Search Results (3,434)

Background: Multidrug efflux proteins, frequently overexpressed in cancer cells, reduce intracellular drug accumulation and limit chemotherapeutic efficacy. Short drug-binding peptides containing the WXXW motif have been shown to non-covalently bind multidrug resistance (MDR)-associated drugs, potentially masking structural features recognized by efflux transporters. We hypothesized that incorporating this motif into a membrane-active peptide would generate a hybrid analogue capable of reversible drug binding and enhanced cellular uptake. Methods: A melittin-derived peptide (M3) was rationally designed by introducing the WXXW motif into the flexible region adjacent to the conserved proline kink to generate a dual-functional peptide with membrane activity and reversible drug binding. Membrane activity was evaluated using liposome leakage assays, and drug-binding interactions with doxorubicin were characterized using fluorescence quenching and microscale thermophoresis (MST). Molecular dynamics simulations were performed to elucidate binding mechanisms, and functional effects were assessed using calcein AM efflux assays, confocal imaging, and cytotoxicity studies across cancer cell lines. Results: M3 retained membrane activity and exhibited moderate, reversible binding to doxorubicin, with simulations showing binding initiation at the WXXW motif and extension to tryptophan residues W12, W15, and W19, forming a multivalent aromatic interface that suggested shielding of key drug functionalities. Functionally, M3 enhanced intracellular calcein retention and increased doxorubicin accumulation, and combination treatment produced synergistic cytotoxicity in the multidrug-resistant H69AR cell line with reduced toxicity toward normal epithelial cells. Conclusions: M3 acts as a membrane-active, reversible drug-binding peptide that enhances intracellular drug accumulation, supporting its potential as a modular strategy to overcome efflux-mediated MDR. Full article

Nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H₂S) were once regarded solely as toxic environmental gases. However, accumulating evidence over the past several decades has established them as the three principal endogenous gasotransmitters that regulate a wide spectrum of physiological and pathological processes. Unlike conventional signaling molecules, gasotransmitters diffuse freely across biological membranes and exert potent biological effects through receptor-independent mechanisms, including redox-sensitive post-translational modifications and modulation of heme-containing proteins. Although the individual functions of NO, CO, and H₂S have been extensively reviewed, emerging studies indicate that these gaseous mediators rarely operate in isolation. Instead, they form a highly integrated signaling network characterized by direct chemical interactions, reciprocal enzymatic regulation, and convergence upon common downstream pathways. In this mini-review, we propose the concept of a “Gasotransmitter Trio Network,” emphasizing the molecular crosstalk among NO, CO, and H₂S as a fundamental determinant of cellular homeostasis. We first summarize the biosynthetic pathways and major signaling mechanisms of the gasotransmitter trio, including S-nitrosylation, persulfidation, and heme-dependent regulation. We then discuss recent advances revealing how interactions among these gases generate novel bioactive intermediates and coordinate redox signaling. Particular attention is given to the emerging roles of gasotransmitters in regulating ferroptosis, autophagy, and mitophagy by modulating iron metabolism, lipid peroxidation, mitochondrial quality control, and antioxidant defense systems. These findings support a unified framework in which gasotransmitters function as master regulators of cellular fate under conditions of physiological and pathological stress. Finally, we highlight recent progress in stimuli-responsive donors, CO-releasing molecules (CORMs), NO-releasing materials (NORMs), H₂S donors, and advanced nanoplatforms that enable spatiotemporally controlled gas delivery. We propose that future therapeutic strategies will increasingly rely on programmable multi-gas systems that recapitulate endogenous gasotransmitter networks. Collectively, this review provides a systems-level perspective on gasotransmitter biology and outlines emerging opportunities for the development of precision gas medicine in cardiovascular, neurodegenerative, inflammatory, metabolic, and malignant diseases. Full article

Background/Objectives: Metabolic dysfunction-associated alcoholic liver disease (MetALD) is a serious worldwide health concern, exhibiting metabolic dysfunction-associated lipid accumulation, alcohol-associated oxidative damage, and endotoxin-induced inflammation. Rb1-enriched red ginseng saponin fraction (RGSF) has been known to exhibit anti-inflammatory and anti-oxidative properties, but its role in MetALD remains to be fully elucidated. This study aims to investigate the specific mechanism of RGSF in the MetALD mouse model. Methods: The MetALD mouse model was administered with or without Rb1-RGSF for 7 weeks. Histopathological and molecular analyses, along with primary cell isolation, were conducted for in vivo and ex vivo investigations. M1 macrophage polarization was assessed by analyzing pro-inflammatory cytokine expression. NF-kB/p65 and TLR4 protein expression were measured before being visualized using immunofluorescence assays and confocal microscopy. Results: Histopathological examination revealed that RGSF treatment markedly reduced hepatic steatosis and attenuated inflammatory lesions in MetALD independent of oxidative stress. Notably, RGSF administration suppressed the LPS-induced internalization of surface TLR4. During the early inflammatory phase, RGSF prevented the LPS-mediated loss of the 130 kDa TLR4 form at the cell membrane, thereby limiting the generation of its 110 kDa cytoplasmic form. LPS-binding assay confirmed the direct interactions between TLR4 and RGSF. Conclusions: Collectively, these findings demonstrate that RGSF regulates TLR4 expression and trafficking, leading to the suppression of M1 macrophage polarization by inhibiting LPS–TLR4 surface interactions, thus exhibiting hepatoprotective effects. Full article

B-cell receptor (BCR) is indispensable for B-cell responses, and its signaling relies on the rearrangement of cytoskeletal proteins. Cytoskeletal protein 4.1R has been previously implicated in the regulation of immune function. However, the specific role of 4.1R in BCR-mediated B-cell activation remains unknown. Here, we performed single-cell RNA (scRNA) sequencing on splenic B cells isolated from wild-type (WT) and 4.1R-knockout (4.1R-KO) mice to systematically characterize the functional contribution of 4.1R to B-cell biology. Transcriptomic analyses suggested a critical role for 4.1R in modulating BCR signaling. Ex vivo stimulation of primary B cells with anti-IgM demonstrated that 4.1R-KO B cells exhibited marked overactivation, hyperproliferation, and enhanced antibody secretion. Furthermore, unbiased phosphoproteomic profiling, identified sustained AKT1 phosphorylation as a key feature in 4.1R-KO B cells. Subsequent functional validation confirmed that 4.1R regulates BCR signaling by constraining AKT1 activation. Mechanistically, 4.1R rapidly colocalized with the coreceptor CD19 at the plasma membrane upon BCR engagement, and co-immunoprecipitation confirmed their physical interaction. Loss of 4.1R disrupted this interaction and resulted in sustained and amplified AKT1 phosphorylation (but not AKT2) in stimulated B cells. Collectively, our findings identify 4.1R as a novel negative regulator of BCR signaling that interacts with CD19 to constrain AKT1 activation. Full article

Bovine viral diarrhea virus (BVDV) infection is associated with inflammatory responses, but the mechanisms underlying inflammasome activation remain unclear. In this study, Madin–Darby bovine kidney (MDBK) cells were used to compare the inflammatory responses induced by the cytopathogenic NADL strain and the non-cytopathogenic TC strain. Both strains significantly increased IL-1β and IL-18 production and promoted NLRP3 inflammasome assembly, indicating activation of upstream inflammasome signaling. However, only the NADL strain markedly induced Gasdermin D (GSDMD) cleavage, membrane pore formation, lactate dehydrogenase release, and pyroptotic cell death. Further mechanistic analyses demonstrated that the NADL core protein C interacted with the inflammasome adaptor ASC, thereby facilitating NLRP3 inflammasome assembly and enhancing inflammatory cytokine secretion. Silencing ASC significantly impaired inflammasome activation and pyroptosis induced by protein C, confirming its essential role in this process. Collectively, these findings demonstrate that the cytopathogenic BVDV NADL strain activates ASC-dependent NLRP3 inflammasome signaling and GSDMD-mediated pyroptosis through its core protein C, providing a molecular explanation for the distinct inflammatory responses and pathogenic outcomes associated with different BVDV biotypes. Full article

Macrophage membrane-coated nanoparticles (MMNPs) are an emerging class of biomimetic nanoplatforms that combine the immune-regulatory functions of macrophages with the structural versatility of synthetic nanoparticles (NPs). By retaining key membrane proteins and receptors, MMNPs exhibit natural targeting capabilities, immune interactions, and inflammatory site homing, making them promising tools for immunomodulation and targeted therapy. This review summarizes macrophage biology relevant to immune regulation and discusses how nanoparticle core properties, including size, surface charge, composition, and mechanical characteristics, influence membrane coating efficiency, stability, and biological performance. Current fabrication and characterization strategies for MMNPs are also discussed. Particular emphasis is placed on the therapeutic applications of MMNPs in inflammatory disorders, tissue regeneration, and oral and dental implant-related applications. Recent studies demonstrate that MMNPs can modulate macrophage polarization, sequester pro-inflammatory cytokines, remodel the immune microenvironment, and promote tissue repair and bone regeneration, highlighting their potential to improve implant integration and reduce inflammation-associated implant failure. Despite these promising advances, challenges remain regarding large-scale manufacturing, membrane preservation, reproducibility, and long-term biosafety. Continued interdisciplinary research in nanotechnology, immunology, and biomaterials engineering is expected to accelerate the clinical translation of MMNPs for regenerative and immunomodulatory therapies. Full article

Objectives: Malaria remains a major global health burden, particularly in endemic regions such as Djibouti, where Plasmodium falciparum and Plasmodium vivax co-circulate, complicating disease control strategies. Increasing resistance to current antimalarial drugs reduces treatment effectiveness and highlights the urgent need for new, safe, and affordable therapeutic agents. This study aimed to identify potential inhibitors from Djiboutian medicinal plants using an integrated in silico approach targeting key proteins from both parasite species. Methods: A library of 222 phytoconstituents was screened against Plasmodium vivax FK506-binding protein 35 (PDB ID: 3IHZ) and Plasmodium vivax dihydrofolate reductase–thymidylate synthase (PDB ID: 1J3K) using molecular docking. Top-ranked compounds were further analyzed for binding interactions and evaluated for drug-likeness and pharmacokinetic properties using QikProp in Maestro v11.5. Selected protein–ligand complexes were subjected to 100 ns molecular dynamics simulations, and their stability was assessed using multiple descriptors, including structural deviation, flexibility, compactness, solvent exposure, and hydrogen bond persistence. Results: Several phytoconstituents exhibited strong binding affinities, with docking scores ranging from −6.09 to −7.54 kcal/mol, outperforming the reference drug artemisinin. Interaction analysis revealed key hydrogen bonds and hydrophobic contacts with essential active-site residues. ADMET predictions indicated favorable pharmacokinetic profiles, including high oral absorption, good membrane permeability, and low predicted toxicity. Molecular dynamics simulations demonstrated stable behavior for most complexes, with compound 121 showing enhanced stability in the 1J3K system and compound 123 exhibiting consistent dynamic stability in the 3IHZ system. In contrast, compound 82 displayed greater structural fluctuations despite maintaining stable hydrogen bond interactions. Conclusions: The integration of molecular docking, ADMET prediction, and molecular dynamics simulations identified compounds 121 and 123 as the most promising antimalarial candidates, exhibiting an optimal balance of binding affinity, favorable pharmacokinetic properties, and dynamic stability. These findings highlight the potential of Djiboutian medicinal plants as a valuable source of novel antimalarial agents and provide a strong computational foundation for future experimental validation. Full article

Background: Brazilian wasp venoms represent a clinically relevant yet underexplored source of bioactive molecules with important implications for allergy, toxicology, and neuropharmacology. This review discusses the biological and immunological activities of venoms from Neotropical wasp species prevalent in Brazil, particularly within the genera Polybia, Synoeca, Polistes, and Agelaia, with emphasis on venom composition, IgE-mediated hypersensitivity, and ion-channel modulation. Methods: A narrative literature review was conducted using studies focused on venom characterization, electrophysiological effects, immune responses, and clinical manifestations associated with Brazilian and other Hymenoptera species. Results: Brazilian wasp venoms contain a diverse repertoire of peptides, enzymes, and low-molecular-weight compounds that act synergistically on multiple cellular targets. Among these, mastoparan-like peptides exhibit antimicrobial, immunomodulatory, and membrane-disruptive activities, contributing to inflammation and cellular dysfunction. In addition, several venom components interact with ion channels and neuronal receptors, modulating neuronal excitability and synaptic signaling, which highlights their potential applications in neuropharmacology. Simultaneously, allergenic proteins can induce IgE sensitization and immediate hypersensitivity reactions ranging from localized manifestations to systemic anaphylaxis. The marked taxonomic and biochemical diversity of Brazilian wasps contributes to substantial variability in venom composition and clinical outcomes. Conclusions: Overall, these venoms constitute a valuable and still insufficiently explored source of biologically active compounds with potential applications in allergy diagnosis, venom immunotherapy, and drug development. Full article

This research evaluated the biocontrol potential of the bacterial flora from cured sugarcane bagasse (SCB) against Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato Fusarium wilt. Screenings of twenty SCB-derived isolates revealed consistent antagonistic activity, inhibiting mycelial growth from 32.08% to 55.00%. The most effective isolate, 100MTN1, was identified via 16S rRNA sequencing (GenBank: PX506225) as Bacillus atrophaeus. Interaction between B. atrophaeus 100MTN1 and Fol FOLViF has revealed a distinct profile of bioactive metabolites produced specifically during co-cultivation. Transcriptomic profiling of Fol FOLViF exposure to 100MTN1 identified 189 differentially expressed genes, with downregulation of genes involved in DNA replication, translation, and membrane transport, and upregulation of those linked to secondary metabolism and oxidative stress. KEGG pathway mapping further supported the possible causes of disruptions within the pathogen. Molecular docking suggested that the B. atrophaeus 100MTN1 derived metabolite, 6-Hydroxy-3′-methoxyflavone and exhibits binding affinity for key Fol proteins that compares favorably with the commercial fungicides. Greenhouse trials using tomato cv. Kalyan confirmed that treatment with strain 100MTN1 was associated with reduced disease severity and enhanced plant growth. These findings suggest that B. atrophaeus 100MTN1 suppresses Fol FOLViF through a combination of metabolite-driven inhibition and transcriptional interference, signifying its potential as a biological control agent for managing Fusarium wilt. 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

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

Sickle cell disease (SCD) is an autosomal recessive hemoglobin disorder that is mainly characterized by the presence of hemoglobin S (HbS; point mutation [Glu6Val] in the beta-globin gene). Under deoxygenated conditions, HbS polymerizes and serves as the primary trigger of oxidative stress in red blood cells (RBCs), promoting polymerization of Band 3, a major membrane scaffold protein that links the lipid bilayer to the spectrin–ankyrin cytoskeletal network. Phosphorylation at key residues within the cytosolic domain of Band 3 induces conformational changes that weaken ankyrin binding and enhance lateral mobility and clustering of Band 3. These effects are mediated through a coordinated network of erythrocyte tyrosine kinases, primarily spleen tyrosine kinase (SYK) and sarcoma (Src) family kinases, which act sequentially to modify distinct tyrosine residues. Structural features of these kinases, including tandem SH2 domains in SYK and conserved SH2–SH3–kinase domain architecture of Src family members, enable precise recognition of phosphotyrosine motifs and propagation of phosphorylation cascades. Sequence alignment and structural superimposition of SH2 domains across studied kinases demonstrate a highly conserved fold that is critical for phosphotyrosine recognition, suggesting potential overlap in substrate engagement. Therapeutically, targeting these kinases has shown considerable promise, as tyrosine kinase inhibitors (TKIs) reduce Band 3 phosphorylation, restore RBC deformability, and decrease hemolysis and vaso-occlusive interactions in vitro. Thus, in this narrative review, we focus on the regulation of Band 3 by the above-mentioned tyrosine kinases, as well as the therapeutic potential of TKIs in SCD. Full article

Carbohydrate-active enzymes (CAZymes) encoded by the human gut microbiome are central mediators of dietary glycan metabolism and host–microbe biochemical homeostasis. Among these, β-glucuronidases represent functionally pivotal hydrolases implicated in metabolism, intestinal physiology, and therapeutic modulation. The present study performs an integrative in silico structural and functional interrogation of β-glucuronidases derived from Acidobacterium capsulatum (3VNY), Bacteroides ovatus (6D8K), and Faecalibacterium prausnitzii (6ED2). An integrated computational framework encompassing physicochemical parameters profiling, hierarchical structural prediction, tertiary-structure validation, salt-bridge energetics, functional domain and motif annotation, protein–protein interaction reconstruction, ligand-binding thermodynamics via molecular docking, and residue-resolved non-covalent interaction network mapping using the Protein Contacts Atlas (PCA) was employed. Physicochemical analyses indicated that all enzymes are thermostable, intracellular, and hydrophilic, while secondary-structure organization revealed a functional balance between helix-mediated rigidity and coil-driven flexibility. Structural validation metrics identified 6ED2 as the most conformationally stable architecture, whereas 6D8K displayed enhanced functional complexity, including enriched motif composition, membrane-associated features, and superior ligand-binding affinity. Docking simulations highlighted castanospermine and calcium saccharate as the most favorable interacting ligands across enzyme variants. Importantly, PCA-based interaction analysis revealed distinct ligand-centered atomic contact networks, with immediate contact counts of 57 (3VNY), 32 (6D8K), and 41 (6ED2), providing residue-level insight into stabilization mechanisms and interaction topology beyond conventional docking metrics. Collectively, these findings establish a multidimensional computational framework linking structural stability, functional diversification, ligand recognition, and atomic interaction networks in gut microbial β-glucuronidases, thereby supporting future biochemical validation, microbiome-targeted therapeutics, and biotechnological or cosmeceutical applications. Full article

Crayfish with cyan soft-carapace and red hard-carapace differ considerably in market value. To investigate the causes underlying this difference in shell color, we selected 120 healthy Procambarus clarkii of similar size (9–10 cm), equally divided by shell color and sex. Muscle quality, pigment deposition, and DGAT2 mRNA expression were compared between the two shell-color types. The results showed that: (1) Muscle hardness was significantly higher in red hard-carapace crayfish than in cyan soft-carapace crayfish (p < 0.05), whereas no significant difference in muscle elasticity was observed among groups (p > 0.05). (2) A significant interaction between shell color and sex influenced crude fat and ash content (p < 0.05). Crude fat content was higher in red hard-carapace crayfish, and ash content was highest in male red hard-carapace crayfish, significantly exceeding that in male cyan soft-carapace crayfish (p < 0.05). (3) Moisture and crude protein content were not significantly affected by the interaction between shell color and sex (p > 0.05), with no notable differences across groups. (4) The contents of astaxanthin, lutein, and β-carotene in the shell were significantly influenced by the interaction between sex and shell color (p < 0.05). Astaxanthin was lowest in female cyan soft-carapace crayfish, and lutein was highest in male red hard-carapace crayfish, and β-carotene showed no significant differences. (5) DGAT2 mRNA expression was highest in hepatic tissue across all groups (p < 0.05). In gonads, expression was higher in ovaries of cyan soft-carapace crayfish and in testes of red hard-carapace crayfish (p < 0.05). (6) DGAT2 mRNA expression in the inner membrane, muscle, and intestine was significantly affected by the interaction between shell color and sex (p < 0.05), with specific expression patterns varying among tissues and groups. These findings indicate that shell color and sex interact to influence nutritional composition, carotenoid profile, and gene expression, providing insights into the mechanisms of body color formation and its physiological correlates. Full article

Small open reading frames (sORFs) encode micropeptides, which are a promising yet largely untapped resource for creating peptide design templates. Owing to their concise nature and functional efficiency, micropeptides often rely on essential structural elements and brief linear motifs, such as domains for membrane interaction, targeting sequences, and sites for protein–protein interactions, to fulfill their biological functions. This inherent simplicity makes them particularly suitable for a bottom-up design approach aimed at identifying, extracting, and systematically refining functional motifs to develop novel bioactive peptides. This review addresses the critical question of how micropeptides, particularly those involved in tumor regulation, can be explored as emerging therapeutic targets, functional templates for peptide design, and potential future therapeutic agents, by synthesizing current understanding of their mechanisms, functional significance in cancer, and the computational and design strategies for their clinical translation. We examined the current methods for analyzing the sequence and structural characteristics that underpin their functional activity and investigated how these attributes can be leveraged for drug discovery and design. Finally, we underscore the primary challenges and future prospects in converting sORF-encoded micropeptides into clinically relevant molecules with the aim of broadening the current scope of the druggable proteome. Full article