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Biomolecules
Volume 15
Issue 8
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Biomolecules, Volume 15, Issue 8 (August 2025) – 154 articles

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24 pages, 3590 KiB  
Article
Palmitic Acid Esterification Boosts Epigallocatechin Gallate’s Immunomodulatory Effects in Intestinal Inflammation
by Raúl Domínguez-Perles, Concepción Medrano-Padial, Cristina García-Viguera and Sonia Medina
Biomolecules 2025, 15(8), 1208; https://doi.org/10.3390/biom15081208 - 21 Aug 2025
Abstract
Lipophenols, combining phenolic and lipid moieties in a single molecule, are valuable candidates for providing enhanced bioactive properties with therapeutic potential, including anti-inflammatory functions associated with immune-mediated diseases such as intestinal bowel disease (IBD). Thus, palmitoyl–epigallocatechin gallate (PEGCG), a lipophilic derivative of epigallocatechin [...] Read more.
Lipophenols, combining phenolic and lipid moieties in a single molecule, are valuable candidates for providing enhanced bioactive properties with therapeutic potential, including anti-inflammatory functions associated with immune-mediated diseases such as intestinal bowel disease (IBD). Thus, palmitoyl–epigallocatechin gallate (PEGCG), a lipophilic derivative of epigallocatechin gallate (EGCG), has been highlighted for its enhanced stability in lipid-rich environments and bioavailability due to improved cellular uptake. However, the contribution of lipophilic esterification to PEGCG’s capacity to inhibit inflammation and the development of harmful autoimmune responses remains underexplored. This work uncovered the differential efficiency of EGCG and its palmitoyl derivative in modulating, in vitro, the interleukin profile generated by intestinal epithelium under inflammatory conditions. Therefore, both could attenuate the immune response by lowering macrophage migration and polarisation towards pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes. While the fatty acid moiety gave PEGCG a functional advantage over EGCG in adjusting the interleukin-based response of intestinal epithelium to inflammation—since both of them decreased, to a similar extent, the expression of pro-inflammatory interleukins, namely IL-6, IL-17, IL-18, IL-23, and TNF-α (which lowered by 11.2%, on average)—the former was significantly more efficient in cushioning the increase in IL-1β and IL-12p70 (by 9.2% and 10.4%, respectively). This immune modulation capacity did not significantly impact the migration and expression of costimulatory molecules featuring M1 (CD86+) or M2 (CD206+) phenotypes by THP-1-derived macrophages, for which both bioactive compounds exhibited equivalent efficiency. Nonetheless, the analysis of the pro- and anti-inflammatory interleukins secreted by differentiated macrophages allowed the identification of an advantage for PEGCG, which decreased the expression of the pro-inflammatory immune mediators IL-1β and IL-12p70, IL-23, and TNF-α more efficiently. These results suggest that lipophilisation of phenolic compounds presents exciting potential for extending their application as functional molecules by combining the effects of their polar head with their ability to interfere with membranes, conveyed by their lipophilic tail. In addition, the enhanced reactivity would confer a higher capacity to interact with cellular signalling molecules and thus inhibit or attenuate the immune response, which is of special interest for preventing the onset and severity of immune-mediated pathologies such as IBD. Full article
(This article belongs to the Special Issue Recent Advances in the Enzymatic Synthesis of Bioactive Compounds)
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10 pages, 229 KiB  
Editorial
Effects of Weightlessness on Molecular Changes in Cellular Organisms, Animals and Plants
by Daniela Grimm
Biomolecules 2025, 15(8), 1207; https://doi.org/10.3390/biom15081207 - 21 Aug 2025
Abstract
Space travel is a dream of humankind [...] Full article
(This article belongs to the Special Issue Effects of Weightlessness on Molecular Changes in Cellular Organisms, Animals and Plants)
18 pages, 2240 KiB  
Article
Role of Tpm Isoforms Produced by the TPM4 Gene in the Regulation of Actin Filament Dynamics by Cofilin
by Svetlana G. Roman, Victoria V. Nefedova and Alexander M. Matyushenko
Biomolecules 2025, 15(8), 1206; https://doi.org/10.3390/biom15081206 - 21 Aug 2025
Abstract
The actin cytoskeleton determines a huge number of intracellular processes, as well as maintaining the cell shape, transport, formation of intercellular contacts, etc. The actin cytoskeleton’s function is largely determined by actin-binding proteins. Here, the mutual influence of two actin-binding proteins, cofilin (cof) [...] Read more.
The actin cytoskeleton determines a huge number of intracellular processes, as well as maintaining the cell shape, transport, formation of intercellular contacts, etc. The actin cytoskeleton’s function is largely determined by actin-binding proteins. Here, the mutual influence of two actin-binding proteins, cofilin (cof) and tropomyosin (Tpm), is studied. In the present work, using various biochemical approaches, we reveal the effects of two TPM4 gene-derived isoforms (Tpm4.1 and Tpm4.2) in the presence of cofilin-1 and cofilin-2. The cofilin severing activity was estimated in F-actin and Tpm/F-actin complexes using viscosity measurements and electron microscopy. Both cofilins prompted the disassembly of F-actin filaments with Tpms attached to them, and the Tpm4.2 isoform demonstrated a better protective effect. We also estimated the ability of cofilin-1 and cofilin-2 to displace Tpms from actin filaments by using the co-sedimentation method. Both cofilin isoforms efficiently displaced Tpm4.1 and Tpm4.2 and bound to actin filaments. Both Tpms decreased the initial rate of actin polymerization in the presence of cofilin-1 and cofilin-2. Overall, we can assume that Tpm4.1 and Tpm4.2 do not affect the binding of cofilin to actin filaments, which may be important for cofilin to exhibit its severing activity and lead to the remodeling of the actin cytoskeleton. Full article
(This article belongs to the Section Cellular Biochemistry)
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19 pages, 7031 KiB  
Article
Integrated Multi-Omics Investigation of Gypenosides’ Mechanisms in Lowering Hepatic Cholesterol
by Qin Jiang, Tao Yang, Hao Yang, Yi Chen, Yuan Xiong, Lin Qin, Qianru Zhang, Daopeng Tan, Xingdong Wu, Yongxia Zhao, Jian Xie and Yuqi He
Biomolecules 2025, 15(8), 1205; https://doi.org/10.3390/biom15081205 - 21 Aug 2025
Abstract
(1) Objective: This study aimed to systematically elucidate the molecular mechanisms by which gypenosides (GP), a major active component of Gynostemma pentaphyllum, ameliorate hypercholesterolemia by modulating the hepatic steroidogenesis pathway, and to identify key therapeutic targets. (2) Methods: We established a high-fat [...] Read more.
(1) Objective: This study aimed to systematically elucidate the molecular mechanisms by which gypenosides (GP), a major active component of Gynostemma pentaphyllum, ameliorate hypercholesterolemia by modulating the hepatic steroidogenesis pathway, and to identify key therapeutic targets. (2) Methods: We established a high-fat diet (HFD)-induced hypercholesterolemia (HC) mouse model and performed GP intervention. An integrated multi-omics approach, combining transcriptomics and proteomics, was utilized to comprehensively analyze GP’s effects on the expression of genes and proteins associated with hepatic cholesterol synthesis, transport, and steroid hormone metabolism. (3) Results: HFD induced significant dysregulation, with 48 steroidogenesis pathway-related genes and 35 corresponding proteins exhibiting altered expression in HC mouse livers. GP treatment remarkably reversed these HFD-induced abnormalities, significantly restoring the expression levels of 42 genes and 14 proteins. Multi-omics integration identified seven critical genes/proteins—Cyp3a25, Fdft1, Tm7sf2, Hmgcs1, Fdps, Mvd, and Pmvk—that were consistently and significantly regulated by GP at both transcriptional and translational levels. Furthermore, correlation analyses demonstrated that Cyp3a25 was significantly negatively correlated with serum total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C), whereas Fdft1, Tm7sf2, Hmgcs1, Fdps, Mvd, and Pmvk showed significant positive correlations. (4) Conclusions: GP effectively ameliorates cholesterol dyshomeostasis through a multi-targeted mechanism in the liver. It inhibits endogenous cholesterol synthesis by downregulating key enzymes (Hmgcs1, Fdft1, Pmvk, Mvd, Fdps, Tm7sf2), promotes cholesterol efflux and transport (upregulating Abca1, ApoB), and accelerates steroid hormone metabolism (upregulating Cyp3a11, Cyp3a25). These findings provide robust scientific evidence for the development of GP as a safe and effective novel therapeutic agent for hypercholesterolemia. Full article
(This article belongs to the Special Issue Lipid Signaling in Human Disease)
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16 pages, 2432 KiB  
Article
PInteract: Detecting Aromatic-Involving Motifs in Proteins and Protein-Nucleic Acid Complexes
by Dong Li, Fabrizio Pucci and Marianne Rooman
Biomolecules 2025, 15(8), 1204; https://doi.org/10.3390/biom15081204 - 21 Aug 2025
Abstract
With the recent development of accurate protein structure prediction tools, virtually all protein sequences now have an experimental or a modeled structure. It has therefore become essential to develop fast algorithms capable of detecting non-covalent interactions not only within proteins but also in [...] Read more.
With the recent development of accurate protein structure prediction tools, virtually all protein sequences now have an experimental or a modeled structure. It has therefore become essential to develop fast algorithms capable of detecting non-covalent interactions not only within proteins but also in protein-protein, protein-DNA, protein-RNA, and protein-ligand complexes. Interactions involving aromatic compounds, particularly their π molecular orbitals, hold unique significance among molecular interactions due to the electron delocalization, which is known to play a key role in processes such as protein aggregation. In this paper, we present PInteract, an algorithm that detects π-involving interactions in input structures based on geometric criteria, including π-π, cation-π, amino-π, His-π, and sulfur-π interactions. In addition, it is capable of detecting chains and clusters of π interactions as well as particular recurrent motifs at protein-DNA and protein-RNA interfaces, called stair motifs, consisting of a particular combination of π-π stacking, cation/amino/His-π and H-bond interactions. Full article
(This article belongs to the Special Issue Computational Analysis and Conformational Modeling for Protein Structure and Interaction)
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33 pages, 1724 KiB  
Review
Retinal Gatekeepers: Molecular Mechanism and Therapeutic Role of Cysteine and Selenocysteine
by Eleonora Maceroni, Annamaria Cimini, Massimiliano Quintiliani, Michele d’Angelo and Vanessa Castelli
Biomolecules 2025, 15(8), 1203; https://doi.org/10.3390/biom15081203 - 21 Aug 2025
Abstract
Oxidative stress is a key contributor to retinal degeneration, as the retina is highly metabolically active and exposed to constant light stimulation. This review explores the crucial roles of cysteine and selenocysteine in redox homeostasis and retinal protection. Cysteine, primarily synthesized via the [...] Read more.
Oxidative stress is a key contributor to retinal degeneration, as the retina is highly metabolically active and exposed to constant light stimulation. This review explores the crucial roles of cysteine and selenocysteine in redox homeostasis and retinal protection. Cysteine, primarily synthesized via the transsulfuration pathway, is the rate-limiting precursor for glutathione (GSH), the most abundant intracellular antioxidant. Selenocysteine enables the enzymatic activity of selenoproteins, particularly glutathione peroxidases (GPXs), which counteract reactive oxygen species (ROS). Experimental evidence from retinal models confirms that depletion of cysteine or selenocysteine results in impaired antioxidant defense and photoreceptor death. Furthermore, dysregulation of these amino acids contributes to the pathogenesis of age-related macular degeneration (AMD), retinitis pigmentosa (RP), and diabetic retinopathy (DR). Therapeutic approaches including N-acetylcysteine, selenium compounds, and gene therapy targeting thioredoxin systems have demonstrated protective effects in preclinical studies. Targeting cysteine and selenocysteine-dependent systems, as well as modulating the KEAP1–NRF2 pathway, may offer promising strategies for managing retinal neurodegeneration. Advancing our understanding of redox mechanisms and their role in retinal cell viability could unlock new precision treatment strategies for retinal diseases. Full article
(This article belongs to the Special Issue Cysteine and Selenocysteine in Antioxidant Defense, Protein Synthesis and Signaling Pathways)
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15 pages, 2296 KiB  
Article
Histone H3 N-Terminal Tail Residues Important for Meiosis in Saccharomyces cerevisiae
by Amy Prichard, Marnie Johansson, David T. Kirkpatrick and Duncan J. Clarke
Biomolecules 2025, 15(8), 1202; https://doi.org/10.3390/biom15081202 - 21 Aug 2025
Abstract
Histone tail phosphorylation has diverse effects on a myriad of cellular processes, including cell division, and is highly conserved throughout eukaryotes. Histone H3 phosphorylation at threonine 3 (H3T3) during mitosis occurs at the inner centromeres and is required for proper biorientation of chromosomes [...] Read more.
Histone tail phosphorylation has diverse effects on a myriad of cellular processes, including cell division, and is highly conserved throughout eukaryotes. Histone H3 phosphorylation at threonine 3 (H3T3) during mitosis occurs at the inner centromeres and is required for proper biorientation of chromosomes on the mitotic spindle. While H3T3 is also phosphorylated during meiosis, a possible role for this modification has not been tested. Here, we asked if H3T3 phosphorylation is important for meiotic division by quantifying sporulation efficiency and spore viability in Saccharomyces cerevisiae mutants with a T3A amino acid substitution. The T3A substitution resulted in reduced sporulation efficiency and reduced spore viability. Analysis of two other H3 tail mutants, K4A and S10A, revealed different effects on sporulation efficiency and spore viability compared to the T3A mutant, suggesting that these phenotypes may be due to failures in distinct functions. To determine if the spindle checkpoint promotes spore viability of the T3A mutant, the MAD2 gene was deleted. This resulted in a severe reduction in spore viability following meiosis. Altogether, the data reveal an important function for histone H3 threonine 3 that requires monitoring by the spindle checkpoint to ensure successful completion of meiosis. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin and Chromosome Molecular Research)
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15 pages, 1908 KiB  
Article
Enhancement of Protein–Protein Interactions by Destabilizing Mutations Revealed by HDX-MS
by Yoshitomo Hamuro, Anthony Armstrong, Jeffrey Branson, Sheng-Jiun Wu, Richard Y.-C. Huang and Steven Jacobs
Biomolecules 2025, 15(8), 1201; https://doi.org/10.3390/biom15081201 - 20 Aug 2025
Abstract
Enhancing protein–protein interactions is a key therapeutic strategy to ensure effective protein function in terms of pharmacokinetics and pharmacodynamics and can be accomplished with methods like directed evolution or rationale design. Previously, two papers suggested the possible enhancement of protein–protein binding affinity via [...] Read more.
Enhancing protein–protein interactions is a key therapeutic strategy to ensure effective protein function in terms of pharmacokinetics and pharmacodynamics and can be accomplished with methods like directed evolution or rationale design. Previously, two papers suggested the possible enhancement of protein–protein binding affinity via destabilizing mutations. This paper reviews the results of the previous literature and adds new data to show the generality of the strategy that destabilizing the unbound protein without significantly changing the free energy of the complex can enhance protein–protein interactions for therapeutic benefit. The first example presented is that of a variant of human growth hormone (hGHv) containing 15 mutations that improve the binding to the hGH binding protein (hGHbp) by 400-fold while retaining full biological activity. The second example is that of the YTE mutations (M252Y/S354T/T256E) in the Fc region of a monoclonal antibody (mAb). The YTE mutations improve the binding of the mAb to FcRn at pH 6.0 10-fold, resulting in elongated serum half-life of the mAb. In both cases, (i) chemical titration or differential scanning calorimetry (DSC) showed the mutations destabilize the unbound mutant proteins, (ii) isothermal titration calorimetry (ITC) showed extremely favorable enthalpy (ΔH) and unfavorable entropy (ΔS) upon binding to their respective target molecule compared with the wildtype, and (iii) hydrogen/deuterium exchange–mass spectrometry (HDX-MS) revealed that these mutations increase the free energy of unbound mutant protein without significantly affecting the free energy of the bound state, resulting in an enhancement to the binding affinities. The third example presented is that of the JAWA mutations (T437R/K248E) also located in the Fc region of a mAb. The JAWA mutations facilitate antibody multimerization upon binding to cell surface antigens, allowing for enhanced agonism and effector functions. Both DSC and HDX-MS showed that the JAWA mutations destabilize the unbound Fc, although the complex was not characterized due to weak binding. Enhancement of protein–protein interactions through incorporation of mutations that increase the free energy of a protein’s unbound state represents an alternative route to decreasing the protein–protein complex free energy through optimization of the binding interface. Full article
(This article belongs to the Special Issue The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed Issue in Honor of Professor S. Walter Englander)
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18 pages, 1425 KiB  
Review
TMCO1 as an Endoplasmic Reticulum Calcium Load-Activated Channel: Mechanisms and Disease Implications
by Jingbo Wang, Panpan Zhu, Zhuohang Li, Xiaohui Su, Mingzhu Qi, Aimin Zhou and Xiangying Kong
Biomolecules 2025, 15(8), 1200; https://doi.org/10.3390/biom15081200 - 20 Aug 2025
Abstract
Calcium ions (Ca2+) play a vital role in many biological processes. Transmembrane and coiled-coil domain 1 (TMCO1) has been characterized as an endoplasmic reticulum (ER) transmembrane protein in recent years. It keeps the cytoplasm and ER’s Ca2+ homeostasis stable by [...] Read more.
Calcium ions (Ca2+) play a vital role in many biological processes. Transmembrane and coiled-coil domain 1 (TMCO1) has been characterized as an endoplasmic reticulum (ER) transmembrane protein in recent years. It keeps the cytoplasm and ER’s Ca2+ homeostasis stable by acting as a novel calcium channel. Studies from different laboratories have revealed that the mutation or deficiency of TMCO1 is closely correlated with several diseases, including cerebro-facio-thoracic dysplasia (CFTD), glaucoma, premature ovarian failure (POF), osteoporosis, and cancer. Here, we review the characteristics of TMCO1 and its involvement in related diseases, which may provide useful information for developing therapeutic strategies for these diseases, as well as promote further research on this protein. Full article
(This article belongs to the Section Molecular Biology)
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12 pages, 793 KiB  
Article
Protein Translocation Control in E. coli via Temperature-Dependent Aggregation: Application to a Conditionally Lethal Enzyme, Levansucrase
by Young Kee Chae
Biomolecules 2025, 15(8), 1199; https://doi.org/10.3390/biom15081199 - 20 Aug 2025
Abstract
Precise control of protein translocation is essential for synthetic biology and protein engineering. Here, we present a temperature-responsive system using elastin-like polypeptides (ELPs) to regulate the translocation of a conditionally lethal enzyme in Escherichia coli. The enzyme, levansucrase, whose activity becomes lethal [...] Read more.
Precise control of protein translocation is essential for synthetic biology and protein engineering. Here, we present a temperature-responsive system using elastin-like polypeptides (ELPs) to regulate the translocation of a conditionally lethal enzyme in Escherichia coli. The enzyme, levansucrase, whose activity becomes lethal in the presence of sucrose, was engineered with an N-terminal signal peptide and a C-terminal ELP tag. At 37 °C, the ELP tag induced intracellular aggregation of the fusion protein, preventing its secretion and allowing cell survival, as indicated by translucent colony formation. In contrast, at 16 °C, the ELP remained soluble, permitting levansucrase secretion into the medium. The resulting conversion of sucrose into levan by the secreted enzyme led to host cell death. These findings highlight ELP-mediated aggregation as a reversible and tunable strategy for regulating protein localization and secretion in E. coli, with potential applications in synthetic biology, metabolic engineering, and biocontainment systems. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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26 pages, 2100 KiB  
Review
Recent Advances in the Role of Fibroblast Growth Factors in Hair Follicle Growth
by Junchao Wang, Lusheng Wang, Shuang Gao and Xiaokun Li
Biomolecules 2025, 15(8), 1198; https://doi.org/10.3390/biom15081198 - 20 Aug 2025
Viewed by 62
Abstract
Hair follicles are essential to hair formation and cyclic regeneration, experiencing growth and degeneration, and quiescence phases involving complex signaling pathways. Among these, fibroblast growth factors (FGFs) play a critical role in follicular morphogenesis, but the role of FGF receptor signaling in hair [...] Read more.
Hair follicles are essential to hair formation and cyclic regeneration, experiencing growth and degeneration, and quiescence phases involving complex signaling pathways. Among these, fibroblast growth factors (FGFs) play a critical role in follicular morphogenesis, but the role of FGF receptor signaling in hair follicle development remains underexplored. Current treatments for hair loss, such as medical, surgical, light-based, and nutraceutical interventions, are often expensive, require long-term commitment, and are associated with substantial side effects. This review discusses the mechanisms and biological functions of the FGF signaling pathway within the hair follicle growth cycle, providing an overview of how these elements influence hair follicle dynamics and the pathogenesis of alopecia. Manipulating the FGF signaling pathway could offer new therapeutic options for androgenetic alopecia and other hair loss conditions, potentially exceeding current treatment modalities in efficacy and safety. Full article
(This article belongs to the Section Cellular Biochemistry)
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19 pages, 5378 KiB  
Article
Dual Regulation of Mitochondrial Complexes by H2S via S-Sulfhydration Controls Respiration in Type 1 Diabetic Hearts
by Tong Su, Li Han Zhu, Jun Xian Liu, Li Yuan Jin, Huixing Cui, Longhao Yu and Yin Hua Zhang
Biomolecules 2025, 15(8), 1197; https://doi.org/10.3390/biom15081197 - 20 Aug 2025
Abstract
Hydrogen sulfide (H2S) has been established to regulate mitochondrial respiration and ATP production, but whether the regulation is through S-sulfhydration (-SSH) of mitochondrial complexes is not well understood. Recently, H2S is known to exert diverse and dose-dependent effects [...] Read more.
Hydrogen sulfide (H2S) has been established to regulate mitochondrial respiration and ATP production, but whether the regulation is through S-sulfhydration (-SSH) of mitochondrial complexes is not well understood. Recently, H2S is known to exert diverse and dose-dependent effects on mitochondrial complexes. However, the involvement of S-sulfhydration of each mitochondrial complex and the activities in diabetic hearts have not been revealed. Here, we conducted comprehensive investigations into S-sulfhydration and the activities of mitochondrial complexes I–V in normal and Streptozotocin (STZ)-induced type 1 diabetic (DM) heart mitochondria. Results showed that proteins of H2S-producing enzymes were downregulated in DM heart mitochondria, which was accompanied by reduced mitochondrial membrane potential (MMP), greater ROS, and lower complex I and V activities, reduced complex V-SSH in DM. In both groups, supplementation with the H2S donor NaHS increased the S-sulfhydration of all mitochondrial complexes, and the activities of complexes I–III and V were significantly increased but complex IV activity was reduced. Consequently, mitochondrial MMP, ROS, and ATP production were normalized with NaHS in DM, whereas inhibition of H2S generation increased mitochondrial ROS and reduced MMP via reducing complex activities in both groups. Ischemic reperfusion did not affect NaHS-increment of S-sulfhydration of complexes I–V, but significantly impaired complex V activity in DM. Collectively, H2S-dependent S-sulfhydration of mitochondrial complexes I–V in normal and DM heart mitochondria were involved in the activation of mitochondrial complexes I–III/V and the inhibition of complex IV, which control cardiac mitochondrial respiration and ATP production. Full article
(This article belongs to the Special Issue Biomolecules in Myocarditis and Inflammatory Heart Disease)
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12 pages, 1439 KiB  
Article
Humanized Monoclonal Antibody Against Citrullinated Histone H3 Attenuates Myocardial Injury and Prevents Heart Failure in Rodent Models
by Matthew Weber, Yuchen Chen, Xinyu Zhou, Heejae Chun, Di Wu, Ki Ho Park, Chuanxi Cai, Yongqing Li, Jianjie Ma and Zequan Yang
Biomolecules 2025, 15(8), 1196; https://doi.org/10.3390/biom15081196 - 20 Aug 2025
Viewed by 72
Abstract
Background: Excessive formation of neutrophil extracellular traps (NETs) leads to NETosis, accompanied by the release of citrullinated histone H3 (CitH3), a key mediator of septic inflammation. However, the role of CitH3 in sterile inflammation, such as acute myocardial infarction (MI) and post-MI heart [...] Read more.
Background: Excessive formation of neutrophil extracellular traps (NETs) leads to NETosis, accompanied by the release of citrullinated histone H3 (CitH3), a key mediator of septic inflammation. However, the role of CitH3 in sterile inflammation, such as acute myocardial infarction (MI) and post-MI heart failure, remains incompletely understood. Methods and Results: We investigated the role of CitH3, a byproduct of NETosis, in myocardial ischemia/reperfusion (I/R) injury using a murine MI model. C57BL/6J mice were subjected to left coronary artery (LCA) occlusion followed by reperfusion and treated with either a humanized anti-CitH3 monoclonal antibody (hCitH3-mAb) or control human IgG. In mice undergoing 40 min of LCA occlusion and 24 h of reperfusion, hCitH3-mAb administered 10 min before reperfusion significantly reduced infarct size by 36% compared to control (p < 0.05). Plasma levels of CitH3, IL-1β, and interferon-β were significantly elevated following MI but were attenuated by hCitH3-mAb. In addition, plasma and cardiac tissue from treated mice showed significantly lower levels of citrate synthase, a marker of mitochondrial injury, suggesting that hCitH3-mAb preserved mitochondrial integrity after MI. In mice undergoing 50 min of LCA occlusion and 21 days of reperfusion, longitudinal echocardiography revealed preservation of left ventricular ejection fraction (LVEF) in hCitH3-mAb-treated mice, with significant improvement observed on days 7, 14, and 21 post-MI (p < 0.05 vs. control). hCitH3-mAb also mitigated myocardial fibrosis and preserved tissue architecture. Conclusions: These findings demonstrated CitH3 as a critical mediator of myocardial injury and adverse remodeling following acute MI. Neutralization of CitH3 via hCitH3-mAb attenuates I/R injury and preserves cardiac function by mitigating inflammation and protecting mitochondrial integrity. Targeting CitH3 represents a promising therapeutic strategy to prevent heart failure following MI. Full article
(This article belongs to the Special Issue Advancing Innovations in Biomedical Research for Translational Applications)
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26 pages, 1606 KiB  
Review
Extracellular Vesicles Derived from Breast Cancer Cells: Emerging Biomarkers of Tumor Progression and Metastasis
by Sona Bernatova, Andreas Nicodemou, Michaela Cehakova, Lubos Danisovic and Martin Bohac
Biomolecules 2025, 15(8), 1195; https://doi.org/10.3390/biom15081195 - 19 Aug 2025
Viewed by 92
Abstract
Breast cancer (BC) remains one of the most prevalent and life-threatening malignancies worldwide, marked by significant heterogeneity and complex mechanisms of progression. Despite major advances in understanding its molecular and cellular basis, the processes driving tumor progression and metastasis continue to challenge effective [...] Read more.
Breast cancer (BC) remains one of the most prevalent and life-threatening malignancies worldwide, marked by significant heterogeneity and complex mechanisms of progression. Despite major advances in understanding its molecular and cellular basis, the processes driving tumor progression and metastasis continue to challenge effective treatment. Among the emerging research areas, extracellular vesicles (EVs) have gained considerable attention for their key role in intercellular communication and their contribution to cancer biology. In BC, tumor cell-derived EVs are implicated in multiple processes that promote disease progression, including tumor growth, remodeling of the tumor microenvironment, and facilitation of metastasis. By transferring oncogenic signals to recipient cells, EVs critically shape the metastatic niche and support the spread of cancer cells to distant organs. Recent studies highlight the diverse functions of BC-derived EVs in modulating immune responses, inducing angiogenesis, and enhancing cancer cell invasiveness. This review explores the role of BC-derived EVs in tumor progression and metastasis. We discuss their molecular composition, mechanisms of action, and impact on the tumor microenvironment, aiming to provide insights into their role in BC pathophysiology and discuss potential clinical applications. A deeper understanding of the complex interplay between EVs and cancer progression may pave the way for innovative strategies to combat BC and improve patient outcomes. Full article
(This article belongs to the Special Issue New Insights into Stem Cell-Derived Exosomes in Human Health and Disease)
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21 pages, 802 KiB  
Article
Study of the Lipophilicity of Tetracyclic Anticancer Azaphenothiazines
by Małgorzata Jeleń, Beata Morak-Młodawska, Małgorzata Dołowy and Adam Konefał
Biomolecules 2025, 15(8), 1194; https://doi.org/10.3390/biom15081194 - 19 Aug 2025
Viewed by 152
Abstract
Although chlorpromazine is primarily used in psychiatry, it has been shown since its introduction to influence the course of neoplastic diseases. According to the strategy of drug repurposing, chlorpromazine has been successfully tested for its potential antitumor effects on multiple cancer cell lines. [...] Read more.
Although chlorpromazine is primarily used in psychiatry, it has been shown since its introduction to influence the course of neoplastic diseases. According to the strategy of drug repurposing, chlorpromazine has been successfully tested for its potential antitumor effects on multiple cancer cell lines. This effect is consistent with the overlap of molecular pathways observed for years between schizophrenia and cancer. The main objective of this work was to evaluate the lipophilicity of 17 previously synthesized tetracyclic chlorpromazine analogues exhibiting diverse anticancer and antimicrobial activity using thin-layer chromatography and computational methods. For a compound to become an effective drug, it must have a favorable ADMET profile, which determines its pharmacokinetic properties as a drug candidate. Lipophilicity is one of the key parameters widely employed in designing new bioactive compounds as potential therapeutic agents. In this article, chromatographic plates precoated with silica gel 60 RP-18F254 and a mixture of acetone and TRIS buffer were used as the mobile phase. The chromatographic parameter of lipophilicity (RM0) of the investigated compounds determined by means of the Soczewinski–Wachtmeister formula was useful to obtain the values of the experimental lipophilicity parameter expressed as logPTLC. The results of logPTLC were compared with theoretical values of logP obtained using different algorithms (iLOGP, XLOGP3, WLOGP, MLOGP, SILCOS-IT, and ClogP). Furthermore, the online platforms, such as SwissADME and pkCSM, allowed the determination of the remaining ADME parameters of the quinoline derivatives of chlorpromazine. The study of lipophilicity and ADME factors enabled confirmation that the tested compounds demonstrated favorable properties. Therefore, they can be considered as promising starting structures for further studies. Full article
(This article belongs to the Special Issue Design, Synthesis, and Evaluation of New Anticancer Substances and Radiopharmaceuticals)
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24 pages, 1380 KiB  
Review
A TRPM2-Driven Signalling Cycle Orchestrates Abnormal Inter-Organelle Crosstalk in Cardiovascular and Metabolic Diseases
by Maali AlAhmad, Esra Elhashmi Shitaw and Asipu Sivaprasadarao
Biomolecules 2025, 15(8), 1193; https://doi.org/10.3390/biom15081193 - 19 Aug 2025
Viewed by 211
Abstract
Cardiovascular and metabolic disorders significantly reduce healthspan and lifespan, with oxidative stress being a major contributing factor. Oxidative stress, marked by elevated reactive oxygen species (ROS), disrupts cellular and systemic functions. One proposed mechanism involves TRPM2 (Transient Receptor Potential Melastatin2)-dependent Ca2+ dysregulation. [...] Read more.
Cardiovascular and metabolic disorders significantly reduce healthspan and lifespan, with oxidative stress being a major contributing factor. Oxidative stress, marked by elevated reactive oxygen species (ROS), disrupts cellular and systemic functions. One proposed mechanism involves TRPM2 (Transient Receptor Potential Melastatin2)-dependent Ca2+ dysregulation. These channels, activated by ROS (via ADP-ribose), not only respond to ROS but also amplify it, creating a self-sustaining cycle. Recent studies suggest that TRPM2 activation triggers a cascade of signals from intracellular organelles, enhancing ROS production and affecting cell physiology and viability. This review examines the role of TRPM2 channels in oxidative stress-associated cardiovascular and metabolic diseases. Oxidative stress induces TRPM2-mediated Ca2+ influx, leading to lysosomal damage and the release of Zn2+ from lysosomal stores to the mitochondria. In mitochondria, Zn2+ facilitates electron leakage from respiratory complexes, reducing membrane potential, increasing ROS production, and accelerating mitochondrial degradation. Excess ROS activates PARP1 in the nucleus, releasing ADP-ribose, a TRPM2 agonist, thus perpetuating the cycle. Lysosomes act as Ca2+-sensitive signalling platforms, delivering toxic Zn2+ signals to mitochondria. This represents a paradigm shift, proposing that the toxic effects of Ca2+ on mitochondria are not direct, but are instead mediated by lysosomes and subsequent Zn2+ release. This cycle exhibits a ‘domino’ effect, causing sequential and progressive decline in the function of lysosomes, mitochondria, and the nucleus—hallmarks of ageing and oxidative stress-related cardiovascular and metabolic diseases. These insights could lead to new therapeutic strategies for addressing the widespread issue of cardiovascular and metabolic diseases. Full article
(This article belongs to the Special Issue Ion Channels in Cardiovascular and Metabolic Diseases)
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18 pages, 3824 KiB  
Article
Changes in Artemin Correlate with Anxiety- and Depression-like Behaviors in a Lipopolysaccharide-Induced Rat Neuroinflammation Model
by Hasan Çalışkan and Seda Koçak
Biomolecules 2025, 15(8), 1192; https://doi.org/10.3390/biom15081192 - 19 Aug 2025
Viewed by 168
Abstract
Artemin is a neurotrophic factor that belongs to the four-member family of Glial-derived growth factors. This study aims to investigate changes in artemin correlated with anxiety and depression-like behaviors in a neuroinflammation rodent model. In adult male Wistar rats, neuroinflammation was established through [...] Read more.
Artemin is a neurotrophic factor that belongs to the four-member family of Glial-derived growth factors. This study aims to investigate changes in artemin correlated with anxiety and depression-like behaviors in a neuroinflammation rodent model. In adult male Wistar rats, neuroinflammation was established through administration of 2 mg/kg LPS. Anxiety-like behaviors and locomotor activity were evaluated by the open field test. The sucrose preference test and the splash test analyzed depression-like behaviors. Tumor necrosis factor alpha (TNF-α), interleukin-1 beta (IL-1β), and artemin levels were measured in the prefrontal cortex, striatum, and serum. In the neuroinflammation group, rearing, total distance traveled, time spent in the central region, and sucrose solution consumption decreased in the open-field test (p < 0.0001). Grooming time and frequency were shortened, and grooming latency was prolonged in the neuroinflammation group (p < 0.0001). TNF-α was significantly increased in the prefrontal cortex (p < 0.05) and striatum (p < 0.01). lL-1β did not change between groups (p > 0.05). Artemin levels decreased in the prefrontal cortex and striatum (p < 0.05). No difference was observed in serum artemin levels; however, artemin levels of brain regions were higher than those in the serum. An increase in anxiety–depression-like behaviors has accompanied decreased levels of artemin in the brain. Artemin may be a target molecule in psychiatric disorders. Further studies are needed to examine the role of artemin in neuropsychiatric disorders. Full article
(This article belongs to the Special Issue Neuroimmune Interactions in Neuropsychiatric Diseases)
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13 pages, 1376 KiB  
Article
The Role of BRCT Domain from LmjPES in Leishmania major Pathogenesis
by Esther Larrea, José Peña-Guerrero, Celia Fernández-Rubio, Aroia Burguete-Mikeo, Elizabeth Guruceaga and Paul Nguewa
Biomolecules 2025, 15(8), 1191; https://doi.org/10.3390/biom15081191 - 19 Aug 2025
Viewed by 150
Abstract
Leishmaniasis is caused by protozoan parasites from the genus Leishmania and remains one of the major threats to global health, impacting millions of people worldwide as well as animals including dogs. Several treatments have been used for managing leishmaniasis; nevertheless, drug resistance has [...] Read more.
Leishmaniasis is caused by protozoan parasites from the genus Leishmania and remains one of the major threats to global health, impacting millions of people worldwide as well as animals including dogs. Several treatments have been used for managing leishmaniasis; nevertheless, drug resistance has emerged as an important obstacle to disease control. Therefore, there is an urgent need to discover new therapeutic targets. The aim of this work was to study the role played by the breast cancer associated 1 C-terminal (BRCT) domain from LmjPES protein (Pescadillo ribosomal biogenesis factor) in Leishmania major‘s pathogenesis through the construction of novel genomic tools. For this purpose, Leishmania integrative plasmids that were able to express the BRCT domain from LmjPES and a hypothetical defective LmjPES lacking this BRCT domain were constructed. It was observed that the overexpression of the aforementioned BRCT domain in L. major dysregulated the mRNA expression of 152 genes (95 up-regulated and 57 down-regulated) in respect to control parasites. Furthermore, clustering studies of these altered genes revealed an enrichment in genes related to metabolic processes, transporter activity, response to stimuli, and protein folding, which are categories described to be associated with the metacyclogenesis process and parasite survival. Interestingly, these genes reached normal levels of expression in parasites transfected with a defective LmjPES (a mutated gene lacking the coding sequence of the BRCT domain). In addition, it was found that the footpad of mice inoculated with LmjPES BRCT-overexpressing parasites had significantly greater inflammation compared to the size of the footpad of animals infected with the control parasites. Based on all these results, it was suggested that the BRCT domain from LmjPES might play a role in L. major‘s infection process and pathogenesis. Full article
(This article belongs to the Special Issue Cellular and Molecular Basis of Parasite Infection)
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23 pages, 6102 KiB  
Review
Contribution and Regulation of HIF-1α in Testicular Injury Induced by Diabetes Mellitus
by Defan Wang, Zhenghong Zhang, Renfeng Xu and Zhengchao Wang
Biomolecules 2025, 15(8), 1190; https://doi.org/10.3390/biom15081190 - 19 Aug 2025
Viewed by 192
Abstract
Diabetes mellitus, as a metabolic disorder, has received growing attention for its detrimental effects on the male reproductive system (particularly the testes) manifesting as increased oxidative stress, reduced blood perfusion, heightened inflammation, and germ cell apoptosis under hyperglycemic conditions. Hypoxia-inducible factor (HIF)-1α, a [...] Read more.
Diabetes mellitus, as a metabolic disorder, has received growing attention for its detrimental effects on the male reproductive system (particularly the testes) manifesting as increased oxidative stress, reduced blood perfusion, heightened inflammation, and germ cell apoptosis under hyperglycemic conditions. Hypoxia-inducible factor (HIF)-1α, a pivotal transcription factor in cellular hypoxia responses, plays a crucial role in regulating metabolism, angiogenesis, and apoptosis. Emerging evidence underscores its significant physiological and pathological roles in diabetic testicular injury. This review outlines the structural domains, activation mechanisms, and key target genes of HIF-1α, and further examines its involvement in diabetes-induced oxidative stress, impaired perfusion, endocrine dysregulation, and the imbalance of apoptosis and autophagy in testicular tissue. Notably, HIF-1α exerts protective effects by activating canonical signaling pathways such as phosphoinositide-3 kinase (PI-3K)/protein kinase B (Akt), mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK), and nuclear factor (NF)-κB, thereby enhancing antioxidant gene expression, promoting angiogenesis, and upregulating anti-apoptotic proteins. Furthermore, HIF-1α may help stabilize androgen levels by preserving Leydig cell function, potentially alleviating diabetes-associated gonadal dysfunction. This review also discusses the feasibility of targeting HIF-1α as a novel therapeutic strategy. In conclusion, a comprehensive understanding of HIF-1α’s mechanistic role in diabetic testicular damage provides valuable insights into the pathogenesis of diabetes-related reproductive disorders and offers new avenues for therapeutic intervention. Full article
(This article belongs to the Special Issue Obesity, Hormones and Reproductive Health)
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56 pages, 1727 KiB  
Review
From Natriuretic Peptides to microRNAs: Multi-Analyte Liquid Biopsy Horizons in Heart Failure
by Evelina Charidemou, Kyriacos Felekkis and Christos Papaneophytou
Biomolecules 2025, 15(8), 1189; https://doi.org/10.3390/biom15081189 - 19 Aug 2025
Viewed by 472
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality worldwide, underscoring the need for improved diagnostic, prognostic, and therapeutic strategies. Circulating microRNAs (c-miRNAs) have emerged as promising non-invasive biomarkers due to their stability, tissue specificity, and regulatory roles in cardiac pathophysiology. [...] Read more.
Heart failure (HF) is a leading cause of morbidity and mortality worldwide, underscoring the need for improved diagnostic, prognostic, and therapeutic strategies. Circulating microRNAs (c-miRNAs) have emerged as promising non-invasive biomarkers due to their stability, tissue specificity, and regulatory roles in cardiac pathophysiology. This review highlights the potential of c-miRNAs in enhancing HF diagnosis, risk stratification, and therapeutic monitoring, particularly when integrated with conventional biomarkers such as natriuretic peptides, galectin-3, soluble ST2, and high-sensitivity troponins. We explore the roles of key miRNAs in HF pathogenesis—including cardiac hypertrophy, fibrosis, inflammation, apoptosis, and vascular remodeling—and discuss their diagnostic and prognostic significance. The potential of multi-analyte liquid biopsy approaches that combine c-miRNAs with protein biomarkers is also examined within the context of precision medicine. Despite promising data, challenges related to standardization, assay variability, and clinical validation remain. Addressing these gaps through harmonized protocols and large-scale studies will be essential for translating c-miRNAs into routine HF management. Full article
(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)
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21 pages, 4617 KiB  
Article
Apelin-13-Mediated Upregulation of METTL3 Ameliorates Alzheimer’s Disease via Inhibiting Neuroinflammation Through m6A-Dependent Regulation of lncRNA BDNF-AS
by Li Han, Siwen Wei, Rong Wang, Yiran Liu, Yi Zhong, Juan Fu, Huaiqing Luo and Meihua Bao
Biomolecules 2025, 15(8), 1188; https://doi.org/10.3390/biom15081188 - 18 Aug 2025
Viewed by 215
Abstract
Apelin-13, a neuropeptide, has been recognized for its neuroprotective properties. Our previous study found apelin-13 improves cognitive function in Alzheimer’s disease (AD) rats by inhibiting neuroinflammation through upregulation of BDNF/TrkB signaling pathway. However, the precise mechanism by which apelin-13 modulates BDNF remains unclear. [...] Read more.
Apelin-13, a neuropeptide, has been recognized for its neuroprotective properties. Our previous study found apelin-13 improves cognitive function in Alzheimer’s disease (AD) rats by inhibiting neuroinflammation through upregulation of BDNF/TrkB signaling pathway. However, the precise mechanism by which apelin-13 modulates BDNF remains unclear. Thus, this study aimed to unravel the specific regulatory mechanism by which apelin-13 regulates BDNF. Bilaterally intracerebroventricular injection with Aβ25–35 was used to establish an in vivo model of AD. For the generation of METTL3 KO rats, the Crispr/Cas9 method was applied. PC12 cells were treated with Aβ25–35 to establish an in vitro model of AD. The cognitive function of the rats was evaluated with the Morris water maze and the novel object recognition test. Hippocampal damage and neuron loss were detected through H&E and immunofluorescent staining. METTL3, BDNF, TrkB, and p-TrkB were examined by Western blotting. Inflammation-related cytokines, IBA1, GFAP, IL-1β, and TNF-α were detected by Western blotting, immunofluorescent staining, ELISA, and qRT-PCR. m6A modification level was evaluated through MeRIP. A flow cytometer was applied to evaluate cell apoptosis. Cell proliferation was examined using MTT. m6A methylation inhibitor DAA reverses the improvement effect of apelin-13 on cognitive function, hippocampal nerve damage, neuron loss, and neuroinflammation in Aβ25–35-treated rats. Further results showed that apelin-13 upregulated METTL3, BDNF-AS m6A methylation, inhibited BDNF-AS expression, and subsequently upregulated BDNF/TrkB signaling pathway and reduced neuroinflammation in in vivo and in vitro AD models in a dose-dependent manner. Knockdown of METTL3 abolished apelin-13’s improvement effect in AD rats. Apelin-13-mediated upregulation of METTL3 enhances neuroinflammation inhibition and BDNF/TrkB signaling pathway via m6A-dependent downregulation of lncRNA BDNF-AS, thus ameliorating AD. Our study offers novel insights into the pathogenesis of AD and identifies potential drug targets for its treatment. Full article
(This article belongs to the Section Molecular Medicine)
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17 pages, 2167 KiB  
Article
Expression of Reelin, Aβ1-42, Tau and FTH1 in Idiopathic Epiretinal Membranes: Exploring the Link Between Reelin and Neurodegenerative Biomarkers
by Bijorn Omar Balzamino, Esposito Graziana, Cosimi Pamela, Squitti Rosanna, Amadoro Giuseppina, Latina Valentina, Ripandelli Guido, Cacciamani Andrea and Micera Alessandra
Biomolecules 2025, 15(8), 1187; https://doi.org/10.3390/biom15081187 - 18 Aug 2025
Viewed by 195
Abstract
Growing evidence suggests that Reelin signals and cleavages are affected in neurodegenerative diseases, prospecting a potential role for Reelin in the pathogenesis of neurodegenerative processes occurring in insulted retinas. We sought to determine whether Reelin, Aβ1-42, FTH1 and TAU proteins accumulate in ocular [...] Read more.
Growing evidence suggests that Reelin signals and cleavages are affected in neurodegenerative diseases, prospecting a potential role for Reelin in the pathogenesis of neurodegenerative processes occurring in insulted retinas. We sought to determine whether Reelin, Aβ1-42, FTH1 and TAU proteins accumulate in ocular fluids of idiopathic epiretinal membrane (iERM) specimens and whether such accumulations depend on disease severity. Comparisons and correlation studies were used to verify the hypothesis of a Reelin, Aβ1-42, TAU and FTH1 marker expressions in this vitreoretinal disease, extending the knowledge on the pathological spectrum of neurodegenerative eye diseases. Aqueous, vitreous and peeled-off ERM samples were collected from patients who had undergone vitrectomy and grouped according to disease severity. We found out that Reelin and Aβ1-42 were expressed in ocular fluids and affected ERMs depending on disease severity. At stage 3, higher Reelin and Aβ1-42 immunofluorescence staining was detected in ERMs, in agreement with the higher Reelin, Aβ1-42, FTH1 and TAU transcript expressions by RT-PCR. Differential expressions of transcripts specific to Aβ1-42, FTH1, GFAP and TAU occurred in vitreal hyalocytes and astrocytes, which selectively responded to vitreal exposure. This is the first study reporting the association between Reelin and ERM disease, highlighting the potential role of Reelin in neurodegenerating and Drusen-affected retinas. The potential association of neurodegenerative mediators with ERM would suggest that part of the neuronal damage activated at the vitreoretinal interphase might be driven by Reelin. Full article
(This article belongs to the Special Issue Biomarkers in Neurodegenerative Diseases: Shaping the Future of Diagnosis and Treatment)
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16 pages, 1354 KiB  
Article
Dynamic Interplay Between miR-124-3p and EGF in the Regulation of Overgrowth via RNA Signaling
by Keziban Korkmaz Bayram, Arslan Bayram, Zeynep Yilmaz Sukranli, Ecmel Mehmetbeyoglu Duman, Fatma Aybuga, Esra Tufan Benli, Serpil Taheri, Yusuf Ozkul and Minoo Rassoulzadegan
Biomolecules 2025, 15(8), 1186; https://doi.org/10.3390/biom15081186 - 18 Aug 2025
Viewed by 191
Abstract
Background: Epigenetic mechanisms and RNA signalling profoundly impact body growth during the early stages of embryonic development. RNA molecules, like microRNAs, play a vital role in early embryonic development, laying the groundwork for future growth and function. miR-124-3p microinjected into mouse fertilised eggs [...] Read more.
Background: Epigenetic mechanisms and RNA signalling profoundly impact body growth during the early stages of embryonic development. RNA molecules, like microRNAs, play a vital role in early embryonic development, laying the groundwork for future growth and function. miR-124-3p microinjected into mouse fertilised eggs (miR-124-3p*) exhibited a significantly overgrowth phenotype. Behavioural test results showed that miR-124-3p mice were more physically active, as indicated by total distance and movement velocity. However, the molecular mechanism leading to these phenotypic changes mediated by miR-124-3p remains a mystery. This study aimed to investigate the role of epidermal growth factor (EGF) in developing an overgrowth phenotype in miR-124-3p* mice. Results: In this research, we preferred to work with neurospheres (NSs) due to the challenges of handling a single embryo, as NSs exhibit similar features, especially regarding cell growth, differentiation, and capacity for self-renewal. We examined the mRNA expression levels of Sox8, Sox9, Sox10, Doublecortin (Dcx), and Neurod1 genes, which are linked to a tiny phenotype in knockout mice, in total embryos at E7.5 and hippocampal cells isolated from E19.5-day fetus and neurospheres aged 12 and 21 days, which were derived from these hippocampal cells through primary cell culture. These genes are significantly overexpressed in miR-124-3p* NSs, but not in the E7.5 total embryos or the hippocampus of the E19.5 fetus. Conclusions: These findings suggest a possible link between miR-124-3p microinjection and EGF activation, which may be associated with early neurogenesis and neuronal differentiation in embryos. This molecular shift might contribute to the development of mice exhibiting increased physical activity and enlarged body size, although these observations remain correlative and require further validation. Full article
(This article belongs to the Section Molecular Genetics)
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18 pages, 969 KiB  
Review
Obesity-Mediated Inflammation and Its Influence on Inflammatory Bowel Disease: Pathophysiology, Clinical Impact, and Therapeutic Implications
by Diego Casas-Deza, Santiago García-López, Vanesa Bernal-Monterde, Cristina Polo-Cuadro, Carmen Yagüe-Caballero and José M. Arbones-Mainar
Biomolecules 2025, 15(8), 1185; https://doi.org/10.3390/biom15081185 - 18 Aug 2025
Viewed by 270
Abstract
Obesity and inflammatory bowel disease (IBD) are two chronic conditions whose prevalence continues to rise globally. Emerging evidence suggests a bidirectional interplay between them, mediated by shared pathophysiological pathways. This narrative review explores the mechanisms Ilinking obesity to IBD development and progression, focusing [...] Read more.
Obesity and inflammatory bowel disease (IBD) are two chronic conditions whose prevalence continues to rise globally. Emerging evidence suggests a bidirectional interplay between them, mediated by shared pathophysiological pathways. This narrative review explores the mechanisms Ilinking obesity to IBD development and progression, focusing on the role of adipose tissue dysfunction. Both diseases exhibit intestinal dysbiosis, low-grade systemic inflammation, and impaired epithelial barrier integrity, contributing to immune activation. Visceral adiposity, particularly mesenteric fat, acts as an immunometabolic organ producing cytokines and adipokines that may exacerbate intestinal inflammation. In Crohn’s disease, mesenteric fat expansion, or “creeping fat”, is associated with transmural inflammation, fibrosis, and luminal narrowing. Epidemiological data on obesity as a risk factor for IBD remain inconsistent due to methodological heterogeneity and confounders. Similarly, the impact of obesity on IBD outcomes, including disease activity, phenotype, and the need for surgery, is debated. While mesenteric surgical approaches like Kono-S anastomosis showed initial promise in reducing recurrence, recent randomized trials offer conflicting results. Finally, metabolic drugs such as statins, metformin, and GLP-1 receptor agonists have demonstrated anti-inflammatory properties with potential utility in IBD management. Prospective studies are warranted to elucidate the clinical significance of obesity and metabolic dysfunction in IBD and evaluate targeted therapeutic strategies. Full article
(This article belongs to the Special Issue Metabolic Inflammation and Insulin Resistance in Obesity)
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17 pages, 4158 KiB  
Article
Exploring the Role of Ferroptosis in the Pathophysiology and Circadian Regulation of Restless Legs Syndrome
by Maria Paola Mogavero, Giovanna Marchese, Giovanna Maria Ventola, Giuseppe Lanza, Oliviero Bruni, Luigi Ferini-Strambi and Raffaele Ferri
Biomolecules 2025, 15(8), 1184; https://doi.org/10.3390/biom15081184 - 18 Aug 2025
Viewed by 142
Abstract
The study objectives were to investigate the role of ferroptosis, the mechanism linking iron accumulation, oxidative stress, and dopaminergic dysfunction, in restless legs syndrome (RLS), and to explore its connection with circadian regulation, a key feature of RLS and a known modulator of [...] Read more.
The study objectives were to investigate the role of ferroptosis, the mechanism linking iron accumulation, oxidative stress, and dopaminergic dysfunction, in restless legs syndrome (RLS), and to explore its connection with circadian regulation, a key feature of RLS and a known modulator of ferroptosis. We conducted pathway and gene expression analyses in 17 RLS patients and 39 controls, focusing on pathways related to ferroptosis, oxidative stress, iron metabolism, dopaminergic signaling, circadian rhythms, and immune responses. Enrichment analysis, differential gene expression, and cross-pathway gene overlaps were assessed. Ferroptosis and efferocytosis pathways were significantly upregulated in RLS, while oxidative phosphorylation, phosphatidylinositol signaling, PI3K-Akt, FoxO, and adipocytokine pathways were downregulated. The circadian rhythm pathway was markedly suppressed, with 12 circadian genes downregulated, suggesting that circadian disruption may drive ferroptosis activation. Decreased expression of protective pathways, including antioxidant responses and autophagy, was associated with increased iron accumulation, oxidative stress, and inflammation. Dopaminergic synapse genes were upregulated, possibly as a compensatory response to neuronal damage. Several genes overlapped across ferroptosis, circadian, and dopaminergic pathways, indicating a shared pathogenic mechanism. Our findings support a model in which circadian disruption promotes ferroptosis in RLS, contributing to iron overload, oxidative damage, and dopaminergic dysfunction. This pathogenic cascade may also enhance immune activation and inflammation. Circadian regulation and ferroptosis emerge as promising therapeutic targets in RLS. Further studies in larger cohorts are warranted to validate these mechanistic insights. Full article
(This article belongs to the Special Issue Biomolecules and Materials Based Approaches in Biomedical Field: 2nd Edition)
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15 pages, 3483 KiB  
Article
Engineering Protein–Peptide Interfaces via Combinatorial Mutagenesis and Mass Photometric Screening
by Bitasadat Hosseini, Mohammed Ashraf, Philip Kitchen, Anupama Chembath, Russell Collighan, Corinne M. Spickett, Lynne Regan and Anna V. Hine
Biomolecules 2025, 15(8), 1183; https://doi.org/10.3390/biom15081183 - 18 Aug 2025
Viewed by 177
Abstract
The SpyTag–SpyCatcher system, developed by the Howarth lab, is based on splitting the CnaB2 domain from Streptococcus pyogenes into two parts: a 13-amino-acid SpyTag and a 116-amino-acid SpyCatcher. Upon incubation, they spontaneously form a covalent isopeptide bond between Asp7 (SpyTag) and Lys31 (SpyCatcher). [...] Read more.
The SpyTag–SpyCatcher system, developed by the Howarth lab, is based on splitting the CnaB2 domain from Streptococcus pyogenes into two parts: a 13-amino-acid SpyTag and a 116-amino-acid SpyCatcher. Upon incubation, they spontaneously form a covalent isopeptide bond between Asp7 (SpyTag) and Lys31 (SpyCatcher). This study explores whether the interaction specificity can be modulated by altering hydrophobic residues within the SpyCatcher binding pocket and corresponding SpyTag positions, potentially to create orthogonal SpyTag–SpyCatcher pairs. Libraries of SpyCatcher and SpyTag were created by partial saturation mutagenesis using overlap PCR and MAX randomisation, respectively. To assess the specificity of the SpyCatcher–SpyTag interaction within the resulting protein mixtures, a novel screening strategy based on mass photometry was developed to detect isopeptide bond formation. We demonstrate tolerance to mutation in the hydrophobic binding pocket of SpyCatcher in terms of binding native SpyTag and demonstrate what to our knowledge constitutes the first example of using mass photometry to examine the interactions of small libraries of proteins with a given ligand. Mass photometry detects stable interactions whether covalent or not and so this study suggests the prospect of employing mass photometry for more general application in protein engineering. Full article
(This article belongs to the Special Issue Functional Peptides and Their Interactions (3rd Edition))
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41 pages, 868 KiB  
Review
Reconstructing the Antibiotic Pipeline: Natural Alternatives to Antibacterial Agents
by Chiemerie T. Ekwueme, Ifeoma V. Anyiam, David C. Ekwueme, Christian K. Anumudu and Helen Onyeaka
Biomolecules 2025, 15(8), 1182; https://doi.org/10.3390/biom15081182 - 18 Aug 2025
Viewed by 351
Abstract
The discovery of penicillin led to remarkable progress in the treatment of diseases and far-reaching advancements in novel antibiotics’ development and use. However, the uncontrolled use and abuse of antibiotics in subsequent years have led to the emergence of the antimicrobial resistance (AMR) [...] Read more.
The discovery of penicillin led to remarkable progress in the treatment of diseases and far-reaching advancements in novel antibiotics’ development and use. However, the uncontrolled use and abuse of antibiotics in subsequent years have led to the emergence of the antimicrobial resistance (AMR) crisis, which now threatens modern medicine. There is an increasing number of emerging and reemerging infectious diseases, which have worsened the state of AMR and pose a serious threat to global health. The World Health Organization (WHO) reports the inadequacy of the drug development pipeline to meet the needs of the pharmaceutical sector in the face of AMR, and this poses a significant challenge in the treatment of diseases. Natural products (NPs) represent a promising group of antibiotic alternatives that can potentially mitigate AMR, as they bypass the pharmacodynamics of traditional antibiotics, thereby making them immune to the mechanisms of AMR. NPs, including plant derivatives, bacteriophages, metals, antimicrobial peptides, enzymes, and immune modulators, as monotherapies or in synergism with existing antibiotics, are gaining attention in a bid to reconstruct the antibiotic pipeline. Harnessing these as antimicrobial agents to curb AMR can help to provide sufficient defence against these infectious pathogens. The current review provides a comprehensive overview of the state of AMR and the potential of the above-mentioned antibiotic alternatives. Additionally, we discuss progress made and research breakthroughs in the application of these alternative therapies in humans, exploring findings from clinical trials and experimental models. The review further evaluates the advancement in technology, interdisciplinary approaches to the formulation and utilisation of NPs, and collaborations in alternative drug development. The research gaps present in this ever-evolving field are highlighted and evaluated together with regulatory issues, safety concerns, and technical difficulties in implementation. Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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21 pages, 3385 KiB  
Article
Targeting HMGCS2: Ketogenesis Suppression Accelerates NAFLD Progression in T2DM Comorbidity, While Cynaroside Ameliorates NASH in Concomitant T2DM
by Yongsheng Shu, Wanqing Shen, Wanyu Feng, Meijun Pan, Xinyi Xu, Shuguo Zheng and Huanhuan Jin
Biomolecules 2025, 15(8), 1181; https://doi.org/10.3390/biom15081181 - 18 Aug 2025
Viewed by 194
Abstract
Patients with concurrent non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) exhibit increased susceptibility to non-alcoholic steatohepatitis (NASH), advanced hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. This study investigated the contribution of ketogenesis to T2DM-mediated NAFLD exacerbation and elucidated the therapeutic [...] Read more.
Patients with concurrent non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) exhibit increased susceptibility to non-alcoholic steatohepatitis (NASH), advanced hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. This study investigated the contribution of ketogenesis to T2DM-mediated NAFLD exacerbation and elucidated the therapeutic mechanism of cynaroside in NASH-complicated T2DM. Male C57BL/6J mice were given CDAHFD combined with streptozotocin to establish stage-specific NAFLD with T2DM models. Hepatic HMGCS2 expression was modulated via tail vein injection of adenoviral vectors for HMGCS2 overexpression or knockdown. Cynaroside was administered orally from week 5 to week 8. The results showed that concurrent T2DM accelerated NAFLD progression, accompanied by a dysregulated ketogenesis that was correlated with disease severity. Hepatic HMGCS2 expression paralleled circulating ketone body concentrations, indicating that HMGCS2-mediated ketogenic dysregulation contributed to NAFLD pathogenesis in T2DM contexts. HMGCS2 overexpression in NASH-T2DM models significantly attenuated steatohepatitis progression through the enhancement of ketogenesis. Cynaroside administration ameliorated hepatic pathology in NASH-T2DM mice by (1) reducing hepatocellular injury and lobular inflammation; (2) decreasing intrahepatic lipid accumulation; and (3) suppressing hepatocyte senescence and the secretion of SASP factors. Mechanistically, cynaroside exerted therapeutic effects via HMGCS2-mediated ketogenesis. Our data demonstrated that ketogenic modulation is a viable therapeutic strategy to delay T2DM-NAFLD progression. Full article
(This article belongs to the Section Molecular Medicine)
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26 pages, 3299 KiB  
Article
Discovery of Novel 2-Substituted Aniline Pyrimidine Based Derivatives as Potent Mer/c-Met Dual Inhibitors with Improvement Bioavailability
by Jixia Yang, Daowei Huang, Ruojin Wang, Pengxin Fan, Rourou Li and Donglai Ma
Biomolecules 2025, 15(8), 1180; https://doi.org/10.3390/biom15081180 - 18 Aug 2025
Viewed by 244
Abstract
This study reports the rational design and systematic evaluation of a novel series of 2-substituted aniline pyrimidine derivatives as dual Mer/c-Met inhibitors. Among the synthesized compounds, 17c demonstrated potent dual kinase inhibition, with IC50 values of 6.4 ± 1.8 nM (Mer) and [...] Read more.
This study reports the rational design and systematic evaluation of a novel series of 2-substituted aniline pyrimidine derivatives as dual Mer/c-Met inhibitors. Among the synthesized compounds, 17c demonstrated potent dual kinase inhibition, with IC50 values of 6.4 ± 1.8 nM (Mer) and 26.1 ± 7.7 nM (c-Met). The compound exhibited significant antiproliferative activity across multiple cancer cell lines (HepG2, MDA-MB-231, and HCT116), while showing minimal hERG channel inhibition (IC50 > 40 μM), indicating favorable cardiac safety. Pharmacokinetic profiling revealed high metabolic stability in human liver microsomes (t1/2 = 53.1 min) and moderate oral bioavailability (F: 45.3%), with strong plasma protein-binding affinity (>95%). Mechanistic studies further demonstrated that 17c dose-dependently suppressed HCT116 cell migration and induced apoptosis. These integrated pharmacological properties position 17c as a promising therapeutic candidate for dual Mer/c-Met drive malignancies. Full article
(This article belongs to the Section Molecular Medicine)
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21 pages, 1238 KiB  
Review
Complement Cascades and Brain Disorders
by Ivana Jovčevska, Alja Videtič Paska and Katarina Kouter
Biomolecules 2025, 15(8), 1179; https://doi.org/10.3390/biom15081179 - 17 Aug 2025
Viewed by 302
Abstract
The complement system is a vital component of innate immunity. Besides its roles in pathogen defense, its significance in neurodevelopment, neurodegeneration, and cancer progression is beginning to be recognized. We performed a comprehensive literature review to summarize the involvement and dysregulation of the [...] Read more.
The complement system is a vital component of innate immunity. Besides its roles in pathogen defense, its significance in neurodevelopment, neurodegeneration, and cancer progression is beginning to be recognized. We performed a comprehensive literature review to summarize the involvement and dysregulation of the complement system in three main CNS-associated conditions: Alzheimer’s disease, schizophrenia, and glioma. In Alzheimer’s disease, activation of the complement system contributes to neuroinflammation, synaptic loss, and neuronal death. In glioblastoma, complement promotes tumor growth, immune evasion, and therapy resistance. In schizophrenia, genetic variations in complement components, particularly C4A, are associated with synaptic pruning abnormalities and disease susceptibility. We conclude that the complement system has a dual role of protector and pathogenic mediator in the central nervous system. While it is critical in neurodegenerative, oncological, and psychiatric disorders, its role is not understood well enough. For therapeutic purposes, targeting the complement system may open new frontiers for therapeutic interventions without disrupting important physiological processes. More research is needed to elucidate the exact roles of the complement and help translate these findings into clinical settings. Full article
(This article belongs to the Special Issue Biomarkers in Neurodegenerative Diseases: Shaping the Future of Diagnosis and Treatment)
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