolipid sphingosine-1-phosphate (S1P) regulates cell death/survival and the inflammatory response by acting on S1P receptors (S1PRs). Unfortunately, the role of [...] Read more.

Background: Type 2 diabetes mellitus (T2DM) is a rapidly expanding worldwide health issue associated with impairments in memory and executive functions. The bioactive sphingolipid sphingosine-1-phosphate (S1P) regulates cell death/survival and the inflammatory response by acting on S1P receptors (S1PRs). Unfortunately, the role of S1PRs signaling in the T2DM brain remains elusive. Methods: The effect of fingolimod (FTY720, S1PRs modulator) on the behavior and expression profile of genes encoding S1PRs, sphingosine kinases (SPHK1 and 2), glucose transporters, proteins engaged in insulin signaling, sirtuin 1 (SIRT1), and proinflammatory cytokines in the brain cortex and hippocampus of diabetic mice was examined. Results: We observed a significant reduction in S1pr1, Sirt1, and insulin-like growth factor-1 (Igf1) gene expression that was accompanied by elevation of Sphk2, S1pr3, Il6, and Tnf in T2DM mice. Moreover, animals showed anxiety-like behavior and memory deficits. Fingolimod administration recovered downregulated S1pr1, Sirt1, and Igf1 expression and upregulated Slc2a4 (GLUT-4) and Ide (insulin-degrading enzyme). Furthermore, FTY720 reduced the elevated expression of Il6 and Tnf. Fingolimod also exerted an anxiolytic effect in T2DM. Conclusions: Results indicate an important role of S1PR modulation in T2DM. Moreover, fingolimod affected mRNA levels of proteins engaged in glucose metabolism/insulin signaling and improved the behavior of diabetic mice. Full article

(This article belongs to the Section Molecular Biology)

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20 pages, 2934 KB

Open AccessArticle

Protective Effects and Potential Mechanisms of D-Aspartate on Testicular Damage Induced by Polystyrene Microplastics

by Sara Falvo, Giulia Grillo, Imed Messaoudi, Nada Fradi, Gabriella Chieffi Baccari, Maria Maddalena Di Fiore, Alessandra Biasi, Maria Rosaria Ambruosi, Alessandra Santillo and Massimo Venditti

Biomolecules 2025, 15(11), 1484; https://doi.org/10.3390/biom15111484 - 22 Oct 2025

Abstract

Polystyrene Microplastics (PS-MPs) affect testicular activity, as evidenced by increased oxidative stress, apoptosis, and autophagy activation, impairing steroidogenesis and spermatogenesis. The present study investigates, for the first time in vivo, the potential protective effect of D-aspartate (D-Asp) against PS-MPs-induced damage on the testicular [...] Read more.

Polystyrene Microplastics (PS-MPs) affect testicular activity, as evidenced by increased oxidative stress, apoptosis, and autophagy activation, impairing steroidogenesis and spermatogenesis. The present study investigates, for the first time in vivo, the potential protective effect of D-aspartate (D-Asp) against PS-MPs-induced damage on the testicular function of adult rats. D-Asp, well-known stimulator of testosterone biosynthesis and spermatogenesis progression, possesses pharmacological properties, including antioxidant and anti-apoptotic ones. The results showed that PS-MP’s adverse effects on testicular activity were reversed by D-Asp treatment. Mechanistically, D-Asp inhibited testicular oxidative stress by modulating the protein levels of CAT, SOD1, SOD2, and 4-HNE; affecting TBARS levels; and reducing apoptosis, as suggested by CYT C analysis and a TUNEL assay. Furthermore, D-Asp administration mitigated PS-MPs-induced autophagy activation by modulating the expression of LC3BI, LC3BII, and p62 proteins. Finally, the amino acid counteracts PS-MPs damage on steroidogenesis and spermatogenesis by restoring normal levels of steroidogenic (StAR, 3β-HSD, and 17β-HSD) and spermatogenic (PCNA and SYCP3) markers. This study encourages further research to understand the potential value of the amino acid in improving human testicular health and male fertility. Full article

(This article belongs to the Section Biological Factors)

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26 pages, 4441 KB

Open AccessArticle

Rapid Biochemical Analysis of Postmortem Serum and Myocardial Homogenates—An Exploratory Study

by Niki Sarri, Henrik Druid, Ali-Reza Rezaie, Klaske Osinga, Nargis Sultana and Kanar Alkass

Biomolecules 2025, 15(10), 1483; https://doi.org/10.3390/biom15101483 - 21 Oct 2025

Abstract

Postmortem diagnosis of sudden cardiac death (SCD) may escape detection due to the absence of thrombi and slow development of structural and immunohistochemical changes. Therefore, this study explores the possibility of analyzing relevant clinical chemistry biomarkers in myocardial homogenates and serum. Following an [...] Read more.

Postmortem diagnosis of sudden cardiac death (SCD) may escape detection due to the absence of thrombi and slow development of structural and immunohistochemical changes. Therefore, this study explores the possibility of analyzing relevant clinical chemistry biomarkers in myocardial homogenates and serum. Following an initial pilot study, myocardial samples from 113 autopsy cases were homogenized with distilled water, T-PER or 2M urea. Aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatine kinase (CK-MB), lactate dehydrogenase (LDH), orosomucoid and total protein were analyzed with an IndikoPlus and a subset was also analyzed with a Roche Cobas 8000 c701 analyzer, which also provided results for cardiac Troponin T, myoglobin and NT-proBNP. Although the yields varied with different extraction buffers depending on the analyte, distilled water was often as effective as T-PER and 2M urea extraction for most analytes. Biomarker levels were consistently higher in the myocardial homogenates than in serum. Proteomic profiling on a subset confirmed higher concentrations of the cardiac markers in the tissue samples than in serum. Finally, we investigated whether selected markers could support the diagnosis of acute cardiac disease by. classifying cases as sudden cardiac death (SCD) or controls. There was no significant difference in serum concentrations of the selected biomarkers between SCD cases and controls, whereas a significant loss of several markers was observed in SCD myocardial samples as compared to controls. Hence, our results suggest that analysis of tissue homogenates is likely better for detecting early ischemia, and we show that an in-house benchtop multi-analyzer can provide rapid results to assist the pathologist’s decision-making during autopsy. Full article

(This article belongs to the Special Issue Molecular Biomarkers in Cardiology 2025)

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17 pages, 2192 KB

Open AccessArticle

Arctic Diatoms as a Source of Antibiofilm Compounds: Identification of Methyl 3-Hydroxyoctadecanoate and Pheophorbide a

by Marit Huizer, Renate Osvik, Espen H. Hansen, Terje Vasskog, Jeanette H. Andersen, Kim van Wezel, Hans Christian Eilertsen, Johan Isaksson, Kine Ø. Hansen and Richard A. Ingebrigtsen

Biomolecules 2025, 15(10), 1482; https://doi.org/10.3390/biom15101482 - 21 Oct 2025

Abstract

Marine diatoms are prolific producers of bioactive metabolites, but Arctic species remain underexplored as sources of antibacterial and antibiofilm agents. Here, seven species were grown in photobioreactors (PBRs) and systematically screened for antibacterial, antibiofilm, and cytotoxic activities. All strains inhibited Gram-positive bacteria, and [...] Read more.

Marine diatoms are prolific producers of bioactive metabolites, but Arctic species remain underexplored as sources of antibacterial and antibiofilm agents. Here, seven species were grown in photobioreactors (PBRs) and systematically screened for antibacterial, antibiofilm, and cytotoxic activities. All strains inhibited Gram-positive bacteria, and four reduced Staphylococcus epidermidis biofilm formation. Porosira glacialis emerged as a lead species, combining potent antibiofilm activity with favourable traits for large-scale cultivation, and no detectable cytotoxicity. Bioactivity-guided fractionation of P. glacialis yielded two antibiofilm compounds: methyl 3-hydroxyoctadecanoate, the first time reported in diatoms and newly associated with antibiofilm bioactivity, and pheophorbide a, a chlorophyll degradation product. Both inhibited S. epidermidis biofilm formation without any observed cytotoxicity. Notably, Cylindrotheca closterium exhibited cultivation-dependent antibiofilm activity, underscoring the importance of growth conditions for metabolite production. These findings highlight the potential of Arctic diatoms as a sustainable source of antibiofilm agents and support further exploration of their metabolites for antimicrobial and industrial applications. Full article

(This article belongs to the Special Issue Recent Advances in Bioactive Compounds from Microalgae)

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24 pages, 3969 KB

Open AccessArticle

Kynurenic Acid Protects Against Myocardial Ischemia/Reperfusion Injury by Activating GPR35 Receptors and Preserving Mitochondrial Structure and Function

by Dóra Nógrádi-Halmi, Barbara Erdélyi-Furka, Dóra Csóré, Éva Plechl, Nóra Igaz, László Juhász, Marietta Zita Poles, Bernát Nógrádi, Roland Patai, Tamás Ferenc Polgár, Mónika Kiricsi, László Vécsei, Renáta Gáspár and Tamás Csont

Biomolecules 2025, 15(10), 1481; https://doi.org/10.3390/biom15101481 - 21 Oct 2025

Abstract

Acute myocardial infarction, often associated with ischemia/reperfusion injury (I/R), is a major healthcare issue ranking among the leading causes of death globally. Although kynurenic acid (KYNA), an endogenous tryptophan metabolite, has been previously shown to protect the cardiac tissue against I/R injury, its [...] Read more.

Acute myocardial infarction, often associated with ischemia/reperfusion injury (I/R), is a major healthcare issue ranking among the leading causes of death globally. Although kynurenic acid (KYNA), an endogenous tryptophan metabolite, has been previously shown to protect the cardiac tissue against I/R injury, its mechanism of action remains unclear. Therefore, here, we examined whether KYNA administration rescues H9c2 cardiac cells exposed to I/R through the preservation of the structural and functional integrity of the mitochondria. In addition, we assessed whether KYNA-derived agonism on G-protein coupled receptor 35 (GPR35) is involved in the protection of cardiac cells against simulated I/R (SI/R)-induced cellular demise. Our results demonstrated that KYNA attenuated the SI/R-induced calcium overload as well as impairments in the mitochondrial ultrastructure. Furthermore, administration of KYNA was shown to reduce mitochondrial superoxide production and preserve mitochondrial function in cells exposed to SI/R. Activation of the GPR35 receptors using an agonist other than KYNA rescued cardiac cells undergoing SI/R, attenuated the apoptotic activity, and improved various parameters of mitochondrial respiration. The administration of a synthetic GPR35 antagonist in parallel with KYNA attenuated the KYNA-induced cytoprotection. Our findings provide evidence that the protective effect of KYNA against SI/R-induced cardiac cell injury involves mitoprotective mechanisms, acting, at least in part, through the activation of GPR35 receptors. Full article

(This article belongs to the Special Issue Bioactive Compounds as Modifiers of Mitochondrial Function)

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20 pages, 4626 KB

Open AccessArticle

Predicting the Impact of Glycosylation on the Structure and Thermostability of Helicobacter pylori Blood Group Binding Adhesin

by Daniel Sijmons, Heber Islas Rios, Benjamin R. Turner, Emma Wanicek, Jessica K. Holien, Anna K. Walduck and Paul A. Ramsland

Biomolecules 2025, 15(10), 1480; https://doi.org/10.3390/biom15101480 - 21 Oct 2025

Abstract

Post-translational modifications (PTMs) are critically important for protein structure and function, with glycosylation being one of the most common forms of PTM. The gastric pathogen Helicobacter pylori has a general glycosylation system, which performs complex glycosylation of lipopolysaccharide, flagella proteins, and outer membrane [...] Read more.

Post-translational modifications (PTMs) are critically important for protein structure and function, with glycosylation being one of the most common forms of PTM. The gastric pathogen Helicobacter pylori has a general glycosylation system, which performs complex glycosylation of lipopolysaccharide, flagella proteins, and outer membrane proteins (OMPs). One of the best-described OMPs of H. pylori is the blood group binding adhesin (BabA), which interacts with the Lewis histo-blood group antigen, Lewis b. The 3D structure for BabA has been determined, and the ligand specifically described. Although BabA is reported to be a glycoprotein, there are limited data examining the effects of glycosylation on the structure and function of this protein. This study examined the folding and thermostability of non-glycosylated recombinant BabA and used computational approaches to predict the effect of glycosylation on the protein, with a focus on its possible heterologous expression in mammalian cells. Three potential O-linked and three potential N-linked glycosylation sites were predicted. Furthermore, the effect of glycan shielding on the solvent-accessible surface area of BabA was examined. Molecular dynamics simulations highlighted local indicators, including root mean square fluctuation and the number of protein-glycan contacts that were affected by glycosylation. Taken together, the findings support a role of glycans in surface shielding and promoting local stabilization in specific areas of the BabA protein. This study helps to strengthen the understanding of the importance of glycosylation and the role it plays in the structure, function, and stability of H. pylori proteins. Full article

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)

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16 pages, 4279 KB

Open AccessArticle

Surfactin Structural Variants Differentially Modulate Plant Immune Responses

by Ning Ding, Hansong Dong, Romain Thomas, Guillaume Gilliard, Jelena Pršić and Marc Ongena

Biomolecules 2025, 15(10), 1479; https://doi.org/10.3390/biom15101479 - 21 Oct 2025

Abstract

Cyclic lipopeptides (CLPs), produced by beneficial rhizobacteria such as Bacillus and Pseudomonas species, are specialized metabolites retaining key functions for the plant protective activity of the producers, which shows their potential as biocontrol agents in agriculture. Beyond their strong antimicrobial properties, CLPs can [...] Read more.

Cyclic lipopeptides (CLPs), produced by beneficial rhizobacteria such as Bacillus and Pseudomonas species, are specialized metabolites retaining key functions for the plant protective activity of the producers, which shows their potential as biocontrol agents in agriculture. Beyond their strong antimicrobial properties, CLPs can act as potent elicitors of plant immunity and systemic resistance. However, the molecular mechanisms underlying these immune-modulatory effects and the role of CLPs’ structural diversity remain poorly understood. Here, we demonstrate that specific structural features of surfactin-type CLPs critically influence their ability to trigger early immune responses in plants, including reactive oxygen species bursts, nitric oxide (NO) production, calcium fluxes, and systemic resistance. In Arabidopsis thaliana roots, we show that surfactin-induced NO generation requires calcium signaling. Moreover, we reveal that contrasting immune effects of CLPs may stem from the ecological lifestyles of their microbial producers, shedding light on the evolutionary basis of plant–microbe interactions. Altogether, our findings underscore the importance of CLP structural variation in shaping plant defense responses and highlight the potential for structure-informed design of next-generation biosourced small molecules with broad-spectrum efficacy as plant protectants. Full article

(This article belongs to the Special Issue Probiotics and Their Metabolites, 2nd Edition)

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17 pages, 1522 KB

Open AccessArticle

Oxidative Stress and Iron Addiction: A Comparative Study of 1321N1 Astrocytoma and T98G Glioblastoma Cells with Differential Expression of L-Cysteine-Metabolizing Enzymes

by Halina Jurkowska, Ewa Jasek-Gajda, Konrad Kaleta, Leszek Rydz, Dominika Szlęzak and Maria Wróbel

Biomolecules 2025, 15(10), 1478; https://doi.org/10.3390/biom15101478 - 20 Oct 2025

Abstract

Gliomas are central nervous system primary tumors that are distinguished by heterogeneity, broad-based infiltration, and metabolic reprogramming that sustains proliferation, invasion, and therapy refractoriness. Oxidative stress—a state of imbalance between the production of reactive oxygen species (ROS) and the antioxidant defense—and disturbed iron [...] Read more.

Gliomas are central nervous system primary tumors that are distinguished by heterogeneity, broad-based infiltration, and metabolic reprogramming that sustains proliferation, invasion, and therapy refractoriness. Oxidative stress—a state of imbalance between the production of reactive oxygen species (ROS) and the antioxidant defense—and disturbed iron metabolism are central drivers of glioma biology. The aim of this study was to evaluate ROS production, sulfane sulfur levels, the expression of proteins with antioxidant properties, such as L-cysteine-metabolizing enzymes (cystathionine β-synthase, CBS; cysteine dioxygenase 1, CDO1; cystathionine γ-lyase, CTH; 3-mercaptopyruvate sulfurtransferase, MPST; thiosulfate sulfurtransferase, TST) and non-enzymatic proteins (p53; transferrin receptor 1, TfR1), in human brain cancer cells differing in malignancy: 1321N1 astrocytoma and T98G glioblastoma. Western blotting analysis demonstrated that the expression of CBS, CDO1, and TfR1 was significantly increased in T98G cells, while CTH, MPST, TST, and p53 were comparably expressed in both cell lines. Quantitative assays revealed that T98G cells harbored significantly higher sulfane sulfur levels and higher numbers of ROS-positive cells compared to 1321N1 cells. Our results suggest that glioblastoma but not astrocytoma cells adapt sulfur and iron metabolism to provide proliferation capacity against chronic oxidative stress. It seems that CBS as well as CDO1 may significantly increase the antioxidant potential of T98G cells. In summary, this study suggests a differing metabolic vulnerability identifiable only in high-grade glioma cells and provides a potential novel molecular target for therapy. Full article

(This article belongs to the Special Issue Cysteine and Selenocysteine in Antioxidant Defense, Protein Synthesis and Signaling Pathways)

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25 pages, 1099 KB

Open AccessReview

Bispecific Antibody and Antibody-Drug Conjugate as Novel Candidates for Treating Pancreatic Ductal Adenocarcinoma

by Hyeryeon Seo, Dabin Go, Se Young Jung, Shinwoo Han, Van Quy Nguyen, Minseok Kwak and Wooram Um

Biomolecules 2025, 15(10), 1477; https://doi.org/10.3390/biom15101477 - 20 Oct 2025

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, characterized by a dense and immunosuppressive tumor microenvironment. With the limited actions of drugs and conventional monovalent antibodies, the success of existing cancer therapies is restricted so far. Recently, bispecific antibodies (BsAbs) [...] Read more.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, characterized by a dense and immunosuppressive tumor microenvironment. With the limited actions of drugs and conventional monovalent antibodies, the success of existing cancer therapies is restricted so far. Recently, bispecific antibodies (BsAbs) have emerged as a promising therapeutic platform, capable of overcoming the limitations of current PDAC treatments by engaging T cells and delivering drugs to multiple targets in a selective manner. Furthermore, the recruitment of additional payloads expands their therapeutic potential, offering more selective drug delivery and presenting new possibilities for treating PDAC. However, a limited number of relevant studies and a lack of comprehensive research have hindered trials for the development of BsAbs and bispecific antibody-drug conjugates (BsADCs) in PDAC therapeutics. This review aims to provide the characteristics of BsAbs and BsADCs and their recent applications in PDAC treatment. Additionally, frequent targets of PDAC treatments will be discussed to suggest how to design BsAbs and BsADCs for PDAC treatments. Full article

(This article belongs to the Special Issue Advances in Nano-Based Drug Delivery Systems)

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18 pages, 1248 KB

Open AccessReview

Multiple Organ Phenotype of Fatigue

by Xiaohua Liu, Zhonghan Zhao, Yuan Zhang, Jun Zou and Lingli Zhang

Biomolecules 2025, 15(10), 1476; https://doi.org/10.3390/biom15101476 - 20 Oct 2025

Abstract

Fatigue is not only a widespread subjective experience but also a complex physiological and pathological state involving multiple organs and systems. Currently, there is no consensus on the definition and classification of fatigue. Based on its causes, this paper categorizes fatigue into sports [...] Read more.

Fatigue is not only a widespread subjective experience but also a complex physiological and pathological state involving multiple organs and systems. Currently, there is no consensus on the definition and classification of fatigue. Based on its causes, this paper categorizes fatigue into sports fatigue, occupational fatigue, and pathological fatigue. It elaborates on the specific manifestations and underlying mechanisms of fatigue in the motor, nervous, cardiovascular, digestive, urinary, endocrine, and reproductive systems, aiming to uncover the intrinsic connections of fatigue phenotypes across different systems. These findings may provide key targets for gene-assisted therapy of fatigue-related complications, thereby establishing a new theoretical foundation for the clinical management of fatigue and related research. Full article

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12 pages, 240 KB

Open AccessReview

Inflammatory Mechanisms in Myocarditis—Recent Therapeutic Strategies

by Stergios Soulaidopoulos, Dimitris Tousoulis, Marios Sagris, Svetlana Aghayan, Konstantinos Platanias, Alexios Giannakodimos, Emilia Lazarou, Konstantinos Tsioufis and George Lazaros

Biomolecules 2025, 15(10), 1475; https://doi.org/10.3390/biom15101475 - 20 Oct 2025

Abstract

Myocarditis is an inflammatory disease of the heart characterized by a complex interplay between innate and adaptive immune responses. The innate immune system provides first-line defense and includes soluble molecules, including macrophages, neutrophils, dendritic cells, and molecular mediators, but lacks immunological memory. In [...] Read more.

Myocarditis is an inflammatory disease of the heart characterized by a complex interplay between innate and adaptive immune responses. The innate immune system provides first-line defense and includes soluble molecules, including macrophages, neutrophils, dendritic cells, and molecular mediators, but lacks immunological memory. In contrast, the adaptive immune system, via T and B lymphocytes, offers high specificity and long-term memory, which can sometimes target myocardial tissue, causing autoimmune injury. Particularly, acute myocarditis is characterized by dysregulated immune signaling, with cytokines (IL-2, IFN-γ, IL-12, IL-4, IL-10) and chemokines (MCP-1, CXCL4, CXCL10) driving disease progression, while adhesion molecules (ICAM-1, VCAM-1, VAP-1) promote leukocyte trafficking and cardiac inflammation. The balance between pro-inflammatory and regulatory responses determines disease outcomes, ranging from resolution with recovery to fulminant myocarditis or progression to dilated cardiomyopathy. Emerging therapeutic approaches targeting cytokines, chemokines, and adhesion molecules, along with established immunosuppressive treatments, underline the potential for modulating immune responses in myocarditis and, thereby, improving patient outcomes. Full article

(This article belongs to the Special Issue Cellular and Molecular Mechanisms in Cardiopathy and Therapeutic Strategies)

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18 pages, 2287 KB

Open AccessArticle

Metabolomics in the Context of Exercise in Subjects with Multimorbidity: A Pilot Study

by Rebecca Bankamp, Simone Schweda, Nils Janzen, Andreas M. Nieß, Inga Krauß and Barbara Munz

Biomolecules 2025, 15(10), 1474; https://doi.org/10.3390/biom15101474 - 20 Oct 2025

Abstract

Lifestyle-related diseases, such as overweight/obesity, diabetes mellitus type 2 (T2DM), cardiovascular disease, or osteoarthritis, are a major health burden in Western societies. Due to common risk factors, most patients suffer from multimorbidity, i.e., have been diagnosed with more than one of these diseases. [...] Read more.

Lifestyle-related diseases, such as overweight/obesity, diabetes mellitus type 2 (T2DM), cardiovascular disease, or osteoarthritis, are a major health burden in Western societies. Due to common risk factors, most patients suffer from multimorbidity, i.e., have been diagnosed with more than one of these diseases. Physical activity (PA) is known to have a positive effect on all of these diseases; however, little is known about the effects of PA on patients with multimorbidity. In particular, so far, no reliable biomarkers have been found to predict and monitor the effects of PA-based lifestyle intervention programs on these subjects. Employing a metabolomics approach with dried blood spots, we analyzed the concentrations of different metabolites in subjects with multimorbidity over the course of the lifestyle intervention program MultiPill-Exercise. We found increased concentrations of all tested amino acids (AAs), total carnitine (Cx), and short- (C2-C6) and long- (>C12) chain acylcarnitines (ACs) after 12 weeks (t1) and/or 24 weeks (t2) of intervention. When correlating baseline (t0) metabolite concentrations with changes in physiological and clinical parameters, we observed associations of various metabolite concentrations with changes in metabolic and cardiovascular parameters. When analyzing metabolite acute reactions in response to exhaustive exercise (ergometer test), however, few overall changes were observed. Nevertheless, a significant negative correlation was found between the mobilization of medium-chain acylcarnitines (MC-ACs) at t2 and changes in peak power output (PPO) between t0 and t2. Taken together, these data suggest that specific AAs and ACs might be candidate biomarkers to predict and monitor the effects of PA-based lifestyle intervention programs in subjects with multimorbidity, a hypothesis that should be further tested in larger cohorts. Full article

(This article belongs to the Section Molecular Biomarkers)

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18 pages, 1617 KB

Open AccessReview

ZC3H12A: A Critical Mediator of Inflammation, Tumor Immunotherapy, and Metabolic–Immune Crosstalk—Implications for Disease Treatment

by Mingjun Lu, Jingwei Guo, Chenyang Wang, Bingbing Wan and Teng Ma

Biomolecules 2025, 15(10), 1473; https://doi.org/10.3390/biom15101473 - 19 Oct 2025

Abstract

ZC3H12A is a key RNA-binding protein and ribonuclease that plays a central role in negatively regulating inflammation and maintaining immune homeostasis. It does this by degrading the mRNA of multiple inflammatory mediators (such as IL-6 and IL-1β), as well as through its [...] Read more.

ZC3H12A is a key RNA-binding protein and ribonuclease that plays a central role in negatively regulating inflammation and maintaining immune homeostasis. It does this by degrading the mRNA of multiple inflammatory mediators (such as IL-6 and IL-1β), as well as through its deubiquitinating enzyme activity. Not only does it limit excessive immune activation by regulating innate and adaptive immune cells (e.g., macrophages and T cells), but it also exerts bidirectional effects in tumors, acting as an anti-tumor factor to inhibit angiogenesis and oncogenic signal pathways, while promoting tumor progression under specific conditions. In recent years, ZC3H12A has emerged as a critical target for tumor immunotherapy, particularly CAR-T cell therapy. Its knockout significantly enhances T-cell persistence and anti-tumor efficacy, demonstrating broad translational potential. Furthermore, ZC3H12A plays a crucial role in systemic metabolic–immune crosstalk and infectious diseases. This review systematically summarizes the multifunctional roles of ZC3H12A in immune regulation, tumor therapy, metabolic disorders and inflammation-related diseases, with the aim of providing new insights into its potential application in the treatment of human diseases. Full article

(This article belongs to the Section Molecular Medicine)

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23 pages, 996 KB

Open AccessReview

The Role of Preimplantation Genetic Testing for Monogenic Disorders (PGT-M) in Hemoglobinopathy Management—Techniques, Accuracy, and the Balancing of Benefits and Drawbacks

by Rasrawee Chantrasiri, Tawiwan Pantasri, Siriporn Chattipakorn, Nipon Chattipakorn, Sirinart Kumfu and Wirawit Piyamongkol

Biomolecules 2025, 15(10), 1472; https://doi.org/10.3390/biom15101472 - 17 Oct 2025

Abstract

Preimplantation genetic testing for monogenic disorders (PGT-M) is a powerful tool for identifying genetic disorders prior to gestation. For hemoglobinopathies like thalassemias and sickle cell disease, PGT-M offers a preventative strategy to ensure that only embryos deemed genetically healthy are transferred. A comprehensive [...] Read more.

Preimplantation genetic testing for monogenic disorders (PGT-M) is a powerful tool for identifying genetic disorders prior to gestation. For hemoglobinopathies like thalassemias and sickle cell disease, PGT-M offers a preventative strategy to ensure that only embryos deemed genetically healthy are transferred. A comprehensive review of 22 original articles explores and summarizes the existing evidence on PGT-M techniques in hemoglobinopathies. The review focuses on key aspects such as accuracy, benefits, and drawbacks related to various hemoglobinopathies. Given the limited quantity of DNA obtained from an embryo biopsy, whole genome amplification (WGA) is a critical step for amplifying the sample. One of the available methods of WGA, multiple displacement amplification (MDA) is one of the most widely adopted method with acceptable allele drop-out (ADO) rates for hemoglobinopathies compared with traditional methods. Dealing with ADO constitutes a primary technical obstacle in PGT-M. The failure to amplify one allele in single-cell analysis is a major factor limiting the overall diagnostic accuracy of the procedure. To mitigate this issue, PCR-based and next-generation sequencing (NGS)-based approaches are employed. These methods incorporate linkage analysis with genetic markers such as short tandem repeats (STRs) or single-nucleotide polymorphisms (SNPs) to reduce the risk of incorrect interpretations from ADO and enhance the proportion of conclusive results. A future direction for PGT-M that involves the development of non-invasive methods (niPGT) will be included and discussed. Full article

(This article belongs to the Section Molecular Genetics)

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23 pages, 5188 KB

Open AccessReview

Dynamic Executors of Bacterial Signals: Functional Versatility and Regulatory Networks of c-di-GMP Effectors

by Jia Jia, Ge Yun, Bingxin Liu, Xinxin Li, Meiling Jiang, Xinlu Yu, Jing Zhang, Yufei Han, Dan Liu, Junlong Zhao, Yuanyuan Wang and Gukui Chen

Biomolecules 2025, 15(10), 1471; https://doi.org/10.3390/biom15101471 - 17 Oct 2025

Abstract

Cyclic di-GMP (c-di-GMP), a universal second messenger in bacteria, orchestrates a wide array of essential life processes. Its intracellular dynamics are meticulously regulated by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), ensuring precise spatiotemporal control. The functional output of c-di-GMP signaling hinges on effector [...] Read more.

Cyclic di-GMP (c-di-GMP), a universal second messenger in bacteria, orchestrates a wide array of essential life processes. Its intracellular dynamics are meticulously regulated by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), ensuring precise spatiotemporal control. The functional output of c-di-GMP signaling hinges on effector proteins—molecular decoders that translate c-di-GMP signals into specific cellular responses. This review systematically examines diverse classes of c-di-GMP effectors, using several representative bacterial species as model systems, to dissect their structural and mechanistic diversity. Particular emphasis is placed on their pivotal roles in bacterial pathogenicity, antibiotic tolerance, and host–pathogen interactions, offering fresh insights into the regulatory mechanisms underlying c-di-GMP signaling. Full article

(This article belongs to the Section Molecular Biology)

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12 pages, 1651 KB

Open AccessArticle

Engineered N-TIMP2 Variant Specifically Targeting MMP-9 Exhibits Potent Anti-Glioblastoma Activity

by Mark Feldman, Naama Rotenberg and Julia M. Shifman

Biomolecules 2025, 15(10), 1470; https://doi.org/10.3390/biom15101470 - 17 Oct 2025

Abstract

Glioblastoma (GB) is the most aggressive form of brain cancer. However, despite intensive intervention, GB almost invariably recurs due to the highly invasive nature of its tumor cells, which infiltrate surrounding healthy brain tissue, underscoring the urgent need for more effective therapies. One [...] Read more.

Glioblastoma (GB) is the most aggressive form of brain cancer. However, despite intensive intervention, GB almost invariably recurs due to the highly invasive nature of its tumor cells, which infiltrate surrounding healthy brain tissue, underscoring the urgent need for more effective therapies. One such approach could be based on targeting matrix metalloproteinase-9 (MMP-9), an enzyme that plays a crucial role in GB progression and is closely associated with enhanced invasiveness and poor prognosis. Previously, we engineered a potent and selective MMP-9 inhibitor derived from the N-terminal domain of the endogenous tissue inhibitor of metalloproteinases-2 (N-TIMP2). In this study, we evaluate the efficacy and toxicity of this engineered N-TIMP2 variant (REY) in adult GB U251 and normal Vero cells using multiple in vitro assays. Our results demonstrate that REY significantly inhibits colony formation and cell invasion, and markedly reduces spheroid spreading at nanomolar concentrations. Importantly, the engineered variant, which is highly specific for MMP-9, consistently outperforms the wild-type N-TIMP2, which broadly targets multiple MMPs, and exhibits no cytotoxicity toward healthy cells. Together, these findings support MMP-9 as a viable therapeutic target in GB and highlight the potential of our engineered N-TIMP2 variant as a promising candidate for further therapeutic development. Full article

(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)

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11 pages, 779 KB

Open AccessReview

Chemerin in Pulmonary Fibrosis: Advances in Mechanistic and Fundamental Research

by Yongshuai Jiang, Ziyang Li, Zhenghang Huang, Junsheng Dong and Li Qian

Biomolecules 2025, 15(10), 1469; https://doi.org/10.3390/biom15101469 - 17 Oct 2025

Abstract

Pulmonary fibrosis is a progressive interstitial lung disease that involves stimulated growth of fibroblasts, over-deposition of extracellular matrix (ECM), and permanent damage of the lung structure. Among its various forms, idiopathic pulmonary fibrosis (IPF) is the most common and life-threatening type with few [...] Read more.

Pulmonary fibrosis is a progressive interstitial lung disease that involves stimulated growth of fibroblasts, over-deposition of extracellular matrix (ECM), and permanent damage of the lung structure. Among its various forms, idiopathic pulmonary fibrosis (IPF) is the most common and life-threatening type with few treatment options and a poor prognosis. Such obstacles highlight the urgency to find new molecular targets by better understanding the cellular and signaling processes that contribute to the pathogenesis of the disease. Chemerin is an adipokine and chemoattractant protein that has recently come into the limelight as a major controller of immune cell trafficking, inflammation, and tissue remodeling. Its biological activity is mainly mediated by binding to its receptors Chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and C-C chemokine receptor-like 2 (CCRL2), and has been linked to numerous pathological conditions, such as metabolic diseases, cancer, and inflammatory diseases. Emerging data now indicate that chemerin can also be a key factor in the initiation and progression of pulmonary fibrosis. The aim of the review is to overview the existing evidence regarding regulatory processes of chemerin expression, signaling pathways, and effects of this protein in cells in the fibrotic lung microenvironment. Moreover, we will comment on the findings of in vitro and in vivo experiments supporting the possibility of chemerin as a promising molecular target in basic research on pulmonary fibrosis. Full article

(This article belongs to the Section Molecular Medicine)

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28 pages, 3654 KB

Open AccessReview

Proximity Ligation Assay: From a Foundational Principle to a Versatile Platform for Molecular and Translational Research

by Hengxuan Li, Xiangqi Ma, Dawei Shi and Peng Wang

Biomolecules 2025, 15(10), 1468; https://doi.org/10.3390/biom15101468 - 17 Oct 2025

Abstract

The precise analysis of protein interactions in their native cellular context and the sensitive quantification of protein abundance in biological fluids are both fundamental to understanding health and disease. Traditional methods for cellular imaging and biochemical quantification often face limitations in specificity, sensitivity, [...] Read more.

The precise analysis of protein interactions in their native cellular context and the sensitive quantification of protein abundance in biological fluids are both fundamental to understanding health and disease. Traditional methods for cellular imaging and biochemical quantification often face limitations in specificity, sensitivity, or the preservation of spatial information. The proximity ligation assay (PLA) is a versatile technological platform developed to overcome these challenges by converting protein recognition events into amplifiable DNA signals, thereby achieving exceptional sensitivity. This foundational principle has given rise to two major formats: in situ PLA (isPLA) and solution-phase PLA. In basic research, isPLA provides high-resolution visualization of protein–protein interactions (PPIs), post-translational modifications (PTMs), and subcellular architecture directly within fixed cells and tissues. In translational and clinical applications, solution-phase PLA enables the highly sensitive quantification of low-abundance biomarkers in liquid samples, which is critical for diagnostics and prognostics in fields such as oncology, neuroscience, and infectious diseases. This review discusses the foundational principles, development, and diverse applications of PLA platforms. We also highlight significant technological advancements, including the development of high-throughput formats, integration with advanced readouts, and the use of alternative affinity reagents. These innovations continue to transform PLA from a targeted validation method into a powerful and multifaceted platform for both fundamental systems biology and clinical diagnostics. Full article

(This article belongs to the Section Chemical Biology)

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19 pages, 1722 KB

Open AccessReview

Natural Compounds with Antiviral Activity Against Clinically Relevant RNA Viruses: Advances of the Last Decade

by David Mauricio Cañedo-Figueroa, Daniela Nahomi Calderón-Sandate, Jonathan Hernández-Castillo, Manuel Josafat Huerta-Garza, Ximena Hernández-Rodríguez, Manuel Adrián Velázquez-Cervantes, Giovanna Berenice Barrera-Aveleida, Juan Valentin Trujillo-Paez, Flor Itzel Lira-Hernández, Blanca Azucena Marquez-Reyna, Moisés León-Juárez, Ana Cristina García-Herrera, Juan Fidel Osuna-Ramos and Luis Adrián De Jesús-González

Biomolecules 2025, 15(10), 1467; https://doi.org/10.3390/biom15101467 - 16 Oct 2025

Abstract

RNA viruses remain a significant public health concern due to their rapid evolution, genetic variability, and capacity to trigger recurrent epidemics and pandemics. Over the last decade, natural products have gained attention as a valuable source of antiviral candidates, offering structural diversity, accessibility, [...] Read more.

RNA viruses remain a significant public health concern due to their rapid evolution, genetic variability, and capacity to trigger recurrent epidemics and pandemics. Over the last decade, natural products have gained attention as a valuable source of antiviral candidates, offering structural diversity, accessibility, and favorable safety profiles. This review highlights key replication mechanisms of RNA viruses and their associated therapeutic targets, including RNA-dependent RNA polymerase, viral proteases, and structural proteins mediating entry and maturation. We summarize recent advances in the identification of bioactive compounds such as flavonoids, alkaloids, terpenes, lectins, and polysaccharides that exhibit inhibitory activity against clinically relevant pathogens, including the Influenza A virus (IAV), human immunodeficiency viruses (HIV), dengue virus (DENV), Zika virus (ZIKV), and Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Special emphasis is placed on the integration of in silico screening, in vitro validation, and nanotechnology-based delivery systems that address challenges of stability, bioavailability, and specificity. Furthermore, the growing role of artificial intelligence, drug repurposing strategies, and curated antiviral databases is discussed as a means to accelerate therapeutic discovery. Despite persistent limitations in clinical translation and standardization, natural products represent a promising and sustainable platform for the development of next-generation antivirals against RNA viruses. Full article

(This article belongs to the Special Issue Molecular Mechanism and Detection of SARS-CoV-2)

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