Identification of the Mechanism of Action of the Index Components of Banxia Xiexin Decoction for Gastric Cancer through Network Pharmacology, Bioinformatics, and Molecular Docking Analysis

<bold>Objective</bold> To further explore the mechanism of Babao Dan (BBD) combined with oxaliplatin (L-OHP) in treating colorectal cancer (CRC) through a network pharmacology analysis. <bold>Methods</bold> The analysis involved the following steps: screen the chemical components of BBD through literature review of Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Chemistry Database, PubChem, and other databases; obtain L-OHP-related targets through GeneCards database; and search CRC-related targets through OMIM, GeneMap, TTD, DisGeNET, CTD, GeneCards, and other databases. After the intersection and mapping of drugs and disease, the protein-protein interaction (PPI) network and core targets were obtained using STRING database and CytoScape software. MetaScape database was used to analyze the core targets to obtain GO biological processes and KEGG pathways. <bold>Results</bold> BBD contained 495 chemical components with 204 active components screened out through the Swiss ADME database and 770 targets were obtained through the Swiss Target Prediction database. After the intersection of BBD and 775 targets of L-OHP with the CRC targets, it resulted in 74 potential targets. Twenty-four core targets were determined from the 74 intersection targets, which were related to the positive regulation of kinase activity, the positive regulation of cell migration, and peptidyl-serine modification in GO biological process. The KEGG pathway analysis showed that the core targets were related to pathway in cancer, proteoglycan in cancer, endocrine resistance, and microRNA in cancer, TNF signaling pathway, platinum resistance, and other pathways. Molecular docking showed that the core targets could bind to the most examined compounds. <bold>Conclusion</bold> Quercetin-7-olate, cyclo (L-tyrosyl-L-phenylalanyl), panaxadiol, and other compounds in BBD may play an anti-colorectal cancer effect in multiple pathways, including EGFR, AKT1, mTOR, and other targets in synergy with L-OHP.

Epimedii herba (EH) showed numerous activities and has the potential to treat periodontitis. However, the pharmacological mechanism has not been exhaustively elucidated. This study predicted the specific targets and mechanisms of EH to prevent and treat periodontitis. A traditional Chinese medicine system pharmacology database and analysis platform was used to screen key compounds of EH and their corresponding targets. Therapeutic Target Database and Comparative Toxicogenomics Database were used to identify targets related to periodontitis. Intersection targets were observed using a Venn diagram. The key components and corresponding protein targets of EH were searched. The intersection targets were obtained and then they were imported into the STRING database to construct a PPI network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Molecular docking between the screened chemical components of EH and key targets was performed using Discovery Studio 2019. The binding stability between components and target proteins was confirmed using molecular dynamics simulations. The binding stability between components and target proteins was confirmed using molecular dynamics simulations. Through network pharmacological analysis, 23 active compounds of EH were identified, including kaempferol and icariin. Based on GeneCards, GEO, and other databases, 3291 periodontitis-related genes were obtained. Venn diagram analysis revealed 137 intersection targets of EH and periodontitis, and Protein kinase B (AKT1) and Tumor necrosis factor (TNF) were identified as the key targets of EH for periodontitis treatment. GO and KEGG analyses revealed that the primary pathways mediating the therapeutic effects of EH were related to cancer, lipid, and atherosclerosis. Molecular docking showed that 8-isopentenyl-kaempferol had the best binding ability to ESR1, which was confirmed by dynamics simulations. This study demonstrated that EH can be used for periodontitis treatment, and the corresponding targets and potential mechanisms were investigated based on network pharmacology, molecular docking, and dynamics simulation analysis. Notably, 8-isopentenyl-kaempferol exhibited good binding affinity and stability to ESR1, which may partially explain the molecular mechanisms of EH for treating periodontitis. Hence, EH can be a novel choice for the clinical treatment of periodontitis in the future.

To explore the active compounds of the Chinese medicine prescriptions of Bushen Hugu Decoction (BHD) and demonstrate its mechanisms against malignant tumor bone metastasis (BM) through network pharmacology and molecular docking analysis. The main components and targets of BHD were retrieved from the TCMSP database, and the targets were normalized by UniProt. The Herbs-Components-Targets network of BHD was established by Cytoscape. The main BM targets were obtained from GeneCards, TTD, DrugBank, and OMIM. STRING and Cytoscape were used to construct a PPI network and obtain hub genes. DAVID and Metascape were used for GO and KEGG enrichment analyses. According to the network topology parameters, the top 4 components were selected for molecular docking verification with the core targets. Compound-target network of BHD mainly contained 51 compounds and 259 corresponding targets including 107 BHD-BM targets. PPI interaction network and subnetworks identified ten hub genes. GO enrichment analysis found 1970 terms (p < 0.05), and 164 signaling pathways (p < 0.05) were found in KEGG, including PI3K-Akt signaling pathway, proteoglycans in cancer, prostate cancer, MAPK signaling pathway, and IL-17 signaling pathway. Molecular docking analysis showed that the active components of BHD, quercetin, luteolin, kaempferol, and aureusidin have good binding activity to the core targets. The potential molecular target and signaling pathways were found for BHD major active components. It provides guidance for the future mechanism research of the BHD in malignant tumor bone metastasis. This study also established the foundation for the new strategy for the pharmacology study of Chinese medicine.

Oral squamous cell carcinoma (OSCC) is a tumor type with a high mortality rate. Chlorogenic acid, abundant in resources and widely utilized in cancer treatments, has seen limited studies regarding its efficacy against OSCC. This paper investigates chlorogenic acid's mechanism in treating OSCC, aiming to guide the development of novel drugs. The study employed network pharmacology, molecular docking, and survival analysis methods. Network pharmacological analysis revealed chlorogenic acid targets 23 OSCC-related proteins, including ESR1, MMP2, MMP9, SRC, MAPK8, MAPK1, CDC42, ERBB2, ATM, and BRAF. Molecular docking simulations indicated that the primary target exhibits significant binding capacity with chlorogenic acid, with MMP9 associated with tumor migration and angiogenesis standing out. Survival analysis demonstrated that the downregulation of most primary targets correlates with improved survival rates in OSCC patients. Enrichment analysis of therapeutic targets highlighted the pivotal role of MAPK-ERK and MAPK-JNK signaling pathways in chlorogenic acid's efficacy against OSCC. This paper predicts chlorogenic acid's potential targets and proposes its molecular mechanism in treating OSCC, offering a theoretical foundation for its application in OSCC treatment. We used traditional Chinese medicine, a disease pharmacology-related information base, and an analysis platform to predict targets. The Cytoscape 3.9.1 and STING databases were used to address common targets for drugs and diseases, establish networks of protein interaction relationships, and screen core targets. Meastro11.5 was used for molecular docking simulation. R4.2.2 was used for survival analysis and joint target enrichment analysis. Network pharmacological analysis identified chlorogenic acid acting on 23 OSCC targets. Molecular docking simulations revealed a strong binding affinity of chlorogenic acid compounds with these targets, particularly MMP9, essential for tumor migration and angiogenesis. Survival analysis indicated that the downregulation of most core targets was correlated with improved OSCC patient survival. Enrichment analysis of therapeutic targets highlighted the critical roles of the MAPK-ERK and MAPK-JNK signaling pathways in the effectiveness of chlorogenic acid against OSCC. This study predicted the potential targets of chlorogenic acid in OSCC treatment and hypothesized its molecular mechanism, offering a theoretical foundation for its use in OSCC therapy.

Wuzi Yanzong Pill (WZYZP) is a traditional Chinese medicine formula extensively used in China to treat male reproductive dysfunction, with a specific focus on invigorating the kidney. Despite its observed efficacy, the exact mechanisms and therapeutic targets remain unclear. The primary goal of this study is to elucidate the potential molecular targets and underlying mechanisms of WZYZP in the treatment of asthenozoospermia (AZS). It will be achieved through the integration of network pharmacology and bioinformatics analyses in a comprehensive and systematic approach. This study employed bioinformatics analysis and network pharmacology methodologies, encompassing: construction of protein-protein interaction (PPI) networks; development of 'Ingredients-Potential Target Genes-Signaling Pathways' (IPS) networks; Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; differential gene analysis; molecular docking; and molecular dynamics simulations (MDS). Through network pharmacology analysis, we identified 485 potential targets of WZYZP. Cross-referencing with disease databases resulted in 57 intersecting targets pertinent to both WZYZP and AZS. Construction of the IPS network further determined eight core candidate targets: PIK3R1, MAPK3, GSK3B, AKT1, MAPK14, ESR1, ESR2, and CYP17A1. GO and KEGG pathway enrichment analyses highlighted significant involvement in prolactin signaling, endocrine resistance, and estrogen signaling pathways. Molecular docking and MDS confirmed stable binding of WZYZP components to all eight core targets. Our findings suggest that WZYZP may exert therapeutic effects in AZS by targeting eight pivotal genes (PIK3R1, MAPK3, GSK3B, AKT1, MAPK14, ESR1, ESR2, and CYP17A1). This is achieved through modulation of prolactin signaling, estrogen signaling, and endocrine resistance, thereby inhibiting inflammatory damage, antagonizing apoptotic signaling, maintaining hormonal homeostasis, and restoring metabolic imbalance.

Exploring the mechanism by which BXSD decoction treats cervical cancer through the combination of network pharmacology and molecular docking analysis: Molecular mechanism of AKT1 and CASP3 protein.

Objectives Bellidifolin (BEL) is one type of tetraoxygenated xanthone that is particularly found in Swertia and Gentiana (Gentianaceae). Despite its broad range of pharmacological activities, it is still unclear whether BEL could be used for lung cancer treatment. Hence, we presently demonstrate the roles of BEL towards the proliferative inhibition of the prototypical A549 lung cancer cells. Materials and Methods The antiproliferative activity of BEL was initially verified by cellular experiments. A network pharmacology method was then pursued to assess BEL potential molecular targets from the platform for pharmacological analysis of Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Disease enrichment of potential targets and construction of compound-target-disease network maps were performed based on a total of 20 diseases. Two core targets related to the BEL-mediated effect in A549 cells were obtained by importing potential targets into a protein-protein interaction database (STRING) and also analyzing respective data of related targets into this database. Last, these core targets were examined by in vitro analysis and molecular docking. Results CCK8 assays indicated that treatment with 50–100 μm BEL had an inhibitory effect on the proliferation of human A549 lung cancer cells, whereas this effect was time- and concentration-dependent. As control, treatment with 50–100 μm BEL did not inhibit the proliferation of normal lung epithelial cells (BEAS-2b cell line). H&E staining of BEL-treated A549 cells showed that, upon an increase of drug concentration, nuclear condensation and fragmentation were largely observed. Cell cycle analysis showed that in vitro treatment with 75–100 μm BEL could block A549 cells in S and G2 phases. Western blot analyses showed that after 72 hours of BEL treatment, the level of caspase-8/3 in A549 cells increased, and the level of PARP1 decreased in a dose-dependent manner. Network pharmacology analysis also indicated that lung cancer was the major disease susceptible to BEL treatment. At the same time, STAT3 and COX-2 were identified as two core targets of BEL in lung cancer treatment. Functional analyses further revealed that the cytotoxicity effect of BEL in A549 cells potentially involved the STAT3/COX-2 pathway. Moreover, molecular docking analysis indicated that BEL structure properly matches with COX-2 and STAT3 in space shape, thus illustrating the putative molecular mechanism of BEL's anticancer effect. Conclusions Based on a series of in vitro analyses, network pharmacology, and molecular docking, the potential mechanism involving the antiproliferative and cytotoxic effects of BEL in lung cancer cells was investigated. Our study may help providing some theoretical basis for the discovery of novel phytotherapy drugs applicable for the treatment of lung cancer.

Patients with gastric cancer (GC) are more likely to be infected with 2019 coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the prognosis is worse. It is urgent to find effective treatment methods. This study aimed to explore the potential targets and mechanism of ursolic acid (UA) on GC and COVID-19 by network pharmacology and bioinformatics analysis. The online public database and weighted co-expression gene network analysis (WGCNA) were used to screen the clinical related targets of GC. COVID-19-related targets were retrieved from online public databases. Then, a clinicopathological analysis was performed on GC and COVID-19 intersection genes. Following that, the related targets of UA and the intersection targets of UA and GC/COVID-19 were screened. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome Analysis (KEGG) pathway enrichment analyses were performed on the intersection targets. Core targets were screened using a constructed protein-protein interaction network. Finally, molecular docking and molecular dynamics simulation (MDS) of UA and core targets were performed to verify the accuracy of the prediction results. A total of 347 GC/COVID-19-related genes were obtained. The clinical features of GC/COVID-19 patients were revealed using clinicopathological analysis. Three potential biomarkers (TRIM25, CD59, MAPK14) associated with the clinical prognosis of GC/COVID-19 were identified. A total of 32 intersection targets of UA and GC/COVID-19 were obtained. The intersection targets were primarily enriched in FoxO, PI3K/Akt, and ErbB signaling pathways. HSP90AA1, CTNNB1, MTOR, SIRT1, MAPK1, MAPK14, PARP1, MAP2K1, HSPA8, EZH2, PTPN11, and CDK2 were identified as core targets. Molecular docking revealed that UA strongly binds to its core targets. The MDS results revealed that UA stabilizes the protein-ligand complexes of PARP1, MAPK14, and ACE2. This study found that in patients with gastric cancer and COVID-19, UA may bind to ACE2, regulate core targets such as PARP1 and MAPK14, and the PI3K/Akt signaling pathway, and participate in antiinflammatory, anti-oxidation, anti-virus, and immune regulation to exert therapeutic effects.

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

To explore potential therapeutic targets and underlying mechanisms of apigenin (API) for papillary thyroid carcinoma (PTC) treatment. Methods: In the present study, network pharmacological analysis combined with molecular docking was used to identify API-related therapeutic targets for PTC treatment. Firstly, potential API-interacting and PTC-related targets were obtained from online databases. Furthermore, we constructed drug-target-disease interaction networks followed by functional enrichment analysis, expression patterns and prognostic values of predicted core targets by using bioinformatic tools. Moreover, we performed molecular docking to validate binding activity of API to core pharmacological targets. Results: A total of 110 API-related therapeutic targets were found to be engaged in the treatment of PTC. Moreover, TP53, HSP90AA1, AKT1, EGFR, SRC, VEGFA, ACTB, JUN and ESR1 were identified as core pharmacological targets of API for treating PTC. The enrichment analysis suggested that API played a comprehensive role in regulating the apoptotic process, modulating cell proliferation, and that multiple pathways were involved in API-related PTC treatment. Further results indicated that the PI3k-Akt/p53 signaling pathway was the key signaling pathway. Moreover, JUN was found mostly correlated with survival and molecular docking results demonstrating strong affinities between API and these core targets. Conclusion: Our findings systematically demonstrated API-associated pharmacological targets and mechanisms for treating PTC and demonstrated that API could function against PTC by inducing apoptosis, cell death and immunological reactions. Our research gives valuable insights and a theoretical basis for API-related PTC treatment.

Context: Breast cancer therapy currently presents several uncomfortable side effects in patients, including effects on non-malignant tissues, recurrence, and resistance, which restrict their utilization. Consequently, researchers have directed their attention toward studying plant-derived anticancer compounds that exhibit high efficacy and safety profiles. Eugenol, a major component found in clove plants, demonstrates promising potential as a therapeutic agent for both estrogen receptor-positive and estrogen receptor-negative breast cancer. Aims: To predict the target of eugenol in estrogen receptor–positive breast cancer using network pharmacology and molecular docking analyses. Methods: Network pharmacology analysis was performed using the Chemical Toxigenomic Database, STITCH, GeneCards, Cytoscape, Enrichr, and Stringdb. Subsequently, molecular docking was performed using protein targets obtained from the RCSB-PDB and analyzed using AutoDock software. Results: Network pharmacology study and molecular docking revealed the anticancer effect of eugenol against breast cancer estrogen receptor–positive, especially in cancer and apoptotic pathways, by acting on caspase-3 (CASP3), epidermal growth factor receptor (EGFR), and poly [ADP-ribose] polymerase 1 (PARP1) signaling pathways. The docking results between the protein targets and eugenol showed that eugenol has the strongest binding with CASP3 (ligand binding energy: -5.78 kcal/mol), followed by eugenol binding with EGFR (ligand binding energy: -5.58 kcal/mol), and eugenol binding with PARP1 (ligand binding energy: -5.58 kcal/mol). Conclusions: Eugenol is a potential candidate for breast cancer therapy, especially for apoptosis mediated by CASP3 in breast cancer luminal A.

Objective The aim of the study is to verify the active ingredients of peach blossom and to explore the molecular mechanisms of their therapeutic effects against constipation through network pharmacology and molecular docking analysis. Methods The potential active ingredients of peach blossom were identified from published literature and the BAT-TCM database, and their potential targets were predicted using the SwissTargetPrediction and PharmMapper platforms. In addition, targets related to constipation were retrieved using OMIM, DrugBank, GeneCards, TTD, and DisGeNET databases. The intersection of drug targets and disease targets was considered as the potential targets of peach blossom in the treatment of constipation. The STRING platform was used to construct a protein interaction network. Gene ontology (GO) functional analysis and KEGG pathway enrichment analysis were performed on key targets using the DAVID database. Molecular docking verification between the active ingredients of peach blossom and the targets was conducted using AutoDock software. Results A total of 33 active ingredients of peach blossom and 185 corresponding targets were identified, and 88 intersection targets were obtained after Venny mapping. These 33 active ingredients (including naringenin, aromadendrin, and cordycepin) in peach blossom may play a role in the treatment of constipation by regulating signaling pathways through targets such as EGFR, VEGFA, ESR1, GSTP1, and PTGS2. Conclusion A variety of active ingredients of peach blossom regulate multiple signaling pathways by acting on targets, which reflects the characteristic of “multiple ingredients-multiple targets-multiple pathways,” thereby playing a role in the treatment of constipation.

Houshiheisan modulates the NF-κB/MLCK signaling pathway to protect the endothelial barrier in cerebral small vessel disease.

Although the protective effects of naringenin (Nar) on vascular smooth muscle cells (VSMCs) have been confirmed, whether it has anti-proliferation and anti-migration effects in high-glucose-induced VSMCs has remained unclear. This study aimed to clarify the potential targets and molecular mechanism of Nar when used to treat high-glucose-induced vasculopathy based on transcriptomics, network pharmacology, molecular docking, and in vivo and in vitro assays. We found that Nar has visible anti-proliferation and anti-migration effects both in vitro (high-glucose-induced VSMC proliferation and migration model) and in vivo (type 1 diabetes mouse model). Based on the results of network pharmacology and molecular docking, vascular endothelial growth factor A (VEGFA), the proto-oncogene tyrosine-protein kinase Src (Src) and the kinase insert domain receptor (KDR) are the core targets of Nar when used to treat diabetic angiopathies, according to the degree value and the docking score of the three core genes. Interestingly, not only the Biological Process (BP), Molecular Function (MF), and KEGG enrichment results from network pharmacology analysis but also transcriptomics showed that phosphatidylinositol-3-kinase (PI3K)/protein kinase B (Akt) is the most likely downstream pathway involved in the protective effects of Nar on VSMCs. Notably, according to the differentially expressed genes (DEGs) in the transcriptomic analysis, we found that cAMP-responsive element binding protein 5 (CREB5) is a downstream protein of the PI3K/Akt pathway that participates in VSMCs proliferation and migration. Furthermore, the results of molecular experiments in vitro were consistent with the bioinformatic analysis. Nar significantly inhibited the protein expression of the core targets (VEGFA, Src and KDR) and downregulated the PI3K/Akt/CREB5 pathway. Our results indicated that Nar exerted anti-proliferation and anti-migration effects on high-glucose-induced VSMCs through decreasing expression of the target protein VEGFA, and then downregulating the PI3K/Akt/CREB5 pathway, suggesting its potential for treating diabetic angiopathies.

Ferroptosis refers to a lytic cell death avenue that may be related to the development of neuropathological disorders. Traumatic brain injury (TBI) is the brain impairments and ferroptosis is found with the pathological role in TBI development. Our previous findings showed that ferulic acid exerts pharmacological benefited against TBI. However, the therapeutic efficacy and mechanism targeting of ferroptosis in ferulic acid against TBI is still unclear. In current report, an integrated approach by using network pharmacology and molecular docking analyses was subjected to identify the ferulic acid-anti-TBI mechanisms and targets associated with ferroptosis. The network pharmacology analysis had screened 184 ferulic acid-related targets, 1834 TBI-associated targets and 616 ferroptosis-linked targets, characterized with 14 overlapping genes among ferulic acid, TBI, and ferroptosis. All core targets in ferulic acid treating TBI via regulation of ferroptosis were identified through parametric determination, including PTGS2, TLR4, RELA, GSK3B, NFE2L2, EGFR, and MIF. Following with enrichment analysis, anti-TBI functions of ferulic acid against TBI targeting ferroptosis were revealed in multiple biological processes, including regulation of polymerase activities, transcription factor functions, ubiquitin protease binding capabilities. Pharmacological mechanisms were detailed in signaling pathways mainly involved in neuroprotection, microenvironmental restoration and neural regeneration were the key functional characteristics. Further in silico validation exhibited that PTGS2 was a potential pharmacological target associated with ferroptosis in ferulic acid against TBI owing to the potent binding energy. Collectively, current bioinformatics data provide a new preclinical insight of the pharmacological function and mechanism targeting of ferroptosis in ferulic acid treating TBI. Compared to other correlative researches, this study may effectively exhibit the preclinical perspective in new drug research and development on ferulic acid against TBI through revealing multiple targets and pathways.