Search Results (466)

West Nile virus (WNV) is a mosquito-borne pathogen of escalating epidemiological importance and a growing global health concern, driven by the climate-associated expansion of its Culex mosquito vectors. Although WNV is an extensively studied flavivirus, most host–pathogen interaction studies focus on static and structural aspects rather than dynamic and functional ones. Delineating phosphorylation-mediated interactions between WNV proteins and human kinases bridges a critical gap by providing important insight into the molecular mechanisms underlying infection. In this study, we investigated potential phosphorylation-mediated interactions between WNV proteins and human kinases using an integrative computational framework combining motif prediction, phosphoproteomic data analysis and structural docking. Key interactions were predicted between viral proteins and regulatory kinases within the AKT-ERK pathway and the AMPK-mediated autophagy, including major network kinases such as RAF1, IKBKB, and ULK1. In addition, experimentally validated phosphorylation sites in viral proteins were found to be associated with multiple candidate host kinases, including MAP2K7 and MAP2K9, suggesting complex regulatory networks. Integration with phosphoproteomic datasets supported the relevance of multiple predicted kinases, including those associated with antiviral responses and translational regulation. Protein–protein docking demonstrated stable, energetically favorable interactions between selected host kinases and viral proteins, particularly the viral polymerase (NS5), helicase (NS3), and NS1. The findings of this study establish a framework for future research on the development of host-directed antiviral strategies. Full article

The herpes simplex virus 1 (HSV-1) US3 is a multifunctional serine/threonine kinase that promotes HSV-1 replication and spread. But its role and the mechanisms by which US3 regulates actin cytoskeletal remodeling remain poorly defined. We combined flow cytometry, confocal microscopy, immunoprecipitation-mass spectrometry (IP-MS), protein complex mapping, and machine learning to characterize US3-mediated F-actin dynamics. Flow cytometry and confocal microscopy showed that wild-type HSV-1 induces significant F-actin remodeling, while the ΔUS3 mutant displays F-actin levels comparable to uninfected cells, identifying US3 as a key regulator. IP-MS identified 47 high-confidence US3 interactors enriched in conserved actin regulatory complexes, including Arp2/3 nucleation machinery, formin-associated assemblies, cofilin severing complexes, and Rho-family GTPase modules. Mapping interactors to the CORUM database revealed clustering within actin nucleation, polymerization, and severing complexes, indicating that US3 operates through organized cellular machines. Machine-learning classifiers trained on label-independent mass-spectrometry features were used to prioritize interactors resembling known actin regulators; under protein-group-aware cross-validation, logistic regression performed best (average precision 0.24; ROC-AUC 0.66), and the analysis was interpreted as prioritization rather than de novo discovery. Pharmacological inhibition of Arp2/3 and formin pathways significantly attenuated US3-dependent F-actin remodeling, supporting the functional involvement of these pathways. Together, these findings are consistent with an inferred hierarchical axis in which US3 modulates Rho GTPase signaling and cofilin activation to promote F-actin disassembly, coordinating cytoskeletal remodeling required for efficient viral egress and spread. Full article

Ebola virus disease (EVD) is characterized by immune dysregulation and damaging hyperinflammation. We aimed to characterize the signaling pathways and regulatory mechanisms dysregulated during EVD. To avoid hyperinflammation, innate immune signaling is regulated by post-translational modifications (PTMs), including protein phosphorylation. Here, we show that the protein tyrosine phosphatase nonreceptor type 13 (PTPN13) negatively regulates Interferon (IFN)-β while also positively regulating the neutrophil chemoattractant CXCL1. Using vectors encoding IRF3 with mutations on phosphorylation sites, we identified Y292 on IRF3 as a PTPN13 target of dephosphorylation. Knockout of PTPN13 increased IRF3 phosphorylation and expression of IFNβ and IFN-stimulated genes (ISGs) following poly(I:C) stimulation. Intriguingly, depletion of PTPN13 during Ebola virus (EBOV) infection resulted in decreased IFNβ and ISG induction at later time points post-infection, which correlated with increased viral titers. We identified PTPN13-mediated dephosphorylation of the viral protein VP35 as one potential mechanism inhibiting virus replication. Additionally, the induction of inflammatory chemokines, including CXCL1, decreased in PTPN13 knockout cells late during EBOV infection. These effects could be explained by increased phosphorylation of the regulatory p85 subunit of PI3K. Dephosphorylation of p85 promotes its degradation, subsequently enhancing PI3K kinase activity and downstream signaling via AKT. Together, our study suggests that PTPN13 is involved in immune regulation and efficient antiviral responses by dephosphorylation of IRF3, EBOV-VP35 and PI3K-p85. Full article

Ostreid herpesvirus 1 (OsHV-1) is a major pathogen associated with summer mortality in bivalve mollusks, but the host-side determinants of susceptibility remain poorly characterized outside oysters. In this study, we compared the responses of Chinese (CS) and Korean (KS) populations of the ark clam Scapharca broughtonii to experimental OsHV-1 challenge. The results showed that OsHV-1 established a markedly strong infection in the CS population but not the KS population, as indicated by high viral DNA loads, severe tissue pathology, detection of viral particles by transmission electron microscopy, broad viral transcription, and substantially high mortality. To explore the molecular basis of this contrasting outcome, we further performed comparative transcriptomic and proteomic analyses. Transcriptomic analysis identified two membrane-associated genes, atrial natriuretic peptide receptor A (NPR-A) and tyrosine-protein kinase receptor (TYRO3-like), that were more highly expressed in the susceptible CS population, suggesting that early host–virus interaction may differ between populations as a result of differentially expressed membrane molecules. Proteomic analysis identified 94 differentially abundant proteins between CS and KS populations; notably, ferritin and superoxide dismutase (SOD) were highly expressed in the less susceptible KS population, leading to stronger basal antioxidant and stress-defense capacity. Taken together, these findings definitively confirmed the significant differential susceptibility to OsHV-1 infection between the two S. broughtonii geographic populations and revealed that this divergent phenotype might involve both population-biased expression of candidate membrane-associated factors and differences in defense-related protein abundance. This study provides candidate markers for future disease-resistance evaluation and breeding in ark clam and offers a basis for further investigation of population-level variation in bivalve–virus interactions. Full article

Virus infection requires coordinated activation of pathogen-sensing, innate immune, and cellular stress response pathways to mount an effective antiviral defense. Recognition of nucleic acid pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs) initiates signaling cascades that drive the production of type I interferons (IFNs) and proinflammatory cytokines. These responses are often accompanied by the activation of integrated stress response pathways that help optimize host defense. Cytosolic double-stranded dsDNA, generated during viral infection or released from damaged mitochondria, is sensed by cyclic GMP-AMP synthase (cGAS), which generates 2′3′-cGAMP to activate stimulator of interferon genes (STING). Activated STING translocates from the endoplasmic reticulum to the Golgi, where it drives TBK1-dependent IFN and cytokine production. Previous reports show that cGAS activity is enhanced by Ras-GAP SH3 domain binding protein 1 (G3BP1), a key nucleator of stress granules (SGs), independent of its role in SG assembly. Here, we identify a non-canonical role of G3BP1 as a regulator of DNA sensing responses at multiple levels, including STING intracellular trafficking, in addition to potentiating cGAS activity. Loss of G3BP1 impaired STING-dependent IFN and cytokine responses to HSV-1 infection and viral DNA. G3BP1-deficient cells showed reduced cGAMP-induced STING translocation to the Golgi, induction of type I IFN and proinflammatory cytokines, and activation of the ER stress kinase PERK and stress granule formation. Together, these findings demonstrate G3BP1-STING as a node linking DNA sensing, innate immunity, and stress signaling with broad implications for antiviral defense and diseases characterized by aberrant DNA sensing and stress responses, including neurodegeneration, fibrosis, and autoimmunity. Full article

Recently, there has been great interest in AI-based approaches for de novo design of novel drug candidates. However, the generation of useful lead drug candidate compounds requires more than predicting engagement with the desired protein target. Candidate molecules must also be anchored in the real world of medicinal chemistry for their synthesis and modification as well as satisfying multiple drug development-related criteria. Here, we present Nevermore, an AI target-conditioned, database-grounded workflow for prioritizing candidate ligands from large compound libraries. Nevermore uses a geometry-aware protein–ligand affinity oracle to score target-specific binding and perform sparse integer edits in count-based Morgan fingerprint space. Nevermore then retrieves the most structurally similar molecules from public chemical databases. This design enables multi-objective search over predicted affinity and absorption, distribution, metabolism, excretion, and toxicity (ADMET) proxies while keeping all candidates anchored to valid database compounds. We evaluated Nevermore’s performance across three biologically distinct targets: Menin, a protein-interaction target relevant to leukemia; SARS-CoV-2 M^pro, a viral cysteine protease relevant to antiviral discovery; and epidermal growth factor receptor (EGFR), a kinase-superfamily oncology target with extensive experimentally tested compounds. Nevermore retrieved candidate sets with favorable predicted affinity–property trade-offs. These results support database-grounded fingerprint steering as a practical computational strategy for lead prioritization and for generating testable molecular hypotheses, although the prioritized candidates remain predictions, requiring follow-up experimental validation. Full article

Dengue is an arboviral disease of global significance caused by Orthoflavivirus denguei (DENV), which has four antigenically distinct serotypes. The envelope (E) protein plays a critical role in viral entry and eliciting immune responses. This study aimed to compare the biochemical and immunological properties of the E protein across the four DENV serotypes using in silico approaches. E protein reference sequences were retrieved from RefSeq and analyzed with various bioinformatics tools. Sequence alignment revealed identities ranging from 63.08% to 77.69%. Biochemical analysis showed minimal variation in molecular weight and isoelectric point; however, the net charge of DENV-3 E protein was notably lower. Secondary structure predictions indicated a predominance of alpha-helices in DENVs-1/2, while DENVs-3/4 featured more beta-sheets. Post-translational modification analysis revealed mostly casein kinase II phosphorylation sites across all serotypes, with DENV-4 uniquely presenting also tyrosine kinase sites. Amino acids W231/D341 in DENV-1, Q86 in DENVs-2/4, and D87/D339 in DENV-3 showed maximum antigenicity scores in B cell recognition, while the human leukocyte antigen (HLA) alleles B*08:01/B*39:01 and DRB4*01:01, recognized by T cells, presented the highest number of predicted epitopes for the different DENV serotypes. Conservation analysis showed that the major antigenic regions highlighted in this study are highly conserved among contemporary DENV isolates despite the genetic variability observed within each serotype. These findings suggest that subtle structural differences in the E protein may contribute to distinct immunogenic profiles, highlighting candidate regions for future investigation. Full article

Extensive efforts have been undertaken by numerous researchers to control respiratory viruses across the domains of diagnosis, prevention, and treatment. In this study, we developed a niclosamide–polysaccharide nasal spray (NPNS) formulation based on xanthan gum (XG), a naturally derived polysaccharide, and niclosamide, a conventional anthelmintic agent. We then evaluated its therapeutic efficacy following intranasal administration under influenza virus-infected conditions. NPNS was assessed for cytotoxicity under Good Laboratory Practice (GLP) conditions in accordance with ISO 10993-5, and no cytotoxic effects were observed. In influenza virus-infected human nasal epithelial cells (HNEc), NPNS treatment resulted in at least 92.5% suppression of viral gene expression. Furthermore, NPNS demonstrated significantly greater antiviral activity compared to Placebo 1 and Placebo 2, which were formulated by excluding niclosamide and XG, respectively. Owing to the physicochemical properties conferred by XG, NPNS exhibited prolonged retention on the nasal mucosa in a mouse model. Consistently, NPNS showed potent antiviral efficacy in influenza-infected mice. In addition, NPNS treatment was associated with the downregulation of S-phase kinase-associated protein 2 (SKP2), a host factor known to facilitate intracellular viral replication. Collectively, these findings suggest that NPNS may serve as a first-line protective barrier during the early stage of influenza infection by simultaneously blocking viral entry and suppressing viral replication through its dual physicochemical and molecular mechanisms. Full article

The liver circadian clock coordinates hepatic lipid metabolism, bile acid synthesis, and glucose homeostasis through interlocking transcription–translation feedback loops. Disruption of this temporal organization is increasingly recognized as a shared pathological feature across the chronic liver disease spectrum. Transcriptomic profiling alone cannot capture the full scope of circadian dysregulation. Approximately half of rhythmically abundant hepatic proteins lack correspondingly rhythmic mRNAs. Roughly 25% of hepatic phosphosites oscillate with a 24-h period. Integrating transcriptomics, proteomics, post-translational modification profiling, metabolomics, and emerging single-cell and spatial approaches is therefore necessary for an accurate account of how circadian programs are remodeled in disease. This narrative review delineates the multi-omics landscape of circadian clock dysregulation across six chronic liver disease categories. These encompass metabolic dysfunction-associated fatty liver disease (MAFLD), alcoholic liver disease (ALD), viral hepatitis, hepatocellular carcinoma (HCC), liver fibrosis, and cholestatic disease. Four molecular features recur across these contexts. BMAL1 functional downregulation, REV-ERBα oscillatory output attenuation, NAD⁺ oscillatory amplitude reduction, and gut–liver axis circadian desynchronization together constitute an inferential framework for hepatic circadian failure. These features represent recurring disease-associated motifs rather than an established pan-disease mechanism. The upstream mechanisms and evidence depth differ substantially by disease category. Oncogenic kinase-driven CLOCK post-translational modifications in HCC, phosphoproteomic remodeling in MAFLD, and epigenomic clock disruption persisting after HCV clearance represent findings that transcriptomics alone would not resolve. The near-complete absence of temporally resolved human tissue data remains the principal barrier to translational progress. This evidence gap limits the clinical actionability of current mechanistic findings across all disease categories. Circadian phase inference algorithms and prospective temporally designed cohort studies offer a methodologically grounded path toward clinically actionable circadian hepatology. Full article

The Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has evolved sophisticated immune-evasion strategies to establish a productive infection in the host, primarily by counteracting the innate antiviral response. Here, we demonstrate for the first time that the PRRSV non-structural protein NSP8 suppresses NF-κB-dependent antiviral signalling by hijacking the host ubiquitin-conjugating enzyme UBE2K and inducing the degradation of IKKα, a pivotal kinase in the NF-κB pathway. PRRSV infection led to significant upregulation of host UBE2K, which in turn facilitated viral replication. Mechanistically, we found that NSP8 interacts directly with IKKα, triggering its degradation by the proteasome. Furthermore, we revealed that this process was facilitated by the host protein UBE2K, which acted as a crucial cofactor by directly interacting with NSP8 and thereby enhancing its activity against IKKα. This disruption blocked the activation of the NF-κB pathway and suppressed the expression of downstream antiviral factors, such as TNF-α, IL-6 and IFN-β, ultimately facilitating PRRSV replication. All of these findings showed that NSP8 is an important part of the process by which the host NF-κB pathway is blocked by viruses. This is a new way in which PRRSV avoids the immune system. Full article

Feline infectious peritonitis virus (FIPV) remains one of the most challenging viral diseases in veterinary medicine, largely owing to the absence of a consistently effective and safe vaccine. Despite widespread feline coronavirus infection, only a subset of infected cats progresses to feline infectious peritonitis, indicating that host immune responses are key determinants of disease outcomes. Accumulating evidence indicates that disease severity is driven not only by viral replication but also by macrophage- and monocyte-centered immune signaling, leading to excessive inflammation and systemic immunopathology in the host. Previous vaccine approaches against FIPV have failed to provide consistent protection and, in some cases, have been associated with enhanced disease. These outcomes suggest that vaccine-induced immune responses that recapitulate pathogenic signaling patterns may exacerbate disease rather than confer protection. In this review, we discuss the current knowledge of immune cell signaling pathways implicated in FIPV infection, including innate sensing through Toll-like receptors, downstream mitogen-activated protein kinases and NF-κB signaling, cytokine production profiles, Fc receptor-associated processes, and intracellular pathways such as autophagy, and how these mechanisms shape vaccine-induced immunity. By integrating insights from immune signaling kinetics, antibody functionality, adjuvant-driven pathway engagement, and platform-specific immune signatures, this review emphasizes the need to reframe FIPV vaccine development strategies that actively shape host immune responses. Rather than maximizing immunogenicity, successful vaccine design is likely to depend on limiting sustained macrophage activation and pro-inflammatory cytokine amplification while supporting antiviral immune functions, thereby reducing the risk of antibody-dependent enhancement and immunopathology. Beyond feline diseases, these considerations provide broader lessons for vaccine design in settings where immune-mediated pathology contributes to disease severity. Full article

Dengue infection remains a major global health concern, with a subset of patients progressing from self-limited dengue fever to severe disease characterised by plasma leakage, shock, and organ dysfunction. The dengue non-structural protein 1 (NS1), a multifunctional glycoprotein expressed on infected cells and secreted into circulation, has emerged as a key mediator linking viral infection to immune-driven vascular pathology. This review synthesises experimental, animal, and human clinical evidence on NS1-driven immunopathogenesis, focusing on mechanisms leading to endothelial dysfunction and increased vascular permeability. NS1 modulates the complement system in a context-dependent manner, contributing to immune evasion by inhibiting terminal complement complex formation, while also promoting antibody-dependent complement activation associated with severe disease. Additionally, NS1 directly disrupts endothelial barrier integrity through disruption of adherens and tight junction architecture, Ang-2/Tie2 imbalance, activation of RhoA/ROCK (RhoA/Rho-associated coiled-coil-containing protein kinase) signalling, and enzymatic degradation of the endothelial glycocalyx, with further amplification through inflammatory mediators. In addition, evidence shows that NS1 activates innate immune signalling, perturbs platelet biology and haemostasis, and forms pro-inflammatory complexes with lipoproteins. Moreover, anti-NS1 antibodies may be both protective and pathogenic. Collectively, these data position NS1-linked pathways as rational targets for adjunctive therapies and next-generation vaccines aimed at preventing vascular leakage and severe dengue infection. Full article

Background/Objectives: Kaposi’s sarcoma (KS) is an angioproliferative malignancy caused by Kaposi’s sarcoma-associated herpesvirus (KSHV), characterized by aberrant angiogenesis, chronic inflammation, and endothelial cell transformation. Given the multi-factorial nature of KS pathogenesis, strategies that simultaneously modulate multiple mo-lecular targets are considered more promising than single-target approaches. However, effective multi-target therapeutic agents for KS remain limited, prompting this study to employ an integrative in silico pipeline. Methods: An integrative in silico pipeline combining compound screening, target predic-tion, network pharmacology, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Ge-nomes (KEGG) enrichment, protein–protein interaction (PPI) analysis, molecular docking, and molecular dynamics (MD) simulations was employed. Streptomyces-derived metabolites were prioritized based on chemical diversity, annotation, and clinical prece-dent. Predicted targets were intersected with KS-associated genes, with hubs ranked by network topology. Docking and MD simulations evaluated binding affinity and stability. Results: Endostemonine I emerged as the top candidate, engaging nine of ten hub proteins, including EGFR, mTOR, PTGS2, SRC, PARP1, PPARγ, MAPK1, MAPK14, and ICAM1. Key nodes such as mTOR, PTGS2, PPARγ, and MAPK14 are central to KS-related an-gi-ogenesis, inflammation, and viral oncogenesis. GO and KEGG analyses revealed en-richment in kinase activity, cell adhesion, and PI3K–Akt/mTOR and MAPK signaling pathways. Docking indicated strong binding to mTOR, PTGS2, PARP1, PPARγ, and MAPK14, while MD simulations confirmed stable interactions for mTOR, PTGS2, PPARγ, and MAPK14. Conclusions: Collectively, these proteins represent high-confidence, druggable KS targets, with Endostemonine I as a promising multi-target scaffold. These findings highlight the therapeutic potential of Endostemonine I and warrant further validation through future in vitro and in vivo studies. Full article

Background: The coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, remains a significant threat to global health. This continued threat is due to the emergence of new variants, the immune system’s limited ability to respond, and the limited effectiveness of available treatments for all individuals. Therefore, leveraging drug repurposing, a fast and inexpensive way to find other drugs that have already been shown to be safe and efficacious, becomes useful. This study leverages ADMET profiling, network pharmacology, and molecular docking to evaluate the repurposing of Product Nkabinde for COVID-19 treatment. Methods: ADMET analysis involving the bioactive phytochemicals of PN was evaluated for pharmacokinetic appropriateness and drug-likeness. Using topological analysis, a network of protein–protein interactions was built to identify hub genes, and predicted compound targets were intersected with COVID-19-associated genes to find shared targets. Their biological importance was characterized using functional enrichment analysis. The binding affinities of PN phytochemicals against hub proteins and SARS-CoV-2 viral proteases (Mpro and PLpro) were assessed by molecular docking using AutoDock Vina. To confirm docking accuracy, co-crystallized ligands were redocked using Schrodinger 2022-1. The multi-target therapeutic potential of PN in COVID-19 was assessed using this integrative network pharmacology and molecular docking technique. Results: Molecular docking demonstrated that PN phytochemicals displayed robust and persistent binding affinities for both viral and host targets. Oleanolic acid showed the best affinity toward Mpro (−12.9 kcal/mol vs. −8.3 kcal/mol), while quercetin-3-O-β-D-(6′-galloyl)-glucopyranoside showed better binding to PLpro (−8.4 kcal/mol vs. −6.4 kcal/mol). Procyanidin B2 toward HCK (−10.5 vs. −7.9 kcal/mol), diosgenin toward EGFR (−9.4 vs. −8.4 kcal/mol), rutin toward SRC (−10.5 vs. −7.8 kcal/mol), and pimelea factor P2 toward PIK3R1 (−11.0 vs. −8.2 kcal/mol) all showed significantly higher affinities than their corresponding co-crystallized ligands. Furthermore, procyanidin B2 demonstrated consistent binding to STAT1 and STAT3, confirming its role in modulating immune signals. Most of the PN phytochemicals show advantageous pharmacokinetic properties, including elevated anticipated gastrointestinal absorption and adherence to Lipinski’s rule of five, signifying favorable oral bioavailability and drug-like properties. Moreover, PN exhibits a remarkable multi-target binding capacity against both SARS-CoV-2 proteases and key host signaling proteins involved in immune regulation and inflammatory responses, as determined by this integrative network pharmacology and molecular docking investigation. Conclusions: PN’s prospects as a host-directed, antiviral treatment for COVID-19 are demonstrated by its coordinated modulation of the PI3K/AKT, JAK–STAT, SRC-family kinase, EGFR, and SYK pathways. These results necessitate further experimental and clinical validation, providing a solid computational basis for repurposing PN in the treatment of COVID-19. Full article

Zika virus (ZIKV) remains a significant global public health threat due to its association with severe neurological and ocular abnormalities, including microcephaly and congenital glaucoma in infants. Viruses often exploit host metabolic programs, such as energy and lipid metabolism, to support their replication. However, how ZIKV-driven metabolic reprogramming affects the anterior segment of the eye, especially trabecular meshwork (TM) cells, remains poorly defined. In this study, we investigated the roles of AMP-activated protein kinase (AMPK) signaling, fatty acid (FA) metabolism, and lipid droplet (LD) biogenesis in ZIKV-induced ocular pathogenesis using primary human TM cells and an IFNAR1-deficient mouse model. ZIKV infection triggered time-dependent activation of the LKB1-AMPK-ACC signaling axis and significantly increased LD accumulation. Pharmacological activation of AMPK suppressed viral replication, whereas its inhibition enhanced infection, highlighting an antiviral role for AMPK signaling. In contrast, ZIKV promoted LD biogenesis, and inhibition of DGAT1 reduced both LD formation and viral replication, indicating a proviral role for LDs. Modulation of FA metabolism further revealed differential effects on ZIKV infection: saturated FA (palmitate) enhanced viral replication, whereas inhibition of FA oxidation with etomoxir reduced infection. Conversely, unsaturated FAs (oleate and linoleate) suppressed viral replication, in part by impairing viral binding and entry. Collectively, these findings show that ZIKV reshapes host metabolic pathways in TM by differentially engaging AMPK signaling, FA metabolism, and LD biogenesis to promote viral replication and spread in ocular tissue. Targeting these metabolic pathways may offer promising therapeutic avenues for preventing and/or treating ZIKV-associated ocular complications. Full article