Unveiling the potential mechanisms of Amomi fructus against gastric ulcers via integrating network pharmacology and in vivo experiments

Metabolomics combined with network pharmacology reveals the regional and variety heterogeneity of grape metabolites and their potential antioxidant mechanisms

China is one of the world's three major grape-producing regions. However, limited research has focused on the differential metabolites of cross-regional and cross-varietal grapes, and the specific metabolites responsible for their pharmacological effects. Thus, this study comparatively analyzed the antioxidant activities and metabolite compositions of grapes from different regions and varieties to explore the potential antioxidant mechanisms of flavonoid metabolites. The results revealed that the production region primarily influenced the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) of grapes, whereas variety significantly affected the ferric ion reducing antioxidant power (FRAP). Both region and variety had highly significant effects on the total phenolic content (TPC) and total flavonoid content (TFC) of grapes (P < 0.001) and showed significant effects on the 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS+) and grape metabolites (P < 0.05). However, variety exerted a stronger influence on metabolite composition than region (P < 0.001). Flavonoid metabolites have emerged as key antioxidants, with compounds such as kaempferol, fisetin, and 6-hydroxyluteolin playing critical roles. These metabolites primarily exert their antioxidant effects through signaling pathways, notably the PI3K-Akt pathway. Among all samples, Xinjiang's 'Summer Black' grapes showed the best antioxidant capacity. These findings provide insights into the biochemical basis underlying the differences grapes in China, offering a theoretical foundation for further research on the pharmacological efficacy and antioxidant mechanisms of secondary metabolites in Chinese grapes.

Asymmetric total synthesis of amovillosumins A and B and their hypoglycemic and anti-inflammatory activities

Motivated by the significant bioactivities and therapeutic potential of 1,4-benzodioxan derivatives, we reported the asymmetric total synthesis of amovillosumins A (1) and B (2), two architecturally unique norlignans isolated from Amomum villosum. The target compounds were achieved in nine and seven steps, respectively, from commercially available materials, delivering exceptional overall yields (45-47 %) with excellent enantiopurity (91-95 % ee). The key synthesis strategies encompassed Williamson ether formation, stereocontrolled ketone reduction, and Ullmann coupling to establish the pivotal 1,4-dioxan scaffold. This synthetic approach unambiguously confirmed the absolute configurations of amovillosumins A and B while providing sufficient quantities for comprehensive biological evaluation. Biological studies demonstrated that (+)-7S,8S-1 significantly stimulated GLP-1 secretion by 344.4 % at 25 μM, obviously stronger than its enantiomer (-)-7R,8R-1 (149.5 %). All isomers displayed significant anti-inflammatory activity in LPS-stimulated Raw264.7 cells, and especially, (+)-R-2 and (-)-S-2 (IC50 = 20.2 and 17.8 μΜ) showed six-fold greater NO inhibition than indometacin (IC50 = 113.2 μM). Mechanistic study demonstrated that (-)-S-2 significantly suppressed the mRNA expression of both Inos and Ptgs2. Network pharmacological analysis further confirmed PTGS2 as the primary target mediating the anti-inflammatory effects of (-)-S-2. This study integrates synthetic chemistry with pharmacological evaluation, offering structural confirmation and therapeutic insights into amovillosumins A and B.

Advances in bioinformatic methods for the acceleration of the drug discovery from nature

BACKGROUND

Drug discovery from nature has a long, ethnopharmacologically-based background. Today, natural resources are undeniably vital reservoirs of active molecules or drug leads. Advances in (bio)informatics and computational biology emphasized the role of herbal medicines in the drug discovery pipeline.

PURPOSE

This review summarizes bioinformatic approaches applied in recent drug discovery from nature.

STUDY DESIGN

It examines advancements in molecular networking, pathway analysis, network pharmacology within a systems biology framework and AI for assessing the therapeutic potential of herbal preparations.

METHODS

A comprehensive literature search was conducted using Pubmed, SciFinder, and Google Database. Obtained data was analyzed and organized in subsections: AI, systems biology integrative approach, network pharmacology, pathway analysis, molecular networking, structure-based virtual screening.

RESULTS

Bioinformatic approaches is now essential for high-throughput data analysis in drug target identification, mechanism-based drug discovery, drug repurposing and side-effects prediction. Large datasets obtained from "omics" approaches require bioinformatic calculations to unveil interactions, and patterns in disease-relevant conditions. These tools enable databases annotations, pattern-matching, connections discovery, molecular relationship exploration, and data visualisation.

CONCLUSION

Despite the complexity of plant metabolites, bioinformatic approaches assist in characterization of herbal preparations and selection of bioactive molecule. It is perceived as powerful tool for uncovering multi-target effects and potential molecular mechanisms of compounds. By integrating multiple networks that connect gene-disease, drug-target and gene-drug-target, drug discovery from natural sources is experiencing a remarkable comeback.

Exploring the potential mechanisms of polysaccharides against gastric ulcer: Network pharmacology analysis and molecular docking validation

Gastric ulcer is a common peptic ulcer that affects human health and life quality seriously. As anti‐gastric ulcer drugs usually cause side‐effects, polysaccharides may be the potential alternatives because of better effectiveness and less toxicity. Although the anti‐gastric ulcer activities of polysaccharides have been widely reported, the mechanisms have not yet been well‐disclosed. In this study, network pharmacology analysis was performed to explore the potential mechanisms of polysaccharides against gastric ulcer, and the results were validated by molecular docking. Results indicated that β‐glucan, arabinogalactan, xylan, and arabinan were the key structures, and ABL1, AKT1, androgen receptor, epidermal growth factor receptor, v‐Ha‐ras Harvey rat sarcoma viral oncogene homolog, HSP90AA1, mitogen‐activated protein kinase 8 (MAPK8), MAPK14, NOS2, PIK3R1, RAC1, ras homolog gene family member A, and proto‐oncogene tyrosine‐protein kinase Src were the core targets for polysaccharides in treating gastric ulcer. Polysaccharides have influences on 1958 GO items and 199 KEGG pathways, and their anti‐gastric ulcer activities are related to MAPK, Ras, PI3K‐Akt, vascular endothelial growth factor, prolactin, FoxO and Rap1 signaling pathways, etc. Molecular docking validation showed that the results of network pharmacology analysis were credible, and interactions between polysaccharide structures and core targets were observed. This study contributes to understanding the mechanisms of polysaccharides in treating gastric ulcer and provides references for future activity screening and mechanism research in anti‐gastric ulcer.

Untargeted serum and gastric metabolomics and network pharmacology analysis reveal the superior efficacy of zingiberis rhizoma recens-/euodiae fructus-processed Coptidis Rhizoma on gastric ulcer rats

ETHNOPHARMACOLOGICAL RELEVANCE

Zingiberis rhizoma recens-/wine-/euodiae fructus-processed Coptidis Rhizoma (CR, zCR/wCR/eCR) are the commonly used processed products of CR in clinic. After being processed with different excipients, the efficacy of CR will change accordingly. I.e., wCR could resolve excessive heat of the upper energizer, zCR could eliminate gastric heat and harmonize the stomach, eCR could smooth the liver and harmonize the stomach. However, the underlying mechanisms were still unclear.

AIM OF THE STUDY

To further verify the differential efficacy of the three processed CR products and compare the mechanisms on gastric ulcer.

MATERIAL AND METHODS

First, a GU model, whose onset is closely related to the heat in stomach and the disharmony between liver and stomach, was established, and the therapeutic effects of zCR/wCR/eCR/CR were evaluated by pathologic observation and measurement of cytokine levels. Second, metabolomics analysis and network pharmacology were conducted to reveal the differential intervening mechanism of zCR/eCR on GU. Third, the predicted mechanisms from metabolomics analysis and network pharmacology were validated using western blotting, flow cytometry and immunofluorescence.

RESULTS

zCR/wCR/eCR/CR could alleviate the pathologic damage to varying degrees. In metabolomics research, fewer metabolic pathways were enriched in serum samples, and most of them were also present in the results of gastric tissue samples. The gastroprotective, anti-inflammatory, antioxidant, and anti-apoptotic effects of zCR/wCR/eCR/CR might be due to their interference on histidine, arachidonic acid, and glycerophospholipids metabolism. Quantitative results indicated that zCR/eCR had a better therapeutic effect than wCR/CR in treating GU. A comprehensive analysis of metabolomics and network pharmacology revealed that zCR and eCR exerted anti-GU effects via intervening in five core targets, including AKT, TNF, IL6, IL1B and PPARG. In the validation experiment, zCR/eCR could significantly reverse the abnormal expression of proteins related to apoptosis, inflammation, oxidative stress, gastric function, as well as the PI3K/AKT signaling pathways.

CONCLUSION

zCR and eCR could offer gastroprotective benefits by resisting inflammation and apoptosis, inhibiting gastric-acid secretion, as well as strengthening gastric mucosal defense and antioxidant capacity. Integrating network pharmacology and metabolomics analysis could reveal the acting mechanism of drugs and promote the development of medications to counteract GU.

Integrating chemical similarity and bioequivalence: an overall evaluation of the quality consistency of traditional decoction and dispensing granule decoction of Amomum villosum

OBJECTIVE

This study aims to investigate the quality consistency between traditional decoction (TD) of Amomum villosum and its dispensing granule decoction (DGD). Fifteen batches of TD and nine batches of dispensing granules (manufactured by A, B, and C) were prepared and evaluated for their consistency.

METHODS

Firstly, The chemical similarity of TD and DGD was examined using GC and HPLC, coupled with hierarchical cluster analysis (HCA), criteria importance though intercrieria correlation(CRITIC) weighting method, and principal component analysis (PCA). Secondly, the gastrointestinal motility experiments in mice, along with the CRITIC weighting method, were employed to assess the bioequivalence of TD and DGD of Amomum villosum. Finally, the entropy weight technique-gray relative analysis(GRA) method was used to compare the quality of Amomum villosum decoctions.

RESULTS

①The CRITIC weighting method indicated significantly higher scores for TD than DGD (p < 0.01). HCA and PCA results demonstrated a clear distinction between TD and DGD. ②Gastrointestinal motility test results revealed no significant difference between TD and DGD in other indicators (p > 0.05).③Gray relative analysis results showed that the relative correlation of TD was more significant than that of DGD.

CONCLUSION

The chemical composition of DGD and TD differed. The biological activity of DGD-A/B was consistent with that of TD, while the difference between DGD-C and TD was significant. A comprehensive evaluation showed that TD exhibited better quality than DGD. DGD manufacturers should optimize the preparation process to enhance product quality.

Integrated ultra-high-performance liquid chromatography coupled with quadrupole-orbitrap mass spectrometry-based components analysis and network pharmacology strategy of Gancao Xiexin Decoction in treating gastric ulcer

Gancao Xiexin Decoction (GCXXD) is a traditional Chinese decoction that is often used in treating gastric ulcers. However, the substance basis and mechanism of action remain unclear. In this study, in vivo and in vitro components of GCXXD were analyzed by ultra-high-performance liquid chromatography coupled with quadrupole-orbitrap mass spectrometry. The compound Discover platform was used to ultimately enable rapid identification of compounds. Acquire X intelligent data acquisition technology software was innovatively adopted. In the process of collecting drug-containing plasma, all components detected in blank plasma samples were excluded to eliminate the interference and influence of endogenous components in plasma, making the analysis results more accurate and reliable. At the same time, the possibility of selecting precursor parent ions with low concentration levels within the chromatographic peak can be increased, improving the coverage and integrality of the detection of components in vivo. Also, the targeted network pharmacology strategy combined with molecular docking was established to explore the mechanism of GCXXD in treating gastric ulcers. As a result, 113 components were identified, 41 of which could enter the bloodstream and exert therapeutic effects in vivo. The main effective components are glycyrrhizic acid, 6-gingerol, jatrorrhizine, wogonin, palmatine, and liquiritigenin, main targets in vivo were related to ALB, IL6, and VEGF, which play an important role in anti-inflammatory and promoting angiogenesis. In summary, this study adopted a comprehensive analysis strategy to reveal the pharmacodynamic material basis and mechanism of GCXXD against gastric ulcers, providing a scientific basis for its clinical application.