Biomolecules

18 pages, 8275 KiB

Open AccessArticle

Targeted Regulation of HSP70 by the ARP2/3 Complex in Mammary Epithelial Cells and Its Impact on Host Cell Apoptosis

by Tingji Yang, Bo Fang, Yan Chen, Dan Bao, Jiang Zhang, Peiwen Liu, Zhiwei Duan, Yuxuan He, Xingxu Zhao, Quan-Wei Zhang, Wei-Tao Dong and Yong Zhang

Biomolecules 2025, 15(4), 538; https://doi.org/10.3390/biom15040538 (registering DOI) - 7 Apr 2025

Abstract

Mastitis is frequently triggered by the bacterial disruption of the epithelial cell barrier. The actin-related protein 2/3 complex (Arp2/3), a major endogenous protein involved in cytoskeletal regulation, plays a crucial role in preserving epithelial barrier integrity during inflammation; however, its specific role in [...] Read more.

Mastitis is frequently triggered by the bacterial disruption of the epithelial cell barrier. The actin-related protein 2/3 complex (Arp2/3), a major endogenous protein involved in cytoskeletal regulation, plays a crucial role in preserving epithelial barrier integrity during inflammation; however, its specific role in mastitis progression remains unclear. This study aims to use lipopolysaccharide (LPS) to establish mammary alveolar cells-large T antigen cells (MAC-T is a bovine mammary epithelial cell line) and mouse models of mastitis, investigating the functional relationship between actin-related protein 2/3 complex subunits 3 (ARPC3) and 4 (ARPC4) and heat shock protein 70 (HSP70) during mammary epithelial cell inflammation and assessing its effects on apoptosis. Transcriptomic sequencing initially identified 48 differentially expressed genes associated with the bacterial invasion of epithelial cells and apoptosis. Further molecular biology analyses showed a significant upregulation of ARPC3/ARPC4 and HSP70 expression during inflammation, along with a marked increase in apoptosis rates. When ARPC3/ARPC4 was inhibited using CK666, HSP70 expression further increased compared to the LPS group, while inflammatory factors, apoptosis rates, and apoptosis-related protein expression were notably reduced. These findings indicate that targeting ARPC3/ARPC4 to regulate HSP70 can promote inflammation and apoptosis, highlighting its potential as a therapeutic target for mastitis. Full article

(This article belongs to the Section Cellular Biochemistry)

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14 pages, 4444 KiB

Open AccessCommunication

A pH-Responsive Dendritic-DNA-Based Nanohydrogel for Dual Drug Delivery

by Jing Zhao, Jingyuan Wu, Yiqi Fan, Chao Yu, Le Yu and Fangwei Shao

Biomolecules 2025, 15(4), 537; https://doi.org/10.3390/biom15040537 (registering DOI) - 6 Apr 2025

Abstract

The rational design of multifunctional drug delivery systems capable of achieving precise drug release remains a huge challenge. Herein, we designed a stimuli-responsive dendritic-DNA-based nanohydrogel as a nanocarrier to achieve the co-delivery of doxorubicin and HMGN5 mRNA-targeting antisense oligonucleotides, thus achieving dual therapeutic [...] Read more.

The rational design of multifunctional drug delivery systems capable of achieving precise drug release remains a huge challenge. Herein, we designed a stimuli-responsive dendritic-DNA-based nanohydrogel as a nanocarrier to achieve the co-delivery of doxorubicin and HMGN5 mRNA-targeting antisense oligonucleotides, thus achieving dual therapeutic effects. The nanocarrier, constructed from dendritic DNA with three crosslinking branches and one loading branch, formed biocompatible and programmable DNA nanohydrogels. The C-rich sequences in the crosslinking branches conferred pH sensitivity, while the loading strand enabled efficient incorporation of a shielding DNA/ASO complex. DOX encapsulation yielded a chemo–gene co-delivery platform. Upon cellular uptake by cancer cells, the nanocarrier disassembled in the acidic tumor microenvironment, releasing DOX for chemotherapy and ASOs via toehold-mediated strand displacement (TMSD) for targeted gene silencing. Cellular studies demonstrated significantly enhanced cancer cell inhibition compared to single-agent treatments, highlighting strong combined effects. This study provides a novel strategy for tumor-microenvironment-responsive co-delivery, enabling precise, on-demand release of therapeutic agents to enhance combined chemo–gene therapy. Full article

(This article belongs to the Section Bio-Engineered Materials)

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39 pages, 3420 KiB

Open AccessArticle

Synergistic Effects of UVB and Ionizing Radiation on Human Non-Malignant Cells: Implications for Ozone Depletion and Secondary Cosmic Radiation Exposure

by Angeliki Gkikoudi, Gina Manda, Christina Beinke, Ulrich Giesen, Amer Al-Qaaod, Elena-Mihaela Dragnea, Maria Dobre, Ionela Victoria Neagoe, Traimate Sangsuwan, Siamak Haghdoost, Spyridon N. Vasilopoulos, Sotiria Triantopoulou, Anna Georgakopoulou, Ioanna Tremi, Paraskevi N. Koutsoudaki, Sophia Havaki, Vassilis G. Gorgoulis, Michael Kokkoris, Faton Krasniqi, Georgia I. Terzoudi and Alexandros G. Georgakilas Show full author list Hide full author list

Biomolecules 2025, 15(4), 536; https://doi.org/10.3390/biom15040536 (registering DOI) - 6 Apr 2025

Abstract

The ozone layer in the Earth’s atmosphere filters solar radiation and limits the unwanted effects on humans. A depletion of this ozone shield triggered by a violent Sun would permit hazardous levels of UV solar radiation, especially in the UVB range, to bombard [...] Read more.

The ozone layer in the Earth’s atmosphere filters solar radiation and limits the unwanted effects on humans. A depletion of this ozone shield triggered by a violent Sun would permit hazardous levels of UV solar radiation, especially in the UVB range, to bombard Earth’s surface, resulting in potentially significant effects on human health. The concern for these adverse effects intensifies if we consider that the UVB solar radiation is combined with secondary cosmic radiation (SCR) components, such as protons and muons, as well as terrestrial gamma rays. This research aims to delve into the intricate interplay between cosmic and solar radiation on earth at the cellular level, focusing on their synergistic effects on human cell biology. Through a multidisciplinary approach integrating radiobiology and physics, we aim to explore key aspects of biologic responses, including cell viability, DNA damage, stress gene expression, and finally, genomic instability. To assess the impact of the combined exposure, normal human cells (skin fibroblasts, keratinocytes, monocytes, and lymphocytes) were exposed to high-energy protons or gamma rays in combination with UVB. Cellular molecular and cytogenetic biomarkers of radiation exposure, such as DNA damage (γΗ2ΑΧ histone protein and dicentric chromosomes), as well as the expression pattern of various stress genes, were analyzed. In parallel, the MTS reduction and lactate dehydrogenase assays were used as indicators of cell viability, proliferation, and cytotoxicity. Results reveal remaining DNA damage for the co-exposed samples compared to samples exposed to only one type of radiation in all types of cells, accompanied by increased genomic instability and distinct stress gene expression patterns detected at 24–48 h post-exposure. Understanding the impact of combined radiation exposures is crucial for assessing the health risks posed to humans if the ozone layer is partially depleted, with structural and functional damages inflicted by combined cosmic and UVB exposure. Full article

(This article belongs to the Special Issue Molecular Mechanisms in DNA and RNA Damage and Repair)

26 pages, 712 KiB

Open AccessReview

Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy

by Saud Alqahtani, Taha Alqahtani, Krishnaraju Venkatesan, Durgaramani Sivadasan, Rehab Ahmed, Hassabelrasoul Elfadil, Premalatha Paulsamy and Kalaiselvi Periannan

Biomolecules 2025, 15(4), 535; https://doi.org/10.3390/biom15040535 (registering DOI) - 5 Apr 2025

Abstract

Pharmacogenomics is revolutionizing precision medicine by enabling tailored therapeutic strategies based on an individual genetic and molecular profile. Circular RNAs (circRNAs), a distinct subclass of endogenous non-coding RNAs, have recently emerged as key regulators of drug resistance, tumor progression, and therapeutic responses. Their [...] Read more.

Pharmacogenomics is revolutionizing precision medicine by enabling tailored therapeutic strategies based on an individual genetic and molecular profile. Circular RNAs (circRNAs), a distinct subclass of endogenous non-coding RNAs, have recently emerged as key regulators of drug resistance, tumor progression, and therapeutic responses. Their covalently closed circular structure provides exceptional stability and resistance to exonuclease degradation, positioning them as reliable biomarkers and novel therapeutic targets in cancer management. This review provides a comprehensive analysis of the interplay between circRNAs and pharmacogenomics, focusing on their role in modulating drug metabolism, therapeutic efficacy, and toxicity profiles. We examine how circRNA-mediated regulatory networks influence chemotherapy resistance, alter targeted therapy responses, and impact immunotherapy outcomes. Additionally, we discuss emerging experimental tools and bioinformatics techniques for studying circRNAs, including multi-omics integration, machine learning-driven biomarker discovery, and high-throughput sequencing technologies. Beyond their diagnostic potential, circRNAs are being actively explored as therapeutic agents and drug delivery vehicles. Recent advancements in circRNA-based vaccines, engineered CAR-T cells, and synthetic circRNA therapeutics highlight their transformative potential in oncology. Furthermore, we address the challenges of standardization, reproducibility, and clinical translation, emphasizing the need for rigorous biomarker validation and regulatory frameworks to facilitate their integration into clinical practice. By incorporating circRNA profiling into pharmacogenomic strategies, this review underscores a paradigm shift toward highly personalized cancer therapies. circRNAs hold immense potential to overcome drug resistance, enhance treatment efficacy, and optimize patient outcomes, marking a significant advancement in precision oncology. Full article

(This article belongs to the Special Issue The Role of Non-Coding RNAs in Health and Disease)

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20 pages, 4755 KiB

Open AccessArticle

Genome Mining of Pseudarthrobacter sp. So.54, a Rhizospheric Bacteria from Colobanthus quitensis Antarctic Plant

by Dayaimi González, Pablo Bruna, María J. Contreras, Karla Leal, Catherine V. Urrutia, Kattia Núñez-Montero and Leticia Brrientos

Biomolecules 2025, 15(4), 534; https://doi.org/10.3390/biom15040534 (registering DOI) - 5 Apr 2025

Abstract

Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study [...] Read more.

Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study its genomic characteristics and metabolic potential, linked to environmental adaptation and the production of secondary metabolites with possible biotechnological applications. Whole-genome sequencing, assembly, phylogenetic analysis, functional annotation, and genomic islands prediction were performed to determine the taxonomic affiliation and differential characteristics of the strain So.54. Additionally, Biosynthetic Gene Clusters (BGCs) responsible for secondary metabolites production were identified. The assembled genome of strain So.54 has 3,871,805 bp with 66.0% G + C content. Phylogenetic analysis confirmed that strain So.54 belongs to the Pseudarthrobacter genus; nevertheless, its nucleotide and amino acid identity values were below the species threshold. The main metabolic pathways and 64 genomic islands associated with stress defense and environmental adaptation, such as heavy metal resistance genes, were identified. AntiSMASH analysis predicted six BGCs with low or no similarity to known clusters, suggesting potential as novel natural products. These findings indicate that strain So.54 could be a novel Pseudarthrobacter species with significant environmental adaptation and biotechnological potential. Full article

(This article belongs to the Topic Natural Products and Drug Discovery—2nd Edition)

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13 pages, 1395 KiB

Open AccessArticle

The Flavonoids and Monoterpenes from Citrus unshiu Peel Contained in Ninjinyoeito Synergistically Activate Orexin 1 Receptor: A Possible Mechanism of the Orexigenic Effects of Ninjinyoeito

by Kaori Ohshima, Kanako Miyano, Miki Nonaka, Sayaka Aiso, Mao Fukuda, Saho Furuya, Hideaki Fujii and Yasuhito Uezono

Biomolecules 2025, 15(4), 533; https://doi.org/10.3390/biom15040533 (registering DOI) - 5 Apr 2025

Abstract

Cancer cachexia, often observed in patients with advanced-stage cancer, is characterized by the loss of body weight and appetite. The Japanese herbal medicine Ninjinyoeito (NYT), which is composed of 12 crude herbal components, has been used as a therapeutic in Japan to improve [...] Read more.

Cancer cachexia, often observed in patients with advanced-stage cancer, is characterized by the loss of body weight and appetite. The Japanese herbal medicine Ninjinyoeito (NYT), which is composed of 12 crude herbal components, has been used as a therapeutic in Japan to improve anorexia and fatigue, which are commonly observed in cancer patients with cancer cachexia. We have previously reported that Citrus unshiu peel (CUP) contained in NYT can enhance food intake by activating the orexin 1 receptor (OX1R). Using the CellKey™ system, which offers detection of OXR activity in intracellular impedance changes, NYT and CUP were found to activate OX1R, which in turn was inhibited by SB674042, a selective OX1R antagonist. Among the flavonoids contained in CUP, nobiletin and hesperidin, but not naringin, activated OX1R. Furthermore, some monoterpenes contained in CUP, including limonene and linalool, but not terpineol, activated OX1R. In addition, nobiletin and limonene synergistically activated OX1R when added simultaneously. However, neither NYT nor CUP induced OX2R activity. The results collectively suggested that the CUP contained in NYT activates OX1R, but not OX2R, and that flavonoids and monoterpenes in CUP can synergistically activate OX1R. These findings could provide evidence supporting the therapeutic potential of NYT in cancer patients with cachexia. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Metabolic Regulation Used by G Protein-Coupled Receptors)

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22 pages, 4224 KiB

Open AccessArticle

The Role of Glutamatergic Neurons in Changes of Synaptic Plasticity Induced by THz Waves

by Lequan Song, Ji Dong, Wenjing Cheng, Zhengjie Fei, Rui Wang, Zhiwei He, Junmiao Pan, Li Zhao, Hui Wang and Ruiyun Peng

Biomolecules 2025, 15(4), 532; https://doi.org/10.3390/biom15040532 (registering DOI) - 4 Apr 2025

Abstract

Background: Terahertz (THz) waves, lying between millimeter waves and infrared light, may interact with biomolecules due to their unique energy characteristics. However, whether THz waves are neurally regulated remains controversial, and the underlying mechanism is elusive. Methods: Mouse brain slices were [...] Read more.

Background: Terahertz (THz) waves, lying between millimeter waves and infrared light, may interact with biomolecules due to their unique energy characteristics. However, whether THz waves are neurally regulated remains controversial, and the underlying mechanism is elusive. Methods: Mouse brain slices were exposed to 1.94 THz waves for 1 h. Synaptic plasticity was evaluated via transmission electron microscopy (TEM), long-term potentiation (LTP), and neuronal class III β-tubulin (Tuj1) and synaptophysin (SYN) expression. Immunofluorescence (IF) and electrophysiology were used to identify neurons sensitive to THz waves. The calcium activity of excitatory neurons, glutamate receptor currents, and glutamate neuron marker expression was also assessed using calcium imaging, a patch clamp, and Western blotting (WB). Optogenetics and chemogenetics were used to determine the role of excitatory neurons in synaptic plasticity impairment after THz wave exposure. NMDA receptor 2B (GluN2B) was overexpressed in the ventral hippocampal CA1 (vCA1) by a lentivirus to clarify the role of GluN2B in THz wave-induced synaptic plasticity impairment. Results: Exposure to 1.94 THz waves increased postsynaptic density (PSD) thickness and reduced the field excitatory postsynaptic potential (fEPSP) slope and Tuj1 and SYN expression. THz waves diminished vCA1 glutamatergic neuron activity and excitability, neural electrical activity, and glutamate transporter function. THz waves reduced N-methyl-D-aspartate receptor (NMDAR) current amplitudes and NMDAR subunit expression. Activating vCA1 glutamatergic neurons through optogenetics and chemogenetics mitigated THz wave-induced synaptic plasticity impairment. GluN2B subunit overexpression improved synaptic plasticity marker expression, synaptic ultrastructure, and the fEPSP slope. Conclusions: Exposure to 1.94 THz waves decreased synaptic plasticity, glutamatergic neuron excitability, and glutamatergic synaptic transmission in the vCA1. Glutamatergic neuron activation and GluN2B overexpression alleviated THz wave-induced synaptic plasticity impairment; thus, neuromodulation could be a promising therapeutic strategy to mitigate the adverse effects of THz radiation. Full article

(This article belongs to the Section Molecular Medicine)

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23 pages, 8144 KiB

Open AccessArticle

Altering the Properties of Laccases from Ensifer meliloti (Sinorhizobium meliloti) and Cerrena unicolor by Chemical Modifications of Proteins

by Anna Pawlik, Radosław Drozd and Grzegorz Janusz

Biomolecules 2025, 15(4), 531; https://doi.org/10.3390/biom15040531 - 4 Apr 2025

Abstract

Due to their catalytic performance, laccases constitute one of the most promising groups of enzymes for potential applications in modern biotechnology. In this study, we aimed to chemically modify Ensifer meliloti (Sinorhizobium meliloti) and Cerrena unicolor laccase and comparatively characterize the [...] Read more.

Due to their catalytic performance, laccases constitute one of the most promising groups of enzymes for potential applications in modern biotechnology. In this study, we aimed to chemically modify Ensifer meliloti (Sinorhizobium meliloti) and Cerrena unicolor laccase and comparatively characterize the structures of both enzymes. The most characteristic feature was the spatial localization of lysine residues, predominantly positioned distal to the active site region for both compared enzymes. The solvent-accessible surface area (SASA) analysis showed that bacterial laccase was characterized by a larger hydrophobic SASA than the fungal enzyme. The pK_a prediction identified only one Lys in the E. meliloti laccase structure susceptible to modification. Modifications were achieved by using mono- and bifunctional crosslinking agents, and glycosylations were also performed. The degree of protein modification ranged from 0% for glucose- and galactose-modified E. meliloti laccase and citraconic anhydride-modified (CA) C. unicolor laccase to 62.94% for the palmitic acid N-hydroxysuccinimide ester-modified E. meliloti enzyme. The stability of covalently modified laccases over a wide pH and temperature ranges and in the presence of inhibitors was investigated. Protein modifications with polymeric sucrose (PS) and ethylene glycol bis-(succinimidyl succinate) (EGNHS) significantly increased the activity of the bacterial and fungal laccases by 15 and 19%, respectively. Although pH optima remained relatively unchanged by modifications, certain variants, especially CA-modified bacterial protein and EGNHS-modified C. unicolor enzyme, exhibited improved stability at near-neutral pH (6–7). Modification of the bacterial enzyme with glutaraldehyde-carbodiimide (GA-CDI-ver) and of the fungal enzyme with CA was the most effective in improving its thermal stability. Chemical modifications using GA, CDI, GA-CDI, and PS allowed E. meliloti L 3.8 laccase to retain full activity in the presence of 5 mM NaI, whereas CA-, PS-, and EGNHS-modified C. unicolor variants retained their activity even at elevated NaCl concentrations. The results clearly demonstrate that the outcome of chemical modifications is closely linked to enzyme-specific structural features and that selecting an appropriate modification strategy is critical to achieving the desired effect. Full article

(This article belongs to the Special Issue Recent Advances in Laccases and Laccase-Based Bioproducts)

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20 pages, 3206 KiB

Open AccessReview

Modeling Necroptotic and Pyroptotic Signaling in Saccharomyces cerevisiae

by Óscar Barbero-Úriz, Marta Valenti, María Molina, Teresa Fernández-Acero and Víctor J. Cid

Biomolecules 2025, 15(4), 530; https://doi.org/10.3390/biom15040530 - 4 Apr 2025

Abstract

The yeast Saccharomyces cerevisiae is the paradigm of a eukaryotic model organism. In virtue of a substantial degree of functional conservation, it has been extensively exploited to understand multiple aspects of the genetic, molecular, and cellular biology of human disease. Many aspects of [...] Read more.

The yeast Saccharomyces cerevisiae is the paradigm of a eukaryotic model organism. In virtue of a substantial degree of functional conservation, it has been extensively exploited to understand multiple aspects of the genetic, molecular, and cellular biology of human disease. Many aspects of cell signaling in cancer, aging, or metabolic diseases have been tackled in yeast. Here, we review the strategies undertaken throughout the years for the development of humanized yeast models to study regulated cell death (RCD) pathways in general, and specifically, those related to innate immunity and inflammation, with an emphasis on pyroptosis and necroptosis. Such pathways involve the assembly of distinct modular signaling complexes such as the inflammasome and the necrosome. Like other supramolecular organizing centers (SMOCs), such intricate molecular arrangements trigger the activity of enzymes, like caspases or protein kinases, culminating in the activation of lytic pore-forming final effectors, respectively, Gasdermin D (GSDMD) in pyroptosis and MLKL in necroptosis. Even though pathways related to those governing innate immunity and inflammation in mammals are missing in fungi, the heterologous expression of their components in the S. cerevisiae model provides a “cellular test tube” to readily study their properties and interactions, thus constituting a valuable tool for finding novel therapies. Full article

(This article belongs to the Section Cellular Biochemistry)

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17 pages, 2880 KiB

Open AccessReview

Thyroid Hormone Deiodination—Mechanisms and Small Molecule Enzyme Mimics

by Debasish Giri and Govindasamy Mugesh

Biomolecules 2025, 15(4), 529; https://doi.org/10.3390/biom15040529 - 4 Apr 2025

Abstract

Thyroid hormones, biosynthesized in the follicular cells in the thyroid gland, play a crucial role in regulating various important biological processes. The thyroid hormone is synthesized as pro-hormone L-thyroxine (T4), while the active form is primarily produced through the phenolic ring deiodination of [...] Read more.

Thyroid hormones, biosynthesized in the follicular cells in the thyroid gland, play a crucial role in regulating various important biological processes. The thyroid hormone is synthesized as pro-hormone L-thyroxine (T4), while the active form is primarily produced through the phenolic ring deiodination of T4 by iodothyronine deiodinase enzymes (DIOs). Three distinct isoforms of the enzyme are known, which, despite having almost similar amino acid sequences in their active site, differ in their regioselectivity of deiodination towards T4 and its metabolites. However, the precise mechanism and the origin of the differences in the regioselectivity of deiodination by DIOs are still not fully understood. Over the years, several research groups have attempted to mimic this system with small molecules to gain some insight into the reactivity and mechanism. In this review, we will explore the recent developments on the biomimetic deiodination of T4 and its derivatives by using selenium-based enzyme mimetics. For example, naphthalene-based molecules, featuring a 1,8-dichalcogen atom, have been shown to perform tyrosyl ring deiodination of T4 and T3, producing rT3 and 3,3′-T2, respectively. The modification of the electron density around the phenolic ring through substitutions in the 4′-hydroxyl group can alter the regioselectivity of the deiodination by deiodinase mimics. Additionally, we will highlight the recent progress in the development of a dipeptide-based DIO1 mimic, as well as the deiodination of other halogenated thyronine derivatives by mimics. Full article

(This article belongs to the Special Issue Biosynthesis and Function of Thyroid Hormones)

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14 pages, 3899 KiB

Open AccessArticle

The Inhibition of Bromodomain and Extraterminal Domain (BET) Proteins Protects Against Microglia-Mediated Neuronal Loss In Vitro

by Marta Matuszewska, Anna Wilkaniec, Magdalena Cieślik, Marcin Strawski and Grzegorz A. Czapski

Biomolecules 2025, 15(4), 528; https://doi.org/10.3390/biom15040528 - 4 Apr 2025

Abstract

Neuroinflammation is a key feature of all neurodegenerative disorders, including Alzheimer’s disease, and is tightly regulated by epigenetic mechanisms. Among them, bromodomain and extraterminal domain (BET) proteins play a crucial role by recognizing acetylated histones and acting as transcriptional co-regulators to modulate gene [...] Read more.

Neuroinflammation is a key feature of all neurodegenerative disorders, including Alzheimer’s disease, and is tightly regulated by epigenetic mechanisms. Among them, bromodomain and extraterminal domain (BET) proteins play a crucial role by recognizing acetylated histones and acting as transcriptional co-regulators to modulate gene expression. This study investigates the potential of inhibiting BET proteins in preventing microglia-mediated neuronal damage in vitro. Murine BV2 microglial cells were exposed to lipopolysaccharide (LPS) or amyloid-β (Aβ) to induce an inflammatory response, and the subsequent effects on murine HT22 neuronal cells were examined. Among the BET proteins tested, only Brd4 was significantly upregulated in BV2 cells upon pro-inflammatory stimulation. JQ1, a potent pan-inhibitor of BET proteins, suppressed LPS-induced upregulation of pro-inflammatory cytokine mRNA levels, including Il1b, Il6, and Tnf, in BV2 microglia. Pre-treatment with JQ1 attenuated the cytotoxicity of LPS-activated BV2 cells toward neurons. Additionally, conditioned media from Aβ fibril-stimulated BV2 cells induced neuronal cell death, which was partially prevented by pre-treatment with JQ1. Co-culture assays further demonstrated the beneficial effect of BET inhibition. Our findings suggest that targeting BET proteins may offer a neuroprotective strategy by modulating microglial activation, potentially providing therapeutic benefits in neurodegenerative diseases. Full article

(This article belongs to the Special Issue Molecular and Genetic Basis of Neurodegenerative Diseases)

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19 pages, 983 KiB

Open AccessReview

Oxidative Stress in Huntington’s Disease

by Félix Javier Jiménez-Jiménez, Hortensia Alonso-Navarro, Elena García-Martín, Alba Cárcamo-Fonfría, María del Mar Caballero-Muñoz and José A. G. Agúndez

Biomolecules 2025, 15(4), 527; https://doi.org/10.3390/biom15040527 - 4 Apr 2025

Abstract

Although the pathogenesis of the neurodegenerative phenomena of Huntington’s disease (HD) is not well known, in the last 30 years, numerous data have been published that suggest a possible role of oxidative stress. The majority of studies regarding this issue were performed in [...] Read more.

Although the pathogenesis of the neurodegenerative phenomena of Huntington’s disease (HD) is not well known, in the last 30 years, numerous data have been published that suggest a possible role of oxidative stress. The majority of studies regarding this issue were performed in different experimental models of this disease (neurotoxic models such as intraperitoneal injection of 3-nitropropionic acid or intrastriatal injection of quinolinic acid, transgenic animal models for HD, and cell cultures) and, less frequently, in samples of brain tissue, plasma/serum, blood cells, and other tissues from patients with a genetic–molecular diagnosis of presymptomatic and symptomatic HD compared to healthy controls. In this narrative review, we have summarized the data from the main studies in which oxidative stress parameters have been measured both in patients with HD and in experimental models of the same disease, as well as the few studies on gene variants involved in oxidative stress in patients with HD. Most studies addressing this issue in experimental models of HD have shown an increase in markers or oxidative stress, a decrease in antioxidant substances, or both. However, the results of studies on patients with HD have not been conclusive as few studies have been published on the matter. However, a meta-analysis of blood studies on HD patients (including a pool of serum and blood cell studies) has shown an increase in lipid peroxidation markers, OH8dG concentrations, and GPx activity and a decrease in GSH levels. Future prospective and multicenter studies with a long-term follow-up period involving a large number of HD patients and healthy controls are needed to address this topic. Full article

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34 pages, 831 KiB

Open AccessReview

Improving Fat Graft Survival Using Soluble Molecule Preconditioning

by Nabil Amraoui, Isabelle Xu, Jorge Robles Cortés, Chanel Beaudoin Cloutier and Julie Fradette

Biomolecules 2025, 15(4), 526; https://doi.org/10.3390/biom15040526 - 3 Apr 2025

Abstract

Fat grafting is widely used in plastic surgery to correct soft tissue deformities. A major limitation of this technique is the poor long-term volume retention of the injected fat due to tissue remodeling and adipocyte death. To address this issue, various optimizations of [...] Read more.

Fat grafting is widely used in plastic surgery to correct soft tissue deformities. A major limitation of this technique is the poor long-term volume retention of the injected fat due to tissue remodeling and adipocyte death. To address this issue, various optimizations of the grafting process have been proposed. This scoping review focuses on preclinical and clinical studies that investigated the impact of various classes of soluble molecules on fat grafting outcomes. Globally, we describe that these molecules can be classified as acting through three main mechanisms to improve graft retention: supporting adipogenesis, improving vascularization, and reducing oxidative stress. A variety of 18 molecules are discussed, including insulin, VEGF, deferoxamine, botulinum toxin A, apocynin, N-acetylcysteine, and melatonin. Many biomolecules have shown the potential to improve long-term outcomes of fat grafts through enhanced cell survival and higher volume retention. However, the variability between experimental protocols, as well as the scarcity of clinical studies, remain obstacles to clinical translation. In order to determine the best preconditioning method for fat grafts, future studies should focus on dosage optimization, more sustained delivery of the molecules, and the design of homogenous experimental protocols and specific clinical trials. Full article

(This article belongs to the Section Molecular Medicine)

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26 pages, 1750 KiB

Open AccessReview

The Emerging Roles of Vacuolar-Type ATPase-Dependent Lysosomal Acidification in Cardiovascular Disease

by Yan-Yan Chen, Cai-Xia Liu, Hai-Xin Liu and Shi-Yuan Wen

Biomolecules 2025, 15(4), 525; https://doi.org/10.3390/biom15040525 - 3 Apr 2025

Abstract

The vacuolar-type ATPase (V-ATPase) is a multi-subunit enzyme complex that maintains lysosomal acidification, a critical process for cellular homeostasis. By controlling the pH within lysosomes, V-ATPase contributes to overall cellular homeostasis, helping to maintain a balance between the degradation and synthesis of cellular [...] Read more.

The vacuolar-type ATPase (V-ATPase) is a multi-subunit enzyme complex that maintains lysosomal acidification, a critical process for cellular homeostasis. By controlling the pH within lysosomes, V-ATPase contributes to overall cellular homeostasis, helping to maintain a balance between the degradation and synthesis of cellular components. Dysfunction of V-ATPase impairs lysosomal acidification, leading to the accumulation of undigested materials and contributing to various diseases, including cardiovascular diseases (CVDs) like atherosclerosis and myocardial disease. Furthermore, V-ATPase’s role in lysosomal function suggests potential therapeutic strategies targeting this enzyme complex to mitigate cardiovascular disease progression. Understanding the mechanisms by which V-ATPase influences cardiovascular pathology is essential for developing novel treatments aimed at improving outcomes in patients with heart and vascular diseases. Full article

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

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45 pages, 2793 KiB

Open AccessReview

Molecular Modelling in Bioactive Peptide Discovery and Characterisation

by Clement Agoni, Raúl Fernández-Díaz, Patrick Brendan Timmons, Alessandro Adelfio, Hansel Gómez and Denis C. Shields

Biomolecules 2025, 15(4), 524; https://doi.org/10.3390/biom15040524 - 3 Apr 2025

Abstract

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties and interactions with biological targets. Many models predicting bioactive peptide function or structure rely on their intrinsic properties, including the influence of amino [...] Read more.

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties and interactions with biological targets. Many models predicting bioactive peptide function or structure rely on their intrinsic properties, including the influence of amino acid composition, sequence, and chain length, which impact stability, folding, aggregation, and target interaction. Homology modelling predicts peptide structures based on known templates. Peptide–protein interactions can be explored using molecular docking techniques, but there are challenges related to the inherent flexibility of peptides, which can be addressed by more computationally intensive approaches that consider their movement over time, called molecular dynamics (MD). Virtual screening of many peptides, usually against a single target, enables rapid identification of potential bioactive peptides from large libraries, typically using docking approaches. The integration of artificial intelligence (AI) has transformed peptide discovery by leveraging large amounts of data. AlphaFold is a general protein structure prediction tool based on deep learning that has greatly improved the predictions of peptide conformations and interactions, in addition to providing estimates of model accuracy at each residue which greatly guide interpretation. Peptide function and structure prediction are being further enhanced using Protein Language Models (PLMs), which are large deep-learning-derived statistical models that learn computer representations useful to identify fundamental patterns of proteins. Recent methodological developments are discussed in the context of canonical peptides, as well as those with modifications and cyclisations. In designing potential peptide therapeutics, the main outstanding challenge for these methods is the incorporation of diverse non-canonical amino acids and cyclisations. Full article

(This article belongs to the Special Issue Computational Analysis and Conformational Modeling for Protein Structure and Interaction)

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24 pages, 6008 KiB

Open AccessArticle

Phlorizin Protects Against Oxidative Stress and Inflammation in Age-Related Macular Degeneration Model

by Zhen-Yu Liao, Chih-Yu Hung, Yu-Jou Hsu, I-Chia Liang, Yi-Chun Chen, Chao-Hsien Sung and Chi-Feng Hung

Biomolecules 2025, 15(4), 523; https://doi.org/10.3390/biom15040523 - 3 Apr 2025

Abstract

Background:Sweet Tea (Lithocarpus polystachyus Rehd.), a traditional ethnobotanical medicine, contains phlorizin, a dihydrochalcone compound with antioxidative and anti-inflammatory properties. Given the critical role of oxidative stress and inflammation in age-related macular degeneration (AMD), this study tested the hypothesis that phlorizin mitigates oxidative [...] Read more.

Background:Sweet Tea (Lithocarpus polystachyus Rehd.), a traditional ethnobotanical medicine, contains phlorizin, a dihydrochalcone compound with antioxidative and anti-inflammatory properties. Given the critical role of oxidative stress and inflammation in age-related macular degeneration (AMD), this study tested the hypothesis that phlorizin mitigates oxidative damage and inflammation in AMD models, thereby offering therapeutic potential. Materials and Methods: Adult retinal pigmented epithelial cells (ARPE-19) were pre-treated with phlorizin (0.01–0.1 μM) and subjected to oxidative stress induced by ultraviolet A (UVA) radiation or sodium iodate (NaIO₃). Cell viability, reactive oxygen species (ROS) production, MAPK/NF-κB signaling, and the level of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and pro-angiogenic factors (VEGF, MMP2, MMP9) expression were assessed using MTT assays, fluorescence imaging, Western blotting, and RT-qPCR. In vivo, a laser-induced choroidal neovascularization (CNV) mouse model was used to evaluate phlorizin’s effects on CNV formation and vascular leakage via fundus photography and fluorescence angiography. Result: Phlorizin significantly enhanced cell viability, reduced ROS production, inhibited MAPK/NF-κB activation, and downregulated inflammatory and angiogenic mediators. In vivo studies confirmed the reduced CNV formation and vascular leakage following the phlorizin treatment. Conclusions: Phlorizin demonstrated significant protective effects against oxidative stress and inflammation, highlighting its therapeutic potential for treating AMD. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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16 pages, 586 KiB

Open AccessReview

Iatrogenic Dementia: Providing Insight into Transmissible Subtype of Alzheimer’s Disease, Creutzfeldt–Jakob Disease and Cerebral Amyloid Angiopathy

by Stella Karatzetzou, Serafeim Ioannidis, Eleni Konstantinopoulou, Dimitrios Parisis, Theodora Afrantou and Panagiotis Ioannidis

Biomolecules 2025, 15(4), 522; https://doi.org/10.3390/biom15040522 - 3 Apr 2025

Abstract

Within the phenotypic spectrum of Alzheimer’s disease (AD), Creutzfeldt–Jakob disease (CJD) and cerebral amyloid angiopathy (CAA), dementia that is attributed to iatrogenic transmission has increasingly gained scientific attention recently. Newly recognized, this treatment-induced form of dementia may result from exposure to certain medical [...] Read more.

Within the phenotypic spectrum of Alzheimer’s disease (AD), Creutzfeldt–Jakob disease (CJD) and cerebral amyloid angiopathy (CAA), dementia that is attributed to iatrogenic transmission has increasingly gained scientific attention recently. Newly recognized, this treatment-induced form of dementia may result from exposure to certain medical or surgical procedures. The present review aims to explore the distinct features of acquired dementia encompassing a history of potential exposure and relatively early age of onset, highlighting transmission potential with a rather prion-like pattern. Having reviewed all available relevant literature, dementia of iatrogenic etiology represents a new disease entity that requires an individualized investigation process and poses a great clinical challenge as far as patients with AD, CJD and CAA are concerned. Understanding the underlying pathophysiology of these rare forms of dementia may significantly enhance awareness within clinical field of neurodegenerative diseases and facilitate their prompt management. Full article

(This article belongs to the Special Issue Molecular and Genetic Basis of Neurodegenerative Diseases)

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22 pages, 3362 KiB

Open AccessReview

Stimulus–Transcription Coupling of TRPM3 Channels: A Signaling Pathway from the Plasma Membrane to the Nucleus

by Gerald Thiel and Oliver G. Rössler

Biomolecules 2025, 15(4), 521; https://doi.org/10.3390/biom15040521 - 2 Apr 2025

Abstract

Transient receptor potential melastatin-3 (TRPM3) channels are cation channels activated by heat and chemical ligands. TRPM3 regulates heat sensation, secretion, neurotransmitter release, iris constriction, and tumor promotion. Stimulation of TRPM3 triggers an influx of Ca²⁺ ions into the cells and the initiation [...] Read more.

Transient receptor potential melastatin-3 (TRPM3) channels are cation channels activated by heat and chemical ligands. TRPM3 regulates heat sensation, secretion, neurotransmitter release, iris constriction, and tumor promotion. Stimulation of TRPM3 triggers an influx of Ca²⁺ ions into the cells and the initiation of an intracellular signaling cascade. TRPM3 channels are regulated by phosphatidylinositol 4,5-bisphosphate, the βγ subunit of G-protein-coupled receptors, phospholipase C, and calmodulin. Extracellular signal-regulated protein kinase ERK1/2 and c-Jun N-terminal protein kinase (JNK) function as signal transducers. The signaling cascade is negatively regulated by the protein phosphatases MKP-1 and calcineurin and increased concentrations of Zn²⁺. Stimulation of TRPM3 leads to the activation of stimulus-responsive transcription factors controlled by epigenetic regulators. Potential delayed response genes encoding the pro-inflammatory regulators interleukin-8, calcitonin gene-related peptide, and the prostaglandin-synthesizing enzyme prostaglandin endoperoxide synthase-2 have been identified. Elucidating the TRPM3-induced signaling cascade provides insights into how TRPM3 stimulation alters numerous biochemical and physiological parameters within the cell and throughout the organism and offers intervention points for manipulating TRPM3 signaling and function. Full article

(This article belongs to the Special Issue TRP Channels in Cardiovascular and Inflammatory Disease, 2nd Edition)

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19 pages, 2275 KiB

Open AccessArticle

Metabolomics Insights into Salivary Profile in Dogs with Babesia canis Infection

by Josipa Kuleš, Ivana Rubić, Dina Rešetar Maslov, Maša Efendić, Krešimir Martinković, Elizabeta Pongrac, Iva Šmit, Dalibor Potočnjak, Renata Barić Rafaj and Vladimir Mrljak

Biomolecules 2025, 15(4), 520; https://doi.org/10.3390/biom15040520 - 1 Apr 2025

Abstract

Babesiosis is a significant vector-borne zoonotic disease with major global economic and health implications, affecting various vertebrate hosts. Babesia parasites are auxotrophic for essential nutrients, relying on their hosts for metabolic support. This study investigated salivary metabolomic changes in dogs naturally infected with [...] Read more.

Babesiosis is a significant vector-borne zoonotic disease with major global economic and health implications, affecting various vertebrate hosts. Babesia parasites are auxotrophic for essential nutrients, relying on their hosts for metabolic support. This study investigated salivary metabolomic changes in dogs naturally infected with Babesia canis (N = 14) compared to healthy controls (N = 14) using untargeted and targeted mass spectrometry-based approaches. Saliva, a biofluid rich in metabolites, undergoes alterations in response to systemic diseases, making it a promising medium for studying host–pathogen interactions. Metabolomic profiling was performed using a Dionex UltiMate 3000 UHPLC system coupled with a Thermo Orbitrap Q Exactive mass spectrometer. An untargeted analysis detected 2257 salivary features, of which, 868 were significantly altered, with seven metabolites identified by reference to standards. A targeted analysis revealed significant changes in seven metabolites. Functional bioinformatics indicated disruptions in amino acid, nucleotide, and lipid metabolism, alongside alterations in energy production pathways, and purine metabolism. These findings provide critical insights into the metabolic shifts underlying canine babesiosis, supporting the development of advanced diagnostic and therapeutic strategies in the future. This study highlights the intricate interplay between host and pathogen, particularly in nutrient acquisition and metabolic regulation. Full article

(This article belongs to the Section Molecular Biomarkers)

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