Mechanism of Modified Danggui Sini Decoction for Knee Osteoarthritis Based on Network Pharmacology and Molecular Docking

Integrating network pharmacology and experimental validation via PPAR signaling to ameliorate rheumatoid arthritis: Insights from Corydalis Decumbentis Rhizoma (Xiatianwu)

Corydalis Decumbentis Rhizoma (Xiatianwu, XTW) exhibits a positive effect in treating rheumatoid arthritis (RA). However, the precise molecular mechanisms underlying its effects remain unclear. In this study, TNF-α was used to induce inflammation and establish and in vitro RA model. Network pharmacology was employed to identify the important active components and targets in the treatment of XTW on RA. CCK-8 was used to investigate the cell viability. GW9662 (a PPARG antagonist) was applied to validate the network pharmacology prediction. ELISA was used to measure pro-inflammatory cytokines (IL-6, IL-1β, and INF-γ) and oxidative stress markers (MMP-2, MDA, and ROS). HPLC-MS was conducted to validate the four important active ingredients (bicuculline, ferulic acid, berberine, and jatrorrhizine) in XTW. Western blotting was carried out to detect the protein levels of PPAR-γ. In vitro experiments demonstrated that XTW exerted dose-dependent anti-RA effects by downregulating pro-inflammatory cytokines and oxidative stress markers. Through Network pharmacology, three targets (RXRA, PPARG, and PPARA) and four active ingredients (bicuculline, ferulic acid, berberine, and jatrorrhizine) were demonstrated important in the treatment of XTW on RA. Besides, PPAR signaling pathway may be a therapeutic target for XTW treating RA. Further experiments confirmed that XTW administration significantly inhibited inflammation and oxidative stress by upregulating the PPAR signaling pathway. In conclusion, XTW modulates RXRA, PPARG, and PPARA through the PPAR signaling pathway, thereby mitigating inflammation and oxidative stress in RA.

A comprehensive study on the impact of Ligustrum vicaryi L. fruit polysaccharide on myocardial fibrosis through animal experiments, network pharmacology and molecular docking

Background

Myocardial fibrosis (MF) is a prevalent pathological condition associated with various heart diseases, such as heart failure and arrhythmias, which disrupt electrical signals and reduce pumping efficiency. This research explored the therapeutic effects and potential mechanisms of Ligustrum vicaryi L. fruit polysaccharide (LVFP) on MF.

Methods

In vivo experiments, including fibrosis markers assay, echocardiography, HE staining, Sirius red staining, and Masson's trichrome staining, were performed to evaluate the therapeutic efficacy of LVFP in treating isoproterenol (ISO)-induced MF. We utilized the PharmMapper database to identify targets of LVFP, aiming to explore potential targets. Additionally, we obtained MF-related targets from the GeneCards database. We utilized Venny, a bioinformatics tool, to identify the intersection between the targets of LVFP and those related to MF. We utilized the STRING database to construct a protein interaction network for the overlapping targets and identified key targets for LVFP in treating MF through cytoHubba analysis. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the intersection targets. We also examined the interaction between LVFP and the key targets using molecular docking techniques.

Results

LVFP significantly inhibited fibrosis biomarker such as hydroxyproline (HYP) and decreased myocardial fibrosis level as shown by heart weight to tibia length (HW/TL) measurement when compared to ISO-treated mice. Additionally, it increased ejection fraction (EF) and fractional shortening (FS) levels. LVFP showed decreased collagen levels compared to the ISO-treated mice by histological quantification of cardiac fibrosis. Based on the monosaccharide structures of LVFP, 413 targets were identified, with 67 associated with MF. Analysis indicated that the 9 hub genes (AKT1, HSP90AA1, SRC, GSK3β, VEGFR2, RHOA, ENO1, PKM, and IL-2) play roles in MF treatment by participating in signaling pathways related to prostate cancer, lipid and atherosclerosis, and insulin resistance. Molecular docking results showed that LVFP exhibited strong binding potential to VEGFR2 (-8.65 kcal/mol), AKT1 (-7.36 kcal/mol) and GSK3β (-7.68 kcal/mol).

Conclusion

LVFP shows promise as a therapeutic agent for MF, primarily through the regulation of various signaling pathways and targets. These findings provide novel insights for the treatment of MF utilizing LVFP.

Exploring the Mechanisms of Sanguinarine in the Treatment of Osteoporosis by Integrating Network Pharmacology Analysis and Deep Learning Technology

BACKGROUND

Sanguinarine (SAN) has been reported to have antioxidant, antiinflammatory, and antimicrobial activities with potential for the treatment of osteoporosis (OP).

OBJECTIVE

This work purposed to unravel the molecular mechanisms of SAN in the treatment of OP.

METHODS

OP-related genes and SAN-related targets were predicted from public databases. Differential expression analysis and VennDiagram were adopted to detect SAN-related targets against OP. Protein-protein interaction (PPI) network was served for core target identification. Molecular docking and DeepPurpose algorithm were further adopted to investigate the binding ability between core targets and SAN. Gene pathway scoring of these targets was calculated utilizing gene set variation analysis (GSVA). Finally, we explored the effect of SAN on the expressions of core targets in preosteoblastic MC3T3-E1 cells.

RESULTS

A total of 21 candidate targets of SAN against OP were acquired. Furthermore, six core targets were identified, among which CASP3, CTNNB1, and ERBB2 were remarkably differentially expressed in OP and healthy individuals. The binding energies of SAN with CASP3, CTNNB1, and ERBB2 were -6, -6.731, and -7.162 kcal/mol, respectively. Moreover, the GSVA scores of the Wnt/calcium signaling pathway were significantly lower in OP cases than in healthy individuals. In addition, the expression of CASP3 was positively associated with Wnt/calcium signaling pathway. CASP3 and ERBB2 were significantly lower expressed in SAN group than in DMSO group, whereas the expression of CTNNB1 was in contrast.

CONCLUSION

CASP3, CTNNB1, and ERBB2 emerge as potential targets of SAN in OP prevention and treatment.

Exploring the Anti-inflammatory Potential of Novel Chrysin Derivatives through Cyclooxygenase-2 Inhibition

Inducible cyclooxygenase-2 (COX-2) is a crucial enzyme involved in the processes of inflammation and carcinogenesis, primarily by catalyzing the production of prostaglandin E2 (PGE2), a significant mediator of inflammation. In this study, we designed and synthesized a series of novel chrysin derivatives to evaluate their anti-inflammatory potential through COX-2 inhibition using in vitro cultures of RAW264.7 macrophages and in silico molecular docking assays. Among the synthesized derivatives, compounds 1a and 8 demonstrated significant inhibition of lipopolysaccharide (LPS)-stimulated proinflammatory cytokine production, including interleukin-6 and tumor necrosis factor-alpha, in RAW264.7 cells. Additionally, these derivatives effectively inhibited PGE2 secretion through COX-2 enzyme inhibition in LPS-stimulated RAW264.7 cells. Molecular docking simulation results revealed that 1a and 8 possess high binding affinities for the COX-2 active site, indicating a strong potential for enzyme inhibition. Furthermore, druglikeness and ADMET predictions for these compounds indicated favorable pharmacokinetic properties, suggesting their suitability as drug candidates. Therefore, compounds 1a and 8 hold promise as potential anti-inflammatory agents for further development.

Study on the anti-atherosclerosis mechanisms of Tanyu Tongzhi formula based on network pharmacology, Mendelian randomization, and experimental verification

CONTEXT

Tanyu Tongzhi Formula (TTF) exhibits potential against atherosclerosis; however, its mechanisms remain unclear.

OBJECTIVE

This study explores the pharmacological mechanisms of TTF in treating atherosclerosis.

MATERIALS AND METHODS

Network pharmacology, molecular docking, mendelian randomization (MR), and liquid chromatography-mass spectrometry (LC-MS) analyses were utilized to reveal potential targets and compounds of TTF against atherosclerosis. After exploring the appropriate concentration of TTF to treat HCAECs using Cell Counting Kit-8 (CCK-8), the HCAECs were divided into three groups: control, oxidized low-density lipoprotein (ox-LDL, 50 μg/mL), and ox-LDL (50 μg/mL) + TTF (1 mg/mL). After 24-h incubation, the efficacy of TTF was verified by CCK-8, Oil red O staining, and ELISA. The expression of key targets was detected by real-time polymerase chain reaction (qPCR) and western blotting.

RESULTS

A total of 137 active compounds and 127 potential TTF targets against atherosclerosis were identified. MR identified ALB, TNF, PPARα, and PPARγ as key targets. Molecular docking indicated that baicalin, naringenin, and curcumin exhibited suitable binding activities to these targets, further confirming by LC-MS analysis. The IC50 of TTF in HCAECs was 18.25 mg/mL. TTF treatment significantly improved atherosclerosis by enhancing cell viability, reducing lipid accumulation, and inhibiting inflammation factors (IL6, IL1B and TNF-α) in ox-LDL-treated HCAECs. Moreover, qPCR or western blotting indicated that TTF could up-regulate PPARα and PPARγ while down-regulate TNF expression.

DISCUSSION AND CONCLUSIONS

Our results revealed active compounds, key pathways, and core targets of TTF against atherosclerosis, providing experimental support for its application in treating of atherosclerosis.

Molecular mechanisms underlying Tao-Hong-Si-Wu decoction treating hyperpigmentation based on network pharmacology, Mendelian randomization analysis, and experimental verification

CONTEXT

Hyperpigmentation, a common skin condition marked by excessive melanin production, currently has limited effective treatment options.

OBJECTIVE

This study explores the effects of Tao-Hong-Si-Wu decoction (THSWD) on hyperpigmentation and to elucidate the underlying mechanisms.

MATERIALS AND METHODS

We employed network pharmacology, Mendelian randomization, and molecular docking to identify THSWD's hub targets and mechanisms against hyperpigmentation. The Cell Counting Kit-8 (CCK-8) assay determined suitable THSWD treatment concentrations for PIG1 cells. These cells were exposed to graded concentrations of THSWD-containing serum (2.5%, 5%, 10%, 15%, 20%, 30%, 40%, and 50%) and treated with α-MSH (100 nM) to induce an in vitro hyperpigmentation model. Assessments included melanin content, tyrosinase activity, and Western blotting.

RESULTS

ALB, IL6, and MAPK3 emerged as primary targets, while quercetin, apigenin, and luteolin were the core active ingredients. The CCK-8 assay indicated that concentrations between 2.5% and 20% were suitable for PIG1 cells, with a 50% cytotoxicity concentration (CC50) of 32.14%. THSWD treatment significantly reduced melanin content and tyrosinase activity in α-MSH-induced PIG1 cells, along with downregulating MC1R and MITF expression. THSWD increased ALB and p-MAPK3/MAPK3 levels and decreased IL6 expression in the model cells.

DISCUSSION AND CONCLUSION

THSWD mitigates hyperpigmentation by targeting ALB, IL6, and MAPK3. This study paves the way for clinical applications of THSWD as a novel treatment for hyperpigmentation and offers new targeted therapeutic strategies.

Molecular docking and network pharmacology research on the Danggui Sini Decoction's mechanism of action for treating erectile dysfunction

Utilizing network pharmacology and molecular docking, we evaluated the possible pharmacological mechanism of Danggui Sini Decoction (DGSND) for treating erectile dysfunction (ED). DGSND's chemical components and targets were found utilizing the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Disease-related genes associated with ED were identified through GeneCards, OMIM, TTD, DrugBank, and DisGeNET databases. These datasets intersected to identify possible DGSND targets for treating ED. We developed an interactive visual network that linked herbs, active components, diseases, and targets using Cytoscape 3.7.1. The protein-protein interactions (PPI) were analyzed using the STRING database. The DAVID database was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment studies to determine the mechanism of action of the discovered genes. The pathways most strongly associated with ED were analyzed through histograms and bubble maps. From the PPI network, the 6 promising targets were selected for molecular docking with the top ranked compounds in terms of degree value. DGSND contains 7 Chinese herbal medicines, 142 main components, and 73 latent targets for treating ED. GO and KEGG analyses suggest that DGSND may have the ability to modulate oxidative stress, apoptosis, and inflammatory responses. Through the PPI network and topology analysis, 6 core genes were pinpointed. Molecular docking revealed that beta-sitosterol exhibited the lowest binding energy with BCL2, indicating a more stable structure. This study demonstrates that DGSND's compounds stimulate NO synthesis and reduce inflammation and cell apoptosis to improve ED by acting on AKTI, ALB, IL6, TNF, TP53, and BCL2. The findings show that DGSND's compounds These findings offer a valuable scientific foundation for further understanding the mechanism of DGSND in treating ED.

Multi-omics association study integrating GWAS and pQTL data revealed MIP-1α as a potential drug target for erectile dysfunction

Background

Erectile dysfunction (ED) brings heavy burden to patients and society. Despite the availability of established therapies, existing medications have restricted efficacy. Therefore, we utilized a two-sample Mendelian randomization (MR) approach to find the drug targets that might enhance the clinical outcome of ED.

Methods

Genetic instruments associated with circulating inflammatory proteins were obtained from a genome-wide association study (GWAS) involving 8,293 European participants. Summary statistics for ED were extracted from a meta-analysis of the United Kingdom Biobank cohort compromised of 6,175 cases and 217,630 controls with European descent. We utilized multi-omics method and MR study to explore potential drug targets by integrating GWAS and protein quantity trait loci (pQTL) data. Inverse-variance weighted (IVW) method was applied as the primary approach. Cochran's Q statistics was employed to investigate the presence of heterogeneity. Furthermore, we identify the potential therapeutic drug targets for the treatment of ED utilizing molecular docking technology.

Results

This MR analysis of integrating GWAS and pQTL data showed that macrophage inflammatory protein-1 alpha (MIP-1α) was causally associated with the risk of ED (OR:1.19, 95%CI:1.02-1.39, p = 0.023). Meanwhile, the results of the weighted median model were consistent with the IVW estimates (OR:1.26, 95%CI:1.04-1.52, p = 0.018). Sensitivity analysis revealed no horizontal pleiotropy and heterogeneity. Furthermore, four anti-inflammatory or tonifying small molecular compounds, encompassing echinacea, pinoresinol diglucoside, hypericin, and icariin were identified through molecular docking technology.

Conclusion

This study identified MIP-1α as an underlying druggable gene and promising novel therapeutic target for ED, necessitating further investigation to detect the potential mechanisms by which MIP-1α might impact the development of ED.

Causal effects of systemic inflammatory proteins on Guillain-Barre Syndrome: insights from genome-wide Mendelian randomization, single-cell RNA sequencing analysis, and network pharmacology

Background

Evidence from observational studies indicates that inflammatory proteins play a vital role in Guillain-Barre Syndrome (GBS). Nevertheless, it is unclear how circulating inflammatory proteins are causally associated with GBS. Herein, we conducted a two-sample Mendelian randomization (MR) analysis to systematically explore the causal links of genetically determined systemic inflammatory proteins on GBS.

Methods

A total of 8,293 participants of European ancestry were included in a genome-wide association study of 41 inflammatory proteins as instrumental variables. Five MR approaches, encompassing inverse-variance weighted, weighted median, MR-Egger, simple model, and weighted model were employed to explore the causal links between inflammatory proteins and GBS. MR-Egger regression was utilized to explore the pleiotropy. Cochran's Q statistic was implemented to quantify the heterogeneity. Furthermore, we performed single-cell RNA sequencing analysis and predicted potential drug targets through molecular docking technology.

Results

By applying MR analysis, four inflammatory proteins causally associated with GBS were identified, encompassing IFN-γ (OR:1.96, 95%CI: 1.02-3.78, PIVW=0.045), IL-7 (OR:1.86, 95%CI: 1.07-3.23, PIVW=0.029), SCGF-β (OR:1.56, 95%CI: 1.11-2.19, PIVW=0.011), and Eotaxin (OR:1.99, 95%CI: 1.01-3.90, PIVW=0.046). The sensitivity analysis revealed no evidence of pleiotropy or heterogeneity. Additionally, significant genes were found through single-cell RNA sequencing analysis and several anti-inflammatory or neuroprotective small molecular compounds were identified by utilizing molecular docking technology.

Conclusions

Our MR analysis suggested that IFN-γ, IL-7, SCGF-β, and Eotaxin were causally linked to the occurrence and development of GBS. These findings elucidated potential causal associations and highlighted the significance of these inflammatory proteins in the pathogenesis and prospective therapeutic targets for GBS.

Elucidation of the anti-colorectal cancer mechanism of Atractylodes lancea by network pharmacology and experimental verification

Atractylodes lancea which was listed in "Shennong's Materia Medica" and could be used to treat gastrointestinal-associated diseases. However, its roles, core and active ingredients, and mechanisms in treatment of colorectal cancer (CRC) were still unknown. Therefore, network pharmacology and experimental validation were used to clarify the effects, core active ingredients and molecular mechanisms of Atractylodes lancea. We found that Atractylodes lancea has 28 effective active components and 213 potential targets. Seventy-three genes which demonstrate interaction between the Atractylodes lancea and CRC were confirmed. Enrichment analysis showed that 2033 GO biological process items and 144 KEGG pathways. Survival and molecular docking analysis revealed that luteolin as the core component interacted with these genes (Matrix metalloproteinase 3 (MMP3), Matrix metalloproteinase 9 (MMP9), Tissue inhibitor of metalloproteinases 1 (TIMP1), Vascular endothelial growth factor A (VEGFA)) with the lowest binding energy, and these genes were involved in building a prognostic model for CRC. Cellular phenotyping experiments showed that luteolin could inhibit the proliferation and migration of CRC cells and downregulate the expression of MMP3, MMP9, TIMP1, VEGFA probably by Phosphoinositide 3-kinase/ serine/threonine kinase Akt (PI3K/AKT) pathway. To conclude, Atractylodes lancea could inhibit proliferation and migration of CRC cells through its core active ingredient (luteolin) to suppress the expression of MMP3, MMP9, TIMP1, VEGFA probably by PI3K/AKT pathway.

Safflower Alleviates Pulmonary Arterial Hypertension by Inactivating NLRP3: A Combined Approach of Network Pharmacology and Experimental Verification

INTRODUCTION

Traditional Chinese medicinal plant, safflower, shows effective for treating pulmonary arterial hypertension (PAH), yet the underlying mechanisms remain largely unexplored. This study is aimed at exploring the potential molecular mechanisms of safflower in the treatment of PAH.

METHODS

Network pharmacology approach and molecular docking were applied to identify the core active compounds, therapeutic targets, and potential signaling pathways of safflower against PAH. Meanwhile, high-performance liquid chromatography (HPLC) assay was performed to determine the core compounds from safflower. Further, the mechanism of action of safflower on PAH was verified by in vivo and in vitro experiments.

RESULTS

A total of 15 active compounds and 177 targets were screened from safflower against PAH. Enrichment analysis indicated that these therapeutic targets were mainly involved in multiple key pathways, such as TNF signaling pathway and Th17 cell differentiation. Notably, molecular docking revealed that quercetin (core compound in safflower) displayed highest binding capacity with NLRP3. In vivo, safflower exerted therapeutic effects on PAH by inhibiting right ventricular hypertrophy, inflammatory factor release, and pulmonary vascular remodeling. Mechanistically, it significantly reduced the expression of proangiogenesis-related factors (MMP-2, MMP-9, Collagen 1, and Collagen 3) and NLRP3 inflammasome components (NLRP3, ASC, and Caspase-1) in PAH model. Similarly, these results were observed in vitro. Besides, we further confirmed that NLRP3 inhibitor had the same therapeutic effect as safflower in vitro.

CONCLUSION

Our findings suggest that safflower mitigates PAH primarily by inhibiting NLRP3 inflammasome activation. This provides novel insights into the potential use of safflower as an alternative therapeutic approach for PAH.

Dang-Gui-Si-Ni decoction facilitates wound healing in diabetic foot ulcers by regulating expression of AGEs/RAGE/TGF-β/Smad2/3

Diabetic foot ulcer (DFU) is a predominant complication of diabetes mellitus with poor prognosis accompanied by high amputation and mortality rates. Dang-Gui-Si-Ni decoction (DSD), as a classic formula with a long history in China, has been found to improve DFU symptoms. However, mechanism of DSD for DFU therapy remains unclear with no systematic elaboration. In vivo, following establishment of DFU rat model, DSD intervention with low, medium and high doses was done, with Metformin (DM) as a positive control group. With wound healing detection, pathological changes by HE staining, inflammatory factor expression by ELISA and qRT-PCR, oxidative stress levels by ELISA, and AGEs/RAGE/TGF-β/Smad2/3 expression by Western blot were performed. In vitro, intervention with LY2109761 (TGF-β pathway inhibitor) based on DSD treatment in human dermal fibroblast-adult (HDF-a) cells was made. Cell viability by CCK8, migration ability by cell scratch, apoptosis by flow cytometry, and AGEs/RAGE/TGF-β/Smad2/3 expression by Western blot were measured. DFU rats exhibited elevated AGEs/RAGE expression, whereas decreased TGF-β1 and p-Smad3/Smad3 protein expression, accompanied by higher IL-1β, IL-6, TNF-α levels, and oxidative stress. DSD intervention reversed above effects. Glucose induction caused lower cell viability, migration, TGF-β1 and p-Smad3/Smad3 protein expression, with increased apoptosis and AGEs/RAGE expression in HDF-a cells. These effects were reversed after DSD intervention, and further LY2109761 intervention inhibited DSD effects in cells. DSD intervention may facilitate wound healing in DFU by regulating expression of AGEs/RAGE/TGF-β/Smad2/3, providing scientific experimental evidence for DSD clinical application for DFU therapy.

Exploration of the Mechanisms Underlying Yu's Enema Formula in Treating Ulcerative Colitis by Blocking the RhoA/ROCK Pathway based on Network Pharmacology, High-performance Liquid Chromatography Analysis, and Experimental Verification

BACKGROUND

The traditional Chinese medicine formula, Yu's Enema Formula (YEF), has demonstrated potential in the treatment of Ulcerative Colitis (UC).

OBJECTIVE

This study aimed to unveil the anti-UC mechanisms of YEF.

METHODS

Utilizing public databases, we obtained YEF and UC-related targets. GO and KEGG analyses were conducted via clusterProfiler and Reactome. The STRING database facilitated the construction of the PPI network, and hub targets were selected using cytoHubba. We used R software for differential expression and correlation analyses, and molecular docking was performed with PyMOL and AutoDock. HPLC analysis identified the compounds in YEF. For in vivo validation, a UC rat model was employed.

RESULTS AND DISCUSSION

495 YEF-UC overlapping targets were identified. GO and KEGG analyses indicated enrichment in exogenous stimuli response, peptide response, positive MAPK cascade regulation, interleukin- related signaling, and the TLR4 cascade. Hub targets included CTNNB1, JUN, MAPK1, MAPK3, SRC, STAT3, TLR4, TP53, and RELA, which were often interconnected. Molecular docking revealed quercetin's strong binding affinity with CTNNB1, MAPK1, MAPK3, SRC, STAT3, TLR4, and TP53, consistent with HPLC analysis. In vivo experiments suggested that YEF has the potential to alleviate UC symptoms and protect the intestinal mucosal barrier by inhibiting the RhoA/ROCK pathway.

CONCLUSION

YEF may safeguard the intestinal mucosal barrier in UC by targeting CTNNB1, MAPK1, MAPK3, SRC, STAT3, TLR4, and TP53, while blocking the RhoA/ROCK pathway.

Study of Therapeutic Mechanisms of Bupi Yichang Formula against Colon Cancer Based on Network Pharmacology, Machine Learning, and Experimental Verification

Bupi Yichang formula (BPYCF) has shown the anti-cancer potential; however, its effects on colon cancer and the mechanisms remain unknown. This study intended to explore the effects of BPYC on colon cancer and its underlying mechanisms. BPYCF-related and colon cancer-related targets were acquired from public databases, followed by differentially expressed genes (DEG) identification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using clusterProfiler. A protein-protein interaction (PPI) network was constructed using STRING database. CytoHubba and MCODE to screen the hub targets. A diagnostic model was built using random forest algorithm. Molecular docking was conducted using PyMOL and AutoDock. High-performance liquid chromatograph-mass spectrometry (HPLC-MS) analysis and in vitro validation were performed. Forty-six overlapping targets of BPYCF-related, colon cancer-related targets, and DEGs were obtained. GO and KEGG analyses showed that the targets were mainly enriched in response to lipopolysaccharide, neuronal cell body, protein serine/threonine/tyrosine, as well as C-type lectin receptor, NOD-like receptor, and TNF signaling pathways. Five targets were identified as the pivotal targets, among which, NOS3, CASP8, RIPK3, and TNFRSF10B were stably docked with the core active component, naringenin. Naringenin was also identified from the BPYCF sample through HPLC-MS analysis. In vitro experiments showed that BPYCF inhibited cell viability, reduced NOS3 expression, and elevated CASP8, RIPK3, and TNFRSF10B expression in colon cancer cells. BPYCF might treat colon cancer mainly by regulating NOS3, CASP8, RIPK3, and TN-FRSF10B. This study first revealed the therapeutic effects and mechanisms of BPYCF against colon cancer, paving the path for the development of targeted therapeutic strategies for this cancer in the clinic.

Exploring the Mechanism of Zilongjin in Treating Lung Adenocarcinoma Based on Network Pharmacology Combined with Experimental Verification

Zilongjin (ZLJ) is a common traditional Chinese medicine for lung adenocarcinoma (LUAD) treatment. However, its mechanisms of action remain to be elucidated. Network pharmacology was used to explore the underlying mechanisms of ZLJ on LUAD treatment. The disease-related targets were determined from the Gene-Cards and DisGeNET databases. Active compounds and targets of ZLJ were obtained from the HIT, TCMSP, and TCMID databases. Then the protein-protein interaction (PPI) network was built by the STRING database to identify core-hub targets of ZLJ in LUAD. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to analyze the enriched regulatory pathways of targets. Molecular docking analysis was used to evaluate interactions between potential targets and active compounds. Finally, qRT-PCR was used to further verify the results of network pharmacology. A total of 124 LUAD-related targets of ZLJ and 5 active compounds of ZLJ from the relevant databases were screened out. Among these target proteins, JUN, CDH1, PPARG, and FOS were core hub-genes in the PPI network. GO and KEGG pathway enrichment analysis indicated that these targets might regulate the PPAR signaling pathway in LUAD. JUN, PPARG, and FOS levels were upregulated, while CDH1 level was downregulated in LUAD cells. This study discerned that ZLJ may target genes such as JUN, FOS, PPARG, and CDH1 via the PPAR signaling pathway in LUAD, offering foundational insights for further exploration of ZLJ in clinical applications.

Integrating network pharmacology and Mendelian randomization to explore potential targets of matrine against ovarian cancer

BACKGROUND

Matrine has been reported inhibitory effects on ovarian cancer (OC) cell progression, development, and apoptosis. However, the molecular targets of matrine against OC and the underlying mechanisms of action remain elusive.

OBJECTIVE

This study endeavors to unveil the potential targets of matrine against OC and to explore the intricate relationships between these targets and the pathogenesis of OC.

METHODS

The effects of matrine on the OC cells (A2780 and AKOV3) viability, apoptosis, migration, and invasion was investigated through CCK-8, flow cytometry, wound healing, and Transwell analyses, respectively. Next, Matrine-related targets, OC-related genes, and ribonucleic acid (RNA) sequence data were harnessed from publicly available databases. Differentially expressed analyses, protein-protein interaction (PPI) network, and Venn diagram were involved to unravel the core targets of matrine against OC. Leveraging the GEPIA database, we further validated the expression levels of these core targets between OC cases and controls. Mendelian randomization (MR) study was implemented to delve into potential causal associations between core targets and OC. The AutoDock software was used for molecular docking, and its results were further validated using RT-qPCR in OC cell lines.

RESULTS

Matrine reduced the cell viability, migration, invasion and increased the cell apoptosis of A2780 and AKOV3 cells (P< 0.01). A PPI network with 578 interactions among 105 candidate targets was developed. Finally, six core targets (TP53, CCND1, STAT3, LI1B, VEGFA, and CCL2) were derived, among which five core targets (TP53, CCND1, LI1B, VEGFA, and CCL2) differential expressed in OC and control samples were further picked for MR analysis. The results revealed that CCND1 and TP53 were risk factors for OC. Molecular docking analysis demonstrated that matrine had good potential to bind to TP53, CCND1, and IL1B. Moreover, matrine reduced the expression of CCND1 and IL1B while elevating P53 expression in OC cell lines.

CONCLUSIONS

We identified six matrine-related targets against OC, offering novel insights into the molecular mechanisms underlying the therapeutic effects of matrine against OC. These findings provide valuable guidance for developing more efficient and targeted therapeutic approaches for treating OC.

Mechanism Study of Polydatin in Treating Spinal Cord Injury by Modulating Mitochondrial Membrane Potential Based on Network Pharmacology and Molecular Docking

Spinal cord injury (SCI) is one of the most devastating central lesions, and mitochondrial function plays an important role in secondary injury after SCI. Polydatin (PD) is a natural glycosylated precursor of resveratrol, showing mitochondrial preservation effects in the central nervous system. This study aimed to identify the hub target genes of PD on mitochondrial membrane potential (MMP) in SCI. A comprehensive analysis was performed on SCI-related genes, MMP-related genes, and PD targets screening from public databases. Differential expression analysis was conducted to identify differentially expressed genes (DEGs) in SCI. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were employed to assess pathway enrichment. Protein-protein interaction (PPI) network analysis and molecular docking were conducted to identify key genes and evaluate the binding affinity between PD and hub genes. A total of 16,958 SCI-related genes, 2,786 MMP-related genes, 318 PD-related target genes, and 7229 DEGs were identified. Intersection analysis revealed 46 genes common to all four categories. GSEA and GSVA analysis identified significant enrichment of pathways associated with suppressed and activated SCI biological processes. The PPI network analysis identified seven core hub genes: EGFR, SRC, VEGFA, STAT3, ERBB2, TP53, and RHOA. Molecular docking revealed strong binding affinities between PD and ERBB2, EGFR, and RHOA. The findings based on computational investigation from public databases suggest that PD may have therapeutic potential for SCI by modulating MMP. These results contribute to the understanding of SCI pathogenesis and the development of novel therapeutic strategies.

Mechanism of Wenshen Xuanbi Decoction in the treatment of osteoarthritis based on network pharmacology and experimental verification

To investigate the mechanism of Wenshen Xuanbi Decoction (WSXB) in treating osteoarthritis (OA) via network pharmacology, bioinformatics analysis, and experimental verification. The active components and prediction targets of WSXB were obtained from the TCMSP database and Swiss Target Prediction website, respectively. OA-related genes were retrieved from GeneCards and OMIM databases. Protein-protein interaction and functional enrichment analyses were performed, resulting in the construction of the Herb-Component-Target network. In addition, differential genes of OA were obtained from the GEO database to verify the potential mechanism of WSXB in OA treatment. Subsequently, potential active components were subjected to molecular verification with the hub targets. Finally, we selected the most crucial hub targets and pathways for experimental verification in vitro. The active components in the study included quercetin, linolenic acid, methyl linoleate, isobergapten, and beta-sitosterol. AKT1, tumor necrosis factor (TNF), interleukin (IL)-6, GAPDH, and CTNNB1 were identified as the most crucial hub targets. Molecular docking revealed that the active components and hub targets exhibited strong binding energy. Experimental verification demonstrated that the mRNA and protein expression levels of IL-6, IL-17, and TNF in the WSXB group were lower than those in the KOA group (p < 0.05). WSXB exhibits a chondroprotective effect on OA and delays disease progression. The mechanism is potentially related to the suppression of IL-17 and TNF signaling pathways and the down-regulation of IL-6.

Mechanistic prospective and pharmacological attributes of quercetin in attenuation of different types of arthritis

Arthritis is a frequent autoimmune disease with undefined etiology and pathogenesis. Scientific community constantly fascinating quercetin (QUR), as it is the best-known flavonoid among others for curative and preventive properties against a wide range of diseases. Due to its multifaceted activities, the implementation of QUR against various types of arthritis namely, rheumatoid arthritis (RA), osteoarthritis (OA), gouty arthritis (GA) and psoriotic arthritis (PsA) has greatly increased in recent years. Many research evidenced that QUR regulates a wide range of pathways for instance NF-κB, MAK, Wnt/β-catenine, Notch, etc., that are majorly associated with the inflammatory mechanisms. Besides, the bioavailability of QUR is a major constrain to its therapeutic potential, and drug delivery techniques have experienced significant development to overcome the problem of its limited application. Hence, this review compiled the cutting-edge experiments on versatile effects of QUR on inflammatory diseases like RA, OA, GA and PsA, sources and bioavailability, therapeutic challenges, pharmacokinetics, clinical studies as well as toxicological impacts. The use of QUR in a health context would offer a tearing and potential therapeutic method, supporting the advancement of public health, particularly, of arthritic patients worldwide.

Osteoarthritis related epigenetic variations in miRNA expression and DNA methylation

Osteoarthritis (OA) is chronic arthritis characterized by articular cartilage degradation. However, a comprehensive regulatory network for OA-related microRNAs and DNA methylation modifications has yet to be established. Thus, we aimed to identify epigenetic changes in microRNAs and DNA methylation and establish the regulatory network between miRNAs and DNA methylation. The mRNA, miRNA, and DNA methylation expression profiles of healthy or osteoarthritis articular cartilage samples were downloaded from Gene Expression Omnibus (GEO) database, including GSE169077, GSE175961, and GSE162484. The differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs), and differentially methylated genes (DMGs) were analyzed by the online tool GEO2R. DAVID and STRING databases were applied for functional enrichment analysis and protein-protein interaction (PPI) network. Potential therapeutic compounds for the treatment of OA were identified by Connectivity map (CMap) analysis. A total of 1424 up-regulated DEGs, 1558 down-regulated DEGs, 5 DEMs with high expression, 6 DEMs with low expression, 1436 hypermethylated genes, and 455 hypomethylated genes were selected. A total of 136 up-regulated and 65 downregulated genes were identified by overlapping DEGs and DEMs predicted target genes which were enriched in apoptosis and circadian rhythm. A total of 39 hypomethylated and 117 hypermethylated genes were obtained by overlapping DEGs and DMGs, which were associated with ECM receptor interactions and cellular metabolic processes, cell connectivity, and transcription. Moreover, The PPI network showed COL5A1, COL6A1, LAMA4, T3GAL6A, and TP53 were the most connective proteins. After overlapping of DEGs, DMGs and DEMs predicted targeted genes, 4 up-regulated genes and 11 down-regulated genes were enriched in the Axon guidance pathway. The top ten genes ranked by PPI network connectivity degree in the up-regulated and downregulated overlapping genes of DEGs and DMGs were further analyzed by the CMap database, and nine chemicals were predicted as potential drugs for the treatment of OA. In conclusion, TP53, COL5A1, COL6A1, LAMA4, and ST3GAL6 may play important roles in OA genesis and development.

A Network Pharmacology Method Combined with Molecular Docking Verification to Explore the Therapeutic Mechanisms Underlying Simiao Pill Herbal Medicine against Hyperuricemia

Objective

Hyperuricemia (HUA) is a common metabolic disease caused by disordered purine metabolism. We aim to reveal the mechanisms underlying the anti-HUA function of Simiao pill and provide therapeutic targets.

Methods

Simiao pill-related targets were obtained using Herbal Ingredients' Targets (HIT), Traditional Chinese Medicine Systems Pharmacology (TCMSP), and Traditional Chinese Medicine Integrated Database (TCMID). HUA-associated targets were retrieved from GeneCards, DisGeNET, and Therapeutic Targets Database (TTD). Protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, ggraph and igraph R packages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using ClusterProfiler. The top 10 core targets were identified through cytoHubba. Molecular docking was conducted using PyMOL and AutoDock high-performance liquid chromatograph (HPLC) analysis was performed to identify effective compounds of Simiao pill.

Results

Simiao pill-HUA target network contained 80 targets. The key targets were mainly involved in inflammatory responses. Insulin (INS), tumor necrosis factor (TNF), interleukin-6 (IL6), interleukin 1 beta (IL1B), vascular endothelial growth factor A (VEGFA), leptin (LEP), signal transducer and activator of transcription 3 (STAT3), C-C motif chemokine ligand 2 (CCL2), interleukin-10 (IL10), and toll like receptor 4 (TLR4) were the top 10 targets in the PPI network. GO analysis demonstrated the main implication of the targets in molecular responses, production, and metabolism. KEGG analysis revealed that Simiao pill might mitigate HUA through advanced glycation end-product- (AGE-) receptor for AGE- (RAGE-) and hypoxia-inducible factor-1- (HIF-1-) associated pathways. IL1B, IL6, IL10, TLR4, and TNF were finally determined as the promising targets of Simiao pill treating HUA. Through molecular docking and HPLC analysis, luteolin, quercetin, rutaecarpine, baicalin, and atractylenolide I were the main active compounds.

Conclusions

Simiao pill can mitigate HUA by restraining inflammation, mediating AGE-RAGE- and HIF-1-related pathways, and targeting IL1B, IL6, IL10, TLR4, and TNF.

Identification of therapeutic targets for osteosarcoma by integrating single-cell RNA sequencing and network pharmacology

Background: Osteosarcoma (OS) is a common primary tumor with extensive heterogeneity. In this study, we used single-cell RNA sequencing (scRNA-seq) and network pharmacology to analyze effective targets for Osteosarcoma treatment. Methods: The cell heterogeneity of the Osteosarcoma single-cell dataset GSE162454 was analyzed using the Seurat package. The bulk-RNA transcriptome dataset GSE36001 was downloaded and analyzed using the CIBERSORT algorithm. The key targets for OS therapy were determined using Pearson's correlation analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on key targets. The DeepDR algorithm was used to predict potential drugs for Osteosarcoma treatment. Molecular docking analysis was performed to verify the binding abilities of the predicted drugs and key targets. qRT-PCR assay was used to detect the expression of key targets in osteoblasts and OS cells. Results: A total of 21 cell clusters were obtained based on the GSE162454 dataset, which were labeled as eight cell types by marker gene tagging. Four cell types (B cells, cancer-associated fibroblasts (CAFs), endothelial cells, and plasmocytes) were identified in Osteosarcoma and normal tissues, based on differences in cell abundance. In total, 17 key targets were identified by Pearson's correlation analysis. GO and KEGG analysis showed that these 17 genes were associated with immune regulation pathways. Molecular docking analysis showed that RUNX2, OMD, and CD4 all bound well to vincristine, dexamethasone, and vinblastine. The expression of CD4, OMD, and JUN was decreased in Osteosarcoma cells compared with osteoblasts, whereas RUNX2 and COL9A3 expression was increased. Conclusion: We identified five key targets (CD4, RUNX2, OMD, COL9A3, and JUN) that are associated with Osteosarcoma progression. Vincristine, dexamethasone, and vinblastine may form a promising drug-target pair with RUNX2, OMD, and CD4 for Osteosarcoma treatment.

Network Pharmacology to Reveal the Molecular Mechanisms of Rutaceous Plant-derived Limonin Ameliorating Non-alcoholic Steatohepatitis

BACKGROUND

Limonin shows promise in alleviating non-alcoholic fatty liver disease. We investigated the mechanisms of limonin against non-alcoholic steatohepatitis (NASH) using network pharmacology and molecular docking.

METHODS

Public databases provided NASH- and limonin-associated targets. VennDiagram identified potential limonin targets for NASH. Enrichment analysis explored the limonin-NASH relationship. PPI network analysis, CytoHubba models, and bioinformatics identified hub genes for NASH treatment. Molecular docking assessed limonin's binding ability to hub targets.

RESULTS

We found 37 potential limonin targets in NASH, involved in oxidative stress, inflammation, and signaling pathways. PPI network analysis revealed seven hub genes (STAT3, NFKBIA, MTOR, TLR4, CASP8, PTGS2, NFKB1) as NASH treatment targets. Molecular docking confirmed limonin's binding to STAT3, CASP8, and PTGS2. Animal experiments on high-fat diet mice showed limonin reduced hepatic steatosis, lipid accumulation, and expression of p-STAT3/STAT3, CASP8, and PTGS2.

CONCLUSION

Limonin's therapeutic effects in NASH may stem from its antioxidant and anti-inflammatory properties. STAT3, CASP8, and PTGS2 are potential key targets for NASH treatment, warranting further investigation.

Study of Therapeutic Mechanisms of Puerarin against Sepsis-Induced Myocardial Injury by Integrating Network Pharmacology, Bioinformatics Analysis, and Experimental Validation

Myocardial injury is the most prevalent and serious complication of sepsis. The potential of puerarin (Pue) to treat sepsis-induced myocardial injury (SIMI) has been recently reported. Nevertheless, the specific anti-SIMI mechanisms of Pue remain largely unclear. Integrating network pharmacology, bioinformatics analysis, and experimental validation, we aimed to clarify the anti-SIMI mechanisms of Pue, thereby furnishing novel therapeutic targets. Pue-associated targets were collected from HIT, GeneCards, SwissTargetPrediction, SuperPred, and CTD databases. SIMI-associated targets were acquired from GeneCards and DisGeNET. Differentially expressed genes (DEGs) were identified from GEO database. Potential anti-SIMI targets of Pue were determined using VennDiagram. ClusterProfiler was employed for GO and KEGG analyses. STRING database and Cytoscape were used for protein-protein interaction (PPI) network construction, and cytoHubba was used for hub target screening. PyMOL and AutoDock were utilized for molecular docking. An in vitro SIMI model was built to further verify the therapeutic mechanisms of Pue. Seventy-three Pue-SIMI-DEG intersecting target genes were obtained. GO and KEGG analyses revealed that the targets were principally concentrated in cellular response to chemical stress, response to oxidative stress (OS), and insulin and neurotrophin signaling pathways. Through PPI analysis and molecular docking, AKT1, CASP3, TP53, and MAPK3 were identified as the pivotal targets. In vivo experiments indicated that Pue promoted cell proliferation, downregulated AKT1, CASP3, TP53, and MAPK3, and inhibited inflammation, myocardial injury, OS, and apoptosis in the cell model. Pue might inhibit inflammation, myocardial injury, OS, and apoptosis to treat SIMI by reducing AKT1, CASP3, TP53, and MAPK3.

Identification of Autophagy-Related Targets of Berberine against Non-Small Cell Lung Cancer and Their Correlation with Immune Cell Infiltration By Combining Network Pharmacology, Molecular Docking, and Experimental Verification

OBJECTIVE

Non-small cell lung cancer (NSCLC) is the most common lung cancer type with high incidence. This study aimed to reveal the anti-NSCLC mechanisms of berberine and identify novel therapeutic targets.

METHODS

Berberine-related targets were acquired from SuperPred, SwissTargetPrediction, and GeneCards. NSCLC-re-lated targets were collected from GeneCards and DisGeNET. Differentially expressed genes (DEGs) were identified GEO database, UCSC Xena, and limma. GO and KEGG analyses were performed using clusterProfiler. Autophagy-related genes and transcriptional factors were collected from HADb and KnockTF, respectively. STRING and Cytoscape were used for PPI network analysis. Immune cell infiltration in NSCLC was assessed using CIBERSORT, and its correlation with autophagy-related targets was evaluated. Molecular docking was conducted using PyMOL and AutoDock. qRT-PCR and CCK-8 assay was used for in vitro verification.

RESULTS

Thirty intersecting targets of berberine-related targets, NSCLC-related targets, and DEGs were obtained. GO and KEGG analyses revealed that the intersecting targets were mainly implicated in oxidative stress, focal adhesion, and cell-substrate junction, as well as AGE-RAGE, relaxin, FoxO, and estrogen signaling pathways. Significantly, CAPN1, IKBKB, and SIRT2 were identified as the foremost autophagy-related targets, and 21 corresponding transcriptional factors were obtained. PPI network analysis showed that CAPN1, IKBKB, and SIRT2 interacted with 50 other genes. Fifty immune cell types, such as B cells naive, T cells CD8, T cells CD4 naive, T cells follicular helper, and monocytes, were implicated in NSCLC pathogenesis, and CAPN1, IKBKB, and SIRT2 were related to immune cells. Molecular docking revealed the favorable binding activity of berberine with CAPN1, IKBKB, and SIRT2. In vitro assays showed lower CAPN1, IKBKB, and SIRT2 expression in NSCLC cells than that in normal cells. Notably, berberine inhibited the viability and elevated CAPN1, IKBKB, and SIRT2 expression in NSCLC cells.

CONCLUSIONS

Berberine might treat NSCLC mainly by targeting CAPN1, IKBKB, and SIRT2.

Efficacy and safety of Chinese herbal medicine Danggui Sini decoction for knee osteoarthritis: A protocol for systematic review and meta-analysis

BACKGROUND

Knee osteoarthritis (KOA) often causes joint pain, weakness and mobility disorders, which seriously affects people's daily life and makes them unable to work and study normally. Traditional Chinese medicine (TCM) prescription Danggui Sini Decoction (DGSND) has been widely used in clinical practice and achieved good results. But there is no high-level evidence to support this result. The aim of this study is to evaluate DGSND's efficacy and safety in the management of KOA.

METHODS

We will search 7 electronic databases including Chinese National Knowledge Infrastructure (CNKI), Wanfang Data (WF), Chinese Scientific Journals Database (VIP), Chinese databases SinoMed (CBM), PubMed, Embase, and Cochrane Library databases. All the publications, with no time restrictions, will be searched without any restriction of language and status, the time from the establishment of the database to September 2022. Two reviewers will independently assess the quality of the selected studies, NoteExpress and Excel software will be used to extract data, and the content will be stored in an electronic chart. Different researchers will separately screen the titles and abstracts of records acquired potential eligibility which comes from the electronic databases. Full-text screening and data extraction will be conducted afterward independently. Statistical analysis will be conducted using RevMan 5.4 software.

RESULTS

This study will compare the effects of DGSND and any other different methods on patients with KOA to provide high-quality, evidence-based clinical recommendations.

CONCLUSION

The study provides a trustable clinical foundation for DGSND in the treatment of KOA.

Mechanism of Yangxin Tongmai Decoction in the Treatment of Coronary Heart Disease with Blood Stasis Syndrome Based on Network Pharmacology and Molecular Docking

This study aimed to explore the mechanism of Yangxin Tongmai decoction (YXTMD) in the treatment of coronary heart disease (CHD) with blood stasis syndrome (BSS) using network pharmacology and molecular docking, and to verify these results through clinical trials. The active compounds of YXTMD were identified using the Traditional Chinese Medicine Systems Pharmacology database, and the targets of the active compounds were predicted using the SwissTarget Prediction database. The targets of CHD and BSS were predicted using the GeneCards, OMIM, PharmGKB, TTD, and DrugBank databases. The common targets of “herb-disease-phenotype” were obtained using a Venn diagram, then used Cytoscape software 3.8.2 and its plug-in CytoNCA and STRING database to construct the “herb active compounds-common target” and protein–protein interaction networks. R language software and bioconductor plug-in were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. AutoDock was used for the molecular docking analysis. Finally, clinical trials were conducted to confirm the results of network pharmacology. Eighty-three active components were obtained, and the core active components were 5,7,4′-trimethoxyflavone, tetramethoxyluteolin, isosinensetin, sinensetin, and 5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one. A total of 140 common targets were identified, and the core targets were EGFR, VEGFA, AKT1, STAT3, TP53, ERBB2, and PIK3CA. Biological processes identified by the GO analysis primarily involved wound healing, regulation of body fluid levels, and vascular process in circulatory system. The cellular components were primarily located in the membrane raft, membrane microdomain, and plasma membrane raft. The primary molecular functions were activity of transmembrane receptor protein kinase, transmembrane receptor protein tyrosine kinase, and protein tyrosine kinase. KEGG analysis showed that the PI3K-Akt signaling pathway was closely related to the treatment of CHD with BSS by YXTMD. Molecular docking results showed that the core active components had a good binding activity with the core targets. The clinical trial results showed that YXTMD improved the BSS scores and decreased the serum levels of total cholesterol and low-density lipoprotein cholesterol. Moreover, the levels of PI3k and AKt mRNA were upregulated and the levels of GSK-3β mRNA were downregulated. YXTMD has multicomponent, multitarget, and multipathway effects in the treatment of CHD with BSS, and its mechanism of action may involve activation of the PI3K-AKt signaling pathway, downregulation of GSK-3β, and mediation of in vivo lipid metabolism-based metabolic processes.

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.

Network Pharmacology and Molecular Docking Analysis on Pharmacological Mechanisms of Astragalus membranaceus in the Treatment of Gastric Ulcer

BACKGROUND

Astragalus membranaceus (AM, family: Leguminosae) exerts significant therapeutic effect on gastric ulcer (GU); however, there are scarce studies on its molecular mechanism against GU. This study aims to explore the key ingredients, key targets, and potential mechanisms of AM in the treatment of GU by utilizing network pharmacology and molecular docking.

METHODS

Several public databases were used to predict the targets of AM and GU, respectively, and the drug and disease targets were intersected to obtain the common targets. Next, the key ingredients and key targets were identified by constructing ingredient-target network and protein-protein-interaction (PPI) network. Gene Ontology biological processes (GOBP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were carried out on the common targets in order to ascertain the biological processes and signaling pathways involved. Finally, molecular docking was conducted to verify the binding affinity between the key ingredients and key targets.

RESULTS

A total of 552 predicted targets were obtained from 23 screened active ingredients, of which 203 targets were the common targets with GU. Quercetin, kaempferol, and isorhamnetin were identified as the key ingredients by constructing ingredient-target network, and TP53, AKT1, VEGFA, IL6, TNF, CASP3, and EGFR were selected as the key targets by constructing PPI network. GOBP and KEGG pathway enrichment analysis suggested that the therapeutic effect of AM on GU involved multiple biological processes and signaling pathways related to inflammation, oxidative stress, apoptosis, cell proliferation, and angiogenesis. Molecular docking validation demonstrated that all key ingredients had good binding affinity with the key targets.

CONCLUSION

This study revealed the key ingredients, key targets, and potential mechanisms of AM against GU, and these data may provide some crucial references for subsequent research and development of drugs for treating GU.

Pharmacological Mechanism of Danggui-Sini Formula for Intervertebral Disc Degeneration: A Network Pharmacology Study

Background

Intervertebral disc degeneration (IVDD) is the most significant cause of low back pain, the sixth-largest disease burden globally, and the leading cause of disability. This study is aimed at investigating the molecular biological mechanism of Danggui-Sini formula (DSF) mediated IVDD treatment.

Methods

A potential gene set for DSF treatment of IVDD was identified through TCMSP, UniProt, and five disease gene databases. A protein interaction network of common targets between DSF and IVDD was established by using the STRING database. GO and KEGG enrichment analyses were performed using the R platform to discover the potential mechanism. Moreover, AutoDock Vina was used to verify molecular docking and calculate the binding energy.

Results

A total of 119 active ingredients and 136 common genes were identified, including 10 core genes (AKT1, IL6, ALB, TNF, VEGFA, TP53, MAPK3, CASP3, JUN, and EGF). Enrichment analysis results showed that the therapeutic targets of DSF for diseases mainly focused on the AGE-RAGE signaling pathway involved in diabetic complications, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, apoptosis, cellular senescence, PI3K-Akt signaling pathway, and FoxO signaling pathway. These biological processes are induced mainly in response to oxidative stress and reactive oxygen species and the regulation of apoptotic signaling pathways. Molecular docking showed that there was a stable affinity between the core genes and the key components.

Conclusions

The combination of network pharmacology and molecular docking provides a practical way to analyze the molecular biological mechanism of DSF-mediated IVDD treatment, which confirms the “multicomponent, multitarget and multipathway” characteristics of DSF and provides an essential theoretical basis for clinical practice.