Revealing the Mechanism of Astragali Radix against Cancer-Related Fatigue by Network Pharmacology and Molecular Docking

An integrative approach for mechanistic insights into the atherosclerotic plaque-stabilizing properties of Danggui Buxue decoction

ETHNOPHARMACOLOGICAL RELEVANCE

Danggui Buxue Decoction (DBD), a traditional Chinese medicinal formula, has historically been used for cardiovascular health, including managing atherosclerotic plaques (ASP). However, its precise mechanisms remain elusive.

AIM OF THE STUDY

The purpose of this study was to use a novel integrative bioinformatics analysis and experimental validation approach to provide a molecular basis for ASP's stabilization by DBD.

MATERIALS AND METHODS

A mice model of ApoE-deficient atherosclerosis fed with a high-fat diet was employed to evaluate the efficacy of DBD in stabilizing ASP. The potential mechanism underlying the stabilization effect of DBD on ASP was systematically investigated using an integrated approach combining network pharmacology, molecular docking, and molecular dynamics simulation. Additionally, an ox-LDL-induced macrophage foam cell model and multivariate statistical analysis were utilized to validate the pharmacodynamic material basis and target of DBD in stabilizing ASP.

RESULTS

Firstly, it was found that DBD can significantly alleviate ASP, which was manifested as a significant reduction in the atherosclerosis index, ratio of area for plaque to lumen, and vulnerability index. Afterwards, network pharmacology investigation identified quercetin and kaempferol as the primary active compounds in DBD anti-ASP. Key core targets mainly involved TP53, AKT1, IL-6 and TNF. The main action pathways included lipid and atherosclerosis, PI3K-Akt signaling, and other pathways. Subsequently, molecular docking and molecular dynamics simulation results confirmed the strong stability of the main active compounds with the key target. Finally, the cell validation experiment in vitro revealed that both quercetin and kaempferol could significantly inhibit RAW264.7 macrophage foaming formation induced by ox-LDL and improve its lipid metabolism disorder. Meanwhile, they could also significantly reverse ox-LDL induced abnormal expression of core protein predicted by network pharmacology in RAW264.7 foam cells. Further correlation analysis revealed that the improvement effect of quercetin and kaempferol on macrophage foaming had a close correlation with the inhibition of core protein expression.

CONCLUSION

DBD mainly utilized active ingredients such as quercetin and kaempferol, through regulating multiple targets like TP53, AKT1, IL-6 and TNF, to stabilize ASP.

Network pharmacology and in silico approach to study the mechanism of quercetin against breast cancer

Breast cancer is a significant health concern among females with an estimated 2.3 million cases reported worldwide in 2022. Traditional treatment methods have now developed resistance and various adverse effects, highlighting an urgent need for attention. Therefore, it is advisable to substitute these conventional therapies with innovative medications. Quercetin is a flavonoid, commonly found in various vegetables and fruits and have been shown to possess anti-cancer properties. Network pharmacology is a comprehensive approach that has significantly assisted in investigating the potential of quercetin as a therapeutic option for breast cancer. The first step includes target fishing for quercetin-targeted genes in breast cancer through various online available databases. All intersecting genes were analysed for the phenotypic- genotypic correlation via online VarElect analysis tool. Using the result from the result the GO enrichment and pathway enrichment analysis was done on 52 common genes; followed by PPI network construction and based on topological parameters top 8 genes were filtered. Based on theVenny2.1 and then GEPIA and HPA analysis the key target were identifies as ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4 and ABCG2. Further, Molecular docking was done to investigate the possible interaction of the identified gene with quercetin. Our finding shows quercetin is the potential natural drug that can treat breast cancer effectively. Quercetin interacts with ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 at cellular as well as molecular level. The ADMET analysis suggests the bioavaibility of quercetin is around 0.55. Suggesting that quercetin satisfies drug-likeness rules but may face challenges like low bioavailability, which can be enhanced through structural modifications or formulations (e.g., nanoparticles). The molecular docking result assures the interaction of quercetin with the ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 with the binding affinity of - 7.2, - 10.1, - 10.4, - 8.0, - 8.2, - 8.2, - 9.0 and - 8.9 respectively. These results suggest quercetin has a stable interaction with the ABCC4 gene. Considering this interaction the quercetin molecules can rescue the cellular condition by inducing apoptosis, inhibiting proliferation, and suppressing metastasis. Quercetin, a natural compound found in fruits and vegetables, has been found to have significant therapeutic roles in treating breast cancer. It inhibits cell cycle arrest, promotes apoptosis, and reduces blood vessel formation. It also reverses drug resistance and has antioxidant and anti-inflammatory properties. This study concludes that the therapeutic influence of quercetin plays a significant role in treating breast cancer and aids in the advancement of the clinical application of quercetin in future studies.

Graphical Abstract

Efficacy of Astragalus Membranaceus (Huang Qi) for Cancer-Related Fatigue: A Systematic Review and Meta-Analysis of Randomized Controlled Studies

Background: Cancer-related fatigue is the most common complication in patients. Astragalus membranaceus is widely used in many countries to treat cancer, but its efficacy and safety is uncertain. Objectives: This study aimed to summarize the evidence on Astragalus membranaceus on cancer-related fatigue and quality of life in patients with cancer. Methods: Nine electronic databases were explored for the clinical randomized controlled trial of intervention with Astragalus membranaceus alone for cancer-related fatigue and quality of life in cancer patients from inception to July 1, 2022. The risk of bias assessment tool was adopted by Cochrane Handbook 6.1.0. The effect size was estimated using relative risk and mean difference with a corresponding 95% confidence interval. Review Manager 5.4 was used for meta-analysis. The evidence level was assessed using Grading of Recommendation, Assessment, Development and Evaluation (GRADE). Results: Eight studies were included. The results of the meta-analysis showed that the addition of Astragalus membranaceus to the control group was effective in reducing cancer-related fatigue (SMD = -1.63, 95% CI [-1.90, -1.36], P < .00001) and (RR = 1.55, 95% CI [1.19, 2.02], P = 0.001) in patients with cancer and improving quality of life (SMD = 0.86, 95% CI [0.17, 1.55], P = 0.01) and (RR = 1.57, 95% CI [1.10, 2.23], P = 0.01). Conclusion: The current evidence is supportive of the efficacy of Astragalus membranaceus in patients with cancer-related fatigue and their quality of life, but due to the small and low quality of the included literature and the lack of uniformity in terms of cancer type as well as treatment modalities, there is currently insufficient evidence to provide strong support for the clinical use of Astragalus membranaceus in the treatment of cancer-related fatigue. More high-quality evidence is needed in the future to further validate the use of Astragalus membranaceus in the treatment of clinical cancer-related fatigue. Registration: A review protocol was developed and registered in the International Prospective Register of Systematic Reviews (PROSPERO). Registration number: CRD42023442277. Registered 20 July 2023.

Medicinal plants for the management of post-COVID-19 fatigue: A literature review on the role and mechanisms

Background

COVID-19 infection has a lasting impact on human health, which is known as post-COVID-19 conditions. Fatigue is one of the most commonly reported post-COVID-19 conditions. Management of fatigue in the post-COVID-19 era is necessary and emerging. The use of medicinal plants may provide a strategy for the management of post-COVID-19 fatigue.

Methods

A literature search has been conducted by using PubMed, Embase and Cochrane library databases is performed for studies published up to March 2024. Keywords, such as "post-COVID-19 conditions, persistent COVID-19 symptoms, chronic COVID-19, long-term sequelae, fatigue, post-COVID-19 fatigue, herbal plants, medicinal herbs, traditional Chinese medicine, pharmacological mechanisms, pharmacological actions" are thoroughly searched in Englsih and Chinese. This study reviews the pathophysiology of post-COVID-19 fatigue and potential herbal plants for managing post-COVID-19 fatigue.

Results and conclusion

Representative medicinal plants that have been extensively investigated by previous studies are presented in the study. Three common mechanisms among the most extensively studied for post-COVID-19 fatigue, with each mechanism having medicinal plants as an example. The latest clinical studies concerning the management of post-COVID-19 fatigue using medicinal plants have also been summarized. The study shows the potential for improving post-COVID-19 fatigue by consuming medicinal plants.

Biological network comparison identifies a novel synergistic mechanism of Ginseng Radix-Astragali Radix herb pair in cancer-related fatigue

ETHNOPHARMACOLOGICAL RELEVANCE

Ginseng Radix and Astragali Radix are commonly combined to tonify Qi and alleviate fatigue. Previous studies have employed biological networks to investigate the mechanisms of herb pairs in treating different diseases. However, these studies have only elucidated a single network for each herb pair, without emphasizing the superiority of the herb combination over individual herbs.

AIM OF THE STUDY

This study proposes an approach of comparing biological networks to highlight the synergistic effect of the pair in treating cancer-related fatigue (CRF).

METHODS

The compounds and targets of Ginseng Radix, Astragali Radix, and CRF diseases were collected and predicted using different databases. Subsequently, the overlapping targets between herbs and disease were imported into the STRING and DAVID tools to build protein-protein interaction (PPI) networks and analyze enriched KEGG pathways. The biological networks of Ginseng Radix and Astragali Radix were compared separately or together using the DyNet application. Molecular docking was used to verify the predicted results. Further, in vitro experiments were conducted to validate the synergistic pathways identified in in silico studies.

RESULTS

In the PPI network comparison, the combination created 89 new interactions and an increased average degree (11.260) when compared to single herbs (10.296 and 9.394). The new interactions concentrated on HRAS, STAT3, JUN, and IL6. The topological analysis identified 20 core targets of the combination, including three Ginseng Radix-specific targets, three Astragali Radix-specific targets, and 14 shared targets. In KEGG enrichment analysis, the combination regulated additional signaling pathways (152) more than Ginseng Radix (146) and Astragali Radix (134) alone. The targets of the herb pair synergistically regulated cancer pathways, specifically hypoxia-inducible factor 1 (HIF-1) signaling pathway. In vitro experiments including enzyme-linked immunosorbent assay and Western blot demonstrated that two herbs combination could up-regulate HIF-1α signaling pathway at different combined concentrations compared to either single herb alone.

CONCLUSION

The herb pair increased protein interactions and adjusted metabolic pathways more than single herbs. This study provides insights into the combination of Ginseng Radix and Astragali Radix in clinical practice.

Molecular network mechanism in cerebral ischemia-reperfusion rats treated with human urine stem cells

Objective

To explore the effect of human urine-derived stem cells (husc) in improving the neurological function of rats with cerebral ischemia-reperfusion (CIR), and report new molecular network by bioinformatics, combined with experiment validation.

Methods

After CIR model was established, and husc were transplanted into the lateral ventricle of rats，neurological severe score (NSS) andgene network analysis were performed. Firstly, we input the keywords "Cerebral reperfusion" and "human urine stem cells" into Genecard database and merged data with findings from PubMed so as to get their targets genes, and downloaded them to make Venny intersection plot. Then, Gene ontology (GO) analysis, kyoto encyclopedia of genes and genomes (KEGG) pathway analysis and protein-protein interaction (PPI) were performed to construct molecular network of core genes. Lastly, the expressional level of core genes was validated via quantitative real-time polymerase chain reaction (qRT-PCR), and localized by immunofluorescence.

Results

Compared with the Sham group, the neurological function of CIR rats was significantly improved after the injection of husc into the lateral ventricle; at 14 days, P = 0.028, which was statistically significant. There were 258 overlapping genes between CIR and husc, and integrated with 252 genes screened from PubMed and CNKI. GO enrichment analysis were mainly involved neutrophil degranulation, neutrophil activation in immune response and platelet positive regulation of degranulation, Hemostasis, blood coagulation, coagulation, etc. KEGG pathway analysis was mainly involved in complement and coagulation cascades, ECM-receptor. Hub genes screened by Cytoscape consist ofCD44, ACTB, FN1, ITGB1, PLG, CASP3, ALB, HSP90AA1, EGF, GAPDH. Lastly, qRT-PCR results showed statistic significance (P < 0.05) in ALB, CD44 and EGF before and after treatment, and EGF immunostaining was localized in neuron of cortex.

Conclusion

husc transplantation showed a positive effect in improving neural function of CIR rats, and underlying mechanism is involved in CD44, ALB, and EGF network.

Network pharmacology and molecular docking to explore the mechanism of a clinical proved recipe for external use of clearing heat and removing dampness in the treatment of immune-related cutaneous adverse events

Immune-related cutaneous adverse events (ircAEs) will undermine the patients' quality of lives, and interrupt the antitumor therapy. A clinical proved recipe for external use of clearing heat and removing dampness (Qing-Re-Li-Shi Formula, hereinafter referred to as "QRLSF") is beneficial to the treatment of ircAEs in clinical practice. Our study will elucidate the mechanism of QRLSF against ircAEs based on network pharmacology and molecular docking. The active components and corresponding targets of QRLSF were collected through traditional Chinese medicine systems pharmacology database. GeneCards, online Mendelian inheritance in man, and pharmacogenomics knowledgebase were used to screen the targets of ircAEs. The intersecting targets between drug and disease were acquired by venn analysis. Cytoscape software was employed to construct "components-targets" network. Search tool for the retrieval of interacting genes/proteins database was applied to establish the protein-protein interaction network and then its core targets were identified. Gene ontology and Kyoto encyclopedia of genes and genomes analysis was performed to predict the mechanism. The molecular docking verification of key targets and related phytomolecules was accomplished by AutoDock Vina software. Thirty-nine intersecting targets related to QRLSF against ircAEs were recognized. The analysis of network clarified 5 core targets (STAT3, RELA, TNF, TP53, and NFKBIA) and 4 key components (quercetin, apigenin, luteolin, and ursolic acid). The activity of QRLSF against ircAEs could be attributed to the regulation of multiple biological effects via multi-pathways (PI3K-Akt pathway, cytokine-cytokine receptor interaction, JAK-STAT pathway, chemokine pathway, Th17 cell differentiation, IL-17 pathway, TNF pathway, and Toll-like receptor pathway). The binding activities were estimated as good level by molecular docking. These discoveries disclosed the multi-component, multi-target, and multi-pathway characteristics of QRLSF against ircAEs, providing a new strategy for such medical problem.

Exploring the Molecular Mechanism of Tong Xie Yao Fang in Treating Ulcerative Colitis Using Network Pharmacology and Molecular Docking

Objective. The purpose of this study was to investigate the mechanisms of action of Tong Xie Yao Fang (TXYF) against ulcerative colitis (UC) by employing a network pharmacology approach. Methods. The network pharmacology approach, including screening of the active ingredients and targets, construction of the active ingredient-drug target network, the active ingredient-diseasetarget network, the protein–protein interaction (PPI) network, enrichment analyses, molecular docking, and targets validation, was used to explore the mechanisms of TXYF against UC. Results. 34 active ingredients and 129 and 772 targets of TXYF and UC, respectively, were identified. The intersection of the active ingredient-drug target network, the active ingredient-disease target network, and the PPI network suggested that kaempferol, beta-sitosterol, wogonin, and naringenin were the core ingredients and prostaglandin-endoperoxide synthase 2 (PTGS2) was the core target. Enrichment analyses showed that regulation of exogenous protein binding and other functions were of great significance. Nuclear factor-kappa B (NF-κB) signaling pathway, interleukin-17 (IL-17) signaling pathway, and tumor necrosis factor (TNF) signaling pathway were important pathways. Results of molecular docking indicated that the core ingredients and the target molecule had strong binding affinities. We have validated the high levels of expression of PTGS2 in UC by analyzing three additional datasets from the Gene Expression Omnibus (GEO) database. Conclusions. There are multiple ingredients, targets, and pathways involved in TXYF’s effectiveness against UC, and these findings will promote further research and clinical applications.

Potential Mechanisms of White Peony against Primary Sjögren's Syndrome Based on Network Pharmacology and Molecular Docking

BACKGROUND

Multiple system and organ damage occurs with the continuous progression of primary Sjögren's syndrome (pSS), and the lack of specific drugs against this disease is a huge challenge. White peony (WP), a widely used traditional Chinese herb, has been confirmed to have a therapeutic value in pSS. However, the specific mechanisms of WP in the treatment of pSS are unknown.

METHODS

The active ingredients and their targets in WP were searched on the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and disease-related targets were collected from GeneCards, Online Mendelian Inheritance in Man (OMIM), and the Therapeutic Target Database (TTD). The overlapping targets were acquired by taking the intersection. A protein-protein interaction (PPI) network was structured using the STRING database. A disease-drug-ingredient-target (D-D-I-T) network was built using Cytoscape software. By filtering twice, core targets were acquired. Gene Ontology (GO) and Kyoto Encyclopedia Gene and Genome (KEGG) pathway enrichment analysis were accompanied by R packages. Finally, molecular docking was used to verify the abovementioned results.

RESULTS

In total, we screened 88 WP-related targets, 1480 pSS-related targets, and 32 overlapping targets. D-D-I-T Network analysis displayed six main active ingredients of WP, which played a significant therapeutic role in pSS. Further topological analysis selected seven core target genes, including IL-6, TNF, PPARγ, AKT1, CASP3, NOS3, and JUN. GO and KEGG analysis were used to elucidate pharmacological mechanisms, mainly acting in the AGE-RAGE signaling pathway. Molecular docking proved that paeoniflorin bound well with core targets.

CONCLUSION

Our study revealed that IL-6, TNF, AKT1, CASP3, NOS3, and JUN may be pathogenic target genes, and PPARγ may be a protective target gene. The main active ingredients of WP mainly played a therapeutic role via the AGE-RAGE signaling pathway. These findings provide a fundamental and theoretical basis for the clinical application of WP.

Network pharmacology and molecular docking-based investigations of Kochiae Fructus’s active phytomolecules, molecular targets, and pathways in treating COVID-19

COVID-19 disease is caused by SARS-CoV-2. Hyper-inflammation mediated by proinflammatory cytokines is humans’ primary etiology of SARS-CoV-2 infection. Kochiae Fructus is widely used in China as traditional Chinese medicine (TCM) to treat inflammatory diseases. Due to its anti-inflammatory properties, we hypothesized that Kochiae Fructus would be a promising therapeutic agent for COVID-19. The active phytomolecules, targets, and molecular pathways of Kochiae Fructus in treating COVID-19 have not been explored yet. Network pharmacology analysis was performed to determine the active phytomolecules, molecular targets, and pathways of Kochiae Fructus. The phytomolecules in Kochiae Fructus were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and their potential targets were predicted with the SwissTargetPrediction webserver. COVID-19-related targets were recovered from the GeneCards database. Intersecting targets were determined with the VENNY tool. The Protein-protein interaction (PPI) and Molecular Complex Detection (MCODE) network analyses were constructed using the Cytoscape software. Using the DAVID tool, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the intersecting targets. AutoDock Vina (version 1.2.0.) was used for molecular docking analysis. Six active phytomolecules and 165 their potential targets, 1,745 COVID-19-related targets, and 34 intersecting targets were identified. Network analysis determined 13 anti-COVID-19 core targets and three key active phytomolecules (Oleanolic acid, 9E,12Z-octadecadienoic acid, and 11,14-eicosadienoic acid). Three key pathways (pathways in cancer, the TNF signaling pathway, and lipid and atherosclerosis) and the top six anti-COVID-19 core targets (IL-6, PPARG, MAPK3, PTGS2, ICAM1, and MAPK1) were determined to be involved in the treatment of COVID-19 with active phytomolecules of Kochiae Fructus. Molecular docking analysis revealed that three key active phytomolecules of Kochiae Fructus had a regulatory effect on the identified anti-COVID-19 core targets. Hence, these findings offer a foundation for developing anti-COVID-19 drugs based on phytomolecules of Kochiae Fructus.