Integrative analysis of network pharmacology and proteomics to identify key targets of Tuomin-Zhiti-Decoction for allergic rhinitis

Green carbon dots derived from Zingiberis Rhizoma Carbonisatum alleviate ovalbumin-induced allergic rhinitis

Background

Allergic rhinitis (AR) affects up to 40% of the population, leading to significant healthcare expenditures. Current mainstream treatments, while effective, can lead to side effects and do not address the underlying immunological imbalances. Zingiberis Rhizoma Carbonisatum (ZRC), the partially charred product of Zingiberis Rhizoma (ZR), has been widely used clinically in China since ancient times to treat respiratory disorders.

Methods

Inspired by the similarity between high-temperature pyrolysis and carbonization processing of herbal medicine, ZRC derived CDs (ZRC-CDs) were extracted and purified through several procedures. Then, the physicochemical characteristics of CDs were delineated through a suite of characterization methods. Moreover, our investigation zeroed in on elucidating the ameliorative impacts of CDs on ovalbumin-induced rat models alongside their underlying mechanisms.

Results

ZRC-CDs with particle sizes ranging from 1.0 to 3.5 nm and rich surface functional groups. Additionally, we observed that ZRC-CDs significantly attenuated nasal symptoms and pathological damage in ovalbumin-induced AR rats, and modulated lipid metabolism and type 2 inflammatory responses. They also inhibit PI3K/AKT and JAK/STAT pathways, which are associated with metabolism and inflammation. Importantly, ZRC-CDs demonstrated high biocompatibility, underscoring their potential as a novel therapeutic agent.

Conclusion

ZRC-CDs offer a promising alternative for AR treatment and could help facilitate broader clinical use of the ZRC. In addition, the exploration of the inherent bioactivity of CDs can help to broaden their biological applications.

Predicting prospective therapeutic targets of Bombyx batryticatus for managing diabetic kidney disease through network pharmacology analysis

We conducted network pharmacology and molecular docking analyses, and executed in vitro experiments to assess the mechanisms and prospective targets associated with the bioactive components of Bombyx batryticatus in the treatment of diabetic kidney disease (DKD). The bioactive components and potential targets of B batryticatus were sourced from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. Using 5 disease databases, we conducted a comprehensive screening of potential disease targets specifically associated with DKD. Common targets shared between the bioactive components and disease targets were identified through the use of the R package, and subsequently, a protein-protein interaction network was established using data from the STRING database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses pertaining to the identified common targets were conducted using the Database for Annotation, Visualization, and Integrated Discovery. Molecular docking simulations involving the bioactive components and their corresponding targets were modeled through AutoDock Vina and Pymol. Finally, to corroborate and validate these findings, experimental assays at the cellular level were conducted. Six bioactive compounds and 142 associated targets were identified for B batryticatus. Among the 796 disease targets associated with DKD, 56 targets were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed the involvement of these shared targets in diverse biological processes and signaling pathways, notably the PI3K-Akt signaling pathway. Molecular docking analyses indicated a favorable binding interaction between quercetin, the principal bioactive compound in B batryticatus, and RAC-alpha serine/threonine-protein kinase. Subsequently, in vitro experiments substantiated the inhibitory effect of quercetin on the phosphorylation level of PI3K and Akt. The present study provides theoretical evidence for a comprehensive exploration of the mechanisms and molecular targets by which B batryticatus imparts protective effects against DKD.

Network pharmacology analysis of the Huangqi-Gancao herb pair reveals quercetin as a therapeutics for allergic rhinitis via the RELA-regulated IFNG/IRF1 axis response

Despite the complexity of allergic rhinitis (AR) pathogenesis, no FDA-approved drug has been developed to achieve optimal therapeutic effects. The present study explored the efficacy and mechanism of Huangqi (Hedysarum Multijugum Maxim)-Gancao (Glycyrrhizae Radix et Rhizoma or licorice) herb pair in treating AR by network pharmacology and experimental approaches. The bioactive ingredients of Huangqi and Gancao were identified and used to predict the targets of these herbs in AR and generate the pharmacological network. Ovalbumin (OVA)-induced AR mouse model was established to assess the anti-AR effect of the Huangqi decoction (HQD) prepared based on both herbs. We identified 90 active ingredients of the Huangqi-Gancao pair, targeting 69 AR-related genes. Quercetin (QUE) was identified as the hub ingredient of this pair, with 57 targets in AR. The protein-protein interaction (PPI) network analysis and molecular docking revealed IL1B, TNF, STAT1, IL6, PTGS2, RELA, IL2, NFKBIA, IFNG, IL10, IL1A, IRF1, EGFR, and CXCL10 as important targets of QUE in AR treatment. Experimentally, QUE or HQD significantly alleviated the AR-induced histopathological changes, AR symptoms, and IgE level and counteracted AR-induced expression changes of IFNG, IRF1, RELA, and NFKBIA. These effects were promoted by the NF-kB inhibitor helenalin, indicating that HQD and QUE counteracted AR in mice by regulating the IFNG/IRF1 signaling via the NF-κB pathway in AR mice. These findings shed light on the efficacy of the constituents of Huangqi-Gancao pair, their potential targets, and the molecular mechanisms of HQD in treating AR, which could advance the development of tailored therapeutic interventions for this disorder.

Integrative analysis of network pharmacology and proteomics reveal the protective effect of Xiaoqinglong Decotion on neutrophilic asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Xiaoqinglong Decotion (XQLD) is a commonly used Chinese herbal formula in clinical practice, especially for allergic diseases such as asthma. However, its intrinsic mechanism for the treatment of neutrophilic asthma (NA) remains unclear.

AIM OF THE STUDY

The aim of this study was to evaluate the efficacy and potential mechanisms of XQLD on NA using network pharmacology and in vivo experiments.

MATERIALS AND METHODS

First, the active compounds, potential targets and mechanisms of XQLD against NA were initially elucidated by network pharmacology. Then, OVA/CFA-induced NA mice were treated with XQLD to assess its efficacy. Proteins were then analyzed and quantified using a Tandem Mass Tags approach for differentially expressed proteins (DEPs) to further reveal the mechanisms of NA treatment by XQLD. Finally, the hub genes, critical DEPs and potential pathways were validated.

RESULTS

176 active compounds and 180 targets against NA were identified in XQLD. Protein-protein interaction (PPI) network revealed CXCL10, CX3CR1, TLR7, NCF1 and FABP4 as hub genes. In vivo experiments showed that XQLD attenuated inflammatory infiltrates, airway mucus secretion and remodeling in the lungs of NA mice. Moreover, XQLD significantly alleviated airway neutrophil inflammation in NA mice by decreasing the expression of IL-8, MPO and NE. XQLD also reduced the levels of CXCL10, CX3CR1, TLR7, NCF1 and FABP4, which are closely associated with neutrophil inflammation. Proteomics analysis identified 28 overlapping DEPs in the control, NA and XQLD groups, and we found that XQLD inhibited ferroptosis signal pathway (elevated GPX4 and decreased ASCL3) as well as the expression of ARG1, MMP12 and SPP1, while activating the Rap1 signaling pathway.

CONCLUSION

This study revealed that inhibition of ARG1, MMP12 and SPP1 expression as well as ferroptosis pathways, and activation of the Rap1 signaling pathway contribute to the therapeutic effect of XQLD on NA.

Methylation-driven mechanisms of allergic rhinitis during pollen and non-pollen seasons using integrated bioinformatics analysis

Background

Allergic rhinitis (AR) is a widespread allergic airway disease that results from a complex interplay between genetic and environmental factors and affects approximately 10%-40% of the global population. Pollen is a common allergen, and exposure to pollen can cause epigenetic changes. However, the mechanism underlying pollen-induced DNA methylation changes and their potential effects on the allergic march are still unclear. The purpose of this study was to explore the methylation-driven mechanisms of AR during the pollen and non-pollen seasons using bioinformatics analysis and to investigate their relationship with asthma.

Methods

We downloaded DNA methylation and gene expression data from the GEO database (GSE50387: GSE50222, GSE50101) and identified differentially methylated positions (DMPs) and differentially expressed genes (DEGs) during the pollen and non-pollen seasons using the CHAMP and limma packages. Through correlation analysis, we identified methylation-driven genes and performed pathway enrichment analysis to annotate their functions. We incorporated external data on AR combined with asthma (GSE101720) for analysis to identify key CpGs that promote the transformation of AR to asthma. We also utilized external data on olive pollen allergy (GSE54522) for analysis to validate the methylation-driven genes. Weighted correlation network analysis (WGCNA) was employed to identify gene modules significantly correlated with pollen allergy. We extracted genes related to the key methylation-driven gene ZNF667-AS1 from the significant module and performed pathway intelligent clustering using KOBAS-i. We also utilized gene set enrichment analysis to explore the potential function of ZNF667-AS1.

Results

We identified 20 and 24 CpG-Gene pairings during the pollen and non-pollen seasons. After incorporating external data from GSE101720, we found that ZNF667-AS1 is a key gene that may facilitate the transformation of AR into asthma during the pollen season. This finding was further validated in another external dataset, GSE54522, which is associated with pollen allergy. WGCNA identified 17 modules, among which the blue module showed significant correlation with allergies. ZNF667-AS1 was located in the blue module. We performed pathway analysis on the genes correlated with ZNF667-AS1 extracted from the blue module and identified a prominent cluster of pathways in the KOBAS-i results, including Toll-like receptor (TLR) family, MyD88, MAPK, and oxidative stress. Gene set enrichment analysis around cg05508084 (paired with ZNF667-AS1) also indicated its potential involvement in initiating and modulating allergic inflammation from the perspective of TLR and MAPK signaling.

Conclusion

We identified methylation-driven genes and their related pathways during the pollen and non-pollen seasons in patients with AR and identified key CpGs that promote the transformation of AR into asthma due to pollen exposure. This study provides new insights into the underlying molecular mechanisms of the transformation of AR to asthma.

Network pharmacology: a bright guiding light on the way to explore the personalized precise medication of traditional Chinese medicine

Network pharmacology can ascertain the therapeutic mechanism of drugs for treating diseases at the level of biological targets and pathways. The effective mechanism study of traditional Chinese medicine (TCM) characterized by multi-component, multi-targeted, and integrative efficacy, perfectly corresponds to the application of network pharmacology. Currently, network pharmacology has been widely utilized to clarify the mechanism of the physiological activity of TCM. In this review, we comprehensively summarize the application of network pharmacology in TCM to reveal its potential of verifying the phenotype and underlying causes of diseases, realizing the personalized and accurate application of TCM. We searched the literature using "TCM network pharmacology" and "network pharmacology" as keywords from Web of Science, PubMed, Google Scholar, as well as Chinese National Knowledge Infrastructure in the last decade. The origins, development, and application of network pharmacology are closely correlated with the study of TCM which has been applied in China for thousands of years. Network pharmacology and TCM have the same core idea and promote each other. A well-defined research strategy for network pharmacology has been utilized in several aspects of TCM research, including the elucidation of the biological basis of diseases and syndromes, the prediction of TCM targets, the screening of TCM active compounds, and the decipherment of mechanisms of TCM in treating diseases. However, several factors limit its application, such as the selection of databases and algorithms, the unstable quality of the research results, and the lack of standardization. This review aims to provide references and ideas for the research of TCM and to encourage the personalized and precise use of Chinese medicine.

Lotus leaf extract can attenuate salpingitis in laying hens by inhibiting apoptosis

This study aimed to determine whether the lotus leaf extract (LLE) had the effect of treating salpingitis in laying hens. First, the salpingitis model was established by the method of bacterial infection. Differential genes between salpingitis and healthy laying hens were identified by transcriptome sequencing, and GO and KEGG enrichment analyses were performed. Groups of treatment of antibiotics and LLE were established to verify the feasibility of the lotus leaf extract in treating salpingitis. Furthermore, the active component and pharmacological effects of LLE were identified using the UPLC-Q-TOF-MS and network pharmacology technique. At last, the mechanism of LLE treating salpingitis was further evaluated by DF-1 cells infected with bacteria. The results showed that LLE significantly reduced the levels of TLR4 and IFN-γ (P < 0.05), accelerated the levels of IgA and IgG (P < 0.05), regulated the levels of SOD and MDA (P < 0.05) in laying hens with salpingitis. A total of 1,874 differential genes were obtained according to the transcriptome sequencing. It was revealed a significant role in cell cycle and apoptosis by enrichment analysis. In addition, among the 28 components identified by UPLC-Q-TOF-MS, 20 components acted on 58 genes, including CDK1, BIRC5, and CA2 for treating salpingitis. After bacterial infection, cells were damaged and unable to complete the normal progression of the cell cycle, leading to cell cycle arrest and further apoptosis formation. However, with the intervention of LLE, bacterial infection was resisted. The cells proliferation was extensively restored, and the expression of NO was increased. The addition of LLE significantly decreased cell apoptosis. The G1 phase increased, the S phase and the G2 phase decreased in the model group; after the intervention of LLE, the G1 phase gradually returned to the average level, and G2 and S phases increased. The mRNA expression levels of BIRC5, CDK1, and CA2 were consistent with the predicted results in network pharmacology. At the same time, the mRNA expression levels of Caspase-3 and Caspase-7 were reduced after added with LLE. The mRNA expression levels of TNF-α, TRADD, FADD, Caspase-8, Caspase-10, and Caspase-9 (P < 0.05), which would inhibit death receptor activation and decrease the apoptotic cascade, were upregulated after bacterial infection. However, the results in LLE groups were downregulated (P < 0.05). Meanwhile, the mRNA expression levels of BCL-2 in LLE groups were increased significantly compared with it in model group (P < 0.05). Notably, LLE administration inhibited apoptosis and regulated the cell cycle distribution in the salpingitis induced by bacterial infection. These results indicated that the LLE attenuated bacterial-induced salpingitis by modulating apoptosis and immune function in laying hens.

LC-MS-based metabolomics reveals the mechanism of anti-gouty arthritis effect of Wuwei Shexiang pill

Wuwei Shexiang Pill (WSP) is a Tibetan traditional medicine, which has been demonstrated to exhibit potent anti-inflammatory and anti-gout effects. However, the specific pharmacological mechanism is not elucidated clearly. In the present study, liquid chromatography-mass spectrometry (LC-MS)-based metabolomics was applied to investigate the alteration of serum metabolites induced by WSP treatment in MSU-induced gouty rats. Subsequently, bioinformatics was utilized to analyze the potential metabolic pathway of the anti-gout effect of WSP. The pharmacodynamic data discovered that WSP could ameliorate ankle swelling and inflammatory cell infiltration, as well as downregulate the protein expression of IL-1β, p-NF-κB p65, and NLRP3 in the synovial membrane and surrounding tissues of gouty ankles. LC-MS-based metabolomics revealed that there were 30 differential metabolites in the serum between sham-operated rats and gouty ones, which were mainly involved in the metabolism of fructose and mannose, primary bile acid biosynthesis, and cholesterol metabolism. However, compared to the model group, WSP treatment upregulated 11 metabolic biomarkers and downregulated 31 biomarkers in the serum. KEGG enrichment analysis found that 27 metabolic pathways contributed to the therapeutic action of WSP, including linoleic acid metabolism, phenylalanine metabolism, and pantothenate and CoA biosynthesis. The comprehensive analysis-combined network pharmacology and metabolomics further revealed that the regulatory network of WSP against gout might be attributed to 11 metabolites, 7 metabolic pathways, 39 targets, and 49 active ingredients of WSP. In conclusion, WSP could ameliorate the inflammation of the ankle in MSU-induced gouty rats, and its anti-gout mechanism might be relevant to the modulation of multiple metabolic pathways, such as linoleic acid metabolism, phenylalanine metabolism, and pantothenate and CoA biosynthesis. This study provided data support for the secondary development of Chinese traditional patent medicine.

Integrated LC-MS and network pharmacology methods to screen quantitative indicators in the Hippocampus histrix Kaup and method transfer

Hippocampus histrix Kaup is a popular marine medicine with high medicinal and healthcare values. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis combined with network pharmacological method was used to screen for suitable quantitative indicators for the quality control of H. histrix Kaup. Firstly, an LC-MS analytical method for the simultaneous determination of 12 nucleosides in extracts of H. histrix Kaup was established. And then, a network pharmacological method incorporated target prediction, protein-protein interaction network, components-targets network, and targets-pathways network was performed to screen for quantitative indicators. Finally, the developed LC-MS method was transferred to liquid chromatographs to improve the generalizability of the method. All 12 nucleotides were authenticated in extracts of H. histrix Kaup by comparing with the standards. The optimal chromatographic separation conditions are as follows: the chromatographic separation was achieved on an Acquire BEH-C18 column (2.1 mm * 100 mm, 1.7 µm) and gradient elution was performed using methanol solution and buffer (0.30% formic acid and 10 mmol/L ammonium acetate) as mobile phase at a flow rate of 0.15 mL/min and an acquisition wavelength of 260 nm. Network pharmacology results showed that adenosine, and uridine show excellent pharmacological activity. Integration the content, correlation, chromatographic separation, and pharmacological activity of each compound in H. histrix Kaup, uridine and adenosine were tentatively determined as quantitative indicators for quality control in H. histrix Kaup. The established LC-MS method was successfully transferred to liquid chromatographs, and the method is stable and reliable for the quality control of H. histrix Kaup. This developed integrated strategy was successfully used to screen quantitative indicators in the H. histrix Kaup.

Identification of pharmacokinetic markers for safflower injection using a combination of system pharmacology, multicomponent pharmacokinetics, and quantitative proteomics study

Safflower injection (SI), a water-extract preparation from safflower (Carthamus tinctorius L.), has been widely used for the treatment of cardio-cerebrovascular diseases. This work aims to develop an approach for identifying PK markers of cardiovascular herbal medicines using SI as a case study. Firstly, qualitative and quantitative analyses were performed to reveal ingredients of the preparation via HPLC-MS. Subsequently, multiple PK ingredients and integrated PK investigations were carried out to ascertain ingredients with favorable PK properties (e.g., easily detected at conventional PK time points and high system exposure) for the whole preparation. Next, ingredients against cardiovascular diseases (CVDs) in the preparation were predicted with target fishing and system pharmacology studies. Finally, ingredients with favorable PK properties, satisfactory PK representativeness for the preparation, and high relevance to CVDs were considered as potential PK markers. Their therapeutic effect was further evaluated using the H₂O₂-induced H9c2 cardiomyocyte-injured model and a proteomics study to identify objective PK markers. As results, it disclosed that SI mainly contains 11 ingredients. Among them, five ingredients, namely, hydroxysafflor yellow A (HSYA), syringin (SYR), p-coumaric acid (p-CA), scutellarin (SCU), and p-hydroxybenzaldehyde (p-HBA), showed favorable PK properties. HSYA, SYR, and rutin (RU) were predicted to show high relevance to CVDs and screened as potential PK markers. However, only HSYA and SYR were confirmed as therapeutic ingredients against CVDs. Combined with these findings, only HSYA demonstrated satisfactory representativeness on PK properties and therapeutic effects of multiple ingredients of the preparation, thereby indicating that HSYA is a potential PK marker for the SI. The results of this study can provide a reference for the characterization of PK markers for traditional Chinese medicines.