Methodology improvement for network pharmacology to correct the deviation of deduced medicinal constituents and mechanism: Xian-Ling-Gu-Bao as an example

Network pharmacology and transcriptomics to determine Danggui Yifei Decoction mechanism of action for the treatment of chronic lung injury

ETHNOPHARMACOLOGICAL RELEVANCE

Several children with pneumonia (especially severe cases) have symptoms of cough and expectoration during the recovery stage after standard symptomatic treatment, which eventually results in chronic lung injury. Danggui yifei Decoction (DGYFD), a traditional Chinese formula, has shown clinical promise for the treatment of chronic lung injury during the recovery stage of pneumonia, however, its mechanism of action is yet to be deciphered.

AIM OF THIS STUDY

To investigate the therapeutic mechanism of DGYFD for the treatment of chronic lung injury by integrating network pharmacology and transcriptomics.

MATERIALS AND METHODS

BALB/c mice were used to establish the chronic lung injury mouse model by intratracheal instillation of lipopolysaccharide (LPS). Pathological analysis of lung tissue, lung injury histological score, lung index, protein levels in bronchoalveolar lavage fluid (BALF), immunohistochemical staining, blood rheology, inflammatory cytokines, and oxidative stress levels were used to evaluate the pharmacological effects of DGYFD. Chemical components of DGYFD were identified using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Integrated network pharmacology together with transcriptomics was used to predict potential biological targets. Western blot analysis was used to verify the results.

RESULTS

In this study, we demonstrated that DGYFD could improve lung injury pathological changes, decreases lung index, down-regulate NO and IL-6 levels, and regulate blood rheology. In addition, DGYFD was able to reduce the protein levels in BALF, up-regulate the expression levels of occludin and ZO-1, improve the ultrastructure of lung tissues, and reverse the imbalance of AT I and AT II cells to repair the alveolar-capillary permeability barrier. Twenty-nine active ingredients of DGYFD and 389 potential targets were identified by UPLC-MS/MS and network pharmacology, and 64 differentially expressed genes (DEGs) were identified using transcriptomics. GO and KEGG analysis revealed that the MAPK pathway may be the molecular target. Further, we found that DGYFD inhibits phosphorylation levels of p38 MAPK and JNK in chronic lung injury mouse models.

CONCLUSIONS

DGYFD could regulate the imbalance between the excessive release of inflammatory cytokines and oxidative stress, repair the alveolar-capillary permeability barrier and improve the pathological changes during chronic lung injury by regulating the MAPK signaling pathway.

Integrated network analysis and metabolomics reveal the molecular mechanism of Yinchen Sini decoction in CCl4-induced acute liver injury

Objective: Yinchen Sini decoction (YCSND), a traditional Chinese medicine (TCM) formula, plays a crucial role in the treatment of liver disease. However, the bioactive constituents and pharmacological mechanisms of action remain unclear. The present study aimed to reveal the molecular mechanism of YCSND in the treatment of acute liver injury (ALI) using integrated network analysis and metabolomics. Methods: Ultra-high-performance liquid chromatography coupled with Q-Exactive focus mass spectrum (UHPLC-QE-MS) was utilized to identify metabolites in YCSND, and high-performance liquid chromatography (HPLC) was applied to evaluate the quality of four botanical drugs in YCSND. Cell damage and ALI models in mice were established using CCl4. 1H-NMR metabolomics approach, along with histopathological observation using hematoxylin and eosin (H&E), biochemical measurements, and reverse transcription quantitative real-time PCR (RT-qPCR), was applied to evaluate the effect of YCSND on CCl4- induced ALI. Network analysis was conducted to predict the potential targets of YCSND in ALI. Result: Our results showed that 89 metabolites in YCSND were identified using UHPLC-QE-MS. YCSND protected against ALI by reducing the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and malondialdehyde (MDA) contents and increasing those of superoxide dismutase (SOD), and glutathione (GSH) both in vivo and in vitro. The 1H-NMRmetabolic pattern revealed that YCSND reversed CCl4-induced metabolic abnormalities in the liver. Additionally, the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis identified five pathways related to liver injury, including the PI3K-AKT, MAPK, HIF-1, apoptosis, and TNF signaling pathways. Moreover, RT-qPCR showed YCSND regulated the inflammatory response (Tlr4, Il6, Tnfα, Nfκb1, Ptgs2, and Mmp9) and apoptosis (Bcl2, Caspase3, Bax, and Mapk3), and inhibited PI3K-AKT signaling pathway (Pi3k and Akt1). Combined network analysis and metabolomics showed a link between the key targets (Tlr4, Ptgs2, and Mmp9) and vital metabolites (choline, xanthine, lactate, and 3-hydroxybutyric acid) of YCSND in ALI. Conclusion: Overall, the results contribute to the understanding of the therapeutic effects of YCSND on ALI, and indicate that the integrated network analysis and metabolomics could be a powerful strategy to reveal the pharmacological effects of TCM.

Network and experimental pharmacology on mechanism of Si-Wu-tang improving ovarian function in a mouse model of premature ovarian failure induced by cyclophosphamide

ETHNOPHARMACOLOGICAL RELEVANCE

Si-Wu-Tang (SWT) has become a common basic prescription for supplementing blood and regulating menstruation, and enjoys the reputation of "the first prescription in gynecology". It is often reported in the treatment of premature ovarian failure (POF). However, knowledge of its specific mechanism is still limited.

AIM OF THE STUDY

This study aimed to identify the potential effects and underlying mechanisms of SWT on POF.

MATERIALS AND METHODS

After confirming the therapeutic effect of SWT on POF mice induced by cyclophosphamide, we further clarified the promoting effect of SWT on ovarian follicle development by detecting the expression of key factors related to follicle development in the ovary in different ways.Then, network pharmacology and gene expression profiling of POF from the GEO database were used to clarify the underlying mechanisms. Molecular biology and molecular docking analysis were applied for final mechanism verification.

RESULTS

Our results showed that SWT increased body weight, ovarian index, reversed disordered serum hormone levels, and menstrual cycle in POF mice. After SWT treatment, the number of follicles at all levels in mice with POF also recovered. Using molecular biology techniques, it was proven that SWT can improve follicle development and angiogenesis in the microenvironment. The network pharmacology and gene expression profiling from the GEO database indicated that the PI3K/Akt signaling pathway may be the reason why SWT improves ovarian function in mice with POF. Subsequently, further Western blot and immunoprecipitation indicated that SWT indeed inhibited the PI3K/Akt signaling pathway in mice with POF. In addition, this conclusion was further confirmed by molecular docking experiments.

CONCLUSIONS

SWT can improve ovarian function in POF mice induced by cyclophosphamide, and its mechanism is related to the inhibition of the PI3K/Akt signaling pathway.

Multitech-Based Study on Medicinal Material Basis and Action Mechanism of Herbal Formula Xian-Ling-Gu-Bao Capsule in Treatment of Osteoarthritis

Currently, osteoarthritis (OA) is thought to be the most prevalent chronic joint disease worldwide. The epidemiology of this disorder is complex, and the treatment is challenging. Xian-Ling-Gu-Bao (XLGB) capsule, a herbal compound preparation, is widely used for the treatment of bone disorders, including OA. Although its efficacy and safety have been demonstrated in clinical trials and practice, the underlying medicinal constituents and mechanism have not been clearly elucidated. Therefore, this study aimed to explore the medicinal constituents and mechanism of XLGB for OA treatment. The phytochemical constituents in XLGB capsule were detected by liquid chromatography-mass spectrometry (LC-MS), the medicinal constituents and therapeutic mechanism for OA treatment were deduced by network analysis, and the deduced mechanism was validated by in vitro experiment. As a result, a total of 55 constituents were detected in XLGB extract, in which 16 constituents were screened out for target collection. Based on the analysis of target profile, XLGB targets showed a high degree of similarity with OA targets. Network analysis revealed that XLGB had a holistic effect of multiple active constituents on multiple targets and pathways. The core targets of XLGB were presumed to be MAPKs, PI3K, AKT, BCL2, RELA, TNF, NOS2, and so on, and the mechanism was speculated to mainly inhibit chondrocyte apoptosis and inflammatory response through JNK and PI3K/AKT/NF-κB signaling cascades. Finally, in vitro study confirmed that XLGB extract protected ATDC5 cells against lipopolysaccharide- (LPS-) induced apoptosis and inflammatory response, and these effects were supposed to be involved in the inhibition of JNK and PI3K/AKT/NF-κB pathways. Our study could provide a scientific basis for further research and clinical use of XLGB capsule.

Study on the Mechanism of Xiaotan Sanjie Recipe in the Treatment of Colon Cancer Based on Network Pharmacology

The aim of the study is to investigate the mechanism of action of Disulfiram against colon cancer through a network pharmacology approach. The targets were then imported into the Cytoscape 3.7.2 software to construct a network of active ingredient targets and were imported into the STRING database to construct a protein-protein interaction (PPI) network, and the Bisogenet plug-in in Cytoscape 3.7.2 was used for network topology analysis. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the potential targets of Yiqi and Baiyu Tang for colon cancer using the R-language Bioconductor platform, and the results were imported into Cytoscape 3.7.2 to obtain KEGG network relationship maps. Molecular docking software Autodock Vina was used to map the core targets to the active ingredients. A total of 119 chemical components and 694 disease targets were obtained, including 113 intersecting targets. The key targets included AKT1 and TP53, and GO functional analysis mainly related to ubiquitination and apoptosis, etc. KEGG analysis showed that the treatment of colon cancer with Ganchenzan mainly acted through cancer-related signaling pathways such as AGE-RAGE and P13K-Akt, and the molecular docking results showed the best binding performance with TP53.

A systematic study of traditional Chinese medicine treating hepatitis B virus-related hepatocellular carcinoma based on target-driven reverse network pharmacology

Hepatocellular carcinoma (HCC) is a serious global health problem, and hepatitis B virus (HBV) infection remains the leading cause of HCC. It is standard care to administer antiviral treatment for HBV-related HCC patients with concurrent anti-cancer therapy. However, a drug with repressive effects on both HBV infection and HCC has not been discovered yet. In addition, drug resistance and side effects have made existing therapeutic regimens suboptimal. Traditional Chinese medicine (TCM) has multi-ingredient and multi-target advantages in dealing with multifactorial HBV infection and HCC. TCM has long been served as a valuable source and inspiration for discovering new drugs. In present study, a target-driven reverse network pharmacology was applied for the first time to systematically study the therapeutic potential of TCM in treating HBV-related HCC. Firstly, 47 shared targets between HBV and HCC were screened as HBV-related HCC targets. Next, starting from 47 targets, the relevant chemical components and herbs were matched. A network containing 47 targets, 913 chemical components and 469 herbs was established. Then, the validated results showed that almost 80% of the herbs listed in chronic hepatitis B guidelines and primary liver cancer guidelines were included in the 469 herbs. Furthermore, functional analysis was conducted to understand the biological processes and pathways regulated by these 47 targets. The docking results indicated that the top 50 chemical components bound well to targets. Finally, the frequency statistical analysis results showed the 469 herbs against HBV-related HCC were mainly warm in property, bitter in taste, and distributed to the liver meridians. Taken together, a small library of 913 chemical components and 469 herbs against HBV-related HCC were obtained with a target-driven approach, thus paving the way for the development of therapeutic modalities to treat HBV-related HCC.