Integration of metabolomics and network pharmacology to reveal the protective mechanism underlying Wogonoside in acute myocardial ischemia rats

Molecular mechanism of rapamycin-induced autophagy activation to attenuate smoking-induced COPD

Chronic obstructive pulmonary disease (COPD) is one of the severe lung and respiratory airway disorders, with high prevalence rate in China. In this paper, we employed network pharmacology predictions to identify autophagy as a signaling pathway associated with COPD. To explore the protective effect of autophagy against COPD and its specific mechanism, we established a mouse model of COPD and administered 3-methyladenine (3-MA) and rapamycin (RAPA) to intervene in autophagy. The lung function of the mice was assessed using an animal pulmonary function analysis system, and lung tissue structure was evaluated through hematoxylin and eosin (HE) staining. The TUNEL staining method was employed to determine the level of apoptosis in lung tissue. Western blot analysis was conducted to measure the expression of autophagy and apoptosis-related proteins, while RT-qPCR was used to assess the expression of apoptosis-related mRNA. The results showed that RAPA effectively improved lung function, attenuated pathological lung injury and increased autophagy level in COPD mice. Apoptosis analysis showed that the apoptosis rate was elevated in COPD and 3- MA mice, whereas it was significantly reduced in RAPA mice. Our findings suggest that stimulation of autophagy may be a potential therapy for the future treatment of COPD.

Integrated network pharmacology and metabolomics analysis to reveal the potential mechanism of Ershen Wan in ameliorating ulcerative colitis

ETHNOPHARMACOLOGICAL RELEVANCE

Ershen Wan (ESW), a classic traditional Chinese medicine (TCM) prescription composed of Psoralea corylifolia Linn. and Myristica fragrans Houtt., has been applied to treat gastrointestinal disorders in clinical practices for thousands of years. However, its potential molecular mechanism in alleviating ulcerative colitis (UC) remains to be elusive.

AIM OF THE STUDY

The purpose of the study is to explore the underlying mechanism of ESW in treating UC.

MATERIALS AND METHODS

The protective effect of ESW on dextran sodium sulfate (DSS)-induced UC mice was assessed by body weight, disease activity index (DAI), colon length, colon tissue pathology, and colonic inflammatory factors. Furthermore, network pharmacology was applied to dissect the possible targets and biological pathways regulated by ESW. The plasma and fecal metabolomics were comprehensively analyzed by UPLC-Q-TOF/MS. Subsequently, an efficient and feasible approach integrating network pharmacology, metabolomics, and molecular docking was used to explore the key targets obtained from the metabolite-reaction-enzyme-gene network. And the effect of ESW on the MAPK signaling mediated intestinal epithelial cell apoptosis was further investigated by in vitro and in vivo experiments.

RESULTS

ESW could notably alleviate colon injury and inflammation of UC mice. Network pharmacology suggested that the bioactive components of ESW could mainly modulate signaling pathways associated with inflammation and metabolism. Consistently, plasma and fecal metabolomics further indicated that ESW could regulate the metabolic pathways of arachidonic acid, linoleic acid, sphingolipid, tryptophan, and glycerophospholipid. And the combined analysis of network pharmacology and metabolomics revealed that 14 pivotal targets were modulated by ESW, including PTGS1, PTGS2, CYP1A1, FADS1, CBR1, ALOX5, EPHX1, EPHX2, HPGD, PLA2G1B, PLA2G7, MGLL, ACHE, and SPHK1. Additionally, molecular docking suggested that bioactive components of ESW could bind well to these potential targets. And in vitro and in vivo experiments further verified that ESW could markedly ameliorate pathological symptoms of UC mice through inhibiting MAPK signaling mediated colonic epithelial cell apoptosis.

CONCLUSION

Collectively, these findings indicated that ESW could effectively alleviate the pathological symptoms of UC mice, mainly involving in the modulation of lipid and amino acid metabolism pathways, and the suppression of MAPK signaling-mediated apoptosis. In this study, the potential mechanism of ESW for the treatment of UC was first clarified, which provided a solid scientific foundation for its clinical application. Notably, the proposed strategy facilitated a comprehensive prediction and validation of the efficacy and molecular mechanism of TCMs, and also provided a novel approach for revealing the intricate biological pathogenesis of diseases.

Decoding gelsenicine-induced neurotoxicity in mice via metabolomics and network toxicology

BACKGROUND

Gelsenicine, the most toxic constituent of Gelsemium elegans Benth., is known for its diverse pharmacological activities alongside potent neurotoxicity, frequently leading to poisoning incidents following mistaken ingestion. However, its molecular mechanisms remain largely unexplored.

PURPOSE

This study aimed to elucidate the key mechanistic network underlying gelsenicine-induced neurotoxicity by employing a comprehensive strategy that integrated metabolomics, network toxicology, molecular docking, and experimental validation.

METHODS

Acute oral toxicity tests were conducted in C57BL/6J mice to assess toxic symptoms, determine the median lethal dose (LD50), and evaluate histopathological changes. Untargeted metabolomics was performed to identify differential metabolites and associated pathways in serum, hippocampus (HIP), and medulla oblongata (MO). Integration of network toxicology pinpointed core targets and pathways, which were further validated through molecular docking and RT-qPCR. A core "compound-target-metabolite-pathway" network involved in gelsenicine-induced neurotoxicity was established.

RESULTS

Gelsenicine exhibited an oral LD50 of approximately 1.82 mg/kg and induced neurotoxic damage in the HIP and MO. Two untargeted metabolomic approaches detected a broad range of metabolites, revealing that gelsenicine markedly altered the metabolic profiles of serum, HIP, and MO. Network toxicology analysis identified 187 key targets associated with gelsenicine neurotoxicity. Integrated analyses with the predicted targets of differential metabolites indicated that gelsenicine primarily interferes with the energy metabolism network centered on the malate-aspartate shuttle (MAS), affecting pathways such as carbon metabolism, amino acid metabolism, TCA cycle, and PPAR signaling pathway. Malate, glutamate, and aspartate were identified as core metabolites and potential biomarkers of gelsenicine poisoning. RT-qPCR validation revealed that gelsenicine interfered with the expression of core targets, including GLUD1, MDH, GOT and ME, all of which exhibited good binding energy with gelsenicine.

CONCLUSION

This study unveiled a novel mechanistic insight into gelsenicine-induced neurotoxicity, demonstrating its capacity to perturb multiple energy metabolism pathways associated with MAS. These findings could enhance the theoretical understanding of gelsenicine's neurotoxic effects and highlight potential applications in clinical diagnosis and forensic identification.

Multimodal Metabolomics Analysis Reveals That Classic Decoction Mitigates Myocardial Ischemia-Induced Damage by Modulating Energy and Branched-Chain Amino Acid Metabolism

Gualou-Xiebai-Banxia (GXB) decoction shows potential for treating myocardial ischemia (MI), although its underlying mechanism is not fully understood. In this study, a multimodal metabolomics approach, combining gas chromatography-mass spectrometry (GC-MS) and 1H-NMR, was employed to investigate the cardioprotective effects of GXB in a rat model of myocardial ischemia induced by ligation. ELISA assays and HE staining demonstrated that GXB effectively reduced myocardial injury, oxidative stress markers, and myocardial fibrosis. Orthogonal partial least-squares discriminant analysis identified 62 biomarkers, 20 of which were confirmed using standard compounds. The GC-MS method showed excellent linearity across a wide concentration range (0.004-29.7 μg/mL, R2 > 0.9995), with intra- and inter-day precision RSD values below 4.72% and 4.96%, respectively. Method recoveries ranged from 95.40% to 104.83%, with RSD values under 4.84%. Pathway enrichment analysis revealed that GXB decoction alleviates myocardial ischemia-induced damage primarily by modulating energy metabolism and branched-chain amino acid metabolism. These findings provide valuable support for the clinical application of GXB decoction in treating myocardial ischemia.

Mechanisms of wogonoside in the treatment of atherosclerosis based on network pharmacology, molecular docking, and experimental validation

BACKGROUND

Atherosclerosis serves as the fundamental pathology for a variety of cardiovascular disorders, with its pathogenesis being closely tied to the complex interplay among lipid metabolism, oxidative stress, and inflammation. Wogonoside is a natural flavonoid extracted from Scutellaria baicalensis with a variety of biological activities, including anti-inflammatory, hypolipidemic, and cardiac function improvement properties. Despite these known effects, the specific role of wogonoside in the context of atherosclerosis remains to be elucidated.

PURPOSE

To validate the efficacy of wogonoside in the treatment of atherosclerosis and to investigate its possible therapeutic mechanisms.

METHODS

Network pharmacology was used to obtain the core targets and signaling pathways that may be efficacious in the treatment of atherosclerosis with wogonoside, which were validated using molecular docking and molecular dynamics simulations. To further validate the core targets in the signaling pathway, we performed in vivo experiments using apolipoprotein E (ApoE)-/- mice. This included pathological morphology and lipid deposition analysis of mouse aorta, serum lipid level analysis, Elisa analysis, oxidative stress analysis, reactive oxygen species (ROS) fluorescence assay, immunohistochemical analysis and protein blot analysis.

RESULTS

Predictions were obtained that wogonoside treatment of atherosclerosis has 31 core targets, which are mainly focused on pathways such as Toll-like receptor (TLR) signaling pathway and NF-kappa B (NF-κB ) signaling pathway. Molecular docking and molecular dynamics simulations showed that wogonoside has good binding properties to the core targets. In vivo experimental results showed that wogonoside significantly inhibited aortic inflammatory response and lipid deposition, significantly reduced the release levels of total cholesterol (TC), triglycerides (TG), low-density-lipoprotein cholesterol (LDL-C), oxidized low density (ox-LDL) and free fatty acid (FFA), and significantly inhibited the release of inflammatory factors TNF-α, IL-1β, IL-6 and oxidative stress in ApoE-/- mice. Further molecular mechanism studies showed that wogonoside significantly inhibited the activation of TLR4/NF-κB signaling pathway in ApoE-/- mice.

CONCLUSION

Wogonoside may be an effective drug monomer for the treatment of atherosclerosis, and its mechanism of action is closely related to the inhibition of the activation of the TLR4/NF-κB signaling pathway.

Cardiovascular protective effects of natural flavonoids on intestinal barrier injury

Natural flavonoids may be utilized as an important therapy for cardiovascular diseases (CVDs) caused by intestinal barrier damage. More research is being conducted on the protective properties of natural flavonoids against intestinal barrier injury, although the underlying processes remain unknown. Thus, the purpose of this article is to present current research on natural flavonoids to reduce the incidence of CVDs by protecting intestinal barrier injury, with a particular emphasis on intestinal epithelial barrier integrity (inhibiting oxidative stress, regulating inflammatory cytokine expression, and increasing tight junction protein expression). Furthermore, the mechanisms driving intestinal barrier injury development are briefly explored, as well as natural flavonoids having CVD-protective actions on the intestinal barrier. In addition, natural flavonoids with myocardial protective effects were docked with ZO-1 targets to find natural products with higher activity. These natural flavonoids can improve intestinal mechanical barrier function through anti-oxidant or anti-inflammatory mechanism, and then prevent the occurrence and development of CVDs.

Study on the protective mechanism of Xuemaitong Capsule against acute myocardial ischemia rat based on network pharmacology and metabolomics

BACKGROUND

Xuemaitong Capsule (XMT) is a widely recognized traditional Miao medicine extensively utilized in Chinese clinical settings. Previous studies have demonstrated XMT protective effects against acute myocardial ischemia (AMI). However, the mechanism by which XMT provides protection to AMI rats is yet to be fully understood.

AIM OF THE STUDY

The purpose of this study was to investigate the protective mechanism of XMT on AMI rats through network pharmacology, traditional pharmacodynamics and metabolomics.

MATERIAL AND METHODS

The components and potential targets of XMT were identified through the application of traditional Chinese medicine system pharmacology and traditional Chinese medicine molecular mechanism bioinformatics analysis tools. We constructed herb-composition-target networks and analyzed protein-protein interaction (PPI) networks. The potential mechanism was explored by pathway enrichment analysis. Subsequently, the AMI model was constructed by ligation of the anterior descending branch of the left coronary artery, and XMT protective effects on AMI rats were evaluated by analyzing the myocardial enzyme profiles, electrocardiograms(ECG), Triphenyltetrazolium chloride(TTC) staining, and Hematoxylin-Eosin (HE) staining in AMI rats. Metabolomics based on UHPLC-Q-Exactive Orbitrap MS was used to observe the protective effect of XMT on the serum metabolic profile of AMI, and multivariate statistical analysis further revealed the differential patterns of metabolites after XMT treatment. Finally, integrated pathway analysis was carried out to reveal the biological metabolic mechanism.

RESULTS

A total of 392 active components of XMT acted with 624 targets for treating AMI. Pathway enrichment analysis revealed that XMT could treat AMI through TNF, MAPK and PI3K-Akt signaling pathways. Further, XMT could effectively prevent ST-segment elevation in the ECG, reduce the size of myocardial infarction, decrease cardiac weight index and cardiac enzyme levels, and mitigate histological damage in the hearts of AMI rats. In addition, XMT callback 117 metabolites and four metabolic pathways, including taurine and hypotaurine metabolism, phenylalanine metabolism, pyrimidine metabolism and retinol metabolism. Through integrating network pharmacology and metabolomics, we explored the biological mechanism by which XMT treats AMI. It was speculated that the mechanism of XMT is to regulate TNF signaling, PI3K-Akt pathway and MAPK signaling pathway, and participate in cell apoptosis, oxidative stress, immune and inflammatory reaction and other biological processes.

CONCLUSION

XMT plays a protective role in AMI rats by regulating multiple metabolic biomarkers, multiple targets and pathways. Therefore, XMT may provide a potential strategy for the treatment of AMI.

Scutellaria baicalensis and its flavonoids in the treatment of digestive system tumors

Scutellaria baicalensis has been used for the treatment of digestive system disorders for thousands of years in China and other regions. Modern research have revealed its therapeutic efforts in digestive system tumors. Thus, to review the updated progress of S. baicalensis and its main flavonoids in the treatment of digestive system tumors in the past 10 years, this article summarized the therapeutic effect and molecular mechanisms of S. baicalensis and its 5 flavonoids on tumors in oral cavity, esophagus, stomach, colon, liver, pancreas by inhibiting tumor cell proliferation, inducing autophagy, stimulating immune response, and increasing drug sensitivity. In conclusion, S. baicalensis and its flavonoids could be applied to treat digestive system tumors with different type of methods.

Yam protein ameliorates cyclophosphamide-induced intestinal immunosuppression by regulating gut microbiota and its metabolites

Yam is a dual-purpose crop used in both medicine and food that is commonly used as a dietary supplement in food processing. Since yam proteins are often lost during the production of yam starch, elucidating the functionally active value of yam proteins is an important guideline for fully utilizing yam in industrial production processes. This study aimed to explore the potential protective effect of yam protein (YP) on cyclophosphamide (CTX)-induced immunosuppression in mice. The results showed that YP can reduce immune damage caused by CTX by reversing immunoglobulins (IgA, IgG and IgM), cytokines (TNF-α, IL-6, etc.) in the intestines of mice. Moreover, YPs were found to prevent CTX-induced microbiota dysbiosis by enhancing the levels of beneficial bacteria within the microbiome, such as Lactobacillus, and lowering those of Desulfovibrio_R and Helicobacter_A. Metabolomics analyses showed that YP significantly altered differential metabolites (tryptophan, etc.) and metabolic pathways (ABC transporter protein, etc.) associated with immune responses in the gut. Furthermore, important connections were noted between particular microbiomes and metabolites, shedding light on the immunoprotective effects of YPs by regulating gut flora and metabolism. These findings deepen our understanding of the functional properties of YPs and lay a solid foundation for the utilization of yam.

Exploring the anti-ischemic stroke potential of wogonoside: Insights from Nrf2/Sirt3 signaling pathway and UPLC-TripleTOF-MS/MS-based metabolomics

Ischemic stroke, accounting for 80 % of all strokes, is a major cause of morbidity and mortality worldwide. However, effective and safe pharmacotherapy options for ischemic injury are limited. This study investigated the therapeutic effects of wogonoside, a compound derived from Radix Scutellariae, on ischemia/reperfusion (I/R) injury. The results showed that wogonoside treatment had significant therapeutic effects in rats with middle cerebral artery occlusion. It effectively reduced mortality rates, neurological deficits, cerebral infarct size, and brain water content. In an in vitro model using PC12 cells, wogonoside activated the Nrf2/Sirt3 signaling pathway. This activation contributed to the attenuation of oxidative damage and inflammation. Metabolomics analysis revealed increased levels of γ-aminobutyric acid (GABA) and glutathione in response to wogonoside treatment, suggesting their potential as therapeutic biomarkers for ischemic stroke. Additionally, wogonoside restored perturbed energy metabolism, including the tricarboxylic acid cycle. Wogonoside has the potential to ameliorate cerebral ischemic injury by targeting GABA-related amino acid metabolism, energy metabolism, and glutathione metabolism, maintaining redox homeostasis, and attenuating oxidative stress. These findings provide valuable insights into the protective mechanisms of wogonoside in cerebral I/R injury and highlight the promising therapeutic approach of wogonoside in the treatment of ischemic stroke.

Danggui Jixueteng decoction for the treatment of myelosuppression after chemotherapy: A combined metabolomics and network pharmacology analysis

Objective

This study aimed to explore the mechanism of the Danggui Jixueteng decoction (DJD) in treating Myelosuppression after chemotherapy (MAC) through network pharmacology and metabolomics.

Methods

We obtained the chemical structures of DJD compounds from TCMSP and PubMed. SwissTargetPrediction, STITCH, CTD, GeneCards, and OMIM were utilized to acquire component targets and MAC-related targets. We identified the key compounds, core targets, main biological processes, and signaling pathways related to DJD by constructing and analyzing related networks. The main active compounds and key proteins of DJD in treating AA were confirmed by molecular docking. A MAC rat model was established through intraperitoneal injection of cyclophosphamide to confirm DJD's effect on the bone marrow hematopoietic system. Untargeted metabolomics analyzed serum metabolite differences between MAC rats and the control group, and before and after DJD treatment, to explore DJD's mechanism in treating MAC.

Results

Of the 93 active compounds identified under screening conditions, 275 compound targets and 3113 MAC-related targets were obtained, including 95 intersecting targets; AKT1, STAT3, CASP3, and JUN were key proteins in MAC treatment. The phosphatidylinositol-3-kinase/RAC-alpha serine/threonine-protein kinase (PI3K/AKT) signaling pathway may play a crucial role in MAC treatment with DJD. Molecular docking results showed good docking effects of key protein AKT1 with luteolin, β-sitosterol, kaempferol, and glycyrrhizal chalcone A. In vivo experiments indicated that, compared to the model group, in the DJD group, levels of WBCs, RBCs, HGB, and PLTs in peripheral blood cells, thymus index increased, spleen index decreased, serum IL-3, GM-CSF levels increased, and IL-6, TNF-α, and VEGF levels decreased (p < 0.01); the pathological morphology of femoral bone marrow improved. Eleven differential metabolites were identified as differential serum metabolites, mainly concentrated in phenylalanine, tyrosine, and tryptophan biosynthesis pathways, phenylalanine metabolism, and arachidonic acid metabolism.

Conclusion

This study revealed that DJD's therapeutic effects are due to multiple ingredients, targets, and pathways. DJD may activate the PI3K/AKT signaling pathway, promote hematopoietic-related cytokine production, regulate related metabolic pathways, and effectively alleviate cyclophosphamide-induced myelosuppression after chemotherapy in rats.