BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

Using network pharmacology and molecular docking technology, proteomics and experiments were used to verify the effect of Yigu decoction (YGD) on the expression of key genes in osteoporotic mice

BACKGROUND

Yigu decoction (YGD) is a traditional Chinese medicine prescription for the treatment of osteoporosis, although many clinical studies have confirmed its anti-OP effect, but the specific mechanism is still not completely clear.

METHODS

In this study, through the methods of network pharmacology and molecular docking, the material basis and action target of YGD in preventing and treating OP were analyzed, and the potential target and mechanism of YGD in preventing and treating OP were clarified by TMT quantitative protein and experiment.

RESULTS

Network pharmacology and molecular docking revealed that the active components of YGD were mainly stigmasterol and flavonoids. Molecular docking mainly studied the strong binding ability of stigmasterol to the target. Animal proteomics verified the related mechanism of YGD in preventing and treating OP. Based on the KEGG enrichment of network pharmacology and histology, our animal experiments in vivo verified that YGD may play a role in the treatment of OP by mediating hif1- α/vegf/glut1 signal pathway.

CONCLUSIONS

YGD prevention and treatment of OP may be achieved by interfering with multiple targets. This study confirmed that it may promote osteoblast proliferation and protect osteoblast function by up-regulating the expression of proteins related to HIF signal pathway.

PEBL, a component-based Chinese medicine, reduces virus-induced acute lung injury by targeting FXR to decrease ACE2 levels

INTRODUCTION

Despite the growing clinical need, the therapeutic efficacy of drugs for acute lung injury (ALI) remains inadequate. Traditional Chinese Medicine (TCM) holds potential in managing ALI due to its unique therapeutic properties. However, the intricate nature of TCM formulations hinders global adoption. Component-based Chinese medicine (CCM) offers a promising pathway for TCM's internationalization. Phillyrin-Emodin-Baicalin-Liquiritin (PEBL), a CCM with significant anti-inflammatory activity, is derived from the well-established TCM formula Liang-Ge-San. Whether PEBL effectively addresses viral ALI, however, remains unclear.

OBJECTIVES

This study aims to investigate the therapeutic effects and underlying mechanisms of PEBL on viral ALI.

METHODS

The efficacy of PEBL against Poly(I:C)-induced ALI was assessed by analyzing cytokine production, macrophage infiltration, pulmonary damage, and mortality. Bioinformatics and network pharmacology were employed to identify key targets and signaling pathways. The molecular mechanisms were further validated using Poly(I:C)-treated RAW264.7 cells, Tg(coro1α: GFP) zebrafish, BALB/c mice, and models of Influenza A/Puerto Rico/8/1934 (H1N1) virus strain (PR8)-induced ALI in BALB/c mice and SARS-CoV-2 Omicron XBB.1.16 subvariant (XBB)-induced ALI in hACE2-transgenic C57BL/6 mice.

RESULTS

PEBL mitigated Poly(I:C)-induced ALI, as evidenced by reduced cytokine levels, diminished macrophage infiltration, alleviated lung damage, and decreased mortality. Virtual screening identified the farnesyl X receptor (FXR) and angiotensin-converting enzyme 2 (ACE2) as key therapeutic targets for viral pneumonia. Mechanistically, PEBL downregulated FXR expression, inhibiting FXR binding to ACE2 promoters, which subsequently suppressed NF-κB-p65 nuclear translocation and cytokine production. In vivo, PEBL attenuated cytokine production by inhibiting ACE2 transcription through FXR downregulation, leading to alleviation of Poly(I:C)-induced ALI in both zebrafish and mice. Additionally, PEBL significantly improved symptoms of ALI caused by PR8 and XBB infections, by disrupting the FXR/ACE2 signaling axis, resulting in reduced weight loss, lower lung indices, diminished viral load and titer, fewer pulmonary lesions, and suppressed NF-κB-p65 nuclear translocation, along with decreased cytokine storm.

CONCLUSIONS

This study provides the first evidence that PEBL offers protective effects against ALI induced by acute respiratory viruses. PEBL prevents FXR from binding to ACE2 by inhibiting FXR transcription, which reduces macrophage infiltration, cytokine storm formation, and inflammatory injury, thereby ameliorating viral ALI. These findings underscore the potential of PEBL as a candidate for further exploration in the treatment of viral ALI.

Synergistic mechanism of olaparib and cisplatin on breast cancer elucidated by network pharmacology

Cisplatin is an important chemotherapeutic agent is widely used to treat breast cancer and olaparib is the most studied PARP inhibitor to date. To explore the combinational anti-cancer potential and synergistic mechanism of Olaparib and cisplatin in breast cancer using network pharmacology. Drugs targets were drawn from PharmMapper, DrugBank, BATMAN-TCM, DrugCentral, STITCH, Swiss Institude of Bioinformatics and Comparative Toxigenomics Database (CTD). Breast cancer targets were extracted from OMIM, KEGG, GeneCards and DrugBank. The protein-protein interaction (PPI) network was created using the STRING database. Core targets were selected by incorporating PPI networks using Cytoscape 3.9.1. GO and KEGG analyses were performed to investigate common targets of Olaparib and cisplatin in breast cancer. The drug-disease-target network contained 82 nodes and 901 edges. The common targets obtained from Olaparib, cisplatin and breast cancer were identified, including ATK, p53, caspase-3, HSP90AA1, IL-6, IL-1β, ANXA5, SIRT1, caspase-9 and PARP. Core targets were primarily related to response to reactive oxygen species, regulation of apoptotic signaling pathway, regulation of DNA metabolic process, and regulation of cell activation. The KEGG pathway analysis revealed that Olaparib and cisplatin may affect breast cancer through platinum drug resistance and longevity regulating pathway. Furthermore, Olaparib combined with cisplatin downregulated the expression of caspase-3 and caspase-9 proteins and upregulated p53, PARP, and SIRT1 protein levels in MCF-7 cells. Functionally, the cooperative effect of Olaparib and cisplatin reduced the applied concentration of cisplatin and enhanced the anticancer effect, emphasizing the importance of combination therapy to overcome side effects and significantly improve the anticancer efficacy of cisplatin.

Network Pharmacology and Experimental Validation of the Effects of Shenling Baizhu San, Quzhi Ruangan Fang and Gexia Zhuyu Tang on the Intestinal Flora of Rats with NAFLD

Objective

In this study, we investigated the effect of Shenling Baizhu San(SLBZS), Quzhi Ruangan Fang(QZRGF) and Gexia Zhuyu Tang(GXZYT) on the intestinal flora of NAFLD rats through network pharmacology and experimental validation.

Materials and Methods

Protein-protein interaction, Gene Ontology (GO), and molecular docking were performed. Male Sprague-Dawley (SD) rats were divided into 6 groups: Normal, Model, SLBZS (7.2g/kg), QZRGF (27.72g/kg), GXZYT (28.8 g/kg) and positive control (Fenofibrate, 18mg/kg); the NAFLD model was established by High-fat diet. After one week of acclimatisation feeding consecutively, continuous gavage was given for 8 W and 12 W. Serum, liver and faeces were collected and biochemical and pathological indices were determined. The diversity and abundance of intestinal flora were also analyzed using 16S rDNA amplified sequencing.

Results

A total of 132 active ingredients were obtained from the screening results of SLBZS. A total of 202 active ingredients were obtained from the screening results of GXZYT. The screening results of QZRGF obtained 34 active ingredients. Nine common hub genes were screened from the PPI network. GO functional analysis reported that these targets were mainly closely related to the response to bacterial molecules. The molecular docking results indicated that the 11 core constituents in three compound prescriptions has good binding ability with MAPK1, AKT1, CASP3, FOS, TP53, STAT3, MAPK3.

Conclusion

The Chinese herbal compounds SLBZS, QZRGF and GXZYT may exert lipid-lowering effects through multi-components, multi-targets and multi-methods for the treatment of NAFLD while improving the diversity and abundance of the intestinal flora of the rats, and the best effect was achieved with SLBZS.

JTCD attenuates HF by inhibiting activation of HSCs through PPARα-TFEB axis-mediated lipophagy

BACKGROUND

Hepatic fibrosis (HF) is an intermediate stage in the progression of chronic liver disease to cirrhosis and has been shown to be a reversible pathological process. Known evidence suggests that activation of hepatic stellate cells (HSCs) and degradation of their lipid droplets (LDs) play an indispensable role in the process of HF. Jiawei Taohe Chengqi Decoction (JTCD) can inhibit the activation of HSCs in the process of HF, but the exact mechanism remains to be elucidated.

PURPOSE

The aim of this study is to determine whether JTCD inhibits lipophagy and to explore the possible mechanisms of its HF effect in HSCs by regulating the PPARα/TFEB axis.

METHODS

Network pharmacology and molecular docking were firstly applied to predict the potential mechanism of JTCD for the treatment of HF. In vivo, a mouse model of HF was constructed using carbon tetrachloride (CCl4) solution, and the efficacy of JTCD was assessed by staining of pathological sections, oil red O staining, immunofluorescence (IF), immunohistochemistry (IHC) staining, Western blotting and qRT-PCR. The intervention of JTCD was verified in vitro by induction of activated LX-2 cells with TGF-β solution and intervention using agonists and antagonists of PPARα. Finally, transient transfection of cells using TFEB siRNA was performed for validation studies.

RESULTS

JTCD effectively alleviated CCl4-induced HF in mice and reduced the levels of HF markers α-smooth muscle actin (α-SMA) and collagen I (COL1A1), and inhibited PPARα expression and lipophagy process. In vitro, JTCD delayed the degradation of LDs and reduced lipophagy in LX-2 cells, suggesting a mechanism involving PPARα/TFEB axis signaling regulation.

TCM-ADIP: A Multidimensional Database Linking Traditional Chinese Medicine to Functional Brain Zones of Alzheimer's Disease

Alzheimer's disease (AD) is a complex neurodegenerative disorder, with existing therapeutic drugs typically targeting specific disease stages. Traditional Chinese medicine (TCM), known for its multi-target and multi-mechanism therapeutic approach, has demonstrated efficacy in treating various stages of AD. In the present work, through a systematic review of classical Chinese medical texts, the formulae for preventing and treating AD were identified. Meanwhile, the active ingredients within these formulae were extracted and cataloged. A comprehensive bioinformatics analysis of omics data was performed to identify differentially expressed genes across different functional brain zones in AD patients at various stages. Finally, by integrating the multidimensional data, we proposed the first database, TCM-ADIP, dedicated to TCM based AD prevention and treatment, which is freely available at https://cbcb.cdutcm.edu.cn/TCM-ADIP/. TCM-ADIP not only supports interactive searching of multidimensional data, but also provides tools for gene localization and functional enrichment analysis of formulae, herbs, and ingredients for AD intervention in specific brain zones. TCM-ADIP fills a crucial gap in existing databases, offering a comprehensive resource for TCM in the treatment of AD.

Mechanisms of Huhuang decoction in treating diabetic wounds: a network pharmacological and experimental study

Background: Huhuang (HH) decoction, a composition of seven traditional Chinese medicines, has demonstrated clinical efficacy in wound healing. However, its pharmacological foundation and potential mechanisms remain unclear. This study aimed to elucidate the mechanisms of action of HH decoction in the treatment of diabetic wounds. Methods: The chemical composition of HH decoction was analysed using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. The targets of the HH decoction in treating diabetic wounds were predicted using network pharmacology. The gene ontology and pathway enrichment analyses were performed using the DAVID functional annotation tool. The compound targets and PPI networks were established using Cytoscape. Molecular docking was implemented using the AutoDock Vina software. Experimental verification was performed on the target prediction of the HH decoction in treating diabetic wounds, both in vivo and in vitro. Results: The study identified 53 chemical components in HH decoction, with tetrahydropalmatine, emodin, rosmarinic acid, citric acid, berberine, and cryptotanshinone as key components for treating diabetic wounds. Twenty-one target genes were identified as core genes. Gene ontology analysis indicated that the therapeutic effects of HH on diabetic foot ulcers may occur through the regulation of cell proliferation, migration, and inflammation. Pathway enrichment was found to be mainly related to the HIF-1 and TNF signalling pathways. HH promoted proliferation, migration, and tube formation in vascular endothelial cells in vitro. Compared with the control group, the expression levels of HIF-1α, VEGF-α, cyclinD1 in the HH group were higher while the phosphorylation level of p65 in the HH group was significantly lower. The concentrations of IL-6, TNF-α, and IL-1β in wound tissue in the HH group were significantly lower than those in the control group. The expression levels of CD31, VEGF-α, Ki67 and HIF-1α in the wounds of diabetic rats in the HH group were higher than those in the control group. Conclusions: The HH decoction promotes diabetic wound healing via multiple components, targets, and pathways. It may enhance vascular endothelial cell proliferation via cyclinD1, promote vascularization through the HIF-1α/VEGF-α signalling pathway, and inhibit inflammation through NF-κB signalling pathways.

Computer-Aided Drug Design in Research on Chinese Materia Medica: Methods, Applications, Advantages, and Challenges

Chinese materia medica (CMM) refers to the medicinal substances used in traditional Chinese medicine. In recent years, CMM has become globally prevalent, and scientific research on CMM has increasingly garnered attention. Computer-aided drug design (CADD) has been employed in Western medicine research for many years, contributing significantly to its progress. However, the role of CADD in CMM research has not been systematically reviewed. This review briefly introduces CADD methods in CMM research from the perspectives of computational chemistry (including quantum chemistry, molecular mechanics, and quantum mechanics/molecular mechanics) and informatics (including cheminformatics, bioinformatics, and data mining). Then, it provides an exhaustive discussion of the applications of these CADD methods in CMM research through rich cases. Finally, the review outlines the advantages and challenges of CADD in CMM research. In conclusion, despite the current challenges, CADD still offers unique advantages over traditional experiments. With the development of the CMM industry and computer science, especially driven by artificial intelligence, CADD is poised to play an increasingly pivotal role in advancing CMM research.

Concoctive principles of detoxification and retention of the main toxicity of Tripterygium wilfordii and its anti-inflammatory efficacy by concocting with the medicinal excipient Spatholobi Caulis juice

Tripterygium wilfordii (TW), which has severe hepatotoxicity, is commonly used as anti-rheumatism. Using the juice of auxiliary herbs in concocting poisonous herbs is a conventional method for toxicity reduction or efficacy enhancement. Traditional Chinese Pharmacy textbooks record that Spatholobi Caulis (SC) can alleviate the side effects caused by TW and also possesses excellent hepatoprotective effect. However, it is still unclear how the concoctive principles of hepatotoxicity reduction and anti-inflammatory efficacy retention of TW after being concocted with the medicinal excipient SC juice. Therefore, this study aimed to evaluate the hepatotoxicity and anti-inflammatory efficacy of concoction with SC juice on TW and preliminarily explored its detoxification mechanism. The attenuation effect of TW concocted with SC juice was determined by triptolide (TP) content, hepatic histological and serum biochemical indexes. The detoxification mechanism was predicted by network pharmacology and molecular docking, and confirmed by quantitative real-time PCR (qRT-PCR) and Western blot. Moreover, the anti-inflammatory efficacy was evaluated by paw edema test, and the major active ingredients in the SC juice introduced to TW concoction were detected. Concoction with SC juice significantly reduced TP content and serum biochemical indicator levels, alleviated liver pathological damage, introduced the main active ingredients, and inhibited the expression of hypoxia inducible factor-1α (HIF-1α) and vascular endothelial growth factor A (VEGFA). Furthermore, the anti-inflammatory efficacy was retained. In summary, this study elucidated that concoction with SC juice alleviated the hepatotoxicity of TW by inhibiting HIF-1α/VEGFA signaling, decreasing TP content, and introducing the main active components. Moreover, the anti-inflammatory efficacy was retained.

Compound kushen injection improves radiation enteritis via cannabinoid receptor 1 in rats

BACKGROUND

Clinical studies have shown that Compound Kushen Injection (CKI) can alleviate the inflammatory symptoms of radiation enteritis. However, the mechanism of action remains unclear. The aim of this study was to explore the possible targets and mechanisms of CKI in the treatment of radiation enteritis.

METHODS

Network pharmacology was used to predict the potential targets of CKI for the treatment of radiation enteritis, and GO and KEGG enrichment analyses were subsequently performed. SD rats were randomly divided into one of the following groups: control, model, CB1 agonist, CKI and CKI + CB1 antagonist. Except for the control group, the remaining groups were irradiated the abdomen with 6 MV medical high-energy x-ray linear accelerator to establish the model of radiation enteritis. After one week of treatment, the expression of inflammatory factors, SOD and GSH-Px activities, MDA, ROS and NO contents; NF-κB signaling activation and the expression of NOX4, CB1, p38 MAPK, p-p38 MAPK in the ileal tissues of rats were examined to assess the therapeutic effect and possible mechanism of CKI on radiation enteritis, respectively.

RESULTS

According to network pharmacology, CB1 might be a target of CKI. GO and KEGG enrichment analyses revealed that CKI was significantly enriched in analgesic, endocannabinoid and inflammatory pathways. In the rat model, Compared with that in the radiotherapy group, the extent of ileal injury was significantly improved in the CKI group compared to the control group. In addition, the infiltration of CD68 and CD16b was significantly reduced, and the expression of MCP1, TNF-α, IL-1β and IL-10 was significantly decreased. In addition, the activities of SOD and GSH-Px were increased, and the activities of MDA, ROS and NO were decreased. The CKI group also showed inhibition of NF-κB signaling and a significant decrease in the expression of NOX4, CB1 and p-p38 MAPK/p38 MAPK. The use of a CB1 agonist could also alleviate radiation enteritis, whereas the addition of a CB1 antagonist could interfere with the ameliorative effect of CKI on radiation enteritis.

CONCLUSIONS

CKI might exert an anti-radiation enteritis effect by targeting the cannabinoid receptor 1.

Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer's disease

Isoliquiritigenin (ISL), a flavone isolated from licorice, has been demonstrated to exhibit anti-inflammatory and antioxidant properties in the treatment of Alzheimer's disease (AD). However, the molecular details of the contribution of ISL to AD remain largely elusive. The present study aimed to investigate the molecular mechanisms of ISL against AD. In this study, AD targets and ISL targets were collected via different databases. The overlapped targets between AD and ISL were generated with Venny. Then we performed Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses on these common targets. The protein-protein interaction (PPI) network was constructed and clusters were obtained using the Molecular Complex Detection (MCODE) and the Cytohubba plugins. Further, molecular docking study was performed for these core targets. Subsequently, the receiver operating characteristic (ROC) curve analysis and the assessment of hub gene expression levels between AD and healthy individuals were used to estimate a possible link between target genes in AD. Finally, experiments were conducted to verify the therapeutic mechanism of ISL in lipopolysaccharide (LPS)-induced BV2 microglial cells. GO and KEGG pathway analysis found that ISL was significantly enriched in regulation of mitogen-activated protein kinase (MAPK) signaling pathway. The PPI network manifested 7 key targets including albumin (ALB), epidermal growth factor receptor (EGFR), solute carrier family 2 member 1 (SLC2A1), insulin-like growth factor 1 (IGF1), mitogen-activated protein kinase 1 (MAPK1), peroxisome proliferator activated receptor alpha (PPARA) and peroxisome proliferator activated receptor gamma (PPAR-γ, PPARG). Molecular docking showed that ISL had high binding affinity with these key targets. The experimental results revealed that ISL decreased extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation and increased the expression of PPAR-γ, and suppressed the production of proinflammatory mediators. Our work revealed that ISL might be an effective treatment strategy in the treatment of AD by its anti-inflammatory effect towards microglia through the ERK/PPAR-γ pathway.

Pharmacological mechanisms of carvacrol against hepatocellular carcinoma by network pharmacology and molecular docking

BACKGROUND

Preclinical studies have demonstrated that carvacrol possesses various biological and pharmacological properties, including anti-hepatocellular carcinoma (HCC) effects. However, the molecular basis of its therapeutic action on HCC remains unclear.

OBJECTIVE

The aim of this study was to investigate and further validate the multi-target therapeutic mechanism of carvacrol against HCC.

METHODS

The chemical structure of carvacrol was obtained from the PubChem database, and its potential targets were identified using SwissTargetPrediction, HERB, and BATMAN-TCM. HCC-specific genes were screened from the TCGA-LIHC cohort. The therapeutic targets of carvacrol against HCC were determined through the intersection of these datasets. Subsequently, a multivariate Cox regression prognostic model was established. Molecular docking was performed to analyze the interactions between carvacrol and its therapeutic targets. Additionally, molecular dynamics simulations were conducted to validate the molecular docking results using Discovery Studio 2019 software.

RESULTS

A total of 223 carvacrol targets and 882 HCC-specific genes were identified. Fifteen therapeutic targets of carvacrol against HCC were obtained, including CA2, AR, ALB, AURKA, ALPL, EPHX2, BCHE, IL1RN, AGRN, CRP, DMGDH, APOA1, SOX9, HPX, and CHKA. The prognostic model accurately and independently predicted survival outcomes. AGRN and AURKA were significantly associated with HCC overall survival. Molecular docking and molecular dynamics simulations demonstrated that carvacrol exhibited strong potential for stable binding to the therapeutic targets AGRN and AURKA.

CONCLUSION

Our findings elucidate the multi-target mechanism of action of carvacrol against HCC, providing a foundation for future research on its application in HCC management.

Systems pharmacology-based drug discovery from Amaryllidaceae alkaloids and investigation of mechanisms of action in treatment of Alzheimer's disease

OBJECTIVES

Given the success of galanthamine in treating Alzheimer's disease, this study aims to establish an effective method to find drugs from Amaryllidaceae alkaloids and to clarify its mechanism in treating Alzheimer's disease.

METHODS

The pharmacodynamic basis and mechanism of action between Amaryllidaceae alkaloids and Alzheimer's disease were explored by constructing a compound-target-disease network, targets protein-protein interaction, gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and molecular docking verification.

KEY FINDINGS

In total, a chemical library of 357 potential alkaloids was constructed. A total of 100 active alkaloid components were identified. Thirty-nine associated targets were yielded based on network construction, and the key targets were defined as HSP90AA1, ESR1, NOS3, PTGS2, and PPARG using protein-protein interaction network. Gene ontology items (490) and 68 Kyoto Encyclopedia of Genes and Genomes pathways were selected through the enrichment of target functions, including neuroactive ligand-receptor interaction, calcium signaling pathway, cAMP signaling pathway, Alzheimer disease, and serotonergic synapse that were related to Alzheimer's disease. Lastly, molecular docking demonstrated good stability in combining selected alkaloids with targets.

CONCLUSIONS

This study explained the mechanisms of Amaryllidaceae alkaloids in preventing and treating Alzheimer's disease and established a novel strategy to discover new drugs from biological chemical sources.

Exploring the mechanisms of Shugan-Jieyu-Jianpi formula against irritable bowel syndrome combined with non-alcoholic fatty liver disease by network pharmacology and experimental validation

The study was aimed to investigate the clinical effect and mechanism of Shugan-Jieyu-Jianpi (SGJYJP) formula for the treatment of irritable bowel syndrome (IBS) combined with non-alcoholic fatty liver disease (NAFLD). The clinical efficacy of SGJYJP was evaluated in 54 patients with IBS-NAFLD. The potential molecular mechanism of SGJYJP formula was investigated by network pharmacology. Animal models were constructed to explore the related mechanism. From clinical studies, the total effective rate of patients in SGJYJP group was significantly higher than that in pinaverium group. The protein expression of TGFB1 was declined in IBS-NAFLD rats, together with the increased expression of PTGS2 and TNF, which was abolished by SGJYJP treatment. SGJYJP significantly reduced the expression of TNF signalling related molecules of TRAF2, caspase-8, and elevated the expression of Bcl-xl in IBS-NAFLD animal models. SGJYJP may exert therapeutic effect on IBS-NAFLD by targeting PTGS2, TGFB1, and TNF genes and TNF signalling.

β-Elemene inhibits epithelial-mesenchymal transformation in non-small cell lung cancer by targeting ALDH3B2/RPSA axis

The pharmacological mechanism of β-elemene in non-small cell lung cancer (NSCLC) remains poorly understood. In this study, we identified aldehyde dehydrogenase 3B2 (ALDH3B2) as a pivotal target for β-elemene's anti-tumor effects in NSCLC by bioinformatic analysis. The overexpression of ALDH3B2 is specifically associated with the malignancy of NSCLC and the poor prognosis in patients with lung adenocarcinoma. Furthermore, we observed a positive correlation between ALDH3B2 levels and the sensitivity of cells to β-elemene. Additionally, we confirmed that β-elemene suppresses ALDH3B2 expression in PC-9 and NCI-H1373 cell lines. Notably, ALDH3B2 overexpression in NCI-H1373 cells resulted in enhanced migration, invasion, and a prominent epithelial-mesenchymal transition (EMT), which could be attenuated by β-elemene via inhibition of ALDH3B2 expression. Subsequent investigations demonstrated that ALDH3B2 overexpression upregulated ribosomal protein SA (RPSA) expression. β-elemene counteracted the upregulation of RPSA by suppressing ALDH3B2. Furthermore, knocking down of ALDH3B2 and β-elemene treatment significantly reduced the activation of protein kinase B (AKT) and extracellular signal-regulated kinase (ERK) signaling pathways via suppression of RPSA. In summary, our research uncovers that in NSCLC, ALDH3B2 functions as an oncogenic protein, promoting tumor progression. Meanwhile, β-elemene inhibits EMT of NSCLC by inhibition of ALDH3B2/RPSA axis and subsequently downregulating AKT and ERK signaling pathways. Our study highlights the significant role of ALDH3B2 in the progression of NSCLC, signifying it as a potential pharmacodynamic biomarker for β-elemene. These findings enrich the understanding of anti-tumor pharmacological mechanism of β-elemene, and provides new theoretical and experimental foundations for its potential application in the treatment of NSCLC.

Network Pharmacology Analysis and Biological Validation Systemically Identified the Active Ingredients and Molecular Targets of Kudzu Root on Osteoporosis

As a traditional medicinal food, Kudzu root (KR) has been proven to be an effective medicine for treating osteoporosis (OP). However, its precise targets and underlying integrated pharmacological mechanisms on OP have not yet been systematically investigated. The aim of the present study was to systemically explore the active ingredients, molecular targets, and ingredient-target network of KR against OP by the methods of network pharmacology followed by biological validation in a glucocorticoid-induced bone loss model of zebrafish. Our results identified a total of 15 active compounds with good pharmacokinetic properties in KR and 119 targets related to OP from correspondent databases, forming an ingredient-target network. Additionally, the protein-protein interaction (PPI) network further identified 39 core targets. Enrichment analyses with functional annotation revealed that the TNF signaling pathway and osteoclast differentiation process were significantly enriched by multi-targets including AKT1, P65, MAPK14, JUN, TNF-α, MMP9, IL6, and IL1B, etc., and served as the critical targets for molecular docking, molecular dynamics simulation, and in vivo experiment validation. These critical targets performed effectively in molecular docking and molecular dynamics, with AKT1, MMP9, and TNF-α exhibiting more prominent binding energy with Coumestrol, Genistein, and Genistein 7-glucoside, respectively. Further experimental validation in a zebrafish model indicated that KR could regulate the expressions of critical targets (AKT1, P65, MAPK14, JUN, TNF-α, and MMP9). This study provides a systemic perspective of the relationships between the active ingredients of KR and their multi-targets in OP, thereby constructing a pharmacological network to clarify the mechanisms by which KR ameliorates OP.

TarIKGC: A Target Identification Tool Using Semantics-Enhanced Knowledge Graph Completion with Application to CDK2 Inhibitor Discovery

Target identification is a critical stage in the drug discovery pipeline. Various computational methodologies have been dedicated to enhancing the classification performance of compound-target interactions, yet significant room remains for improving the recommendation performance. To address this challenge, we developed TarIKGC, a tool for target prioritization that leverages semantics enhanced knowledge graph (KG) completion. This method harnesses knowledge representation learning within a heterogeneous compound-target-disease network. Specifically, TarIKGC combines an attention-based aggregation graph neural network with a multimodal feature extractor network to simultaneously learn internal semantic features from biomedical entities and topological features from the KG. Furthermore, a KG embedding model is employed to identify missing relationships among compounds and targets. In silico evaluations highlighted the superior performance of TarIKGC in drug repositioning tasks. In addition, TarIKGC successfully identified two potential cyclin-dependent kinase 2 (CDK2) inhibitors with novel scaffolds through reverse target fishing. Both compounds exhibited antiproliferative activities across multiple therapeutic indications targeting CDK2.

Network Pharmacology and Bioinformatics Study of Six Medicinal Food Homologous Plants Against Colorectal Cancer

Integrating network pharmacological analysis and bioinformatic techniques, this study systematically investigated the molecular mechanisms of six medicinal food homologous plants (Astragalus membranaceus, Ganoderma lucidum, Dioscorea opposite, Curcuma longa, Glycyrrhiza uralensis, and Pueraria lobata) against colorectal cancer. Through screening the TCMSP database, 303 active compounds and 453 drug targets were identified. By integrating differential expression gene analysis with WGCNA on the GSE41258 dataset from the GEO database, 49 potential therapeutic targets were identified. GO and KEGG enrichment analyses demonstrated that these targets are primarily involved in drug response, fatty acid metabolism, and key cancer-related pathways. Cross-validation using three machine learning algorithms-LASSO regression, SVM-RFE, and Random Forest-pinpointed four critical target genes: CA1, CCND1, CXCL2, and EIF6. Further, CIBERSORT immune infiltration analysis revealed strong associations between these core genes and the tumor immune microenvironment in colorectal cancer patients, notably in modulating M0 macrophage infiltration and mast cell activity. Molecular docking analyses confirmed robust binding interactions between active compounds and core target proteins. This study systematically elucidated the molecular mechanisms of six medicinal food homologous plants against colorectal cancer, providing scientific evidence for their rational clinical application.

Mechanistic insights into pachymic acid's action on triple-negative breast Cancer through TOP2A targeting

Triple-negative breast cancer (TNBC) is characterized by the absence of estrogen and progesterone receptors, and lack of human epidermal growth factor receptor 2 (HER2) expression. Traditional Chinese medicine (TCM) has demonstrated promising efficacy in treating TNBC. This study explored the mechanisms of pachymic acid (PA) on TNBC by merging network pharmacology with experimental validation. We acquired Microarray data of TNBC from the Gene Expression Omnibus (GEO). The related targets of PA were predicted and screened using the following 6 databases: Swiss Target Prediction, HERB (Herbal Medicine Database), ETCM (Encyclopedia of Traditional Chinese Medicine), BATMAN (Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine), HIT (Herb Ingredients' Targets Database), and PharmMapper. The STRING interaction network analysis tool was used to create Protein-Protein Interaction (PPI) networks. Enrichment analysis included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We conducted a pan-cancer analysis, tumor immune microenvironment analysis, and molecular docking. We performed cell experimental, included cytotoxicity assay, apoptosis analysis, proliferation assay, and migration and invasion assays. PA has potential for treating TNBC with the target of TOP2A, and platinum drug resistance possibly serving as the KEGG pathway through which PA exerts its therapeutic effects. PA is involved in processes such as nuclear division, chromosome segregation, mitotic nuclear division, condensed chromosome formation, and protein C-terminus binding. PA probably exert its therapeutic effects through the tumor immune microenvironment, involving elements such as Dendritic cells activated, Eosinophils, Macrophages M0, Macrophages M1, and T cells CD4 memory activated. The therapeutic effects of PA may vary across different subtypes of TNBC such as TNBC-BL1, TNBC-Metaplastic, and TNBC-BL2. This study provides compelling evidence that PA holds significant promise as a therapeutic agent for TNBC, primarily through its action on TOP2A and its influence on the TNBC.

Active Ingredients and Potential Mechanism of Additive Sishen Decoction in Treating Rheumatoid Arthritis with Network Pharmacology and Molecular Dynamics Simulation and Experimental Verification

Background

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease in which macrophages produce cytokines that enhance inflammation and contribute to the destruction of cartilage and bone. Additive Sishen decoction (ASSD) is a widely used traditional Chinese medicine for the treatment of RA; however, its active ingredients and the mechanism of its therapeutic effects remain unclear.

Methods

To predict the ingredients and key targets of ASSD, we constructed "drug-ingredient-target-disease" and protein-protein interaction networks. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the potential mechanism. The activity of the predicted key ingredients was verified in lipopolysaccharide-stimulated macrophages. The binding mode between the key ingredients and key targets was elucidated using molecular docking and molecular dynamics simulation.

Results

In all, 75 ASSD active ingredients and 1258 RA targets were analyzed, of which kaempferol, luteolin, and quercetin were considered key components that mainly act through inflammation-related pathways, such as the PI3K-AKT, TNF, and IL-17 signaling pathways, to ameliorate RA. Transcriptome sequencing suggested that kaempferol-, luteolin-, and quercetin-mediated inhibition of glycolysis reduced the lipopolysaccharide-induced production of proinflammatory factors. In vitro experiments indicated that kaempferol, luteolin, and quercetin decreased Glut1 and LDHA expression by diminishing PI3K-AKT signaling to inhibit glycolysis. Molecular dynamic simulation revealed that kaempferol, luteolin, and quercetin stably occupied the hydrophobic pocket of PI3Kδ.

Conclusion

Our results show that the PI3Kδ-mediated anti-inflammatory responses elicited by kaempferol, luteolin, and quercetin are crucial for the therapeutic efficacy of ASSD against RA.

Study based on metabolomics and network pharmacology to explore the mechanism of Ginseng-Douch compound fermentation products in the treatment of hyperlipidemia

BACKGROUND

Ginseng-Douchi (GD) is a complex fermented product of ginseng and soybean, similar to natto, and is effective in the treatment of hyperlipidemia, but the mechanism of action involved needs to be further explored.

RESULTS

The present study combines a comprehensive strategy of network pharmacology and metabolomics to explore the lipid-lowering mechanism of GD. First, a hyperlipidemia rats model induced by a high-fat diet was established to evaluate the therapeutic effects of GD. Second, potential biomarkers were identified using serum metabolomics and metabolic pathway analysis was performed with MetaboAnalyst. Third, network pharmacology is used to find potential therapeutic targets based on the blood-influencing components of GD. Finally, core targets were obtained through a target-metabolite and the enrichment analysis of biomarkers-genes. Biochemistry analysis showed that GD exerted hypolipidemic effects on hyperlipidemic rats. Nineteen potential biomarkers for the GD treatment of hyperlipidemia were identified by metabolomics, which was mainly involved in linoleic acid metabolism, glycerophospholipid metabolism, ether lipid metabolism, alpha-linolenic acid metabolism and glycosylphosphatidylinositol-anchor biosynthesis. GD had a callback function for ether lipid metabolism and glycerophospholipid metabolism pathways. Eighteen blood components were identified in serum, associated with 85 potential therapeutic targets. The joint analysis showed that three core therapeutic targets were regulated by GD, including PIK3CA, AKT1 and EGFR.

CONCLUSION

This study combines serum medicinal chemistry of traditional Chinese medicine, network pharmacology and metabolomics to reveal the regulatory mechanism of GD on hyperlipidemia. © 2024 Society of Chemical Industry.

Anthocyanin-Mediated Autophagy in Hepatocellular Carcinoma: Gene Associations and Prognostic Implications

BACKGROUND

Hepatocellular carcinoma (HCC) is a globally prevalent malignancy accompanied by high incidence, poor outcomes, and high mortality. Anthocyanins can inhibit tumor proliferation, migration, invasion, and promote apoptosis. Moreover, autophagy-related genes (ARGs) may play vital roles in HCC progression. This study aimed to decipher the mechanisms through which anthocyanins influence HCC via ARGs and to establish a novel prognostic model.

METHODS

Based on data from public databases, differential analysis and the Venn algorithm were employed to detect intersecting genes among differentially expressed genes (DEGs), anthocyanin- related targets, and ARGs. Consensus clustering was implemented to delineate molecular subtypes of HCC. The prognostic model was developed by Cox regression analyses. CIBIRSORT was engaged to assess the immune cell infiltration. Kaplan-Meier (KM) analysis and receiver operating characteristic (ROC) curve were utilized to evaluate the predictive efficiency of the prognostic signature.

RESULTS

A total of 36 intersecting genes were identified from overlapping 1524 ARGs, 537 anthocyanin- related targets, and 5247 DEGs. Consensus clustering determined three molecular subtypes (cluster 1, cluster 2, and cluster 3). Cluster 1 showed worse outcomes and remarkably higher abundances of plasma cells and T follicular helper cells. Furthermore, four prognostic signatures (KDR (Kinase insert domain receptor), BAK1 (BCL2 antagonist/killer 1), HDAC1 (Histone deacetylase 1), and CDK2 (Cyclin-dependent kinase 2)) were identified and showing substantial predictive efficacy.

CONCLUSION

This investigation identified three molecular subtypes of HCC patients and proposed a promising prognostic signature comprising KDR, BAK1, HDAC1, and CDK2, which could supply further robust evidence for additional clinical and functional studies.

Protective Role of Electroacupuncture Against Cognitive Impairment in Neurological Diseases

Many neurological diseases can lead to cognitive impairment in patients, which includes dementia and mild cognitive impairment and thus create a heavy burden both to their families and public health. Due to the limited effectiveness of medications in treating cognitive impairment, it is imperative to develop alternative treatments. Electroacupuncture (EA), a required method for Traditional Chinese Medicine, has the potential treatment of cognitive impairment. However, the molecular mechanisms involved have not been fully elucidated. Considering the current research status, preclinical literature published within the ten years until October 2022 was systematically searched through PubMed, Web of Science, MEDLINE, Ovid, and Embase. By reading the titles and abstracts, a total of 56 studies were initially included. It is concluded that EA can effectively ameliorate cognitive impairment in preclinical research of neurological diseases and induce potentially beneficial changes in molecular pathways, including Alzheimer's disease, vascular cognitive impairment, chronic pain, and Parkinson's disease. Moreover, EA exerts beneficial effects through the same or diverse mechanisms for different disease types, including but not limited to neuroinflammation, neuronal apoptosis, neurogenesis, synaptic plasticity, and autophagy. However, these findings raise further questions that need to be elucidated. Overall, EA therapy for cognitive impairment is an area with great promise, even though more research regarding its detailed mechanisms is warranted.

Network Pharmacological Analysis of Hydroxychloroquine Intervention in the Treatment of Iga Nephropathy

BACKGROUND

IgA nephropathy (IgAN) is the most prevalent primary glomerulonephritis globally and has a high propensity to develop into end-stage renal disease (ESRD). Hydroxychloroquine has been proven to reduce proteinuria in IgAN patients, but the precise mechanism remains unclear. Therefore, network pharmacology was used to investigate the mechanism.

METHODS

PubChem and SwissADME databases were utilized to acquire the structure of hydroxychloroquine. The SwissTargetPrediction, PharmMapper, DrugBank, TargetNet, and BATMAN-TCM databases were then utilized to obtain the targets. The target genes related to IgAN were then gathered from the databases, which included GeneCards, PHARMGKB, DrugBank, OMIM, and DisGeNET. Common targets were obtained by UniProt. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to define the main molecular mechanisms and pathways. Furthermore, a protein-protein interaction (PPI) network was constructed using the STRING tool, and the core targets were obtained by Cytoscape. Finally, molecular docking between the core targets and hydroxychloroquine was performed.

RESULTS

167 common target genes were acquired by overlapping. The core targets were TNF, ALB, IL1B, JUN, FOS, SRC, and MMP9. The GO and KEGG results showed the targets to be related to the production of inflammatory cytokines and chemokines and were engaged in the toll-like receptor (TLR) signaling pathway. At the same time, the molecular docking results showed that the core targets all combined with hydroxychloroquine closely.

CONCLUSION

This study proved that hydroxychloroquine may treat IgAN through the TLR signaling pathway, and the restraint of TNF, TLR, IL1B, and JUN may be essential for the treatment.

Shexiang Baoxin Pills alleviate doxorubicin-induced cardiotoxicity via the reactive oxygen species-mediated AKT/Bcl-2 pathway

BACKGROUND

Shexiang Baoxin Pill (SBP) is a classical Chinese medicine that improves endothelial function and antioxidant and inflammatory responses. It may also alleviate doxorubicin (DOX)-induced cardiotoxicity. The aim of this study is to explore the potential influence and molecular mechanisms of SBP in DOX-induced cardiotoxicity using network pharmacology.

METHODS

We established control, SBP, DOX, and DOX + SBP groups to evaluate cell function using a Cell Counting Kit-8 assay, reactive oxygen species (ROS) measurement, cell cycle analysis, and apoptosis assessment. Network pharmacology was employed to predict potential targets and pathways of SBP in DOX-induced cardiotoxicity; the predictions were validated using protein blotting assays.

RESULTS

SBP (2.5 mg/L) significantly mitigated DOX-induced cardiotoxicity. DOX elevated ROS levels, induced phosphorylation of the AKT pathway, and altered the expression of apoptosis-related proteins Bcl-2 and Bax. SBP attenuated the impact of DOX on cardiomyocytes. Network pharmacology identified 10 candidate targets.

CONCLUSION

SBP ameliorates DOX-induced cardiomyocyte apoptosis by activating the ROS-mediated AKT/Bcl-2 signaling pathway.

Evaluating current status of network pharmacology for herbal medicine focusing on identifying mechanisms and therapeutic effects

INTRODUCTION

Network pharmacology has gained significant traction as a tool for identifying the mechanisms and therapeutic effects of herbal medicines. However, despite the usefulness of these approaches, their diversity underscores the critical need for a systematic evaluation to ensure consistency and reliability.

OBJECTIVES

We aimed to evaluate the network pharmacological analyses, focusing on identifying the mechanisms and therapeutic effects of herbal medicines.

METHODS

We employed a comprehensive approach involving systematic data retrieval, network construction, and analysis. Herbal compounds and their targets were meticulously extracted from five distinct network pharmacology databases to ensure extensive coverage and high data reliability. Advanced network-based methods were used to identify key herbal targets and predict therapeutic effects, thereby enriching the depth and breadth of the analysis. Experimental validation was performed on prostate cancer models to substantiate the computational predictions.

RESULTS

The results of the recapitulating task for known herbal ingredient targets revealed distinct patterns in performance and coverage based on network construction and aggregation methods. We performed the same analysis to identify herbal targets and found that network centrality, path counts, and downweighted path counts had their own pros and cons. By comparing network-based methods, we found that considering the impact on the multiscale interactome yielded the highest accuracy in discriminating known therapeutic effects. Using optimal conditions, we successfully identified new indications for herbal medicines and validated these findings through follow-up in vitro and in vivo experiments.

CONCLUSION

This study presents the first comprehensive and critical evaluation of the current network pharmacology analyses in the field of herbal medicine and provides valuable guidance for continued advances in the elucidation of the mechanisms and therapeutic effects.

Gegen Qinlian Decoction Attenuates Colitis-Associated Colorectal Cancer via Suppressing TLR4 Signaling Pathway Based on Network Pharmacology and In Vivo/In Vitro Experimental Validation

Background: Gegen Qinlian Decoction (GQD), is used for intestinal disorders like ulcerative colitis, irritable bowel syndrome, and colorectal cancer. But the precise mechanisms underlying its anti-inflammatory and anti-tumor effects are not fully elucidated. Methods: Use network pharmacology to identify targets and pathways of GQD. In vivo (azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colitis-associated colorectal cancer (CAC) mouse model) and in vitro (lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages) experiments were conducted to explore GQD's anti-inflammatory and anti-tumor effects. We monitored mouse body weight and disease activity index (DAI), and evaluated colon cancer tissues using hematoxylin and eosin staining. Expression of Ki67 and F4/80 was determined by immunohistochemistry analysis. The protein levels of TLR4 signaling pathway were assessed by western blotting analysis. Enzyme-linked immunosorbent assay measured IL-1β, IL-6, and TNF-α levels. Immunofluorescence (IF) staining visualized NF-κB and IRF3 translocation. Results: There were 18, 9, 24 and 77 active ingredients in the four herbs of GQD, respectively, targeting 435, 156, 485 and 691 genes. Through data platform analysis, it was concluded that there were 1104 target genes of GQD and 2022 target genes of CAC. Moreover, there were 99 intersecting genes between GQD and CAC. The core targets of GQD contained NFKB1, IL1B, IL6, TLR4, and TNF, and GQD reduced inflammation by inhibiting the TLR4 signaling pathway. In vivo experiment, GQD increased mouse body weight, lowered DAI scores, while also alleviating histopathological changes in the colon and decreasing the expressions of Ki67 and F4/80 in the AOM/DSS-induced mice. GQD reduced IL-1β, IL-6, and TNF-α levels in the serum and downregulated TLR4, MyD88, and phosphorylation of IκBα, P65, and IRF3 in the colon tissue from AOM/DSS-induced mice. In vitro, GQD suppressed pro-inflammatory cytokines and TLR4 signaling pathway in the LPS-induced RAW264.7 cells, and combined with TAK242, it further reduced the phosphorylation of IκBα, P65. Conclusions: GQD mitigated CAC by inhibiting the TLR4 signaling pathway, offering a potential therapeutic approach for CAC management.

Active Targets and Potential Mechanisms of Erhuang Quzhi Formula in Treating NAFLD: Network Analysis and Experimental Assessment

The purpose of this research was to investigate the main active components, potential targets of action, and pharmacological mechanisms of Erhuang Quzhi Formula (EHQZF) against NAFLD using network pharmacology, molecular docking, and experimental validation. The main active chemical components of EHQZF and the potential targets for treating NAFLD were extracted and analyzed. The PPI network diagram of "Traditional Chinese Medicine-Active Ingredients-Core Targets" was constructed and the GO, KEGG, and molecular docking analysis were carried out. Identification of components in traditional Chinese medicine compounds was conducted by LC-MS. NAFLD models were established and relevant pathologic indicators and Western blot were analyzed in vivo and ex vivo. Totally 8 herbs attributed to the liver meridian and 20 corresponding targets of NAFLD were obtained from EHQZF. Flavonoids and phenolic acids as the main components of EHQZF treated NAFLD through the MAPK/AKT signaling pathway. Pathway enrichment analysis focused on the MAPK/AKT signaling pathway and apoptosis signaling pathway. Molecular docking showed that Quercetin and Luteolin had stable binding structures with AKT1, STAT3, and other targets. Experiments showed that EHQZF reduced lipid accumulation, regulated changes in adipose tissue, inhibited the MAPK/AKT signaling pathway and exert multiple components, several targets, and multiple pathway interactions to treat NAFLD.

Study of the multitarget mechanism of Astragalus (HUANGQI) in the treatment of Alzheimer's disease based on network pharmacology and molecular docking technology

CONTEXT

In China, HUANGQI is widely used for the treatment of Alzheimer's disease (AD). However, a comprehensive understanding of its mechanism of anti-AD effects is lacking.

OBJECTIVE

To explore the active ingredients of HUANGQI and its potential targets and mechanisms of action in AD.

MATERIALS AND METHODS

The active ingredients and targets of HUANGQI were screened from databases (TCSMP, ETCM, and BATMan), and AD-related genes were obtained from DrugBank and GeneCards. The same target genes were screened, and a drug-target disease network was constructed. The PPI network was constructed and GO and KEGG pathway enrichment analyses of the targets. The Cell Counting Kit-8 (CCK-8) assay was used to determine suitable HUANGQI treatment concentrations for HT-22 cells between 0-480 μg/mL. CCK-8, FITC-phalloidin and propidium iodide (PI) assays were used to examine the protective effect of (0, 60, 120, 240 μg/mL) of HUANGQI on 20 μM Aβ1-42-induced HT-22 cell cytotoxicity.

RESULTS

Twelve active ingredients of HUANGQI were selected, with 679 common targets associated with AD. GO and KEGG analysis revealed that the therapeutic mechanisms of HUANGQI involve TNF, AGE, the NF-κB pathway, and nuclear receptor activity-related processes. The CCK-8 assay indicated that HUANGQI was not cytotoxic to HT-22 cells at concentrations less than 240 μg/mL and was able to attenuate Aβ1-42-induced cellular damage (EC50 = 83.46 μg/mL). FITC-phalloidin and PI assays suggested that HUANGQI could alleviate 20 μM Aβ1-42-induced neuronal cell cytotoxicity in a dose-dependent manner.

CONCLUSION

HUANGQI has a protective effect on Aβ1-42-induced nerve cell injury; further mechanism research was needed.

Reveal the potent antidepressant effects of Zhi-Zi-Hou-Pu Decoction based on integrated network pharmacology and DDI analysis by deep learning

Background and objective

The multi-targets and multi-components of Traditional Chinese medicine (TCM) coincide with the complex pathogenesis of depression. Zhi-Zi-Hou-Pu Decoction (ZZHPD) has been approved in clinical medication with good antidepression effects for centuries, while the mechanisms under the iceberg haven't been addressed systematically. This study explored its inner active ingredients - potent pharmacological mechanism - DDI to explore more comprehensively and deeply understanding of the complicated TCM in treatment.

Methods

This research utilized network pharmacology combined with molecular docking to identify pharmacological targets and molecular interactions between ZZHPD and depression. Verification of major active compounds was conducted through UPLC-Q-TOF-MS/MS and assays on LPS-induced neuroblastoma cells. Additionally, the DDIMDL model, a deep learning-based approach, was used to predict DDIs, focusing on serum concentration, metabolism, effectiveness, and adverse reactions.

Results

The antidepressant mechanisms of ZZHPD involve the serotonergic synapse, neuroactive ligand-receptor interaction, and dopaminergic synapse signaling pathways. Eighteen active compounds were identified, with honokiol and eriocitrin significantly modulating neuronal inflammation and promoting differentiation of neuroimmune cells through genes like COMT, PI3KCA, PTPN11, and MAPK1. DDI predictions indicated that eriocitrin's serum concentration increases when combined with hesperidin, while hesperetin's metabolism decreases with certain flavonoids. These findings provide crucial insights into the nervous system's effectiveness and potential cardiovascular or nervous system adverse reactions from core compound combinations.

Conclusions

This study provides insights into the TCM interpretation, drug compatibility or combined medication for further clinical application or potential drug pairs with a cost-effective method of integrated network pharmacology and deep learning.

Sanguinarine identified as a natural dual inhibitor of AURKA and CDK2 through network pharmacology and bioinformatics approaches

Cervical cancer (CA) continues to be a female malignant tumor with limited therapeutic options, resulting in a high mortality rate. Sanguinarine (SANG), a naturally occurring alkaloid, has demonstrated notable efficacy in preclinical treatment of CA. However, the mechanism through which SANG acts against CA is not fully understood. To address this, utilizing nine drug target prediction databases, we have successfully identified 379 potential targets for SANG. Venn diagram analysis compared 2367 CA-related targets from the GeneCards disease database, 2618 CA-closely related targets derived from multiple datasets in GEO through WGCNA analysis, and the 379 potential targets of SANG, resulting in 35 shared targets. Subsequently, by employing PPI network analysis, the Cytohubba plugin, the Human Protein Atlas, TCGA database data, and ROC curve analysis, we have identified AURKA and CDK2 as key targets of SANG in combating CA. Single-gene GSEA results suggest that the overexpression of AURKA and CDK2 is closely correlated with DNA replication, cell cycle progression, and various DNA repair pathways in CA. Molecular docking and molecular simulation dynamics analyses have confirmed the stable binding of both AURKA and CDK2 to SANG. In summary, by integrating diverse methodological approaches, this study discovered that SANG potentially inhibits the malignant features of CA by targeting AURKA and CDK2, thereby regulating DNA replication, cell cycle progression, and multiple DNA repair pathways. This lays a solid foundation for further exploring the pharmacological role of SANG in CA therapy. However, further in-depth in vitro and in vivo experiments are required to corroborate our findings.

Molecular targets and mechanisms of Sijunzi decoction in the treatment of Parkinson's disease: evidence from network pharmacology, molecular docking, molecular dynamics simulation, and experimental validation

Aim

To explore the molecular mechanism of Sijunzi Decoction (SJZD) in the treatment of Parkinson's disease (PD) through the application of network pharmacology, molecular docking, and molecular dynamics simulations, complemented by experimental verification.

Methods

The BATMAN-TCM, GeneCards, and DisGeNet databases were searched to screen the active components and therapeutic targets of SJZD. Cytoscape (3.7.1) was used to create a network diagram of the components and targets. The STRING platform was used to construct a protein-protein interaction (PPI) network. The Bioconductor database and RX64 (4.0.0) software were used to conduct Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the core target genes. The binding sites and binding energies between SJZD active components and the target were analyzed by molecular docking and dynamic simulation. Finally, the therapeutic effect and mechanism of SJZD were verified by Cell Counting Kit-8 (CCK-8) and Western blotting (WB).

Results

This research identified 188 active compounds in SJZD, 1568 drug targets, 2069 PD targets, and 451 intersection targets related to PD. According to network analysis, Adenosine Triphosphate, Tridecanoic Acid, Hexadecanoic Acid, Pentadecanoic Acid, and Adenosine were identified as the core components of SJZD in the treatment of PD. The five targets with the highest Degree values in the PPI network were AKT1, INS, TNF, IL-6, and TP53. The GO and KEGG enrichment analyses, in turn, determined that the administration of SJZD for the treatment of PD may engage processes such as xenobiotic stimulation and biological stimulus response. Furthermore, AGE-RAGE and cAMP signaling pathways related to diabetic complications may be involved. Molecular docking and kinetic simulations showed that IL-6 and AKT1 bind best to Adenosine. Experimental results showed that SJZD significantly reduced 6-OHDA-induced apoptosis of SH⁃SY5Y cells by activating the PI3K/AKT signaling pathway and regulating the expression of apoptosis factors such as Bcl⁃2 and Bax.

Conclusion

SJZD is essential in the processes of apoptosis and neuronal protection, acting through various components that target multiple pathways. Notably, the PI3K/AKT pathway is a verified SJZD-PD target, providing a reference for clinical precision drug use for PD.

NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine

The biological targets of traditional Chinese medicine (TCM) are the core effectors mediating the interaction between TCM and the human body. Identification of TCM targets is essential to elucidate the chemical basis and mechanisms of TCM for treating diseases. Given the chemical complexity of TCM, both in silico high-throughput compound-target interaction predicting models and biological profile-based methods have been commonly applied for identifying TCM targets based on the structural information of TCM chemical components and biological information, respectively. However, the existing methods lack the integration of TCM chemical and biological information, resulting in difficulty in the systematic discovery of TCM action pathways. To solve this problem, we propose a novel target identification model NP-TCMtarget to explore the TCM target path by combining the overall chemical and biological profiles. First, NP-TCMtarget infers TCM effect targets by calculating associations between herb/disease inducible gene expression profiles and specific gene signatures for 8233 targets. Then, NP-TCMtarget utilizes a constructed binary classification model to predict binding targets of herbal ingredients. Finally, we can distinguish TCM direct and indirect targets by comparing the effect targets and binding targets to establish the action pathways of herbal component-direct target-indirect target by mapping TCM targets in the biological molecular network. We apply NP-TCMtarget to the formula XiaoKeAn to demonstrate the power of revealing the action pathways of herbal formula. We expect that this novel model could provide a systematic framework for exploring the molecular mechanisms of TCM at the target level. NP-TCMtarget is available at http://www.bcxnfz.top/NP-TCMtarget.

Fucoxanthin Prevents Lipopolysaccharide-Induced Acute Lung Injury by Inhibiting Ferroptosis via Nrf2/STAT3 and Glutathione Pathways

Fucoxanthin, sourced from marine brown algae, diatoms, and microalgae, is known to possess strong anti-inflammatory activity. To explore its intrinsic mechanism, we investigated its effects on acute lung injury (ALI) with an experiment using lipopolysaccharide (LPS)-induced RAW264.7 inflammatory cells and an ALI animal model. Fucoxanthin was observed to suppress the inflammatory response in vitro by reducing the levels of inflammatory markers such as PTGS2, iNOS, and TNF-α. Network pharmacology analysis revealed that fucoxanthin could potentially inhibit ferroptosis through 10 targets, including PTGS2. This was further confirmed by the dose-dependent increase in lipid peroxidation and Fe[Formula: see text] levels caused by fucoxanthin, as well as the regulation of ferroptosis-associated proteins ACSL4, SLC7A11, GPX4, and FTH1. Furthermore, fucoxanthin was found to significantly reduce the inflammatory response and ferroptosis in a mouse model of LPS-induced ALI. Further research revealed that fucoxanthin could raise the levels of [Formula: see text]-Glu-Cys and carbamyl glycine, which are intermediate metabolites of glutathione synthesis, in RAW264.7 cells. This implies that fucoxanthin can inhibit ferroptosis by regulating the [Formula: see text]-glutamyl cycle. Our research demonstrated that fucoxanthin is capable of activating phosphorylated STAT3 and raising the expression of Nrf2 and HO-1, implying that fucoxanthin may be able to prevent LPS-induced ferroptosis in ALI through the Nrf2/STAT3 pathway.

Exploring the mechanism of sesamin for the treatment of PM2.5-induced cardiomyocyte damage based on transcriptomics, network pharmacology and experimental verification

Introduction

Exposure to fine particulate matter (PM2.5) is known to be associated with cardiovascular diseases. Sesamin (Ses) is a natural phenolic compound found in sesame seeds and sesame oil. Ferroptosis is a novel mode of cell death characterised by iron-dependent lipid peroxidation. This study aims to explore whether PM2.5 can induce ferroptosis in H9C2 cells and to investigate the precise protective mechanism of Ses.

Methods

Based on transcriptomic data, PM2.5 may induce ferroptosis in cardiomyocytes. The ferroptosis inducer erastin and ferroptosis inhibitor ferrostatin-1 (Fer-1) were used to illustrate the mechanisms involved in PM2.5-induced H9C2 cell injury. Using network pharmacology, the pharmacological mechanism and potential therapy targets of Ses were explored for the treatment of PM2.5-induced cardiomyocyte injury. H9C2 cells were cultured and pretreated with Fer-1 or different concentrations of Ses, and then cardiomyocyte injury model was established using erastin or PM2.5. Indicators of oxidative responses, including total superoxide dismutase, reduced glutathione, glutathione peroxidase and malondialdehyde, were measured. The expression levels of ferroptosis-related proteins were determined through Western blot analysis.

Results

Results demonstrate that PM2.5 induces ferroptosis in H9C2 cells and Ses exerts a protective effect by suppressing ACSL4-mediated ferroptosis.

Discussion

Overall, these findings elucidate a novel mechanism by which Ses ameliorates the detrimental effects of PM2.5 on cardiomyocytes.

Jiao-tai-wan and its effective component-coptisine alleviate cognitive impairment in db/db mice through the JAK2/STAT3 signaling pathway

BACKGROUND

Cognitive impairment (CI) is now well-accepted as a complication and comorbidity of diabetes mellitus (DM), becoming a serious medical and social problem. Jiao-tai-wan (JTW), one of noted traditional Chinese medicine (TCM), showed dual therapeutic effects on DM and CI. Nevertheless, the potential mechanism is unclear.

PURPOSE

This study sought to investigate the mechanism how JTW protected against DM and CI and screen the active component in JTW.

METHODS

Db/db mice were used as mouse models. Mice were treated by gavage with 0.9 % saline (0.1 mL/10g/d), low dose of JTW (2.4 g/kg/d) or high dose of JTW (4.8 g/kg/d) for 8 weeks separately. To access the effects of JTW, the levels of OGTT, HOMA-IR, blood lipids, inflammatory cytokines in serum and hippocampus were measured, behavioral tests were conducted, and histopathological changes were observed. The mechanism exploration was performed via network pharmacology, RT-qPCR, western blot, and immunofluorescence staining (IF). The impact and mechanism of coptisine in vitro were investigated using BV2 cells induced by LPS as cellular models. In vitro experiments were conducted in two parts. The first part comprised four groups: Control group, LPS group, LPS+LCOP group and LPS+HCOP group. The second part consisted of four groups: Control group, LPS group, LPS+HCOP group, and LPS+ Fed group. The western blot and RT-qPCR methods were used to examine the changes in biomarkers of the JAK2/STAT3 signaling pathways in BV2 cells.

RESULTS

The results demonstrated that JTW could improve OGTT and HOMA-IR, reduce the serum levels of LDL-C, HDL-C, TG, and TC, restore neuronal dysfunction and synaptic plasticity, and decrease the deposition of Aβ in the hippocampus. The findings from ELISA, IF, and RT-qPCR revealed that JTW could alleviate microglial activation and inflammatory status in vivo and coptisine could play the same role in vitro. Moreover, the changes of the JAK2/STAT3 signaling pathway in LPS-induced BV2 cells or hippocampus of db/db mice were distinctly reversed by coptisine or JTW, respectively.

CONCLUSION

Our study suggested that JTW and its effective component coptisine could alleviate diabetes mellitus-related cognitive impairment, closely linked to the JAK2/STAT3 signaling pathway.

Demethylzeylasteral ameliorates podocyte damage in murine lupus by inhibiting inflammation and enhancing autophagy

BACKGROUND

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with multiorgan and tissue involvement. Lupus nephritis (LN), an inflammatory condition of the kidneys associated with SLE, represents a significant cause of morbidity and mortality in SLE patients. Current immunosuppressive therapies for LN have limited efficacy and can lead to significant side effects. Demethylzeylasteral (DML) has shown promise in the treatment of LN, but its precise mechanism of action remains unclear.

PURPOSE

To assess the therapeutic effects and potential molecular mechanisms of DML in LN METHODS: The study evaluated the renal protective effects of DML in MRL/lpr mice through assessments of immune complex levels, renal function, and pathological changes. Network pharmacology and transcriptomics approaches were used to elucidate the underlying mechanisms. Molecular docking, biacore assay, monoclonal antibody blocking experiments, and in vitro studies were conducted to verify the mechanisms of action.

RESULTS

DML treatment reduced levels of anti-Sm and anti-dsDNA IgG antibodies, as well as serum creatinine and blood urea nitrogen levels. DML also mitigated glomerular damage and fibrosis. Mechanistically, DML alleviated podocyte damage by suppressing inflammation and enhancing autophagy through inhibition of the IL-17A/JAK2-STAT3 pathways. Additionally, DML exhibited high binding affinity with IL17A, JAK2, and STAT3.

CONCLUSION

These findings provide strong evidence for the beneficial effects of DML in LN, suggesting its potential as a novel therapeutic strategy for improving renal function in autoimmune kidney diseases.

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.

Exploration of the potential mechanism of aqueous extract of Artemisia capillaris for the treatment of non-alcoholic fatty liver disease based on network pharmacology and experimental verification

OBJECTIVES

Non-alcoholic fatty liver disease (NAFLD) is a nutritional and metabolic disease with a high prevalence today. Artemisia capillaris has anti-inflammatory, antioxidant, and other effects. However, the mechanism of A. capillaris in treating NAFLD is still poorly understood.

METHODS

This study explored the mechanism of A. capillaris in the treatment of NAFLD through network pharmacology and molecular docking, and verified the results through in vivo experiments using a high-fat diet-induced mouse model and in vitro experiments using an oleic acid-induced HepG2 cell model.

KEY FINDINGS

Aqueous extract of A. capillaris (AEAC) can reduce blood lipids, reduce liver lipid accumulation and liver inflammation in NAFLD mice, and improve NAFLD. Network pharmacology analysis revealed that 51 drug ingredients in A. capillaris correspond to 370 targets that act on NAFLD. GEO data mining obtained 93 liver differentially expressed genes related to NAFLD. In the UHPLC-MS detection results, 36 components were characterized and molecular docked with JNK. Verified in vitro and in vivo, the results show that JNK and the phosphorylation levels of IL-6, IL-1β, c-Jun, c-Fos, and CCL2 are key targets and pathways.

CONCLUSIONS

This study confirmed that AEAC reduces lipid accumulation and inflammation in the liver of NAFLD mice by inhibiting the JNK/AP-1 pathway.

Exploration of compatibility rules and discovery of active ingredients in TCM formulas by network pharmacology

Network pharmacology is an interdisciplinary field that utilizes computer science, technology, and biological networks to investigate the intricate interplay among compounds/ingredients, targets, and diseases. Within the realm of traditional Chinese medicine (TCM), network pharmacology serves as a scientific approach to elucidate the compatibility relationships and underlying mechanisms of action in TCM formulas. It facilitates the identification of potential active ingredients within these formulas, providing a comprehensive understanding of their holistic and systematic nature, which aligns with the holistic principles inherent in TCM theory. TCM formulas exhibit complexity due to their multi-component characteristic, involving diverse targets and pathways. Consequently, investigating their material basis and mechanisms becomes challenging. Network pharmacology has emerged as a valuable approach in TCM formula research, leveraging its holistic and systematic advantages. The manuscript aims to provide an overview of the application of network pharmacology in studying TCM formula compatibility rules and explore future research directions. Specifically, we focus on how network pharmacology aids in interpreting TCM pharmacological theories and understanding formula compositions. Additionally, we elucidate the process of utilizing network pharmacology to identify active ingredients within TCM formulas. These findings not only offer novel research models and perspectives for integrating network pharmacology with TCM theory but also present new methodologies for investigating TCM formula compatibility. All in all, network pharmacology has become an indispensable and crucial tool in advancing TCM formula research.

Discovery and Prediction Study of the Dominant Pharmacological Action Organ of Aconitum carmichaeli Debeaux Using Multiple Bioinformatic Analyses

Herbs, such as Aconitum carmichaeli Debeaux (ACD), have long been used as therapies, but it is difficult to identify which organs of the human body are affected by the various compounds. In this study, we predicted the organ where the drug predominantly acts using bioinformatics and verified it using transcriptomics. We constructed a computer-aided brain system network (BSN) and intestinal system network (ISN). We predicted the action points of ACD using network pharmacology (NP) analysis and predicted the dockable proteins acting in the BSN and ISN using statistical-based docking analysis. The predicted results were verified using ACD-induced transcriptome analysis. The predicted results showed that both the NP and docking analyses predominantly acted on the BSN and showed better hit rates in the hub nodes. In addition, we confirmed through verification experiments that the SW1783 cell line had more than 10 times more differentially expressed genes than the HT29 cell line and that the dominant acting organ is the brain, using network dimension spanning analysis. In conclusion, we found that ACD preferentially acts in the brain rather than in the intestine, and this multi-bioinformatics-based approach is expected to be used in future studies of drug efficacy and side effects.

Exploring the role of Yuxuebi tablet in neuropathic pain with the method of similarity research of drug pharmacological effects based on unsupervised machine learning

Introduction

Having multiple pharmacological effects is a characteristic of Traditional Chinese Medicine (TCM). Currently, there is a lack of suitable methods to explore and discover modern diseases suitable for TCM treatment using this characteristic. Unsupervised machine learning technology is an efficient strategy to predict the pharmacological activity of drugs. This study takes Yuxuebi Tablet (YXB) as the research object. Using the unsupervised machine learning technology of drug cell functional fingerprint similarity research, the potential pharmacological effects of YXB were discovered and verified.

Methods

LC-MS combined with the in vitro intestinal absorption method was used to identify components of YXB that could be absorbed by the intestinal tract of rats. Unsupervised learning hierarchical clustering was used to calculate the degree of similarity of cellular functional fingerprints between these components and 121 marketed Western drugs whose indications are diseases and symptoms that YXB is commonly used to treat. Then, based on the Library of Integrated Network-based Cellular Signatures database, pathway analysis was performed for selected Western drugs with high similarity in cellular functional fingerprints with the components of YXB to discover the potential pharmacological effects of YXB, which were validated by animal experiments.

Results

We identified 40 intestinally absorbed components of YXB. Through predictive studies, we found that they have pharmacological effects very similar to non-steroidal anti-inflammatory drugs (NSAIDs) and corticosteroids. In addition, we found that they have very similar pharmacological effects to anti-neuropathic pain medications (such as gabapentin, duloxetine, and pethidine) and may inhibit the NF-κB signaling pathway and biological processes related to pain perception. Therefore, YXB may have an antinociceptive effect on neuropathic pain. Finally, we demonstrated that YXB significantly reduced neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI). Transcriptome analysis further revealed that YXB regulates the expression of multiple genes involved in nerve injury repair, signal transduction, ion channels, and inflammatory response, with key regulatory targets including Sgk1, Sst, Isl1, and Shh.

Conclusion

This study successfully identified and confirmed the previously unknown pharmacological activity of YXB against neuropathic pain through unsupervised learning prediction and experimental verification.

Identification of molecular targets and underlying mechanisms of Fuzheng Shengbai Decoction against colon cancer based on network pharmacology

OBJECTIVES

To investigate the molecular targets and underlying mechanisms of Fuzheng Shengbai Decoction (FZSBD) against colon cancer (CC).

METHODS

Multiple network pharmacology approaches were used to predict the molecular targets and underlying mechanisms of FZSBD against CC. The expression of potential molecular targets was determined. The effects of FZSBD on cell viability, proliferation, migration, invasion, and the cell cycle of CC cells were investigated. The therapeutic efficacy, hematological, immunological, and inflammatory data in patients with CC were evaluated after treatment with the XELOX regimen with and without FZSBD.

RESULTS

A total of 912 potential targets in FZSBD and 2765 DEGs in CC specimens were screened. Five hub genes (TP53, MYC, VEGFA, CCND1, and IL1B) closely associated with immune-related signaling pathways and the cell cycle process were identified. The five hub genes were of prognostic value in CC. The gene and protein expression of the five hub genes was significantly higher in CC tumor tissue samples than that of normal tissue samples. Furthermore, with increasing doses, FZSBD increasingly inhibited growth, migration, and invasion, and suppressed the cell cycle process of CC cells. Supplementing of FZSBD to the XELOX regimen enhanced immune modulation and alleviated inflammatory responses.

CONCLUSIONS

This study identified the molecular targets and underlying mechanisms of FZSBD treatment against CC and may provide clues for future research on the treatment of CC with FZSBD.

Exploring the high-quality ingredients and mechanisms of Da Chuanxiong Formula in the treatment of neuropathic pain based on network pharmacology, molecular docking, and molecular dynamics simulation

Da Chuanxiong Formula (DCXF) is a traditional herbal prescription used for pain management. It consists of Chuanxiong Rhizoma (CR) and Gastrodiae Rhizoma (GR). Despite its long history of use, the underlying therapeutic mechanism of DCXF remains insufficiently understood. Therefore, in this study, key target genes were obtained through network pharmacology research methods and molecular docking techniques, including transient receptor potential vanilloid 1 (TRPV1), adenosine A2a receptor (ADORA2A), nuclear receptor subfamily 3 group C member 1 (NR3C1), and protein kinase C beta (PRKCB). Molecular dynamics simulations demonstrated the favorable binding between all four key genes and their corresponding compounds. Notably, chronic constriction injury (CCI) treatment resulted in a significant decrease in mechanical threshold and thermal latency period for rat foot contraction, which was ameliorated upon administration of DCXF. Furthermore, real-time quantitative reverse transcription PCR (RT-qPCR) and western blot (WB) analyses indicated an upregulation of TRPV1, ADORA2A, NR3C1, and PRKCB expression in the rat dorsal root ganglion following CCI, which was attenuated by treatment with DCXF. The expressions of inflammatory factors, including tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6), in the rat dorsal root ganglion were assessed using ELISA, confirming consistent trends with the aforementioned findings. The results of this study offer a promising theoretical foundation for the utilization of DCXF in the treatment of neuropathic pain (NP).

A practical guide to implementing artificial intelligence in traditional East Asian medicine research

In this paper, we present a comprehensive guide for implementing artificial intelligence (AI) techniques in traditional East Asian medicine (TEAM) research. We cover essential aspects of the AI model development pipeline, including research objective establishment, data collection and preprocessing, model selection, evaluation, and interpretation. The unique considerations in applying AI to TEAM datasets, such as data scarcity, imbalance, and model interpretability, are discussed. We provide practical tips and recommendations based on best practices and our own experience. The potential of large language models in TEAM research is also highlighted. Finally, we discuss the challenges and future directions of AI application in TEAM, emphasizing the need for standardized data collection and sharing platforms.

Kurarinone, a flavonoid from Radix Sophorae Flavescentis, inhibits RANKL-induced osteoclastogenesis in mouse bone marrow-derived monocyte/macrophages

Inflammation-induced osteoclast proliferation is a crucial contributor to impaired bone metabolism. Kurarinone (KR), a flavonoid extracted from the Radix Sophorae Flavescentis, exhibits notable anti-inflammatory properties. Nevertheless, the precise influence of KR on osteoclast formation remains unclear. This study's objective was to assess the impact of KR on osteoclast activity in vitro and unravel its underlying mechanism. Initially, a target network for KR-osteoclastogenesis-osteoporosis was constructed using network pharmacology. Subsequently, the intersecting targets were identified through the Venny platform and a PPI network was created using Cytoscape 3.9.1. Key targets within the network were identified employing topological algorithms. GO enrichment and KEGG pathway analysis were then performed on these targets to explore their specific functions and pathways. Additionally, molecular docking of potential core targets of KR was conducted, and the results were validated through cell experiments. A total of 83 target genes overlapped between KR and osteoclastogenesis-osteoporosis targets. Enrichment analysis revealed their role in inflammatory response, protein tyrosine kinase activity, osteoclast differentiation, and MAPK and NF-κB signaling pathways. PPI analysis and molecular docking demonstrate that key targets MAPK14 and MAPK8 exhibit more stable binding with KR compared to other proteins. In vitro experiments demonstrate that KR effectively inhibits osteoclast differentiation and bone resorption without cellular toxicity. It suppresses key osteoclast genes (NFATc1, c-Fos, TRAP, MMP9, Ctsk, Atp6v2), hinders IκB-α degradation, and inhibits ERK and JNK phosphorylation, while not affecting p38 phosphorylation. The results indicate that KR may inhibit osteoclast maturation and bone resorption by blocking NF-κB and MAPK signaling pathways, suggesting its potential as a natural therapeutic agent for osteoporosis.

Potential mechanism prediction of indole-3-propionic acid against diminished ovarian reserve via network pharmacology, molecular docking and experimental verification

BACKGROUND

Oxidative stress (OS) is one of the major causes of ovarian aging and dysfunction. Indole-3-propionic acid (IPA) is an indole compound derived from tryptophan with free radical scavenging and antioxidant properties, and thus may have potential applications in protecting ovarian function, although the exact mechanisms are unknown. This study aims to preliminarily elucidate the potential mechanisms of IPA that benefit ovarian reserve function through network pharmacology, molecular docking, and experimental verification.

METHODS

The related protein targets of IPA were searched on SwissTargetPrediction, TargetNet, BATMAN-TCM, and PharmMapper databases. The potential targets of diminished ovarian reserve (DOR) were identified from OMIM, GeneCards, DrugBank, and DisGeNET databases. The common targets were uploaded directly to the STRING database to construct PPI networks. We then performed GO and KEGG enrichment analysis on the targets. Subsequently, molecular docking and molecular dynamics simulation were used to validate the binding conformation of IPA to candidate targets. Furthermore, we carried out in vitro experiments to validate the prediction results of network pharmacology.

RESULTS

We identified a total of 61 potential targets for the interaction of IPA with DOR. The PPI network topological parameter analysis yielded 13 hub genes for DOR treatment. The GO biological process enrichment analysis identified 293 entries, mainly enriched in aging, signal transduction, response to hypoxia, negative regulation of apoptotic process, and positive regulation of cell proliferation. The KEGG enrichment analysis mainly included lipid and atherosclerosis, progesterone-mediated oocyte maturation, AGE-RAGE, relaxin, estrogen, and other signaling pathways. The molecular docking further revealed the direct binding of IPA with six hub proteins including NOS3, AKT1, EGFR, PPARA, SRC, and TNF. In vitro experiments showed that IPA pretreatment attenuated H2O2-induced cellular oxidative stress damage, while IPA exerted cytoprotective and antioxidant damage effects by regulating the six hub genes and antioxidant proteins.

CONCLUSION

We systematically illustrated the potential protective effects of IPA against DOR through multiple targets and pathways using network pharmacology, and further verified the cytoprotective effect and antioxidant properties of IPA through in vitro experiments. These findings provide new insights into the targets and molecular mechanisms whereby IPA improves DOR.

Mechanism investigation of anti-NAFLD of Shugan Yipi Granule based on network pharmacology analysis and experimental verification

As a classical traditional Chinese patent medicine, Shugan Yipi Granule is widely used in China to treat non-alcoholic fatty liver disease (NAFLD) recently. Our previous study confirmed that Shugan Yipi Granule are effective in NAFLD. However, its underlying mechanism is still unknown. This study aims to investigate the mechanism of Shugan Yipi Granule on NAFLD based on network pharmacology prediction, liquid chromatography-mass spectrometry (LC-MS) analysis and in vitro verification. We obtained the active ingredients and targets of Shugan Yipi Granule and NAFLD from 6 traditional Chinese medicine databases, and the crucial components and targets screened by protein-protein interaction (PPI) network were used for molecular docking. Plasma metabolomics of NAFLD patients treated with Shugan Yipi Granule for one month was analyzed using LC-MS methods and MetaboAnalyst 4.0 to obtain significant differential metabolites and pathways. Finally, free fatty acid (FFA) induced HepG2 cells were treated with different concentrations of quercetin and kaempferol, then oil red o (ORO) and triglyceride (TG) level were tested to verify the lipid deposition of the cell. Network pharmacology analysis showed that the main active ingredients of Shugan Yipi Granule include quercetin, kaempferol and other 58 ones, as well as 188 potential targets. PI3K/Akt signaling pathway was found to be the most relevant pathway for the treatment of NAFLD. Non-targeted metabolomics showed that quercetin and kaempferol were significantly up-regulated differential metabolites and were involved in metabolic pathways such as thyroid hormone signaling. In vitro results showed that quercetin, kaempferol were effective in reducing lipid deposition and TG content by inhibiting cellular fatty acid uptake. Ultimately, with the network pharmacology and serum metabolomics analysis, quercetin and kaempferol were found to be the important active ingredients and significantly up-regulated differential metabolites of Shugan Yipi Granule against NAFLD, which we inferred that they may regulate NAFLD through PI3K/Akt signaling pathway and thyroid hormone metabolism pathway. The in vitro experiment verification results showed that quercetin and kaempferol attenuated the lipid accumulation and TG content by inhibiting the fatty acid uptake in the FFA-induced HepG2 cell. Current study provides the necessary experimental basis for subsequent in-depth mechanism research.

Screening of active components of Ganoderma lucidum and decipher its molecular mechanism to improve learning and memory disorders

Learning and memory impairment (LMI), a common degenerative central nervous system disease. Recently, more and more studies have shown that Ganoderma lucidum (GL) can improve the symptoms of LMI. The active ingredients in GL and their corresponding targets were screened through TCMSP (Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform) and BATMAN-TCM (Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine) databases, and the potential LMI targets were searched for through GeneCard (GeneCards Human Gene Database) and DrugBank. Then, we construct a 'main active ingredient-target' network and a protein-protein interaction (PPI) network diagram.The GO (Gene Ontology) functional enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway annotation analysis were performed on the common targets through DAVID (Database for Annotation Visualization and Integrated Discovery) to clarify the potential molecular mechanism of action of active ingredients in GL. The tumor necrosis factor (TNF) protein was verified by Western blot; Twenty one active ingredients in GL and 142 corresponding targets were screened out, including 59 targets shared with LMI. The 448 biological processes shown by the GO functional annotation results and 55 signal pathways shown by KEGG enrichment analysis were related to the improvement of LMI by GL, among which the correlation of Alzheimer's disease pathway is the highest, and TNF was the most important protein; TNF can improve LMI. GL can improve LMI mainly by 10 active ingredients in it, and they may play a role by regulating Alzheimer's disease pathway and TNF protein.

PTGS2 as target of compound Huangbai liquid in the nursing of pressure ulcer

OBJECTIVE

Pressure ulcer refers to ulceration and necrosis caused by local skin and cell tissues being compressed for a long time, continuous ischemia, hypoxia, and malnutrition. However, role of prostaglandin-endoperoxide synthase 2 (PTGS2) in the management of pressure ulcers in with compound Huangbai liquid is still unclear.

METHODS

Traditional Chinese medicine components and related targets of compound Huangbai liquid were collected through traditional Chinese medicine systems pharmacology (TCMSP) and Batman-traditional Chinese medicine database. Disease-related targets were obtained using the Gene Cards database. The protein-protein interaction (PPI) network was constructed using the Search tool for retrieval of interacting genes (STRING) and analyzed by Cytoscape to obtain the core components. To evaluate the clinical efficacy of the compound Huangbai liquid in the treatment of pressure ulcers, 40 patients with pressure ulcers were selected and divided into an observation group and a control group, with 20 individuals in each group. The observation group received treatment with compound Huangbai liquid.

RESULTS

Sixty-five components and 480 targets of compound Huangbai liquid were obtained from TCMSP and Batman - traditional Chinese medicine databases. Two hundred seventy-three pressure ulcer-related targets were obtained. Seventy-two potential targets of compound Huangbai pigment in treatment of pressure ulcer were obtained, and 2 unrelated targets were deleted. There were 70 nodes and 1167 edges in PPI network. Gene ontology (GO) function is involved in biological processes such as reactive oxygen species metabolism and cellular response to chemical stress. Cellular components such as platelet α granules lumen and membrane rafts were involved. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that compound Huangbai liquid in treatment of pressure ulcer. The clinical results indicate that the compound Huangbai liquid has a good therapeutic effect on pressure ulcers.

CONCLUSION

PTGS2 may be a target for treatment of pressure ulcers with compound Huangbai liquid, providing a new direction for its treatment.