Biomolecules

27 pages, 27119 KiB

Open AccessReview

Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations

by Zhaonan Chai, Yawei Feng, Tong Zhao, Xiaolong Wang, Maksudbek Yusupov, Maryam Ghasemitarei, Tayebeh Ghorbi, Annemie Bogaerts and Yuantao Zhang

Biomolecules 2025, 15(7), 952; https://doi.org/10.3390/biom15070952 (registering DOI) - 30 Jun 2025

Abstract

In this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an efficient and [...] Read more.

In this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an efficient and hygienic advanced oxidation technology, CAP demonstrates tremendous potential in fields such as biomedicine and environmental protection. Through simulations, this paper provides a detailed analysis of the interaction mechanisms between ROS and components of biological tissues and environmental toxins. In this paper, we review the reactions involving four major ROS (OH radicals, O atoms,

O_{3}

molecules, and

H_{2} O_{2}

molecules) and organic compounds, including proteins, DNA, polysaccharides, fatty acids, antibiotics, and mycotoxins. Atomic-level analysis reveals various oxidative modification reactions induced by ROS and their resulting products, including dehydrogenation reactions, bond-formation reactions, oxygen-addition reactions, and bond-cleavage reactions. Additionally, the study elucidates the role of active functional groups in various organic compounds, the presence of special elements, and the specific reactive nature of

H_{2} O_{2}

. Furthermore, the influence of different ROS species and concentrations on reaction types is explored, aiming to provide a solid theoretical foundation for the application of CAP technology in biomedicine and environmental remediation. Full article

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

► Show Figures

Figure 1

15 pages, 1854 KiB

Open AccessArticle

Administration of Purified Alpha-1 Antitrypsin in Salt-Loaded Hypertensive 129Sv Mice Attenuates the Expression of Inflammatory Associated Proteins in the Kidney

by Van-Anh L. Nguyen, Yunus E. Dogan, Niharika Bala, Erika S. Galban, Sihong Song and Abdel A. Alli

Biomolecules 2025, 15(7), 951; https://doi.org/10.3390/biom15070951 (registering DOI) - 30 Jun 2025

Abstract

Background: Alpha-1 antitrypsin (AAT) is a multifunctional protease inhibitor that has been shown to have anti-inflammatory properties in various diseases. AAT has been reported to protect against renal injury via anti-apoptotic, anti-fibrotic, and anti-inflammatory effects. However, its role in mitigating renal inflammation and [...] Read more.

Background: Alpha-1 antitrypsin (AAT) is a multifunctional protease inhibitor that has been shown to have anti-inflammatory properties in various diseases. AAT has been reported to protect against renal injury via anti-apoptotic, anti-fibrotic, and anti-inflammatory effects. However, its role in mitigating renal inflammation and reducing high blood pressure induced by salt-loading has never been studied. Methods: In this study, we salt-loaded 129Sv mice to induce hypertension and then administered purified human AAT (hAAT) or the vehicle to investigate whether renal inflammation and associated inflammatory/signaling pathways are mitigated. Results: Western blotting and densitometric analysis showed administration of hAAT attenuated protein expression of kidney injury molecule-1 (KIM1), CD93, CD36, and the toll-like receptor 2 and 4 (TLR-2/4) in kidney lysates. Similarly, protein expression of two key inflammatory transcription factors, signal transducer and activator of transcription 3 (STAT3) and NF-Kappa B were shown to be attenuated in the kidneys of 129Sv mice that received hAAT. Conversely, hAAT treatment upregulated the expression of heat shock protein 70 (HSP70) and immunohistochemistry confirmed these findings. Conclusions: Purified hAAT administration may be efficacious in mitigating renal inflammation associated with the development of hypertension from salt-loading, potentially through a mechanism involving the reduction of pro-inflammatory and injury-associated proteins. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Figure 1

15 pages, 5078 KiB

Open AccessArticle

Intratracheal Aerosolization of Nocardia farcinica in Mice Optimizes Bacterial Distribution and Enhances Pathogenicity Compared to Intranasal Inoculation and Intratracheal Instillation

by Bingqian Du, Ziyu Song, Jirao Shen, Jiang Yao, Shuai Xu, Xiaotong Qiu, Min Yuan and Zhenjun Li

Biomolecules 2025, 15(7), 950; https://doi.org/10.3390/biom15070950 (registering DOI) - 30 Jun 2025

Abstract

Nocardia, an easily missed but potentially fatal opportunistic pathogen, can lead to serious infections like lung and brain abscesses. Intranasal inoculation (IN) is the traditional approach for constructing a Nocardia-induced pneumonia mice model, while it usually only results in limited local [...] Read more.

Nocardia, an easily missed but potentially fatal opportunistic pathogen, can lead to serious infections like lung and brain abscesses. Intranasal inoculation (IN) is the traditional approach for constructing a Nocardia-induced pneumonia mice model, while it usually only results in limited local bacterial infection in the lungs. To comprehensively assess infection dynamics across distinct pulmonary inoculation routes in mice models, this study compared the pathogenicity of three different Nocardia farcinica pneumonia models established via IN, intratracheal aerosolization (ITA), and intratracheal instillation (ITI). C57BL/6J mice were infected with N. farcinica through IN, ITA and ITI with comparative analyses of bacterial distribution in lungs, survival rate, weight, bacterial load, inflammatory cytokines, histopathological characteristics and transcriptome differences. The findings suggest that ITA N. farcinica infections caused severer clinical symptoms, higher mortality, pulmonary bacterial load, levels of inflammatory cytokines in bronchoalveolar lavage fluid, and more significant histopathological damage to lungs than IN and ITI. Furthermore, ITA resulted in better lung bacterial distribution and delivery efficiency than ITI and IN. Transcriptome analysis of lungs from N. farcinica infected mice via IN, ITA and ITI revealed significant differential gene expression, whereas ITA route resulted in a larger fold change. ITA provides a more consistent and severe model of N. farcinica pneumonia in mice than IN and ITI, which can make the bacteria more evenly distributed in the lungs, leading to more severe pathological damage and higher mortality rates. In conclusion, ITA is an optimal route for developing animal models of N. farcinica pneumonia infections. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)

18 pages, 3501 KiB

Open AccessArticle

A Transcriptomics Approach to Unveil the Antioxidant Effects of Tryptophan on Oocyte Quality Under Oxidative Stress in Pigs

by Zhekun Zhu, Yanlong Li, Xinyin Fan, Shuang Cai, Siyu Li, Yutian Wang, Xinyu Wang and Fengjuan Yang

Biomolecules 2025, 15(7), 949; https://doi.org/10.3390/biom15070949 (registering DOI) - 30 Jun 2025

Abstract

This study investigates the effect of tryptophan treatment on aged pig oocytes, focusing on its potential to reduce oxidative stress and improve oocyte quality. An oxidative stress model was induced using hydrogen peroxide (H₂O₂) to mimic aging effects on [...] Read more.

This study investigates the effect of tryptophan treatment on aged pig oocytes, focusing on its potential to reduce oxidative stress and improve oocyte quality. An oxidative stress model was induced using hydrogen peroxide (H₂O₂) to mimic aging effects on oocytes. Fresh ovaries from young sows were collected, and oocytes were aspirated and cultured for in vitro maturation. Oocytes in the H₂O₂and the H₂O₂+Trp groups were exposed to 100 µM H₂O₂ for 30 min, with the H₂O₂+Trp group receiving an additional 50 µM tryptophan supplementation. RNA-sequencing was performed to study the underlying mechanism through which tryptophan mitigated the H₂O_2-induced oxidative stress in oocytes. The results demonstrated that tryptophan supplementation significantly reduced oxidative stress markers such as H₂O₂ and malonaldehyde (MDA) while restoring key antioxidant enzymes such as superoxide dismutase (SOD), and catalase (CAT) confirming its antioxidant role. Furthermore, tryptophan improved cumulus cell expansion, and oocyte quality, which were compromised by oxidative stress. Transcriptomics study revealed the enrichment of several KEGG pathways, such as P13K-Akt signaling pathways as a critical regulator of cell survival and function, emphasizing the protective effects of tryptophan on oocyte integrity. Moreover, the protein–protein interaction (PPI) network identified several hub genes in the tryptophan-treated group compared with H₂O₂, including TIMP1, CCN2, and MMP12 as key players in ECM remodeling and cellular adhesion, which are critical for restoring oocyte quality. These findings suggest that tryptophan supplementation not only mitigated oxidative stress but also modulated gene expression related to cellular functions and stress response. These results propose that tryptophan could be a valuable therapeutic strategy for improving reproductive outcomes in aging sows and other mammals facing age-related oocyte dysfunction. Full article

(This article belongs to the Special Issue Placental-Related Disorders of Pregnancy: 2nd Edition)

15 pages, 4150 KiB

Open AccessArticle

PRMT5 Identified as a Viable Target for Combination Therapy in Preclinical Models of Pancreatic Cancer

by Xiaolong Wei, William J. Kane, Sara J. Adair, Sarbajeet Nagdas, Denis Liu and Todd W. Bauer

Biomolecules 2025, 15(7), 948; https://doi.org/10.3390/biom15070948 (registering DOI) - 30 Jun 2025

Abstract

Pancreatic cancer is the third leading cause of cancer-related death in the US. First-line chemotherapy regimens for pancreatic ductal adenocarcinoma (PDAC) include FOLFIRINOX or gemcitabine (Gem) with or without paclitaxel (Ptx); however, 5-year survival with these regimens remains poor. Previous work has demonstrated [...] Read more.

Pancreatic cancer is the third leading cause of cancer-related death in the US. First-line chemotherapy regimens for pancreatic ductal adenocarcinoma (PDAC) include FOLFIRINOX or gemcitabine (Gem) with or without paclitaxel (Ptx); however, 5-year survival with these regimens remains poor. Previous work has demonstrated protein arginine methyltransferase 5 (PRMT5) to be a promising therapeutic target in combination with Gem for the treatment of PDAC; however, these findings have yet to be confirmed in relevant preclinical models of PDAC. To test the possibility of PRMT5 as a viable therapeutic target, clinically relevant orthotopic and metastatic patient-derived xenograft (PDX) mouse models of PDAC growth were utilized to evaluate the effect of PRMT5 knockout (KO) or pharmacologic inhibition on treatment with Gem alone or Gem with Ptx. Primary endpoints included tumor volume, tumor weight, or metastatic tumor burden as appropriate. The results showed that Gem-treated PRMT5 KO tumors exhibited decreased growth and were smaller in size compared to Gem-treated wild-type (WT) tumors. Similarly, the Gem-treated PRMT5 KO metastatic burden was lower than the Gem-treated WT metastatic burden. The addition of a PRMT5 pharmacologic inhibitor to Gem and Ptx therapy resulted in a lower final tumor weight and fewer metastatic tumors. The depletion of PRMT5 results in increased DNA damage in response to Gem and Ptx treatment. Thus, PRMT5 genetic depletion or inhibition in combination with Gem-based therapy improved the response in primary and metastatic PDAC in clinically relevant mouse models, suggesting that PRMT5 is a viable therapeutic target for combination therapy in PDAC. Full article

(This article belongs to the Special Issue Advancing Innovations in Biomedical Research for Translational Applications)

► Show Figures

Figure 1

15 pages, 3758 KiB

Open AccessReview

Unraveling the Role of Microcystin-LR in Ferroptosis and Sepsis Pathogenesis: A Comprehensive Review

by Honglian Ying, Hongli Zhao, Xiaqiu Zhang, Haoyuan Feng, Manjuan Zhou, Zunqiu Wu and Ning Wu

Biomolecules 2025, 15(7), 947; https://doi.org/10.3390/biom15070947 (registering DOI) - 30 Jun 2025

Abstract

Sepsis, a systemic inflammatory response syndrome triggered by infection, is characterized by acute onset, rapid progression, and high mortality. Ferroptosis, a form of programmed cell death induced by iron-dependent lipid peroxidation, is closely associated with the occurrence and development of various diseases. Microcystin-LR [...] Read more.

Sepsis, a systemic inflammatory response syndrome triggered by infection, is characterized by acute onset, rapid progression, and high mortality. Ferroptosis, a form of programmed cell death induced by iron-dependent lipid peroxidation, is closely associated with the occurrence and development of various diseases. Microcystin-LR (MC-LR) can exacerbate sepsis by causing multi-organ damage via the ferroptosis pathway. Currently, the relationship between MC-LR, ferroptosis, and sepsis remains unclear. Understanding its pathogenesis and identifying potential therapeutic targets may reduce the mortality of sepsis patients and lead to clinical improvement. This article reviews the relationship among MC-LR, ferroptosis, and sepsis, focusing on the mechanism by which MC-LR exposure induces sepsis from the ferroptosis perspective, providing a theoretical basis for the prevention and treatment of MC-LR-exposure-induced sepsis in the population. Full article

► Show Figures

Figure 1

27 pages, 9300 KiB

Open AccessArticle

Genome-Wide Identification of the GRAS Transcription Factor Family in Sweet Orange and the Regulation of Salt Stress-Enhanced Plant Salt Tolerance in Sweet Orange by CsGRAS15 and CsGRAS27

by Hailin Ren, Rong Xu, Jie Wang, Qian Zhang, Lili Nie, Li Zhang, Xianyan Zhou, Xiaozhen Liu and Hanyao Zhang

Biomolecules 2025, 15(7), 946; https://doi.org/10.3390/biom15070946 (registering DOI) - 29 Jun 2025

Abstract

Background: GRAS transcription factors are crucial for plant development and stress responses but remain poorly characterized in citrus. Soil salinization increasingly threatens sweet orange (Citrus sinensis) yield. Identifying salt-responsive GRAS genes could reveal key tolerance determinants for breeding resistant cultivars. Methods: [...] Read more.

Background: GRAS transcription factors are crucial for plant development and stress responses but remain poorly characterized in citrus. Soil salinization increasingly threatens sweet orange (Citrus sinensis) yield. Identifying salt-responsive GRAS genes could reveal key tolerance determinants for breeding resistant cultivars. Methods: We systematically identified and analyzed sweet orange GRAS transcription factors using bioinformatics. Results: Forty-three CsGRAS genes were identified, phylogenetically classified into ten subfamilies, and found to be structurally conserved. A promoter analysis revealed a high prevalence (58.78%) of hormone- and stress-responsive cis-elements. These genes reside on nine chromosomes, with segmental duplication being the primary evolutionary driver (eight duplicated pairs). Functional enrichment implicated hormone signaling pathways in regulating growth under stress. Transcriptome profiling identified 42 differentially expressed CsGRAS genes (19 upregulated and 23 downregulated) under salt stress. qRT-PCR validated the expression patterns of selected genes (e.g., CsGRAS15 and CsGRAS27). Notably, DELLA subfamily members CsGRAS15 and CsGRAS27, key negative regulators in gibberellin (GA) signaling, were differentially expressed. Modulating these DELLA proteins presents a promising strategy to enhance sweet orange salt tolerance by mitigating GA-mediated growth inhibition during stress. Conclusion: This study identifies salt-responsive CsGRAS genes, highlighting CsGRAS15 and CsGRAS27 as potential targets for improving salt tolerance in citrus. Full article

(This article belongs to the Section Molecular Genetics)

► Show Figures

Figure 1

16 pages, 2118 KiB

Open AccessReview

Recent Advances in Combination Therapy of YAP Inhibitors with Physical Anti-Cancer Strategies

by Junchi Zhou, Changyan Yu, Wanhong Yang, Nian Jiang, Sanhua Li, Yun Liu and Xinting Zhu

Biomolecules 2025, 15(7), 945; https://doi.org/10.3390/biom15070945 (registering DOI) - 29 Jun 2025

Abstract

In recent years, physical anti-cancer strategies using radiation, light, sound, electricity, and magnetism have shown great potential in cancer treatment. Photodynamic therapy, radiation therapy, photothermal therapy, and other treatments have different advantages. As a critical transcriptional coactivator in the Hippo signaling pathway, Yes-Associated [...] Read more.

In recent years, physical anti-cancer strategies using radiation, light, sound, electricity, and magnetism have shown great potential in cancer treatment. Photodynamic therapy, radiation therapy, photothermal therapy, and other treatments have different advantages. As a critical transcriptional coactivator in the Hippo signaling pathway, Yes-Associated Protein (YAP) is closely related to tumor proliferation, radiation resistance, and immunosuppression. YAP has been a target in immunotherapy, and YAP inhibitors are used in clinical practice. Combining immunotherapy and physical anti-cancer strategies is an anti-cancer program with clinical potential to enhance the therapeutic effect. This review summarizes the role of photodynamic therapy, radiotherapy, and other physical anti-cancer strategies combined with YAP-targeted therapy in cancer treatment. YAP inhibitors and these physical anti-cancer strategies provide new directions and ideas for cancer treatment. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Graphical abstract

18 pages, 7501 KiB

Open AccessArticle

Probing the Active Site of Class 3 L-Asparaginase by Mutagenesis: Mutations of the Ser-Lys Tandems of ReAV

by Kinga Pokrywka, Marta Grzechowiak, Joanna Sliwiak, Paulina Worsztynowicz, Joanna I. Loch, Milosz Ruszkowski, Miroslaw Gilski and Mariusz Jaskolski

Biomolecules 2025, 15(7), 944; https://doi.org/10.3390/biom15070944 (registering DOI) - 29 Jun 2025

Abstract

The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly [...] Read more.

The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly specific zinc-binding site created by two cysteines, a lysine, and a water molecule. Two Ser-Lys tandems (Ser48-Lys51, Ser80-Lys263) are located in the close proximity of the metal binding site, with Ser48 hypothesized to be the catalytic nucleophile. To further investigate the catalytic process of ReAV, site-directed mutagenesis was employed to introduce alanine substitutions at residues from the Ser-Lys tandems and at Arg47, located near the Ser48-Lys51 tandem. These mutational studies, along with enzymatic assays and X-ray structure determinations, demonstrated that substitution of each of these highly conserved residues abolished the catalytic activity, confirming their essential role in enzyme mechanism. Full article

(This article belongs to the Special Issue State-of-the-Art Protein X-Ray Crystallography)

► Show Figures

Figure 1

20 pages, 3210 KiB

Open AccessArticle

Significant Reduction of Chenodeoxycholic Acid and Glycochenodeoxycholic Acid in the Elderly with Severe COVID-19

by Shiyang Liu, Wen Xu, Bo Tu, Zhiqing Xiao, Xue Li, Lei Huang, Xin Yuan, Shengdong Luo, Juanjuan Zhou, Xinxin Yang, Junlian Yang, De Chang, Weiwei Chen and Fu-Sheng Wang

Biomolecules 2025, 15(7), 943; https://doi.org/10.3390/biom15070943 (registering DOI) - 28 Jun 2025

Abstract

Elderly individuals infected with SARS-CoV-2 are at higher risk of developing cytokine storms and severe outcomes, yet specific biomarkers remain unclear. In this study, we investigated the alteration of primary bile acid metabolism in elderly patients with severe COVID-19 using untargeted metabolomics ( [...] Read more.

Elderly individuals infected with SARS-CoV-2 are at higher risk of developing cytokine storms and severe outcomes, yet specific biomarkers remain unclear. In this study, we investigated the alteration of primary bile acid metabolism in elderly patients with severe COVID-19 using untargeted metabolomics (n = 31), followed by targeted metabolomics to compare patients with disease progression (n = 16) to those without (n = 48). Significant reductions in chenodeoxycholic acid (CDCA) and glycochenodeoxycholic acid (GCDCA) levels were identified in severe cases, with GCDCA levels at admission correlating strongly with peak inflammatory markers. In vitro, CDCA, GCDCA, and their receptors, Farnesoid X Receptor (FXR) and Takeda G-protein-coupled receptor 5 (TGR5), effectively inhibited the inflammatory response induced by SARS-CoV-2. NOD-like receptor pathway, activated by SARS-CoV-2, may modulate inflammatory cytokines under the treatment of CDCA, GCDCA, and TGR5. CDCA and GCDCA levels at admission predicted disease progression, suggesting their potential as biomarkers for severe COVID-19 in the elderly and highlighting their regulatory role in inflammation, pointing to new therapeutic avenues. Full article

(This article belongs to the Special Issue Metabolic Pathways, COVID-19 and Other Viral Acute Respiratory Infections: Mechanisms and Clinical Implications: 2nd Edition)

► Show Figures

Figure 1

19 pages, 11830 KiB

Open AccessArticle

Single-Nucleus Transcriptomics Reveals Glial Metabolic–Immune Rewiring and Intercellular Signaling Disruption in Chronic Migraine

by Shuangyuan Hu, Zili Tang, Shiqi Sun, Lu Liu, Yuyan Wang, Longyao Xu, Jing Yuan, Ying Chen, Mingsheng Sun and Ling Zhao

Biomolecules 2025, 15(7), 942; https://doi.org/10.3390/biom15070942 (registering DOI) - 28 Jun 2025

Abstract

Chronic migraine (CM) is a debilitating neurological disorder, yet the glial-specific mechanisms underlying its pathophysiology in the trigeminal nucleus caudalis (TNC)—a critical hub for craniofacial pain processing—remain poorly understood. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to resolve cell-type-specific transcriptional landscapes in a [...] Read more.

Chronic migraine (CM) is a debilitating neurological disorder, yet the glial-specific mechanisms underlying its pathophysiology in the trigeminal nucleus caudalis (TNC)—a critical hub for craniofacial pain processing—remain poorly understood. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to resolve cell-type-specific transcriptional landscapes in a nitroglycerin (NTG)-induced CM rat model, with a particular focus on microglia and astrocytes. We identified 19 transcriptional clusters representing nine major cell types, among which reactive microglia (NTG-Mic) and astrocytes (NTG-Asts) were markedly expanded. The NTG-Mic displayed a glycolysis-dominant, complement-enriched state, whereas the NTG-Asts exhibited concurrent activation of amino acid transport and cytokine signaling pathways. Pseudotime trajectory analysis revealed bifurcated glial activation paths, with NTG driving both cell types toward terminal reactive states. Intercellular communication inference uncovered suppressed homeostatic interactions (e.g., CSF1-CSF1R) alongside enhanced proinflammatory signaling (e.g., FGF1-FGFR2, PTN-SDC4), particularly affecting neuron–glia and glia–glia crosstalk. Together, these findings define a high-resolution atlas of glial reprogramming in CM, implicating state-specific metabolic–immune transitions and dysregulated glial communication as potential targets for therapeutic intervention. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Figure 1

27 pages, 11349 KiB

Open AccessArticle

Uric Acid, the End-Product of Purine Metabolism, Mitigates Tau-Related Abnormalities: Comparison with DOT, a Non-Antibiotic Oxytetracycline Derivative

by Bianca Andretto de Mattos, Rodrigo Hernán Tomas-Grau, Thaís Antonia Alves Fernandes, Florencia González-Lizárraga, Aurore Tourville, Ismaila Ciss, Jean-Michel Brunel, Rosana Chehin, Annie Lannuzel, Laurent Ferrié, Rita Raisman-Vozari, Bruno Figadère, Elaine Del Bel and Patrick Pierre Michel

Biomolecules 2025, 15(7), 941; https://doi.org/10.3390/biom15070941 (registering DOI) - 28 Jun 2025

Abstract

We aimed to simulate tau abnormalities—specifically hyperphosphorylation and aggregation—that are hallmarks of tauopathies, including Alzheimer’s disease, to evaluate tau-targeting therapies. To model pathological p-tau accumulation at early disease stages, we exposed mouse cortical cultures to redox-active iron from hemin (Hm), a breakdown product [...] Read more.

We aimed to simulate tau abnormalities—specifically hyperphosphorylation and aggregation—that are hallmarks of tauopathies, including Alzheimer’s disease, to evaluate tau-targeting therapies. To model pathological p-tau accumulation at early disease stages, we exposed mouse cortical cultures to redox-active iron from hemin (Hm), a breakdown product of hemoglobin, or challenged them with the excitatory neurotransmitter glutamate. Using the AT8 phospho-specific antibody, we demonstrate that a subtoxic concentration of Hm (3 µM) promotes pathological p-tau accumulation in a subpopulation of cultured cortical neurons and their proximal neurites. Uric acid (UA; 0.1–200 µM), the metabolic end-product of purines in humans, prevented p-tau build-up. Neither xanthine, the immediate precursor of UA, nor allantoin, its oxidized product, reproduced this effect. Live cell imaging studies revealed that UA operates by repressing iron-driven lipid peroxidation. DOT (3 µM), a brain-permeant tetracycline (TC) without antibiotic activity, mimicked UA’s anti-tau and antioxidant effects. Interestingly, both UA and DOT remained effective in preventing p-tau accumulation induced by glutamate (10 µM). To simulate tau aggregation at more advanced disease stages, we conducted a Thioflavin-T aggregation assay. Our findings revealed that UA and DOT prevented tau aggregation seeded by heparin. However, only DOT remained effective when heparin-assembled tau fibrils were used as the seeding material. In summary, our results indicate that UA-elevating agents may hold therapeutic utility for tauopathies. The non-purine compound DOT could serve as an effective alternative to UA-related therapies. Full article

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

► Show Figures

Figure 1

28 pages, 2110 KiB

Open AccessReview

Adeno-Associated Virus Vectors in Retinal Gene Therapy: Challenges, Innovations, and Future Directions

by Jiayu Huang, Jiajun Li, Xiangzhong Xu and Keran Li

Biomolecules 2025, 15(7), 940; https://doi.org/10.3390/biom15070940 (registering DOI) - 28 Jun 2025

Abstract

Adeno-associated virus (AAV) vectors have emerged as the leading platform for retinal gene therapy due to their favorable safety profile, low immunogenicity, and ability to mediate long-term transgene expression within the immune-privileged ocular environment. By integrating diverse strategies such as gene augmentation and [...] Read more.

Adeno-associated virus (AAV) vectors have emerged as the leading platform for retinal gene therapy due to their favorable safety profile, low immunogenicity, and ability to mediate long-term transgene expression within the immune-privileged ocular environment. By integrating diverse strategies such as gene augmentation and gene editing, AAV-based therapies have demonstrated considerable promise in treating both inherited and acquired retinal disorders. However, their clinical translation remains limited by several key challenges, including restricted packaging capacity, suboptimal transduction efficiency, the risk of gene therapy-associated uveitis, and broader societal concerns such as disease burden and ethical oversight. This review summarizes recent advances aimed at overcoming these barriers, with a particular focus on delivery route-specific disease applicability, multi-vector systems, and capsid engineering approaches to enhance payload capacity, targeting specificity, and biosafety. By synthesizing these developments, we propose a conceptual and technical framework for a more efficient, safer, and broadly applicable AAV platform to accelerate clinical adoption in retinal gene therapy. Full article

(This article belongs to the Special Issue Retinal Diseases: Molecular Mechanisms and Therapies)

► Show Figures

Figure 1

18 pages, 3693 KiB

Open AccessArticle

β-Secosterol, an Oxyphytosterol Produced Through the Reaction of β-Sitosterol with Ozone, Demonstrates Different Cytotoxic Effects on BRL-3A and HTC Cells

by Bianca S. Takayasu, Igor R. Martins, Miriam Uemi, Janice Onuki and Glaucia M. Machado-Santelli

Biomolecules 2025, 15(7), 939; https://doi.org/10.3390/biom15070939 (registering DOI) - 27 Jun 2025

Abstract

Sitosterol (Sito) is a phytosterol with bioactive properties, including reducing atherosclerosis risk and anti-inflammatory and antitumoral effects. However, it can be oxidized by reactive oxygen species such as ozone (O₃), producing oxyphytosterols with harmful effects such as cytotoxicity, oxidative stress, and [...] Read more.

Sitosterol (Sito) is a phytosterol with bioactive properties, including reducing atherosclerosis risk and anti-inflammatory and antitumoral effects. However, it can be oxidized by reactive oxygen species such as ozone (O₃), producing oxyphytosterols with harmful effects such as cytotoxicity, oxidative stress, and proatherogenicity. Ozone, a strong oxidant and common pollutant, can alter plant steroid compounds, raising concerns about dietary oxyphytosterol intake. Studies identify β-Secosterol (βSec) as the primary ozone-derived oxyphytosterol from Sito, exhibiting cytotoxic effects on HepG2 human liver tumor cells. This study investigated βSec’s biological effects on two rat liver cell lines: BRL-3A (immortalized) and HTC (tumoral), examining cell death, cell cycle progression, morphology, and cytoskeleton organization. While Sito influenced cell metabolic activity without affecting cell survival or morphology, βSec demonstrated significant cytotoxicity in both cell lines. It induced G0/G1 cell cycle arrest and disrupted cytoskeleton organization, with different implications: BRL-3A cells showed persistent cytoskeletal changes potentially linked to tumor induction, while HTC cells displayed chemoresistance, restoring cytoskeletal integrity and enhancing metastatic potential. These findings reveal βSec’s complex, context-dependent effects, suggesting it may promote tumor-like behavior in non-tumoral cells and resistance mechanisms in cancer cells, contributing to understanding oxyphytosterols’ implications for physiological and pathological conditions. Full article

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

► Show Figures

Graphical abstract

17 pages, 7434 KiB

Open AccessArticle

Cell-Type Annotation for scATAC-Seq Data by Integrating Chromatin Accessibility and Genome Sequence

by Guo Wei, Long Wang, Yan Liu and Xiaohui Zhang

Biomolecules 2025, 15(7), 938; https://doi.org/10.3390/biom15070938 (registering DOI) - 27 Jun 2025

Abstract

Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) technology enables single-cell resolution analysis of chromatin accessibility, offering critical insights into gene regulation, epigenetic heterogeneity, and cellular differentiation across various biological contexts. However, existing cell annotation methods face notable limitations. Cross-omics approaches, which rely [...] Read more.

Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) technology enables single-cell resolution analysis of chromatin accessibility, offering critical insights into gene regulation, epigenetic heterogeneity, and cellular differentiation across various biological contexts. However, existing cell annotation methods face notable limitations. Cross-omics approaches, which rely on single-cell RNA sequencing (scRNA-seq) as a reference, often struggle with data alignment due to fundamental differences between transcriptional and chromatin accessibility modalities. Meanwhile, intra-omics methods, which rely solely on scATAC-seq data, are frequently affected by batch effects and fail to fully utilize genomic sequence information for accurate annotation. To address these challenges, we propose scAttG, a novel deep learning framework that integrates graph attention networks (GATs) and convolutional neural networks (CNNs) to capture both chromatin accessibility signals and genomic sequence features. By utilizing the nucleotide sequences corresponding to scATAC-seq peaks, scAttG enhances both the robustness and accuracy of cell-type annotation. Experimental results across multiple scATAC-seq datasets suggest that scAttG generally performs favorably compared to existing methods, showing competitive performance in single-cell chromatin accessibility-based cell-type annotation. Full article

(This article belongs to the Section Molecular Biology)

► Show Figures

Figure 1

26 pages, 3666 KiB

Open AccessReview

Human Blood-Derived lncRNAs in Autism Spectrum Disorder

by Carmela Serpe, Paola De Sanctis, Marina Marini, Silvia Canaider, Provvidenza Maria Abruzzo and Cinzia Zucchini

Biomolecules 2025, 15(7), 937; https://doi.org/10.3390/biom15070937 (registering DOI) - 27 Jun 2025

Abstract

Autism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder with a significant impact on public health. ASD diagnosis is based on clinical observation and typically occurs around three years of age. The identification of reliable ASD markers could facilitate early diagnosis [...] Read more.

Autism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder with a significant impact on public health. ASD diagnosis is based on clinical observation and typically occurs around three years of age. The identification of reliable ASD markers could facilitate early diagnosis and help pinpoint therapeutic targets for effective interventions. Long non-coding RNAs (lncRNAs), particularly those derived from blood, have been recently proposed as potential biomarkers in many pathological conditions, including neurological diseases. This manuscript summarizes original studies examining human dysregulated blood-derived lncRNAs as potential ASD biomarkers. LncRNAs are described by grouping them according to the selection strategy used by the authors: (i) lncRNAs involved in biological processes impaired in ASD or in pathological conditions sharing the disrupted signaling pathways of ASD; and (ii) lncRNAs identified through high-throughput analysis. The study highlights key priorities for future research: assessing the ability of lncRNAs to distinguish ASD from other neurological disorders, extending analyses to larger and younger cohorts to validate candidate biomarkers in early life, and integrating multiple data sources to establish validated biomarker networks for clinical application. This review indicates that research on blood-derived lncRNAs in ASD is still in its early stages. Full article

(This article belongs to the Special Issue Molecular, Cellular, and Blood Biomarkers in Diagnosis, Prognosis, Monitoring, and Treatment)

► Show Figures

Graphical abstract

20 pages, 600 KiB

Open AccessReview

Macropinocytosis: Both a Target and a Tool for Cancer Therapy

by Manhan Zhao, Liming Zhou, Yifei Zhai, Aiqin Sun, Genbao Shao and Qiong Lin

Biomolecules 2025, 15(7), 936; https://doi.org/10.3390/biom15070936 (registering DOI) - 26 Jun 2025

Abstract

Macropinocytosis is a non-selective, clathrin-independent endocytic process that facilitates bulk internalization of extracellular fluid and its dissolved components (including proteins, lipids, and nucleotides) through plasma membrane remodeling and the subsequent formation of macropinosomes. This evolutionarily conserved cellular process plays important roles in nutrient [...] Read more.

Macropinocytosis is a non-selective, clathrin-independent endocytic process that facilitates bulk internalization of extracellular fluid and its dissolved components (including proteins, lipids, and nucleotides) through plasma membrane remodeling and the subsequent formation of macropinosomes. This evolutionarily conserved cellular process plays important roles in nutrient supply, immune response, and metabolism. Particularly, cancer cells exploit activated macropinocytosis to obtain nutrients for supporting proliferation and survival under nutritional stress. Thus, macropinocytosis emerges as an important target for cancer therapy. Furthermore, as activated macropinocytosis constitutively uptakes extracellular fluids into cancer cells, it has been utilized for delivering anti-tumor drugs in cancer therapy. In this review, we systematically addressed progress in cancer therapeutic strategies in both targeting macropinocytosis and utilizing macropinocytosis as an anti-cancer drug delivering tool, including therapeutic applications with macropinocytosis inhibitors; metabolic modulators; methuosis (the macropinocytosis-associated cell death) inducers; and macropinocytosis-mediated anti-cancer drug delivery strategies such as nanoparticles, viral vectors, extracellular vesicles, and targeted conjugates. We conclude that developing targeted macropinocytosis anti-cancer drugs and exploring macropinocytosis-dependent anti-cancer drug delivery systems open new avenues for cancer therapy. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Figure 1

18 pages, 535 KiB

Open AccessReview

Overcoming Immune Barriers in Allogeneic CAR-NK Therapy: From Multiplex Gene Editing to AI-Driven Precision Design

by Hyunyoung Kim

Biomolecules 2025, 15(7), 935; https://doi.org/10.3390/biom15070935 (registering DOI) - 26 Jun 2025

Abstract

Chimeric antigen receptor (CAR)-engineered natural killer (NK) cells are a promising platform for off-the-shelf immunotherapy due to their safety advantages over CAR-T cells, including lower risk of graft-versus-host disease, cytokine release syndrome, and neurotoxicity. However, their persistence and efficacy are limited by immunological [...] Read more.

Chimeric antigen receptor (CAR)-engineered natural killer (NK) cells are a promising platform for off-the-shelf immunotherapy due to their safety advantages over CAR-T cells, including lower risk of graft-versus-host disease, cytokine release syndrome, and neurotoxicity. However, their persistence and efficacy are limited by immunological challenges such as host T-cell-mediated rejection, NK cell fratricide, and macrophage-mediated clearance. This review summarizes gene editing strategies to overcome these barriers, including β2-microglobulin (B2M) knockout and HLA-E overexpression to evade T and NK cell attacks, CD47 overexpression to inhibit phagocytosis, and TIGIT deletion to enhance cytotoxicity. In addition, we discuss functional enhancements such as IL-15 pathway activation, KIR modulation, and transcriptional reprogramming (e.g., FOXO1 knockout) to improve persistence and antitumor activity. We also highlight the role of induced pluripotent stem cell (iPSC)-derived NK platforms, enabling standardized, scalable, and multiplex gene-edited products. Finally, we explore artificial intelligence (AI) applications in immunogenomic profiling and predictive editing to tailor NK cell therapies to patient-specific HLA/KIR/SIRPα contexts. By integrating immune evasion, functional reinforcement, and computational design, we propose a unified roadmap for next-generation CAR-NK development, supporting durable and broadly applicable cell-based therapies. Full article

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

► Show Figures

Figure 1

15 pages, 3547 KiB

Open AccessArticle

Discovery of Dietary Plant Flavonols as Novel Potent Inhibitors Targeting DYRK1A Kinase

by Jin Jin, Qihong Zhou, Bin Guo and Zongchao Jia

Biomolecules 2025, 15(7), 934; https://doi.org/10.3390/biom15070934 (registering DOI) - 26 Jun 2025

Abstract

DYRK1A kinase is a critical regulator in cellular signaling pathways and a promising therapeutic target for neurodegenerative diseases, diabetes and cancers. Despite its significance, the development of potent, selective and safe inhibitors remains a significant challenge. Several natural flavonoids have been reported to [...] Read more.

DYRK1A kinase is a critical regulator in cellular signaling pathways and a promising therapeutic target for neurodegenerative diseases, diabetes and cancers. Despite its significance, the development of potent, selective and safe inhibitors remains a significant challenge. Several natural flavonoids have been reported to inhibit DYRK1A by binding in the ATP-binding pocket, exhibiting antidiabetic properties. However, a systematic screening of these structural derivatives remains lacking. In this study, we aimed to expand the pool of flavonoid-based DYRK1A inhibitor candidates for drug development against DYRK1A through targeted screening and structure-based analysis. A focused library of 13 flavonoid derivatives was screened to identify novel DYRK1A inhibitors, revealing eight new flavonol inhibitors with IC₅₀ values ranging from 149.5 nM to 737.9 nM. Among these, fisetin demonstrated the highest potency with an IC₅₀ of 149.5 nM, followed by kaempferol (296.3 nM), isorhamnetin (418 nM), morin (478.4 nM), myricetin (633.2 nM) and luteolin (797.8 nM), all exhibiting submicromolar inhibitory activity. Additional novel inhibitors, Apigenin and Kaempferide, also showed effective inhibition. As controls, the previously known inhibitors quercetin and curcumin were evaluated, yielding IC₅₀ values of 737.9 nM and 2.35 μM, respectively, which validated the assay conditions. To the best of our knowledge, fisetin is the most potent known DYRK1A inhibitor among flavonoids. Cellular assays further demonstrated that the top flavonoid hits induced dose-dependent cytotoxicity and morphological changes in HeLa cells. Structure-activity relationship and molecular simulation analysis revealed that the selected flavonols interact with key residues for DYRK1A inhibition. These results highlight flavonols as a promising scaffold for DYRK1A inhibition and provide valuable natural inhibitor leads for further optimization and therapeutic development. Full article

(This article belongs to the Special Issue Novel Molecules for Cancer Treatment (3rd Edition))

► Show Figures

Figure 1

Journal Description

Biomolecules

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI