Network pharmacology: curing causal mechanisms instead of treating symptoms

Integrated network pharmacology, proteomics, molecular docking, and experiments in vivo and in vitro to explore the efficacy and potential mechanism of bufalin against hepatocellular carcinoma angiogenesis

ETHNOPHARMACOLOGICAL RELEVANCE

Bufalin is a potent bioactive compound extracted from the venom of toads such as Bufo gargarizans. It has rich pharmacological effects, and its traditional applications mainly include anti-cancer, anti-inflammatory and analgesic, especially in cancer treatment, which has been a hot topic of research. Prior research has suggested that bufalin may have anti-tumor angiogenic effects. However, the efficacy and mechanism of bufalin inhibiting hepatocellular carcinoma (HCC) angiogenesis have yet to be further investigated.

AIM OF THE STUDY

An extensive detailed strategy via network pharmacology, proteomics, histopathological analysis, molecular docking, in vitro experiments, and in vivo magnetic resonance imaging (MRI) examinations were adopted to investigate the efficacy and mechanisms of bufalin against HCC angiogenesis.

MATERIALS AND METHODS

Micro-vessel density (MVD) and intravoxel incoherent motion (IVIM) perfusion-related parameters based on magnetic resonance diffusion-weighted imaging were used to identify the effect of bufalin against HCC angiogenesis. Potential bufalin and HCC targets were gathered from appropriate databases. The STRING database was used to construct the target protein interaction networks. The "clusterprofiler" package (version 4.2.2) in R was applied to conduct the target-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology (GO) analysis. Network pharmacology and proteomics were integrated to identify key targets and pathways related to bufalin against HCC angiogenesis. Molecular docking and Western Blot were utilized to validate the findings.

RESULTS

Analysis through IVIM and MVD showed that bufalin could inhibit HCC angiogenesis in nude mice models. A total of 159 common targets of bufalin and HCC were identified by network pharmacology. GO analysis revealed that these targets focused on multiple angiogenesis-related biological processes, including endothelial cell proliferation and migration, sprouting angiogenesis, and regulation of angiogenesis. The KEGG enrichment results suggested that bufalin could regulate multiple signaling pathways to inhibit HCC angiogenesis, including VEGF, MAPK, PI3K-Akt, mTOR, and HIF-1 signaling pathways. MAPK1, MAPK14, PRKCA, EIF4E, and APEX1 might be critical targets in regulating the above pathways. The molecular docking and Western blot analysis verified the effects of bufalin on target proteins.

CONCLUSION

This study demonstrated that bufalin might inhibit HCC angiogenesis by regulating multiple targets and pathways. These findings offer theoretical insights and experimental foundations for the clinical application and commercial development of bufalin in the treatment of HCC.

Integration of network pharmacology and experimental validation to explore the pharmacological mechanism of andrographolide against asthma

Andrographolide (AG), one of the main active components of Andrographis paniculata (Burm.f.) Wall. ex Nees, has been proved to possess the pharmacological function of anti-inflammation in multiple disease including asthma. But the potential mechanism is still not clear. In this study, network pharmacology, molecular docking and experimental validation were utilized to explore the molecular mechanism of AG in the treatment of asthma. AG-related targets and asthma-related targets were screened by Swiss Target Prediction, DrugBank, STITCH, OMIM, Genecards and TTD databases. A protein-protein interaction (PPI) network was obtained through the STRING Database. The plug-in of "Network Analyzer" in Cytoscape 3.7.1 software was used to conduct the topological analysis. GO enrichment and KEGG pathway analysis were achieved by Metascape database and Bioinformatics platform. The target-pathway network was acquired by Cytoscape 3.7.1 software. The binding affinity between AG and the target genes was evaluated by Molecular docking with AutoDockTools 1.5.6. Flow cytometry was also used to verify the mechanism behind the treatment of asthma by AG, which was predicted in network pharmacology. In total, 38 targets were identified as potential targets of AG against asthma. The top 10 targets revealed by PPI are: IL-6, IL-1B, NFKB1, MMP9, CDK2, CREBBP, MAP2K1, JAK1, AR, PRKCA. GO and KEGG analysis showed that AG treatment of asthma mainly involved protein phosphorylation, peptidyl-serine phosphorylation, peptidyl-amino acid modification and other biological processes. The main signaling pathways are Th17 cell differentiation, JAK-STAT signaling pathway and PI3K-Akt signaling pathway. Molecular docking showed that AG has higher affinity with MMP9, PRKCA, JAK2, LTGAL and LRRK2. Flow cytometry showed that Th17 cell differentiation may be the potential target of AG in the treatment of asthma. This study successfully revealed the underlying target genes and mechanism involved in the treatment of asthma for AG, providing a reference and guidance for future mechanism research.

Exploration of the molecular mechanism of modified Danggui Liuhuang Decoction in treating central precocious puberty and its effects on hypothalamic-pituitary-gonadal axis hormones

AIM

To evaluate the molecular mechanism of modified Danggui Liuhuang Decoction (MDGLHD) in treating central precocious puberty (CPP).

METHODS

CPP-related genes were obtained from GEO dataset, MalaCard, DisGeNET and GeneCards databases. MDGLHT ingredients and targets were obtained in TCMSP, HERB, and SwissTargetPrediction databases. Protein-protein interaction (PPI) network was constructed and analyzed using STRING database and Cytoscape 3.9.1. Genetic ontological (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed with DAVID and Metascape databases. Molecular docking was performed with PyMoL and AutoDock-Vina software. The GnRH secretion model was established by E2 induction of GT1-7 cells. CCK-8, ELISA and qRT-PCR were used to detect the effects of MDGLHD on gonadotropin-releasing hormone (GnRH) secretion and endocrine signaling receptor gene expression.

RESULTS

318 potential targets of MDGLHD in CPP treatment were screened out. Quercetin, kaempferol, and (S)-Canadine were considered to be the most important active ingredients in MDGLHD. Bioinformatics analysis showed that these targets were associated with response to hormone, JAK-STAT signaling pathway and HIF-1 signaling pathway. Quercetin, kaempferol, and (s)-Canadine had good binding affinity with tumor protein p53 (TP53), estrogen receptor 1(ESR1), Jun proto-oncogene (JUN), MYC proto-oncogene (MYC) and AKT serine/threonine kinase 1 (AKT1). In vitro experiments showed that MDGLHD extract can inhibit GnRH secretion and the expression of neuroendocrine signaling receptor protein gene.

CONCLUSION

MDGLHD treatment of CPP is achieved through multi-components, multi-targets and multi-pathways, and inhibition of GnRH secretion and neuroendocrine signaling.

Warfarin use and vestibular dysfunction insights from NHANES data, network pharmacology, Mendelian randomization, and molecular docking

Despite numerous anticoagulants available, warfarin is widely used due to its efficacy and cost-effectiveness in treating thromboembolic diseases. However, its potential impact on vestibular function remains unexplored. This study investigates the association between warfarin use and vestibular dysfunction using data from the NHANES database and examines underlying mechanisms through network pharmacology, Mendelian randomization (MR), and molecular docking. We conducted a cross-sectional analysis of NHANES data (1999-2004) to evaluate the prevalence of vestibular dysfunction among warfarin users. Network pharmacology identified overlapping genes between warfarin targets and vestibular dysfunction-related genes. MR analysis assessed the causal relationship, and molecular docking examined interactions between warfarin and significant genes. The study included 1681 participants, revealing a higher prevalence of vestibular dysfunction in warfarin users. Multiple regression analysis confirmed a significant association between warfarin use and vestibular dysfunction. Network pharmacology identified 31 overlapping genes, with MAPK8 emerging as a key gene through MR analysis. Molecular docking showed a strong binding affinity between warfarin and MAPK8. Findings suggest that warfarin use is significantly associated with vestibular dysfunction, potentially through interactions with MAPK8. This highlights the importance of monitoring vestibular function in patients on warfarin therapy and considering genetic factors to personalize treatment. Future research should explore these mechanisms further and validate findings in broader populations.

Isorhamnetin inhibits cholangiocarcinoma proliferation and metastasis via PI3K/AKT signaling pathway

BACKGROUND

Cholangiocarcinoma (CCA), which is a malignant tumor originating from the epithelial cells of the bile ducts, has witnessed an increasing incidence year by year. Owing to the dearth of effective treatments, the prognosis for CCA is rather poor. Isorhamnetin is known to possess anti-tumor, anti-inflammatory and oxidative stress modulating effects; however, its role in CCA remains unclear.

METHODS

Firstly, we screened the core targets and pathways of isorhamnetin for the treatment of CCA through a network pharmacology approach. Subsequently, we verified via molecular docking that the core targets could dock stably with isorhamnetin. Finally, we verified the inhibitory effect of isorhamnetin on the malignant biological behavior of CCA in vitro and in vivo experiments.

RESULTS

Based on the network pharmacology analysis, we came to the conclusion that AKT1 might be a core target of isorhamnetin in the treatment of CCA. Molecular docking indicated that AKT1 was capable of binding stably to isorhamnetin. Subsequently, In vitro experiments demonstrated that isorhamnetin was able to suppress the proliferation and metastasis of CCA cells, and AKT1 played a pivotal role in this process. Mechanistically speaking, isorhamnetin exerts its inhibitory effect on tumor growth via the PI3K/AKT signaling pathway.

CONCLUSIONS

Our study demonstrated for the first time that isorhamnetin can inhibit the progression of CCA through PI3K/AKT, and that AKT1 may be a target of isorhamnetin for the treatment of CCA.

Reversal of sorafenib resistance in hepatocellular carcinoma by curcumol: insights from network pharmacology, molecular docking, and experimental validation

Background

Curcumol, a bioactive sesquiterpenoid extracted from traditional Chinese medicine (TCM), has demonstrated potential in overcoming tumor drug resistance. However, its mechanisms in reversing drug resistance, particularly in hepatocellular carcinoma (HCC) resistant to sorafenib, are not yet fully elucidated. This study aims to explore the molecular mechanisms by which curcumol reverses sorafenib resistance in HCC using a combination of network pharmacology, molecular docking, and in vivo and in vitro experiments.

Methods

We identified curcumol targets and genes associated with sorafenib-resistant HCC, resulting in a set of overlapping targets. These intersection targets underwent enrichment analysis using DAVID, and a protein-protein interaction (PPI) network was constructed via the STRING database and Cytoscape. Molecular docking confirmed the binding of curcumol to core targets. In vitro assays, including CCK-8, colony formation assay, apoptosis detection, wound healing, and Transwell assays, evaluated curcumol's effects on sorafenib-resistant HCC cells. Western blotting assessed the impact on PI3K/AKT and JAK/STAT3 signaling pathways. Additionally, a sorafenib-resistant HCC xenograft mouse model was established to observe the in vivo efficacy of curcumol combined with sorafenib.

Results

We identified 117 potential targets for curcumol in reversing sorafenib resistance in HCC. Among them, five core targets-ALB, STAT3, HSP90AA1, HSP90AB1, and SRC-showed strong binding affinity with curcumol. KEGG pathway analysis of the intersecting genes highlighted significant involvement of the PI3K/AKT, JAK/STAT3, Ras, Rap1, HIF-1, FoxO, and mTOR signaling pathways. In vitro experiments revealed that curcumol significantly enhanced the sensitivity of sorafenib-resistant HCC cells to sorafenib, inhibiting cell proliferation, invasion, and migration while promoting apoptosis. In vivo studies further confirmed that curcumol combined with sorafenib effectively inhibited tumor growth in sorafenib-resistant HCC models.

Conclusion

This study provides compelling evidence that curcumol can reverse sorafenib resistance in HCC by modulating multiple signaling pathways, including PI3K/AKT and JAK/STAT3 pathways. Our findings suggest that curcumol holds promise as a novel therapeutic agent for overcoming drug resistance in HCC, offering a new avenue for clinical intervention.

Integrated cell metabolomics and network pharmacology approach deciphers the mechanisms of Astragali Radix MIX in repairing podocyte injury

To elucidate the molecular mechanisms of the MIX (combined in proportion to the content in Astragali Radix (AR), named the MIX) repairing podocyte damage to ameliorate nephropathy. MTT assay and western blot analysis were used to evaluate the protective effects of MIX on MPC5 cells induced by Adriamycin (ADR). Screening of potential pharmacodynamic markers, relevant drugs and disease targets were conducted by using metabolomics combined with bioinformatics, and the most relevant metabolic pathways were identified by analyzing shared target and KEGG pathways. The key mechanism was subsequently validated by cell adhesion assays, western blot assays, and immunofluorescence staining. The results showed that the MIX has the capacity to repair adriamycin-induced damage in MPC5 cells, as evidenced by enhanced cell viability and synaptopodin expression. Additionally, the MIX shows promise in potentially reinstating the podocyte adhesion through the modulation of the expression of podocyte adhesion-related proteins linked to nucleotide metabolites. The MIX has the potential to beneficially affect podocyte injury by modulating the cell adhesion pathway, contributing to one of the pharmacodynamic mechanisms of AR treatment of nephrotic syndrome. This has implications for the development and utilization of AR resources and achievement the social benefit of empowering rural revitalization.

Leveraging machine learning for drug repurposing in rheumatoid arthritis

Rheumatoid arthritis (RA) presents a significant challenge in clinical management because of the dearth of effective drugs despite advances in understanding its mechanisms. Drug repurposing has emerged as a promising strategy to address this gap, offering potential cost savings and expediting drug discovery. Notably, computational methods, particularly machine learning (ML), have shown promise in RA drug repurposing. In this review, we survey various drug-repurposing approaches, both classical and contemporary, highlighting the pivotal role of ML. We summarize RA candidate drugs identified through computational strategies and discuss prevailing challenges in this domain. Leveraging ML, alongside a deepening understanding of RA mechanisms, holds promise for enhancing pharmacological treatment options for patients with RA.

Network Pharmacology and in vitro Experimental Verification on Intervention of Oridonin on Non-Small Cell Lung Cancer

OBJECTIVE

To explore the key target molecules and potential mechanisms of oridonin against non-small cell lung cancer (NSCLC).

METHODS

The target molecules of oridonin were retrieved from SEA, STITCH, SuperPred and TargetPred databases; target genes associated with the treatment of NSCLC were retrieved from GeneCards, DisGeNET and TTD databases. Then, the overlapping target molecules between the drug and the disease were identified. The protein-protein interaction (PPI) was constructed using the STRING database according to overlapping targets, and Cytoscape was used to screen for key targets. Molecular docking verification were performed using AutoDockTools and PyMOL software. Using the DAVID database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted. The impact of oridonin on the proliferation and apoptosis of NSCLC cells was assessed using cell counting kit-8, cell proliferation EdU image kit, and Annexin V-FITC/PI apoptosis kit respectively. Moreover, real-time quantitative PCR and Western blot were used to verify the potential mechanisms.

RESULTS

Fifty-six target molecules and 12 key target molecules of oridonin involved in NSCLC treatment were identified, including tumor protein 53 (TP53), Caspase-3, signal transducer and activator of transcription 3 (STAT3), mitogen-activated protein kinase kinase 8 (MAPK8), and mammalian target of rapamycin (mTOR). Molecular docking showed that oridonin and its key target molecules bind spontaneously. GO and KEGG enrichment analyses revealed cancer, apoptosis, phosphoinositide-3 kinase/protein kinase B (PI3K/Akt), and other signaling pathways. In vitro experiments showed that oridonin inhibited the proliferation, induced apoptosis, downregulated the expression of Bcl-2 and Akt, and upregulated the expression of Caspase-3.

CONCLUSION

Oridonin can act on multiple targets and pathways to exert its inhibitory effects on NSCLC, and its mechanism may be related to upregulating the expression of Caspase-3 and downregulating the expressions of Akt and Bcl-2.

An integrated serum pharmacochemistry, network pharmacology, and metabolomics strategy: A study on raw and wine-processed Paeoniae Radix Alba in promoting blood circulation to alleviate blood stasis

Paeoniae Radix Alba (PRA) is a traditional Chinese medicine that can be processed with wine to achieve an enhanced effect of promoting blood circulation, thus alleviating blood stasis. However, to date, the changes in the bioactive compounds of PRA before and after wine-processing, as well as the mechanisms of action and the effects on ameliorating blood stasis syndrome (BSS), have not been adequately investigated. Therefore, we systematically elucidated the material basis and mechanisms of action of PRA in the treatment of BSS before and after wine processing by integrating serum pharmacochemistry, network pharmacology, and metabolomics approaches. The wine processing method significantly affected 11 components of PRA, including gallic acid, ethyl gallate, paeoniflorin, and 3-O-methylellagic acid 4-O-β-D-glucopyranoside. Benzoylpaeoniflorin and desbenzoylpaeoniflorin are key serum components of PRA both before and after wine processing. SRC and GAPDH are the central targets through which benzoylpaeoniflorin and desbenzoylpaeoniflorin exert their ameliorative effects on BSS, respectively. The metabolomics results indicated that six metabolic pathways-pyrimidine metabolism, ascorbate and aldarate metabolism, steroid hormone biosynthesis, pentose and glucuronate interconversions, tryptophan metabolism, and lysine degradation-play important roles in the amelioration of BSS by PRA and WPRA. 2'-Deoxycytidine, cortexolone, dihydrocortisol, L-gulonic gamma-lactone, L-uridine, D-ribulose, 4-trimethylammoniobutanoic acid, and indoleacetic acid have been identified as potential biomarkers for the amelioration of BSS by PRA and WPRA. The present study significantly contributes to elucidating the processing mechanism of PRA in "promoting blood circulation to remove blood stasis through wine processing".

Xin-Ji-Er-Kang balances mitochondrial fusion and fission to protect cardiomyocytes in mice with heart failure by regulating the ERα/SIRT3 pathway

BACKGROUND

Mitochondrial dynamics imbalance is an essential pathological mechanism in heart failure (HF). The Chinese herbal formula Xin-Ji-Er-Kang (XJEK) has demonstrated good therapeutic effects in various cardiovascular disease models. However, whether XJEK treats HF by regulating mitochondrial dynamics homeostasis and its specific molecular mechanisms remain elusive.

PURPOSE

To investigate the effect of XJEK on restoring the disrupted mitochondrial dynamics homeostasis in HF and elucidate the potential regulatory mechanism.

STUDY-DESIGN/METHODS

A mouse model of myocardial ischemia-reperfusion (MIR)-induced HF was established to assess the cardioprotection of XJEK. Subsequently, network pharmacology was employed to predict the mechanism by which XJEK treated HF. Moreover, gene silencing was employed to explore the potential mechanisms behind the cardioprotective effects of XJEK in AC16 cells subjected to hypoxia/reoxygenation (H/R).

RESULTS

XJEK treatment significantly attenuated myocardial fibrosis and ameliorated ventricular remodeling in post-MIR-induced HF mice. Network pharmacology analysis identified the estrogen receptor α (ERα) as a key regulator of XJEK-mediated cardioprotection. XJEK disordered mitochondrial dynamics in the hearts of MIR-induced HF mice. In addition, XJEK restored mitochondrial fusion-fission imbalance and facilitated ERα nuclear translocation to up-regulate sirtuin 3 (SIRT3) expression in the hearts of MIR-induced HF mice and H/R-induced AC16 cells. Notably, ERα depletion in cardiomyocytes completely abrogated the cardioprotective effects of XJEK.

CONCLUSION

XJEK safeguards the hearts in mice with MIR-induced HF by facilitating ERα nuclear translocation to up-regulate SIRT3 expression to rescue the mitochondrial fusion-fission imbalance. This study establishes a new theoretical basis for treating HF with XJEK.

Exploring the molecular mechanism of Tripterygium Wilfordii Hook F in treating systemic lupus erythematosus via network pharmacology and molecular docking

BACKGROUND

Tripterygium wilfordii Hook F (TwHF) is a prominent Chinese herbal formula. It exhibits significant clinical efficacy in treating systemic lupus erythematosus (SLE), though its mechanisms remain unclear. Our study employs network pharmacology and molecular docking to explore active compounds of TwHF and their associated targets for SLE treatment.

METHODS

Primary active compounds of TwHF and their targets were sourced from the TCMSP, SwissTargetPrediction, and UniProt databases. SLE-relevant target proteins were identified from the OMIM and GeneCards databases. Enrichment analyses were conducted to reveal results of common TwHF-SLE targets. STRING and Cytoscape software were used to systematically analyze and construct protein-protein interaction (PPI) networks, compound-target-pathway, and target-organ networks. Molecular docking was utilized to confirm the binding of key targets to the top active compounds.

RESULTS

A total of 14 active compounds and 300 overlapping targets between TwHF and SLE were identified. PPI network analysis revealed 29 core targets. Several pathways were found to contribute to the potential therapeutic effects of TwHF in SLE, including PI3K-Akt signaling pathway, Th17 cell differentiation, chemokine signaling, and T cell receptor signaling. Disease Ontology (DO) analysis highlighted the involvement of TwHF in genes associated with myocardial infarction (MI), atherosclerosis (AS), breast carcinoma, and ischemia. Molecular docking results demonstrated strong binding affinities, with 37 signal molecule-receptor interactions in SLE and 97 interactions in SLE-related MI and AS showing binding energies lower than -7 kJ/mol.

CONCLUSIONS

This research effectively anticipates the potent constituents, probable targets, and pathways implicated in treating SLE with TwHF, specifically addressing complications such as MI and AS. Comprehending the precise molecular mechanism targeting SLE of TwHF and its efficacious bioactive components furnishes a theoretical groundwork for enhancing its clinical utilization. Key Points •SLE is characterized by aberrant immune activation and persistent inflammation. •TwHF exerts immunomodulatory and anti-inflammatory effects. •TwHF exhibits prospects in the treatment of SLE with unknown molecular mechanisms. •Network pharmacology and molecular docking reveal promise in the mechanism of TwHF.

Discovery of novel oleanolic acid glycoside derivatives targeting PTP1B/PI3K/AKT signaling pathway for the treatment of breast cancer

Protein tyrosine phosphatase 1B (PTP1B) has been identified as a key drug target for anti-tumor drug development. Oleanolic acid (OA) has been proved to be an inhibitor of PTP1B, but its poor water solubility, low bioavailability and poor activity in vivo limit its clinical efficacy. In this study, a total of 47 new OA derivatives including heteroatom derivatives, ester derivatives, amino substitution derivatives and Schiff base derivatives were designed and synthesized. Among them, OA-Br-1 had stronger inhibition and selectivity on PTP1B than OA, with IC50 value of 7.08 ± 5.05 μM for PTP1B and 222.28 ± 0.11 μM for TCPTP. In addition, OA-Br-1 significantly inhibited the proliferation and induced apoptosis of breast cancer cells, and in vivo nude mice experiments also showed that OA-Br-1 could inhibit the growth of breast tumors. Then network pharmacology was used to predict the targets of OA-Br-1, and the PPI network map between compound - breast cancer - target was constructed. The results showed that the probability value of PTPN1 ranked first among all predicted targets, which was consistent with the results of enzyme activity experiments in vitro. The enrichment results of KEGG pathway and GO functional annotation analysis showed that the effect of OA-Br-1 on breast cancer was significantly correlated with the PI3K/AKT pathway. Subsequent Western Blot results also proved that OA-Br-1 could significantly inhibit the expression of PTP1B, p-PI3K and p-AKT, indicating that OA-Br-1 played an anti-breast cancer role through the PTP1B/PI3K/AKT signaling pathway. Collectively, these findings identify OA-Br-1 as a promising PTP1B inhibitor for breast cancer treatment.

6'-O-caffeoylarbutin of Vaccinium dunalianum alleviated ischemic stroke through the PI3K/AKT/NF-κB pathway

BACKGROUND

Vaccinium dunalianum ("Que Zui Tea") has been traditionally consumed as a tea substitute in Yunnan, China, for its health benefits, i.e., improving vascular health. 6'-O-caffeoylarbutin (CA) is its major bioactive compound (∼20 %). However, the potential of CA against ischemic stroke remains unknown.

PURPOSE

This study explores the protective properties of CA in ischemic stroke, providing empirical support for the folk use of the plant and further drug development.

METHODS

An oxygen-glucose deprivation/reoxygenation (OGD/R)-induced BV2 cells were utilized to identify potential bioactive compounds. Moreover, the pathway and targets were predicted and further verified in OGD/R-induced microglia, nerve cells and in mice of middle cerebral artery occlusion.

RESULTS

CA effectively reduced nitric oxide (NO) release and transcript-level expression of inflammatory factors in OGD/R-stimulated BV2 cells. NF-κB1, IL-6, AKT1, CASP3, and MMP9 were identified as key CA targets for ischemic stroke treatment. In silico predictions suggested that phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PI3K/AKT), mitogen-activated protein kinase (MAPK), and tumor necrosis factor (TNF) were the relevant pathways. These predictions were supported in vitro by an observed decrease in NO, reactive oxygen species, lactate dehydrogenase, and inflammatory cytokines (IL-6, IL-1β, and TNF-α) levels following CA treatment. Western blotting confirmed the regulation of p-IκBα, P65, AKT, and apoptosis-related proteins (further confirmed by PI3K inhibitor LY294002 treatment). These findings were further supported in vivo, with CA ameliorating neurological functions and deficits in ischemic mice. This amelioration correlated with increased cerebral blood flow, and alleviated neuron wrinkling, necrosis, and cell shrinkage. CA also increased brain superoxide dismutase, catalase, and glutathione peroxidase levels.

CONCLUSION

CA exerts neuroprotective effects in ischemic stroke by inhibiting inflammation and oxidative stress through the PI3K/AKT/NF-κB pathway, suggesting its therapeutic potential for cerebral ischemia and supporting the traditional use of V. dunalianum.

Characterization of the Molecular Mechanisms Underlying Lurasidone-Induced Acute Manic Episodes in Bipolar Depression: A Network Pharmacology and Molecular Docking Approach

BACKGROUND

Lurasidone monotherapy has been approved for the treatment of bipolar depression. However, several case reports have indicated treatment with lurasidone-induced acute mania in people with bipolar depression. The mechanism by which this occurs remains to be elucidated.

OBJECTIVE

In this study, we systematically explored the mechanism of action of lurasidone-induced acute mania in bipolar depression using network pharmacology and molecular docking.

METHODS

Putative target genes for lurasidone were obtained from the GeneCards, PharmMapper, SwissTargetPrediction, and DrugBank databases. Targets for bipolar depression and acute mania were collected from the DisGeNET and GeneCards databases. A protein-protein interaction (PPI) network was built to screen the hub targets. The Bioinformatics platform and Database for Annotation, Visualization, and Integrated Discovery were used for the visualization of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the top 20 core targets. The drug-pathway-target-disease network was constructed using Cytoscape. Finally, molecular docking was performed to evaluate the binding affinity between lurasidone and potential targets.

RESULTS

In total, 327, 1253, and 429 targets of lurasidone, bipolar depression, and acute mania were identified, respectively. A topological analysis of the PPI network revealed the top 20 hub targets. Based on PPI, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the top 20 hub targets, lurasidone was found to induce acute manic episodes in people with bipolar depression by targeting the serotonergic synapse signaling pathway via MAOB, HTR1A, HTR2A, HTR3A, SLC18A2, HTR1B, and HTR7. Molecular docking revealed good binding affinities between lurasidone and these potential targets.

CONCLUSIONS

This study revealed that lurasidone may regulate the serotonergic synapse signaling pathway by interacting with the identified core targets MAOB, HTR1A, HTR2A, HTR3A, SLC18A2, HTR1B, and HTR7 to induce treatment-emergent mania in people with bipolar depression. Our work provides a theoretical basis for the pharmacology of lurasidone-induced acute mania in bipolar depression and further basic research.

Mechanism of Protective Effect of Mongolia Medicine Nagab-9 on LPS-Induced Acute Lung Injury Based on an Integrated Network Pharmacology and Experimental Verification

Objectives

To investigate the potential mechanisms of Nagab-9 in alleviating acute lung injury (ALI) by integrating network pharmacology analysis with in vivo and in vitro validation experiments.

Methods

Active compounds of Nagab-9 were identified using TCMSP and ETCM databases. ALI-related targets were collected from relevant disease databases, and an intersection of these targets was used to construct a protein-protein interaction (PPI) network to identify core targets. Functional analysis through Gene Ontology (GO) and KEGG pathway enrichment was performed. The key targets of Nagab-9 intervention in ALI were further validated in LPS-induced ALI mouse models and in mouse alveolar epithelial cell injury models.

Results

A total of 25 active components were identified from Nagab-9. PPI network analysis highlighted core targets, and GO and KEGG pathway analyses identified significant pathways involved. Six core components were selected based on topological parameters of the "compound-target-pathway-disease" network. In vivo, Nagab-9 was shown to alleviate ALI-induced lung damage, inhibit inflammatory infiltration, and modulate inflammatory factors by downregulating Ly6G, Cit-H3, and phosphorylated proteins SRC, ERK1/2, and STAT3 in lung tissue. In vitro experiments demonstrated that Nagab-9 effectively inhibits LPS-induced inflammatory responses, protecting lung tissue and suppressing neutrophil infiltration and NET formation, likely through the SRC/ERK1/2/STAT3 pathway.

Conclusion

Nagab-9 exerts a protective effect against ALI by modulating inflammatory responses and reducing neutrophil infiltration and NET formation, primarily via the SRC/ERK1/2/STAT3 signaling pathway. This study supports Nagab-9 as a promising therapeutic agent for ALI intervention.

Personalized assessment and monitoring of bone health from sweat: unveiling TEGO doped wearable, non-invasive hydrogel nanocomposite biosensor empowered by IL-6 detection

Portable biosensing is crucial for rapid detection and continuous monitoring of bone diseases such as osteoporosis and bone cancer. It is well established that such bone disorders or diseases trigger release of inflammatory cytokines including interleukin-6 (IL6), detectable in sweat by electrochemical immunosensors. To this end, this study presents a novel hydrogel nanocomposite based immunosensor with highly conductive dual-layer of thermally exfoliated graphene oxide, toward precise detection and determination of loading level of IL-6 biomarker, and in turn, developing a label-free flexible bone biosensing platform. The immunosensor employed antibody immobilization process, which was further facilitated by the modification of the dual-layer by using 1-pyrenebutyric acid N-hydroxy succinimide ester. A thorough analysis of the effects of surface modification was conducted utilizing spectroscopic, electrochemical, and morphological methods. The biosensor's response was assessed through the utilization of the cyclic voltammetry measurement, which exhibited remarkable selectivity, achieving a low limit of detection of 15.4 pg ml-1across a wide linear range. Additionally, field emission scanning electron microscopy, Fourier transform infrared spectroscopy and Raman spectroscopy were successfully used to validate the sensing substrate in bio-fluidic samples and to understand the structure-property correlation. This innovative portable and flexible biosensor thus offers a practical and effective tool for potential application in continuous monitoring of bone health.

Network pharmacology-based investigation of the pharmacological mechanisms of diosgenin in nonalcoholic steatohepatitis

The prevalence of nonalcoholic steatohepatitis (NASH) is rising annually, posing health and economic challenges, with limited treatments available. Diosgenin, a natural steroidal compound found in various plants, holds potential as a therapeutic candidate. Recent studies have confirmed diosgenin's anti-inflammatory and metabolism-modulating properties. However, its therapeutic effects on NASH and the underlying mechanisms are still unclear. This study aims to explore diosgenin's protective effects and pharmacological mechanisms against NASH using network pharmacology, molecular docking, and experimental validation. We gathered potential targets of diosgenin and NASH from various databases to generate protein-protein interaction (PPI) networks. GO and KEGG pathway enrichment analyses identified key targets and mechanisms. Molecular docking confirmed the binding capacity between diosgenin and core target proteins. Additionally, a NASH cell model was developed to validate the pharmacological effects of diosgenin. Our investigation identified nine key targets (ALB, AKT1, TP53, VEGFA, MAPK3, EGFR, STAT3, CASP3, IGF1) that interact with diosgenin. Molecular docking indicated potential bindings interactions, while enrichment analyses revealed that diosgenin may enhance fatty acid metabolism via the PI3K-Akt pathway. Cellular experiments confirmed that diosgenin activates this pathway, reduces SCD1 expression, and decreases triglyceride and IL-6 levels. Our study elucidates that diosgenin may ameliorate triglyceride deposition and inflammation through the PI3K-Akt pathway.

The effects and mechanisms of Xiaoyao San on nonalcoholic fatty liver disease rat based on transcriptomics and proteomics analysis

Nonalcoholic Fatty Liver Disease (NAFLD) is characterized by excessive lipid accumulation in hepatocytes and is closely associated with metabolic disturbances such as obesity, dyslipidemia, and insulin resistance. Despite its increasing prevalence and potential progression to severe liver conditions, there is currently no approved pharmaceutical intervention for NAFLD. Traditional Chinese Medicine (TCM) formulations, such as Xiaoyao San (XYS), have shown therapeutic efficacy in treating NAFLD, but the underlying mechanisms remain unclear. This study employed a multi-omics approach to elucidate the therapeutic mechanisms of XYS in NAFLD. A rat model of NAFLD was established using a high-fat diet (HFD). The chemical constituents of XYS were analyzed using UPLC-MS/MS. Transcriptomics and proteomics analyses were performed to identify potential biological targets and signaling pathways involved in the therapeutic effects of XYS. The results were validated using ELISA and Western blotting. UPLC-MS/MS identified 225 prototype chemical components of XYS in the blood. XYS significantly reduced body weight, liver index, and Lee's index in NAFLD model rats. It ameliorated HFD-induced hepatic steatosis, down-regulated serum levels of ALT, AST, GGT, TG, TC, LDL-C, FBG, IL-1β, IL-6, TNF-α, and ROS, and up-regulated HDL-C levels. Transcriptomics and proteomics analyses revealed that XYS modulated key signaling pathways, including cAMP, TGF-β, NF-κB, and necroptosis. Specifically, XYS down-regulated the expressions of NF-κB, p-NF-κB, FOXO1, TGF-β1, RIP3, and p-MLKL, while up-regulating cAMP, PKA, p-PKA, and PPARα. XYS improves NAFLD by regulating the cAMP/PKA-mediated PPARα, FOXO1, and NF-κB signaling pathways. This study provides a comprehensive understanding of the molecular mechanisms underlying the therapeutic effects of XYS in NAFLD and supports its potential as a novel therapeutic intervention for this condition.

Umbelliferone attenuates calcium oxalate crystal-induced renal injury and inflammation by attenuating autophagy through the PI3K/AKT pathway

Calcium oxalate (CaOx) crystals are a major component of human kidney crystals and can induce renal tubular inflammation and damage, ultimately leading to renal calcium deposits and kidney stone formation. Umbelliferone (Umb) is a common coumarin compound. In this study, we used in vivo, in vitro experiments and network pharmacology were performed to assess the therapeutic effects of Umb on kidney stones and investigate its pharmacological mechanism. First, we established cellular and mouse models of calcium oxalate renal calcinosis, and we found that Umb reduces renal crystalline deposits, as well as the inflammation and damage they cause. Subsequently, we screened the PI3K/AKT signalling pathway via network pharmacology and experimentally demonstrated that Umb exerts its protective effects through the PI3K/AKT signalling pathway. Finally, molecular docking techniques and experiments were used to find out that Umb acts directly on PIK3CA to play its role.Our results indicate that Umb alleviates inflammation and injury by attenuating renal autophagy induced by kidney stones via the PI3K/AKT pathway.

A new paradigm for drug discovery in the treatment of complex diseases: drug discovery and optimization

In the past, the drug research and development has predominantly followed a "single target, single disease" model. However, clinical data show that single-target drugs are difficult to interfere with the complete disease network, are prone to develop drug resistance and low safety in clinical use. The proposal of multi-target drug therapy (also known as "cocktail therapy") provides a new approach for drug discovery, which can affect the disease and reduce adverse reactions by regulating multiple targets. Natural products are an important source for multi-target innovative drug development, and more than half of approved small molecule drugs are related to natural products. However, there are many challenges in the development process of natural products, such as active drug screening, target identification and preclinical dosage optimization. Therefore, how to develop multi-target drugs with good drug resistance from natural products has always been a challenge. This article summarizes the applications and shortcomings of related technologies such as natural product bioactivity screening, clarify the mode of action of the drug (direct/indirect target), and preclinical dose optimization. Moreover, in response to the challenges faced by natural products in the development process and the trend of interdisciplinary and multi-technology integration, and a multi-target drug development strategy of "active substances - drug action mode - drug optimization" is proposed to solve the key challenges in the development of natural products from multiple dimensions and levels.

Recent advancement in prevention against hepatotoxicity, molecular mechanisms, and bioavailability of gallic acid, a natural phenolic compound: challenges and perspectives

Drug-induced liver injury (DILI) results from the liver toxicity caused by drugs or their metabolites. Gallic acid (GA) is a naturally occurring secondary metabolite found in many fruits, plants, and nuts. Recently, GA has drawn increasing attention due to its potent pharmacological properties, particularly its anti-inflammatory and antioxidant capabilities. To the best of our knowledge, this is the first review to focus on the pharmacological properties of GA and related molecular activation mechanisms regarding protection against hepatotoxicity. We also provide a thorough explanation of the physicochemical properties, fruit sources, toxicity, and pharmacokinetics of GA after reviewing a substantial number of studies. Pharmacokinetic studies have shown that GA is quickly absorbed and eliminated when taken orally, which restricts its use in development. However, the bioavailability of GA can be increased by optimizing its structure or changing its form of administration. Notably, according to toxicology studies conducted on a range of animals and clinical trials, GA rarely exhibits toxicity or side effects. The antioxidation mechanisms mainly involved Nrf2, while anti-inflammatory mechanisms involved MAPKs and NF-κB signaling pathways. Owing to its marked pharmacological properties, GA is a prospective candidate for the management of diverse xenobiotic-induced hepatotoxicity. We also discuss the applications of cutting-edge technologies (nano-delivery systems, network pharmacology, and liver organoids) in DILI. In addition to guiding future research and development of GA as a medicine, this study offers a theoretical foundation for its clinical application.

Network Pharmacology and Experimental Validation Reveal Sishen Pill's Efficacy in Treating NSAID-Induced Small Intestinal Ulcers

Purpose

Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used but often cause small intestinal ulcers (SIUs), for which effective therapies are lacking. Sishen Pill (SSP), a traditional Chinese medicine, shows therapeutic promise, yet its mechanisms remain unclear. This study integrates network pharmacology, molecular docking, and experimental validation to systematically investigate SSP's protective mechanisms against NSAID-induced SIUs.

Patients and Methods

Active SSP ingredients were screened using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Encyclopedia of Traditional Chinese Medicine (ETCM) databases. SIU-related targets were retrieved from GeneCards and DisGeNET. Protein-protein interaction (PPI) networks were constructed via STRING and Cytoscape, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Molecular docking (AutoDock Vina, PyMOL) validated ligand-target interactions. In vivo validation employed an indomethacin-induced SIU rat model to assess SSP's effects on ulcer severity, inflammation, oxidative stress, and PI3K/AKT signaling.

Results

We identified 66 bioactive SSP ingredients, 222 drug targets, and 144 SIU-related targets. Molecular docking revealed high binding affinity of SSP components (quercetin, bavachinin, rutaecarpine, evodiamine) to key targets (AKT1, HSP90AA1, IL6, MAPK1, BCL2). KEGG analysis highlighted the PI3K/AKT pathway as central. In vivo, SSP reduced ulcer indices, suppressed pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and attenuated oxidative stress. SSP also downregulated PI3K and AKT1 mRNA expression, confirming pathway modulation.

Conclusion

This study elucidates SSP's multi-target mechanism against NSAID-induced SIUs, emphasizing its role in suppressing inflammation, oxidative stress, and PI3K/AKT signaling. These findings provide a scientific foundation for SSP's clinical application and highlight its potential as a safe, effective alternative to conventional therapies.

Ginsenoside Rh2 Ameliorates Myocardial Infarction by Regulating Cardiomyocyte Pyroptosis Based on Network Pharmacology, Molecular Docking, and Experimental Verification

Myocardial infarction (MI) is a significant threat to human health worldwide. Following MI, cardiomyocytes (CMs) undergo pyroptosis, exacerbating the damage caused by infarction. Ginseng may play a role in alleviating CM pyroptosis. However, further exploration is needed regarding its main active ingredients and effects. By employing network pharmacology on the active ingredients of ginseng, MI and pyroptosis, and employing molecular docking between such ingredients and pyroptosis-related proteins, we screened for the main ingredient of ginseng. Through network pharmacology and molecular docking, we identified ginsenoside Rh2, which acts on MI and cell pyroptosis, as the most likely active ingredient that stably binds to pyroptosis-related proteins. We subsequently constructed a neonatal rat CM oxygen-glucose deprivation (OGD) model in vitro and an MI mouse model in vivo. Ginsenoside Rh2 was administered, with losartan used as a positive control. In the in vitro OGD model, ginsenoside Rh2 increased the viability of primary rat CMs and mitigated OGD-induced pyroptosis. In the in vivo MI model, ginsenoside Rh2 reduced CM pyroptosis, decreased infarct size, and subsequently improved cardiac function. Our study provides a novel therapeutic strategy for MI by attenuating CM pyroptosis.

Network pharmacology and experimental validation reveal dexmedetomidine's protective mechanisms against acute liver injury in mice

This study explored the role and molecular mechanisms of dexmedetomidine (DEX), an α2-adrenergic receptor agonist, in the treatment of a mouse model of acute liver injury (ALI). DEX significantly mitigated hepatic tissue damage and reduced serum levels of liver function biomarkers and proinflammatory cytokines. Network pharmacology analysis revealed 81 common targets between DEX and ALI, identifying 10 crucial hub genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that DEX's therapeutic effect on ALI is likely linked to the activation of the PI3K/AKT pathway. Immunohistochemical experiments verified DEX's activation of the PI3K/AKT pathway. Molecular docking and dynamic simulations confirmed the stable interaction between DEX and the epidermal growth factor receptor (EGFR). Immunohistochemistry and western blotting further validated that DEX pretreatment upregulated EGFR expression. Our findings indicate that DEX may mitigate ALI by interacting with EGFR and triggering the PI3K/AKT pathway. These findings provide a solid theoretical and experimental basis for using DEX as a potential therapeutic regimen for treating inflammatory liver diseases.

UPLC-Q-TOF-MS and network pharmacology to reveal the mechanism of Guizhi Gegen decoction against type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease. Clinical studies have shown that the incidence and prevalence of T2DM has been on the rise globally in recent years, and the mortality rate is also increasing. Chinese herbs is multiple target for disease. Guizhi Gegen decoction (GZGGD) is one of the most alternative treatment for T2DM. However, the treatment mechanism is unclear. The composition of the GZGGD was determined by ultra-high-performance liquid chromatography with quadrupole time-of-flight mass spectrometry. The key targets and pathways were predicted by network pharmacology and molecular docking. In vivo experiments were performed to further verify and reveal the potential mechanism of action. We identified 44 active components of GZGGD (genistein, 26-hydroxyporicoic acid DM, puerarin, eugenol, and gentiobiose). Network pharmacology predicted key targets such as TNF, AKT1, TP53, EGFR, and STAT3, and AGE-RAGE, IL-17 signaling pathways were enriched. Molecular docking showed that the active components of GZGGD have good binding activity with the potential targets of T2DM. In vivo animal experiments showed improvement in white blood, fasting blood glucose, and inflammatory factor levels (INS, TC, TNF-α, and IL-6). This study clarifies the potential role of GZGGD in T2DM, which can help in the study of T2DM.

Revealing the multi-target compounds of Sarcandra glabra identification and inhibition of novel target genes for the treatment of pancreatic cancer

BACKGROUND

S. glabra has been widely used to treat tumors in traditional Chinese medicine (TCM). However, the specific mechanism of action of S. glabra in pancreatic cancer remains unclear. In this study, network pharmacological analysis was used to identify the active components of S. glabra and their corresponding targets for the treatment of pancreatic cancer. Furthermore, molecular docking, molecular dynamic simulations, and in vitro experiments were performed to validate the findings.

METHODS

The active components of S. glabra and their corresponding targets for the treatment of pancreatic cancer were identified using the TCMSP database and a literature search. Differentially expressed genes were identified using data from the Gene Expression Omnibus (GEO) database, and their protein-protein interaction (PPI) network was constructed using the STRING platform. The target genes of S. glabra were further assessed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses in the R software. Subsequently, a protein-protein interaction (PPI) network and a composite target-pathway network were established. The target genes were subjected to survival and mutation analyses. Molecular docking and molecular dynamic simulations were used to validate the interaction between the hub target genes and S. glabra in vitro. In addition, cell viability and qRT-PCR verification of S. glabra against pancreatic cancer in vitro.

RESULTS

A total of 20 active components and 70 targets were identified. Based on the PPI network, CASP3, MMP9, CCND1, EGF, MMP2, CASP8, ERBB2, STAT1, and PPARG were identified as hub target genes. Enrichment analysis showed that S. glabra may primarily affect pathways such as p53 signaling, transcriptional dysregulation in cancer, proteoglycans in cancer, pancreatic cancer, and cell cycle. Molecular docking and molecular dynamic simulations indicated stable binding between anhydroicaritin-GSK3B and quercetin-PPARG. In vitro experiments demonstrated that treatment with S. glabra significantly inhibited the growth of PANC-1 cells and downregulated expression of GSK3B and PPARG (P < 0.05).

CONCLUSION

This study demonstrates the potential of S. glabra, a herb in traditional Chinese medicine, for treating pancreatic cancer. The findings provide insights into the mechanism of action of the active ingredients of S. glabra, offering a strong theoretical foundation for its various clinical applications.

CLINICAL TRIAL NUMBER

Not applicable.

An integrated approach using molecular docking, network pharmacology, and UPLC-Q-TOF-MS analysis to investigate the chemical makeup and mechanism of Xiaoqinglong decoction against asthma

OBJECTIVE

This study aims to investigate the potential mechanisms by which Xiaoqinglong decoction (XQLD) exerts its therapeutic effects on asthma. This will be achieved through the application of the UPLC-Q-TOF-MS coupling technique, integrated with network pharmacology and molecular docking methodologies.

METHODS

The UPLC-Q-TOF-MS technique was employed to perform a qualitative analysis of both the aqueous extract of XQLD and the drug-containing serum. The Swiss TargetPrediction, OMIM, and GeneCards databases were utilized to identify blood-derived components and disease-associated targets. Subsequently, a protein-protein interaction (PPI) network was constructed by intersecting these datasets to identify key targets, which were then subjected to Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Cytoscape software facilitated the construction of a 'drug-component-disease-target' network to enable visualization and analysis, thereby aiding in the prediction of targets and signaling pathways of XQLD in the treatment of asthma. Finally, molecular docking of the pertinent incoming components to the central target was conducted utilizing AutoDock Vina and PyMol software.

RESULTS

A comprehensive analysis identified 102 components within the aqueous extract of XQLD, alongside 93 components in the drug-containing serum. Additionally, 90 compound-disease shared targets and 45 key targets were identified through PPI network analysis. Notably, compounds such as apigenin, l-asarinin, 6-shogaol, ellagic acid, kaempferol, and naringenin are pivotal in mediating the therapeutic effects of XQLD in asthma treatment. The primary molecular targets of XQLD for asthma include SRC, AKT1, EGFR, ESR1, HIF1A, and PIK3CA. The results of the molecular docking analysis indicated that the binding energies between the core target and the active ingredient were ≤ -5.5 kcal/mol, demonstrating a strong affinity.

CONCLUSION

This study elucidated the chemical composition, potential targets, and action pathways of the aqueous extract of XQLD and its drug-containing serum. It preliminarily identified the material basis and mechanism of action, thereby providing a foundation for further in-depth research into the mechanisms underlying XQLD and its clinical applications.

To investigate the effect and mechanism of tetrahydrocurcumin on hepatocellular carcinoma based on phosphoinositide 3-kinases/AKT signaling pathway

BACKGROUND

Liver cancer has a high incidence and mortality worldwide, especially in China. Herein, we investigated the therapeutic effect and mechanism of tetrahydrocurcumin against hepatocellular carcinoma (HCC), with a focus on the of phosphoinositide 3-kinases (PI3K)/AKT signaling pathway.

AIM

To investigate the effects and mechanism of tetrahydrocurcumin in HCC cell lines HepG2 and Huh7.

METHODS

Using Metascape, we analyzed the potential targets of tetrahydrocurcumin in HCC. Molecular docking validation was performed using SYBYL2.0. Cell Counting Kit-8, wound healing, and transwell assays were performed to evaluate the effects of tetrahydrocurcumin on HepG2 and Huh7 cell migration, invasion, and apoptosis. The expression of PI3K/AKT signaling pathway-related proteins was detected by western blotting.

RESULTS

Network pharmacology and molecular docking showed that tetrahydrocurcumin has high binding affinity for phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha. In vitro experiments demonstrated that tetrahydrocurcumin suppressed the migration and invasion of liver cancer cells, promoted their apoptosis, and downregulated the expression of p-PI3K, p-AKT, and B cell leukemia/lymphoma 2, while upregulating caspase-3, p53, and B cell leukemia/lymphoma 2 associated X.

CONCLUSION

In summary, tetrahydrocurcumin suppresses PI3K/AKT signaling, promotes apoptosis, and prevents the migration and invasion of liver cancer cells.

Investigating the pharmacological mechanisms of clopidogrel for carotid stenosis treatment based on network pharmacology and molecular docking techniques

Carotid artery stenosis is a manifestation of atherosclerosis and is associated with an increased risk of various cardiovascular diseases. Clopidogrel is an antiplatelet drug widely used for the prevention and treatment of atherosclerosis-related diseases. This study explores the potential molecular mechanisms of clopidogrel in the treatment of carotid artery stenosis through network pharmacology and molecular docking techniques. First, network pharmacology methods were used to construct a clopidogrel target network and identify its possible 127 action targets. Secondly, the gene ontology enrichment analysis indicated that clopidogrel for treating carotid stenosis is closely related to inflammatory responses, platelet activation, and angiogenesis. The Kyoto Encyclopedia of Genes and Genomes analysis revealed associations with lipid metabolism and atherosclerosis. Subsequently, molecular docking technology was employed to screen the binding affinity of clopidogrel to these targets. The results revealed that clopidogrel exhibited binding energies less than - 4.20 kcal/mol with multiple targets, including TNF, MMP9, PTGS2, CCL2, TLR4, and IL-10. This indicates that clopidogrel has high binding affinity and stable binding modes with these targets, thereby exerting anti-inflammatory effects. This study reveals the potential molecular mechanisms of clopidogrel in the treatment of carotid artery stenosis through network pharmacology and molecular docking techniques. The experimental results provide a theoretical basis for the application of clopidogrel in the treatment of carotid artery stenosis and offer new ideas for further drug development and personalized treatment.

Neuroprotective role of Da Qin Jiu decoction in ischemic stroke: Mitochondrial rescue through PI3K/Akt-mediated UPRmt activation

ETHNOPHARMACOLOGICAL RELEVANCE

Ischemic stroke (IS) is a highly debilitating neurological condition with limited treatment options and suboptimal outcomes. The traditional Chinese medicine formula Da Qin Jiu Decoction (DQJD) has been widely used for its neuroprotective effects. However, its potential mechanisms of action in IS remain unclear.

AIM OF THE STUDY

This study aims to investigate the therapeutic effects of DQJD on IS and elucidate its underlying mechanisms of action.

MATERIALS AND METHODS

The neuroprotective effects of DQJD were evaluated in a mouse model of middle cerebral artery occlusion/reperfusion (MCAO/R). Neurological recovery was assessed using behavioral tests and tissue analysis, including TTC staining, MRI, and HE & Nissl staining. Mitochondrial function was examined through Western blot, JC-1 assay, ROS staining, and electron microscopy. Additionally, network pharmacology, bioinformatics analyses, and Mendelian randomization were employed to identify key molecular targets and mechanisms. Molecular docking was conducted to explore interactions between active components of DQJD and relevant pathways, focusing on PI3K/Akt signaling.

RESULTS

Treatment with DQJD significantly reduced infarct volume, alleviated tissue damage and improved neurological outcomes. Molecular analyses revealed the upregulation of ATF5 and mitochondrial unfolded protein response (UPRmt)-related proteins, including HSP60, LONP1, and ClpP, indicating UPRmt activation. Enhanced mitochondrial membrane potential (ΔΨm), reduced ROS levels, and restoration of mitochondrial dynamics further demonstrated the rescue of mitochondrial function. Network pharmacology and molecular docking analyses highlighted the central role of PI3K/Akt signaling in DQJD-mediated neuroprotection.

CONCLUSIONS

DQJD exerts neuroprotective effects in IS by restoring mitochondrial function through UPRmt activation via the PI3K/Akt pathway. These findings support further exploration of DQJD as a therapeutic option for IS.

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

ETHNOPHARMACOLOGICAL RELEVANCE

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

AIM OF THE STUDY

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

MATERIALS AND METHODS

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

RESULTS

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

CONCLUSION

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

Qingfei Jiedu Huatan Formula inhibits NLRP3 inflammasome activation to attenuates inflammation and pyroptosis in severe pneumonia: Integrating experimental verification, network pharmacology and transcriptomics

ETHNOPHARMACOLOGICAL RELEVANCE

Severe pneumonia (SP) represents an acute, critical condition characterized by high morbidity and mortality rates, along with numerous complications. The Qingfei Jiedu Huatan Formula (QJHF), a traditional Chinese medicine (TCM) formulation, is indicated for the treatment of severe pneumonia. However, its underlying therapeutic mechanisms remain uncertain.

AIM OF THE STUDY

This study aimed to investigate the beneficial effects and molecular mechanisms of QJHF in the treatment of severe pneumonia.

MATERIALS AND METHODS

The anti-inflammatory properties of QJHF were assessed using a Klebsiella pneumoniae-induced rat model of SP and LPS-induced MH-S cells. Network pharmacology and transcriptomics were employed to identify potential targets and elucidate the molecular mechanisms underlying QJHF's action against SP. Pyroptosis in lung tissue and MH-S cells was examined via immunofluorescence and scanning electron microscopy. The expression of the NLRP3 inflammasome and its upstream regulatory pathways was measured through Western blot analysis.

RESULTS

QJHF was found to alleviate pulmonary edema, enhance lung pathology, and improve the blood oxygenation index, while reducing inflammatory cell infiltration, expression of inflammatory factors, and lactic acidosis in SP rats. Serum containing QJHF-containing serum significantly reduced the secretion and transcription of inflammatory factors in MH-S cells. Network pharmacology and RNA-Seq analysis revealed potential targets modulated by QJHF against SP, showing a significant association between these targets and NLRP3 within the PPI network. Pathway enrichment analysis suggested that the NOD-like receptor, TNF, NF-κB, and JAK/STAT signaling pathways might regulate the NLRP3 inflammasome and coordinate the inflammatory response. Additionally, QJHF was shown to suppress NLRP3 inflammasome activation in rats with SP and in MH-S cells, which corresponded with markedly reduced levels of TNFR1, TRAF2, TAK1, phosphorylated p65, IκBα, JAK2, and STAT3.

CONCLUSIONS

QJHF effectively attenuated the inflammatory response in severe pneumonia by inhibiting macrophage-mediated inflammation and NLRP3 inflammasome activation through TNF, NF-κB, and JAK/STAT signaling pathways.

A Mechanistic Study of the Feasibility of Ursodeoxycholic Acid in the Treatment of Colon Adenocarcinoma

Purpose

Bile acids promote the progression of colon adenocarcinoma (COAD), and ursodeoxycholic acid (UDCA) is a key drug in promoting bile acid excretion, but its role in COAD unclear. Our study aims to investigate the relationship between COAD and bile acid metabolism and to assess the feasibility of UDCA for the treatment of COAD.

Methods

Firstly, biological targets closely related to COAD were identified: Based on the cancer genome atlas (TCGA) database, the core genes of COAD were obtained by differential expression analysis and weighted gene-coexpression network analysis (WGCNA), and subjected to gene ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Secondly, finding a drug by target, after identifying UDCA as a candidate drug, the feasibility of UDCA in treating COAD was verified in reverse: Using databases to collect potential targets for COAD and UDCA, and the intersecting genes were the potential targets for UDCA to exert anti-tumor effects. Then Autodock was used for molecular docking to analyze the interaction between UDCA and core target proteins. Finally, experimental validation was performed: MTT assay, wound healing, transwell migration, and angiogenesis assays were used to detect the effects of UDCA on cell proliferation, migration, invasion, and neovascularization.

Results

2064 differential genes were screened from TCGA. WGCNA obtained the module most relevant to CRC, containing 493 genes. KEGG analysis found that overlapping genes were mainly concentrated in bile acid metabolic pathways. A total of 26 UDCA anti-tumor targets were obtained in database, and 5 core targets were selected by STRING database and Cytoscape software: TNF, CYP27B1, MDM2, MMP2, CASP3. Molecular docking results showed that UDCA had good binding activity with the core targets. In vitro experiment showed UDCA effectively inhibited the proliferation, migration, invasion and neovascularization in colon cancer cells.

Conclusion

The antitumor activity of ursodeoxycholic acid may be related to cell apoptosis, proliferation, migration and vascular neogenesis.

Investigating the PI3K/AKT/mTOR axis in Buzhong Yiqi Decoction's anti-colorectal cancer activity

Buzhong Yiqi Decoction (BZYQD) is a traditional Chinese medicine renowned for its anti-colorectal cancer (CRC) properties. However, the bioactive components and mechanisms of BZYQD against CRC remain unknown. In this study, LC-MS was used to analyze the chemical composition of BZYQD. Next, the network pharmacology and molecular docking was used to investigate the core components and targets of BZYQD against CRC. Finally, we experimentally validated the potential mechanism of BZYQD against CRC through in vitro studies. Our results identified 26 chemical components in the BZYQD; 75 "hithubs" targets were screened by network pharmacology, and mainly involving pathways such as including pathways in cancer, P13K-Akt signaling pathway, proteoglycans in cancer, kaposi sarcoma-associated herpesvirus, and lipid and atherosclerosis signaling pathways. Based on the number of "hithubs" targets in the key pathways, the two most critical targets including AKT1 and PIK3CA were selected. The component-target network results indicated that astragaloside IV, gancaonin A, quercetin, poricoic acid A, and licoisoflavanone are key anti-CRC components in BZYQD. Molecular docking showed a strong binding affinity between these components and targets. The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway emerged as the primary target of BZYQD. Further in vitro studies confirmed that BZYQD's anti-CRC activity is mediated through the PI3K/AKT/mTOR axis and influences macrophage polarization. BZYQD exerts its therapeutic effects on CRC through multiple components, targets, and pathways. Our study elucidates the effective components and molecular mechanisms of BZYQD in CRC treatment and provides preliminary validation through molecular docking and experimental studies.

Network pharmacology and molecular docking technology-based predictive study and potential targets analysis of icariin for the treatment of diabetic nephropathy

OBJECTIVE

Epimedium glycoside is a flavonoid compound in Epimedium, which has been found to alleviate various chronic diseases. The effect and mechanism of icariin on the treatment of diabetes nephropathy still need to be clarified. In this study, we conducted network pharmacology and molecular docking analysis to reveal the mechanism of icariin treating DKD, and then validated its efficacy using a cell model.

METHOD

The structure and targets of icariin were screened using Traditional Chinese Medicine Systems Pharmacology (TCMSP), and their targets were annotated. Retrieve DKD targets from OMIM, GeneCards, and TTD databases. We constructed a protein-protein interaction (PPI) network using the STRING platform and visualized the results using Cytoscape 3.9.1 software. We also conducted GO and KEGG enrichment analysis on icariin and then performed molecular docking between icariin and key targets. Finally, we established a cell model of DKD to evaluate the efficacy of icariin in treating DKD.

RESULT

A total of 77 icariin targets were associated with DKD. The GO and KEGG enrichment results showed that the therapeutic effect of icariin on DKD was significantly correlated with inflammatory response, cell apoptosis, epithelial-mesenchymal transition, and PI3K/AKT signaling pathway. The molecular docking results indicate that icariin has a high affinity for key targets EGER, AKT1, and IGF1. Cell experiments showed that icariin inhibited high glucose-induced EMT, fibrosis-related proteins, levels of inflammatory factors TGF-β1, IL-6, and TNF-α, as well as phosphorylation of phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT) in renal tubular epithelial cells. In addition, icariin inhibited the increase in EGER and AKT1 mRNA levels caused by high glucose and alleviated the decrease in IGF1 mRNA levels.

CONCLUSION

Epimedium glycoside may protect DKD by targeting EGER, AKT1, and IGF1 to inhibit PI3K/AKT signaling, but the specific mechanism needs further exploration.

Network pharmacological evaluation of Cressa cretica L.- an integrated approach of modern and ancient pharmacology

Cressa cretica L. is immensely valuable in pharmacology. Computational approach through network pharmacology has been attempted to understand lead molecules of Cressa and their interactions with multiple targets. The phytochemical components of methanolic extracts of Cressa leaves were identified using GC-MS analysis, revealing 16 compounds. Using the identified lead molecules, target proteins were predicted using SWISS-target prediction and were analyzed using Cytoscape. This led to the identification of 56 candidate protein targets, which were used to construct a network using CytoHubba, Centiscape, MCODE, and KEGG pathways. The STRING network was created using Cytoscape for analyzing protein-protein interactions, and the top 5 genes were chosen from a total of 12 algorithms in CytoHubba. The antioxidant effects of C. cretica were investigated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, which showed an increase in the trend activity of the plant extract with an inhibition percentage of 51.53 ± 0.003%. This was further validated by ferric reducing antioxidant power (FRAP) assay that resulted in an antioxidant activity of 6.64 µg/mL at a high concentration of 500 µg/mL. Molecular docking and simulation were performed to study the interaction of human cyclooxygenase-2 (PDB ID: 5KIR) with Cressa metabolites. 5KIR exhibited a higher interaction with methyl stearate, forming two H-bond interactions with Arg 120 and Tyr 355. Molecular dynamics simulation analysis confirmed the stability of the protein-ligand complex. The network pharmacology analysis of putative proteins obtained from C. cretica revealed that the peroxisome proliferator-activated receptor gamma (PPARG) gene is found in numerous cancer pathways and can be inhibited.

Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry Combined With Network Pharmacology to Elucidate the Bioactive Ingredients and Potential Mechanism of Wu-Teng Decoction for Treatment of Rheumatoid Arthritis

Wu-Teng Decoction (WTD) is a significant in-hospital preparation widely used in clinical practice to treat rheumatoid arthritis (RA) in China, however, its active substances and underlying mechanisms remain unclear. In this study, the chemical constituents of WTD were analyzed using ultra-high-performance liquid chromatography-tandem mass spectrometry, identifying a total of 120 compounds, including flavonoids, phenylpropanoids, phenolic acids, alkaloids, etc. Subsequently, network pharmacology analyses revealed that 29 compounds were potential active compounds in WTD for the treatment of RA, as well as 48 core anti-RA targets, including tumor necrosis factor-α, V-Akt murine thymoma viral oncogene homolog 1, and albumin. Further analysis suggested that WTD treats RA via the phosphoinositide 3-kinase-Akt, mitogen-activated protein kinase, and Ras signaling pathways. Molecular docking analysis of the top five pivotal targets with the core active ingredients demonstrated suitable binding interactions at the active site of target proteins. The significant reduction of nitric oxide levels in lipopolysaccharides-induced RAW264.7 cells validated the anti-inflammation activity of WTD.

Nutritional L-Citrulline and Tetrahydrobiopterin in Peripheral Artery Disease: A Phase II Randomized Trial (CIPER Study)

BACKGROUND

Peripheral artery disease (PAD) is a major public health concern due to its high prevalence, severe impact on individuals' health and quality of life, and substantial economic burden. Pharmacological interventions are still limited with numbers needed-to-treat ranging from 6 (cilostazol) to 50 (aspirin, statins, and vorapaxar).

OBJECTIVES

This randomized, placebo-controlled, double-blinded crossover interventional trial aims to measure the effect of L-citrulline and tetrahydrobiopterin (H4Bip) on walking distance in patients with PAD, stratified by plasma levels of asymmetric dimethyl L-arginine (ADMA), the endogenous inhibitor of endothelial nitric oxide (NO) synthase.

METHODS

We measured preinterventional ADMA levels in 51 patients with PAD in Australia and Germany with mean changes in absolute claudication distance (dACD) as the primary outcome upon orally supplementing the L-arginine precursor, L-citrulline (3 g) twice daily for 12 weeks, and, in one arm, additionally H4Bip (0.45 g) once per day for a further 2 weeks.

RESULTS

Preinterventional ADMA levels were pathological (>0.4 μM) in 34 patients. Supplementation with L-citrulline significantly increased the mean plasma levels of both L-citrulline and L-arginine, from 41.8 ± 2.7 μmol/l to 246.3 ± 67.3 μmol/l (P = 0.004) and from 75.2 ± 4.2 μmol/l to 119.2 ± 6.9 μmol/l (P < 0.0001) respectively, when compared with placebo. dACD in % of control was significantly improved by L-citrulline vs placebo (20.11% ± 4.50% vs 5.73% ± 2.74%, respectively; P = 0.011). Further addition of H4Bip increased the mean percentage dACD to 28.15% ± 6.84% (P = 0.021), but only in patients with preinterventional pathological ADMA levels.

CONCLUSIONS

L-citrulline and, when ADMA levels are pathological, H4Bip are effective nutritional interventions in patients with PAD warranting further confirmatory trials.

Anti-pyroptosis biomimetic nanoplatform loading puerarin for myocardial infarction repair: From drug discovery to drug delivery

Pyroptosis is a critical pathological mechanism implicated in myocardial damage following myocardial infarction (MI), and the crosstalk between macrophages and pyroptotic cardiomyocytes presents a formidable challenge for anti-pyroptosis therapies of MI. However, as single-target pyroptosis inhibitors frequently fail to address this crosstalk, the efficacy of anti-pyroptosis treatment post-MI remains inadequate. Therefore, the exploration of more potent anti-pyroptosis approaches is imperative for improving outcomes in MI treatment, particularly in addressing the crosstalk between macrophages and pyroptotic cardiomyocytes. Here, in response to this crosstalk, we engineered an anti-pyroptosis biomimetic nanoplatform (NM@PDA@PU), employing polydopamine (PDA) nanoparticles enveloped with neutrophil membrane (NM) for targeted delivery of puerarin (PU). Notably, network pharmacology is deployed to discern the most efficacious anti-pyroptosis drug (puerarin) among the 7 primary active monomers of TCM formulations widely applied in clinical practice and reveal the effect of puerarin on the crosstalk. Additionally, targeted delivery of puerarin could disrupt the malignant crosstalk between macrophages and pyroptotic cardiomyocytes, and enhance the effect of anti-pyroptosis by not only directly inhibiting cardiomyocytes pyroptosis through NLRP3-CASP1-IL-1β/IL-18 signal pathway, but reshaping the inflammatory microenvironment by reprogramming macrophages to anti-inflammatory M2 subtype. Overall, NM@PDA@PU could enhance anti-pyroptosis effect by disrupting the crosstalk between M1 macrophages and pyroptotic cardiomyocytes to protect cardiomyocytes, ameliorate cardiac function and improve ventricular remodeling, which providing new insights for the efficient treatment of MI.

Active Components of Wen Fei Fu Yang Qu Tan Fang and its Molecular Targets for Chronic Obstructive Pulmonary Disease Based on Network Pharmacology and Molecular Docking

To investigate the mechanism of Wen Fei Fu Yang Qu Tan Fang (WFFYQTF) in the treatment of chronic obstructive pulmonary disease (COPD) using network pharmacology and pharmacodynamics. The TCMSP database was utilized to identify the chemical components and molecular targets of WFFYQTF. Cytoscape software was employed to construct a "drug component-target" network. COPD risk genes and intersecting molecular targets of WFFYQTF were identified using GeneCards, OMIM, and DisGeNET databases. The STRING website was the place where protein-protein interaction (PPI) analysis was performed. Cytoscape topological analysis was applied for screening out key targets of WFFYQTF. GO and KEGG enrichment analyses were conducted using the DAVID database to elucidate the treatment targets of COPD with WFFYQTF. A total of 136 active components of WFFYQTF were identified, including key components such as quercetin, kaempferol, and luteolin, which were found to be particularly significant. Additionally, 412 drug targets and 7121 COPD risk genes were screened out, and 323 treatment targets of COPD with WFFYQTF were determined by Wayne analysis. Core targets identified via PPI analysis included SRC, STAT3, AKT1, HSP90AA1, and JUN. Pathways such as the hypoxia responce, inflammatory response, PI3K/AKT pathway, TH17 pathway and MAPK pathway were obtained with GO and KEGG enrichment analyses. Molecular docking results suggested that quercetin could be soundly bound to STAT3 and AKT1, and kaempferol to SRC. WFFYQTF can effectively impede COPD progression through the coordinated action of multiple components, targets, and pathways during treatment.

Oridonin Alleviates Doxorubicin-Induced Cardiotoxicity by Inhibiting p38 MAPK/MMP3 Signaling Pathway

Although doxorubicin (DOX) is an efficient chemotherapeutic drug for human tumors, severe cardiotoxicity restricts its clinical use. Oridonin (Ori), a bioactive component isolated from Isodon rubescens (Hemsl.) H. Hara, possesses potent anti-inflammatory and anticancer potentials. Therefore, our study aimed to evaluate the protective effects of Ori against DOX-induced cardiotoxicity. DIC models were established in vivo and in vitro. The action targets and pharmaceutical mechanism of Ori against DIC were comprehensively examined by network pharmacology, RNA-sequencing, and experimental validation. Ori relieved Dox-induced cell apoptosis in vitro and in vivo. A total of 7084 DEGs, 196 Ori, and 8172 DIC targets were screened by transcriptomics and network pharmacology, respectively. The three sets contained 11 intersection genes, including Ccl2, Myc, Mmp3, Egfr, p38 MAPK (MAPK14), Esr1, Tnf, Jun, Cdk1, Alb, and Ccnd1. The experimental results showed that Ori significantly decreased MMP-3 activity and the expression of p38 MAPK, thereby attenuating myocardial apoptosis and inflammatory infiltration. This study suggests that Ori is a potential therapeutic agent for DOX-induced cardiotoxicity that exerts its effects by inhibiting the p38 MAPK/MMP-3 signaling pathway.

Research on the mechanism of eugenol in the treatment of liver cancer based on network pharmacology, molecular docking technology, and in vitro experiments

Eugenol, a phenolic natural product with diverse pharmacological activities, remains unexplored in liver cancer. Using network pharmacology, we investigated eugenol's therapeutic mechanisms in liver cancer. We obtained eugenol's molecular structure from PubChem and screened its targets using similarity ensemble approach in Swiss Target Predictiondatabases. Overlapping genes with liver cancer-related genes from GeneCards were identified. Protein-protein interaction networks, Gene Ontology annotations, and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted. A target-pathway network revealed eugenol's interaction with 122 liver cancer-related genes. Molecular docking confirmed eugenol's high affinity for mitochondrial nicotinamide adenine dinucleotide, reduced form (NADH) dehydrogenase 1 (MT-ND1), AKT1, NDUFB7, and NADH dehydrogenase (complex I) subunit S3 (NDUFS3). Expression levels of these targets in normal liver and liver cancer tissues were examined using GEPIA2 and HPA databases. The CCK-8 assay and colony formation assay demonstrated that eugenol significantly inhibited the proliferation of hepatocellular carcinoma cells. Western blot analysis confirmed that eugenol upregulated MT-ND1 while downregulating the expression of targets such as AKT1, NDUFB7, and NDUFS3. Furthermore, it was found that eugenol could influence the expression of the AKT1 target through the AKT/p70 S6K pathway. This study provides new insights into the potential mechanisms of eugenol in liver cancer and offers novel perspectives for network-based liver cancer research.

Bibliometric analysis of literature on natural medicines against chronic kidney disease from 2001 to 2024

BACKGROUND

Chronic kidney disease (CKD) is a globally common and progressive disease. There has been few bibliometric study to analyze the status, hot spots, and trends in the field of natural medicines (NMs) against CKD.

PURPOSE

To comprehensively understand the status, hot spots, and trends in the field of NMs against CKD.

METHODS

The documents concerning NMs against CKD are extracted from the Web of Science Core Collection database (WOSCC). The literature analysis was conducted using VOSviewer 1.6.20 and CiteSpace 6.3.R1 software.

RESULTS

In total, 641 publications were encompassed, which were produced by 3 548 authors and 823 organizations, 241 journals, and 56 countries/regions. The most productive author, institution, country, and journal were Li, Ping, Nanjing University of Chinese Medicine, China, and Journal of Ethnopharmacology, respectively. The first high-cited article was published in Medicinal Research Reviews with 457 citations authored by Huang and colleagues in 2007. Oxidative stress, anti-inflammatory, renal fibrosis, and gut microbiota were the emerging keywords. Rhubarb, Astragalus, Angelica, and Cordyceps, which contain anthraquinones, cordycepin, adenosine, or various polysaccharides, are promising NMs to prevent or treat CKD.

CONCLUSION

Currently, the main hot spot is the elucidation of cellular and molecular mechanisms using novel technologies such as network pharmacology, molecular docking, and experimental validation. Future studies are needed to focus on the inherent molecular mechanisms and clinical applications. In addition, potential side effects of the bioactive compounds cannot be ignored.

Systematic druggable genome-wide Mendelian randomization to identify therapeutic targets and dominant flora for ulcerative colitis

The relationship and mechanism among gut microbiota (GM), metabolites and active ulcerative colitis (UC) are unclear. This study aims to infer the causal relationship between druggable-genes and active UC using Mendelian randomization (MR) and bioinformatics methods. The "microbiota-target" and "microbiota- metabolite" network was constructed to screen the microorganisms and metabolites associated with active UC, and the mechanism of GM, metabolites and active-UC was analyzed. These findings were verified through molecular docking, molecular dynamics (MD) simulations and co-localization analysis. Subsequently, the effects of key GM and targets on mice with UC induced by dextran sulfate sodium (DSS) was investigated. Our findings indicated that four drug targets (IFN-γ, IL24, CXCR6, PRKCZ) are closely associated with the risk of active UC, with IL24 specifically found to be colocalized with UC. These four targets were significantly correlated with differences of immune cell infiltration in active-UC. Faecalibacterium prausnitzii (F. prausnitzii) was predicted to inhibit IFN-γ and promote the remission of active UC. Additionally, seven GM were identified to be associated with the risk of active UC. Molecular docking and MD further confirmed the stable interactions between IFN-γ and metabolites of F. prausnitzii. We also verified the alleviating effect of F. prausnitzii on DSS-induced UC mice. The result indicated that F. prausnitzii can reduce inflammatory cell infiltration and goblet cell death in the colon, lower myeloperoxidase activity, and downregulate IFN-γ expression levels. This study revealed that GM can modify the immune microenvironment of active UC, providing new ideas for the prevention and treatment of UC.

The mechanism of SiJunZi decoction in the treatment of Parkinson's disease

Parkinson's disease (PD) is the second most common neurodegenerative disease, but treatment options for PD are limited, and drug development has reached a bottleneck. With the progress of the aging population, the number of PD patients in China is increasing day by day, imposing a heavy burden on patients and society. Therefore, it is urgent to explore targeted medicine based on the pathogenesis of PD and disease targets. Ancient physicians have used the traditional Chinese medicine formula SiJunZi decoction (SJZD) to treat PD. However, it is less commonly used clinically now, and its pharmacological mechanism still needs to be further elucidated. In this study, based on network pharmacology research and molecular docking technology, the mechanism of SJZD in treating PD was revealed, showing that the extract of SJZD acts on cell microdomain membranes and lipid rafts, affecting ubiquitin-protein ligase binding and ubiquitin-like protein ligase binding processes, and plays a role in neurogenesis. Molecular docking results showed that Ellipticine and Hederagenin in SJZD exhibited significant effects on targets: CASP3, BCL2, and PTGS2. The effect of SJZD reversing MPP+-induced SH-SY5Y cells injury was verified by experiments, concentrations ranging from 5ug/mL to 0.1ug/mL showed significant cell protection at 24 h.

Mitochondria-dependent apoptosis was involved in the alleviation of Jujuboside A on diabetic kidney disease-associated renal tubular injury via YY1/PGC-1α signaling

BACKGROUND

Renal tubular injury was a significant pathological change of diabetic kidney disease (DKD), and the amelioration of renal tubular injury through mitochondrial function was an important treatment strategy of DKD. Our previous study had revealed that Jujuboside A (Ju A), the main active substance isolated from Semen Ziziphi Spinosae (SZS), could restore renal function of diabetic mice. However, its protective mechanism against DKD remains unclear.

PURPOSE

To investigate the effects and the mechanism of Ju A against DKD-associated renal tubular injury.

STUDY DESIGN AND METHODS

The anti-apoptotic effect of Ju A and its protection effect on mitochondria dysfunction of renal tubular epithelial cells (RTECs) were examined in high glucose (HG)-cultured HK-2 cells, and in db/db mice. Subsequently, Network Pharmacology analysis, molecular docking, luciferase assay, chromatin immunoprecipitation (ChIP), Yin Yang 1 (YY1) overexpression lentiviral vector and peroxisome proliferator-activated receptor-γ coactlvator-1α (PGC-1α) specific agonist ZLN005 were all used to identify the protective mechanism of Ju A towards DKD-associated mitochondrial dysfunction of RTECs.

RESULTS

Ju A inhibited RTECs apoptosis and ameliorated mitochondria dysfunction of RTECs of diabetic mice, and HG-cultured HK-2 cells. YY1 was the potential target of Ju A against DKD-related mitochondrial dysfunction, and the down-regulation of YY1 induced by Ju A increased PGC-1α promoter activity, leading to the restored mitochondrial function of HG-treated HK-2 cells. Renal tubule specific overexpression of YY1 intercepted the renal protective effect of Ju A on diabetic mice via blocking PGC-1α-mediated restoration of mitochondrial function of RTECs. The in-depth mechanism research revealed that the protective effect of Ju A towards DKD-associated renal tubular injury was linked to the restored mitochondrial function through YY1/PGC-1α signaling, resulting in the inhibited apoptosis of RTECs in diabetic condition via inactivating CytC-mediated Caspase9/Caspase3 signaling.

CONCLUSION

Ju A through the inhibition of mitochondria-dependent apoptosis alleviated DKD-associated renal tubular injury via YY1/PGC-1α signaling.

α-Lipoic Acid Ameliorates Arsenic-Induced Lipid Disorders by Promoting Peroxisomal β-Oxidation and Reducing Lipophagy in Chicken Hepatocyte

Liver disease poses a significant threat to global public health, with arsenic (As) recognized as a major environmental toxin contributing to liver injury. However, the specific mechanisms and the protective effects of α-lipoic acid (LA) remain unclear. Therefore, this study employs network toxicology and network pharmacology to comprehensively analyze the hepatotoxic mechanism of As and the hepatoprotective mechanism of LA, and further verifies the mechanisms of peroxisomal β-oxidation and lipophagy in the process. The network analysis results show that As induces liver damage mainly through autophagy, apoptosis, lipid metabolism, and oxidative stress, whereas LA exerts its hepatoprotective properties mainly by regulating lipid metabolism. Further verifications find that As inhibits SIRT1 expression, activates the P53 and Notch pathways, damages mitochondria, inhibits peroxisomal β-oxidation, increases lipid accumulation, and enhances lipophagy in the liver, while LA intervention alleviates As-induced lipid accumulation and enhances lipophagy by targeting SIRT1, ameliorating mitochondrial damage, enhancing peroxisomal β-oxidation, thereby alleviating As-induced liver damage. This study further clarifies the mechanism of As hepatotoxicity and provides a theoretical basis for LA as a potential hepatoprotective agent.

Discussion on the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation technology

To explore the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation. The active ingredients and potential targets were screened by the Systematic Pharmacological Analysis Platform of Traditional Chinese Medicine (TCMSP). Hypertension-related targets were obtained from OMIM and GeneCards databases. Common targets between drug and hypertension were screened in the Venny platform. A protein-protein interaction (PPI) network was constructed in the STRING database using intersection targets. Key targets in PPI network were analyzed by Cytoscape. R language program was used for Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, the binding abilities of the main active ingredients to critical targets were verified by molecular simulation. Naringenin, quercetin, kaempferol, and β-sitosterol in Lingguizhugan Decoction, and potential targets such as STAT3, AKT1, TNF, IL6, JUN, PTGS2, MMP9, CASP3, TP53, and MAPK3, were screened out. KEGG Enrichment analysis revealed that the common targets of Lingguizhugan Decoction and hypertension are mainly involved in the lipid and atherosclerosis signaling pathway, AGE-RAGE signaling pathway in diabetic complications, fluid shear stress and atherosclerosis, and IL17 signaling pathway. The molecular simulation results showed that naringenin-MAPK3, quercetin-MMP9, quercetin-PTGS2, and quercetin-TP53 were the top four in the docking scores. Naringenin-MAPK3 and quercetin-MMP9 were stable, with binding free energies of -27.97 ± 1.41 kcal/mol and -21.15 ± 3.17 kcal/mol, respectively. The possible mechanism of Lingguizhugan Decoction in treating hypertension is characterized of multi-component, multi-target, and multi-pathway.Communicated by Ramaswamy H. Sarma.

The Potential Mechanism of Soy Isoflavones in Treating Osteoporosis: Focusing on Bone Metabolism and Oxidative Stress

Osteoporosis is divided into primary and secondary types. Primary osteoporosis may result from estrogen deficiency in postmenopausal women, imbalanced bone remodeling in the elderly, or imbalanced adolescent-type bone development. Secondary osteoporosis can be caused by factors like long-term glucocorticoid treatment, chronic kidney disease (CKD), estrogen deprivation, oxidative stress, diabetes, and obesity. This review focuses on the therapeutic potential of soy isoflavones for osteoporosis. At the cellular level, soy isoflavones, as natural plant extracts and phytoestrogens, are crucial for osteoblastogenesis and differentiation, osteoclastogenesis, osteoclast mineralization, and bone marrow mesenchymal stromal cell differentiation. They also maintain calcium homeostasis by regulating extracellular calcium and vitamin D levels. In terms of oxidative stress, soy isoflavones mitigate it in the endoplasmic reticulum and mitochondria, thus regulating cellular senescence, autophagy, and bone remodeling processes. Moreover, soy isoflavones can relieve symptoms related to CKD and inhibit glucocorticoid secretion, which directly or indirectly benefits the treatment of osteoporosis. Overall, soy isoflavones have the potential to treat osteoporosis by enhancing bone health, regulating metabolism, and alleviating oxidative stress. Future research should explore the potential of soy isoflavones as phytoestrogens for treating osteoporosis. This exploration should focus on clarifying the safety, identifying potential side effects, determining the optimal dosage regimen, and developing strategies to mitigate any adverse reactions. In addition, further large-scale, multicenter human clinical trials are necessary to accurately evaluate the actual therapeutic effect of soy isoflavones on osteoporosis.