The Intersection of Epigenetics and Senolytics in Mechanisms of Aging and Therapeutic Approaches
Ethanol Disrupts the Protective Crosstalk Between Macrophages and HBV-Infected Hepatocytes
Saponins Effect on Human Insulin Amyloid Aggregation
Early-Stage Luminal B-like Breast Cancer Exhibits a More Immunosuppressive Tumor Microenvironment than Luminal A-like Breast Cancer
Synergistic Enzybiotic Effect of a Bacteriophage Endolysin and an Engineered Glucose Oxidase Against Listeria

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. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Biomolecules and their members receive discounts on the article processing charges.

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 18.4 days after submission; acceptance to publication is undertaken in 2.7 days (median values for papers published in this journal in the second half of 2024).
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 (2023); 5-Year Impact Factor: 5.4 (2023)

Imprint Information Journal Flyer Open Access ISSN: 2218-273X

Latest Articles

22 pages, 13635 KiB

Open AccessArticle

Pericarpium Trichosanthis Injection Protects Isoproterenol-Induced Acute Myocardial Ischemia via Suppressing Inflammatory Damage and Apoptosis Pathways

by Zizheng Wu, Xing Chen, Jiahao Ye, Xiaoyi Wang and Zhixi Hu

Biomolecules 2025, 15(5), 618; https://doi.org/10.3390/biom15050618 (registering DOI) - 24 Apr 2025

Abstract

This research proposes to systematically investigate the cardioprotective mechanisms of Pericarpium Trichosanthis injection (PTI) against acute myocardial ischemia through an integrated approach combining ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) constituent profiling, UNIFI database-assisted component identification, network pharmacology-guided target prediction, molecular docking verification, and in vivo experimental validation. The multimodal methodology is designed to comprehensively uncover the therapeutic benefits and molecular pathways underlying this traditional Chinese medicine formulation. Methods: UPLC-Q-TOF/MS and the UNIFI database were used in conjunction with a literature review to screen and validate the absorbed components of PTI. Using network pharmacology, we constructed protein-protein interaction (PPI) networks for pinpointing prospective therapeutic targets. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify potential signaling pathways. In vivo experiments were conducted to investigate the mechanisms by which PTI ameliorated isoproterenol-induced myocardial injury in rats. All animal experiments have adhered to ARRIVE guidelines. Results: UPLC-Q-TOF/MS revealed 11 core active components in PTI. Network pharmacology prioritization identified pseudoaspidin, ciryneol C, cynanoside M, daurinol, and n-butyl-β-D-fructopyranoside as central bioactive constituents within the compound-target interaction network. Topological analysis of the protein interactome highlighted AKT1, EGFR, MMP9, SRC, PTGS2, STAT3, BCL2, CASP3, and MAPK3 as the most interconnected nodes with the highest betweenness centrality. Pathway enrichment analysis established the PI3K/Akt signaling cascade as the principal mechanistic route for PTI’s cardioprotective effects. Molecular docking simulations demonstrated high-affinity interactions between characteristic components (e.g., cynanoside M, darutigenol) and pivotal targets including PTGS2, MAPK3, CASP3, and BCL2. In vivo investigations showed PTI treatment markedly attenuated myocardial tissue degeneration and collagen deposition (p < 0.05), normalized electrocardiographic ST-segment deviations, and suppressed pro-inflammatory cytokine production (IL-6, TNF-α). The formulation concurrently reduced circulating levels of cardiac injury indicators (LDH, cTnI) and oxidative stress parameters (ROS, MDA), Regarding apoptosis regulation, PTI reduced Bax, caspase-3, and caspase-9, while elevating Bcl-2 (p < 0.05), effectively inhibiting myocardial cell apoptosis with all therapeutic outcomes reaching statistical significance. These findings highlight PTI’s protective effects against myocardial injury through multi-target modulation of inflammation, oxidation, and apoptosis. Conclusions: PTI exerts its therapeutic effects in treating acute myocardial ischemia by regulating and suppressing inflammatory responses, and inhibiting cardiomyocyte apoptosis. Full article

(This article belongs to the Section Molecular Medicine)

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21 pages, 1714 KiB

Open AccessReview

The Role of N6-Methyladenosine (m6A) RNA Modification in the Pathogenesis of Parkinson’s Disease

by Yulu Wang, Tianyuan Zhao, Chunsen Yuan and Xuechai Chen

Biomolecules 2025, 15(5), 617; https://doi.org/10.3390/biom15050617 - 23 Apr 2025

Abstract

Parkinson’s disease (PD) is a neurodegenerative disease with a high prevalence among the middle-aged and elderly population. The pathogenesis of PD is closely linked to the misfolding and aggregation of α-synuclein, which contributes to the formation of Lewy bodies. These processes are associated with the degeneration of dopaminergic neurons, a key neuropathological change that underlies the motor symptoms of PD. In addition, genetic susceptibility, mitochondrial dysfunction, oxidative stress and neuroinflammation are involved in the progress of the disease. Previous studies indicated that the dysregulation of epigenetic modifications, including DNA methylation and histone acetylation, may be the key pathophysiological factors in PD. N6-methyladenosine (m6A) is a dynamically reversible modification in eukaryotes RNA, and could regulate mRNA degradation, stability, maturation, and translation. Recently, clinical research has shown that the global m6A level is significantly reduced in PD patients as well as the expression changes in m6A-associated proteins. Moreover, the dysregulation of m6A modification was shown to impact dopamine metabolism and damage dopaminergic neurons, indicating that m6A RNA modification may play a critical role in the pathogenesis of PD. In this review, we summarize recent clinical studies on m6A RNA modification in PD patients and discuss the regulatory role of m6A modification in dopamine metabolism and dopaminergic neurons death. Furthermore, based on the different m6A modification databases and prediction websites, we analyzed the potential m6A modification sites on the mRNA of key PD pathogenic genes (SNCA, PRKN, PINK1, and LRRK2) for the first time, aiming to offer new gene targets and perspectives understanding the pathogenesis of PD. Full article

(This article belongs to the Section Molecular Biology)

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15 pages, 1219 KiB

Open AccessArticle

Pancreatic MicroRNAs in Ictidomys tridecemlineatus Associated with Metabolic Diseases: Nature’s Insights into Important Biomarkers

by Olawale O. Taiwo, Saif Rehman and Kenneth B. Storey

Biomolecules 2025, 15(5), 616; https://doi.org/10.3390/biom15050616 - 23 Apr 2025

Abstract

Hibernation involves a profound metabolic rate depression (MRD) that enables certain species to survive prolonged periods of low energy availability. The thirteen-lined ground squirrel uses MRD to arrange cellular and biochemical pathways which suppress nonvital genetic and cellular pathways to conserve internal energy while preserving all essential processes. This study investigates the role of microRNAs (miRNAs) in controlling key signaling pathways and cellular processes in pancreatic tissue during hibernation. Using next-generation sequencing and broad genomic analysis, we analyzed and identified seven differentially expressed miRNAs (miR-29a-3p, miR-22-3p, miR-125-5p, miR-200a-3p, miR-328-3p, miR-21-5p, and miR-148-3p) in the pancreas of hibernating 13-lined ground squirrels (Ictidomys tridecemlineatus). Our findings reveal that these miRNAs regulate pathways involved in glucose homeostasis, including insulin secretion and metabolic regulation, contributing to the unique adaptations of hibernation. These insights advance our understanding of the molecular adaptations underlying hibernation and may have implications for therapeutic strategies targeting metabolic disorders such as diabetes. Full article

(This article belongs to the Section Molecular Biology)

39 pages, 1641 KiB

Open AccessReview

The Role of Astrocytes in the Molecular Pathophysiology of Schizophrenia: Between Neurodevelopment and Neurodegeneration

by Licia Vellucci, Benedetta Mazza, Annarita Barone, Anita Nasti, Giuseppe De Simone, Felice Iasevoli and Andrea de Bartolomeis

Biomolecules 2025, 15(5), 615; https://doi.org/10.3390/biom15050615 - 23 Apr 2025

Abstract

Schizophrenia is a chronic and severe psychiatric disorder affecting approximately 1% of the global population, characterized by disrupted synaptic plasticity and brain connectivity. While substantial evidence supports its classification as a neurodevelopmental disorder, non-canonical neurodegenerative features have also been reported, with increasing attention given to astrocytic dysfunction. Overall, in this study, we explore the role of astrocytes as a structural and functional link between neurodevelopment and neurodegeneration in schizophrenia. Specifically, we examine how astrocytes contribute to forming an aberrant substrate during early neurodevelopment, potentially predisposing individuals to later neurodegeneration. Astrocytes regulate neurotransmitter homeostasis and synaptic plasticity, influencing early vulnerability and disease progression through their involvement in Ca²⁺ signaling and dopamine–glutamate interaction—key pathways implicated in schizophrenia pathophysiology. Astrocytes differentiate via nuclear factor I-A, Sox9, and Notch pathways, occurring within a neuronal environment that may already be compromised in the early stages due to the genetic factors associated with the ‘two-hits’ model of schizophrenia. As a result, astrocytes may contribute to the development of an altered neural matrix, disrupting neuronal signaling, exacerbating the dopamine–glutamate imbalance, and causing excessive synaptic pruning and demyelination. These processes may underlie both the core symptoms of schizophrenia and the increased susceptibility to cognitive decline—clinically resembling neurodegeneration but driven by a distinct, poorly understood molecular substrate. Finally, astrocytes are emerging as potential pharmacological targets for antipsychotics such as clozapine, which may modulate their function by regulating glutamate clearance, redox balance, and synaptic remodeling. Full article

(This article belongs to the Special Issue The Role of Astrocytes in Neurodegenerative Diseases)

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35 pages, 3801 KiB

Open AccessReview

Targeting the Electron Transport System for Enhanced Longevity

by Marko Radovic, Lucas P. Gartzke, Simon E. Wink, Joris A. van der Kleij, Frouwkje A. Politiek and Guido Krenning

Biomolecules 2025, 15(5), 614; https://doi.org/10.3390/biom15050614 - 23 Apr 2025

Abstract

Damage to mitochondrial DNA (mtDNA) results in defective electron transport system (ETS) complexes, initiating a cycle of impaired oxidative phosphorylation (OXPHOS), increased reactive oxygen species (ROS) production, and chronic low-grade inflammation (inflammaging). This culminates in energy failure, cellular senescence, and progressive tissue degeneration. Rapamycin and metformin are the most extensively studied longevity drugs. Rapamycin inhibits mTORC1, promoting mitophagy, enhancing mitochondrial biogenesis, and reducing inflammation. Metformin partially inhibits Complex I, lowering reverse electron transfer (RET)-induced ROS formation and activating AMPK to stimulate autophagy and mitochondrial turnover. Both compounds mimic caloric restriction, shift metabolism toward a catabolic state, and confer preclinical—and, in the case of metformin, clinical—longevity benefits. More recently, small molecules directly targeting mitochondrial membranes and ETS components have emerged. Compounds such as Elamipretide, Sonlicromanol, SUL-138, and others modulate metabolism and mitochondrial function while exhibiting similarities to metformin and rapamycin, highlighting their potential in promoting longevity. The key question moving forward is whether these interventions should be applied chronically to sustain mitochondrial health or intermittently during episodes of stress. A pragmatic strategy may combine chronic metformin use with targeted mitochondrial therapies during acute physiological stress. 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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24 pages, 3732 KiB

Open AccessArticle

Acute Neurovascular Inflammatory Profile in Patients with Aneurysmal Subarachnoid Hemorrhage

by Ruby R. Taylor, Robert W. Keane, Begoña Guardiola, Raul Martí, Daniel Alegre, W. Dalton Dietrich, Jon Perez-Barcena and Juan Pablo de Rivero Vaccari

Biomolecules 2025, 15(5), 613; https://doi.org/10.3390/biom15050613 - 23 Apr 2025

Abstract

Aneurysmal subarachnoid hemorrhage (aSAH) is a life-threatening condition that results from intracranial aneurysm rupture, leading to the accumulation of blood between the arachnoid and pia mater. The blood breakdown products and damage-associated molecule patterns (DAMPs), which are released as a result of vascular and cellular compromise following aneurysm rupture, elicit local endothelial reactions leading to the narrowing of cerebral arteries and ischemia. In addition, vascular inflammation, characterized by activated endothelial cells, perpetuates disruption of the neurovascular unit and the blood–brain barrier. The uncertain prognosis of aSAH patients contributes to the necessity of a fluid biomarker that can serve as a valuable adjunct to radiological and clinical evaluation. Limited studies have investigated vascular inflammation and angiogenic protein expression following aSAH. Reliable markers of the vascular inflammatory and angiogenic response associated with aSAH may allow for the earlier detection of patients at risk for complications and aid in the identification of novel pharmacologic targets. We investigated whether vascular inflammatory and angiogenesis signaling proteins may serve as potential biomarkers of aSAH. Serum and cerebrospinal fluid (CSF) from fifteen aSAH subjects and healthy age-matched controls as well as hydrocephalus (CSF) no-aneurysm controls were evaluated for levels of vascular inflammatory and angiogenesis proteins. Protein measurement was carried out using electrochemiluminescence. The area under the curve (AUC) was calculated using receiver operating characteristics (ROC) to obtain information on biomarker reliability, specificity, sensitivity, cut-off points, and likelihood ratio. In addition, patients were grouped by Glasgow Outcome Score—Extended at 3 months post-injury to determine the correlation between vascular inflammatory protein levels and clinical outcome measures. aSAH subjects demonstrated elevated vascular inflammatory protein levels in serum and CSF when compared to controls. Certain vascular injury and angiogenic proteins were found to be promising biomarkers of inflammatory response in aSAH in the CSF and serum. In particular, elevated levels of serum amyloid-alpha (SAA) were found to be correlated with unfavorable outcomes following aSAH. Determination of these protein levels in CSF and serum in aSAH may be utilized as reliable biomarkers of inflammation in aSAH and used clinically to monitor patient outcomes. Full article

(This article belongs to the Special Issue Biomarkers of Cardiovascular and Cerebrovascular Diseases, 2nd Edition)

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38 pages, 2476 KiB

Open AccessReview

Understanding the Role of Adipokines in Cardiometabolic Dysfunction: A Review of Current Knowledge

by Sayantap Datta, Saisudha Koka and Krishna M. Boini

Biomolecules 2025, 15(5), 612; https://doi.org/10.3390/biom15050612 - 23 Apr 2025

Abstract

Cardiometabolic risk and associated dysfunctions contribute largely to the recent rise in mortality globally. Advancements in multi-omics in recent years promise a better understanding of potential biomarkers that enable an early diagnosis of cardiometabolic dysfunction. However, the molecular mechanisms driving the onset and progression of cardiometabolic disorders remain poorly understood. Adipokines are adipocyte-specific cytokines that are central to deleterious cardiometabolic alterations. They exhibit both pro-inflammatory and anti-inflammatory effects, complicating their association with cardiometabolic disturbances. Thus, understanding the cardiometabolic association of adipokines from a molecular and signaling perspective assumes great importance. This review presents a comprehensive outline of the most prominent adipokines exhibiting pro-inflammatory and/or anti-inflammatory functions in cardiometabolic dysfunction. The review also presents an insight into the pathophysiological implications of such adipokines in different cardiometabolic dysfunction conditions, the status of adipokine druggability, and future studies that can be undertaken to address the existing scientific gap. A clear understanding of the functional and mechanistic role of adipokines can potentially improve our understanding of cardiovascular disease pathophysiology and enhance our current therapeutic regimen in the years to come. Full article

(This article belongs to the Special Issue Insights from the Editorial Board Members)

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15 pages, 2356 KiB

Open AccessArticle

New Lead Schiff Bases Predominantly Mediate Vasorelaxant Activity Through α₁ Receptor Blocking Activity

by Zakia Subhan, Niaz Ali, Abid Ullah, Wajid Ali, Muhammad Nabi and Syed Wadood Ali Shah

Biomolecules 2025, 15(5), 611; https://doi.org/10.3390/biom15050611 - 23 Apr 2025

Abstract

Schiff bases synthesized in our laboratory have demonstrated pain-relieving effects through both peripheral and central nervous system pathways. Considering that centrally acting analgesics often affect the muscle tone of the gastrointestinal tract (GIT) and related deep internal organs, this study was conducted to examine potential relaxant effects on blood vessels and GIT smooth muscles. The possible relaxant effects of Schiff bases (SB1 and SB2) on isolated rabbit aortic strips were evaluated. The experiments involved assessing their impact on contractions induced by 80 mM potassium chloride (KCL) and 1 µM norepinephrine (NE). Norepinephrine concentration response curves (N. ECRCs) were constructed in the absence and presence of three different concentrations of SB1 and SB2, using N. ECRCs as a negative control. Terazosin served as a standard α1 receptor blocker. Docking studies were employed to validate the mechanism of action for SB1 and SB2. The study outcomes suggest that SB1 is more potent than SB2, demonstrating lower EC₅₀ values for NE-induced contractions in intact (5.50 × 10⁻⁵ ± 2.23 M) and denuded (5.81 × 10⁻⁵ ± 3.80 M) aortae. For NE-induced contractions, SB1 showed percent relaxation values of 48% and 41% in intact and denuded aortae, respectively. In comparison, SB2 exhibited values of 82.5% and 74%, showing that SB1 is more efficacious than SB2. The rightward shift of N. ECRCs for both SB1 and SB2 confirms their inhibition of α1 receptors. Additive effects of SB1 and SB2 were seen in the presence of verapamil (p < 0.0001). Docking analysis revealed that the compounds can properly bind to the target receptor Gq 1D (P25100). Findings show that both Schiff base SB1 and SB2 produce significant (p < 0.05) vasorelaxation via the α1 receptor blocking mechanism. Full article

(This article belongs to the Section Chemical Biology)

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24 pages, 1334 KiB

Open AccessReview

Small but Mighty: Nanobodies in the Fight Against Infectious Diseases

by Wenning Jiang, Chundong Huang, Serge Muyldermans and Lingyun Jia

Biomolecules 2025, 15(5), 610; https://doi.org/10.3390/biom15050610 - 23 Apr 2025

Abstract

Infectious diseases, caused by pathogenic microorganisms and capable of spreading, pose a significant threat to global public health. Developing efficient and cost-effective techniques for treating infectious diseases is crucial in curbing their progression and reducing patients’ morbidity and mortality. Nanobodies (Nbs), a novel class of affinity reagents derived from unique heavy chain-only antibodies in camelids, represent the smallest intact and fully functional antigen-binding fragments. Compared with conventional antibodies and their antigen binding fragments, Nbs offer numerous advantages, including high affinity, exceptional target specificity, cost-effective production, easy accessibility, and robust stability, demonstrating immense potential in infectious disease treatment. This review introduces Nbs and focuses on discussing their mechanisms and intervention strategies in the treatment of viral and bacterial infections. Full article

(This article belongs to the Section Molecular Medicine)

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3 pages, 137 KiB

Open AccessEditorial

Zinc in Health and Disease Condition—2nd Edition

by Xiang-Ping Chu, Qian Jiang and Yuyang Chu

Biomolecules 2025, 15(5), 609; https://doi.org/10.3390/biom15050609 - 23 Apr 2025

Abstract

Zinc is an essential trace element that plays a pivotal role in numerous physiological processes, including immune function, antioxidant defense, cellular signaling, and growth [...] Full article

(This article belongs to the Special Issue Zinc in Health and Disease Conditions: 2nd Edition)

20 pages, 6962 KiB

Open AccessArticle

Topical Delivery of Ceramide by Oil-in-Water Nanoemulsion to Retain Epidermal Moisture Content in Dermatitis

by Yu Zhou, Lichun Wu, Yi Zhang, Jia Hu, Jannatul Fardous, Yasuhiro Ikegami and Hiroyuki Ijima

Biomolecules 2025, 15(5), 608; https://doi.org/10.3390/biom15050608 - 22 Apr 2025

Abstract

External environmental stressors and internal physiological changes frequently compromise the skin barrier, resulting in conditions such as dermatitis and dehydration. A key underlying factor is the depletion of ceramides, essential lipids in the stratum corneum that maintain skin integrity. Although topical ceramide supplementation is effective for barrier repair, its clinical application is limited by poor solubility and low skin permeability. To overcome these challenges, this study developed an oil-in-water nanoemulsion (O/W-NE) using ultrasonic emulsification for the efficient transdermal delivery of ceramide C2. Octyldodecanol was selected as the oil phase to enhance ceramide solubility, while glycerin was incorporated to increase aqueous phase viscosity, reduce particle size, and function as a biocompatible penetration enhancer. The optimized nanoemulsion achieved a particle size of 112.5 nm and an encapsulation efficiency of 85%. Its performance was evaluated via in vitro release, ex vivo skin permeation, and in vivo biocompatibility studies. Mechanistic investigations revealed that both particle size and glycerin concentration significantly influenced ceramide penetration into the epidermis and dermis. Additionally, the nanoemulsion exhibited moisturizing and barrier-repair effects in a damaged skin model. Overall, this O/W-NE offers a stable, non-invasive strategy for enhancing ceramide delivery and restoring skin barrier function. Full article

(This article belongs to the Special Issue Molecular Advances in Wound Healing and Skin Regeneration)

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15 pages, 404 KiB

Open AccessArticle

Adipokines as Potential Biomarkers in Pregnancy: A Naturalistic Study of Adipokines in Pregnant Women and Newborns

by Cristina Mihaela Ormindean, Răzvan Ciortea, Andrei Mihai Măluțan, Carmen Elena Bucuri, Doru Mihai Diculescu, Cristian Ioan Iuhas, Ciprian Gheorghe Porumb, Vlad Ormindean, Maria Patricia Roman, Ionel Daniel Nati, Viorela Suciu, Alexandru Emil Hăprean and Dan Mihu

Biomolecules 2025, 15(5), 607; https://doi.org/10.3390/biom15050607 - 22 Apr 2025

Abstract

Maternal obesity is an escalating public health concern that adversely affects pregnancy outcomes. Adipokines play a key role in regulating metabolism and fetal development, but their dynamic changes during pregnancy remain inadequately understood. Objective: This study investigates maternal and fetal adipokine variations throughout pregnancy and their associations with maternal body mass index (BMI), abdominal wall thickness, and neonatal outcomes. Methods: A prospective case-control study was conducted involving 74 pregnant women categorized by BMI. Maternal blood samples were collected at mid-pregnancy and delivery, and additional analysis of umbilical-cord blood was performed. Clinical parameters such as BMI, abdominal wall thickness, and fetal growth metrics were also recorded. Results: Adiponectin levels were significantly lower in obese pregnancies, whereas leptin and visfatin levels increased with higher maternal BMI. Umbilical-cord blood leptin levels correlated positively with maternal BMI and neonatal birth weight, while ghrelin levels were reduced in neonates born to obese mothers. Significant adipokine fluctuations were observed between mid-pregnancy and delivery. Conclusions: Maternal obesity is associated with distinct alterations in adipokine profiles. These findings highlight the potential of maternal adipokines, given their links to maternal adiposity, as predictive biomarkers for adverse pregnancy outcomes and long-term metabolic risks in offspring. Further interventional research is warranted to evaluate targeted strategies aimed at improving perinatal metabolic health. Full article

21 pages, 3207 KiB

Open AccessArticle

Integrating Biochemical and Computational Approaches Reveal Structural Insights in Trastuzumab scFv-Fc Antibody Engineering

by Olga Bednova, Jessica Pougoue Ketchemen, Hazem Mslati, Mark Barok, Heikki Joensuu, Natalie Zeytuni, Francesco Gentile, Leon Sanche, Humphrey Fonge and Jeffrey Victor Leyton

Biomolecules 2025, 15(5), 606; https://doi.org/10.3390/biom15050606 - 22 Apr 2025

Abstract

Antibody-based agents have become a preferred treatment for various diseases, including cancer, due to significant advances in antibody engineering. The use of single-chain Fv-Fcs (scFv-Fcs) has been a promising engineering approach for therapeutic design. The concept is that the Fc provides increased stability and target binding and ultimately improves performance. However, the structural and dynamic relationship between the variable and Fc domains, which are fused in close proximity, and the impact on stability and target binding are not well understood. This study evaluated trastuzumab-derived scFv-Fc antibodies, focusing on the impact of their design on important biopharmaceutical parameters. Computational modelling and molecular dynamics, alongside experimental studies, were used to ascertain their dynamics, expression and purification, stabilities, and binding potencies. The results showed that the scFv subunits exhibited stochastic interplays that lead to diverse shapes and were associated with functional performance. This new understanding of scFv-Fc antibodies and their structural and functional nuances provides important details to further guide the design of more effective and less toxic therapeutics. Full article

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

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7 pages, 647 KiB

Open AccessPerspective

RNA-Mediated Non-Mendelian Inheritance in Mice: The Power of Memory

by Minoo Rassoulzadegan

Biomolecules 2025, 15(4), 605; https://doi.org/10.3390/biom15040605 - 21 Apr 2025

Abstract

The mouse genome is transcribed at different rates in both directions from the newly formed genome after fertilization. During embryonic genomic activation (EGA/ZGA), the first RNA metabolism creates heterogeneity between blastomeres. Indeed, ZGA-dependent maternal RNA degradation is crucial to regulate gene expression and enable the initiation and acquisition of full developmental competence. Subsequently, from the new genome, in addition to mRNAs, a wide range of regulatory ncRNAs are also transcribed. Regulatory ncRNAs (non-coding RNAs) have profoundly influenced fields ranging from developmental biology to RNA-mediated non-Mendelian inheritance, exhibiting sequence-specific functions. To date, the database cataloging ncRNA is not exhaustive, but their high sequence diversity, length and low expression level can vary within the same genome depending on environmental conditions, making understanding their functions often ambiguous. Indeed, during transcription control, cellular RNA content varies continuously. This phenomenon is observed in genetically identical organisms studied—bacteria, flies, plants and mammals—due to changes in transcription rates, and therefore, it impacts cellular memory. Importantly, experimental data regarding the simple modification of RNAs levels by microinjection into fertilized mouse eggs suggest that they certainly play a driving role in establishing and transmitting newly formed expression information. The idea here is that, even in a stable genome, transcripts can vary rapidly and significantly in response to environmental changes, initiated by transcriptional variations in the genome, thus altering cellular memory. Full article

(This article belongs to the Section Molecular Genetics)

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16 pages, 12866 KiB

Open AccessArticle

Regeneration of Two-Walled Infrabony Periodontal Defects in Swine After Buccal Fat Pad-Derived Dedifferentiated Fat Cell Autologous Transplantation

by Daisuke Akita, Naoki Tsukimura, Tomohiko Kazama, Rie Takahashi, Yoshiki Taniguchi, Jin Inoue, Ayana Suzuki, Nodoka Tanabe, Keisuke Seki, Yoshinori Arai, Masatake Asano, Shuichi Sato, Yoshiyuki Hagiwara, Koichiro Kano, Masaki Honda and Taro Matsumoto

Biomolecules 2025, 15(4), 604; https://doi.org/10.3390/biom15040604 - 20 Apr 2025

Abstract

Mature adipocyte-derived dedifferentiated fat (DFAT) cells show proliferative capabilities and multipotency. Given that the buccal fat pad (BFP) serves as a readily available resource for DFAT cell isolation, BFP-derived DFAT (BFP-DFAT) cells are a promising candidate in orofacial tissue engineering. In this research, we assessed the regenerative capacity of the periodontium through autologous BFP-DFAT cell transplantation in adult swine (micro-minipigs; MMPs). The BFP-DFAT cells were transplanted into inflammation-inducing two-walled infrabony periodontal defects located on the mesial of the second mandibular premolar (n = 6). Twelve weeks post-transplantation, a remarkable attachment gain was noted in the DFAT group, based on probing depths and clinical attachment levels. Histological and immunohistochemical analyses indicated new continuous cellular cementum and alveolar bone formation within the created infrabony defect. Well-organized periodontal ligament-like fibers were embedded between newly formed cementum and the alveolar bone. Histometric analysis demonstrated that the DFAT group had a 2.2-fold increase in new alveolar bone length and a 2.2-fold enhancement in vascularization than those in the control group. Except for minor inflammation in the lungs, no teratomas were detected in the recipient MMPs. BFP-DFAT cells significantly enhanced periodontal tissue regeneration, thus representing an optimal source for tissue engineering applications in dentistry. Full article

(This article belongs to the Special Issue Biologics and Biomaterials for Periodontal Treatment: Current and Future Challenges)

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15 pages, 3023 KiB

Open AccessArticle

Link N Directly Targets IL-1β to Suppress Inflammation and Regulate Sensory Pain in Intervertebral Disc Degeneration

by Michael P. Grant, Muskan Alad, Fajer Yousef, Laura M. Epure, John Antoniou and Fackson Mwale

Biomolecules 2025, 15(4), 603; https://doi.org/10.3390/biom15040603 - 19 Apr 2025

Abstract

Intervertebral disc (IVD) disease is typically characterized by the degradation of IVD tissue, secretion of inflammatory and painful factors, and hyperinnervation of the disc. The pro-inflammatory cytokine interleukin-1β (IL-1β) has been regarded as a principal factor in orchestrating disc degeneration. Link N (LN) is a peptide derived from the link protein that has been shown to promote extracellular disc regeneration even in an inflammatory milieu; however, no mechanism(s) has been described for their behaviour to date. Building on prior studies on LN, we hypothesize that LN directly inhibits IL-1β. IVD degeneration was experimentally induced in New Zealand white rabbits, followed by the injection of either sLN or saline as the vehicle control. To determine the expression of markers of pain, histology was performed. Cultured human Nucleus Pulposus disc cells (hNP) were used to determine the effects of LN on IL-1β-induced changes in gene expression, including the effects on IL-1β, TNFα, and IL6 signalling. Isolated murine dorsal root ganglia (DRG) neurons were used to assess the effect of LN on IL-1β-induced neuronal hyperactivity. LN significantly reduced IL-1β-induced NF-κB activation in a dose-dependent manner in disc cells and was further able to modulate IL-1β-induced gene expression, inflammatory mediators, and neurotrophic factors. Peptide docking simulations revealed that LN could interact with IL-1β. A direct interaction of LN and IL-1β was revealed through co-immunoprecipitation experiments. Although IL-1β was able to hypersensitize DRG neurons following a seven-day exposure, as demonstrated by Ca²⁺ imaging, this effect was significantly blunted when co-treated with LN. LN demonstrates a novel mechanism of action by directly inhibiting IL-1β, in addition to mitigating IL-1β-induced hypersensitivity in DRG neurons. These data suggest a potential role for LN in reducing discogenic pain. Full article

(This article belongs to the Section Molecular Medicine)

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17 pages, 3557 KiB

Open AccessArticle

The Role of Antigen Carbohydrate 125 in Modulating Soluble ST2: Prognostic-Related Effects in Acute Heart Failure

by Arancha Martí-Martínez, Julio Núñez, Herminio López-Escribano, Elena Revuelta-López, Anna Mollar, Marta Peiró, Juan Sanchis, Antoni Bayés-Genís, Arturo Carratala, Òscar Miró, Pere Llorens and Pablo Herrero-Puente

Biomolecules 2025, 15(4), 602; https://doi.org/10.3390/biom15040602 - 18 Apr 2025

Abstract

Background: Acute heart failure (AHF) is a complex syndrome associated with high mortality and hospital readmissions, characterized by volume overload and inflammation. Soluble ST2 (sST2) and antigen carbohydrate 125 (CA125) are emerging biomarkers that reflect these processes and may interact to influence long-term outcomes in AHF patients. This study aims to examine the prognostic relationship between sST2 and CA125 in predicting mortality and heart failure (HF)-related hospitalizations in patients with decompensated heart failure. Methods: In a cohort of 635 patients with AHF, we investigated whether the prognostic value of sST2 varies according to CA125 levels (≤35 vs. >35 U/mL). The endpoints were: (a) time to all-cause death, and (b) the combination of time to death or new HF admission. Results: This study of EAHFE registry data shows that the association between sST2 and long-term adverse outcomes (mortality and HF hospitalizations) in patients with AHF was differentially influenced by CA125 concentrations (p-value for interactions = 0.031 and 0.029, respectively). Higher sST2 was associated with the risk of death and the combined risk of death/HF readmission when CA125 was >35 U/mL [HR = 1.02 (CI 95%: 1.01–1.04), p = 0.006 and 1.02 (CI 95%: 1.01–1.03); p = 0.013 per increase in 10 ng/mL, respectively], but not when CA125 was ≤35 U/mL. Conclusions: This study highlights the prognostic interaction between sST2 and CA125 in AHF. Elevated sST2 predicts poor outcomes mainly in patients with high CA125 levels (>35 U/mL), suggesting CA125’s role in modulating inflammatory activity in HF. Further research is needed. Full article

(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)

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22 pages, 7835 KiB

Open AccessArticle

Identification of TSSK1 and TSSK2 as Novel Targets for Male Contraception

by Saman Nayyab, Marıá Gracia Gervasi, Darya A. Tourzani, Yeva Shamailova, Hiroki Akizawa, Mahboubeh Taghavi, Wei Cui, Rafael Fissore, Ana Maria Salicioni, Gunda I. Georg, Elizabeth Snyder and Pablo E. Visconti

Biomolecules 2025, 15(4), 601; https://doi.org/10.3390/biom15040601 - 18 Apr 2025

Abstract

The testis-specific serine kinases (TSSKs) are post-meiotically expressed in testicular germ cells. Their testis-specific expression, together with their putative role in phosphorylation pathways, suggests that TSSKs have relevant roles in spermiogenesis, sperm function, or both. Independent Tssk3 and Tssk6 knockout mice, as well as the double Tssk1/Tssk2 KO males, are sterile. However, the double KO results are silent regarding the individual roles of TSSK1 and TSSK2. The aim of this study was to develop independent mutant mouse models of Tssk1 and Tssk2, using CRISPR/Cas9, to evaluate their independent roles in reproduction. Male heterozygous pups were used to establish one Tssk1 and two independent Tssk2 mutant lines. Natural mating mutant Tssk1 and Tssk2 homozygous males but not females were found to be sterile. Additionally, homozygous males have lower sperm numbers and decreased motility, and were infertile in vitro. Anti-TSSK2 antibodies were validated against Tssk2 mutants and used in Western blot and immunofluorescence experiments. TSSK2 is localized to the sperm head; importantly, it is present in the testes and sperm from Tssk1 mutant mice, confirming individual mutation. Our results indicate that both TSSK1 and TSSK2 are individually essential for male reproduction and support both kinases as suitable nonhormonal male contraceptive targets. Full article

(This article belongs to the Collection Feature Papers in Section 'Molecular Medicine')

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19 pages, 2854 KiB

Open AccessArticle

Sex-Specific Inflammatory Profiles Affect Neuropsychiatric Issues in COVID-19 Survivors

by Mariagrazia Palladini, Mario Gennaro Mazza, Beatrice Bravi, Margherita Bessi, Maria Cristina Lorenzi, Sara Spadini, Rebecca De Lorenzo, Patrizia Rovere-Querini, Roberto Furlan and Francesco Benedetti

Biomolecules 2025, 15(4), 600; https://doi.org/10.3390/biom15040600 - 18 Apr 2025

Abstract

Post-COVID syndrome has unveiled intricate connections between inflammation, depressive psychopathology, and cognitive impairment. This study investigates these relationships in 101 COVID-19 survivors, focusing on sex-specific variations. Utilizing path modelling techniques, we analyzed the interplay of a one-month 48-biomarker inflammatory panel, with three-months of depressive symptoms and cognitive performance. The findings indicate that cognitive impairment is influenced by both inflammation and depression in the overall cohort. However, prominent sex-specific differences emerged. In females, a lingering imbalance between pro- and anti-inflammatory responses—likely reflecting the long-lasting immune alterations triggered by COVID-19—significantly affects cognitive functioning and shows a marginal, though not statistically significant, association with depressive symptoms. This suggests that a mixed inflammatory profile may contribute to these outcomes. Conversely, in males, inflammation was inversely associated with depression severity, with protective effects from regulatory mediators (IL-2, IL-4, IL-6, IL-15, LIF, TNF-α, β-NGF) against depression. In males, cognitive impairment appeared to be driven mainly by depressive symptoms, with minimal influence from inflammatory markers. These results highlight distinct sex-specific pathways in immune and inflammatory responses post-COVID-19, potentially shaped by endocrine mechanisms. The findings suggest that persistent inflammation may foster long-term neuropsychiatric sequelae, possibly through its effects on the brain, and underscore the need for sex-tailored therapeutic strategies to address the lasting impact of COVID-19. Full article

(This article belongs to the Section Biological Factors)

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23 pages, 2666 KiB

Open AccessFeature PaperArticle

Progression and Augmentation Therapy in PiSZ and PiZZ Alpha-1 Antitrypsin Deficiency: A Longitudinal Functional and Densitometric Study

by Soha Esmaili, Juan Luis Rodríguez Hermosa, Gianna Vargas Centanaro, José Luis Álvarez-Sala, Iman Esmaili and Myriam Calle Rubio

Biomolecules 2025, 15(4), 599; https://doi.org/10.3390/biom15040599 - 17 Apr 2025

Abstract

Background: Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder associated with an increased risk of developing chronic obstructive pulmonary disease (COPD) with variable phenotypic expression among different genotypes. While the PiZZ genotype is well characterized, the clinical and structural progression of PiSZ individuals remains less defined. This study evaluates genotype-specific disease trajectories and the impact of augmentation therapy over a two-year follow-up. Methods: A prospective observational cohort study was conducted, including 74 AATD patients (41 PiSZ, 33 PiZZ), stratified by augmentation therapy status. Disease progression was assessed through lung function decline (forced expiratory volume in one second [FEV1], diffusing capacity for carbon monoxide [DLCO], carbon monoxide transfer coefficient [KCO]) and densitometric changes (15th percentile lung density [PD-15], percentage of lung voxels below −950 Hounsfield units [HU-950]). Mixed-effects models and multivariable regression analyses were performed to evaluate genotype-specific progression patterns and treatment effects. Results: Results: PiZZ individuals exhibited significantly greater annual decline in lung function and densitometric parameters compared to PiSZ individuals, with more pronounced loss in basal lung regions and with greater decline in advanced stages, in contrast to the PiSZ genotype, which showed greater progression in earlier stages. Augmentation therapy was associated with a significant reduction in PD-15 decline in both genotypes, with the greatest benefit observed in PiZZ patients and in those diagnosed within five years of disease onset. Smoking and frequent exacerbations were identified as independent risk factors for accelerated disease progression. Conclusions: PiZZ individuals experience a more aggressive disease trajectory than PiSZ individuals in the absence of treatment. Augmentation therapy effectively mitigates disease progression in both genotypes, with greater efficacy when initiated early. Smoking and frequent exacerbations were identified as independent risk factors for accelerated disease progression. These findings underscore the importance of genotype-specific monitoring and personalized therapeutic strategies in AATD to optimize clinical outcomes. Full article

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

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