International Journal of Molecular Sciences

26 pages, 993 KB

Open AccessArticle

TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features

by Yury V. Milchevskiy, Galina I. Kravatskaya and Yury V. Kravatsky

Int. J. Mol. Sci. 2025, 26(23), 11284; https://doi.org/10.3390/ijms262311284 - 21 Nov 2025

Abstract

Protein structure prediction continues to pose multiple challenges, despite the progress made by ML. While recent deep learning models have achieved a strong performance using embeddings from protein language models, they often ignore non-canonical amino acids and rely heavily on sequence alignments or [...] Read more.

Protein structure prediction continues to pose multiple challenges, despite the progress made by ML. While recent deep learning models have achieved a strong performance using embeddings from protein language models, they often ignore non-canonical amino acids and rely heavily on sequence alignments or evolutionary profiles. Here, we present an improvement to this approach for predicting the secondary protein structure of DSSP classes solely from amino acid sequences. We suggest that ML feature sets should be generated from statistically significant mutually uncorrelated descriptors. The selection of statistically assessed descriptors, including predicting the physicochemical parameters of non-canonical amino acids, is a key component of the proposed method. The statistical significance and influence of each of the suggested features were assessed using a two-step Linear Discriminant Analysis, which permitted the evaluation of the statistical significance of each descriptor and their impact on model accuracy. We applied the set of 109 most influential statistically significant descriptors as a learning model for the two-layer Bi-LSTM network combined with ESMFold2 embeddings. Our method, TruMPET (Training upon Multiple Pre-selected Elements Technique), outperformed all other methods reported in the literature for the non-redundant datasets (CB513: DSSP Q3 = 91.36% and Q8 = 85.41%, TEST2018: DSSP Q3 = 90.64% and Q8 = 84.17%). Full article

(This article belongs to the Special Issue Recent Research of Protein Structure Prediction and Design)

30 pages, 5094 KB

Open AccessReview

Illuminating the Invisible: Fluorescent Probes as Emerging Tools for Micro/Nanoplastic Identification

by Junhan Yang, Kaichao Zheng, Weiqing Chen, Xiaojun Zeng, Yao Chen, Fengping Lin and Daliang Li

Int. J. Mol. Sci. 2025, 26(23), 11283; https://doi.org/10.3390/ijms262311283 - 21 Nov 2025

Abstract

The pervasive environmental contamination by micro- and nanoplastics (MNPs) presents a formidable analytical challenge, necessitating the development of rapid and sensitive detection methods. While conventional techniques often suffer from limitations in sensitivity and throughput, fluorescent probe-based technology has emerged as a powerful alternative. [...] Read more.

The pervasive environmental contamination by micro- and nanoplastics (MNPs) presents a formidable analytical challenge, necessitating the development of rapid and sensitive detection methods. While conventional techniques often suffer from limitations in sensitivity and throughput, fluorescent probe-based technology has emerged as a powerful alternative. This review charts the evolution of these probes, from initial stains relying on hydrophobic adsorption to advanced molecular designs engineered for specific chemical recognition. We critically examine key operational mechanisms, including the solvatochromic response of Nile Red, polarity-discriminatory probes enabling a “microplastic rainbow,” and targeted systems achieving turn-on fluorescence via restriction of intramolecular rotation. Furthermore, we highlight cutting-edge signal enhancement strategies, such as plasmon- and metal-enhanced fluorescence, which amplify detection to the femtogram level. Special emphasis is placed on the distinct challenges posed by nanoplastics, including their propensity for aggregation in aqueous matrices that exacerbates false positives and their superior ability to breach biological barriers, and how AIE luminogens and PEF/MEF strategies mitigate these issues through enhanced signal-to-noise ratios and subcellular resolution, differing from their application to microplastics. Critically, we address the imperative for low-toxicity probe designs, emphasizing biocompatibility and biodegradability criteria to facilitate safe, long-term in vivo tracking and widespread ecological surveillance. The integration of these sophisticated probes with smart, “activate-on-target” systems is paving the way for next-generation MNP analysis, offering critical insights for environmental monitoring and toxicological assessment. Full article

(This article belongs to the Special Issue Toxicity of Metals, Metal-Based Drugs, and Microplastics)

► Show Figures

Graphical abstract

25 pages, 887 KB

Open AccessReview

GAMT Deficiency: Clinical Presentation, Treatment, Diagnosis, Animal Models, Preclinical and Clinical Developments

by Sara Biagiotti, Elena Perla, Serafina Manila Guzzo, Manuela Tolve, Francesca Nardecchia, Luigia Rossi, Claudia Carducci, Tiziana Pascucci, Vincenzo Leuzzi and Mauro Magnani

Int. J. Mol. Sci. 2025, 26(23), 11282; https://doi.org/10.3390/ijms262311282 - 21 Nov 2025

Abstract

Guanidinoacetate Methyl Transferase (GAMT) deficiency is a rare disease characterized by neurodevelopmental derangements, epilepsy, and movement disorders. The condition arises from the combined effect of postnatal brain creatine (Cr) depletion and guanidinoacetate (GAA) toxicity. Consequently, current treatment relies on Cr supplementation [...] Read more.

Guanidinoacetate Methyl Transferase (GAMT) deficiency is a rare disease characterized by neurodevelopmental derangements, epilepsy, and movement disorders. The condition arises from the combined effect of postnatal brain creatine (Cr) depletion and guanidinoacetate (GAA) toxicity. Consequently, current treatment relies on Cr supplementation and metabolic management to reduce GAA accumulation by limiting its synthesis through ornithine supplementation and precursor reduction. Although effective in preventing the severe GAMT phenotype, the therapy is limited in normalizing these metabolites’ concentrations. Recently, interest has been growing in approaches aimed at restoring the mutant enzyme as the primary step toward a cure. Some of these approaches have been investigated at the preclinical level and are here summarized. Interestingly, a mouse model that replicates most of the patients’ features is now available in various labs, and the strong commitment of the Association for Creatine Deficiency has fostered the coordination and support of many of these models’ initiatives. This review introduces readers to the complexity of this ultrarare condition, describes current therapeutic approaches, provides information about the most accurate methods for an early diagnosis, and outlines the main features of the available animal models. Finally, some current preclinical investigations are described, along with some preliminary expectations of emerging data. Full article

(This article belongs to the Collection Feature Papers in Molecular Pathology, Diagnostics, and Therapeutics)

21 pages, 5045 KB

Open AccessArticle

Coprogen B from Talaromyces marneffei ΔsreA: Rapid Iron Chelation and Favorable Partitioning to Deferoxamine

by Bishant Pokharel, Wachiraporn Tipsuwan, Monsicha Pongpom, Teera Chewonarin, Pimpisid Koonyosying, Agostino Cilibrizzi and Somdet Srichairatanakool

Int. J. Mol. Sci. 2025, 26(23), 11281; https://doi.org/10.3390/ijms262311281 - 21 Nov 2025

Abstract

Iron (Fe) chelators are used to treat iron-overloaded disorders, metal detoxification, radionuclides, and molecular imaging; however, they can cause side effects. In this study, we identified and characterized Coprogen B (CPGB), a hexadentate trihydroxamate siderophore secreted by the opportunistic dimorphic fungus Talaromyces marneffei [...] Read more.

Iron (Fe) chelators are used to treat iron-overloaded disorders, metal detoxification, radionuclides, and molecular imaging; however, they can cause side effects. In this study, we identified and characterized Coprogen B (CPGB), a hexadentate trihydroxamate siderophore secreted by the opportunistic dimorphic fungus Talaromyces marneffei and compared its properties with deferoxamine (DFO). Siderophore production was enriched from a ΔsreA strain and purified via Amberlite XAD2 and Sephadex LH20 chromatography, followed by reverse-phase HPLC. Active fractions were confirmed by Ultraviolet–Visible (UV–Vis) spectral fingerprints (≈230 nm) for hydroxamate, with a band at 430–450 nm upon Fe(III) complexation, as well as by chrome azurol A assay, Nuclear Magnetic Resonane (NMR) spectroscopy, High-Performance Liquid Chromatography–Mass Spectrometry (HPLC-MS), and Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF-MS). CPGB exhibited strong molar absorptivity and rapid, concentration-dependent chelation of Fe(III), yielding a sustained binding profile that matched or exceeded that of DFO over time. In determining n-octanol/water partitioning for CPGB and DFO (230 nm) and their Fe(III) complexes, the partitioning (P) assay revealed that CPGB was moderately hydrophilic (P = 0.505 ± 0.063; cLogP = −0.299 ± 0.053), while DFO was strongly hydrophilic (P = 0.098 ± 0.005; cLogP = −1.010 ± 0.022). Fe(III) complexation reduced lipophilicity: CPGB–Fe partitioned ~30–35% into octanol, while DFO–Fe complex partitioned ~7–8%, remaining largely aqueous. Overall, this outcome potentially suggested improved clearance in vivo. These data nominate CPGB as a promising alternative to existing iron chelators. The siderophore exhibited greater lipophilicity, emphasizing better passive membrane permeability than DFO, while siderophore–Fe(III) binding indicated increased biases toward the aqueous phase. Future in vivo studies are warranted to confirm its pharmacokinetics, safety, and therapeutic efficacy. Full article

(This article belongs to the Special Issue Recent Research on Biomimetic Chromatography, QSAR and Chemoinformatics in Molecular Modeling and Drug Design)

► Show Figures

Figure 1

16 pages, 3099 KB

Open AccessArticle

Analysis of Cembrane-Type Diterpenoids from Cultured Soft Coral Sclerophytum flexibile for Inhibition of TGF-β-Induced IL-6 Secretion in Inflammation-Associated Cancer

by Yi-Chen Wang, Shun-Ban Tai, Jenq-Lin Yang, Pei-Feng Liu, Ping-Jyun Sung, Jui-Hsin Su and Chun-Lin Chen

Int. J. Mol. Sci. 2025, 26(23), 11280; https://doi.org/10.3390/ijms262311280 - 21 Nov 2025

Abstract

Cembrane-type diterpenoids (cembranoids), natural compounds derived from soft coral Sclerophytum flexibile, exhibit diverse biological activities including anti-inflammatory, anti-cancer, and anti-viral effects. Our previous research demonstrated that Sinulariolide, a member of this group, effectively inhibits TGF-β-induced IL-6 secretion, thereby suppressing inflammation-associated cancer development. [...] Read more.

Cembrane-type diterpenoids (cembranoids), natural compounds derived from soft coral Sclerophytum flexibile, exhibit diverse biological activities including anti-inflammatory, anti-cancer, and anti-viral effects. Our previous research demonstrated that Sinulariolide, a member of this group, effectively inhibits TGF-β-induced IL-6 secretion, thereby suppressing inflammation-associated cancer development. Building on these findings, the present study employs a structure-activity relationship (SAR) approach to compare the anti-inflammatory properties of various cembranoids extracted from cultured soft coral Sclerophytum flexibile—a sustainable and environmentally friendly source that offers a consistent supply for research and therapeutic development. By isolating multiple cembrane-type analogs and analyzing their structural differences, we identified key chemical features that enhance their ability to interfere with TGF-β signaling and subsequent IL-6 production. The SAR analysis revealed distinct variations in anti-inflammatory efficacy among the tested compounds, pinpointing structural motifs crucial for inhibiting TGF-β-induced IL-6 secretion. These insights deepen our understanding of the molecular basis behind the anti-inflammatory action of cembranoids and guide the optimization of these compounds for potential therapeutic use. Full article

(This article belongs to the Special Issue Bioactive Molecules from Food or Other Natural Sources Against Cancer: 2nd Edition)

25 pages, 1266 KB

Open AccessReview

Monomeric [CRP] and CRP-Controlled Stress and Pain Hypersensitization as Novel Predictors of Cognitive Disturbance and AD in Chronic Inflammatory Disease

by Mark Slevin and Amelia Tero-Vescan

Int. J. Mol. Sci. 2025, 26(23), 11279; https://doi.org/10.3390/ijms262311279 - 21 Nov 2025

Abstract

Chronic low-grade systemic inflammation is increasingly recognized as a key mediator linking stress, pain sensitivity, and cognitive decline. Central to this process are the acute-phase reactants interleukin-6 (IL-6) and C-reactive protein (CRP), which serve as biomarkers of systemic inflammation while promoting neuroimmune dysregulation. [...] Read more.

Chronic low-grade systemic inflammation is increasingly recognized as a key mediator linking stress, pain sensitivity, and cognitive decline. Central to this process are the acute-phase reactants interleukin-6 (IL-6) and C-reactive protein (CRP), which serve as biomarkers of systemic inflammation while promoting neuroimmune dysregulation. Emerging evidence implicates the IL-6–CRP axis in the amplification of pain perception, central sensitization, and stress hypersensitivity, ultimately promoting neurodegenerative processes such as those observed in Alzheimer’s disease (AD) and vascular dementia. Monomeric CRP (mCRP), a proinflammatory isoform generated under mechanical or oxidative stress, can trigger histone modifications (e.g., H3 citrullination), activate endothelial and immune cells, and exacerbate inflammatory pain pathways. These mechanisms are further modulated by genetic and epigenetic factors, including IL-6/CRP/NR3C1 gene variant expression; promoter methylation; and stress-responsive microRNAs, which intersect with dysregulation of the hypothalamic–pituitary–adrenal (HPA) axis, impairing immune resolution and neurocognitive resilience. Psychosocial stressors, such as the burden of caregiving or perfectionistic cognitive patterns, amplify IL-6 and CRP levels, particularly when pain is present, suggesting a synergistic interaction between emotional distress and somatic inflammation. Specifically, elevated CRP is associated with increased pain sensitivity, lower pain thresholds, and cognitive decline even in subclinical populations, providing a feedforward model in which chronic stress and pain potentiate systemic inflammation, disrupt neuroendocrine feedback, and accelerate neurodegenerative pathology. However, in this model, the potentially critical mechanistic and pathological role of mCRP remains to be discovered. This review addresses the missing elements of these overlapping pathways and discusses the therapeutic potential of targeting IL-6–CRP signaling, stress regulation, and epigenetic modifiers as strategies to ameliorate inflammation-driven cognitive decline and enhance stress resistance in chronic disease contexts. We propose that plasma mCRP or more likely the isoform-aware metric, the mCRP/CRP ratio, will provide a biologically anchored, potentially more discriminative approach to vascular-neuroimmune risk and capture the propensity for local effector signaling, likely outperforming hs-CRP or IL-6 alone for risk stratification across neurovascular and stress-sensitized pain phenotypes. Full article

(This article belongs to the Special Issue Novel Therapeutic Strategies for Neurodegenerative Disease)

37 pages, 6282 KB

Open AccessReview

Targeting Lactylation for Cancer: Mechanisms, Effects, and Therapeutic Prospects

by Dong Chang, Daolong Li, Yuxi Sun, Jiekang Shi, Shengping Zhang and Chuangui Wang

Int. J. Mol. Sci. 2025, 26(23), 11278; https://doi.org/10.3390/ijms262311278 - 21 Nov 2025

Abstract

Recent studies reveal that lysine lactylation plays a pivotal and multifaceted role in tumor progression. Here, we provide a systematic overview of the mechanisms underlying lactylation, highlighting its regulation of tumor metabolic reprogramming and immune microenvironment remodeling. We further summarize how lactylation drives [...] Read more.

Recent studies reveal that lysine lactylation plays a pivotal and multifaceted role in tumor progression. Here, we provide a systematic overview of the mechanisms underlying lactylation, highlighting its regulation of tumor metabolic reprogramming and immune microenvironment remodeling. We further summarize how lactylation drives malignancy across diverse cancer types and discuss emerging strategies to therapeutically target lactylation in cancer. By integrating current findings, this review offers a comprehensive framework for understanding lactylation in tumor biology and identifies key gaps for future investigation, thereby providing a valuable reference for both basic research and therapeutic development. Full article

(This article belongs to the Special Issue Molecular Biology of Cancer—Implications for Diagnosis and Treatment: 3rd Edition)

25 pages, 6971 KB

Open AccessArticle

Docetaxel and Gemcitabine Modulate Cellular Effects and Long Non-Coding RNA Profiles in Non-Small Cell Lung Cancer

by Andrei-Alexandru Tirpe, Lajos Raduly, Oana Zanoaga, Stefan Strilciuc and Ioana Berindan-Neagoe

Int. J. Mol. Sci. 2025, 26(23), 11277; https://doi.org/10.3390/ijms262311277 - 21 Nov 2025

Abstract

Lung cancer remains the most prevalent and deadliest malignancy worldwide. According to the European Society for Medical Oncology guidelines for non-oncogene-addicted metastatic non-small-cell lung cancer (NSCLC), patients with metastatic squamous-cell carcinoma (LUSC) or metastatic non-squamous NSCLC with performance status 2 and PD-L1 < [...] Read more.

Lung cancer remains the most prevalent and deadliest malignancy worldwide. According to the European Society for Medical Oncology guidelines for non-oncogene-addicted metastatic non-small-cell lung cancer (NSCLC), patients with metastatic squamous-cell carcinoma (LUSC) or metastatic non-squamous NSCLC with performance status 2 and PD-L1 < 50% may receive single-agent chemotherapy with gemcitabine (GEM), docetaxel (DOC), or vinorelbine. Herein, we investigated the cellular effects of GEM/DOC as monotherapies in NSCLC cell lines—lung adenocarcinoma, A549 and CALU6; LUSC, H520 and H1703. Treatment with GEM/DOC may induce apoptotic cell death in all NSCLC cell lines at 48 h. GEM/DOC can affect cancer cell migration assessed by scratch assay. Both GEM/DOC may produce distinct effects on cell cycle arrest, consistent with their particular pharmacodynamic effects. Furthermore, GEM/DOC induced signals consistent with autophagic activity in LUSC cell lines, but only GEM triggered signals consistent with autophagic activity in the CALU6 cell line. Analysis of three key long non-coding RNAs (lncRNAs)—MALAT1, NEAT1, and HOTAIR—showed variable expression in the studied cell lines as a potential response to DOC and GEM treatment. Our findings indicate different cellular effects of GEM and DOC in NSCLC cell lines and provide an overview of how currently used chemotherapeutics may influence the expression of lncRNAs. Full article

(This article belongs to the Special Issue Apoptosis and Autophagy in Cancer Research)

27 pages, 2474 KB

Open AccessArticle

The Gene Encoding the RCC1 (Regulator of Chromosome Condensation 1) Protein in Drosophila melanogaster and Homo sapiens

by Vera A. Turtapkina, Maria V. Maltseva, Elena V. Evtushenko, Sima S. Gatzkaya, Evgeniya S. Omelina, Nadezhda V. Battulina, Natalia A. Lemskaya, Victor V. Shloma, Alexander V. Vershinin, Tatyana Yu. Vatolina and Igor F. Zhimulev

Int. J. Mol. Sci. 2025, 26(23), 11276; https://doi.org/10.3390/ijms262311276 - 21 Nov 2025

Abstract

The RCC1 gene is active in ensuring many cellular functions related to cell division in Drosophila melanogaster and Homo sapiens. A detailed comparison of the structure and functions of the RCC1 gene in Drosophila melanogaster and Homo sapiens was carried out using [...] Read more.

The RCC1 gene is active in ensuring many cellular functions related to cell division in Drosophila melanogaster and Homo sapiens. A detailed comparison of the structure and functions of the RCC1 gene in Drosophila melanogaster and Homo sapiens was carried out using different analytical techniques (bioinformatics, immunofluorescence and confocal microscopy, FISH, and molecular genetic methods). The Drosophila RCC1 gene belongs to the family of housekeeping genes, since it resides in the interbands and gray bands of polytene chromosomes within aquamarine/lazurite chromatin in D. melanogaster. Furthermore, the databases demonstrate that RCC1 in D. melanogaster is expressed in all the tissues at all the developmental stages. According to The Human Protein Atlas, RCC1 in humans also exhibits low tissue specificity for 29 tissues. Immunostaining of polytene chromosomes with RCC1 antibodies revealed approximately 260 sites of RCC1 protein localization exclusively in black bands (sites of developmental genes) and in heterochromatin. The size of the coding gene portions is almost identical for D. melanogaster and H. sapiens, being ~2 kb. The group of Drosophila proteins related to condensed chromatin, RCC1 being a member of this group, has homologs forming similar interaction networks in humans. The conserved nature of the RCC1 gene has been confirmed by cell cycle studies in both species. It was found that expression of the RCC1 gene is upregulated in glioblastoma; the RCC1 protein predominantly resides on centrioles during metaphase. Full article

(This article belongs to the Special Issue Drosophila: A Versatile Model in Biology and Medicine—2nd Edition)

34 pages, 2315 KB

Open AccessReview

Cardiovascular Disease in the Context of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): A Comprehensive Narrative Review

by Attia Mustafa, Chris Kite, Lukasz Lagojda, Alexander Dallaway, Kamaljit Kaur Chatha, Nwe Ni Than, Eva Kassi, Ioannis Kyrou and Harpal S. Randeva

Int. J. Mol. Sci. 2025, 26(23), 11275; https://doi.org/10.3390/ijms262311275 - 21 Nov 2025

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic hepatic disease with a rising global prevalence (25–38% of the general population). As a new term, MASLD was introduced in 2023 to replace the previous nomenclature of non-alcoholic fatty liver disease (NAFLD) and metabolic [...] Read more.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic hepatic disease with a rising global prevalence (25–38% of the general population). As a new term, MASLD was introduced in 2023 to replace the previous nomenclature of non-alcoholic fatty liver disease (NAFLD) and metabolic dysfunction-associated fatty liver disease (MAFLD). This new term/definition introduced changes in the diagnostic criteria and underscores the direct link between cardio-metabolic risk and this prevalent liver disease. In this context, the present review examines the clinical and pathophysiological links between MASLD and cardiovascular disease (CVD), providing a robust evidence synthesis of primarily systematic review data on the association between MASLD and coronary artery disease (CAD), atrial fibrillation (AF), and heart failure (HF). This association appears to be not only synergistic, but also independent of other known CVD risk factors, highlighting MASLD as a key cardio-metabolic risk factor that merits prompt diagnosis and treatment. The development of MASLD-related cardiovascular morbidity increases with the severity of the underlying hepatic pathology, particularly with progression to steatohepatitis and fibrosis. Notably, growing evidence highlights the links between MASLD and CVD through cardiac structural, electrical, and functional alterations that can progress to CAD, AF, and new-onset HF. Recognizing these links in clinical practice underscores the importance of early detection and multi-disciplinary management of MASLD to prevent disease progression and CVD complications. Full article

(This article belongs to the Special Issue Molecular Advances in Metabolic Dysfunction-Associated Steatotic Liver Disease)

21 pages, 1186 KB

Open AccessArticle

Differential Subcellular Distribution and Physiological Responses of Artemisia argyi to Pb, Cu, and Zn Stress

by Yu Guo, Xiaoqi Zhang, Tianhong Zhou, Qianqian Yu and Wenfang Hao

Int. J. Mol. Sci. 2025, 26(23), 11274; https://doi.org/10.3390/ijms262311274 - 21 Nov 2025

Abstract

Artemisia argyi is recognized as a promising phytoremediation crop due to its high economic value. A 90-day greenhouse pot experiment was conducted to assess the effects of different doses of lead (Pb), copper (Cu), and zinc (Zn) on the growth, heavy metal accumulation, [...] Read more.

Artemisia argyi is recognized as a promising phytoremediation crop due to its high economic value. A 90-day greenhouse pot experiment was conducted to assess the effects of different doses of lead (Pb), copper (Cu), and zinc (Zn) on the growth, heavy metal accumulation, and physiological responses of A. argyi cultivated in alkaline soil. The results indicated that exposure to Pb, Cu, or Zn significantly decreased photosynthetic pigment content and induced substantial reactive oxygen species generation, consequently elevating glutathione and malondialdehyde levels. Biomass and heavy metal accumulation data demonstrated that A. argyi possesses high tolerance to Pb stress, characterized by low translocation rates and predominant accumulation in roots and cell walls. This retention mechanism supports its potential as a lead-enriching plant while maintaining economic value. In contrast, Zn exhibited the highest translocation rate among the metals tested. Although the proportion of Zn in organelles decreased with increasing stress intensity, its enrichment in organelles remained notably higher than that under Pb or Cu stress. Copper exhibited intermediate mobility, with limited accumulation in organelles, thereby inducing relatively minor cellular damage. These findings elucidate the metal-specific accumulation patterns in A. argyi and underscore its potential as a phytoremediation crop for heavy metal-contaminated soils. Full article

(This article belongs to the Section Molecular Toxicology)

17 pages, 2073 KB

Open AccessArticle

Polystyrene Micro- and Nanoplastic Exposure Triggers an Activation and Stress Response in Human Astrocytes

by Sonia Kiran, Uvindu Thilanka, Yu Xue and Qing-Xiang Amy Sang

Int. J. Mol. Sci. 2025, 26(23), 11273; https://doi.org/10.3390/ijms262311273 - 21 Nov 2025

Abstract

Recent evidence indicates the presence of micro- and nanoplastics in the human brain, with higher accumulation observed in patients with dementia. However, their mechanistic effects on the human brain at the cellular level remain underexplored. Astrocytes play a crucial role in repairing neurons [...] Read more.

Recent evidence indicates the presence of micro- and nanoplastics in the human brain, with higher accumulation observed in patients with dementia. However, their mechanistic effects on the human brain at the cellular level remain underexplored. Astrocytes play a crucial role in repairing neurons following injury. The dysfunction of these cells can lead to chronic inflammation, a hallmark of neurodegenerative diseases. Here, we investigated the cytotoxic responses of primary human astrocytes exposed to polystyrene particles of two representative sizes, 25 nm and 1 µm, at concentrations of 1 µg/mL and 5 µg/mL for 48 h. Flow cytometry and confocal microscopy revealed the accumulation of particles of both sizes within the cytoplasm. Functional assays revealed reduced cell viability and elevated lactate dehydrogenase release, indicating cytotoxic effects following microplastic exposure. Gene expression analysis showed significant upregulation of MAPK14 and SOD2, indicating oxidative stress activation, and increased expression of pro-inflammatory mediators IL-6, TNF-α, and NF-κB1. In parallel, GLUT1 transcripts and GLUT1-positive cell populations were markedly reduced, suggesting impaired glucose metabolism. Collectively, these findings demonstrate that microplastics disrupt astrocytic homeostasis by inducing oxidative, inflammatory, and metabolic disturbances, leading to a reactive yet metabolically compromised phenotype. This study demonstrates the cellular damage caused by microplastics in astrocytes, which may contribute to a cellular mechanism linking environmental pollutant exposure to adverse effects on human health. Full article

(This article belongs to the Section Molecular Nanoscience)

20 pages, 2187 KB

Open AccessArticle

Redox on the Clock: Sex-Dependent Dynamics of Xanthine Oxidoreductase Isoforms and Melatonin

by Elżbieta Cecerska-Heryć, Martyn Zoń, Marta Budkowska, Natalia Serwin, Anna Michalczyk, Małgorzata Goszka, Aleksandra Polikowska, Bartosz Wojciuk and Barbara Dołęgowska

Int. J. Mol. Sci. 2025, 26(23), 11272; https://doi.org/10.3390/ijms262311272 - 21 Nov 2025

Abstract

Melatonin, a key regulator of the circadian rhythm, exerts strong antioxidant effects by scavenging reactive oxygen species (ROS) and modulating enzymatic redox balance. Xanthine oxidoreductase (XOR), a molybdenum- and iron–sulfur-containing enzyme, catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid—the [...] Read more.

Melatonin, a key regulator of the circadian rhythm, exerts strong antioxidant effects by scavenging reactive oxygen species (ROS) and modulating enzymatic redox balance. Xanthine oxidoreductase (XOR), a molybdenum- and iron–sulfur-containing enzyme, catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid—the final steps of purine catabolism—serving as an important enzymatic source of ROS under physiological conditions. XOR exists in three interconvertible isoforms: xanthine dehydrogenase (XDH), which uses NAD⁺ as an electron acceptor; xanthine oxidase (XO), which transfers electrons to oxygen, producing superoxide and hydrogen peroxide; and an intermediate form (XDO) that reflects the redox-dependent interconversion between the two. This study aimed to evaluate temporal and sex-dependent variations in XOR isoforms and their relationship with melatonin levels in healthy individuals. Sixty-six volunteers (33 women aged 24–38 and 33 men aged 24–44) were examined. Blood samples were collected at 02:00, 08:00, 14:00, and 20:00. Serum melatonin was measured using ELISA, and XOR isoform activities were determined spectrophotometrically. Melatonin exhibited a precise 24 h rhythm with a nocturnal peak at 02:00 (~98 pg/mL) and a daytime nadir at 14:00 (~9 pg/mL). XO activity varied significantly (p < 0.01), showing an inverse correlation with melatonin in men (ρ = −0.52, p = 0.006), while XDO activity correlated positively with melatonin in women at 14:00 (ρ = 0.48, p = 0.01). These findings indicate sex-specific and time-dependent regulation of XOR isoforms, suggesting that redox homeostasis is modulated differently in men and women throughout the day. Understanding these dynamics may refine the interpretation of oxidative stress biomarkers and help optimize diagnostic and chronotherapeutic approaches in redox-related disorders. Full article

(This article belongs to the Special Issue Molecular Mechanism of Circadian Rhythm)

► Show Figures

Figure 1

27 pages, 577 KB

Open AccessReview

Targeting DNA Damage Response and Immune Crosstalk in Cancer: Mechanistic Insights and Therapeutic Opportunities

by Lavinia Marcut, Roxana Daniela Brata, Alina Cristina Barb, Alexia Manole, Dan Gabriel Stef, Cristina Stefania Dumitru, Flavia Zara and Raul Patrascu

Int. J. Mol. Sci. 2025, 26(23), 11271; https://doi.org/10.3390/ijms262311271 - 21 Nov 2025

Abstract

Cancer progression and therapeutic resistance are driven by complex molecular interactions between genomic instability and immune modulation. Defects in the DNA damage response (DDR) not only promote tumor heterogeneity but also shape the tumor immune landscape through the generation of neoantigens, activation of [...] Read more.

Cancer progression and therapeutic resistance are driven by complex molecular interactions between genomic instability and immune modulation. Defects in the DNA damage response (DDR) not only promote tumor heterogeneity but also shape the tumor immune landscape through the generation of neoantigens, activation of the cGAS–STING pathway, and modulation of immune checkpoints. This review provides an integrative overview of the molecular mechanisms linking DDR dysfunction to immune crosstalk, emphasizing how these processes influence tumor evolution and response to therapy. We discuss emerging therapeutic strategies that exploit DDR–immune interactions, including PARP and ATR inhibitors, synthetic lethality approaches, and combination regimens with immune checkpoint blockade. Understanding the bidirectional connection between DNA repair pathways and immune signaling unveils new translational opportunities for precision oncology and offers a framework for developing combinatorial therapies capable of overcoming resistance and improving long-term cancer control. Full article

(This article belongs to the Special Issue Molecular Biology of Cancer—Implications for Diagnosis and Treatment: 3rd Edition)

► Show Figures

Figure 1

27 pages, 2130 KB

Open AccessArticle

Impact of Octenyl Succinylation and Bee Products on Maize Starch Films and Apple Storage Quality

by Paulina Pająk, Karolina Królikowska, Lesław Juszczak, Gohar Khachatryan and Jacek Grzyb

Int. J. Mol. Sci. 2025, 26(23), 11270; https://doi.org/10.3390/ijms262311270 - 21 Nov 2025

Abstract

Starch is a promising biodegradable polymer for food packaging, offering a competitive alternative to synthetic films, but its native form has limited functionality. This study aimed to develop edible films based on native (N) and octenyl-succinylated (OS) maize starch incorporating honey-bee-derived extracts (HBE), [...] Read more.

Starch is a promising biodegradable polymer for food packaging, offering a competitive alternative to synthetic films, but its native form has limited functionality. This study aimed to develop edible films based on native (N) and octenyl-succinylated (OS) maize starch incorporating honey-bee-derived extracts (HBE), and to evaluate their physicochemical, structural, and bioactive properties. Moreover, the films were applied as a packaging for apple slices stored for seven days. OS starch enhanced film functionality, particularly when combined with bee pollen, bee bread, and propolis extracts. The presence of amphiphilic octenyl groups and bioactive components significantly modified film microstructure and thermal behavior. Compared to native starch films, OS-based films showed higher water solubility and swelling ratio but lower tensile strength. Among the HBE formulations, propolis-enriched films exhibited the highest total phenolic content, strongest antioxidant capacity, and most effective antimicrobial action. Although none of the starch-based films prevented apple weight loss or browning during storage, propolis addition markedly reduced mold growth compared to synthetic packaging. Overall, octenyl-succinylated maize starch combined with propolis extract offers a promising, biodegradable alternative to conventional plastic films for sustainable food packaging applications. Full article

(This article belongs to the Special Issue Molecular Design and Functional Applications of Polysaccharide Composites)

► Show Figures

Figure 1

17 pages, 2069 KB

Open AccessReview

Salivary Oxidative Stress Biomarkers in Peri-Implant Disease: A Systematic Review and Meta-Analysis

by Paul Șerban Popa, Gabriel Valeriu Popa, Kamel Earar, Claudia Elisabeta Popa-Cazacu and Mădălina Nicoleta Matei

Int. J. Mol. Sci. 2025, 26(23), 11269; https://doi.org/10.3390/ijms262311269 - 21 Nov 2025

Abstract

Peri-implantitis, a common biological complication of dental implants, is characterized by soft-tissue inflammation and progressive bone loss. Oxidative stress is increasingly implicated in its pathogenesis, yet the diagnostic potential of salivary redox biomarkers remains unclear. This study’s objective was to assess the association [...] Read more.

Peri-implantitis, a common biological complication of dental implants, is characterized by soft-tissue inflammation and progressive bone loss. Oxidative stress is increasingly implicated in its pathogenesis, yet the diagnostic potential of salivary redox biomarkers remains unclear. This study’s objective was to assess the association between salivary malondialdehyde (MDA) and total antioxidant capacity (TAC) and peri-implant disease via a pre-registered, quantitative meta-analysis of previously published studies using predefined statistical criteria. Following a priori PROSPERO registration, we systematically searched PubMed, Scopus, and Web of Science (2004–September 2025), extracted data in duplicate, and pooled effects using random-effects models; certainty of evidence was appraised with GRADE (Grading of Recommendations Assessment, Development and Evaluation) and risk of bias with ROBINS-I (Risk Of Bias In Non-randomized Studies of Interventions)/QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies-2). Twelve studies were included qualitatively: seven (n = 726) contributed to MDA and five (n = 485) to TAC meta-analyses. Peri-implant disease was associated with elevated MDA (SMD = 1.64, 95% CI 1.39–1.88) and reduced TAC (SMD = −1.88, 95% CI −2.17 to −1.58); statistical heterogeneity was not detected, and results were robust to sensitivity and exploratory assay-based subgroup analyses. Salivary MDA and TAC show consistent, large, standardized differences in peri-implant disease; however, observational designs, assay variability, and the absence of validated diagnostic thresholds warrant cautious interpretation and prospective validation before clinical adoption. Full article

(This article belongs to the Special Issue Molecules and Mechanisms of Oxidative Stress Relevant in the Pathophysiology of Diseases)

► Show Figures

Figure 1

38 pages, 7876 KB

Open AccessReview

Nanosecond Pulsed Electric Fields (nsPEFs) for Precision Intracellular Oncotherapy: Recent Advances and Emerging Directions

by Kainat Gul and Sohail Mumtaz

Int. J. Mol. Sci. 2025, 26(23), 11268; https://doi.org/10.3390/ijms262311268 - 21 Nov 2025

Abstract

Intracellular targeting is the missing dimension in contemporary oncology, and nanosecond pulsed electric fields (nsPEFs) uniquely aim to deliver it. By charging membranes on sub-microsecond timescales, nsPEF bypasses plasma-membrane shielding to porate organelles, collapse mitochondrial potential, perturb ER calcium, and transiently open the [...] Read more.

Intracellular targeting is the missing dimension in contemporary oncology, and nanosecond pulsed electric fields (nsPEFs) uniquely aim to deliver it. By charging membranes on sub-microsecond timescales, nsPEF bypasses plasma-membrane shielding to porate organelles, collapse mitochondrial potential, perturb ER calcium, and transiently open the nuclear envelope. This mechanism reprograms malignant fate while preserving tissue architecture. This review synthesizes the most recent evidence to frame nsPEF as a programmable intracellular therapy, mapping mechanistic design rules that link pulse width, amplitude, repetition, and rise time to specific organelle responses. We outline therapeutic applications, including the induction of apoptosis in resistant tumors, immunogenic cell death with systemic memory, and synergy with checkpoint blockade. We also survey integrations with nanoparticles, calcium, and chemotherapeutic drugs for improved outcomes. We critically appraise safety, selectivity, and scalability, distill translational bottlenecks in dosimetry and standardization, and propose an actionable roadmap to accelerate clinical adoption. Viewed through this lens, nsPEF is not merely another ablation tool but a platform for precision intracellular oncotherapy, capable of drug-sparing efficacy and immune convergence when engineered with rigor. Full article

(This article belongs to the Section Molecular Oncology)

► Show Figures

Figure 1

16 pages, 1960 KB

Open AccessArticle

Photodynamic Inactivation Enhances Antibiotic Efficacy Without Affecting Drug Stability: Insights into Photosensitizer–Antibiotic Combination Therapies

by Rocío B. Acosta, Edgardo N. Durantini and Mariana B. Spesia

Int. J. Mol. Sci. 2025, 26(23), 11267; https://doi.org/10.3390/ijms262311267 - 21 Nov 2025

Abstract

Photodynamic inactivation (PDI) represents a promising strategy to overcome bacterial resistance by combining light, oxygen, and a photosensitizer (PS) to generate reactive oxygen species (ROS) that damage essential cellular components. Combining PDI with conventional antibiotics (ATBs) may further enhance bacterial eradication through complementary [...] Read more.

Photodynamic inactivation (PDI) represents a promising strategy to overcome bacterial resistance by combining light, oxygen, and a photosensitizer (PS) to generate reactive oxygen species (ROS) that damage essential cellular components. Combining PDI with conventional antibiotics (ATBs) may further enhance bacterial eradication through complementary mechanisms. In this study, the tetracationic 5,10,15,20-tetra(4-N,N,N-trimethylammoniophenyl)porphyrin (TMAP⁴⁺) was evaluated in combination with ATBs: ampicillin (AMP) and rifampicin (RIF) against Staphylococcus aureus and cephalexin (CFX) against Escherichia coli. The photostability of all agents was assessed under the experimental irradiation conditions, and no evidence of physical interaction between TMAP⁴⁺ and the ATBs was detected. AMP and CFX remained photostable, while RIF exhibited only minimal photodegradation under white light, confirming its stability during PDI treatments. The antimicrobial assays revealed that irradiation significantly enhanced the bactericidal activity of TMAP⁴⁺. When combined with ATBs, photoactivated TMAP⁴⁺ led to a pronounced reduction in the minimum inhibitory concentration (MIC) values of AMP and RIF for S. aureus and of CFX for E. coli, indicating additive effects. Growth curve analyses corroborated these results, showing delayed bacterial growth and decreased maximal optical densities in the combined treatments compared to single agents. Overall, these findings demonstrate that the photodynamic process can potentiate the antimicrobial effect of conventional ATBs without compromising their stability, supporting the potential of PS–ATB combination therapies as a valuable approach to improve antibacterial efficacy and mitigate ATB resistance. Full article

(This article belongs to the Special Issue New Molecular Insights into Antimicrobial Photo-Treatments)

► Show Figures

Figure 1

19 pages, 2033 KB

Open AccessArticle

Galactooligosaccharide Production Using Immobilized Aspergillus oryzae β-Galactosidase, Part I: Characterization and Influence of Reaction Conditions

by Monika Antošová, Jana Krázel Adamíková and Milan Polakovič

Int. J. Mol. Sci. 2025, 26(23), 11266; https://doi.org/10.3390/ijms262311266 - 21 Nov 2025

Abstract

The enzymatic production of prebiotic galactooligosaccharides (GOS), functional food ingredients with established health benefits, remains an active research area driven by a rising global demand for GOS. These oligosaccharides are synthesized from lactose via transgalactosylation catalyzed by β-galactosidase, accompanied by hydrolysis of both [...] Read more.

The enzymatic production of prebiotic galactooligosaccharides (GOS), functional food ingredients with established health benefits, remains an active research area driven by a rising global demand for GOS. These oligosaccharides are synthesized from lactose via transgalactosylation catalyzed by β-galactosidase, accompanied by hydrolysis of both substrate and products, and the competition between these reactions critically determines the maximum achievable GOS yield. In this study, β-galactosidase from Aspergillus oryzae was immobilized on an anion-exchange resin (Dowex Marathon MSA) using three glutaraldehyde-based crosslinking strategies. The resulting immobilized biocatalysts were characterized and evaluated for GOS synthesis, with product yield as the principal performance indicator. The results demonstrated that the immobilized biocatalysts markedly modulated the balance between transgalactosylation and hydrolytic activities. The biocatalyst prepared by simultaneous resin activation and enzyme crosslinking provided the highest GOS yield and operational stability. This biocatalyst was subsequently used to study the effects of lactose concentration, pH, enzyme loading, and temperature. Among these, lactose concentration most strongly influenced GOS yield, whereas the other factors primarily affected the reaction rate. These findings offer practical insights into enzyme immobilization strategies for optimizing GOS production. Full article

(This article belongs to the Section Biochemistry)

► Show Figures

Figure 1

Journal Description

International Journal of Molecular Sciences

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI