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Integrating systematic biological and proteomics strategies to explore the pharmacological mechanism of danshen yin modified on atherosclerosis.

ABSTRACT: This research utilized the systematic biological and proteomics strategies to explore the regulatory mechanism of Danshen Yin Modified (DSYM) on atherosclerosis (AS) biological network. The traditional Chinese medicine database and HPLC was used to find the active compounds of DSYM, Pharmmapper database was used to predict potential targets, and OMIM database and GeneCards database were used to collect AS targets. String database was utilized to obtain the other protein of proteomics proteins and the protein-protein interaction (PPI) data of DSYM targets, AS genes, proteomics proteins and other proteins. The Cytoscape 3.7.1 software was utilized to construct and analyse the network. The DAVID database is used to discover the biological processes and signalling pathways that these proteins aggregate. Finally, animal experiments and proteomics analysis were used to further verify the prediction results. The results showed that 140 active compounds, 405 DSYM targets and 590 AS genes were obtained, and 51 differentially expressed proteins were identified in the DSYM-treated ApoE-/- mouse AS model. A total of 4 major networks and a number of their derivative networks were constructed and analysed. The prediction results showed that DSYM can regulate AS-related biological processes and signalling pathways. Animal experiments have also shown that DSYM has a therapeutic effect on ApoE-/-mouse AS model (P < .05). Therefore, this study proposed a new method based on systems biology, proteomics, and experimental pharmacology, and analysed the pharmacological mechanism of DSYM. DSYM may achieve therapeutic effects by regulating AS-related signalling pathways and biological processes found in this research.

SUBMITTER: Yang K

PROVIDER: S-EPMC7753997 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Integrating systematic biological and proteomics strategies to explore the pharmacological mechanism of danshen yin modified on atherosclerosis.

Yang Kailin K Zeng Liuting L Ge Anqi A Pan Xiaoping X Bao Tingting T Long Zhiyong Z Tong Qiaozhen Q Yuan Mengxia M Zhu Xiaofei X Ge Jinwen J Huang Zhengde Z

Journal of cellular and molecular medicine 20201102 23

This research utilized the systematic biological and proteomics strategies to explore the regulatory mechanism of Danshen Yin Modified (DSYM) on atherosclerosis (AS) biological network. The traditional Chinese medicine database and HPLC was used to find the active compounds of DSYM, Pharmmapper database was used to predict potential targets, and OMIM database and GeneCards database were used to collect AS targets. String database was utilized to obtain the other protein of proteomics proteins an ...[more]

PMID: 33140562

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Project description:The shock of Coronavirus Disease 2019 (COVID-19) has disrupted food systems worldwide. Such disruption, affecting multiple systems interfaces in smallholder agriculture, is unprecedented and needs to be understood from multi-stakeholder perspectives. The multiple loops of causality in the pathways of impact renders the system outcomes unpredictable. Understanding the nature of such unpredictable pathways is critical to identify present and future systems intervention strategies. Our study aims to explore the multiple pathways of present and future impact created by the pandemic and "Amphan" cyclonic storm on smallholder agricultural systems. Also, we anticipate the behaviour of the systems elements under different realistic scenarios of intervention. We explored the severity and multi-faceted impacts of the pandemic on vulnerable smallholder agricultural production systems through in-depth interactions with key players at the micro-level. It provided contextual information, and revealed critical insights to understand the cascading effect of the pandemic and the cyclone on farm households. We employed thematic analysis of in-depth interviews with multiple stakeholders in Sundarbans areas in eastern India, to identify the present and future systems outcomes caused by the pandemic, and later compounded by "Amphan". The immediate adaptation strategies of the farmers were engaging family labors, exchanging labors with neighbouring farmers, borrowing money from relatives, accessing free food rations, replacing dead livestock, early harvesting, and reclamation of waterbodies. The thematic analysis identified several systems elements, such as harvesting, marketing, labor accessibility, among others, through which the impacts of the pandemic were expressed. Drawing on these outputs, we employed Mental Modeler, a Fuzzy-Logic Cognitive Mapping tool, to develop multi-stakeholder mental models for the smallholder agricultural systems of the region. Analysis of the mental models indicated the centrality of "Kharif" (monsoon) rice production, current farm income, and investment for the next crop cycle to determine the pathways and degree of the dual impact on farm households. Current household expenditure, livestock, and soil fertility were other central elements in the shared mental model. Scenario analysis with multiple stakeholders suggested enhanced market access and current household income, sustained investment in farming, rapid improvement in affected soil, irrigation water and livestock as the most effective strategies to enhance the resilience of farm families during and after the pandemic. This study may help in formulating short and long-term intervention strategies in the post-pandemic communities, and the methodological approach can be used elsewhere to understand perturbed socioecological systems to formulate anticipatory intervention strategies based on collective wisdom of stakeholders.

Project description:BackgroundThis study sought to explore the anti-inflammatory mechanism of Wuyao (radix linderae)-Danshen (salviae miltiorrhiza) in endometriosis (EMS) based on network pharmacology and molecular docking.MethodsThe active constituents of Wuyao-Danshen were collected and identified using the Traditional Chinese Medicine Systems Pharmacology Database, and used to predict and identify the protein targets. The EMS targets and anti-inflammatory targets were obtained from Genecards, Online Mendelian Inheritance in Man, and Drugbank. The Search Tool for the Retrieval of Interacting Genes/Proteins database was used to analyze the protein interactions (PPIs) and core targets, and a target PPI network was constructed by importing the software of Cytoscape. The Metascape database was used to conduct enrichment analyses of the Gene Ontology (GO) functions and the Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways for the key anti-inflammatory targets of EMS. Finally, Autodock Vina software was used to verify the results of the active ingredients and key anti-inflammatory targets.ResultsThere were 8 active components in Wuyao, 65 in Danshen, and 591 corresponding protein targets in Danshen, and 375 in Wuyao, including luteolin, quercetin, vancomyl alcohol, and salvianol. One thousand and six hundred eighty-nine disease targets, 1,216 anti-inflammatory targets, and 144 key anti-inflammatory targets were identified, including the (signal transduction and transcriptional activator 3) STAT3, phosphatidyl inositol-3 kinase regulates subunit 1 (PIK3R1) and mitogen-activated protein kinase 1 (MAPK1) protein kinase B. Three hundred and fifty-three biological processes (BPs), 21 cellular components, and 25 molecular functions (MFs) were enriched with GO functions, and 108 KEGG pathways were enriched and analyzed, including the MAPK and PI3K-Akt signaling pathways. Molecular docking confirmed that luteolin, coumarin, and quercetin could bind to the key target proteins (i.e., STAT3, PIK3R1, and MAPK1).ConclusionsBased on network pharmacology and molecular docking, Wuyao-Danshen was found to act on EMS through anti-inflammatory targets and related signaling pathways. Our findings provide a basis for further research.

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Integrating systematic biological and proteomics strategies to explore the pharmacological mechanism of danshen yin modified on atherosclerosis.

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Integrating systematic biological and proteomics strategies to explore the pharmacological mechanism of danshen yin modified on atherosclerosis.

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