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阐明小青龙汤治疗慢性荨麻疹的机制:网络药理学、生物信息学分析、分子对接和分子动力学模拟的综合方法

Elucidating the Mechanism of Xiaoqinglong Decoction in Chronic Urticaria Treatment: An Integrated Approach of Network Pharmacology, Bioinformatics Analysis, Molecular Docking, and Molecular Dynamics Simulations.

作者信息

Zhu Zhengjin, Liu Lu, Li Meihong, Liang Na, Liu Suoyu, Sun Dan, Li Wenbin

机构信息

The First Clinical Medical College, Shaanxi University of Chinese Medicine, Qindu District, Xianyang, 712046, China.

Department of ICU, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China.

出版信息

Curr Comput Aided Drug Des. 2025 Jul 16. doi: 10.2174/0115734099391401250701045509.

Abstract

INTRODUCTION

Xiaoqinglong Decoction (XQLD) is a traditional Chinese medicinal formula commonly used to treat chronic urticaria (CU). However, its underlying therapeutic mechanisms remain incompletely characterized. This study employed an integrated approach combining network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulations to identify the active components, potential targets, and related signaling pathways involved in XQLD's therapeutic action against CU, thereby providing a mechanistic foundation for its clinical application.

METHODS

The active components of XQLD and their corresponding targets were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. CU-related targets were retrieved from the OMIM and GeneCards databases. Subsequently, core components and targets were determined via protein-protein interaction (PPI) network analysis and component-target-pathway network construction. Topological analyses were performed using Cytoscape software to prioritize core nodes within these networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database to identify enriched biological processes and signaling pathways. Molecular docking was performed to evaluate binding interactions between key components and core targets, while molecular dynamics (MD) simulations were employed to assess the stability of the component-target complexes with the lowest binding energy. Finally, CU-related targets of XQLD were validated using datasets from the Gene Expression Omnibus (GEO) database.

RESULTS

A total of 135 active components and 249 potential targets of XQLD were identified, alongside 1,711 CU-related targets. Core components, such as quercetin, kaempferol, beta-sitosterol, naringenin, stigmasterol, and luteolin, exhibited high degree values in the constructed networks. The core targets identified included AKT1, TNF, IL6, TP53, PTGS2, CASP3, BCL2, ESR1, PPARG, and MAPK3. GO and KEGG pathway enrichment analyses revealed the PI3K-Akt signaling pathway as a central regulatory mechanism. Molecular docking studies demonstrated strong binding affinities between active components and core targets, with the stigmasterol-AKT1 complex exhibiting the lowest binding energy (-11.4 kcal/mol) and high stability in MD simulations. Validation using GEO datasets identified 12 core genes shared between CU-related targets and XQLD-associated targets, including PTGS2 and IL6, which were also prioritized as core targets in the network pharmacology analyses.

DISCUSSION

This study comprehensively integrates multidisciplinary approaches to clarify the potential molecular mechanisms of XQLD in treating CU, highlighting its multitarget and multipathway synergistic effects. Molecular docking and dynamics simulations confirm the stable interaction between stigmasterol and the core target AKT1. Additionally, GEO dataset analysis verifies the pathogenic relevance of targets such as PTGS2 and IL6, significantly enhancing the credibility of our findings. These results provide a modern scientific basis for the traditional therapeutic effects of XQLD on CU and have important implications for developing multitarget treatments for this condition. However, this study mainly relies on database mining and computational simulations. Further in vitro and in vivo experimental validations are needed to confirm the predicted component-target-pathway interactions.

CONCLUSION

This study identifies the active components, potential targets, and pathways through which XQLD exerts therapeutic effects on CU. These findings provide a theoretical foundation for further mechanistic studies and support their clinical application in the treatment of CU.

摘要

引言

小青龙汤是常用于治疗慢性荨麻疹(CU)的中药方剂。然而,其潜在的治疗机制仍未完全明确。本研究采用网络药理学、生物信息学、分子对接和分子动力学模拟相结合的综合方法,以确定小青龙汤治疗慢性荨麻疹的活性成分、潜在靶点和相关信号通路,从而为其临床应用提供作用机制基础。

方法

利用中药系统药理学(TCMSP)数据库确定小青龙汤的活性成分及其相应靶点。从OMIM和GeneCards数据库中检索慢性荨麻疹相关靶点。随后,通过蛋白质-蛋白质相互作用(PPI)网络分析和成分-靶点-通路网络构建确定核心成分和靶点。使用Cytoscape软件进行拓扑分析,以对这些网络中的核心节点进行优先级排序。通过DAVID数据库进行基因本体(GO)和京都基因与基因组百科全书(KEGG)通路富集分析,以识别富集的生物学过程和信号通路。进行分子对接以评估关键成分与核心靶点之间的结合相互作用,同时采用分子动力学(MD)模拟评估结合能最低的成分-靶点复合物的稳定性。最后,使用基因表达综合数据库(GEO)的数据验证小青龙汤的慢性荨麻疹相关靶点。

结果

共确定了小青龙汤的135种活性成分和249个潜在靶点,以及1711个慢性荨麻疹相关靶点。槲皮素、山奈酚、β-谷甾醇、柚皮素、豆甾醇和木犀草素等核心成分在构建的网络中具有较高的度值。确定的核心靶点包括AKT1、TNF、IL6、TP53、PTGS2、CASP3、BCL2、ESR1、PPARG和MAPK3。GO和KEGG通路富集分析表明PI3K-Akt信号通路是核心调控机制。分子对接研究表明活性成分与核心靶点之间具有较强的结合亲和力,豆甾醇-AKT1复合物在分子动力学模拟中表现出最低的结合能(-11.4 kcal/mol)和高稳定性。使用GEO数据集进行验证,确定了慢性荨麻疹相关靶点和小青龙汤相关靶点之间共享的12个核心基因,包括PTGS2和IL6,它们在网络药理学分析中也被列为核心靶点。

讨论

本研究综合运用多学科方法阐明了小青龙汤治疗慢性荨麻疹的潜在分子机制,突出了其多靶点和多途径的协同作用。分子对接和动力学模拟证实了豆甾醇与核心靶点AKT1之间的稳定相互作用。此外,GEO数据集分析验证了PTGS2和IL6等靶点的致病相关性,显著提高了我们研究结果的可信度。这些结果为小青龙汤对慢性荨麻疹的传统治疗效果提供了现代科学依据,并对开发针对该病症的多靶点治疗具有重要意义。然而,本研究主要依赖于数据库挖掘和计算模拟。需要进一步的体外和体内实验验证来确认预测的成分-靶点-通路相互作用。

结论

本研究确定了小青龙汤对慢性荨麻疹发挥治疗作用的活性成分、潜在靶点和通路。这些发现为进一步的机制研究提供了理论基础,并支持其在慢性荨麻疹治疗中的临床应用。

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