Proteomic and network pharmacology analyses reveal S100A8 as the anti-inflammatory target of Yunpi Jiedu Tongluo Qushi Granule in the treatment of rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by synovial inflammation. RA has a global prevalence between 0.5 % and 1 % although its pathogenesis is not completely understood. Chinese herbal medicine such as Yunpi Jiedu Tongluo Qushi Granule (YJTQG) is one of the treatments for RA. However, the underlying mechanism of action is unclear. Here, analysis of clinical samples reveals that YJTQG can reduce the inflammatory factors and alleviate the symptoms of RA patients. Quantitative proteomic analysis of serum proteomes of RA patients identifies the potential therapeutic targets of YJTQG. We use biochemical experiments to validate several differentially expressed proteins, discover S100A8 as a possible therapeutic target of YJTQG, and analyze the correlation between S100A8 and several known RA biomarkers. Network pharmacology analysis discloses COX1/2 and NOS2 as potential targets of key compounds in YJTQG and protein-protein interaction network analysis reveals TNFα, IL-6, and STAT3 as possible core targets of YJTQG. Bioinformatic and patient sample analyses indicate that YJTQG may reduce S100A8 expression by suppressing its transcription. Mechanistically, we find that kaempferol and quercetin in YJTQG may reduce the expression of S100A8 by inhibiting the phosphorylation, nuclear translocation, and transcriptional activity of p65 in the lipopolysaccharide-stimulated RAW264.7 cells. Therefore, our work demonstrates that S100A8 is a potential therapeutic target of YJTQG for RA, which may provide a new direction for developing new treatments for RA patients.

Network pharmacology and experimental verification unraveled the mechanism of Bailing Capsule against asthma.

Asthma is a serious public health challenge around the world. Recent studies into traditional Chinese medicine preparations for asthma have yielded promising findings regarding Bailing Capsule's potential in bronchial asthma prevention and treatment. This study aims to initially clarify the potential mechanism of Bailing Capsule in the treatment of asthma using network pharmacology and in vitro experimental approaches. Network pharmacology was adopted to detect the active ingredients of Bailing Capsule via Traditional Chinese Medicine Systems Pharmacology Database, and the key targets and signaling pathways in the treatment of asthma were predicted. Docking and molecular dynamics simulations were conducted to verify the most important interactions formed by these probes within different regions of the binding site. The predicted targets were validated in lipopolysaccharide-induced 16HBE cell experiment. Seven active ingredients were screened from Bailing Capsule, 294 overlapping targets matched with asthma were considered potential therapeutic targets, such as SRC, TP53, STAT3, and E1A binding protein P300. The main functional pathways involving these key targets include phosphatidylinositol 3-kinase/protein kinase B, mitogen-activated protein kinase, renin-angiotensin system and other signaling pathways, which were mainly involved in the inflammatory response, apoptosis, and xenobiotic stimulus. Moreover, molecular docking showed that Cerevisterol have higher affinity for SRC, TP53, STAT3, and E1A binding protein P300 than other main active components, which is close to the docking results of the co-crystallized ligands to proteins. Consequently, Cerevisterol was selected for molecular dynamics simulation and the results show that Cerevisterol can bind most tightly to SRC, TP53, and STAT3. Bailing Capsule can promote the growth of 16HBE cell, reduce the production of IL-4, TNF-α and IL-6, and down-regulate the levels of SRC and STAT3 mRNA. This study preliminarily reveals the potential mechanism of Bailing Capsule against asthma with the aid of network pharmacology and in vitro cell experiment, which provided reference and guidance for in-depth research and clinical application.

The mechanism of quercetin in treating intracerebral hemorrhage was investigated by network pharmacology and molecular docking.

BACKGROUND: The aim of this study was to explore the molecular mechanism of quercetin in the treatment of intracerebral hemorrhage. METHODS: Quercetin target genes and intracerebral hemorrhage target genes were collected from 5 databases. After standardized conversion of the obtained target genes through uniprot database, cross genes of the 2 were obtained using Venny 2.1 online tool. Further, protein interaction relationships were obtained in the String database, and then core target genes were screened and visualized by Cytoscape software, and cross genes were enriched by GO and KEGG pathways. Finally, the active drug ingredients and target proteins were verified and visualized by computer. RESULTS: In this study, 197 quercetin targets were identified as potential targets for the treatment of intracerebral hemorrhage, and 7 core target genes (TP53, STAT3, AKT1, SRC, JUN, TNF, and IL6) were screened. The GO and KEGG analyses further shed light on the molecular mechanisms underlying quercetin's treatment of intracerebral hemorrhage, involving multiple biological processes and signaling pathways (such as cancer pathways, lipids, and atherosclerosis). The stable binding of quercetin to these 7 key targets was confirmed by molecular docking simulation. CONCLUSION: Quercetin may treat intracerebral hemorrhage through multi-target-multi-pathway mechanisms, including regulating apoptosis, inhibiting inflammatory response, inhibiting iron death, and regulating angiogenesis, which can help alleviate nerve damage caused by intracerebral hemorrhage.

Therapeutic mechanism and key active ingredients of Yinxing Mihuan Oral Solution in coronary heart disease comorbidity with anxiety: A network pharmacology and molecular docking approach.

Yinxing Mihuan Oral Solution (YMOS) is a Chinese patent medicine for treating coronary heart disease combined anxiety (CHDCA), but the molecular mechanism of its treatment is still unclear. This article aims to understand the molecular mechanism, optimize clinical drug use, and guide new drug development. Using the Swiss Target Prediction database, we obtained the main chemical composition of YMOS. Then we used network pharmacology to identify their potential targets. Network construction, coupled with protein-protein interaction and enrichment analysis was used to identify representative components and core targets. Finally, molecular docking simulation was conducted to further refine the drug-target interaction. Forty-two active chemicals were found in YMOS and 91 target genes related to CHDCA. The treatment effect was found to be associated with 1908 biological processes and 160 pathways, as revealed by the outcomes of the enrichment analysis. The potential therapeutic mechanisms of the drug are closely related to its antioxidant, anti-inflammatory, and vascular function regulation pathways, and the main core targets include albumin, tumor necrosis factor, TP53, AKT serine/threonine kinase 1, interleukin 1 beta, and vascular endothelial growth factor A. The potential molecular mechanisms of YMOS in CHDCA treatment were identified using network pharmacology and molecular docking approaches. The results reveal the systemic biological implications of YMOS. This study has systematically uncovered the molecular mechanism of YMOS for the first time, offering fresh insights for evidence-based clinical applications.

Bioinformatics and network pharmacology discover the molecular mechanism of Liuwei Dihuang pills in treating cerebral palsy.

A collection of chronic central motor, postural, and activity restriction symptoms are referred to as cerebral palsy (CP). Previous research suggests that a number of perinatal variables, including hypoxia, may be linked to CP. And the pathophysiological process that causes brain injury in growing fetuses is mostly caused by amniotic fluid infection and intra-amniotic inflammation. Still, there is still much to learn about the molecular mechanism of CP. The goal of this study was to identify the molecular mechanism of Liuwei Dihuang pill (LWDHP) in the treatment of CP using network pharmacology and bioinformatics. The Chinese medicine database provided the LWDHP components and targets, the CP illness gene data set was gathered from a disease, and the expression profile of children with CP was chosen from anther database. Using the Kyoto Encyclopedia of Genes and Genomes and gene ontology databases, a network of interactions between proteins was created, and functional enrichment analysis was carried out. Analysis of traditional Chinese medicine found that the key active ingredients of LWDHP are quercetin, Stigmasterol and kaempferol. Through enrichment analysis, it was found that the hub genes for LWDHP treatment of CP are CXCL8, MMP9, EGF, PTGS2, SPP1, BCL2L1, MMP1, and AR. K EGG analysis found that LWDHP treatment of CP mainly regulates PI3K-Akt signaling pathway, IL-17 signaling pathway, Jak-STAT signaling pathway, NF-kappa B signaling pathway, etc. To summarize, LWDHP regulates immunological and inflammatory variables through a variety of components, targets, and signaling pathways, which plays a significant role in the development and management of CP.

Elucidation of the molecular mechanism of type 2 diabetes mellitus affecting the progression of nonalcoholic steatohepatitis using bioinformatics and network pharmacology: A review.

Increasing evidence suggests that patients with diabetes are at increased risk of developing nonalcoholic steatohepatitis (NASH), but the underlying mechanisms that affect the progression of NASH remain unclear. In this study, we used bioinformatics and network pharmacology methods to explore the differentially expressed genes of NASH and the related genes of type 2 diabetes mellitus, and a total of 46 common targets were obtained. Gene ontology showed that the common targets were mainly involved in biological processes such as glucocorticoid, hormone, and bacterium responses. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis signal pathways were mainly in colorectal cancer, amphetamine addition, the peroxisome proliferator-activated receptor signaling pathway, and the toll-like receptor signaling pathway. The protein-protein interaction network identified 8 hub genes, and the co-expression network was analyzed to obtain 7 related functions and mutual proportions of hub genes. A total of 120 transcription factors were predicted for hub genes. Hub genes were closely related to immune cells, including neutropils and eosinophils. In addition, we identified 15 potential candidate drugs based on hub genes that are promising for the treatment of NASH. Type 2 diabetes mellitus can affect the progression of NASH by changing hormone levels and inflammatory responses through multiple targets and signaling pathways. Eight hub genes are expected to be potential targets for subsequent treatment.

Clinical Efficacy and Mechanistic Insights of Anshen Dingzhi Prescription on Breast Cancer-Related PTSD Through Network Pharmacology and Molecular Docking.

Anshen Dingzhi prescription (ADP) is a classic prescription of traditional Chinese medicine, which has been used in the treatment of neuropsychiatric diseases. However, its treatment of breast cancer-related post-traumatic stress disorder (BC-PTSD) lacks clinical research evidence and its mechanism is not clear. The present study investigated the efficacy and action mechanism of ADP against BC-PTSD. The results of the clinical trial showed that after 4 weeks of treatment, both groups showed reduced post-traumatic stress disorder checklist-civilian version (PCL-C), Pittsburgh sleep quality index (PSQI), self-rating depression scale (SDS) and self-rating anxiety scale (SAS) scores, and increased functional assessment of cancer therapy-breast (FACT-B) scores. The serum cortisol (CORT), tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1ß) levels were decreased and brain-derived neurotrophic factor (BDNF) level were increased, and the improvement of serum TNF-α, IL-1ß, and BDNF in treatment group was better than that of the control group. The overall treatment efficacy in the treatment group (43.90%) was superior to that in the control group (23.81%), and the overall incidence of adverse effects was lower than that in the control group. The results of network analysis and molecular docking showed that ADP blood components could act on IL1B, TNF, and BDNF. ADP contributes to the treatment of BC-PTSD symptoms, with a mechanism possibly related to its regulatory effect on TNF-α, IL-1ß, and BDNF levels.Trial registration: Chinese Clinical Trial Registry, http://www.chictr.org.cn,ChiCTR2300077801.

Network pharmacology-based study on the mechanism of action of Trollius chinensis capsule in the treatment of upper respiratory tract infection.

BACKGROUND: Upper respiratory tract infection (URTI), one of the most common respiratory diseases, has a high annual incidence. Trollius chinensis capsule has been used to treat URTI in China. However, the underlying-mechanisms remain unclear. METHODS: Network pharmacology was used to explore the potential mechanism of action of Trollius chinensis capsule in URTI treatment. The active compounds in Trollius chinensis were obtained from the TCMSP, SymMap, and ETCM databases. The TCMSP, PubChem, and SwissTargetPrediction databases were used to predict potential targets of Trollius chinensis. URTI-associated targets were gathered from GeneCards and DisGeNET databases. The key targets and signaling pathways associated with URTI were selected by network topology, GO, and KEGG pathway enrichment analysis. Molecular docking was used to verify the binding activity between active compounds and key targets. RESULTS: Quercetin, pectolinarigenin, beta-sitosterol, acacetin and cirsimaritin are major active compounds in Trollius chinensis capsule. Eighty one candidate therapeutic targets were confirmed to be involved in protection of Trollius chinensis capsule against URTI. Among them, 7 key targets (TP53, IL6, AKT1, CASP3, CXCL8, MMP9, and EGFR) were verified to have good binding affinities to the main active compounds. Furthermore, enrichment analyses suggested that inflammatory response, virus infection and oxidative stress related biological processes and pathways were possibly the potential mechanism. CONCLUSION: Overall, the present study clarified that quercetin, pectolinarigenin, beta-sitosterol, acacetin and cirsimaritin are proved to be the main effective compounds of Trollius chinensis capsule treating URTI, possibly by acting on the targets of IL6, AKT1, CASP3, CXCL8, MMP9 and EGFR to play anti-infectious, anti-viral, and anti-oxidative effects. This study provides a new understanding of the active compounds and mechanisms of Trollius chinensis capsule in URTI treatment from the perspective of network pharmacology.

Pharmacological targets and validation of remdesivir for the treatment of COVID-19-associated pulmonary fibrosis: A network-based pharmacology and bioinformatics study.

The objective of this study was to employ bioinformatics and network pharmacology methodologies to investigate the targets and molecular mechanisms of remdesivir in the treatment of coronavirus disease 2019 (COVID-19)-associated pulmonary fibrosis (PF). Several open-source databases were utilized to confirm the shared targets of remdesivir, COVID-19, and PF. Following this, a comprehensive analysis incorporating function enrichment, protein-protein interaction (PPI), transcription factor (TF), and molecular docking was conducted to investigate the potential mechanisms underlying the effectiveness of remdesivir in the treatment of COVID-19-associated PF. The initial validation of these findings was performed using publicly available histological and single-cell sequencing databases. The functional enrichment analysis revealed a strong association between remdesivir and viral defense, inflammatory response, and immune response. The key pathways identified in the study were transforming growth factor (TGF-ß), PI3K-Akt, mTOR, MAPK, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor resistance, HIF-1, and Toll-like receptor signaling pathways. Additionally, the PPI analysis demonstrated the network relationships of 13 important targets, while the TF analysis provided valuable insights into the regulatory networks of these targets. Among the identified TFs, RELA was found to be the most significant. To validate our findings, we utilized publicly available histological and single-cell sequencing databases, successfully confirming the involvement of 8 key targets, including AKT1, EGFR, RHOA, MAPK1, PIK3R1, MAPK8, MAPK14, and MTOR. Furthermore, molecular docking studies were conducted to assess the interaction between remdesivir and the identified key targets, thus confirming its effective targeting effects. Remdesivir has the potential to exert antiviral, anti-inflammatory, and immunomodulatory effects in the context of COVID-19-associated PF.

Analysis of Pathological Factors of Long Head of Biceps Tendinopathy Based on Network Pharmacology.

OBJECTIVES: To investigate the therapeutic effect and mechanism of Danggui Buxue Tang in the treatment of biceps longus tendon lesions, and to preliminarily explore the relevant factors affecting this injury. METHODS: Using network pharmacology analysis methods, the potential mechanism of Danggui Buxue Tang in treating key lesions of the long head of the biceps brachii muscle was studied. RESULTS: Model analysis revealed 44 protein-protein interactions associated with long head binding. The distribution of 19 strongly correlated targets is Pharmaper>SEA>Stitch>Swiss. Further discovery revealed 17 immune system and inflammation related KEGG pathways with P values less than 0.01. The TNF and sphingolipid signaling pathways are associated with inflammation, while the MAPK signaling pathway is associated with immunity. Finally, it was found that the FoxO and HIF-1 signaling pathways are directly associated with long head restraint injury in the biceps brachii muscle. CONCLUSION: Danggui Buxue Tang inhibits related pathways, regulates the immune system, reduces inflammation, and alleviates disease progression. Danggui Buxue Tang can be an effective choice for treating combined lesions of the long head of the biceps brachii muscle.

Transplanting network pharmacology technology into food science research: A comprehensive review on uncovering food-sourced functional factors and their health benefits.

Network pharmacology is an emerging interdisciplinary research method. The application of network pharmacology to reveal the nutritional effects and mechanisms of active ingredients in food is of great significance in promoting the development of functional food, facilitating personalized nutrition, and exploring the mechanisms of food health effects. This article systematically reviews the application of network pharmacology in the field of food science using a literature review method. The application progress of network pharmacology in food science is discussed, and the mechanisms of functional factors in food on the basis of network pharmacology are explored. Additionally, the limitations and challenges of network pharmacology are discussed, and future directions and application prospects are proposed. Network pharmacology serves as an important tool to reveal the mechanisms of action and health benefits of functional factors in food. It helps to conduct in-depth research on the biological activities of individual ingredients, composite foods, and compounds in food, and assessment of the potential health effects of food components. Moreover, it can help to control and enhance their functionality through relevant information during the production and processing of samples to guarantee food safety. The application of network pharmacology in exploring the mechanisms of functional factors in food is further analyzed and summarized. Combining machine learning, artificial intelligence, clinical experiments, and in vitro validation, the achievement transformation of functional factor in food driven by network pharmacology is of great significance for the future development of network pharmacology research.

Network pharmacology-based investigation and experimental validation of the mechanism of metformin in the treatment of acute myeloid leukemia.

Metformin, a widely used anti-diabetic agent, has shown significant anti-cancer properties as reported in in various cancers, including acute myeloid leukemia. However, the detailed mechanisms by which metformin influences acute myeloid leukemia remain unrevealed. Employing a synergistic approach of network pharmacology and experimental validation, this study systematically identifies and analyzes potential metformin targets and AML-related genes. These findings are then cross-referenced with biomedical databases to construct a target-gene network, providing insights into metformin's pharmacodynamics in AML treatment. Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses are utilized. Results show metformin's effectiveness in inhibiting AML cell proliferation and inducing apoptosis through the AKT/HIF1A/PDK1 signaling pathway. This research provides insights into metformin's clinical application in AML treatment.

Discussion on the mechanism of Tiaoqi Xiaowei decoction in the treatment of chronic atrophic gastritis based on network pharmacology and molecular docking: An observational study.

To explore the mechanism of Tiaoqi Xiaowei decoction in the treatment of chronic atrophic gastritis by network pharmacology and molecular docking. The main active components and targets of Tiaoqi Xiaowei decoction were obtained from TCMSP database. The databases of Disgenet, GeneCards, and OMIM were used to obtain chronic atrophic gastritis-related targets. The component-target-disease network was constructed by Cytoscape 3.7.1 software, and the protein-protein interaction network was constructed by String database. The core targets were screened by CytoNCA plug-in. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis were performed using the Metascape database. The core components and targets were subjected to molecular docking verification using AutoDock Tools 1.5.6 software, and the binding score was obtained. A total of 48 active components were identified, involving 82 action targets. Core active components such as quercetin, beta-sitosterol, kaempferol, luteolin, and naringenin, and core targets such as AKT1, TP53, VEGFA, TNF, IL6, and PTGS2 were obtained. A total of 188 signaling pathways were screened out, including cancer pathway, PI3K-Akt, IL-17, and TNF signaling pathway. Molecular docking results showed that the key components of Tiaoqi Xiaowei decoction had a favorable binding affinity with key targets. Tiaoqi Xiaowei decoction acts on multiple targets such as AKT1, TP53, VEGFA, TNF, IL6, PTGS2, and synergistically treats chronic atrophic gastritis by regulating inflammatory responses and tumor-related signaling pathways.

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.

Mechanism of inhibition of TLR4/NFκB/NLRP3 inflammatory pathway against AD based on the network pharmacology of Erjing Pills.

Alzheimer disease is an irreversible neurodegenerative disease, and its pathogenesis involves various mechanisms such as neuroinflammation and ß-amyloid deposition. Erjing Pills can inhibit neuroinflammation by inhibiting toll-like receptor 4/nuclear factor kappa-B/nucleotide-binding domain leucine-rich repeat and pyrin domain-containing protein 3; however, qualitative analysis of the material basis is lacking. Therefore, it is necessary to analyze and explore the material basis of network pharmacology research. This study employed a multifaceted approach, including drug-like screening, molecular docking, and bioinformatic analysis. Preliminary screening identified 59 drug ingredients in Erjing Pills that met the Absorption, Distribution, Metabolism, Excretion and Toxicity screening criteria. Among these, 7 ingredients, including diosgenin, exhibited superior binding properties compared with the positive drugs in molecular docking. Gene ontology annotation and pathway analysis revealed their involvement in crucial biological processes, such as hormone response, insulin resistance, and steroid hormone biosynthesis signaling pathways, which are known for their anti-inflammatory and cognitive enhancement effects. A meta-analysis of relevant literature corroborated the anti-inflammatory activities of diosgenin and 5 other ingredients. These 5 ingredients, with diosgenin as a prominent candidate, exert anti-inflammatory effects by targeting key components of the toll-like receptor 4/nuclear factor kappa-B/nucleotide-binding domain leucine-rich repeat and pyrin domain-containing protein 3 inflammatory pathway, thereby presenting potential efficacy in the treatment of Alzheimer disease.

Integrating serum metabolomics analysis and network pharmacology to reveal the potential mechanism of Shengmai Jianghuang San in the treatment of nasopharyngeal carcinoma.

Shengmai Jianghuang San (SMJHS) is a traditional Chinese herbal compound reported to inhibit Nasopharyngeal Carcinoma (NPC) progression and enhance radiosensitivity. However, the specific active ingredients and regulatory mechanisms of SMJHS against NPC, particularly under hypoxic conditions, remain unclear. In this study, Sprague-Dawley (SD) rats were gavaged with Shengmai Jianghuang San (SMJHS), and their blood was collected from the abdominal aorta. UHPLC-Q-Exactive orbitrap MS/MS was used to identify the metabolite profiles of SMJHS drug-containing serum. A molecular network of the active compositions in SMJHS targeting NPC was constructed through network pharmacology and molecular docking. The HIF-1α/VEGF pathway was in key positions. The effects of SMJHS on the proliferation, migration, and radiosensitivity of hypoxic NPC cells were assessed by in vitro experiments. NPC cell lines stably overexpressing HIF-1α were established using a lentivirus to investigate the regulation of HIF-1α/VEGF signaling in hypoxic NPC cells by SMJHS. Through a combination of network pharmacological analysis, cellular biofunctional validation, and molecular biochemical experiments, our study found that SMJHS had an anti-proliferative effect on NPC cells cultured under hypoxic conditions, inhibiting their migration and increasing their radiosensitivity. Additionally, SMJHS suppressed the expression of HIF-1α and VEGFA, exhibiting potential as an effective option for improving NPC treatment.

MSH-DTI: multi-graph convolution with self-supervised embedding and heterogeneous aggregation for drug-target interaction prediction.

BACKGROUND: The rise of network pharmacology has led to the widespread use of network-based computational methods in predicting drug target interaction (DTI). However, existing DTI prediction models typically rely on a limited amount of data to extract drug and target features, potentially affecting the comprehensiveness and robustness of features. In addition, although multiple networks are used for DTI prediction, the integration of heterogeneous information often involves simplistic aggregation and attention mechanisms, which may impose certain limitations. RESULTS: MSH-DTI, a deep learning model for predicting drug-target interactions, is proposed in this paper. The model uses self-supervised learning methods to obtain drug and target structure features. A Heterogeneous Interaction-enhanced Feature Fusion Module is designed for multi-graph construction, and the graph convolutional networks are used to extract node features. With the help of an attention mechanism, the model focuses on the important parts of different features for prediction. Experimental results show that the AUROC and AUPR of MSH-DTI are 0.9620 and 0.9605 respectively, outperforming other models on the DTINet dataset. CONCLUSION: The proposed MSH-DTI is a helpful tool to discover drug-target interactions, which is also validated through case studies in predicting new DTIs.

Exploring the pharmacological mechanism of Xianlingubao against diabetic osteoporosis based on network pharmacology and molecular docking: An observational study.

Xianlinggubao formula (XLGB), is a traditional Chinese compound Medicine that has been extensively used in osteoarthritis and aseptic osteonecrosis, but its curative effect on diabetic osteoporosis (DOP) and its pharmacological mechanisms remains not clear. The aim of the present study was to investigate the possible mechanism of drug repurposing of XLGB in DOP therapy. We acquired XLGB active compounds from the traditional Chinese medicine systems pharmacology and traditional Chinese medicines integrated databases and discovered potential targets for these compounds by conducting target fishing using the traditional Chinese medicine systems pharmacology and Swiss Target Prediction databases. Gene Cards and Online Mendelian Inheritance in Man® database were used to identify the DOP targets. Overlapping related targets between XLGB and DOP was selected to build a protein-protein interaction network. Next, the Metascape database was utilized to enrich the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. In addition, Auto-Dock Vina software was used to verify drug and target binding. In total, 48 hub targets were obtained as the candidate targets responsible for DOP therapy. The anti-DOP effect mediated by XLGB was primarily centralized on the advanced glycation end products (AGEs)-receptor for AGE signaling pathway in diabetic complications and osteoclast differentiation. In addition, AKT serine/threonine kinase 1, tumor necrosis factor, Interleukin-6, vascular endothelial growth factor A and peroxisome proliferator activated receptor gamma, which were considered as potential therapeutic targets. Furthermore, molecular docking results confirm the credibility of the predicted therapeutic targets. This study elucidates that XLGB may through regulating AGEs formation and osteoclast differentiation as well as angiogenesis and adipogenesis against DOP. And this study provides new promising points to find the exact regulatory mechanisms of XLGB mediated anti-DOP effect.

Exploring the mechanism of Lianhuaqingwen (LHQW) in treating chronic bronchitis based on network pharmacology and experimental validation.

BACKGROUND: Lianhuaqingwen (LHQW) has been used in the treatment of chronic bronchitis, but the precise mechanism through which LHQW exhibits its anti-inflammatory effects in this context is not yet fully understood. The aim of this study was to investigate the active ingredients and signaling pathways responsible for LHQW's effectiveness in managing chronic bronchitis. METHODS: The research leveraged the TCMSP database to determine the active compounds and drug targets of LHQW. In parallel, the GeneCards, DrugBank, and PharmGkb databases were used to uncover targets pertinent to chronic bronchitis. To discern the potential mechanisms by which LHQW's active ingredients might treat chronic bronchitis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Network pharmacology facilitated the construction of a drug-active ingredient-disease target network, aiding in forecasting the core targets for chronic bronchitis treatment by LHQW. Subsequently, molecular docking techniques alongside in vitro experiments were applied to confirm the interactions between the active ingredients and the primary targets. RESULTS: A total of 157 active ingredients, 225 potential drug targets, and 594 bronchitis-related targets were derived from various databases. Following this, 76 potential gene targets were pinpointed by integrating drug and related targets. GO and KEGG enrichment analyses were employed to identify key pathways involved in LHQW's mechanism for treating chronic bronchitis. By constructing a protein-protein interaction (PPI) network for the 76 potential gene targets, four core targets (TNF, IL6, IFNG, and STAT3) were identified as primarily involved in responses to lipopolysaccharide, the TNF pathway, and the JAK-STAT pathway. Molecular docking results revealed a favorable affinity between multiple active ingredients of LHQW and the four core targets, suggesting that the therapeutic effects are mediated through the inhibition of inflammatory responses and signaling pathways. Interestingly, quercetin, an active ingredient of LHQW, was observed to bind to all four core targets simultaneously. Furthermore, cell experiment and western blot analysis indicated that both LHQW and quercetin exhibit anti-inflammatory effects by targeting the four core proteins and the JAK-STAT pathways. CONCLUSION: This research emphasizes the diverse active ingredients, targets, channels, and pathways of LHQW in the treatment of chronic bronchitis, providing important perspectives for the creation of novel therapeutic drugs and clinical uses.

Investigating the mechanism of PAD in the treatment of acne based on network pharmacology and molecular docking: A review.

Acne is a common and chronic skin condition characterized by high incidence, recurrent symptoms and difficult cure. Summarizing the clinical treatment experience, it was found that the powder for ascending and descending was effective in the treatment of acne. Our aim was to use network pharmacology and molecular docking to reveal the hub genes, biological functions, and signaling pathways of powder for ascending and descending against acne. First, the chemical components and target genes of PAD were sifted using the TCMSP and HERB database. The targets of acne were obtained simultaneously from the CTD, OMIM and GeneCards database. The obtained drug targets and disease targets were imported into the R language software to draw Venn diagrams. Then, the potential targets were imported into the String website to construct a protein interaction network diagram. And Cytoscape software was used for topological analysis to screen the core targets, and the core targets were analyzed by GO functional enrichment and KEGG pathway enrichment. Finally, molecular docking was used to verify the predictions of key genes' reliability. The core targets of the treatment of acne were TNF, GADPH, IL-6 and so on. The results of enrichment analysis showed that the treatment of acne with PAD may be related to TNF signaling pathway and AGE-RAGE signaling pathway. The molecular docking verification showed that the components were well bound to the core targets of acne, and the docking ability of stigmasterol and TNF (-12.73 kcal/mol) was particularly outstanding.