Combinatorial Chemistry & High Throughput Screening - Volume 28, Issue 15, 2025

Chemotherapy-induced phlebitis (CIP) is a side product of chemotherapy treatment for malignant tumors, which affects the therapeutic effect and quality of life of cancer patients, and still lacks a clear therapeutic means. In this study, we investigated the therapeutic effects of QLTMP on CIP using network pharmacology and verified the anti-inflammatory mechanism of QLTMP in a mice model induced by vinorelbine.

Network pharmacology analysis was performed to identify bioactive compounds in QLTMP. The protein-protein interaction network was used to identify the core therapeutic targets of QLTMP against CIP, analyze biological function and pathway enrichment based on the identified core therapeutic targets, and evaluate the therapeutic effect of QLTMP in a model of CIP induced by vinorelbine to confirm the reliability of the network pharmacological analysis.

One hundred and sixty-five bioactive compounds of QLTMP matched the screening criteria and identified 19 core therapeutic targets of QLTMP against CIP. Biofunctional analysis showed that the therapeutic effect of QLTMP on CIP was mainly related to the inhibition of inflammation, while pathway enrichment analysis showed that the TNF signaling pathway was involved in the inflammatory process.

Experimental confirmation in a mice model showed that QLTMP exerts anti-inflammatory effects through modulation of the PI3K/AKT/TNF signaling pathway, a discovery consistent with the network pharmacological analysis.

The network pharmacological analysis of the anti-inflammatory mechanism of QLTMP on CIP and its exploration of in vivo experiments provide a theoretical basis for the design of agents that can mitigate or cure CIP.

Renal cell carcinoma is the most common aggressive tumor of the genitourinary system. The main pathological subtype is clear cell renal cell carcinoma (ccRCC), and its treatment options are very limited. Therefore, identifying specific biomarkers of ccRCC is of great significance for diagnosis and prognosis.

First, we obtained transcriptome data and clinical data of 611 patients with renal clear cell carcinoma to analyze the relationship between hypoxia-related lncRNAs and overall survival (OS). We screened hypoxia-related lncRNAs through Pearson correlation and Cox regression analysis. Univariate and multivariate regression analysis were applied to assess survival-related risk factors. According to the median risk score, patients were divided into two groups. Next, a nomogram map was built, and GSEA was used for gene function annotation. RT-qPCR, Western Blot, and Flow Cytometry were used to determine the role of SNHG19 in RCC cells.

By analyzing the co-expression of hypoxia genes and lncRNAs, 310 hypoxia-related genes were obtained. Four sHRlncRs (AC011445.2, PTOV1-AS2, AP004609.3, and SNHG19) with the highest prognostic values were included in the group to construct the HRRS model. The high-risk group had a shorter OS than the low-risk group. HRRS was considered to be an independent prognostic factor and associated with OS. The two groups showed different pathways in GSEA. Experiments showed that SNHG19 plays essential roles in the autophagy and apoptosis of RCC cells.

We constructed and validated a hypoxia-related lncRNA model for ccRCC patients. This study also provides new biomarkers for the poor prognosis of ccRCC patients.

Verbascoside, a compound classified as a phenylethanol glycoside in Dihuang, has been the subject of modern pharmacological investigations. These studies have revealed its noteworthy antioxidant, anti-inflammatory, memory-enhancing, neuroprotective, anti-tumor, and various other pharmacological properties. While verbascoside exhibits favorable antioxidant effects, its precise mechanism of action in ameliorating osteoporosis through the treatment of oxidative stress remains unclear.

This study employed CCK8, ALP, ELISA, and ROS staining techniques to examine the osteoporotic effects of verbascoside on zebrafish and MC3T3-E1 cells. Additionally, this study aimed to investigate the molecular mechanism by which verbascoside improves osteoporosis by mitigating oxidative stress. To identify the common targets of verbascoside in relation to oxidative stress and osteoporosis, network pharmacology and molecular dynamics simulation were employed. The construction of the verbascoside - oxidative stress - osteoporosis - potential target gene network aimed to identify the core targets, while the mechanism of action was elucidated through KEGG analysis, and the accuracy was confirmed by assessing the mRNA expression of the targets.

In vivo experiments demonstrated that verbascoside exhibited therapeutic effects on osteoporosis and reduced ROS production in zebrafish. In vitro experiments further revealed that verbascoside enhanced the proliferation and differentiation of MC3T3-E1 cells, thereby improving the oxidative stress status of osteoblasts. Thirteen core targets and estrogen signaling pathways were identified through the application of network pharmacology. The pivotal role of the estrogen signaling pathway in facilitating the ability of verbascoside to mitigate oxidative stress-induced osteoporosis was substantiated by the modulation of target protein mRNA expression.

The findings underscore the considerable therapeutic potential of verbascoside in ameliorating osteoporosis through the alleviation of oxidative stress, thus establishing it as a promising compound for the treatment of this condition.

This study aimed to investigate the anti-inflammatory effect and mechanism of Sophora alopecuroides L. (KDZ) on lipoteichoic acid (LTA)-induced inflammation in Bovine Mammary Epithelial Cells (BMEC).

The KDZ active ingredient database was established by using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) to detect the chemical components of KDZ and combine it with the TCMSP database. Furthermore, potential targets of KDZ active ingredients were collected through the UniProt database, and mastitis-related targets were screened through the OMIM, Genecard, and DisGeNET databases. Furthermore, common targets were identified between ingredient targets and disease targets, and protein-protein interaction analysis was performed on them using the STRING platform. Furthermore, the protein interaction network was constructed using Cytoscape software. Core targets were screened through network topology analysis. On this basis, GO and KEGG enrichment analyses were performed on the common target, and molecular simulation docking analysis was conducted on the main active ingredients and core targets. Finally, the accuracy of the network analysis results was validated using in vitro cell experiments.

The results of UPLC-QTOF-MS detection and network pharmacology analysis showed that KDZ could intervene in signaling pathways, such as the IL-17 signaling pathway, TNF signaling pathway, MAPK signaling pathway, etc., by acting on 80 common targets through 15 potential active ingredients, thereby regulating biological processes, such as positive regulation of peptidyl serine physiology, apoptotic process, and inflammatory response, to treat mastitis. Besides, molecular simulation docking analysis also showed that the main active ingredients in KDZ, such as quercetin, matrine, calycosin, etc., can form stable bindings with 11 core targets (TNF-α, IL-6, IL-1β, etc.) through hydrogen bonding. Further in vitro validation experiments confirmed that KDZ intervention could inhibit the IL-17 signaling pathway by inhibiting the expression of GSK3β and subsequently inhibiting the production of downstream inflammatory cytokines IL-8, IL-6, IL-1β, and TNF-α, thereby alleviating LTA-induced BMEC inflammatory damage.

KDZ can alleviate LTA-induced BMEC inflammatory damage by inhibiting the IL-17 signaling pathway. This study can provide a scientific basis for the clinical application of KDZ and lay the foundation for the development of new therapeutic drugs for mastitis.

The aim of this study was to elucidate the mechanism of action of Shenbao tablets using metabolomics approach.

Kidney-yang deficiency is a common syndrome type in traditional Chinese Medicine (TCM) syndrome typology, closely related to disorders of multiple metabolic pathways and is the root cause and underlying syndrome type of many diseases. Shenbao tablets can significantly improve the main symptoms of kidney yang deficiency syndrome, but the mechanism of action of Shenbao tablets on kidney yang deficiency syndrome is still unknown.

The rats were intraperitoneally injected with hydrocortisone once a day for 40 days to simulate the syndrome. Traditional pharmacodynamic indicators (body mass, biochemical indicators and pathology) were used to evaluate the efficacy of the medicine. Serum, urine and feces were collected from rats. UPLC/MS metabolomics method was used to study the overall metabolic profile of serum, while GC/MS metabolomics method was used to study the metabolic spectrum of urine and feces.

Results showed that the syndrome was significantly improved in the treatment group, and obvious metabolic disorders were observed in rats with the syndrome, with 47 potential biomarkers identified. Pathway analysis showed that nicotinate and nicotinamide metabolism, glycine, serine and trione metabolism, aminoacyl tRNA biosynthesis, glycoxylate and dicarboxylate metabolism were the major ways for Shenbao tablet to improve kidney-yang deficiency syndrome.

The mechanism of action of Shenbao tablet in improving the syndrome involves the regulation of energy metabolism, amino acid metabolism, bile acid metabolism, fatty acid metabolism and intestinal microorganisms. This work shows that metabolomics is a promising tool for studying the essence of syndrome theory in TCM and the mechanisms of TCM.

Ligusticum striatum DC. (LDC) is often prescribed for Cerebral Ischemia (CI) and is commonly combined with Borneolum (BO) to enhance therapeutic outcomes. However, its specific active ingredients and underlying mechanisms remain unclear.

This study aimed to identify the active ingredients and mechanisms of LDC and BO combination therapy against CI using network pharmacology, molecular docking, and in vivo experiments.

Potential active ingredients and targets were sourced from relevant databases, and a drug-component-target-disease network was constructed to pinpoint key ingredients. Subsequently, a protein-protein interaction analysis was conducted to confirm the key targets. Following enrichment analyses of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), molecular docking was employed to evaluate binding energies. Finally, the therapeutic effects and mechanisms of the combination against CI were validated through in vivo experiments using male ICR mice.

Venn analysis identified a total of 41 components and 292 potential targets. The drug-component-target-disease network revealed that the key components in LDC were palmitic acid, tetramethylpyrazine, and (Z)-ligustilide, while those in BO were (+)-borneol, β-elemene, and (-)-borneol. The PPI analysis highlighted seven crucial targets. Docking results confirmed a stable affinity between these components and their targets. KEGG enrichment analysis indicated that the mechanism involved the PI3K/AKT signaling pathway. Subsequently, in vivo experiments confirmed that the combination ameliorated abnormal hippocampus morphology and reduced the release of inflammatory factors through the activation of the PI3K/AKT signaling pathway.

The combination of LDC and BO markedly improved CI and inhibited inflammation response via activating the PI3K/AKT pathway.

The Precancerous Lesion of Gastric Cancer (PLGC) is an early stage in the development of gastric cancer. The clinical application of HPXLD has been found to be effective in treating PLGC, but the mechanism of how HPXLD acts on PLGC is still unclear.

The objectives of this study were to reveal the molecular mechanism of how HPXLD can be used to treat PLGC and investigate this mechanism through bioinformatics and experimental validation.

PLGC-associated target genes were identified through bioinformatics analysis. A rat model of PLGC was induced using N-methyl-N'-nitro-N-nitrosoquanidine (MNNG) in combination with ranitidine, hot saline, ethanol, and intermittent fasting, with interventions by HPXLD. The pathological alterations in gastric mucosa were assessed through Hematoxylin-eosin staining (HE). Immunohistochemistry (IHC) and Western blot analyses were employed to evaluate the changes in expression levels of inflammation-related proteins.

After conducting bioinformatics analysis, it was found that there were 23 HPXLD-PLGC crossover genes, which were significantly enriched in the IL-17 signaling pathway, TNF signaling pathway, and NF-kappa B signaling pathway. The results of HE showed that HPXLD was effective in improving gastric mucosal histopathological changes. Additionally, the IHC results demonstrated that HPXLD was able to downregulate the expression of IL-6, COX-2, MCP-1, and MMP-9. Furthermore, Western blot analysis revealed that HPXLD was able to downregulate the expressions of IL-6, IL-17RA, ACT1, NF-κB, and TNF-α.

HPXLD has been shown to improve PLGC by reducing the expression of inflammation-related proteins. This suggests that HPXLD may potentially be a treatment option for PLGC.

Rheumatoid Arthritis (RA) is a chronic autoimmune disease with a complex etiology. Siweixizangmaoru Decoction (SXD) has been used to treat RA in Tibet for a long history as a classic Tibetan medicine formula. However, the potential pharmacological mechanism has not been elucidated yet.

The aim of this study was to evaluate the efficacy and mechanism of action of SXD in the treatment of RA using network pharmacology and molecular docking analysis.

Network pharmacology was employed to identify the potential bioactive components and key targets of SXD for the treatment of RA. Molecular docking of key targets and potential compounds was conducted. High-performance liquid chromatography was performed to validate the predicted active components of SXD. We established a rat model of RA and evaluated the histopathology of each group of rats. In addition, the levels of inflammatory factors in serum and the expression levels of PI3K/AKT and MAPK pathway-related proteins in synovial tissue were detected.

The results of network pharmacological analyses indicated that apigenin, rhamnolipids, kaempferol, quercetin, and naringenin are potential bioactive components of SXD for the treatment of rheumatoid arthritis and that their therapeutic effects may be related to the PI3K-Akt and MAPK pathways. The results of in vivo experiments show that SXD improved the arthritis index, significantly reduced joint swelling, and improved synovial inflammation and cartilage destruction.

Network pharmacology, along with experimental validation, provided a useful approach for understanding the pharmacological mechanism of Siweixizangmaoru decoction in RA.

This study aimed to study the inhibitory effect of niraparib alone or in combination with GD2 specific antibody on Bladder Cancer (BCa).

The migration ability of BCa cells was assessed through a scratch assay. CCK-8 assay was performed to evaluate the viability of BCa cells, and Transwell invasion assays were utilized to examine invasive capacity. The expression levels of E-cadherin and vimentin in BCa cells were measured using QRT-PCR.

Western blot showed the EMT level to be the lowest in the niraparib+GD2 group. The transwell invasion assay suggested that the invasion ability of BCa cells was weakened in the niraparib+GD2 group. CCK8 assay indicated that the proliferation ability of BCa cells was decreased. Scratch test suggested that the migration ability of BCa cells was weakened. PCR result showed that the niraparib + GD2 group had the most significant inhibitory effect on mRNA expression of EMT markers.

Niraparib combined with a GD2-specific antibody exerted a more prominent inhibitory effect on BCa.

This study aimed to identify marine-derived protease inhibitors with potential applications in immunogenicity-targeted therapies.

Starting with a pharmacophore model based on the GRL-09510 complex (PDB ID: 5v4y), we isolated three critical features (RAA) that facilitated the selection of 192 candidates from an initial pool of 18,547 compounds.

Subsequent docking analyses, validated with a strong ROC value of 0.74, revealed four high-affinity compounds: Echoside C (CMNPD22461), Anguibactin (CMNPD3610), Hansforester K (CMNPD30598), and Polyandocarpamide A (CMNPD4564), with binding scores of -7.773, -7.770, -7.690, and -7.236 kcal/mol, respectively—each exceeding the reference compound's binding efficacy. Further assessments of drug-likeness (ADME) and toxicity profiles produced favorable results and predicted biological activity from the PASS program supported their potential as potent protease inhibitors. Density Functional Theory (DFT) analysis and molecular dynamics simulations confirmed the stability of these compounds when bound to the protease’s active site, with configurations similar to the GRL-09510 complex.

These findings suggest that the identified marine-derived compounds hold significant promise as effective protease inhibitors, offering new opportunities for immunotherapy and advancements in drug development.

Reproductive endocrine disorder can impair endometrial receptivity, preventing embryo implantation and increasing miscarriage risk. Impaired endometrial receptivity contributes significantly to female infertility. Inflammatory signaling pathways including the IL-6/STAT3 pathway help embryos implant. Therefore, it is crucial to explore the relationship between the IL-6/STAT3 signaling pathway and endometrial receptivity.

To investigate the mechanism by which Bushen Zhuyun decoction (BSZY) enhances endometrial receptivity in rats through the IL-6/STAT3 signaling pathway.

Mifepristone-induced poor endometrial receptivity models of female SD rats were established, followed by histopathological observation. ELISA was used to measure serum sex hormones and VEGF. Western blotting or IHC was used to measure steroid receptors, IGFBP1, and IL-6/STAT3 pathway activation in the uterus during each estrus cycle and early gestation of normal rats. The Treg/Th17 balance was assessed using flow cytometry.

Significant differences were found in the protein expressions of steroid receptors, IL-6, STAT3, and p-STAT3 during each estrus cycle and early gestation of normal rats. The protein expressions of STAT3 and PR were strongly correlated with each other. BSZY notably improved uterine morphology increased the expression of implantation markers and raised the serum concentrations of sex hormones and VEGF. BSZY enhanced the expressions of IL-6 and its receptors and restored the expressions of STAT3 and p-STAT3 in the uterus of pregnant rats. In addition, BSZY effectively restored the Treg/Th17 balance in the peripheral blood of pregnant rats.

BSZY enhances endometrial receptivity and promotes decidualization in SD rats via the IL-6/STAT3 signaling pathway.

Cisplatin is an effective anti-cancer drug with limited clinical applications due to ototoxicity. Resveratrol, known for its antioxidant and anti-inflammatory properties, has been reported to mitigate these adverse effects, although the underlying mechanism remains under-researched.

This study aimed to investigate the effects and underlying mechanisms of resveratrol on cisplatin-induced ototoxicity.

Ototoxicity was modeled in House Ear Institute-Organ of Corti 1 (HEI-OC1) cells by cisplatin exposure, followed by interventions using thioredoxin-interacting protein (TXNIP) siRNA transfection, MitoQ, or resveratrol. Apoptosis and proliferation were quantitatively assessed using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) and Ki67 immunostaining. Quantitative real-time PCR (qRT-PCR) and western blotting were used to measure the changes in mRNA and protein levels. Flow cytometry and enzyme-linked immunosorbent assay (ELISA) were used to analyze pyroptotic cells and inflammatory responses. Reactive oxygen species (ROS) production was tracked using 2', 7'-dichlorofluorescein diacetate (DCFH-DA) staining and flow cytometry. Mitochondrial Membrane Potential (MMP) and mitochondrial permeability transition pore (MPTP) opening levels were analyzed through tetramethylrhodamine ethyl ester (TMRE) staining and specific reagent kits, respectively. Lastly, immunofluorescence staining and co-immunoprecipitation were employed to investigate the co-localization and interactions between TXNIP and thioredoxin (TRX)/NOD-like receptor family pyrin domain-containing 3 (NLRP3) proteins.

Cisplatin exacerbated apoptosis, suppressed cell proliferation, and upregulated NLRP3, pro-Caspase-1, cleaved Caspase-1, Gasdermin D (GSDMD), GSDMD-N, and TXNIP expression. Concurrently, cisplatin resulted in increased pyroptotic cells and increased interleukin-6 (IL-6), IL-18, IL-1β, and tumor necrosis factor-α (TNF-α) levels. These effects were mitigated by TXNIP knockdown. Furthermore, cisplatin led to elevated cellular ROS and mitochondrial ROS (mtROS), decreased MMP, and inhibited MPTP opening. Cisplatin reduced the co-localization and interaction between TRX and TXNIP while enhancing those between TXNIP and NLRP3. These changes were attenuated by MitoQ. Resveratrol displayed effects similar to those of TXNIP knockdown and MitoQ treatment.

Resveratrol alleviated the toxic effects of cisplatin on cochlear hair cells by inhibiting cell pyroptosis process mediated by the mtROS/TXNIP/NLRP3 pathway.

The incidence of Functional Dyspepsia (FD) is gradually increasing, yet there are currently no effective treatment methods available. This study explored the effective components, potential targets, and pathways of Shi-San-Wei-He-Zhong-Wan (SSWHZW) in the treatment of FD, aiming to provide new insights into its treatment.

First, the Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP) and GeneCards databases were utilized to identify the major active components of SSWHZW and potential therapeutic targets of FD. Subsequently, functional enrichment analyses were performed to elucidate the mechanisms of SSWHZW on FD. Molecular docking simulations were then conducted to assess the binding affinity of key targets and major active components. Next, an FD animal model was established, and the therapeutic effects of SSWHZW were validated using Hematoxylin and Eosin (HE) staining and Enzyme-linked Immunosorbent Assay (ELISA). Finally, Western blot analysis was performed to validate the involvement of key signaling pathways.

A total of 229 active ingredients and 283 putative targets were identified from SSWHZW, of which 173 overlapped with the targets of FD and were considered potential therapeutic targets. Key ingredients, such as quercetin, kaempferol, wogonin, and baicalein, were identified as pivotal components of SSWHZW, potentially acting on the 173 overlapping targets and influencing FD through related signaling pathways. Functional enrichment analysis revealed that the PI3K-Akt signaling pathway, VEGF signaling pathway, and NF-kappa B signaling pathway may be involved in the mechanism of SSWHZW in treating FD. Molecular docking predicted that all five ingredients could firmly bind with the top-ranked target TP53 in the Protein-protein Interaction (PPI) network. Further experiments demonstrated that SSWHZW protected the intestinal tissues of FD rats from inflammatory damage by inhibiting the PI3K/AKT signaling pathway.

Based on network pharmacology, this study explored the multi-component, multi-target, and multi-pathway characteristics of SSWHZW in treating FD. The findings suggest that SSWHZW exerts its anti-FD effects by inhibiting the expression of the PI3K/AKT signaling pathway, providing new insights and methods for further research on the mechanism of SSWHZW in treating FD.

The duration of response to immune checkpoint inhibitors (ICIs) varies because of tumor immune heterogeneity, and employing programmed death receptor ligand 1 (PD-L1) expression to evaluate the efficacy of anti-programmed cell death-1 (PD-1)/PD-L1 antibodies remains controversial.

A total of 138 advanced non-small cell lung cancer (NSCLC) patients were subdivided into 2 groups - 52 patients with a PD-L1 Expression≥50% and 86 patients with a PD-L1 Expression <50% - based on next-generation sequencing (NGS) to analyze multiple-dimensional data types, including tumor mutation burden (TMB), gene alterations, gene enrichment analysis, therapy response, and immune-related adverse events (irAEs).

High levels of PD-L1 expression were significantly associated with advanced age and TMB status. The PD-L1≥50% cohort presented mutations of KRAS, NOTCH1, and FAT, while the PD-L1<50% group exhibited mutations of EGFR, PTEN, or LATS1/2. Except for the ascertained DNA damage response regulation. Even though there was no significant difference between PD-L1≥50% and PD-L1<50% cohorts on therapy response, patients with a PD-L1 Expression≥50% elicited a high irAEs incidence rate and increased plasma interleukin 6 (IL-6) concentration.

This real-world retrospective study suggested that high expression of PD-L1 exhibited inappropriate activation of different pathways and collaborated with anti-cytokines and chemokines therapy may optimize clinical therapy efficacy.