“One Pot” Enzymatic Synthesis of Caffeic Acid Phenethyl Ester in Deep Eutectic Solvent
Carnitine O-Acetyltransferase as a Central Player in Lipid and Branched-Chain Amino Acid Metabolism, Epigenetics, Cell Plasticity, and Organelle Function
Integrin and Its Associated Proteins as a Mediator for Mechano-Signal Transduction
Deletion of Murine APP Aggravates Tau and Amyloid Pathologies in the 5xFADXTg30 Alzheimer’s Disease Model
Integrated Clinomics and Molecular Dynamics Simulation Approaches Reveal the SAA1.1 Allele as a Biomarker in Alkaptonuria Disease Severity

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

16 pages, 2164 KiB

Open AccessArticle

The Hepatoprotective Properties of Gentiopicroside, Sweroside, and Swertiamarin Against Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)

by Anthony O. Boateng, Vinood B. Patel and S. W. Annie Bligh

Biomolecules 2025, 15(5), 726; https://doi.org/10.3390/biom15050726 (registering DOI) - 16 May 2025

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic disease characterised by the accumulation of fat in the liver. It is estimated that 30–38% of the world’s adult population have MASLD, making it the most prevalent global chronic liver disease. Due to a lack of a therapy for MASLD, treatment has been mainly focussed on managing the conditions associated with the disease such as obesity, diabetes mellitus, and hyperlipidaemia. This study aimed to investigate the role played by Gentiana phytochemicals including the following: gentiopicroside, sweroside, and swertiamarin, in promoting hepatocyte protection against the cytotoxic effects of fatty acids. Gentiana species such as lutea, macrophylla, rigescens, and scabra are known to protect and enhance hepatocyte viability via their antioxidant, anti-inflammatory, and bitter components including the following: amarogentin gentianine, iso-orientin, swertiamarin, gentiopicroside, and sweroside. In this study, HepG2 cells pre-treated with phytochemicals gentiopicroside, sweroside, swertiamarin, and silymarin followed by an exposure to arachidonic acid (10, 30, 50 and 80 µM) were assessed for cell viability via MTT, mitochondrial function via seahorse assay, ROS levels via DCF assay, and annexin V-FITC for apoptosis. THLE-2 cells were also assayed for validation. The phytochemicals tested improved ATP production notably gentiopicroside, which improved ATP production by over 60% compared to untreated hepatocytes. Significant hepatocyte protection against lipotoxicity leading to apoptosis was also observed in gentiopicroside in the presence of 30 µM arachidonic acid with apoptosis reduced by over 50%. ROS production was reduced up to 60% by the pre-treatment of HepG2 cells with 20 µM, gentiopicroside, sweroside, swertiamarin, and silymarin, with the highest reduction observed in swertiamarin. It was concluded that phytochemicals gentiopicroside, sweroside, and swertiamarin play key roles in the hepatocyte protection against the cytotoxic effects of fatty acids. This protection is conferred by enhancing mitochondrial function in terms of increasing the maximal respiratory capacity in response to a high influx of fatty acids, promoting ATP production as well as scavenging ROS produced as a result of high fatty acid influx and increased mitochondrial respiration. Highlights: Gentiopicroside may minimise lipotoxicity leading to apoptosis and necrosis in hepatocytes in the presence of arachidonic acid. A pre-treatment of hepatocytes with phytochemicals, namely gentiopicroside, sweroside, and silymarin provides a degree of protection which may be attributed to the enhancement of mitochondrial function. Sweroside, silymarin, and swertiamarin may protect HepG2 and THLE-2 cells by scavenging ROS produced by arachidonic acid and the mitochondrial electron transport chain. Full article

(This article belongs to the Special Issue Nonalcoholic Fatty Liver Disease: From Molecular Mechanisms to Therapeutic Approaches)

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24 pages, 761 KiB

Open AccessReview

Unlocking the Potential of Bioactive Compounds in Pancreatic Cancer Therapy: A Promising Frontier

by Silvia Brugiapaglia, Ferdinando Spagnolo and Claudia Curcio

Biomolecules 2025, 15(5), 725; https://doi.org/10.3390/biom15050725 - 15 May 2025

Abstract

Pancreatic ductal adenocarcinoma (PDA) is a highly challenging malignancy to treat, with a high mortality rate and limited therapeutic options. Despite advances in cancer research, the prognosis for patients diagnosed with PDA is often poor due to late-stage detection and resistance to conventional therapies. Consequently, there is growing interest in the potential of bioactive compounds as alternative or adjuvant treatments, given their ability to target multiple aspects of cancer biology, offering a more holistic approach to treatment. In the context of PDA, certain bioactive compounds, such as polyphenols (found in fruits, vegetables, and tea), flavonoids, carotenoids and compounds in cruciferous vegetables, have shown potential in inhibiting cancer cell growth, reducing inflammation, and promoting cancer cell apoptosis. This review aims to elucidate the mechanisms, by which these bioactive compounds exert their effects, modulating the oxidative stress, influencing inflammatory pathways and regulating cell survival and death. It also highlights current clinical trials that are paving the way toward incorporating these natural agents into mainstream treatment strategies, with the goal of boosting the efficacy of conventional therapies for PDA. Full article

(This article belongs to the Special Issue Design and Synthesis of Bioactive Compounds for Therapeutic Applications)

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16 pages, 2496 KiB

Open AccessArticle

High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations

by Bin Wu, Fujia Tian, Yajun Yang, Liang Dai and Xinghua Zhang

Biomolecules 2025, 15(5), 724; https://doi.org/10.3390/biom15050724 - 15 May 2025

Abstract

R-loops are nucleic acid structures composed of an RNA-DNA hybrid (RDH) duplex and a displaced single-stranded DNA (ssDNA), which are fundamentally involved in key biological functions, including transcription and the preservation of genome stability. In an R-loop, the RDH duplex is bent by the folded secondary structures of the displaced ssDNA. Previous experiments and simulations indicated the high bendability of DNA below the persistence length. However, the bendability of a short RDH duplex remains unclear. Here, we report that an RDH duplex exhibits higher bendability than a DNA duplex on the short length scale using single-molecule cyclization experiments. Our molecular dynamics simulations show that an RDH duplex has larger intrinsic curvature and structural fluctuations and more easily forms kinks than DNA, which promote the bending flexibility of RDH from unlooped structures. Interestingly, we found that an RDH duplex composed of a C-rich DNA strand and a G-rich RNA strand shows significantly higher bendability than that composed of a G-rich DNA strand and a C-rich RNA strand in the same CpG island promoter regions, which may contribute to the formation of an R-loop. These findings shape our understanding towards biological processes involving R-loops through the high and sequence-dependent bendability of an RDH duplex. Full article

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

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13 pages, 2564 KiB

Open AccessArticle

Viable Cryopreservation Strategy for Extending the Timeframe of Circulating Tumor Cell Detection in Breast Cancer Clinical Trials

by Cristina Sánchez-Quesada, Estefanía Toledo, José Juan Jiménez-Moleón and José Juan Gaforio

Biomolecules 2025, 15(5), 723; https://doi.org/10.3390/biom15050723 - 15 May 2025

Abstract

Circulating tumor cells (CTCs) hold recognized prognostic value in various cancers, including breast cancer, where their presence correlates with survival outcomes. However, the typical 24 h window for blood processing and CTC isolation poses a logistical challenge, particularly for multicenter studies. This study aimed to evaluate cryopreservation at different stages of CTC isolation and immunocytological detection to extend the blood sample processing period. Using spiked peripheral blood samples with MDA-MB-231, SKBR3, and MCF7 breast cancer cell lines, four distinct cryopreservation points were assessed: following Ficoll gradient separation, immunomagnetic separation, cytocentrifugation, and cytokeratin labeling. Our findings demonstrated that cryopreservation of the mononuclear and granulocytic cell fraction after double-density Ficoll gradient separation was the only viable method for subsequent CTC detection. This approach allowed for consistent recovery of CK+ CTCs, with an average recovery rate of over 81% after one year of cryopreservation. In contrast, cryopreservation at later stages resulted in undetectable CTCs or only cellular debris. In conclusion, cryopreservation following density gradient centrifugation is a feasible strategy for delaying CTC isolation and immunocytological analysis in breast cancer research, facilitating its application in multicenter clinical trials. Full article

(This article belongs to the Section Molecular Medicine)

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17 pages, 15016 KiB

Open AccessArticle

Baicalin Alleviates Piglet Immunosuppression Induced by Glaesserella parasuis via Promoting CD163/Tumor Necrosis Factor-like Weak Inducer of Apoptosis-Mediated Autophagy

by Shulin Fu, Ronghui Luo, Jingyang Li, Yunjian Fu, Qiaoli Dong, Siyu Liu, Yamin Sun, Ling Guo, Jin Hu and Yinsheng Qiu

Biomolecules 2025, 15(5), 722; https://doi.org/10.3390/biom15050722 - 15 May 2025

Abstract

Glaesserella parasuis (G. parasuis) causes vascular inflammation in piglets, resulting in vascular damage. However, the mechanism causing vascular inflammation remains unclear. Baicalin possesses an anti-inflammatory function. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) has been implicated in immunosuppression. CD163, a scavenger receptor expressed on macrophages that acts as a decoy receptor for TWEAK, plays a crucial role in the regulation of autophagy and inflammation. This research investigated the efficacy of baicalin in reducing immunosuppression elicited by G. parasuis through the regulation of CD163/TWEAK-mediated autophagy. The data demonstrated that G. parasuis altered routine blood indicators and biochemical parameters, increased cytokine production, and induced blood vessel tissue damage. G. parasuis reduced the CD3+ T cell proportion, CD3+CD4+ T cell proportion, and CD3+CD8+ T cell proportion in piglet blood. The proteomic analysis revealed that CD163 was differentially expressed in the blood vessels of challenged piglets. Baicalin was found to regulate CD163/TWEAK axis expression, inhibit Notch/Wnt signaling pathway activation, promote autophagy, and reduce NLRP3/Caspase 1 signaling pathway activation. Baicalin also decreased cytokine production and alleviated pathological tissue damage in the blood vessels of G. parasuis-challenged piglets. Taken together, this study indicates that baicalin alleviates G. parasuis-induced immunosuppression and might promote CD163/TWEAK-mediated autophagy. This finding suggests that baicalin could serve as a potential therapeutic agent to control G. parasuis infection and related vascular inflammation. Full article

(This article belongs to the Topic Recent Advances in Veterinary Pharmacology and Toxicology)

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16 pages, 503 KiB

Open AccessReview

Embryonic Origins of Cancer: Insights from Double Homeobox 4 Regulation

by Bo Fu, Hong Ma, Liang Wang, Zhenhua Guo, Fang Wang, Di Liu and Dongjie Zhang

Biomolecules 2025, 15(5), 721; https://doi.org/10.3390/biom15050721 - 14 May 2025

Abstract

Embryogenesis and tumorigenesis share several key biological characteristics, such as rapid cell proliferation, high plasticity, and immune evasion. This similarity indicates that developmental pathways can be hijacked, leading to the formation of malignant cell states. With regard to this, cancer can be regarded as a stem cell disease. On the contrary, a fetus, in many ways, has similar characteristics to the “ideal tumor”, such as immune evasion and rapid growth. Therefore, deciphering the molecular mechanisms beneath these phenomena will help us to understand the embryonic origins of cancer. This review discusses the relationship between embryogenesis and tumorigenesis, highlighting the potential roles played by DUX4. DUX4 is involved in the activation of the zygote genome and then facilitates the establishment of totipotency in pre-implantation embryos, whereas the misexpression of DUX4 is associated with different types of cancer. Taken together, this indicates that DUX4 performs analogous functions in these two processes and connects embryogenesis and tumorigenesis. Through examining DUX4, this review underscores the importance of developmental mechanisms in cancer biology, suggesting that the insights gained from studying embryonic processes may provide novel therapeutic strategies. As we continue to explore the complex relationship between cancer and embryogenesis, elucidating the role of DUX4 in linking these two processes will be critical for developing targeted therapies that exploit developmental pathways. Full article

(This article belongs to the Section Molecular Biology)

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13 pages, 3474 KiB

Open AccessFeature PaperArticle

Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T

by Vincenzo Carbone, Kerri Reilly, Carrie Sang, Linley R. Schofield, William J. Kelly, Ron S. Ronimus, Graeme T. Attwood and Nikola Palevich

Biomolecules 2025, 15(5), 720; https://doi.org/10.3390/biom15050720 - 14 May 2025

Abstract

Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze the demethylesterification of pectin, a key polysaccharide in cell walls. Here we present the crystal structure of the catalytic domain of PmeC5 that is associated with a gene from Butyrivibrio fibrisolvens D1^T that encodes a large secreted pectinesterase family protein (2089 aa) determined to a resolution of 1.33 Å. Protein in silico modelling of the secreted pectinesterase confirmed the presence of an additional pectate lyase (PL9) and adhesin-like domains. The structure of PmeC5 was the characteristic right-handed parallel β-helical topology and active site residues of Asp231, Asp253, and Arg326 typical of the enzyme class. PmeC5 is a large modular enzyme that is characteristic of rumen B. fibrisolvens megaplasmids and plays a central role in degrading plant cell wall components and releasing methanol in the rumen environment. Such secreted PMEs are significant contributors to plant fiber digestion and methane production, making them attractive targets for both methane mitigation strategies and livestock productivity enhancement. Full article

(This article belongs to the Topic Design, Synthesis and Biological Evaluation of Novel Small Molecules as Multi-target Enzyme Inhibitors)

25 pages, 3667 KiB

Open AccessReview

Nicotinamide N-Methyltransferase (NNMT) and Liver Cancer: From Metabolic Networks to Therapeutic Targets

by Shi-Yan Lai, Xiao-Juan Zhu, Wei-Dong Sun, Shuang-Zhou Bi, Chen-Ying Zhang, An Liu and Jiang-Hua Li

Biomolecules 2025, 15(5), 719; https://doi.org/10.3390/biom15050719 - 14 May 2025

Abstract

Hepatocellular carcinoma (HCC), the predominant form of primary liver cancer, remains a global health challenge with limited therapeutic options and high mortality rates. Despite advances in understanding its molecular pathogenesis, the role of metabolic reprogramming in HCC progression and therapy resistance demands further exploration. Nicotinamide N-methyltransferase (NNMT), a metabolic enzyme central to NAD⁺ and methionine cycles, has emerged as a critical regulator of tumorigenesis across cancers. However, its tissue-specific mechanisms in HCC—particularly in the context of viral hepatitis and methionine cycle dependency—remain understudied. This review systematically synthesizes current evidence on NNMT’s dual role in HCC: (1) driving NAD⁺ depletion and homocysteine (Hcy) accumulation via metabolic dysregulation, (2) promoting malignant phenotypes (proliferation, invasion, metastasis, and drug resistance), and (3) serving as a prognostic biomarker and therapeutic target. We highlight how NNMT intersects with epigenetic modifications, immune evasion, and metabolic vulnerabilities unique to HCC. Additionally, we critically evaluate NNMT inhibitors, RNA-based therapies, and non-pharmacological strategies (e.g., exercise) as novel interventions. By bridging gaps between NNMT’s molecular mechanisms and clinical relevance, this review provides a roadmap for advancing NNMT-targeted therapies and underscores the urgency of addressing challenges in biomarker validation, inhibitor specificity, and translational efficacy. Our work positions NNMT not only as a metabolic linchpin in HCC but also as a promising candidate for precision oncology. Full article

(This article belongs to the Section Molecular Biology)

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18 pages, 1035 KiB

Open AccessReview

Erythrocyte Membrane Fingerprints in the Veterinary Field: The Importance of Membrane Profiling and Its Application in Companion Animals

by Benedetta Belà, Alessandro Gramenzi, Paraskevi Prasinou and Carla Ferreri

Biomolecules 2025, 15(5), 718; https://doi.org/10.3390/biom15050718 - 14 May 2025

Abstract

The importance of lipid molecules present at the level of cell membranes is already well known. They can act as secondary messengers, participating in signal transduction processes that regulate various organ functions; furthermore, their nature significantly influences cellular properties and functions. Recent studies have seen how the lipid composition of cell membranes is connected to the animal lifespan and the onset of several pathological conditions. While numerous studies have been conducted aimed at characterizing the membrane lipidomic profile in the human field, in the animal field, especially in pets, the number of studies is very limited. In recent years, preliminary analyses have been conducted to provide initial information on the composition of membrane fatty acids in healthy pets and those with chronic enteropathy. The results of these studies are very interesting as they highlight differences in fatty acid composition between the two groups of animals. Obviously, a greater number of works is needed to obtain more reliable results and to analyze how the membrane lipid composition can vary in different breeds and sizes of dogs and cats in an attempt to understand the mechanisms underlying it. The present review is divided into three main parts: the first one examines the close influence of fatty acids on membrane properties/functions, the second one presents the main lipidomic analyses conducted so far on companion animals, and the third and final part summarizes the latest works on the link between membrane lipid profiles and animal lifespans, also focusing on dietary and non-dietary strategies able to influence it. Membrane lipidomics allows us to obtain a concrete overview of an animal’s metabolism and nutrition; furthermore, lipid alterations could be used as biomarkers for the early diagnosis of pathologies. This represents an innovative tool in the veterinary field to monitor the metabolic/health status of animals. Full article

(This article belongs to the Section Lipids)

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14 pages, 1624 KiB

Open AccessArticle

Factors Determining Kinesin Motors in a Predominant One-Head-Bound or Two-Heads-Bound State During Its Stepping Cycle

by Xiao-Xuan Shi, Yu-Ru Liu and Ping Xie

Biomolecules 2025, 15(5), 717; https://doi.org/10.3390/biom15050717 - 13 May 2025

Abstract

At physiological or saturating ATP concentrations, some families of kinesin motors, such as kinesin-1 and kinesin-2, exhibit a predominant two-heads-bound (2HB) state during their stepping cycle on microtubules, while others, such as kinesin-3, exhibit a predominant one-head-bound (1HB) state. An interesting but unclear issue is what factors determine a kinesin motor in the predominant 1HB and 2HB states. Here, on the basis of the general chemomechanical pathway of the kinesin motors, a theory is given on fractions of 1HB and 2HB states. With the theory, the factors affecting a kinesin motor in the predominant 1HB and 2HB states are determined. The results about the effects of ATP concentration, ADP concentration and external load on the fractions of 1HB and 2HB states are presented. Furthermore, the theory is applied to kinesin-1, kinesin-2, kinesin-3, kinesin-5 and kinesin-13 motors, with the theoretical results agreeing well with published experimental data. Full article

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

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26 pages, 1575 KiB

Open AccessReview

CXCR Family and Hematologic Malignancies in the Bone Marrow Microenvironment

by Yanquan Liu and Huanwen Tang

Biomolecules 2025, 15(5), 716; https://doi.org/10.3390/biom15050716 - 13 May 2025

Abstract

Malignant hematologic diseases, also referred to as hematologic tumors, encompass a series of malignant proliferative disorders of the lymphopoietic system, including leukemia, lymphoma, multiple myeloma, and myeloproliferative neoplasms. The dysregulation of inflammatory factors or chronic inflammatory responses plays an indispensable role in the onset and progression of these tumors. The C-X-C motif chemokine receptor (CXCR) serves as a key mediator of immune-inflammatory responses. Through its specific regulatory mechanisms, CXCR is involved in the transduction and activation of various signaling pathways, thereby mediating the malignant biological characteristics of blood tumor cells, such as uncontrolled proliferation, differentiation, invasion, migration, autophagy, and apoptosis. In the bone marrow microenvironment, CXCR plays a pivotal role. This review systematically analyzes and elucidates the roles and mechanisms of the CXCR family in hematologic malignancies, aiming to provide new insights into the biological mechanisms and clinical significance of these diseases. The CXCR family holds great potential as a molecular marker for both fundamental research and the clinical diagnosis and treatment of hematologic malignancies. Full article

(This article belongs to the Topic Advances in Molecular Pathogenesis and Targeted Therapies for Multiple Myeloma)

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13 pages, 467 KiB

Open AccessReview

OX40–OX40L Axis in Cutaneous T-Cell Lymphomas: Pathogenic, Prognostic, and Potential Therapeutic Perspectives

by Alba Guglielmo, Alessandro Borghi, Corrado Zengarini, Bianca Maria Piraccini, Monica Corazza and Alessandro Pileri

Biomolecules 2025, 15(5), 715; https://doi.org/10.3390/biom15050715 - 13 May 2025

Abstract

Mycosis fungoides (MF) and Sézary syndrome (SS) are the most prevalent forms of cutaneous T-cell lymphoma (CTCL) and are characterized by the proliferation of CD4⁺ T-helper cells. The pathogenesis of CTCLs involves a critical interaction between neoplastic cells and the tumor microenvironment. This interaction is driven not only by cytokines but also by surface proteins that mediate cell–cell contact. One such protein, OX40 (also known as CD134), is a member of the TNF receptor superfamily and serves as an induced costimulatory molecule that facilitates the interaction between T-cells and antigen-presenting cells. In this narrative review, we explore the literature surrounding the OX40–OX40L interaction in CTCLs, highlighting its pathogenic and prognostic significance. Additionally, we compare the expression and function of OX40–OX40L in chronic inflammatory skin diseases, such as atopic dermatitis and psoriasis, with their role in CTCLs. Finally, we provide an overview of the current state of therapeutic research, discussing the potential of targeting the OX40–OX40L axis in CTCL treatment. Full article

(This article belongs to the Section Molecular Biomarkers)

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13 pages, 1023 KiB

Open AccessArticle

Hydroxytyrosyl Eicosapentaenoate as a Potential Antioxidant for Omega-3 Fatty Acids: Improved Synthesis and Comparative Evaluation with Other Natural Antioxidants

by Natalia García-Acosta, Rosa Cert, Marta Jordán, Luis Goya, Raquel Mateos and Jose Luis Espartero

Biomolecules 2025, 15(5), 714; https://doi.org/10.3390/biom15050714 - 13 May 2025

Abstract

Hydroxytyrosol (HT), the primary phenolic compound in virgin olive oil, has notable cardiovascular benefits, particularly in preventing low-density lipoprotein (LDL) oxidation. However, its hydrophilicity limits its solubility and integration into lipid-based formulations. This study aimed to enhance its lipophilicity by synthesizing hydroxytyrosyl eicosapentaenoate (HT-EPA), a derivative of HT and eicosapentaenoic acid (EPA), using a one-step enzymatic catalysis with lipase B from Candida antarctica (CALB). The reaction, performed as a suspension of HT in ethyl eicosapentaenoate (Et-EPA) (1:9 molar ratio) under vacuum, achieved higher yields and shorter reaction times than previously reported, with a purity exceeding 98%, confirmed by ¹H-NMR. For the first time, the antioxidant capacity of HT-EPA in comparison with other natural antioxidants was assessed using the FRAP assay, while its oxidative stability in an omega-3-rich oil matrix was evaluated via the Rancimat method. HT-EPA and hydroxytyrosyl acetate (HT-Ac) displayed antioxidant activity comparable to HT but significantly higher than α-tocopherol, a common food antioxidant. Given the scarcity of effective lipid-soluble antioxidants, HT-EPA represents a promising candidate for omega-3 nutraceuticals, offering enhanced stability and potential health benefits. This study provides a simple, efficient, and scalable strategy for developing functional lipid-based formulations with cardioprotective potential by improving HT solubility while preserving its antioxidant properties. Full article

(This article belongs to the Section Lipids)

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29 pages, 2758 KiB

Open AccessReview

Past, Present and Future Perspectives of Forensic Genetics

by Itzae Adonai Gutiérrez-Hurtado, Mayra Elizabeth García-Acéves, Yolanda Puga-Carrillo, Mariano Guardado-Estrada, Denisse Stephania Becerra-Loaiza, Víctor Daniel Carrillo-Rodríguez, Reynaldo Plazola-Zamora, Juliana Marisol Godínez-Rubí, Héctor Rangel-Villalobos and José Alonso Aguilar-Velázquez

Biomolecules 2025, 15(5), 713; https://doi.org/10.3390/biom15050713 - 13 May 2025

Abstract

Forensic genetics has experienced remarkable advancements over the past decades, evolving from the analysis of a limited number of DNA segments to comprehensive genome-wide investigations. This progression has significantly improved the ability to establish genetic profiles under diverse conditions and scenarios. Beyond individual identification, forensic genetics now enables the inference of physical traits (e.g., eye, hair, and skin color, as well as body composition), biogeographic ancestry, lifestyle habits such as alcohol and tobacco use, and even the transfer of genital microbiomes post-coitus, among other characteristics. Emerging trends point to a future shaped by the integration of cutting-edge technologies, including CRISPR-Cas systems, artificial intelligence, and machine learning, which promise to further revolutionize the field. This review provides a thorough exploration of forensic genetics, tracing its evolution from its foundational methods (past) to its diverse modern applications (present) and offering insights into its potential future directions. Full article

(This article belongs to the Collection Feature Papers in Molecular Genetics)

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22 pages, 683 KiB

Open AccessFeature PaperReview

Interplay Between Vascular Dysfunction and Neurodegenerative Pathology: New Insights into Molecular Mechanisms and Management

by Avanthika Mekala and Hongyu Qiu

Biomolecules 2025, 15(5), 712; https://doi.org/10.3390/biom15050712 - 13 May 2025

Abstract

Vascular dysfunction frequently coexists with neurodegenerative disorders such as dementia and Alzheimer’s disease (AD) in older individuals; however, the cause-and-effect relationship remains unclear. While AD is primarily characterized by neural tissue degeneration, emerging evidence suggests that aging-induced vascular dysfunction contributes to both the onset and progression of cognitive impairment and dementia by decreasing cerebral blood flow (CBF) and disrupting the blood–brain barrier (BBB). This challenges the traditional notion and underscores vascular dysfunction as an early pathogenic stimulus; thus, targeting vascular pathologies could be a promising strategy to slow dementia progression and potentially prevent AD. Conversely, aging-related neurodegeneration exacerbates vascular dysfunction, accelerating dementia pathology through oxidative stress and inflammation as well as deposition of neurotoxic substances such as beta-amyloid (Aβ) and tau in vascular walls. This bidirectional interaction creates a vicious cycle that worsens cognitive decline, underscoring the complexity of these diseases. This review aims to highlight recent advances in research on the mechanisms of aging-related vascular dysfunction in neurodegenerative diseases, focusing on vascular contributions to cognitive impairment and dementia (VCID) and AD. Additionally, we will explore the reciprocal effects and intricate relationship between vascular dysfunction and neurodegenerative pathologies, enhancing our understanding of relative disease pathogenesis and guiding the development of innovative prevention and treatment strategies. Full article

(This article belongs to the Special Issue The Role of Vascular Dysfunction in Neuronal Degeneration and Cognitive Impairment (2nd Edition))

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14 pages, 6294 KiB

Open AccessArticle

Vitamin D and Retinoic Acid Require Protein Kinase C Activity and Reactive Oxygen Species as Opposing Signals Regulating PEIG-1/GPRC5A Expression in Caco-2 and T84 Colon Carcinoma Cells

by Pablo A. Iglesias González, Consuelo Mori, Ángel G. Valdivieso and Tomás A. Santa Coloma

Biomolecules 2025, 15(5), 711; https://doi.org/10.3390/biom15050711 - 13 May 2025

Abstract

PEIG-1/GPRC5A (phorbol ester induced gene-1/G-protein Coupled Receptor Class C Group 5 Member A) was the first identified member of the orphan G protein-coupled receptor family GPRC5. Deregulation of its expression is associated with the development and progression of various types of tumours, particularly colon carcinoma. In this work, we study the effects of vitamin D (VD, cholecalciferol) and retinoic acid (RA) on GPRC5A mRNA expression in the colorectal cancer cell lines Caco-2 and T84. Both VD (10 µM) and all-trans retinoic acid (ATRA, atRA, RA) (10 µM) increased GPRC5A mRNA levels. Protein kinase C (PKC) inhibition with Gö6983 (10 µM) completely abolished the effects of VD and RA on GPRC5A expression. In parallel, VD and RA increased cytosolic and mitochondrial ROS levels (cROS and mtROS). However, the antioxidants NAC (10 mM) and MitoTEMPO (10 µM) raised GPRC5A gene expression levels in the presence of VD or RA, suggesting that elevated ROS may inhibit GPRC5A expression. In conclusion, both VD and RA stimulate GPRC5A expression. The mechanisms involve a common and essential PKC signalling pathway, as Gö6983 inhibited both VD- and RA-induced signalling. Full article

(This article belongs to the Special Issue Biomolecules and Their Impact on Biology and Translational Applications: Celebrating the Pioneering Work of Prof. Ho Jeong Kwon)

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22 pages, 5907 KiB

Open AccessArticle

A Novel Ashwagandha (Withania somnifera) Formulation Mitigates Sleep Deprivation-Induced Cognitive Impairment and Oxidative Stress in a Rat Model

by Besir Er, Busra Ozmen, Emre Sahin, Cemal Orhan, Nurhan Sahin, Abhijeet A. Morde, Muralidhara Padigaru and Kazim Sahin

Biomolecules 2025, 15(5), 710; https://doi.org/10.3390/biom15050710 - 12 May 2025

Abstract

Ashwagandha (Withania somnifera) is a well-known adaptogenic herb traditionally used to enhance sleep quality and mitigate stress-induced cognitive decline. This study investigated the effects of different doses of ashwagandha root extract (AE) formulations on cognitive function, oxidative stress, and neuronal plasticity in a rat model of sleep deprivation (SD). Forty-nine rats were randomly assigned to seven groups: control, wide platform (WP), SD, SD + A1 (15 mg/kg AE 1.5%), SD + A2 (30 mg/kg AE 1.5%), SD + A3 (5.5 mg/kg AE 8.0%), and SD + A4 (11 mg/kg AE 8.0%). The extract was administered orally for four weeks. SD induced via a modified wide platform model significantly impaired spatial memory, increased oxidative stress, and suppressed GABA receptor activity. Treatment with all AE doses, except 15 mg/kg AE 1.5%, considerably reduced serum corticosterone (12% for SD + A2, 15% for SD + A3, and 32% for SD + A4), CRH (11% for SD + A2, 14% for SD + A3, and 17% for SD + A4), ACTH (22% for SD + A2, 26% for SD + A3, and 38% for SD + A4), and MDA levels (31% for SD + A2, 34% for SD + A3, and 46% for SD + A4) (p < 0.05). All doses improved antioxidant enzyme activity and memory performance, while AE 8.0% doses notably increased serotonin (19% for SD + A3 and 33% for SD + A4) and dopamine levels (40% for SD + A3 and 50% for SD + A4). Moreover, AE treatment enhanced markers of neuronal plasticity and partially improved GABAergic function. These findings suggest that AE formulations, particularly at higher concentrations, exert neuroprotective effects against SD-induced cognitive impairment by modulating oxidative stress, neurotransmitter balance, and neuroplasticity, indicating their potential application in managing stress-related neurological disorders. Full article

(This article belongs to the Special Issue Design and Synthesis of Bioactive Compounds for Therapeutic Applications)

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37 pages, 2972 KiB

Open AccessReview

Role of Tumor Necrosis Factor in Tuberculosis

by Fedor D. Kireev, Julia A. Lopatnikova, Alina A. Alshevskaya and Sergey V. Sennikov

Biomolecules 2025, 15(5), 709; https://doi.org/10.3390/biom15050709 - 12 May 2025

Abstract

Tumor necrosis factor (TNF) is a key immunoregulatory cytokine with a dual role in the host response to Mycobacterium tuberculosis. While essential for granuloma formation, macrophage activation, and containment of latent infection, TNF can also contribute to tissue damage and immune pathology. This review systematically analyzes over 300 peer-reviewed studies published between 1980 and 2024, highlighting the molecular and cellular mechanisms of TNF action in tuberculosis (TB). Particular attention is given to TNF receptor signaling pathways, the balance between protective and pathological immune responses, and the modulation of TNF activity during anti-TNF therapy in patients with autoimmune diseases. We discuss how different TNF inhibitors vary in their capacity to interfere with host defense mechanisms, with monoclonal antibodies carrying a higher reactivation risk than receptor-based agents. To enhance conceptual clarity, we provide newly developed schematic representations that integrate current knowledge on TNF-driven immune dynamics, including its interaction with other cytokines, effects on granuloma stability, and role in intracellular bacterial control. Understanding the pleiotropic functions of TNF in tuberculosis pathogenesis is crucial for developing safe immunomodulatory strategies and optimizing the clinical management of patients at risk of latent TB reactivation. Full article

(This article belongs to the Section Biological Factors)

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17 pages, 4071 KiB

Open AccessArticle

Examining the Effects of the RUNX1 p.Leu43Ser Variant on FPD/AML Phenotypes Using a CRISPR/Cas9-Generated Knock-In Murine Model

by Ana Marin-Quilez, Ignacio García-Tuñón, Rocío Benito, José Luis Ordoñez, Lorena Díaz-Ajenjo, Ana Lama-Villanueva, Carmen Guerrero, Jesús Pérez-Losada, José Ramón González-Porras, Jesús María Hernández-Rivas, Mónica del Rey and José María Bastida

Biomolecules 2025, 15(5), 708; https://doi.org/10.3390/biom15050708 - 12 May 2025

Abstract

Germline heterozygous variants in RUNX1 lead to Familial Platelet Disorder with Myeloid Leukemia Predisposition (FPD/AML). Cellular and/or animal models are helpful to uncovering the role of a variant in disease progression. Twenty-five mice per genotype (RUNX1^WT/WT, RUNX1^WT/L43S, RUNX1^L43S/L43S), previously generated by CRISPR/Cas9, and nine sub-lethally irradiated mice per genotype were investigated. Peripheral blood (PB), bone marrow (BM), and spleen samples were analyzed by flow cytometry and histopathology. Deregulated genes were analyzed by RNA-seq in BM. An aberrant myeloid Mac1⁺Sca1⁺ckit⁻ population in the PB, BM, and spleen of two homozygous and one heterozygous mouse was observed, as well as BM hypercellularity. No Mac1⁺Sca1⁺ckit⁻ cells were detected in any RUNX1^WT/WT mice. Moreover, the spleen of both homozygous mice showed destruction of the white/red pulp and the presence of apoptotic cells. The aberrant population was also detected in four irradiated mice, two heterozygous and two homozygous, in their PB, BM, and spleen. RNA-seq studies showed 698 genes significantly deregulated in the three non-irradiated Mac1⁺Sca1⁺ckit⁻ mice vs. six healthy mice, highlighting the alteration of genes involved in apoptosis and DNA repair. These results indicate that the homozygous form of the variant p.Leu43Ser may contribute to the pathogenesis of aberrant cells. Full article

(This article belongs to the Special Issue Molecular Advances in Platelet Disease, Thrombosis and Hemostasis)

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23 pages, 19946 KiB

Open AccessArticle

AMPK Signaling Axis-Mediated Regulation of Lipid Metabolism: Ameliorative Effects of Sodium Octanoate on Intestinal Dysfunction in Hu Sheep

by Huimin Zhang, Shuo Yan, Zimeng Ma, Ruilin Du, Xihe Li, Siqin Bao and Yongli Song

Biomolecules 2025, 15(5), 707; https://doi.org/10.3390/biom15050707 - 12 May 2025

Abstract

At the present stage, heavy metal pollution, led by environmental exposure to cadmium (Cd), has caused incalculable losses in animal husbandry. The potential value of caprylic acid as a medium- and long-chain fatty acid with a unique role in regulating lipid metabolism has attracted much attention. Our previous study found that octanoic acid levels were significantly reduced under Cd-exposed conditions in Hu Sheep, on the basis of which we investigated the protective effect of sodium octanoate, a derivative of octanoic acid, against Cd exposure in Hu Sheep in the present study. In this study, an animal model of Cd exposure in Hu Sheep was established. Comprehensive assessment of Cd-induced intestinal injury using hematoxylin and eosin (H&E) staining, immunostaining and carried out in-depth analyses combined with lipid metabolomics and transcriptomics. The results showed that Cd exposure triggered intestinal inflammation, barrier function damage and oxidative stress imbalance. Lipid metabolomics analysis showed that Cd exposure severely disrupted lipid metabolic processes, especially the glycerophospholipid metabolic pathway, suggesting that lipid metabolic disorders are closely related to intestinal injury. Notably, sodium octanoate could partially reverse the lipid metabolism abnormality by regulating the Adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway, effectively alleviating the Cd toxicity, which provides a brand-new prevention and control strategy for Cd-induced intestinal injury in the livestock industry pollution-mediated disease. Full article

(This article belongs to the Section Lipids)

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