基于网络药理、分子对接和分子动力学模拟探讨蛇床子治疗牙周炎伴骨质疏松的作用机制

doi:10.7518/hxkq.2025.2024275

华西口腔医学杂志 ›› 2025, Vol. 43 ›› Issue (2): 249-261.doi: 10.7518/hxkq.2025.2024275

基于网络药理、分子对接和分子动力学模拟探讨蛇床子治疗牙周炎伴骨质疏松的作用机制

冯苗苗(), 徐小苒, 李宁丽, 杨铭真, 翟远坤()

开封市牙周组织工程重点实验室，河南大学口腔医学院，开封 475001

收稿日期:2024-07-28 修回日期:2024-11-05 出版日期:2025-04-01 发布日期:2025-03-25
通讯作者: 翟远坤 E-mail:fmm1660445237@126.com;zhaiyuankun@ henu.edu.cn;zhaiyuankun@henu.edu.cn
作者简介:冯苗苗，住院医师，硕士，E-mail：fmm1660445237@126.com
基金资助:
河南省科技攻关项目(242102310376);河南省教育厅高等学校重点项目(21A320004);河南省开封市科技攻关项目(2203015);河南大学口腔医学院青年科研基金(HU-SSYS2024005);山西大学医学分子细胞生物学山西省重点实验室开放课题(MMCBOP-2023-03)

Mechanism of Cnidii Fructus in the treatment of periodontitis with osteoporosis based on network pharmacology, molecular docking, and molecular dynamics simulation

Feng Miaomiao(), Xu Xiaoran, Li Ningli, Yang Mingzhen, Zhai Yuankun()

Kaifeng Key Laboratory of Periodontal Tissue Engineering, School of Stomatology, Henan University, Kaifeng 475001, China

Received:2024-07-28 Revised:2024-11-05 Online:2025-04-01 Published:2025-03-25
Contact: Zhai Yuankun E-mail:fmm1660445237@126.com;zhaiyuankun@ henu.edu.cn;zhaiyuankun@henu.edu.cn
Supported by:
Project of Science and Technology Department of Henan Province(242102310376);Key Project of High Education Institutions of Henan Provincial Department of Education(21A320004);Project of Science and Technology Department of Kaifeng City, Henan Province(2203015);Youth Scientific Research Fund of School of Stomatology, Henan University(HUSSYS2024005);Open Project of the Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University(MMC-BOP-2023-03)

摘要/Abstract

摘要：

目的联合使用网络药理学、分子对接和分子动力学模拟技术探讨蛇床子治疗牙周炎伴骨质疏松的活性成分及潜在靶点，并探讨其可能的作用机制。方法通过TCMSP数据库、SwissTargetPrediction数据库并结合文献报道筛选蛇床子的主要化学成分及作用靶点；采用多种数据库预测牙周炎和骨质疏松的作用靶点；利用Venny 2.1获取蛇床子与牙周炎和骨质疏松的交集靶点；采用STRING数据库构建交集靶点的蛋白相互作用网络（PPI）图并使用Cytoscape 3.9.1软件构建活性成分-交集靶点网络，对其进行拓扑分析筛选关键靶点和核心活性成分；基于Metascape平台对交集靶点进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析；选取节度点（degree）值排名前5位的核心靶点和核心活性成分，使用Discovery Studio 2019软件对配体和受体进行分子对接，并将结果可视化；使用Gromacs2022.3进行分子动力学模拟，以评估核心活性成分和关键靶点之间相互作用的稳定性。结果筛选得到蛇床子的20个潜在活性成分，蛇床子治疗牙周炎伴骨质疏松的作用靶点116个；对116个交集靶点进行GO和KEGG通路富集分析发现，蛇床子可能通过磷脂酰肌醇3激酶-蛋白激酶、晚期糖基化终产物-糖基化终末产物受体等信号通路发挥治疗作用；分子对接结果发现核心活性成分与关键靶点能够较好地结合，分子动力学模拟进一步验证了香叶木素-AKT1复合体稳定性。结论本研究揭示蛇床子通过多成分、多靶点、多途径的特点治疗牙周炎伴骨质疏松的潜在分子药理机制，为后续药物开发研究及临床应用提供理论基础。

关键词: 蛇床子, 牙周炎, 骨质疏松, 网络药理学, 分子对接, 分子动力学模拟

Abstract:

Objective This study aimed to explore the active components, potential targets, and mechanism of Cnidii Fructus in the treatment of periodontitis with osteoprosis through network pharmacology, molecular docking, and molecular dynamics simulation technology. Methods The main chemical constituents and targets of Cnidii Fructus were screened using the TCMSP and SwissTargetPrediction databases, as well as literature reports. Targets of periodontitis and osteoporosis were predicted using different databases. The intersection targets of Cnidii Fructus, periodontitis, and osteoporosis were obtained using Venny 2.1. The protein-protein interaction network was formed on the STRING platform. Cytoscape 3.9.1 was used to construct the active component-intersection target interaction network, perform the topological analysis, and screen key targets and core active components. Furthermore, the Metascape database was used to perform gene ontology (GO) function and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis on the intersection targets. The top five key targets and core active components were selected as receptor proteins and ligand small molecules. Discovery Studio 2019 was used to dock ligands and receptors and visualize the docking results. Molecular dynamics simulation was conducted using Gromacs2022.3 to assess the stability of the interactions between the core active components and the main targets. Results A total of 20 potential active ingredients of Cnidii Fructus were screened, and 116 targets of Cnidii Fructus were obtained for treating periodontitis and osteoporosis. GO and KEGG analysis of the 116 targets showed that Cnidii Fructus may play a therapeutic role through the phosphoinositide 3-kinase-protein kinase B (PI3K-Akt) and advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathways. Molecular docking showed that the core constituents were well bound to the main targets. Molecular dynamics simulations confirmed the stability of the Diosmetin-AKT1 complex system. Conclusion The preliminary discovery of the potential molecular pharmacological mechanism of Cnidii Fructus extract in the targeted treatment of periodontitis with osteoporosis through a multi-component, multitarget, and multi-pathway approach can serve as a theoretical foundation for future drug-development research and clinical application.

Key words: Cnidii Fructus, periodontitis, osteoporosis, network pharmacology, molecular docking, molecular dynamics simulation

中图分类号:

R781.4

冯苗苗, 徐小苒, 李宁丽, 杨铭真, 翟远坤. 基于网络药理、分子对接和分子动力学模拟探讨蛇床子治疗牙周炎伴骨质疏松的作用机制[J]. 华西口腔医学杂志, 2025, 43(2): 249-261.

Feng Miaomiao, Xu Xiaoran, Li Ningli, Yang Mingzhen, Zhai Yuankun. Mechanism of Cnidii Fructus in the treatment of periodontitis with osteoporosis based on network pharmacology, molecular docking, and molecular dynamics simulation[J]. West China Journal of Stomatology, 2025, 43(2): 249-261.

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编号	Mol ID	活性成分	OB/%	DL
1	MOL001510	24-epicampesterol	37.58	0.71
2	MOL001771	poriferast-5-en-3beta-ol	36.91	0.75
3	MOL001941	Ammidin	34.55	0.22
4	MOL002881	Diosmetin	31.14	0.27
5	MOL002883	Ethyl oleate （NF）	32.40	0.19
6	MOL000358	beta-sitosterol	36.91	0.75
7	MOL003584	Xanthoxylin N	35.51	0.21
8	MOL003588	Prangenidin	36.31	0.22
9	MOL003591	ar-curcumene	52.34	0.65
10	MOL003600	cnidimol B	68.66	0.26
11	MOL003604	cnidimol F	54.43	0.28
12	MOL003605	（E）-2,3-bis （2-keto-7-methoxy-chromen-8-yl） acrolein	56.38	0.71
13	MOL003606	cniforin A	55.89	0.47
14	MOL003607	cniforin B	36.70	0.60
15	MOL003608	O-Acetylcolumbianetin	60.04	0.26
16	MOL003617	isogosferol	30.07	0.25
17	MOL003624	O-Isovalerylcolum bianetin	64.03	0.36
18	MOL003626	Ostruthin	30.65	0.23
19	MOL000449	Stigmasterol	43.83	0.76
20	MOL000614	osthol	38.75	0.13

靶点	PDB ID	-CIE
靶点	PDB ID	美花椒内酯	蛇床子素	香叶木素	(E)-2,3-bis (2-keto-7-methoxy-chromen-8-yl) acrolein	O-乙酰二氢欧山芹酯
BCL2	4lxd	22.60	26.47	26.39	NA	31.16
CASP3	1rhm	27.27	26.32	34.22	43.43	31.47
JUN	4y46	30.18	33.07	34.59	42.93	35.47
AKT1	4ejn	31.79	38.05	44.33	56.19	40.55
PPARG	6t1s	32.02	34.55	40.70	47.64	36.71

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基于网络药理、分子对接和分子动力学模拟探讨蛇床子治疗牙周炎伴骨质疏松的作用机制

Mechanism of Cnidii Fructus in the treatment of periodontitis with osteoporosis based on network pharmacology, molecular docking, and molecular dynamics simulation

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