Search Results (28,542)

Despite advances in multimodal treatment, head and neck squamous cell carcinoma (HNSCC) remains a major clinical problem owing to its high recurrence rate and frequent development of treatment resistance. Abnormal histone modifications, particularly lysine methylation regulated by methyltransferases (KMTs) and demethylases (KDMs), have emerged as key drivers of HNSCC initiation, progression, and cellular plasticity. This review aims to comprehensively evaluate the role of selected KMTs and KDMs in HNSCC biology, with a focus on their contribution to resistance to immunotherapy, radiotherapy, and cytotoxic chemotherapy. We summarize and critically analyze preclinical and clinical studies investigating histone methylation dynamics in HNSCC, with particular emphasis on enzymes such as KMT2C/D, EZH2, NSD1/NSD2, SMYD3, G9a/EHMT2, LSD1, KDM2A/B, KDM3, KDM4, KDM5, KDM6, KDM7, and KDM8. Attention is given particularly to pharmacological approaches targeting these proteins: we discuss small-molecule inhibitors of EZH2, LSD1, KDM4/5/6, and other KMT/KDMs that are currently in preclinical development or in early clinical trials, and we highlight completed and ongoing studies testing EZH1/2 inhibitors and epigenetic combinations in patients with recurrent and metastatic HNSCC. The deregulation of specific KMTs and KDMs reshapes histone methylation at key residues, thereby controlling cell cycle progression, epithelial–mesenchymal transition (EMT), stem cell phenotypes, DNA damage responses, and multiple interactions with the immune system in HNSCC. Targeting disrupted histone methylation pathways may partially reverse the epigenetic reprogramming of HNSCC cells and represents a promising strategy to improve treatment efficacy in patients with advanced disease. We also summarize the preclinical evidence and the currently limited clinical data on targeting histone methylation dynamics in HNSCC and discuss their therapeutic implications. Full article

Protein–protein interactions (PPIs) represent a vast and largely underexplored landscape of therapeutic targets, yet their structural features—including large, flat, and dynamic interfaces—have historically limited their druggability. In this context, cyclic peptides have emerged as a powerful class of PPI modulators, sitting at the interface between biologics and small molecules, and thus garnering key advantages of both classes. Their conformational constraint enhances binding affinity, proteolytic stability and, in some instances, cell permeability, thus enabling access to intracellular targets. This review provides an updated overview of cyclic peptides as modulators of PPIs, focusing on both conceptual foundations and practical strategies for their discovery and optimization. The main discovery approaches include natural sources, de novo design based on secondary structure mimetics, high-throughput screening, and computational approaches. Integration of these complementary strategies is crucial to enhance success rates in the discovery of effective and developable cyclic peptides. Accordingly, the present review aims to provide a practical guide for researchers entering this rapidly growing field, outlining current opportunities, methodological advances, and remaining challenges in the development of cyclic peptide-based PPI modulators. Full article

The aim of this study was to formulate and optimize a novel functional ingredient based on thermally treated skimmed goat milk enriched with Agrocybe aegerita mushroom extract (ME) and grape pomace seed extract (GPE), intended for application in a dehydrated soup model. A central composite design was applied for preliminary optimization and the formulation based on antioxidant properties. The optimized ingredient exhibited enhanced antioxidant activity, with GPE identified as the dominant factor influencing the responses. However, deviations between predicted and experimental values were observed, reflecting moderate model fitting and differences in assay mechanisms. ATR-FTIR spectra were dominated by milk compounds, while DLS and electrophoretic analysis revealed structural modifications, including polymodal particle size distribution and alterations in the protein profile, indicating interactions between milk proteins, polyphenols, and mushroom-derived compounds. UHPLC-QToF-MS analysis confirmed a high content of grape-derived phenolic compounds. Following simulated gastrointestinal digestion, several phenolic compounds were detected in the soluble fraction, with catechin and ethyl gallate exhibiting the highest bioaccessibility (12.58% and 4.54%). The enriched ingredient showed modified techno-functional properties, including reduced emulsifying capacity but improved foaming behavior, which was attributed to protein structural changes and intermolecular interactions. Application in a dehydrated soup model demonstrated good solubility, stability, and high sensory acceptability without negative effects on flavor. Furthermore, the enriched soup showed enhanced antioxidant properties after simulated gastrointestinal digestion. The developed formulation represents a promising natural functional ingredient, combining enhanced bioactive properties with satisfactory technological performance. Full article

Pneumolysin (PLY), a cholesterol-dependent cytolysin produced by Streptococcus pneumoniae, plays a key role in the pathogenesis of bacterial pneumonia. The present study aimed to identify potential phytocompound inhibitors of pneumolysin and evaluate their protective effects against toxin-induced cytotoxicity using combined in silico and in vitro approaches. A ligand library comprising 200 phytocompounds was constructed using three-dimensional structures obtained from the PubChem database, while the PLY protein structure was retrieved from the Protein Data Bank. Molecular docking was performed to analyse protein-ligand interactions, followed by visualization using BIOVIA Discovery Studio Visualizer. Top-ranked phytocompounds from docking were further screened by computational ADME analysis, followed by molecular dynamics (MD) simulations for stability analysis. Selected compounds were then validated using RAW 264.7 macrophages, and cytotoxicity was assessed by flow cytometry. Among the screened compounds, three showed high binding affinity, with oridonin exhibiting the most favourable interaction profile (−7.906 kcal/mol). MD simulation confirmed the stability of the pneumolysin–oridonin complex. In vitro results demonstrated that pneumolysin induced significant, concentration-dependent cytotoxicity, whereas pre-incubation with oridonin significantly reduced cell death. To provide direct functional evidence of pneumolysin inhibition, haemolysis inhibition assay using sheep erythrocytes was performed where reduction of pneumolysin-mediated haemolysis by oridonin in a concentration-dependent manner was demonstrated. These findings suggest that oridonin may serve as a potential inhibitor of pneumolysin-mediated cytotoxicity and pneumococcal virulence. Full article

Aspartic proteases (APs), a class of proteolytic enzymes involved in protein maturation, degradation, and signaling, are known to contribute to fungal virulence and pathogenicity. However, the AP gene family in Talaromyces marneffei (T. marneffei), a dimorphic opportunistic pathogenic fungus, has not yet been functionally analyzed. In this study, we identified 27 AP genes from the T. marneffei genome, and the encoded APs retained conserved domains and exhibited similar motifs and structural properties crucial for catalytic activity. Phylogenetic and collinearity analyses found that TmAPs were most recently homologous to Aspergillus gene families, with both tandem and segmental duplications contributing to their expansion. Expression patterns, combined with RNA-sequencing data, revealed the specialized roles of TmAP1 and TmAP2 in the dimorphic conversion between the yeast and mycelial phases. Protein–protein interaction network analysis uncovered links to cell fusion, mitochondrial function, and programmed cell death. Under abiotic stress conditions, several TmAP genes displayed significant transcriptional changes, implying their involvement in short-term adaptation and stress responses. This study provides the first comprehensive and systematic analysis of the AP gene family in T. marneffei, highlighting their potential biological roles in fungal development, dimorphic conversion, and stress adaptation. Our findings offer valuable insights into further functional characterization of AP genes in T. marneffei and may facilitate the development of novel therapeutic targets and intervention strategies against T. marneffei infection. Full article

Autophagy is a carefully regulated catabolic process that utilizes assemblies of specific sets of macromolecules operating at multiple stages of the pathway. Discoveries in recent years show that autophagy markedly relies on liquid-liquid phase separation (LLPS). Here, we present parameters that indicate the plasticity of autophagy proteins and their probability to undergo LLPS in macroautophagy and microautophagy. We show that microautophagy is an extremely LLPS-friendly pathway. Several mechanisms involving proteins in the autophagy machinery that drive LLPS on various types of membranes to regulate this process or that undergo LLPS as autophagic cargo are described in detail. We also summarize the factors that modulate the LLPS potential of autophagy proteins. A high probability of autophagy-related proteins to undergo spontaneous LLPS shown here can direct future research on the role of protein droplets in autophagy. Full article

In this study, Apocynum venetum was employed as the raw material to optimize protein extraction and enzymatic hydrolysis processes for the preparation of highly active angiotensin-converting enzyme (ACE)-inhibitory peptides, achieving an ACE inhibition rate of 92.34%. Multispectral analyses and microstructural characterization demonstrated that enzymatic hydrolysis induced the unfolding of protein secondary structures, resulting in a looser and more porous morphology enriched with characteristic amino acids. A total of 2567 peptide sequences were identified by LC–MS/MS, among which 18 potential bioactive peptides were screened. Molecular docking analysis revealed that these peptides interact with the active site of ACE primarily through hydrogen bonding and hydrophobic interactions, with WLRDFL exhibiting the strongest binding affinity. This study systematically elucidates the structural characteristics and antihypertensive molecular mechanisms of ACE-inhibitory peptides derived from Apocynum venetum, providing both theoretical insights and experimental support for the development of natural antihypertensive functional foods and the high-value utilization of this plant. Full article

Stress granules (SGs) are stress-induced ribonucleoprotein condensates assembled around untranslated mRNAs and RNA-binding proteins. G3BP1 is a central regulator of SG formation, yet the molecular events that initiate G3BP1-mediated condensation remain poorly understood. Current models propose that condensation is initiated by RNA–RNA interactions, G3BP1 self-association, or RNA-dependent assembly of G3BP1 into higher-order networks. To define the earliest steps of condensate formation, we employed high-speed atomic force microscopy (HS-AFM) to monitor G3BP1–RNA assembly at the nanometer scale. HS-AFM revealed that G3BP1 first associates with RNA to form discrete nascent assemblies that progressively recruit additional RNA and G3BP1 molecules. These assemblies subsequently grow into higher-order RNA–protein condensates through stepwise assembly. Together, these observations identify RNA-bound G3BP1 assemblies as the initiating structures of condensate formation and provide a framework for understanding the early stages of stress granule assembly. Full article

Schwann cells, the principal glial cells of the peripheral nervous system, play a central role in nerve repair following injury. Upon injury, mature Schwann cells dedifferentiate into repair Schwann cells. These processes are governed by complex gene regulatory networks, yet the quantitative dynamics of these processes remain unclear. Here, using a bottom-up systems biology approach, we constructed an endogenous regulatory network model based on experimentally validated interactions, without relying on high-throughput data as input. The model captures Schwann cell dedifferentiation dynamics and reveals a potential landscape composed of stable states and intermediate transition states. Simulations recapitulate post-injury trajectories and confirm the role of c-Jun upregulation in maintaining repair capacity. Furthermore, the model predicts multiple potential therapeutic targets, including tumor protein p53 (P53), c-Jun N-terminal kinase (JNK), and phosphatase and tensin homolog (PTEN), for sustaining repair competence. We also identify intrinsic heterogeneity within repair Schwann cells. Furthermore, we uncover key transition states that simultaneously connect repair-competent cells to both repair-deficient and apoptotic phenotypes. These intermediate states may represent critical regulatory bottlenecks and serve as key cellular targets for improving peripheral nerve regeneration. Overall, this work provides new insights into the precise regulation of Schwann cell fate and establishes a theoretical framework for regenerative medicine and clinical strategies in peripheral nerve repair. Full article

Background: The endocannabinoid system (ECS) and the Kisspeptin system (KS) play crucial roles in the central and peripheral regulation of male reproduction. The KS comprises Kisspeptins, the cleavage product of the Kiss1 protein, and its receptor Kiss1R; it is a critical central regulatory factor of the Gonadotropin Releasing Hormone (GnRH), but its role in the testis in sustaining spermatogenesis is not fully understood. Similarly, in addition to the brain, the ECS is widely expressed in the testis, where it regulates spermatogenesis, steroidogenesis, and the production of high-quality gametes. Since the possible crosstalk between KS and ECS at the gonadal level is poorly understood, this study investigates the possible mutual modulation between ECS and KS in rat testis. Methods: Experiment 1: Testis pieces collected from adult rats were treated ex vivo for 1 h with the endocannabinoid anandamide (AEA, 10⁻⁸ M) ± SR141716A (10⁻⁷ M, a cannabinoid receptor (CB) 1 antagonist), or with SR141716A alone. Experiment 2: Testis pieces were treated for 4 h with decreasing doses of Kisspeptin-10 (Kp10, 10⁻⁶–10⁻⁹ M) ± Kp234 (a Kiss1R antagonist). Proteins extracted from the treated tissues were analyzed by Western blot for Kiss1R, Kiss1, CB1, CB2, AEA-hydrolyzing enzyme Fatty Acid Amide Hydrolase (FAAH), and AEA-biosynthetic enzyme N-acylphosphatidylethanolamine-specific phospholipase D (NAPE-PLD) proteins. Results: AEA treatment, via CB1, reduced Kiss1R protein in testis. Kp10 treatment increased the expression of CBs and NAPE-PLD at all doses and increased FAAH at 10⁻⁹ M dose only. Pre-incubation with Kp234 abolished Kp10 effects on CB1, NAPE-PLD, and FAAH, suggesting a direct Kp10-dependent modulation; on the other hand, pre-incubation with Kp234 did not abolish Kp10’s effects on CB2, suggesting an indirect action of Kp10 on CB2. Conclusions: Mutual modulation between ECS and KS exists in the testis: AEA, via CB1, suppresses Kisspeptin signaling, while Kisspeptin regulates the ECS through both Kiss1R-dependent and independent mechanisms. These local interactions identify new potential mechanisms in the intratesticular communications sustaining spermatogenesis via ECS and suggest that KS might be a new therapeutic target to rescue ECS impairment in male reproductive dysfunction. Full article

The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. Coronaviruses are a diverse group of RNA viruses classified into alpha, beta, gamma, and delta genera, with SARS-CoV-2 belonging to the beta-coronavirus family. The virus exhibits high transmissibility and causes a wide spectrum of clinical manifestations ranging from mild respiratory symptoms to severe complications such as acute respiratory distress syndrome, multi-organ failure, and death, particularly among elderly and immunocompromised individuals. Structurally, SARS-CoV-2 possesses a large single-stranded RNA genome encoding major structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, which play critical roles in host-cell recognition and viral infection. Understanding the molecular mechanisms of virus–host interactions, especially protein–protein interactions (PPIs), is essential for uncovering viral pathogenesis and identifying potential therapeutic targets. Traditional experimental techniques for PPI detection, such as yeast two-hybrid and affinity purification methods, are often expensive, labor-intensive, and prone to inaccuracies. Consequently, computational approaches based on machine learning (ML) and deep learning (DL) have gained significant attention for efficient and scalable PPI prediction. These methods use diverse biological information, including protein sequences, structural features, genomic data, Gene Ontology annotations, and interaction networks, to model complex biological relationships. This survey reviews computational approaches to PPI prediction, highlighting ML- and DL-based techniques, methodological advances, performance evaluation practices, and limitations that affect benchmark comparability. It also discusses biological databases and data sources commonly used in PPI studies and explicitly considers how models trained in coronavirus-centered settings may generalize to other viral families with different mechanisms of host interaction. Full article

Silver nanoparticles (AgNPs) synthesized via fungal-mediated biosynthesis have gained attention as eco-friendly alternatives to chemically produced nanomaterials, with broad biomedical potential. Fungi represent particularly attractive systems because their secretomes contain diverse biomolecules, including enzymes, proteins, polysaccharides, and secondary metabolites, capable of reducing silver ions and stabilizing the resulting nanoparticles. Despite extensive investigation, the molecular mechanisms underlying fungal-mediated AgNP formation remain poorly defined. This review critically examines the key biomolecular drivers involved in this process, with emphasis on nitrate reductases, oxidoreductases, extracellular proteins, polysaccharides, and secondary metabolites as potential reducing and capping agents. Proposed mechanisms, including nitrate reductase-dependent, superoxide-mediated, and metabolite-driven pathways, are evaluated. The influence of process parameters such as silver nitrate concentration, incubation time, culture medium composition, pH, temperature, and fungal species on nanoparticle yield, size, and stability is also assessed. Analysis of the current literature highlights significant knowledge gaps, including limited application of proteomic and metabolomic approaches, a lack of causal mechanistic studies, and insufficient standardization of experimental protocols. Overall, evidence indicates that fungal AgNP biosynthesis is governed by complex interactions among multiple biomolecular classes rather than a single universal mechanism, underscoring priorities for improving reproducibility, scalability, and mechanistic understanding. Full article

Human endogenous retroviruses (HERVs) originate from ancient retroviral integration into the primate germline. Although most are defective proviruses, the most recently endogenized groups, like the HERV-K family, retain intact ORFs encoding retroviral proteins. HERVs usually remain transcriptionally silent, yet this status is reversible. Multiple HIV-HERV interactions, mainly mediated by the HIV Tat protein, lead to HERV transcription and protein production. The present study investigates HERV-K transcription in particular of Human MMTV-like (HML) group-2 and 6 in peripheral blood of people with HIV (PWH). Using different experimental approaches—such as single-cell and plasma transcriptomics-, we found that HERV-K transcripts may be detected during both acute and chronic phases of the infection, with HML-6 showing higher expression compared to HML-2, predominantly within myeloid cells. Effective combined antiretroviral therapy (cART) was able to significantly reduce HML-6 transcription, regardless of whether the treatment was initiated in the acute or late chronic phases of HIV infection. Notably, chronic infections showed higher HML-6 transcript levels compared to acute infections in both naïve and successfully cART-treated subjects, potentially associated with persistent immune dysregulation observed in chronic HIV infection, although a direct causal role of HML-6 expression remains to be established. Full article

This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions. Full article

Accessory proteins of SARS-CoV-2 play crucial roles in viral pathogenesis, yet their structural properties remain elusive. ORF7b, a small accessory protein comprising only 43 amino acids, is widely assumed to parallel the structure–function relationships of its SARS-CoV ortholog based solely on sequence homology. In this study, we challenge this paradigm through direct physicochemical and structural characterization. Sequence analysis and electrostatic profiling reveal that the SARS-CoV-2 protein is a macromolecular polyanion with a net charge of −4 at neutral pH, featuring a diffuse negative surface that is highly responsive to pH changes. Complete 3D structures generated via ab initio modeling display a helical core flanked by two highly fluctuating, disordered termini. Residue Interaction Network (RIN) topology and Normal Mode Analysis (NMA) identified specific hinges governing these flexible extremities. Furthermore, the calculated dipole moment vector is tilted outward by 24°, misaligning with the central axis. Molecular dynamics simulations suggest that while the soluble structure is highly stable in water, it undergoes severe distortions and insufficient solvation within a membrane-mimetic environment. Thermodynamic association profiles and verified interactomic data from BioGRID reveal a strong propensity for ORF7b to participate in liquid–liquid phase transitions alongside human and viral partners. Taken together, these unique properties suggest that ORF7b operates as a dynamic peripheral membrane protein rather than a sedentary transmembrane component, providing a fresh framework for future therapeutic targeting. Overall, these in silico findings shift the current paradigm on ORF7b2 topology and provide a robust, physically grounded framework that identifies specific molecular priorities for future in vitro and in vivo validation. Full article