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      Molecular mechanism of resveratrol promoting differentiation of preosteoblastic MC3T3-E1 cells based on network pharmacology and experimental validation

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          Abstract

          The purpose of this study was to investigate the mechanism by which resveratrol (Res) inhibits apoptosis and promotes proliferation and differentiation of pre-osteoblastic MC3T3-E1 cells, laying the groundwork for the treatment of osteoporosis (OP). The TCMSP database was used to find the gene targets for Res. The GeneCards database acquire the gene targets for OP. After discovering the potential target genes, GO, KEGG, and Reactome enrichment analysis were conducted. Verifying the major proteins involved in apoptosis can bind to Res using molecular docking. CCK8 measured the proliferative activity of mouse pre-osteoblasts in every group following Res intervention. Alkaline phosphatase staining (ALP) and alizarin red staining to measure the ability of osteogenic differentiation. RT-qPCR to determine the expression levels of Runx2 and OPG genes for osteogenic differentiation ability of cells. Western blot to measure the degree of apoptosis-related protein activity in each group following Res intervention. The biological processes investigated for GO of Res therapeutic OP involved in cytokine-mediated signaling pathway, negative regulation of apoptotic process, Aging, extrinsic apoptotic signaling pathway in absence of ligand, according to potential therapeutic target enrichment study. Apoptosis, FoxO signaling pathway, and TNF signaling pathway are the primary KEGG signaling pathways. Recactome pathways are primarily engaged in Programmed Cell Death, Apoptosis, Intrinsic Apoptotic Pathway, and Caspase activation via extrinsic apoptotic signaling pathways. This research established a new approach for Res treatment of OP by demonstrating how Res controls the apoptosis-related proteins TNF, IL6, and CASP3 to suppress osteoblast death and increase osteoclastogenesis.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12906-024-04396-3.

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

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          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            KEGG: kyoto encyclopedia of genes and genomes.

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            KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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              AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

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              We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. (c) 2009 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Miao Fang: 251401073@qq.com
                Zhenlong Wang: borbylong@swmu.edu.cn
                Journal
                Journal ID (nlm-ta): BMC Complement Med Ther
                Journal ID (iso-abbrev): BMC Complement Med Ther
                Title: BMC Complementary Medicine and Therapies
                Publisher: BioMed Central (London )
                ISSN (Electronic): 2662-7671
                Publication date (Electronic): 29 February 2024
                Publication date PMC-release: 29 February 2024
                Publication date Collection: 2024
                Volume: 24
                Electronic Location Identifier: 108
                Affiliations
                [1 ]Department of Spine Surgery, Chengdu Second People’s Hospital, ( https://ror.org/02q28q956) No.2, Huatai Road, Chenghua District, Chengdu, 610000 Sichuan China
                [2 ]Department of Spine Surgery, RuiKang Hospital affiliated to Guangxi University of Chinese Medicine, ( https://ror.org/024v0gx67) Nanning, 530011 Guangxi China
                [3 ]Department of orthopedics, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, ( https://ror.org/00g2rqs52) No.182, Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan China
                Article
                Publisher ID: 4396
                DOI: 10.1186/s12906-024-04396-3
                PMC ID: 10905894
                PubMed ID: 38424533
                SO-VID: c08a6750-a65b-4f95-844a-fbc38078999f
                Copyright © © The Author(s) 2024
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                Date received : 28 October 2023
                Date accepted : 10 February 2024
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © BioMed Central Ltd., part of Springer Nature 2024

                Keywords: integrative medicine,phytotherapy,resveratrol,apoptosis,osteogenesis,mc3t3-e1,osteoporosis
                Data availability:
                Keywords: integrative medicine, phytotherapy, resveratrol, apoptosis, osteogenesis, mc3t3-e1, osteoporosis

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