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18 pages, 1988 KiB  
Article
Computational Design of Potentially Multifunctional Antimicrobial Peptide Candidates via a Hybrid Generative Model
by Fangli Ying, Wilten Go, Zilong Li, Chaoqian Ouyang, Aniwat Phaphuangwittayakul and Riyad Dhuny
Int. J. Mol. Sci. 2025, 26(15), 7387; https://doi.org/10.3390/ijms26157387 - 30 Jul 2025
Viewed by 247
Abstract
Antimicrobial peptides (AMPs) provide a robust alternative to conventional antibiotics, combating escalating microbial resistance through their diverse functions and broad pathogen-targeting abilities. While current deep learning technologies enhance AMP generation, they face challenges in developing multifunctional AMPs due to intricate amino acid interdependencies [...] Read more.
Antimicrobial peptides (AMPs) provide a robust alternative to conventional antibiotics, combating escalating microbial resistance through their diverse functions and broad pathogen-targeting abilities. While current deep learning technologies enhance AMP generation, they face challenges in developing multifunctional AMPs due to intricate amino acid interdependencies and limited consideration of diverse functional activities. To overcome this challenge, we introduce a novel de novo multifunctional AMP design framework that enhances a Feedback Generative Adversarial Network (FBGAN) by integrating a global quantitative AMP activity regression module and a multifunctional-attribute integrated prediction module. This integrated approach not only facilitates the automated generation of potential AMP candidates, but also optimizes the network’s ability to assess their multifunctionality. Initially, by integrating an effective pre-trained regression and classification model with feedback-loop mechanisms, our model can not only identify potential valid AMP candidates, but also optimizes computational predictions of Minimum Inhibitory Concentration (MIC) values. Subsequently, we employ a combinatorial predictor to simultaneously identify and predict five multifunctional AMP bioactivities, enabling the generation of multifunctional AMPs. The experimental results demonstrate the efficiency of generating AMPs with multiple enhanced antimicrobial properties, indicating that our work can provide a valuable reference for combating multi-drug-resistant infections. Full article
(This article belongs to the Special Issue Application of Artificial Intelligence in Molecular Sciences)
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26 pages, 1785 KiB  
Review
Targeting RHAMM in Cancer: Crosstalk with Non-Coding RNAs and Emerging Therapeutic Strategies Including Peptides, Oligomers, Antibodies, and Vaccines
by Dong Oh Moon
Int. J. Mol. Sci. 2025, 26(15), 7198; https://doi.org/10.3390/ijms26157198 - 25 Jul 2025
Viewed by 196
Abstract
Cancer remains a major cause of mortality worldwide, driven by complex molecular mechanisms that promote metastasis and resistance to therapy. Receptor for hyaluronan-mediated motility (RHAMM) has emerged as a multifunctional regulator in cancer, contributing to cell motility, invasion, proliferation, and fibrosis. In addition [...] Read more.
Cancer remains a major cause of mortality worldwide, driven by complex molecular mechanisms that promote metastasis and resistance to therapy. Receptor for hyaluronan-mediated motility (RHAMM) has emerged as a multifunctional regulator in cancer, contributing to cell motility, invasion, proliferation, and fibrosis. In addition to being regulated by non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, RHAMM serves as a promising therapeutic target. Recent developments in RHAMM-targeted strategies include function-blocking peptides (e.g., NPI-110, NPI-106, and P15-1), hyaluronan (HA) oligomers, and anti-RHAMM antibodies, all shown to modulate tumor stroma and suppress tumor invasiveness. Importantly, RHAMM-targeted peptide vaccines, such as the RHAMM-R3 epitope, have demonstrated immunogenicity and anti-leukemia efficacy in both pre-clinical and early clinical studies, suggesting their potential to elicit specific CD8+ T-cell responses and enhance graft-versus-leukemia effects. This review summarizes the intricate roles of RHAMM in cancer progression, its modulation by ncRNAs, and the translational promise of novel RHAMM-targeting approaches, providing insights into future directions for precision cancer therapy. Full article
(This article belongs to the Section Molecular Oncology)
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14 pages, 1395 KiB  
Article
Cost–Consequence Analysis of Semaglutide vs. Liraglutide for Managing Obese Prediabetic and Diabetic Patients in Saudi Arabia: A Single-Center Study
by Najla Bawazeer, Seham Bin Ganzal, Huda F. Al-Hasinah and Yazed Alruthia
Healthcare 2025, 13(14), 1755; https://doi.org/10.3390/healthcare13141755 - 20 Jul 2025
Viewed by 684
Abstract
Background: Semaglutide and Liraglutide are medications in the Glucagon-like peptide-1 agonists (GLP-1 RAs) class used to manage type 2 diabetes mellitus and obesity in Saudi Arabia. Although the 1.0 mg once weekly dosage of Semaglutide does not have a labeled indication for [...] Read more.
Background: Semaglutide and Liraglutide are medications in the Glucagon-like peptide-1 agonists (GLP-1 RAs) class used to manage type 2 diabetes mellitus and obesity in Saudi Arabia. Although the 1.0 mg once weekly dosage of Semaglutide does not have a labeled indication for the management of obesity, many believe that this dosage is more effective than the 3.0 mg once daily Liraglutide dosage for the management of both diabetes and obesity. Objective: To compare the effectiveness of the dosage of 1.0 mg of Semaglutide administered once weekly versus 3.0 mg of Liraglutide administered once daily in controlling HbA1c levels, promoting weight loss, and evaluating their financial implications among obese patients in Saudi Arabia using real-world data. Methods: A retrospective review of Electronic Medical Records (EMRs) from January 2021 to June 2024 was conducted on patients prescribed Semaglutide or Liraglutide for at least 12 months. Exclusion criteria included pre-existing severe conditions (e.g., cardiovascular disease, stroke, or cancer) and missing baseline data. The primary outcomes assessed were changes in HbA1c, weight, and direct medical costs. Results: Two hundred patients (100 patients on the 1.0 mg once weekly dose of Semaglutide and 100 patients on the 3.0 mg once daily dose of Liraglutide) of those randomly selected from the EMRs met the inclusion criteria and were included in the analysis. Of the 200 eligible patients (65.5% female, mean age 48.54 years), weight loss was greater with Semaglutide (−8.09 kg) than Liraglutide (−5.884 kg). HbA1c reduction was also greater with Semaglutide (−1.073%) than Liraglutide (−0.298%). The use of Semaglutide resulted in lower costs of USD −1264.76 (95% CI: −1826.82 to 33.76) and greater reductions in weight of −2.22 KG (95% CI: −7.68 to −2.784), as well as lower costs of USD −1264.76 (95% CI: (−2368.16 to −239.686) and greater reductions in HbA1c of −0.77% (95% CI: −0.923 to −0.0971) in more than 95% of the cost effectiveness bootstrap distributions. Conclusions: Semaglutide 1.0 mg weekly seems to be more effective and cost-saving in managing prediabetes, diabetes, and obesity compared to Liraglutide 3.0 mg daily. Future studies should examine these findings using a more representative sample and a robust study design. Full article
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25 pages, 1330 KiB  
Review
Cardioprotection Reloaded: Reflections on 40 Years of Research
by Pasquale Pagliaro, Giuseppe Alloatti and Claudia Penna
Antioxidants 2025, 14(7), 889; https://doi.org/10.3390/antiox14070889 - 18 Jul 2025
Viewed by 685
Abstract
Over the past four decades, cardioprotective research has revealed an extraordinary complexity of cellular and molecular mechanisms capable of mitigating ischemia/reperfusion injury (IRI). Among these, ischemic conditioning has emerged as one of the most influential discoveries: brief episodes of ischemia followed by reperfusion [...] Read more.
Over the past four decades, cardioprotective research has revealed an extraordinary complexity of cellular and molecular mechanisms capable of mitigating ischemia/reperfusion injury (IRI). Among these, ischemic conditioning has emerged as one of the most influential discoveries: brief episodes of ischemia followed by reperfusion activate protective programs that reduce myocardial damage. These effects can be elicited locally (pre- or postconditioning) or remotely (remote conditioning), acting mainly through paracrine signaling and mitochondria-linked kinase pathways, with both early and delayed windows of protection. We have contributed to clarifying the roles of mitochondria, oxidative stress, prosurvival kinases, connexins, extracellular vesicles, and sterile inflammation, particularly via activation of the NLRP3 inflammasome. Despite robust preclinical evidence, clinical translation of these approaches has remained disappointing. The challenges largely stem from experimental models that poorly reflect real-world clinical settings—such as advanced age, comorbidities, and multidrug therapy—as well as the reliance on surrogate endpoints that do not reliably predict clinical outcomes. Nevertheless, interest in multi-target protective strategies remains strong. New lines of investigation are focusing on emerging mediators—such as gasotransmitters, extracellular vesicles, and endogenous peptides—as well as targeted modulation of inflammatory responses. Future perspectives point toward personalized cardioprotection tailored to patient metabolic and immune profiles, with special attention to high-risk populations in whom IRI continues to represent a major clinical challenge. Full article
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15 pages, 1455 KiB  
Article
Assessment of Selected Biochemical Parameters of the Renin–Angiotensin–Aldosterone System in Repeat Convalescent Plasma Donors in the Context of Long-Term Changes Following SARS-CoV-2 Infection
by Marta Stanek, Dorota Diakowska, Krzysztof Kaliszewski and Anna Leśków
J. Clin. Med. 2025, 14(14), 4910; https://doi.org/10.3390/jcm14144910 - 10 Jul 2025
Viewed by 284
Abstract
Background: SARS-CoV-2 infection has been associated with long-term health consequences, including dysregulation of the renin–angiotensin–aldosterone system (RAAS). This study aimed to evaluate long-term changes in selected RAAS-related biochemical parameters in repeat convalescent plasma donors, focusing on enzymes and peptides involved in vascular regulation [...] Read more.
Background: SARS-CoV-2 infection has been associated with long-term health consequences, including dysregulation of the renin–angiotensin–aldosterone system (RAAS). This study aimed to evaluate long-term changes in selected RAAS-related biochemical parameters in repeat convalescent plasma donors, focusing on enzymes and peptides involved in vascular regulation and inflammation. Methods: Thirty repeat convalescent plasma donors were enrolled, each providing four serum samples at defined time points post-infection. Samples were collected during Period 1 (≤60 days), Period 2 (61–90 days), Period 3 (91–120 days), and Period 4 (>120 days) after confirmed SARS-CoV-2 infection. The analyzed parameters included angiotensin I (Ang I), angiotensin II (Ang II), angiotensin 1–7 (Ang 1–7), angiotensin 1–9 (Ang 1–9), ACE, ACE2, ADAM10, and ADAM17. Concentrations were determined using ELISA assays. The control group consisted of pre-pandemic serum samples from healthy individuals. Results: An initial post-infection increase was observed in most parameters, particularly in Period 1. Over time, levels of several markers declined, yet Ang 1–7 and Ang 1–9 remained elevated compared to controls even beyond 120 days. Significant correlations (p < 0.05) were found between ADAM10, ADAM17, and angiotensin peptides, suggesting prolonged RAAS modulation. Metalloproteinases were notably elevated early after infection, potentially contributing to inflammatory and cardiovascular responses. Conclusions: The findings indicate a transient but measurable biochemical response of the RAAS following SARS-CoV-2 infection, with most parameters normalizing after 120 days. However, the sustained elevation of certain markers suggests a potential long-term impact on vascular homeostasis, warranting further investigation. Full article
(This article belongs to the Special Issue Post-COVID Symptoms and Causes, 3rd Edition)
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17 pages, 1548 KiB  
Article
CD19-ReTARGTPR: A Novel Fusion Protein for Physiological Engagement of Anti-CMV Cytotoxic T Cells Against CD19-Expressing Malignancies
by Anne Paulien van Wijngaarden, Isabel Britsch, Matthias Peipp, Douwe Freerk Samplonius and Wijnand Helfrich
Cancers 2025, 17(14), 2300; https://doi.org/10.3390/cancers17142300 - 10 Jul 2025
Viewed by 404
Abstract
Background/Objectives: The physiological activation of cytotoxic CD8pos T cells (CTLs) relies on the engagement of the TCR/CD3 complex with cognate peptide-HLA class I (pHLA-I) on target cells, triggering cell lysis with appropriate cytokine release and minimized off-target toxicity. In contrast, current [...] Read more.
Background/Objectives: The physiological activation of cytotoxic CD8pos T cells (CTLs) relies on the engagement of the TCR/CD3 complex with cognate peptide-HLA class I (pHLA-I) on target cells, triggering cell lysis with appropriate cytokine release and minimized off-target toxicity. In contrast, current immunotherapies for CD19-expressing hematological malignancies, such as chimeric antigen receptor (CAR) T cells and bispecific T cell engagers (BiTEs), bypass TCR/pHLA interactions, resulting in CTL hyperactivation and excessive cytokine release, which frequently cause severe immune-related adverse events (irAEs). Thus, there is a pressing need for T cell-based therapies that preserve physiological activation while maintaining antitumor efficacy. Methods: To address this, we developed CD19-ReTARGTPR, a novel fusion protein consisting of the immunodominant cytomegalovirus (CMV) pp65-derived peptide TPRVTGGAM (TPR) covalently presented by a soluble HLA-B*07:02/β2-microglobulin complex fused to a high-affinity CD19-targeting Fab antibody fragment. The treatment of CD19-expressing cancer cells with CD19-ReTARGTPR makes them recognizable for pre-existing anti-CMVpp65 CTLs via physiological TCR-pHLA engagement. Results: Our preclinical data demonstrate that CD19-ReTARGTPR efficiently redirects anti-CMV CTLs to eliminate CD19-expressing cancer cells, including both established cell lines and primary chronic lymphocytic leukemia (CLL) cells. Unlike CD19-directed CAR T cells or the CD19/CD3 BiTE blinatumomab, CD19-ReTARGTPR mediated robust cytotoxic activity without triggering supraphysiological cytokine release. Importantly, this approach retained efficacy even against cancer cells with low CD19 expression. Conclusions: In summary, we provide a robust proof-of-concept study and show that CD19-ReTARGTPR offers a promising alternative strategy for T cell redirection, enabling the selective and effective killing of CD19-expressing malignancies while minimizing cytokine-driven toxicities through physiological CTL activation pathways. Full article
(This article belongs to the Special Issue New Insights of Hematology in Cancer)
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16 pages, 2188 KiB  
Article
Tartary Buckwheat Peptides Prevent Oxidative Damage in Differentiated SOL8 Cells via a Mitochondria-Mediated Apoptosis Pathway
by Yifan Xu, Yawen Wang, Min Yang, Pengxiang Yuan, Weikang Xu, Tong Jiang and Jian Huang
Nutrients 2025, 17(13), 2204; https://doi.org/10.3390/nu17132204 - 2 Jul 2025
Viewed by 476
Abstract
Background: Under oxidative stress conditions, the increased levels of reactive oxygen species (ROS) within cells disrupt the intracellular homeostasis. Tartary buckwheat peptides exert their effects by scavenging oxidative free radicals, such as superoxide anion and hydrogen peroxide, thereby reducing oxidative damage within cells. [...] Read more.
Background: Under oxidative stress conditions, the increased levels of reactive oxygen species (ROS) within cells disrupt the intracellular homeostasis. Tartary buckwheat peptides exert their effects by scavenging oxidative free radicals, such as superoxide anion and hydrogen peroxide, thereby reducing oxidative damage within cells. Meanwhile, these peptides safeguard mitochondria by maintaining the mitochondrial membrane potential, decreasing the production of mitochondrial oxygen free radicals, and regulating mitochondrial biogenesis and autophagy to preserve mitochondrial homeostasis. Through these mechanisms, Tartary buckwheat peptides restore the intracellular redox balance, sustain cellular energy metabolism and biosynthesis, and ensure normal cellular physiological functions, which is of great significance for cell survival and adaptation under oxidative stress conditions. Objectives: In this experiment, a classical cellular oxidative stress model was established. Indicators related to antioxidant capacity and mitochondrial membrane potential changes, as well as pathways associated with oxidative stress, were selected for detection. The aim was to elucidate the effects of Tartary buckwheat oligopeptides on the metabolism of cells in response to oxidative stress. Methods: In this study, we established an oxidative damage model of mouse skeletal muscle myoblast (SOL8) cells using hydrogen peroxide (H2O2), investigated the pre-protective effects of Tartary buckwheat oligopeptides on H2O2-induced oxidative stress damage in SOL8 cells at the cellular level, and explored the possible mechanisms. The CCK-8 method is a colorimetric assay based on WST-8-[2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodiumsalt], which is used to detect cell proliferation and cytotoxicity. Results: The value of CCK-8 showed that, when the cells were exposed to 0.01 mmol/L H2O2 for 1 h and 10 mg/mL Tartary buckwheat oligopeptides intervention for 48 h, these were the optimal conditions. Compared with the H2O2 group, the intervention group (KB/H2O2 group) showed that the production of ROS was significantly reduced (p < 0.001), the malondialdehyde (MDA) content was significantly decreased (p < 0.05), and the activity of catalase (CAT) was significantly increased (p < 0.01); the mitochondrial membrane potential in the KB/H2O2 group tended to return to the level of the control group, and they all showed dose-dependent effects. Compared with the H2O2 group, the mRNA expression of KEAP1 in the KB/H2O2 group decreased, while the mRNA expression of NRF2α, HO-1, nrf1, PGC-1, P62, and PINK increased. Conclusions: Therefore, Tartary buckwheat oligopeptides have a significant pre-protective effect on H2O2-induced SOL8 cells, possibly by enhancing the activity of superoxide dismutase, reducing ROS attack, balancing mitochondrial membrane potential, and maintaining intracellular homeostasis. Full article
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21 pages, 4136 KiB  
Article
Microwave Irradiation Pre-Treatment as a Sustainable Method to Obtain Bioactive Hydrolysates from Chicken Feathers
by Álvaro Torices-Hernández, Marta Gallego, Leticia Mora and Fidel Toldrá
Int. J. Mol. Sci. 2025, 26(13), 6344; https://doi.org/10.3390/ijms26136344 - 30 Jun 2025
Viewed by 504
Abstract
Chicken feathers constitute a major by-product from the poultry industry, with a potential environmental impact and significant difficulties in their management. This study aimed to develop a sustainable method to hydrolyse chicken feathers and evaluate the effects of microwave (MW) irradiation pre-treatment in [...] Read more.
Chicken feathers constitute a major by-product from the poultry industry, with a potential environmental impact and significant difficulties in their management. This study aimed to develop a sustainable method to hydrolyse chicken feathers and evaluate the effects of microwave (MW) irradiation pre-treatment in the generation of bioactive hydrolysates by simple or sequential hydrolysis with Alcalase. The hydrolysate with MW irradiation pre-treatment and Alcalase (2%, 2 h) (MWA) showed the highest overall antioxidant activity and neprilysin-inhibitory activity (55%), whereas samples without MW irradiation pre-treatment exerted the highest inhibitory activity of dipeptidyl peptidase IV (DPP IV) and angiotensin-converting enzyme (ACE-I), with values close to 50 and 70%, respectively. Mass spectrometry in tandem of bioactive hydrolysates was performed, and an in silico approach was used to characterise the obtained sequences. These results confirmed that MW irradiation pre-treatment improved Alcalase hydrolysis, leading to the generation of bioactive peptides with potential multifunctional properties, including antioxidant, antidiabetic, and antihypertensive activities. Moreover, this study highlights the potential of combining MW irradiation and enzymatic hydrolysis as a sustainable strategy for the revalorisation of chicken feathers. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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21 pages, 5739 KiB  
Article
Novel Lung Cell-Penetrating Peptide Targets Alveolar Epithelial Type II Cells, Basal Cells, and Ionocytes
by Jin Wen, Gajalakshmi Singuru, Jeffrey Stiltner, Sanjay Mishra, Kyle S. Feldman, Kayla McCandless, Raymond Yurko, Kazi Islam, Ray Frizzell, Hisato Yagi, Jonathan M. Brown and Maliha Zahid
Pharmaceutics 2025, 17(7), 824; https://doi.org/10.3390/pharmaceutics17070824 - 25 Jun 2025
Viewed by 573
Abstract
Background: Cell-penetrating peptides cross cell membrane barriers while carrying cargoes in a functional form. Our work identified two novel lung-targeting peptides, S7A and R11A. Here, we present studies on biodistribution, the cell types targeted, and an in vitro proof of application. Methods: Studies [...] Read more.
Background: Cell-penetrating peptides cross cell membrane barriers while carrying cargoes in a functional form. Our work identified two novel lung-targeting peptides, S7A and R11A. Here, we present studies on biodistribution, the cell types targeted, and an in vitro proof of application. Methods: Studies were performed in human bronchial epithelial cells (HBECs) with and without various endocytic inhibitors, and coincubation with fluorescently labeled transferrin or endocytic markers. Cyclic R11A (cR11A) was conjugated to siRNA duplexes and anti-viral activity against SARS-CoV-2 was tested. Biodistribution studies were performed by injecting wild-type mice with fluorescently labeled peptides, and various circulation times were allowed for, as well as cross-staining of lung sections or isolated single cells with various cellular markers, followed by fluorescence-activated cell sorting or confocal microscopy. Results: cR11A showed peak uptake in 15 min, with the highest uptake in airway epithelial type II (ATII) cells, followed by p63+ basal cells and ionocytes. Cyclization increased transduction efficiencies ~100-fold. Endocytosis studies showed a decrease in peptide uptake by pre-treatment with Pitstop2 but not Amiloride or Nystatin. Endocytic marker Lamp1 showed colocalization at the earliest time point, with the escape of the peptide from endocytic vesicles later. cR11A conjugated to ant-spike and anti-envelop proteins showed anti-viral effects with an EC90 of 0.6 μM and 1.0 µM, respectively. Conclusions: We have identified a novel peptide, cR11A, that targets ATII, basal cells, and ionocytes, the cyclization of which increased transduction efficiency in vitro and in vivo. The uptake mechanism appears to be via clathrin-mediated endocytosis with escape from endocytic vesicles. cR11A can act as a vector to deliver anti-viral siRNA to epithelial cells. Full article
(This article belongs to the Section Biologics and Biosimilars)
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19 pages, 2694 KiB  
Article
Biphasic CAPA-IVM Improves Equine Oocyte Quality and Subsequent Embryo Development Without Inducing Genetic Aberrations
by Muhammad Fakhar-I-Adil, Daniel Angel-Velez, Emin Araftpoor, Qurratul Ain Amin, Mohamed Hedia, Marcel Bühler, Kris Gevaert, Björn Menten, Ann Van Soom, Susana Marina Chuva de Sousa Lopes, Dominic Stoop, Chloë De Roo, Katrien Smits and Björn Heindryckx
Int. J. Mol. Sci. 2025, 26(12), 5495; https://doi.org/10.3390/ijms26125495 - 8 Jun 2025
Viewed by 921
Abstract
In vitro maturation (IVM) of oocytes retrieved from ovum pick-up (OPU) or ovarian tissue (OT) is a standard approach for patients with specific conditions where prior hormonal stimulation is contraindicated. However, the developmental competence of oocytes matured in vitro is still inferior to [...] Read more.
In vitro maturation (IVM) of oocytes retrieved from ovum pick-up (OPU) or ovarian tissue (OT) is a standard approach for patients with specific conditions where prior hormonal stimulation is contraindicated. However, the developmental competence of oocytes matured in vitro is still inferior to that of oocytes matured in vivo. Capacitation IVM (CAPA-IVM) includes an extra step of pre-maturation culture (PMC) with c-type natriuretic peptide (CNP) as a meiotic arrestor to better synchronize cytoplasmic and nuclear maturity in oocytes by allowing the cytoplasm additional time to acquire essential components critical for optimal competency. This study aims to evaluate the effect of CAPA-IVM on equine oocyte quality and developmental competence. Immature cumulus–oocyte complexes (COCs) were retrieved from slaughterhouse ovaries and matured in vitro either in CAPA-IVM (short 6 h, long 24 h pre-maturation) or standard IVM. Mature oocytes from each group were analyzed for calcium-releasing potential (n = 52) and single-oocyte proteomics (n = 44), and embryo development (n = 229) was assessed after fertilization with piezo-drilled intracytoplasmic sperm injection (ICSI). Genetic analysis of developed blastocysts (n = 41) was performed to detect chromosomal aberrations. Our findings demonstrate that CAPA-IVM of equine COCs yields significantly higher maturation rates than controls. Moreover, short CAPA-IVM with six hours pre-maturation culture showed substantially higher embryo development potential than the control group (20/69 vs. 9/63, respectively). Genetic analysis revealed a high euploidy rate in equine blastocysts regardless of the maturation conditions. Live calcium imaging of the fertilized oocytes demonstrated that the majority of oocytes displayed non-continuous calcium oscillation patterns, irrespective of maturation conditions. Single-oocyte proteomics reveals a comparable proteomic landscape between mature oocytes subjected to short CAPA-IVM and standard IVM. However, we identified four enriched gene sets with positive enrichment scores after short CAPA-IVM, related to cytoskeleton regulation, ribosomal function, and cytosolic components. Our findings indicate that CAPA-IVM holds the potential to improve oocyte quality and competence in horses. However, further fine-tuning of culture conditions would benefit the effective use of these IVM systems. Moreover, given that the mare serves as an excellent model for human reproduction, the molecular trends identified in this study could provide valuable insights for advancing human artificial reproductive technologies. Full article
(This article belongs to the Special Issue Molecular Research on Embryo Developmental Potential)
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20 pages, 2509 KiB  
Article
Substitution of Proline Residues by 4-Fluoro-l-Proline Affects the Mechanism of the Proline-Rich Antimicrobial Peptide Api137
by Maren Reepmeyer, Andor Krizsan, Alexandra Brakel, Lisa Kolano, Jakob Gasse, Benjamin W. Husselbee, Andrea J. Robinson and Ralf Hoffmann
Antibiotics 2025, 14(6), 566; https://doi.org/10.3390/antibiotics14060566 - 31 May 2025
Viewed by 618
Abstract
Background: The well-studied 18-residue-long proline-rich antimicrobial designer peptide Api137 utilizes at least two lethal intracellular mechanisms that target the bacterial 70S ribosome. First, Api137 stalls the ribosome by binding to the peptidyl-transferase center, trapping the release factor, and inhibiting protein expression. Second, [...] Read more.
Background: The well-studied 18-residue-long proline-rich antimicrobial designer peptide Api137 utilizes at least two lethal intracellular mechanisms that target the bacterial 70S ribosome. First, Api137 stalls the ribosome by binding to the peptidyl-transferase center, trapping the release factor, and inhibiting protein expression. Second, Api137 disrupts the assembly of the large 50S subunit of the ribosome, resulting in partially assembled pre-50S dead-end particles that are unable to form the functional 70S ribosome. Methods: All six proline residues in Api137 were substituted with 4S- and 4R-fluoro-l-proline (Fpr), which promote the cis- and trans-conformer ratio of the preceding Xaa-Pro-bond, respectively. The effect on the antibacterial activity was studied using Escherichia coli. The underlying mechanisms were investigated by studying 70S ribosome binding, inhibition of in vitro translation, and ribosome profile analysis. Results: Interestingly, the analogs were equipotent to Api137, except for the 4S-Fpr11 and 4S-Fpr16 analogs, which were four times more or less active, respectively. The most active 4S-Fpr11 analog competed the least with Api137 for its ribosome binding site, suggesting a shifted binding site. Both Fpr14 and the 4S-Fpr16 analogs disturbed 50S subunit assembly less than Api137 or not at all. The strongest effect was observed with the 4R-Fpr16 analog resulting in the lowest 70S ribosome content and the highest pre-50S particle content. This peptide also showed the strongest competition with Api137 for its binding site. However, its antibacterial activity was similar to that of Api137, possibly due to its slower cellular uptake. Conclusions: Api137 inhibits protein translation and disrupts 50S assembly, which can be adjusted by substituting specific proline residues with fluoroproline. 4R-Fpr16 potently inhibits ribosome assembly and offers a novel, unexploited clinical mechanism for future antibiotic development. Full article
(This article belongs to the Special Issue Discovery and Development of Novel Antibacterial Agents—2nd Edition)
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17 pages, 1965 KiB  
Article
The Role of Long-Range Non-Specific Electrostatic Interactions in Inhibiting the Pre-Fusion Proteolytic Processing of the SARS-CoV-2 S Glycoprotein by Heparin
by Yi Du, Yang Yang, Son N. Nguyen and Igor A. Kaltashov
Biomolecules 2025, 15(6), 778; https://doi.org/10.3390/biom15060778 - 28 May 2025
Viewed by 494
Abstract
The proteolytic processing of the SARS-CoV-2 spike glycoprotein by host cell membrane-associated proteases is a key step in both the entry of the invading virus into the cell and the release of the newly generated viral particles from the infected cell. Because of [...] Read more.
The proteolytic processing of the SARS-CoV-2 spike glycoprotein by host cell membrane-associated proteases is a key step in both the entry of the invading virus into the cell and the release of the newly generated viral particles from the infected cell. Because of the critical importance of this step for the viral infectivity cycle, it has been a target of extensive efforts aimed at identifying highly specific protease inhibitors as potential antiviral agents. An alternative strategy to disrupt the pre-fusioviden processing of the SARS-CoV-2 S glycoprotein aims to protect the substrate rather than directly inhibit the proteases. In this work, we focused on furin, a serine protease located primarily in the Golgi apparatus, but also present on the cell membrane. Its cleavage site within the S glycoprotein is located within the stalk region of the latter and comprises an arginine-rich segment (SPRRARS), which fits the definition of the Cardin–Weintraub glycosaminoglycan recognition motif. Native mass spectrometry (MS) measurements confirmed the binding of a hexadecameric peptide representing the loop region at the S1/S2 interface and incorporating the furin cleavage site (FCS) to heparin fragments of various lengths, as well as unfractionated heparin (UFH), although at the physiological ionic strength, only UFH remains tightly bound to the FCS. The direct LC/MS monitoring of FCS digestion with furin revealed a significant impact of both heparin fragments and UFH on the proteolysis kinetics, although only the latter had IC50 values that could be considered physiologically relevant (0.6 ± 0.1 mg/mL). The results of this work highlight the importance of the long-range and relatively non-specific electrostatic interactions in modulating physiological and pathological processes and emphasize the multi-faceted role played by heparin in managing coronavirus infections. Full article
(This article belongs to the Special Issue Molecular Mechanism and Detection of SARS-CoV-2)
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13 pages, 1859 KiB  
Article
The Isolation, Structural Characterization, and Biosynthetic Pathway of Unguisin from the Marine-Derived Fungus Aspergillus candidus
by Wenjiao Diao, Wei Zhang, Xiaoxi Zhang, Siyu Du, Caijuan Zheng, Xuenian Huang and Xuefeng Lu
Mar. Drugs 2025, 23(5), 219; https://doi.org/10.3390/md23050219 - 21 May 2025
Viewed by 739
Abstract
Unguisins, a class of structurally complex cyclic peptides featuring a γ-aminobutyric acid residue embedded in the skeleton, exhibit diverse biological activities. Here, a new unguisin K, along with three known congeners, was isolated from the marine-derived fungus Aspergillus candidus MEFC1001. The biosynthetic [...] Read more.
Unguisins, a class of structurally complex cyclic peptides featuring a γ-aminobutyric acid residue embedded in the skeleton, exhibit diverse biological activities. Here, a new unguisin K, along with three known congeners, was isolated from the marine-derived fungus Aspergillus candidus MEFC1001. The biosynthetic pathway was elucidated through gene disruption coupled with in vitro enzymatic characterization. The ugs biosynthetic gene cluster (BGC) containing ugsA and ugsB, in conjunction with an extra-clustered gene ugsC, collaborates to synthesize these unguisins. The alanine racemase (AR) UgsC catalyzes the isomerization of Ala and provides d-Ala as the starter unit for the non-ribosomal peptide synthetase (NRPS). The unique localization of ugsC outside the ugs BGC is different from previously reported unguisin-producing systems where AR genes reside within BGCs. The methyltransferase UgsB mediates a key pre-modification step by methylating phenylpyruvic acid to yield β-methylphenylpyruvate, which is subsequently incorporated as β-methylphenylalanine during NRPS assembly. This represents the first experimental evidence of the β-carbon methylation of Phe residue occurring at the precursor level rather than through post-assembly modification. The NRPS UgsA recruits a variety of amino acids for assembly and cyclization to form mature unguisins. Additionally, genome mining utilizing UgsA as a query identified homologous NRPSs in diverse fungal species, highlighting the potential for unguisin production in fungi. This study enriches the biosynthetic diversity of cyclic peptides and provides guidance for exploring unguisin-like natural products derived from fungi. Full article
(This article belongs to the Special Issue Biosynthesis of Biologically Active Marine Natural Products 2025)
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22 pages, 3022 KiB  
Article
Circulating Antibodies Against Common Cold Coronaviruses Do Not Interfere with Immune Responses to Primary or Booster SARS-CoV-2 mRNA Vaccines
by Bindu Adhikari, Eugene M. Oltz, Richard J. Gumina, Maryssa K. Kick, Linda J. Saif and Anastasia N. Vlasova
Vaccines 2025, 13(5), 547; https://doi.org/10.3390/vaccines13050547 - 21 May 2025
Viewed by 877
Abstract
Background: Pre-existing cross-reactive antibodies (Abs) against common cold coronaviruses (CCCoVs) have been hypothesized to influence the immune responses to SARS-CoV-2 vaccine-induced Ab responses. Methods: Serum samples from healthy healthcare workers (HCWs, n = 64) receiving mRNA vaccines were collected at seven time points: [...] Read more.
Background: Pre-existing cross-reactive antibodies (Abs) against common cold coronaviruses (CCCoVs) have been hypothesized to influence the immune responses to SARS-CoV-2 vaccine-induced Ab responses. Methods: Serum samples from healthy healthcare workers (HCWs, n = 64) receiving mRNA vaccines were collected at seven time points: pre-COVID-19-vaccination (Pre), post-first dose (Vax1), post-second dose (Vax2), and 6-, 9-, 12-, and 15-months post-Vax2. Booster vaccine doses (n = 23) were received 1–80 days prior to the 9 m sample collection time point. We used peptide-based enzyme-linked immunosorbent assays (ELISAs) to measure SARS-CoV-2/CCCoV-specific IgG/IgA/IgM and SARS-CoV-2 IgG4 (associated with immune tolerance) Ab levels in the HCW serum samples. Additionally, we measured Epstein–Barr/influenza A (unrelated pathogens) virus-specific IgG Ab levels. Results: We observed that vaccination significantly increased SARS-CoV-2 IgG Ab levels at the Vax1 (p ≤ 0.0001) and Vax2 (p ≤ 0.0001) time points compared to Pre-Vax. These Ab levels declined at 6 months post-vaccination but increased again following the booster vaccine dose around the 9-month post-Vax2 time point in a cohort (n = 23) of the HCWs. However, this increase was modest compared to those induced by the primary vaccine series. Interestingly, a moderate but continuous increase in SARS-CoV-2 S IgG4 Ab levels was observed throughout this study, becoming statistically significant by the 15-month time point (p = 0.03). Further, a significant increase in CCCoV IgG (but not IgA/IgM) Ab levels was observed at the Vax1 time point, suggestive of cross-reactive or non-specific immune responses. Finally, we observed no negative correlation between the levels of pre-existing CCCoV-specific Abs and the vaccine-induced Ab response (Vax1/Vax2). Conclusions: Pre-existing CCCoV Abs do not interfere with the development of vaccine-induced immunity. However, vaccine-associated Abs wane over time, which may be associated with the increasing IgG4 Ab response. Full article
(This article belongs to the Section COVID-19 Vaccines and Vaccination)
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10 pages, 1300 KiB  
Perspective
The Molecular Pathology of Pre-Eclamptic Hypertension
by Robin W. Carrell, Randy J. Read and Aiwu Zhou
Curr. Issues Mol. Biol. 2025, 47(5), 375; https://doi.org/10.3390/cimb47050375 - 20 May 2025
Viewed by 400
Abstract
The central role of angiotensinogen in the control of blood pressure is revealed by a series of crystallographic structures, including complexes with renin. Specifically, the structures provide an understanding of the sequential molecular events that lead to the pre-eclamptic hypertensive crises of pregnancy. [...] Read more.
The central role of angiotensinogen in the control of blood pressure is revealed by a series of crystallographic structures, including complexes with renin. Specifically, the structures provide an understanding of the sequential molecular events that lead to the pre-eclamptic hypertensive crises of pregnancy. The release of the precursor vasopressor peptide from the amino-terminal tail of angiotensinogen appears to be modulated by a redox-sensitive disulphide bridge. Our findings indicate that the activation of the thiol-switch in the circulating maternal angiotensinogen occurs at the placental level in response to oxidative stress, exacerbated by placental insufficiency. We propose here that a contributory factor is the inherent redox stress accompanying the placental exchange of oxygenation between the haemoglobin of the mother (oxy-HbA) and the deoxygenated haemoglobin of the foetus (deoxy-HbF). Full article
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