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Neurotropic Viruses as Acute and Insidious Drivers of Aging
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The α5-α6-α7-Pba3-Pba4 Complex: A Starting Unit in Proteasome Core Particle Assembly
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Modeling Human Cell Death Pathways in Budding Yeast
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Salivary MicroRNAs as Non-Invasive Biomarkers for Endometriosis and Therapy Response
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Oxidant-Based Cytotoxic Agents during Aging
Journal Description
Biomolecules
Biomolecules
is a peer-reviewed, open access journal on structures and functions of bioactive and biogenic substances, molecular mechanisms with biological and medical implications as well as biomaterials and their applications. Biomolecules is published monthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q1 (Biochemistry and Molecular Biology) / CiteScore - Q1 (Biochemistry)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 19.4 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Sections: published in 15 topical sections.
- Testimonials: See what our editors and authors say about Biomolecules.
- Companion journal: Receptors.
Impact Factor:
4.8 (2024);
5-Year Impact Factor:
5.6 (2024)
Latest Articles
The NO Pathway as a Target in Patients with Stable and Advanced Heart Failure: An Additional Arrow in Our Quiver!
Biomolecules 2025, 15(10), 1420; https://doi.org/10.3390/biom15101420 - 6 Oct 2025
Abstract
The nitric oxide (NO) pathway is a fundamental regulator of vascular tone, myocardial function, and inflammation. In heart failure (HF), especially in advanced stages, dysregulation of NO–soluble guanylate cyclase (sGC)–cyclic guanosine monophosphate (cGMP) signaling contributes to endothelial dysfunction, increased vascular resistance, myocardial fibrosis,
[...] Read more.
The nitric oxide (NO) pathway is a fundamental regulator of vascular tone, myocardial function, and inflammation. In heart failure (HF), especially in advanced stages, dysregulation of NO–soluble guanylate cyclase (sGC)–cyclic guanosine monophosphate (cGMP) signaling contributes to endothelial dysfunction, increased vascular resistance, myocardial fibrosis, and impaired cardiac performance. Chronic inflammation further reduces NO bioavailability, exacerbating HF progression This review synthesizes current knowledge on the role of the NO pathway in HF pathophysiology, with a focus on stable and advanced HF. Special attention is given to patient subgroups with comorbidities such as chronic kidney disease, where modulation of NO signaling may be particularly beneficial. We also evaluate therapeutic strategies targeting NO bioavailability and sGC stimulation. Evidence shows that impaired NO signaling promotes systemic and pulmonary vasoconstriction, elevates ventricular afterload, and worsens cardiac remodeling. Pharmacological agents that restore NO levels or activate downstream effectors such as sGC improve vasodilation, reduce fibrosis, and enhance myocardial relaxation. These effects are especially relevant in advanced HF patients and those with renal impairment, who often exhibit limited responses to conventional therapies. The NO pathway represents a promising therapeutic target in both stable and advanced HF. Modulating this pathway could improve outcomes, particularly in complex populations with multiple comorbidities, highlighting the need for further clinical research and tailored treatments.
Full article
(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)
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Open AccessArticle
Effects of HDL Structure and Function in Peripheral Artery Disease
by
Yu-Huang Liao, Semon Wu, Yu-Lin Ko and Ming-Sheng Teng
Biomolecules 2025, 15(10), 1419; https://doi.org/10.3390/biom15101419 - 6 Oct 2025
Abstract
The structure and function of high-density lipoprotein (HDL), rather than its concentration, are more important factors in determining HDL activity. HDL particles (HDL-P) are heterogeneous in their composition, size, and antioxidative function. We investigated the levels of HDL subfractions and oxidized high-density lipoprotein
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The structure and function of high-density lipoprotein (HDL), rather than its concentration, are more important factors in determining HDL activity. HDL particles (HDL-P) are heterogeneous in their composition, size, and antioxidative function. We investigated the levels of HDL subfractions and oxidized high-density lipoprotein (Ox-HDL) and validated their correlation with genetic determinants underlying peripheral artery disease (PAD). We recruited a PAD population stratified by claudication severity (group I) and critical limb ischemia (group II) according to the Rutherford classification. We found that the level of Ox-HDL was significantly increased with Rutherford classification (group II; p = 0.001). Conversely, the levels of high-density lipoprotein cholesterol (HDL-C), HDL-P, and small high-density lipoprotein particles (S-HDL-P) were significantly reduced in group II. Three single nucleotide polymorphisms (SNPs) were differentially associated with HDL particles and Ox-HDL. Briefly, rs117685211 and rs7934858 showed opposing effects, with rs117685211 and rs148877054 being associated with low levels of HDL subfractions; rs148877054 was significantly associated with M and S-HDL-P. Our study indicated the significance of HDL subfractions and Ox-HDL in the pathogenesis of PAD.
Full article
(This article belongs to the Section Lipids)
Open AccessReview
Micro- and Nanoplastics Act as Metal Carriers with the Potential to Alter Human Gene Expression Patterns—The Inferences from Bioinformatic Online Tools
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Maja Grabacka and Małgorzata Pierzchalska
Biomolecules 2025, 15(10), 1418; https://doi.org/10.3390/biom15101418 - 6 Oct 2025
Abstract
Micro- and nanoplastic particles (MNPLs) present in the environment have recently become a potential health hazard factor due to the ability to penetrate living organisms, their organs, and cells. MNPLs interact with and absorb chemicals and elements, including metals, such as iron, copper,
[...] Read more.
Micro- and nanoplastic particles (MNPLs) present in the environment have recently become a potential health hazard factor due to the ability to penetrate living organisms, their organs, and cells. MNPLs interact with and absorb chemicals and elements, including metals, such as iron, copper, and zinc, and transport them into the cells. The cells subsequently respond with the altered gene expression profiles. In this study, we applied freely accessible online bioinformatic tools to draw out the sets of genes modulated by the metal ions and MNPLs. We focused on the gene interactome as revealed by The Comparative Toxicogenomics Database (CTD). To achieve a deeper insight into the biological processes that are potentially modulated, the retrieved CTD lists of genes, whose expression was influenced by MNPLs and metals, were subsequently analyzed using online tools: Metascape and String database. The genes from the revealed networks were arranged into functional clusters, annotated mainly as inflammation and immune system activity, regulation of apoptosis, oxidative stress response, Wingless-related Integration Site (WNT) signaling and ferroptosis. The complexity of the interactions between the gene sets altered by MNPLs and metal ions illustrates their pleiotropic effects on living systems.
Full article
(This article belongs to the Special Issue Molecular Advances in Drug Resistance and Novel Therapies for Cancer)
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Open AccessSystematic Review
The Anti-Inflammatory Effects of Resistance Training in Patients with Type 2 Diabetes: A Systematic Review and Meta-Analysis
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Nikolaos P. E. Kadoglou, Chrysostomos Georgiou, Nikolaos Balaskas, Chrystalla Panayiotou, Michail Vardas, Andreas Mitsis and Constantine N. Antonopoulos
Biomolecules 2025, 15(10), 1417; https://doi.org/10.3390/biom15101417 - 5 Oct 2025
Abstract
Type 2 diabetes mellitus (T2DM) is associated with increased cardiovascular risk characterized by low-grade inflammation. The aim of this systematic review and meta-analysis was to assess the effects of resistance exercise training (RET) predominantly on cytokines, along with changes in glucose profile and
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Type 2 diabetes mellitus (T2DM) is associated with increased cardiovascular risk characterized by low-grade inflammation. The aim of this systematic review and meta-analysis was to assess the effects of resistance exercise training (RET) predominantly on cytokines, along with changes in glucose profile and body composition in T2DM patients. The present systematic review and meta-analysis was conducted utilizing PubMed, Web of Science, Embase, and the Cochrane Library databases from their inception up to July 2024 (PROSPERO; registration number CRD420251149352). We screened only for randomized controlled trials investigating the effects of systematic, supervised RET on C-reactive protein (CRP) and adipokines: adiponectin, interleukin 6 (IL-6), tumor necrosis factor-alpha (TNF-α), along with changes in anthropometric indices and glycemic control in adult T2DM patients. Pooled post-exercise weighted mean differences (WMDs) with 95% confidence intervals (CIs) were calculated for all outcomes of interest between exercise-treated patients and controls. Sixteen studies involving a total of 668 T2DM patients were retrieved from the databases for meta-analysis. We used the GRADE framework for assessing the certainty of evidence. Cochran Q-score (I2) was used to estimate heterogeneity among studies (level of significance p < 0.10) and risk of bias analysis was also performed. The cumulative results showed that post-RET inflammatory markers were lower in exercise-treated patients compared to controls regarding CRP (mg/L) (WMD: −0.63; 95%CIs: −1.05, −0.20; p < 0.001); adiponectin (μg/mL) (WMD: −0.94; 95%CIs: −1.49, −0.38; p < 0.001). The results from adiponectin are quite conflicting since they derived from only three studies, where one of them had the greater impact. In parallel, we noticed significant amelioration of fasting glucose and HbA1c (p < 0.001), while body weight remained unaltered. Our meta-analysis demonstrated non-significantly lower levels of IL-6 and TNF-α in RET vs. control group. RET can merely reduce the inflammatory burden in T2DM patients by ameliorating the circulating levels of CRP and adiponectin, while in the rest of the biomarkers, non-significant results were obtained. Hence, the overall clinical impact of those anti-inflammatory effects of RET needs to be determined.
Full article
(This article belongs to the Special Issue Inflammation—The Surprising Bridge between Diseases)
Open AccessArticle
Curcumin Alleviates Doxorubicin-Induced Cardiotoxicity by Modulating Apelin Expression
by
Baris Akca, Olcay Murat Disli, Nevzat Erdil, Yilmaz Cigremis, Hasan Ozen, Merve Durhan, Selahattin Tunc, Onural Ozhan, Zeynep Ulutas and Feray Akgul Erdil
Biomolecules 2025, 15(10), 1416; https://doi.org/10.3390/biom15101416 - 5 Oct 2025
Abstract
Background: Doxorubicin (Dox)-induced cardiotoxicity is the most important side effect of the drug and significantly limits its use in susceptible patients. Therefore, preventive measures are required to alleviate the Dox-induced cardiac failure. In this study, curcumin, a strong antioxidant agent, was investigated for
[...] Read more.
Background: Doxorubicin (Dox)-induced cardiotoxicity is the most important side effect of the drug and significantly limits its use in susceptible patients. Therefore, preventive measures are required to alleviate the Dox-induced cardiac failure. In this study, curcumin, a strong antioxidant agent, was investigated for its potential protective effect on dox-induced cardiotoxicity with its effect on Apelin expression as a mediator of cardiac function. Methods: Wistar albino rats were equally divided into four groups as Control, DOX, CUR, and CUR+DOX. Dox was administered a single dose of 20 mg/kg bw intraperitoneally while 100 mg/kg bw curcumin was given orally for 14 days before the Dox use. Results: DOX group showed a prolonged QT interval on an electrocardiogram and elevated cardiac troponin levels. In biochemical analyses, decreased Superoxide Dismutase activity and increased Malondialdehyde level and Catalase activity were detected in DOX group. Gene expression of Apelin decreased significantly while NF-κB increased in DOX group. Degenerative changes in histopathology, and increased iNOS and nitrotyrosine immunoreactivity were detected in DOX group. However, no significant changes were observed at reduced Glutathione, TNF-, and IL-1β levels. Curcumin use in Dox-given rats altered most of the disturbed parameters investigated in this study, indicating an alleviating effect on Dox-induced cardiotoxicity. Serum and heart Apelin levels and mRNA expression in heart tissue were detected to significantly increase in CUR+DOX group as compared to DOX group. Furthermore, NF-κB mRNA expression was significantly decreased in heart tissue of CUR+DOX group compared with the DOX group. Conclusions: The results suggest that Apelin acts as an important mediator in Dox cardiotoxicity and may be used as a target for treatment of certain cardiomyopathies. By regulating Apelin expression, curcumin may serve as a potential adjunct in cardioprotective approaches.
Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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Open AccessArticle
UHPLC-QTOF-ESI-MS/MS, SNAP-MS Identification, In Silico Prediction of Pharmacokinetic Properties of Constituents from the Stem Bark of Holarrhena floribunda (G. Don) T. Durand and Schinz (Apocynaceae)
by
Franck Landry Djila Possi, Mc Jesus Kinyok, Joseph Eric Mbasso Tameko, Bel Youssouf G. Mountessou, Johanne Kevine Jumeta Dongmo, Mariscal Brice Tchatat Tali, Appolinaire Kene Dongmo, Fabrice Fekam Boyom, Jean Jules Kezetas Bankeu, Norbert Sewald, Jean Rodolphe Chouna and Bruno Ndjakou Lenta
Biomolecules 2025, 15(10), 1415; https://doi.org/10.3390/biom15101415 - 4 Oct 2025
Abstract
The present work reports the bioguided isolation of constituents from the ethanol extract of Holarrhena floribunda stem bark, their identification by UHPLC-ESI-QTOF-MS/MS identification, and the in silico prediction of the pharmacokinetic and toxicity parameters. The crude extract, along with its n-hexane and
[...] Read more.
The present work reports the bioguided isolation of constituents from the ethanol extract of Holarrhena floribunda stem bark, their identification by UHPLC-ESI-QTOF-MS/MS identification, and the in silico prediction of the pharmacokinetic and toxicity parameters. The crude extract, along with its n-hexane and alkaloid-rich fractions, displayed moderate to good antiplasmodial activity in vitro against chloroquine-sensitive (3D7) and multidrug-resistant (Dd2) strains of Plasmodium falciparum, with IC50 values ranging from 6.54 to 43.54 µg/mL. Seventeen steroidal alkaloids (1–17) were identified in the most active fraction using UHPLC-ESI-QTOF-MS/MS, based on their fragmentation patterns and analysis with the Structural Similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS). Furthermore, bioguided isolation of the ethanol extract yielded twenty-one compounds (3, 5, 10, 14–16, 18–31), whose structures were elucidated by spectroscopic methods. Among them, compounds 5, 14, and 27 showed the highest potency against the two strains of P. falciparum, with IC50 values between 25.97 and 55.78 µM. In addition, the in silico prediction of pharmacokinetic parameters and drug-likeness using the SwissADME web tool indicated that most of the evaluated compounds (1, 3–5, and 14–16) complied with Lipinski’s rule of five.
Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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Open AccessReview
Red-Wine Gene Networks Linked to Exceptional Longevity in Humans
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Patricia Lacayo, Alexandria Martignoni, Kenneth Park, Christianne Castro and Shin Murakami
Biomolecules 2025, 15(10), 1414; https://doi.org/10.3390/biom15101414 - 4 Oct 2025
Abstract
Despite the health concerns regarding alcohol and its link to cancer, moderate consumption of red wine has been associated with healthy aging and longevity, defined as up to one drink per day for women and two drinks per day for men (approximately 142
[...] Read more.
Despite the health concerns regarding alcohol and its link to cancer, moderate consumption of red wine has been associated with healthy aging and longevity, defined as up to one drink per day for women and two drinks per day for men (approximately 142 mL or 5 oz per drink). Previous research has revealed the health benefits of red wine, particularly in relation to cardiovascular disease. However, the influence of genetic factors on these benefits remains to be elucidated. In this study, we explored genes linked to red wine and created a curated gene set that intersects with those related to centenarians, which are markers of exceptional longevity. By analyzing literature from over 190 databases, we identified and validated a curated list of 43 genes associated with red wine and centenarians. We conducted gene set enrichment analysis as well as enrichment analysis of diseases and their tissue distributions. The results suggest that these genes play a crucial role in stress response and apoptosis, which are essential for cell survival and renewal. Additionally, these genes were enriched in pathways associated with smooth muscle cell proliferation, neuroinflammation, nucleotide excision repair, and lipoprotein metabolism (false discovery rate, FDR < 3 × 10−7). Gene set enrichment analysis indicated significant tissue distribution in the gastrointestinal, cardiovascular, and respiratory systems. Furthermore, the disease–gene enrichment analysis pointed to associations with diseases related to tissues and organs, including cardiovascular disease (heart disease and stroke), type 2 diabetes, gastrointestinal diseases and metabolic diseases, immune diseases, and cancer (FDR < 9.37 × 10−6); notably, cardiovascular diseases, diabetes, and cancer are leading causes of death, suggesting that these genes may be protective against those diseases. Our review of the literature indicates that individuals who do not currently drink alcohol should not be encouraged to start. However, we propose that moderate consumption of red wine, especially for middle-aged to older adults after 40 years old, can provide significant health benefits due to its components and the positive effects of hormesis. Although further research is necessary to uncover additional genes, this study provides the first genetic overview of the health benefits of red wine, emphasizing its potential in supporting healthy aging and longevity.
Full article
(This article belongs to the Special Issue Molecular Mechanisms of Life-Extending Biomolecules and Interventions with Medical and Technological Implications)
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Open AccessArticle
Engineering a High-Fidelity MAD7 Variant with Enhanced Specificity for Precision Genome Editing via CcdB-Based Bacterial Screening
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Haonan Zhang, Ying Yang, Tianxiang Yang, Peiyao Cao, Cheng Yu, Liya Liang, Rongming Liu and Zhiying Chen
Biomolecules 2025, 15(10), 1413; https://doi.org/10.3390/biom15101413 - 4 Oct 2025
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) nucleases enable precise genome editing, but off-target cleavage remains a critical challenge. Here, we report the development of MAD7_HF, a high-fidelity variant of the MAD7 nuclease engineered through a bacterial screening system leveraging the
[...] Read more.
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) nucleases enable precise genome editing, but off-target cleavage remains a critical challenge. Here, we report the development of MAD7_HF, a high-fidelity variant of the MAD7 nuclease engineered through a bacterial screening system leveraging the DNA gyrase-targeting toxic gene ccdB. This system couples survival to efficient on-target cleavage and minimal off-target activity, mimicking the transient action required for high-precision editing. Through iterative selection and sequencing validation, we identified MAD7_HF, harboring three substitutions (R187C, S350T, K1019N) that enhanced discrimination between on- and off-target sites. In Escherichia coli assays, MAD7_HF exhibited a >20-fold reduction in off-target cleavage across multiple mismatch contexts while maintaining on-target efficiency comparable to wild-type MAD7. Structural modeling revealed that these mutations stabilize the guide RNA-DNA hybrid at on-target sites and weaken interactions with mismatched sequences. This work establishes a high-throughput bacterial screening strategy that allows the identification of Cas12a variants with improved specificity at a given target site, providing a useful framework for future efforts to develop precision genome-editing tools.
Full article
(This article belongs to the Special Issue Advances in Microbial CRISPR Editing)
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Open AccessArticle
2-Hydroxymelatonin Induces Husk-Imposed Vivipary in the Transgenic Rice Overexpressing Melatonin 2-Hydroxylase
by
Kyungjin Lee and Kyoungwhan Back
Biomolecules 2025, 15(10), 1412; https://doi.org/10.3390/biom15101412 - 4 Oct 2025
Abstract
Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin
[...] Read more.
Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin 2-hydroxylase (OsM2H), which catalyzes the hydroxylation of melatonin to 2-hydroxymelatonin (2-OHM). OsM2H overexpression (M2H-OE) showed PHS under paddy conditions. Germination assays revealed that intact seeds harvested at 26 and 36 days after heading (DAH) showed PHS, whereas dehusked seeds did not, indicating husk-imposed PHS. Overproduction of 2-OHM was observed in M2H-OE seeds compared to wild-type control. In addition, M2H-OE lines produced more hydrogen peroxide than the wild-type. 2-OHM-induced reactive oxygen species resulted in the induction of OsGA3ox2, a gibberellin (GA) biosynthesis gene, and repression of OsGA2ox3, a GA degradation gene, in caryopses at 2 DAH, but in the induction of the ABA degradation gene OsABA8ox3 in intact seeds at 26 DAH. In addition, M2H-OE seedlings were longer and showed increased levels of hydrogen peroxide and OsGA3ox2 expression versus the wild-type. This is the first report showing that 2-OHM can induce PHS via the husk pathway in rice seeds through the induction of GA biosynthetic and ABA degradation genes.
Full article
(This article belongs to the Special Issue New Insights into Hormonal Control of Plant Growth and Development)
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Open AccessReview
Anticoagulation Therapies and microRNAs in Heart Failure
by
Lucia Spartano, Maria Lombardi and Chiara Foglieni
Biomolecules 2025, 15(10), 1411; https://doi.org/10.3390/biom15101411 - 3 Oct 2025
Abstract
Heart failure (HF) remains a major cause of mortality despite the advances in pharmacological treatment. Anticoagulation therapies, including Clopidogrel, Aspirin, Warfarin, and novel oral anticoagulants (NOACs) such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, are frequently administered to HF patients to prevent thromboembolism and
[...] Read more.
Heart failure (HF) remains a major cause of mortality despite the advances in pharmacological treatment. Anticoagulation therapies, including Clopidogrel, Aspirin, Warfarin, and novel oral anticoagulants (NOACs) such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, are frequently administered to HF patients to prevent thromboembolism and adverse, life-threatening outcomes (e.g., stroke and myocardial infarction). In these settings, drug resistance and variability in responsivity to therapeutic approaches are challenging issues. Recent studies suggest that non-coding RNAs, particularly microRNAs (miRs) may play a modulatory role in HF therapy context, affecting drug efficacy. Specific miRs have been associated with resistance to Clopidogrel (e.g., miR-223 and miR-26a), Aspirin (e.g., miR-19b-1-5p and miR-92a) and Warfarin (e.g., miR-133 and miR-137). Moreover, Digoxin, a cardiac glycoside acting also over bleeding risk, upregulates miR-132, which is involved in HF-associated cardiac alteration and hypertrophy. Evidence linking miR expression to NOAC pharmacodynamics, cardiac remodeling and regulation of the coagulation is growing. These findings highlight the need of deeply harnessing the potential of miRs as predictive biomarkers or therapeutic targets in HF. Improving the knowledge on the relationship between miR and anticoagulant drugs in HF patients will contribute to personalization of the anticoagulant therapies, aimed at enhancing patient responsivity and minimizing adverse effects, ultimately improving patient life quality.
Full article
(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)
Open AccessArticle
Asiatic Acid from Centella asiatica as a Potent EGFR Tyrosine Kinase Inhibitor with Anticancer Activity in NSCLC Cells Harboring Wild-Type and T790M-Mutated EGFR
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Chaiwat Monmai, Sahachai Sabuakham, Wachirachai Pabuprapap, Waraluck Chaichompoo, Apichart Suksamrarn and Panupong Mahalapbutr
Biomolecules 2025, 15(10), 1410; https://doi.org/10.3390/biom15101410 - 3 Oct 2025
Abstract
Lung cancer is a leading cause of cancer mortality worldwide. Targeted therapies with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) represent a significant advance in the management of lung cancer. However, their long-term efficacy is often limited by acquired resistance, particularly
[...] Read more.
Lung cancer is a leading cause of cancer mortality worldwide. Targeted therapies with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) represent a significant advance in the management of lung cancer. However, their long-term efficacy is often limited by acquired resistance, particularly due to the T790M mutation, highlighting the need for novel EGFR-TKIs. Although compounds derived from Centella asiatica have demonstrated anticancer potential, their role in EGFR inhibition has not yet been reported. In this study, we investigated the inhibitory activity of two primary constituents, asiaticoside and asiatic acid, against wild-type and double-mutant (L858R/T790M) EGFR, as well as the anticancer effects of the more potent compound in lung cancer cells. A kinase activity assay revealed that asiatic acid potently inhibited both wild-type and double-mutant EGFR, whereas asiaticoside showed minimal inhibitory activity. Molecular docking demonstrated that asiatic acid bound to the ATP-binding pocket of both EGFR forms with binding energies superior to those of erlotinib and osimertinib. Treatment with asiatic acid significantly (i) reduced viability of A549 and H1975 cells while remaining non-toxic to BEAS-2B normal lung cells, (ii) enhanced cancer cell apoptosis, (iii) suppressed extracellular signal-regulated kinase (ERK) and protein kinase B (Akt) signaling pathways, and (iv) inhibited EGFR activation in A549 and H1975 cells. These results suggest that asiatic acid is a promising lead compound for anticancer drug development.
Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products: 2nd Edition)
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Open AccessReview
Bioinformatics Strategies in Breast Cancer Research
by
Matteo Veneziano, Isabella Savini, Elisa Cortellesi, Valeria Gasperi, Alessandra Gambacurta and Maria Valeria Catani
Biomolecules 2025, 15(10), 1409; https://doi.org/10.3390/biom15101409 - 2 Oct 2025
Abstract
Breast cancer is a heterogeneous disease and a leading cause of cancer-related deaths worldwide, underscoring the urgent need for effective biomarkers to guide diagnosis, prognosis, and therapeutic decisions. Bioinformatics methodologies, including genomics, transcriptomics, proteomics, and metabolomics data analysis, are essential for deciphering the
[...] Read more.
Breast cancer is a heterogeneous disease and a leading cause of cancer-related deaths worldwide, underscoring the urgent need for effective biomarkers to guide diagnosis, prognosis, and therapeutic decisions. Bioinformatics methodologies, including genomics, transcriptomics, proteomics, and metabolomics data analysis, are essential for deciphering the complex molecular landscape of breast cancer. Bioinformatics tools facilitate the identification of differentially expressed genes, non-coding RNAs, and proteins, unraveling crucial pathways involved in tumor initiation, progression, and metastasis. By constructing and analyzing protein–protein interaction networks and signaling pathways, bioinformatics approaches can identify potential diagnostic, prognostic, and predictive biomarkers. Herein, we explore the role of bioinformatics in breast cancer research and its potential application in identifying novel therapeutic targets and predicting drug response, ultimately enabling the development of tailored treatment strategies. We also address the challenges and future directions in utilizing bioinformatics for biomarker discovery and validation, emphasizing the need for robust statistical methods, standardized data analysis pipelines, and collaborative efforts to translate bioinformatics insights into improved clinical outcomes for breast cancer patients.
Full article
(This article belongs to the Special Issue Experimental and Bioinformatic Approaches for Biomarker Discovery in Disease: From Molecular Mechanisms to Therapeutic Challenges)
Open AccessArticle
Upregulation of GLT-1 Expression Attenuates Neuronal Apoptosis and Cognitive Dysfunction via Inhibiting the CB1-CREB Signaling Pathway in Mice with Traumatic Brain Injury
by
Bin Bu, Ruiyao Ma, Chengyu Wang, Shukun Jiang and Xiaoming Xu
Biomolecules 2025, 15(10), 1408; https://doi.org/10.3390/biom15101408 - 2 Oct 2025
Abstract
Background: Glutamate transporter 1 (GLT-1) plays a vital role in maintaining glutamate homeostasis in the body. A decreased GLT-1 expression in astrocytes can heighten neuronal sensitivity to glutamate excitotoxicity after traumatic brain injury (TBI). Despite its significance, the mechanisms behind the reduced expression
[...] Read more.
Background: Glutamate transporter 1 (GLT-1) plays a vital role in maintaining glutamate homeostasis in the body. A decreased GLT-1 expression in astrocytes can heighten neuronal sensitivity to glutamate excitotoxicity after traumatic brain injury (TBI). Despite its significance, the mechanisms behind the reduced expression of GLT-1 following TBI remain poorly understood. After TBI, the endocannabinoid 2-arachidonoyl glycerol (2-AG) is elevated several times. 2-AG is known to inhibit key positive transcriptional regulators of GLT-1. This study aims to investigate the role of 2-AG in regulating GLT-1 expression and to uncover the underlying mechanisms involved. Methods: A controlled cortical impact (CCI) model was used to establish a TBI model in C57BL/6J mice. The CB1 receptor antagonist (referred to as AM281) and the monoacylglycerol lipase (MAGL) inhibitor (referred to as JZL184) were administered to investigate the role and mechanism of 2-AG in regulating GLT-1 expression following TBI. Behavioral tests were conducted to assess neurological functions, including the open field, Y-maze, and novel object recognition tests. Apoptotic cells were identified using the TUNEL assay, while Western blot analysis and immunofluorescence were employed to determine protein expression levels. Results: The expression of GLT-1 in the contused cortex and hippocampus following TBI showed an initial decrease, followed by a gradual recovery. It began to decrease within half an hour, reached its lowest level at 2 h, and then gradually increased, returning to normal levels by 7 days. The administration of AM281 alleviated neuronal death, improved cognitive function, and reversed the reduction of GLT-1 caused by TBI in vivo. Furthermore, 2-AG decreased GLT-1 expression in astrocytes through the CB1-CREB signaling pathway. Mechanistically, 2-AG activated CB1, which inhibited CREB phosphorylation in astrocytes. This decreased GLT-1 levels and ultimately increased neuronal sensitivity to glutamate excitotoxicity. Conclusions: Our research demonstrated that the upregulation of GLT-1 expression effectively mitigated neuronal apoptosis and cognitive dysfunction by inhibiting the CB1-CREB signaling pathway. This finding may offer a promising therapeutic strategy for TBI.
Full article
(This article belongs to the Special Issue Advancing Molecular Regulation in Brain Injury Research: Mechanisms, Diagnosis, and Rehabilitation)
Open AccessReview
Advancing CAR-T Therapy for Solid Tumors: From Barriers to Clinical Progress
by
Sergei Smirnov, Yuriy Zaritsky, Sergey Silonov, Anastasia Gavrilova and Alexander Fonin
Biomolecules 2025, 15(10), 1407; https://doi.org/10.3390/biom15101407 - 2 Oct 2025
Abstract
Therapy with chimeric antigen receptor (CAR)-T cells has revolutionized the treatment of hematological malignancies. However, their application in solid tumors remains a formidable challenge due to obstacles such as the immunosuppressive tumor microenvironment, tumor heterogeneity, and limited T cell persistence. Although second- and
[...] Read more.
Therapy with chimeric antigen receptor (CAR)-T cells has revolutionized the treatment of hematological malignancies. However, their application in solid tumors remains a formidable challenge due to obstacles such as the immunosuppressive tumor microenvironment, tumor heterogeneity, and limited T cell persistence. Although second- and third-generation CAR-T cells have shown restricted efficacy in clinical trials, next-generation strategies—including cytokine-armored CAR-T cells (e.g., IL-15, IL-7/CCL19), logic-gated systems, and localized delivery approaches—demonstrate promising potential to overcome these limitations. This review examines the major barriers impeding CAR-T cell efficacy in solid tumors, evaluates clinical outcomes from conventional CAR constructs, and highlights innovative strategies being tested in recent clinical trials. Key advances discussed include the use of dominant-negative receptors (e.g., TGFβRII) to combat immunosuppression and the co-expression of bispecific T cell engagers (BiTEs) to address antigen escape.
Full article
(This article belongs to the Section Molecular Medicine)
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Open AccessReview
NEK Family Kinases: Structure, Function, and Role in Disease
by
Brandon M. Baker, Julia R. Boehling, Sarah Knopf, Stephanie Held, Margarite Matossian, Jorge A. Belgodere, Van T. Hoang, Bridgette M. Collins-Burow, Elizabeth C. Martin, Sean B. Lee, Matthew E. Burow, David H. Drewry and Robert H. Newman
Biomolecules 2025, 15(10), 1406; https://doi.org/10.3390/biom15101406 - 2 Oct 2025
Abstract
The Never-in-Mitosis A-Related Kinase (NEK) family is an important, yet largely understudied, family of protein kinases involved in the regulation of a variety of critical cellular processes. Consequently, dysregulation of NEK function has been linked to the etiology and progression of several disorders,
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The Never-in-Mitosis A-Related Kinase (NEK) family is an important, yet largely understudied, family of protein kinases involved in the regulation of a variety of critical cellular processes. Consequently, dysregulation of NEK function has been linked to the etiology and progression of several disorders, including cancer, ciliopathies, neurodegenerative disorders, inflammatory disorders, and other pervasive diseases. In this review, we have summarized recent findings to provide an overview of the NEK family and their diverse functions within various cellular contexts. In parallel, we have highlighted the emerging roles of NEK family members in human health, identifying potential therapeutic targets within the NEK family and exploring their potential for future clinical applications. Finally, we have addressed ongoing challenges and emerging research directions in this rapidly evolving field, aiming to pave the way for future discoveries and innovations.
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(This article belongs to the Section Cellular Biochemistry)
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Open AccessReview
A Review on Low-Dimensional Nanoarchitectonics for Neurochemical Sensing and Modulation in Responsive Neurological Outcomes
by
Mohammad Tabish, Iram Malik, Ali Akhtar and Mohd Afzal
Biomolecules 2025, 15(10), 1405; https://doi.org/10.3390/biom15101405 - 2 Oct 2025
Abstract
Low-Dimensional Nanohybrids (LDNHs) have emerged as potent multifunctional platforms for neurosensing and neuromodulation, providing elevated spatial-temporal precision, versatility, and biocompatibility. This review examines the intersection of LDNHs with artificial intelligence, brain–computer interfaces (BCIs), and closed-loop neurotechnologies, highlighting their transformative potential in personalized neuro-nano-medicine.
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Low-Dimensional Nanohybrids (LDNHs) have emerged as potent multifunctional platforms for neurosensing and neuromodulation, providing elevated spatial-temporal precision, versatility, and biocompatibility. This review examines the intersection of LDNHs with artificial intelligence, brain–computer interfaces (BCIs), and closed-loop neurotechnologies, highlighting their transformative potential in personalized neuro-nano-medicine. Utilizing stimuli-responsive characteristics, optical, thermal, magnetic, and electrochemical LDNHs provide real-time feedback-controlled manipulation of brain circuits. Their pliable and adaptable structures surpass the constraints of inflexible bioelectronics, improving the neuronal interface and reducing tissue damage. We also examined their use in less invasive neurological diagnostics, targeted therapy, and adaptive intervention systems. This review delineates recent breakthroughs, integration methodologies, and fundamental mechanisms, while addressing significant challenges such as long-term biocompatibility, deep-tissue accessibility, and scalable manufacturing. A strategic plan is provided to direct future research toward clinical use. Ultimately, LDNHs signify a transformative advancement in intelligent, tailored, and closed-loop neurotechnologies, integrating materials science, neurology, and artificial intelligence to facilitate the next era of precision medicine.
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(This article belongs to the Special Issue Molecular Mechanisms and Novel Therapeutic Approaches of Neurodegenerative Diseases)
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Open AccessArticle
Thermodynamic Determinants in Antibody-Free Nucleic Acid Lateral Flow Assays (AF-NALFA): Lessons from Molecular Detection of Listeria monocytogenes, Mycobacterium leprae and Leishmania amazonensis
by
Leonardo Lopes-Luz, Paula Correa Neddermeyer, Gabryele Cardoso Sampaio, Luana Michele Alves, Matheus Bernardes Torres Fogaça, Djairo Pastor Saavedra, Mariane Martins de Araújo Stefani and Samira Bührer-Sékula
Biomolecules 2025, 15(10), 1404; https://doi.org/10.3390/biom15101404 - 2 Oct 2025
Abstract
Antibody-free nucleic acid lateral flow assays (AF-NALFA) are an established approach for rapid detection of amplified pathogens DNA but can yield inconsistent signals across targets. Since AF-NALFA depends on dual hybridization of probes to single-stranded amplicons (ssDNA), site-specific thermodynamic (Gibbs free energy-ΔG) at
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Antibody-free nucleic acid lateral flow assays (AF-NALFA) are an established approach for rapid detection of amplified pathogens DNA but can yield inconsistent signals across targets. Since AF-NALFA depends on dual hybridization of probes to single-stranded amplicons (ssDNA), site-specific thermodynamic (Gibbs free energy-ΔG) at probe-binding regions may be crucial for performance. This study investigated how site-specific-ΔG and sequence complementarity at probe-binding regions determine Test-line signal generation, comparing native and synthetic amplicons and assessing the effects of local secondary structures and mismatches. Asymmetric PCR-generated ssDNA amplicons of Listeria monocytogenes, Mycobacterium leprae, and Leishmania amazonensis were analyzed in silico and tested in AF-NALFA prototypes with gold-labeled thiol probes and biotinylated capture probes. T-line signals were photographed, quantified (ImageJ version 1.4k), and statistically correlated with site-specific-ΔG. While native ssDNA from M. leprae and L. amazonensis failed to produce AF-NALFA T-line signals, L. monocytogenes yielded strong detection. Site-specific-ΔG below −10 kcal/mol correlated with reduced hybridization. Synthetic oligos preserved signals despite structural constraints, whereas ~3–4 mismatches, especially at capture probe regions, markedly impaired T-line intensity. The performance of AF-NALFA depends on the synergism between thermodynamic accessibility, site-specific-ΔG-induced site constraints, and sequence complementarity. Because genomic context affects hybridization, target-specific thermodynamic in silico evaluation is necessary for reliable pathogen DNA detection.
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(This article belongs to the Section Molecular Biology)
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Open AccessReview
GLP-1 Receptor Agonists in Heart Failure
by
Ali Reza Rahmani, Simrat Kaur Dhaliwal, Paola Pastena, Eliot Kazakov, Keerthana Jayaseelan and Andreas Kalogeropoulos
Biomolecules 2025, 15(10), 1403; https://doi.org/10.3390/biom15101403 - 2 Oct 2025
Abstract
Heart failure (HF) is a growing public health concern, driven by the increasing prevalence of obesity, diabetes, and aging. Despite therapeutic advances, HF continues to be associated with high morbidity and mortality. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs), originally developed for glycemic control
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Heart failure (HF) is a growing public health concern, driven by the increasing prevalence of obesity, diabetes, and aging. Despite therapeutic advances, HF continues to be associated with high morbidity and mortality. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs), originally developed for glycemic control in type 2 diabetes, have demonstrated cardiovascular benefits in clinical trials. Recent studies, including STEP-HFpEF and SUMMIT, have shown improvement in symptoms and weight loss in patients with HF with preserved ejection fraction (HFpEF). GLP-1 RAs are involved in multiple biological pathways relevant to heart failure pathophysiology. These include pathways related to sympathetic nervous system activity, inflammatory cytokine signaling, oxidative stress, calcium handling, natriuretic peptide signaling, and cardiac metabolism. GLP-1 receptor agonists modulate vascular pathways involving nitric oxide signaling, endothelial function, and renal sodium handling, contributing to improved hemodynamics and neurohormonal balance. Together, these actions intersect with key neurohormonal and cellular processes contributing to chronic heart failure progression. This review explores the mechanistic overlap between GLP-1 receptor signaling and heart failure pathophysiology. This mechanistic overlap suggests a plausible role for these agents as adjunctive treatments in heart failure, especially in metabolically driven phenotypes. While direct cardiac effects remain incompletely defined, systemic metabolic and anti-inflammatory actions provide a mechanistic basis for observed clinical benefits.
Full article
(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)
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Open AccessArticle
Secretome from Uterine Cervical Mesenchymal Stem Cells as a Protector of Neuronal Cells Against Oxidative Stress and Inflammation
by
Javier Mateo, Miguel Ángel Suárez-Suárez, Maria Fraile, Ángel Ramón Piñera-Parrilla, Francisco J. Vizoso and Noemi Eiro
Biomolecules 2025, 15(10), 1402; https://doi.org/10.3390/biom15101402 - 2 Oct 2025
Abstract
Background: The limited self-repair capacity of nerve tissue requires a new therapeutic approach. Mesenchymal stem cells from the uterine cervix, hUCESC, have shown anti-inflammatory, regenerative, and anti-oxidative stress effects through their secretome, which makes them candidates to evaluate their potential in the context
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Background: The limited self-repair capacity of nerve tissue requires a new therapeutic approach. Mesenchymal stem cells from the uterine cervix, hUCESC, have shown anti-inflammatory, regenerative, and anti-oxidative stress effects through their secretome, which makes them candidates to evaluate their potential in the context of neuronal damage. In this study, we aimed to determine whether secretome or conditioned medium of hUCESC (hUCESC-CM) has beneficial action in the treatment of PC-12 and HMC3 cells in vitro under conditions of oxidative stress and inflammation. Methods: Differentiated PC-12 cells and HMC3 cells were subjected to oxidative stress and inflammatory conditions in the presence of hUCESC-CM. The expression of factors related to both processes was evaluated by q-RT-PCR. Results: PC-12 cells treated with hUCESC-CM showed a significant increase in the expression of anti-oxidative stress factors (HO-1 and Nrf2) and a significant decrease in the expression of pro-inflammatory factors (IL1β, IL6 and TNFα). In addition, the treatment of HMC3 cells with hUCESC-CM significantly decreased the expression of IL6 and TNFα and enhanced the expression of neuroprotective factors such as BDNF and GDNF. Conclusions: Considering that both oxidative stress and inflammation are interrelated and implicated in several nerve injuries and neurodegenerative disorders, the effects of hUCESC-CM on neuronal cells are very promising.
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(This article belongs to the Section Biological Factors)
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Open AccessReview
Statistical Methods for Multi-Omics Analysis in Neurodevelopmental Disorders: From High Dimensionality to Mechanistic Insight
by
Manuel Airoldi, Veronica Remori and Mauro Fasano
Biomolecules 2025, 15(10), 1401; https://doi.org/10.3390/biom15101401 - 2 Oct 2025
Abstract
Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput omics technologies—transcriptomics, proteomics, metabolomics, and epigenomics—offer a unique opportunity to link genetic variation to molecular and cellular mechanisms underlying these disorders.
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Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput omics technologies—transcriptomics, proteomics, metabolomics, and epigenomics—offer a unique opportunity to link genetic variation to molecular and cellular mechanisms underlying these disorders. However, the high dimensionality, sparsity, batch effects, and complex covariance structures of omics data present significant statistical challenges, requiring robust normalization, batch correction, imputation, dimensionality reduction, and multivariate modeling approaches. This review provides a comprehensive overview of statistical frameworks for analyzing high-dimensional omics datasets in NDDs, including univariate and multivariate models, penalized regression, sparse canonical correlation analysis, partial least squares, and integrative multi-omics methods such as DIABLO, similarity network fusion, and MOFA. We illustrate how these approaches have revealed convergent molecular signatures—synaptic, mitochondrial, and immune dysregulation—across transcriptomic, proteomic, and metabolomic layers in human cohorts and experimental models. Finally, we discuss emerging strategies, including single-cell and spatially resolved omics, machine learning-driven integration, and longitudinal multi-modal analyses, highlighting their potential to translate complex molecular patterns into mechanistic insights, biomarkers, and therapeutic targets. Integrative multi-omics analyses, grounded in rigorous statistical methodology, are poised to advance mechanistic understanding and precision medicine in NDDs.
Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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