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Keywords = drug–protein interaction

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24 pages, 5754 KB  
Article
Phloretin Modulates STING Ubiquitination Degradation to Restrain Dendritic Cell Overactivation and Alleviate Sjögren’s Syndrome
by Tianle Zhan, Haoran Chen, Jian Yao and Chuangqi Yu
Pharmaceuticals 2026, 19(9), 1398; https://doi.org/10.3390/ph19091398 - 4 Sep 2026
Abstract
Background/Objectives: Sjögren’s Syndrome (SS) is an autoimmune disorder with impaired exocrine gland function. Its pathogenesis remains elusive, but aberrant innate/adaptive immunity and dysregulated interferon signaling are core features. Current SS research lacks exploration of innate immune mechanisms and therapeutic targets. Phloretin, a [...] Read more.
Background/Objectives: Sjögren’s Syndrome (SS) is an autoimmune disorder with impaired exocrine gland function. Its pathogenesis remains elusive, but aberrant innate/adaptive immunity and dysregulated interferon signaling are core features. Current SS research lacks exploration of innate immune mechanisms and therapeutic targets. Phloretin, a natural dihydrochalcone derivative, inhibits excessive innate immune activation, yet its role and mechanism in SS remain unreported. Methods: This study aimed to explore the therapeutic efficacy of phloretin against Sjögren’s syndrome (SS) and elucidate the regulatory mechanism underlying its effects on dendritic cells (DCs) and the Stimulator of Interferon Genes (STING)-driven innate immune cascade. Clinical specimens were utilized to analyze DC infiltration and STING expression in the labial glands of SS patients. In vivo experiments were conducted on NOD/Ltj SS mice with phloretin treatment, using hydroxychloroquine as a positive control. For in vitro studies, DCs were stimulated with poly I:C to verify the functional effects of phloretin and its regulatory role in the STING/TANK-binding kinase 1 (TBK1)/Interferon Regulatory Factor 3 (IRF3) signaling. Salivary secretion, glandular inflammatory responses, and systemic immune overactivation were evaluated in SS mice. In poly I:C-stimulated DCs, cell activation, migration, and co-stimulatory molecule expression were measured. The regulatory effects of phloretin on the STING signaling cascade and STING ubiquitin-mediated degradation were examined by Western blotting. Phloretin, initially identified as a candidate compound via virtual screening, was subjected to thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) and molecular dynamics simulation (MD) for direct binding verification with STING. The STING overexpression rescue experiment further corroborates that phloretin modulates innate immune responses in a STING-dependent manner. Results: Clinical results revealed obvious infiltration of CD11c+STING+ DCs and CD11c+p-TBK1+ DCs in labial gland lesions of SS patients. In NOD/Ltj SS mice, phloretin treatment recovered salivary secretion, relieved glandular inflammatory injury, and restrained excessive activation of innate and adaptive immune responses, showing comparable therapeutic effects compared with hydroxychloroquine. In vitro experiments confirmed that phloretin could alleviate poly I:C-induced abnormal activation and migration of DCs, as well as reduce the expression of co-stimulatory molecules. Mechanistically, phloretin was found to interfere with the STING signaling cascade, alter the ubiquitination level of STING protein, and further inhibit the abnormal activation of DCs, which may contribute to its protective effects against Sjögren’s syndrome. Notably, results from MD, CETSA and DARTS collectively validate the interaction between phloretin and STING protein, providing solid molecular-level evidence for its regulatory effect on STING signaling transduction. Conclusions: DCs and STING-driven innate immunity critically contribute to SS progression. Phloretin effectively ameliorates SS-related immune disorders by restraining DC overactivation and STING signaling, supporting it as a promising candidate agent for SS treatment. Full article
(This article belongs to the Section Pharmacology)
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21 pages, 6332 KB  
Article
Drug Design Studio (DDS) 2.0: A Unified Platform for Network Pharmacology Integrated with Docking and Virtual Screening Workflow for Covalent/Non-Covalent Binders
by Mahmoud E. Soliman
Int. J. Mol. Sci. 2026, 27(17), 7874; https://doi.org/10.3390/ijms27177874 - 3 Sep 2026
Abstract
Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist “one drug, one target” view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains [...] Read more.
Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist “one drug, one target” view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains fragmented and technically demanding: researchers must query several independent databases, install and reconcile multiple standalone tools for target collection, network construction, hub-gene ranking and pathway enrichment, and then manually bridge the results into structure-based follow-up such as molecular docking. This fragmentation is a persistent barrier, particularly for experimental and non-specialist users. Here, we present the network-pharmacology module of Drug Design Studio (DDS) 2.0, a unified, user-friendly platform that streamlines the entire workflow—disease target retrieval, compound–target prediction, shared-target identification, protein–protein interaction (PPI) network construction, hub-gene ranking and Gene Ontology/pathway enrichment—within a single guided interface, consolidating steps that otherwise require several separate tools. Crucially, DDS 2.0 links the resulting hub genes directly to the docking and virtual-screening engine introduced in the previous DDS releases: representative experimental structures and mutant forms—for instance, resistance-conferring variants found in drug-resistant strains—of the target proteins are selected and streamed into a docking-ready workspace, with dedicated support for covalent binders. We validate the module against four independent published network-pharmacology studies spanning diverse diseases; DDS reproduces the reported hub genes with a mean recovery (recall) of 0.85 (range 0.80–0.90) and a mean Jaccard index of 0.74, and recovers the corresponding target sets and enriched pathways. DDS 2.0 thus delivers an integrated route from systems-level analysis to structure-based drug design. DDS 2.0 is freely and publicly accessible. Comprehensive user documentation is built directly into DDS and can be accessed at any time from the Documentation panel. Full article
(This article belongs to the Section Molecular Informatics)
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15 pages, 1923 KB  
Article
Integrative Identification of Candidate Protein Targets and Compounds for Dystonia Using Mendelian Randomization, Single-Cell RNA Sequencing, and Network Pharmacology
by Lin Chen, Ming-Juan Fang, Nan Cheng and Yin Xu
Genes 2026, 17(9), 1067; https://doi.org/10.3390/genes17091067 - 3 Sep 2026
Abstract
Background: Dystonia is a severe neurological disorder with enigmatic pathogenesis. Current treatment options are limited in preventing the disease progression, underscoring the urgent need for new targeted therapeutic agents to develop more effective therapies. Methods: We performed a proteome-wide Mendelian randomization (MR) study [...] Read more.
Background: Dystonia is a severe neurological disorder with enigmatic pathogenesis. Current treatment options are limited in preventing the disease progression, underscoring the urgent need for new targeted therapeutic agents to develop more effective therapies. Methods: We performed a proteome-wide Mendelian randomization (MR) study and sensitivity analyses to evaluate the causal relationships between dystonia and proteins. GO and KEGG enrichment analysis of dystonia-associated proteins was conducted. Then, we built PPI network and identified the expression of hub-genes in specific brain neurons in single-cell sequencing data. Additionally, we performed drug enrichment analysis of hub-genes, and employed network pharmacology and molecular docking methods to identify potential drugs for dystonia. Results: Our study identified genetically predicted associations consistent with a potential causal effect between 51 proteins and risk of dystonia. GO and KEGG enrichment analyses revealed that these proteins are involved cellular response to transforming growth factor-β stimulation and cytokine-cytokine receptor interaction. Notably, the PPI network exhibited 21 community relationships within the regulatory network among the 51 dystonia-associated proteins identified. The single-cell RNA annotations for brain cluster specificity revealed Tumor necrosis factor (TNF) was highly expressed in microglia cells. Drug enrichment analysis identified five traditional Chinese medicine monomers (paeoniflorin, artesunate, ginsenoside Rh1, psoralen, and quercetin dihydrate) as candidates for molecular docking analysis. Among these, paeoniflorin-TNF, quercetin dihydrate-TNF, and artesunate-TNF exhibited the highest binding energy (−9.1 kcal/mol). Conclusions: Our molecular-docking analysis suggested that traditional Chinese medicine monomers including paeoniflorin, quercetin dihydrate, and artesunate may serve as promising candidates for future drug development. Full article
(This article belongs to the Section Neurogenomics)
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30 pages, 49030 KB  
Article
Cytotoxic, Drug-Interaction, and Apoptosis-Associated Effects of β-Boswellic Acid and Doxorubicin in Murine 4T1 TNBC-like Cells
by Zahide Küçük, Mehmet Cudi Tuncer and Şamil Öztürk
Biomedicines 2026, 14(9), 1978; https://doi.org/10.3390/biomedicines14091978 - 2 Sep 2026
Abstract
Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited targeted therapeutic options. Although the anticancer and pro-apoptotic properties of boswellic acids have previously been reported, the interaction profile of chemically defined β-boswellic acid (BA) with doxorubicin (DOX) remains insufficiently [...] Read more.
Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited targeted therapeutic options. Although the anticancer and pro-apoptotic properties of boswellic acids have previously been reported, the interaction profile of chemically defined β-boswellic acid (BA) with doxorubicin (DOX) remains insufficiently characterised in the murine 4T1 TNBC-like model. This study quantitatively evaluated BA–DOX drug interactions using different reference models and characterised the cytotoxic and apoptosis-associated cellular phenotype accompanying combined exposure. Methods: Cytotoxicity was assessed using the MTT assay and BA–DOX interactions were evaluated using the Chou–Talalay combination index (CI), highest single-agent (HSA) and Bliss independence models. Apoptosis and cell-cycle distribution were analysed by flow cytometry and mitochondrial membrane potential was assessed by JC-1 staining. Caspase-3/7 activity, RT-qPCR, live/dead Calcein-AM/PI staining, 4′,6-Diamidino-2-phenylindole (DAPI) nuclear staining, and cytokine measurements were also performed. Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and STRING-based protein–protein interaction (PPI) analyses were used to explore putative molecular pathways associated with experimental findings. Results: The 48 h selectivity index of BA was 1.28, indicating only modest differential cytotoxicity between 4T1 cells and HaCaT keratinocytes under the experimental conditions rather than definitive cancer-cell selectivity. Drug-interaction analyses revealed concentration- and model-dependent effects, with the Chou–Talalay analysis indicating synergism in selected intermediate and higher concentration pairs. Under the selected phenotypic-characterisation condition, BA + DOX produced a greater apoptotic response than either single treatment, accompanied by increased G2/M and Sub-G1 fractions, mitochondrial membrane depolarisation, and increased caspase-3/7 activity. This treatment condition was not included in the drug-interaction analysis and was therefore not interpreted as a pharmacologically validated synergistic combination. RT-qPCR demonstrated increased mRNA expression of Bax, Casp3, and Casp9, decreased mRNA expression of Bcl2, and a marked increase in the Bax/Bcl2 mRNA ratio. Calcein-AM/PI and DAPI analyses further demonstrated increased cell death and apoptotic nuclear alterations. The measured concentrations of TNF-α and IL-6 in culture supernatants were lower after BA + DOX treatment, whereas IL-10 remained unchanged; however, these cytokine measurements were not normalised to viable cell number and therefore require cautious interpretation. Exploratory bioinformatic analyses identified predicted associations with apoptosis-, mitochondrial-, and cell-cycle-related processes and pathways; however, these database-derived findings were considered hypothesis-generating and not evidence of BA-dependent target engagement or pathway activation. Conclusions: Combined BA and DOX exposure produced greater cytotoxic and apoptosis-associated responses than either single treatment in 4T1 cells, whereas formal drug-interaction classifications varied according to concentration and analytical model. The accompanying changes in mitochondrial membrane potential, caspase-3/7 activity, and apoptosis-related gene expression describe a treatment-associated cellular phenotype but do not identify a direct molecular target of BA or establish a causal molecular mechanism. The findings also do not demonstrate TNBC-specific selectivity. Further studies using additional breast cancer and tissue-matched non-malignant models, together with direct target-engagement and functional pathway-validation approaches, are required. Full article
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39 pages, 21142 KB  
Article
Integrated Metabolic and Immune Molecular Subtyping and a Molecular Classification Score for Revealing Disease Heterogeneity in Pulmonary Arterial Hypertension
by Xin Chen, Yuetong Zhu, Qingping Shi, Jianing He, Siyu Chen and Jieru Han
Metabolites 2026, 16(9), 637; https://doi.org/10.3390/metabo16090637 - 1 Sep 2026
Viewed by 139
Abstract
Objectives: Despite the central role of metabolic–immune crosstalk in pulmonary arterial hypertension (PAH), integrative quantitative tools remain lacking. We aimed to construct and validate a metabolic–immune molecular classification score (MIRS) as a quantitative metric to capture the inflammation–metabolism balance and to assess its [...] Read more.
Objectives: Despite the central role of metabolic–immune crosstalk in pulmonary arterial hypertension (PAH), integrative quantitative tools remain lacking. We aimed to construct and validate a metabolic–immune molecular classification score (MIRS) as a quantitative metric to capture the inflammation–metabolism balance and to assess its discriminatory performance for molecular subtyping, cross-cohort applicability, and biological implications. Methods: We integrated five PAH lung tissue transcriptomic datasets from the Gene Expression Omnibus (GEO). A training set was used to identify differentially expressed genes and to derive MIRS as the first principal component of 20 core genes. MIRS was projected onto independent validation cohorts. Immune microenvironment, pathway activities, protein–protein interaction, and drug repositioning analyses were performed. Results: MIRS significantly distinguished Non-IPAH from IPAH in GSE117261 (AUC = 0.718, p = 0.010) and revealed internal heterogeneity in SSc-PAH. MIRS-related gene expression patterns showed significant differences across COPD and ILD lung tissues in independent datasets. A unified fixed PCA projection pipeline with mean imputation for missing core genes was applied to all pulmonary disease datasets, enabling consistent numerical quantification of MIRS across cohorts under the same mathematical framework. MIRS failed to discriminate PAH from controls in PBMCs, indicating that this tissue-derived signature is not readily detectable in peripheral blood—a limitation that restricts its applicability to lung tissue specimens and highlights challenges for blood-based biomarker development in PAH. Higher MIRS correlated with increased immune scores and myeloid cell infiltration in Non-IPAH. Drug prediction identified sirolimus and tocilizumab as top candidates, with MIRS-stratified sensitivity patterns aligning with pathway loading directions. Conclusions: MIRS is a quantitative, tissue-restricted metric that captures metabolic–immune activation in PAH, with exploratory observations in other pulmonary diseases that warrant further validation. It provides a molecular stratification basis for subtype discrimination and a hypothesis-generating framework for future therapeutic investigations. Full article
(This article belongs to the Section Cell Metabolism)
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23 pages, 21277 KB  
Article
Network Pharmacology and Molecular Dynamics Identify CCL5 and CCR2 Small-Molecule Candidates for Intracanal Treatment of Chronic Apical Periodontitis
by Juan Manuel Guzmán-Flores, Raúl Antonio Briseño-Neri, Fernando Martínez-Esquivias and María del Carmen Leal-Moya
Oral 2026, 6(5), 111; https://doi.org/10.3390/oral6050111 - 1 Sep 2026
Viewed by 114
Abstract
Background/Objectives: Chronic apical periodontitis (CAP) is a persistent periapical inflammatory lesion whose treatment still fails in a substantial fraction of cases, and no molecularly targeted adjunct exists. We aimed to identify druggable hub genes and small-molecule candidates suitable for local intracanal delivery using [...] Read more.
Background/Objectives: Chronic apical periodontitis (CAP) is a persistent periapical inflammatory lesion whose treatment still fails in a substantial fraction of cases, and no molecularly targeted adjunct exists. We aimed to identify druggable hub genes and small-molecule candidates suitable for local intracanal delivery using an integrative computational pipeline. Methods: CAP-associated genes were retrieved from GeneCards and the Open Targets Platform. A protein–protein interaction network, MCODE modules, and three CytoHubba centrality algorithms were used to define hub genes. DrugClip virtual screening and ADMET filtering calibrated for intracanal safety selected candidates, which were assessed by molecular docking with AutoDock Vina, 100 ns molecular dynamics simulations, and per-snapshot binding free-energy analysis. Results: Retrieval yielded 110 non-redundant genes; inflammation was the most enriched process. Eighteen hub genes emerged, with CCL5 and CCR2 among the most central. Screening prioritized MCULE-9834903214 for CCL5 and MCULE-9117306970 for CCR2. The CCR2 complex remained stably engaged, whereas the CCL5 complex was only metastable. Per-snapshot binding free energies over 35–100 ns overlapped in central tendency (−30.5 ± 35.4 vs. −21.6 ± 66.7 kJ·mol−1 for CCR2 and CCL5) but separated by dispersion, with the CCR2 energy trace being nearly twofold tighter. Conclusions: Neither docking affinity nor the mean binding free energy distinguished the leads; the consistency of the binding-energy trace did. MCULE-9117306970 is the priority candidate for experimental validation as a locally delivered anti-inflammatory adjunct against CCR2; MCULE-9834903214 requires redesign to achieve a stable polar anchor. This pipeline yields experimentally testable hypotheses rather than validated therapeutics. Full article
(This article belongs to the Special Issue Artificial Intelligence in Oral Medicine: Advancements and Challenges)
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55 pages, 5312 KB  
Review
Harnessing Medicinal Plants Through Advanced Drug Delivery: A New Era in Type 2 Diabetes Management
by Abhishek Dadhich, Vikas Sharma, Shivika Sharma, Sweta Bawari and Iyyakkannu Sivanesan
Pharmaceutics 2026, 18(9), 1100; https://doi.org/10.3390/pharmaceutics18091100 - 1 Sep 2026
Viewed by 207
Abstract
Type 2 diabetes mellitus (T2DM) remains a global health crisis, with nearly 589 million adults currently affected and projections pointing toward 853 million by 2050. Despite an expanding pharmacological armamentarium, a significant proportion of patients fail to achieve adequate glycaemic control, and the [...] Read more.
Type 2 diabetes mellitus (T2DM) remains a global health crisis, with nearly 589 million adults currently affected and projections pointing toward 853 million by 2050. Despite an expanding pharmacological armamentarium, a significant proportion of patients fail to achieve adequate glycaemic control, and the limitations of existing therapies, including adverse effects, cost, and limited accessibility, underscore the compelling need for novel therapeutic approaches. Phytochemicals such as curcumin, berberine, quercetin, resveratrol, and epigallocatechin gallate possess well-documented antidiabetic activity, operating through the PI3K/Akt, AMPK (activated protein kinase), NF-κB/JNK (nuclear factor kappa-B), and GLP-1R (glucagon-like peptide-1) signalling axes to improve insulin sensitivity, suppress gluconeogenesis, protect pancreatic beta-cells, and attenuate chronic metabolic inflammation. However, their clinical utility has been fundamentally constrained by poor oral bioavailability arising from low aqueous solubility, gastrointestinal instability, extensive first-pass metabolism, and P-glycoprotein-mediated efflux. Advanced drug delivery systems, including liposomes, solid lipid nanoparticles (SLN), nanostructured lipid carriers, PLGA (Poly (lactic-co-glycolic acid)) and chitosan nanoparticles, nanoemulsions, self-nanoemulsifying drug delivery systems, and phytosomes have demonstrated the capacity to overcome these barriers, achieving five- to ten-fold improvements in systemic bioavailability and substantially enhanced antidiabetic efficacy in preclinical models. Emerging mechanistic evidence further positions gut microbiota modulation and epigenetic reprogramming as additional therapeutic axes through which nano-encapsulated phytochemicals may exert durable metabolic benefits. Nonetheless, critical translational challenges persist, encompassing nanotoxicological risks, herb–drug interactions, the absence of harmonised regulatory frameworks for nano-phytomedicine products, phytochemical raw material variability, and formidable technical and economic barriers to scalable nanoparticle manufacturing. This review synthesises the current mechanistic, formulation, and clinical evidence within a unified analytical framework and identifies the strategic priorities of rigorous clinical development, regulatory clarity, and manufacturing standardisation required to translate nano-phytomedicine science into evidence-based T2DM therapeutics. Full article
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28 pages, 9399 KB  
Article
Computational Repurposing of Janus Kinase Inhibitors as Potential Therapeutic Candidates for Alzheimer’s Disease
by Ly Thi Huong Nguyen, Mai Thi Nguyen and Thai Uy Nguyen
Medicina 2026, 62(9), 1674; https://doi.org/10.3390/medicina62091674 - 31 Aug 2026
Viewed by 182
Abstract
Background and Objectives: Alzheimer’s disease (AD) is the most common neurodegenerative disorder, and current therapies provide only limited symptomatic relief without effectively slowing its progression. Increasing evidence suggests that aberrant activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling [...] Read more.
Background and Objectives: Alzheimer’s disease (AD) is the most common neurodegenerative disorder, and current therapies provide only limited symptomatic relief without effectively slowing its progression. Increasing evidence suggests that aberrant activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling cascade contributes to AD-associated neuroinflammation. This study investigated the therapeutic potential and molecular mechanisms of JAK inhibitors in AD using integrated bioinformatics and network pharmacology approaches. Materials and Methods: Potential anti-AD targets of JAK inhibitors were identified using the SwissTargetPrediction and GeneCards databases. Functional enrichment, protein–protein interaction (PPI) analysis, transcriptomic validation using public datasets, regulatory network construction, molecular docking, normal mode analysis (NMA), and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction were performed to investigate the potential mechanisms of action of these drugs in AD. Results: Our analysis identified 163 shared targets between JAK inhibitors and AD. Enrichment analysis revealed that these genes were primarily involved in protein phosphorylation and were enriched in key signaling pathways, including the neurotrophin, phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), and mitogen-activated protein kinase (MAPK) signaling pathways. PPI analysis identified AKT1, BCL2, SRC, STAT3, and TNF as five highly ranked hub targets across multiple topological algorithms. Transcriptomic validation confirmed significantly higher expression of these targets in the prefrontal cortex of individuals with AD compared with normal subjects. Molecular docking indicated that pacritinib and momelotinib showed relatively favorable predicted interactions with the hub proteins, while NMA revealed differences in the predicted flexibility of the docked complexes. Furthermore, ADMET prediction showed that pacritinib possesses favorable pharmacokinetic properties for the treatment of AD. Conclusions: Collectively, these findings provide mechanistic insights into the potential effects of JAK inhibitors in AD and identify pacritinib as a computationally prioritized candidate that warrants experimental validation in appropriate AD models. However, as this study is based solely on computational analyses without wet-lab validation, the findings should be considered hypothesis-generating in silico evidence, and the potential safety concerns of pacritinib require further investigation. Full article
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12 pages, 269 KB  
Article
Effect of Oral Supplementation of Kratom (Mitragyna speciosa Korth.) on Gastrointestinal Nematodes and Serum Lipid Peroxidation in Crossbred Saanen Goats
by Sopon Veerapan, Supawit Triwutanon and Theera Rukkwamsuk
Vet. Sci. 2026, 13(9), 893; https://doi.org/10.3390/vetsci13090893 - 31 Aug 2026
Viewed by 109
Abstract
The objective of this study was to compare fecal egg count (FEC) and serum malondialdehyde (MDA) concentration in naturally parasite-infected goats following administration of an anthelmintic drug and Mitragyna speciosa Korth. as the control and treatment groups, respectively. A total of 34 female [...] Read more.
The objective of this study was to compare fecal egg count (FEC) and serum malondialdehyde (MDA) concentration in naturally parasite-infected goats following administration of an anthelmintic drug and Mitragyna speciosa Korth. as the control and treatment groups, respectively. A total of 34 female goats were randomly allocated into two groups. The control group received albendazole at a dose of 15 mg/kg on the first day of the experiment. Then followed by a daily placebo until day 21. The treatment group was orally administered 5 g/head of dried Mitragyna speciosa Korth. daily for 21 days. Hematological parameters were evaluated on days 0 and 21, while blood biochemical parameters, including blood urea nitrogen (BUN), creatinine, aspartate aminotransferase (AST), and gamma-glutamyl transferase (GGT), were measured on day 0 and at 7-day intervals until day 35. Fecal egg count and serum MDA concentration were determined on day 0 and every 7 days until day 42. The results showed that plasma protein levels were significantly affected by time (p < 0.05) and group (p < 0.05), while red blood cell count was significantly influenced by time (p < 0.05). No significant group effects were observed for BUN, creatinine, AST, and GGT. However, AST showed a significant effect over time (p < 0.05). Hematological and blood biochemical parameters remained within physiological ranges in both groups, with no evidence of kratom-associated toxicity. Log2-transformed fecal egg counts per gram of feces (Log2-EPG) showed significant time and time × group interaction effects (p < 0.001 and p = 0.008, respectively). Fecal egg count reduction test (FECRT) showed significant time and time × group interaction effects (p = 0.009 and p = 0.013, respectively). Serum MDA was significantly lower in the kratom group only at day 7 (p < 0.05). In conclusion, Mitragyna speciosa Korth. supplementation did not significantly reduce fecal egg count compared to conventional anthelmintic treatment but demonstrated a transient effect on oxidative stress, as indicated by changes in serum MDA concentration. Full article
16 pages, 4745 KB  
Article
Annexin A5 Maintains Mitochondrial Integrity by Inhibiting mPTP Opening to Protect Against Acetaminophen-Induced Acute Liver Injury
by Xiaowen Zhang, Wenwei Li, Luqi Li, Ying Wang, Wei Tang, Jing Zhang and Zichun Hua
Int. J. Mol. Sci. 2026, 27(17), 7771; https://doi.org/10.3390/ijms27177771 - 30 Aug 2026
Viewed by 129
Abstract
Acetaminophen (APAP) represents a major cause of drug-induced liver injury (DILI), and effective pharmacological interventions remain limited. Annexin A5 (AnxA5), a Ca2+-dependent phospholipid-binding protein, participates in diverse biological processes related to tissue repair. In this study, we evaluated AnxA5 expression in [...] Read more.
Acetaminophen (APAP) represents a major cause of drug-induced liver injury (DILI), and effective pharmacological interventions remain limited. Annexin A5 (AnxA5), a Ca2+-dependent phospholipid-binding protein, participates in diverse biological processes related to tissue repair. In this study, we evaluated AnxA5 expression in APAP-challenged mouse livers and clinical samples from patients with liver injury. Using hepatic cell lines AML12 and HepG2, we performed overexpression-based functional assays to assess the cytoprotective effects of AnxA5 against APAP toxicity. Co-immunoprecipitation assays were applied to characterize protein interactions, and mitochondrial functional parameters were measured to dissect the underlying molecular mechanism. We found that AnxA5 was significantly upregulated in both APAP exposed mice and APAP DILI patients. Cellular functional assays showed that AnxA5 overexpression mitigated APAP triggered cytotoxicity in AML12 and HepG2 cells. Mechanistically, AnxA5 bound to voltage dependent anion channel 1 (VDAC1), restrained VDAC1 mediated mitochondrial Ca2+ influx, and suppressed VDAC1 oligomerization, which further inhibited mitochondrial permeability transition pore (mPTP) opening. In an APAP-induced liver injury mouse model, exogenous recombinant AnxA5 treatment maintained mitochondrial integrity and ameliorated hepatic inflammation and liver damage. Collectively, our data reveal AnxA5 as an endogenous mitochondrial protective factor and support its therapeutic potential against APAP-induced liver injury. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 22216 KB  
Article
A Novel Cell-Based High-Throughput Screening Model for Inhibitors Targeting Influenza Virus Hemagglutinin–α-2,6-Sialic Acid Interaction
by Keyu Guo, Xiaofang Chen, Chenyin Wang, Yaru Liu, Chao Liu, Yexiang Wu, Xiuyong Fan, Yanni Xu, Shuyi Si, Yongxin Zhang and Jing Zhang
Biomolecules 2026, 16(9), 1253; https://doi.org/10.3390/biom16091253 - 29 Aug 2026
Viewed by 268
Abstract
Rising drug resistance undermines current anti-influenza virus therapies. Although targeting the hemagglutinin (HA)–sialic acid receptor interaction is a promising strategy, progress is impeded by the lack of subtype-independent screening models. Herein, we established a fluorescence-based cell high-throughput model using fluorescein isothiocyanate-conjugated Sambucus Nigra [...] Read more.
Rising drug resistance undermines current anti-influenza virus therapies. Although targeting the hemagglutinin (HA)–sialic acid receptor interaction is a promising strategy, progress is impeded by the lack of subtype-independent screening models. Herein, we established a fluorescence-based cell high-throughput model using fluorescein isothiocyanate-conjugated Sambucus Nigra Lectin (FITC-SNA) as a stable HA surrogate and α-2,6-sialyltransferase (ST6GAL1)-overexpressing MDCK cells to mimic the HA–receptor interface. This platform was designed to serve as an efficient primary screening tool to rapidly filter large compound libraries for potential binders to the receptor-binding interface. Screening 10,000 compounds identified Obatoclax Mesylate and Ethylparaben as primary hits. Both exhibited broad-spectrum HA inhibition activity, validating the model’s capability to identify compounds interfering with viral attachment. Further cellular antiviral assays revealed cytotoxicity for both compounds, resulting in low selectivity indexes (SIs), indicating that while these molecules effectively target the interaction site, they require substantial structural optimization for therapeutic use. Molecular docking confirmed their binding to type A H1N1, H3N2, and B/Victoria HA proteins, while ADMET predictions highlighted specific structural optimization needs to mitigate toxicity. In conclusion, this subtype-independent, highly specific high-throughput screening (HTS) model provides an efficient and reliable platform for early-stage influenza drug discovery and lead compound development. Full article
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21 pages, 18293 KB  
Article
Resnet-Driven In Silico Identification of Lead Peptides from the Venom Gland Transcriptome of Orientothele washanensis Coupled with Molecular Docking and Dynamics Simulation
by Xin Zeng, Wen-Feng Du, Wen-Hao Yin, Jun-Yao Zhu, Yu-Bin Yang, Wei-Jun Guo, Wen-Liang Li, Hao Gong, Zi-Zhong Yang and Yi Li
Pharmaceuticals 2026, 19(9), 1368; https://doi.org/10.3390/ph19091368 - 29 Aug 2026
Viewed by 223
Abstract
Background: Orientothele washanensis is a venomous spider with considerable ecological and scientific importance. Its venom, characterized by complex composition and ease of collection, serves as a valuable resource for the discovery of natural peptide drugs. Conventional wet-lab screening methods are limited by [...] Read more.
Background: Orientothele washanensis is a venomous spider with considerable ecological and scientific importance. Its venom, characterized by complex composition and ease of collection, serves as a valuable resource for the discovery of natural peptide drugs. Conventional wet-lab screening methods are limited by rigorous experimental conditions, high resource consumption, and long research cycles, which hinder the efficient identification of functional peptides from the venom gland transcriptome of this spider. Methods: To address these technical bottlenecks, this study developed a novel deep learning model named PepPI-DRN for peptide-protein interaction prediction. The model integrated a residual equivariant graph neural network, a residual 1-dimensional convolutional neural network, and a dual-modal attention mechanism by leveraging both sequence and structural features of peptides and proteins. Results: Results on an independent test set indicated that PepPI-DRN achieved the competitive or superior performance compared with state-of-the-art methods on multiple key evaluation metrics. Candidate peptides with high interaction probabilities against targets were obtained from the venom gland transcriptome of Orientothele washanensis. Furthermore, lead peptides with high binding strength and good structural stability were identified from candidate peptides by molecular docking, and molecular dynamics simulation. Conclusions: These results showed that the pipeline with PepPI-DRN, molecular docking and molecular dynamics simulation enabled efficient and reliable identification of lead peptides from the venom gland transcriptome of Orientothele washanensis, providing a robust and effective strategy for the discovery and development of natural peptide drugs from the spider venom. Full article
(This article belongs to the Section Natural Products)
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23 pages, 22403 KB  
Article
PPE57 Cooperates with MmpL3 to Mediate Bacterial Lipid Transport and Promote Persistent Infection of Mycobacterium tuberculosis
by Shufeng Weng, Qingchun Li, Yamin Zhao, Taiyue Lin, Zihan Wang, Mingrui Zhu, Miaochengyue Xin and Ying Xu
Microorganisms 2026, 14(9), 1912; https://doi.org/10.3390/microorganisms14091912 - 28 Aug 2026
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Abstract
Mycobacterium tuberculosis (M. tb) possesses a unique, lipid-rich cell envelope that is critical for virulence, drug resistance, and persistence. Here, we identify the PPE family protein PPE57 as a key regulator of mycolic acid transport and host lipid exploitation. PPE57 physically [...] Read more.
Mycobacterium tuberculosis (M. tb) possesses a unique, lipid-rich cell envelope that is critical for virulence, drug resistance, and persistence. Here, we identify the PPE family protein PPE57 as a key regulator of mycolic acid transport and host lipid exploitation. PPE57 physically interacts with the essential lipid transporter MmpL3, promoting trehalose monomycolate (TMM) translocation, enhancing trehalose dimycolate (TDM) synthesis, and increasing cell wall lipid content. Site-directed mutagenesis identified G175 as a critical residue for PPE57-MmpL3 binding. Deletion of PPE57 reduces cell wall thickness, alters lipid composition, and impairs biofilm formation. Mechanistically, PPE57 facilitates bacterial cholesterol acquisition, and during infection, activates the host PPAR-γ pathway in macrophages, leading to enhanced cholesterol uptake, lipid droplet accumulation, and increased intracellular triglyceride and cholesteryl ester levels. These changes provide a nutrient-rich niche that promotes bacterial survival and persistence. In a mouse model of infection, PPE57 deficiency results in reduced bacterial burden, milder lung pathology, and diminished lipid droplet-positive cell accumulation in lung tissues. These findings establish PPE57 as an essential accessory component of the MmpL3 lipid transport system, bridging mycobacterial cell wall assembly with host nutrient exploitation during persistent infection. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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26 pages, 77286 KB  
Article
Computational Identification of New Dual PAK4 and NAMPT Inhibitors
by Yiling Wang and Audrey Minden
Int. J. Mol. Sci. 2026, 27(17), 7706; https://doi.org/10.3390/ijms27177706 - 28 Aug 2026
Viewed by 225
Abstract
Dual inhibition of p21-activated kinase 4 (PAK4) and nicotinamide phosphoribosyltransferase (NAMPT) has emerged as a promising therapeutic strategy due to its ability to simultaneously target oncogenic signaling and cellular metabolism in cancer. While existing inhibitors such as KPT9274 and PF-3758309 have demonstrated preclinical [...] Read more.
Dual inhibition of p21-activated kinase 4 (PAK4) and nicotinamide phosphoribosyltransferase (NAMPT) has emerged as a promising therapeutic strategy due to its ability to simultaneously target oncogenic signaling and cellular metabolism in cancer. While existing inhibitors such as KPT9274 and PF-3758309 have demonstrated preclinical activity, their clinical translation has been limited by poor selectivity, suboptimal efficacy, and dose-limiting toxicities. Reliance on a small number of available compounds is therefore insufficient, highlighting the need for systematic optimization to identify candidates with improved therapeutic profiles. Although several dual PAK4 and NAMPT inhibitors such as GNE2861, LCH7749944, and PF3758309 have been identified in our previous study, the number of compounds available is limited. Identification of new candidate compounds would allow researchers to identify those that are the most efficient, those that are the most potent and selective, and those that have optimal pharmacokinetics. In this study, we performed additional large-scale drug screening to identify new candidate dual PAK4 and NAMPT inhibitors and expand the diversity of this inhibitor class. Computational molecular docking was used to evaluate binding affinities toward both targets, followed by drug–protein interaction analyses to assess binding stability and interaction patterns at the molecular level. Several new candidate compounds demonstrated favorable predicted binding to both PAK4 and NAMPT, with distinct interaction profiles compared to previously reported inhibitors. Biochemical assays further demonstrated inhibitory activity against both PAK4 and NAMPT among several selected compounds, supporting their potential as dual-target inhibitors. These findings provide mechanistic insight into dual-target engagement and highlight structural features associated with improved binding behavior. Expanding the pool of dual inhibitors enhances opportunities for preclinical development, supports optimization of pharmacokinetic and safety profiles, and strengthens datasets for drug discovery. Collectively, this work broadens the landscape of dual PAK4 and NAMPT inhibitors and supports their potential application across multiple cancer types beyond triple-negative breast cancer. Full article
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28 pages, 1862 KB  
Review
Food Effects, Pharmacokinetic Drug–Drug Interactions, and Clinical Optimization of Oral Anticancer Agents
by Abdullah A. Assiri
Pharmaceutics 2026, 18(9), 1082; https://doi.org/10.3390/pharmaceutics18091082 - 28 Aug 2026
Viewed by 326
Abstract
Oral targeted therapies now constitute a substantial and growing proportion of anticancer drug therapy, shifting administration from the controlled intravenous setting to patient-managed oral therapy in the outpatient setting, where systemic exposure depends on factors that parenteral therapy largely bypasses. Food effects, gastric [...] Read more.
Oral targeted therapies now constitute a substantial and growing proportion of anticancer drug therapy, shifting administration from the controlled intravenous setting to patient-managed oral therapy in the outpatient setting, where systemic exposure depends on factors that parenteral therapy largely bypasses. Food effects, gastric pH, first-pass metabolism, transporter activity, organ function, concomitant medications and adherence contribute to variability in exposure, and many oral anticancer agents have narrow therapeutic indices in which modest exposure changes carry clinical consequence. This review synthesizes the pharmacokinetic determinants of oral anticancer drug exposure across twenty-seven exemplar agents spanning the main mechanistic classes and translates them into actionable pharmacy practice. Its contribution is a cross-class agent-level comparison in which within-class divergences are made explicit, the integration of determinants usually reviewed separately, and an explicit statement of the evidence level behind every entry. We examine food effects, the interaction between acid-suppressive therapy and pH-dependent agents, the dominant role of cytochrome P450 3A4 and of the efflux transporters P-glycoprotein and breast cancer resistance protein, and the exposure–response relationships that motivate therapeutic drug monitoring, for which the evidence remains uneven and does not yet support routine use. We propose a structured framework for operationalizing these principles in daily practice. Full article
(This article belongs to the Special Issue Pharmacokinetics of Orally Administered Drugs, 3rd Edition)
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