CHEN Jian, CHEN Qilong. Current situation and thinking of network pharmacology in the research of traditional Chinese medicine. [J]. Academic Journal of Shanghai University of Traditional Chinese Medicine 35(5):1-6,13(2021)
DOI:
CHEN Jian, CHEN Qilong. Current situation and thinking of network pharmacology in the research of traditional Chinese medicine. [J]. Academic Journal of Shanghai University of Traditional Chinese Medicine 35(5):1-6,13(2021) DOI: 10.16306/j.1008-861x.2021.05.001.
Current situation and thinking of network pharmacology in the research of traditional Chinese medicine
Network pharmacology has become a popular tool for the research on pharmacological basis and action mechanism of traditional Chinese medicine(TCM) .It is widely used in the screening of active components of Chinese medicines, repositioning of drugs, exploration of the mechanism of compatibility of Chinese medicines, and explanation of the action mechanism of multi-components, multi-targets and multi-pathways of Chinese medicines.The development stages of network pharmacology are reviewed, the databases related to network pharmacology at the present stage, such as TCM database, disease database and functional annotation database, are sorted out, and the application of network pharmacology in the research of TCM modernization is briefly summarized.It also points out the problems and challenges of network pharmacology research, and then looks forward to the development direction of TCM network pharmacology research.The purpose of this paper is to provide guidance for standardized and rational application of network pharmacology in TCM research, and provide ideas for leading the development of TCM original researches and the research and development of new Chinese medicines.
关键词
网络药理学中医药数据库
Keywords
network pharmacologytraditional Chinese medicinedatabase
references
WATTS D J,STROGATZ S H. Collective dynamics of “small-world” networks[J]. Nature,1998,393(6684): 440-442.
BARABÁSI A L,ALBERT R. Emergence of Scaling in Random Networks[J]. Science,1999,286(5439): 509-512.
BARABÁSI A L,OLTVAI Z N. Network biology: understanding the cell’s functional organization[J]. Nat Rev Genet,2004,5(2): 101-113.
HOPKINS A L. Network pharmacology[J]. Nat Biotechnol,2007,25(10): 1110-1111.
LI B Q,MA C F,ZHAO X Y,et al. YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery [J]. Comput Struct Biotechnol J,2018,16: 600-610.
HUANG L,XIE D L,YU Y R,et al. TCMID 2.0: a comprehensive resource for TCM [J]. Nucleic Acids Res,2018,46(D1): D1117-D1120.
RU J L,LI P,WANG J,et al. TCMSP: a database of systems pharmacology for drug discovery from herbal medicines [J]. J Cheminform,2014,6: 13.
XU H Y,ZHANG Y Q,LIU Z M,et al. ETCM: an encyclopaedia of traditional Chinese medicine[J]. Nucleic Acids Res,2019,47(D1): D976-D982.
WU Y,ZHANG F L,YANG K,et al. SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping[J]. Nucleic Acids Res,2019,47(D1): D1110-D1117.
LIU Z Y,GUO F F,WANG Y,et al. BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine[J]. Sci Rep,2016,6: 21146.
PIÑERO J,RAMÍREZ-ANGUITA J M,SAÜCH-PITARCH J,et al. The DisGeNET knowledge platform for disease genomics: 2019 update[J]. Nucleic Acids Res,2020,48(D1): D845-D855.
STELZER G,ROSEN N,PLASCHKES I,et al. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses [J]. Curr Protoc Bioinformatics,2016,54: 1.30.1-1.30.33.
WANG Y X,ZHANG S,LI F C,et al. Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics [J]. Nucleic Acids Res,2020,48(D1): D1031-D1041.
WISHART D S,FEUNANG Y D,GUO A C,et al. DrugBank 5.0: a major update to the DrugBank database for 2018[J]. Nucleic Acids Res,2018,46(D1): D1074-D1082.
AMBERGER J S,BOCCHINI C A,SCOTT A F,et al. OMIM.org: leveraging knowledge across phenotype-gene relationships[J]. Nucleic Acids Res,2019,47(D1): D1038-D1043.
ZHOU Y Y,ZHOU B,PACHE L,et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets [J]. Nat Commun,2019,10(1): 1523.
HUANG D W,SHERMAN B T,LEMPICKI R A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources[J]. Nat Protoc,2009,4(1): 44-57.
SZKLARCZYK D,GABLE A L,LYON D,et al. STRING v11: protein-protein association networks with increased coverage,supporting functional discovery in genome-wide experimental datasets[J]. Nucleic Acids Res,2019,47(D1): D607-D613.
WARDE-FARLEY D,DONALDSON S L,COMES O,et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function[J]. Nucleic Acids Res,2010,38(Web Server issue): W214-W220.
LIU F C,LI L,CHEN J,et al. A Network Pharmacology to Explore the Mechanism of Calculus Bovis in the Treatment of Ischemic Stroke[J]. Biomed Res Int,2021,2021: 6611018.
SUN W J,CHEN Y F,LI H C,et al. Material basis and molecular mechanisms of Dachengqi decoction in the treatment of acute pancreatitis based on network pharmacology [J]. Biomed Pharmacother,2020,121: 109656.
CHEN J,LIANG Z Q,HU C,et al. Protection against peripheral artery disease injury by Ruan Jian Qing Mai formula via metabolic programming[J]. Biotechnol Appl Biochem,2021,68(2): 366-380.
CHEN J,WANG Y K,GAO Y,et al. Protection against COVID-19 injury by qingfei paidu decoction via anti-viral,anti-inflammatory activity and metabolic programming [J]. Biomed Pharmacother,2020,129: 110281.
LUO F,GU J Y,ZHANG X Z,et al. Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease [J]. Sci Rep,2015,5: 10064.
KEISER M J,ROTH B L,ARMBRUSTER B N,et al. Relating protein pharmacology by ligand chemistry [J]. Nat Biotechnol,2007,25(2): 197-206.
NICKEL J,GOHLKE B O,EREHMAN J,et al. SuperPred: update on drug classification and target prediction[J]. Nucleic Acids Res,2014,42(Web Server issue): W26-W31.
LIU X F,OUYANG S S,YU B,et al. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach[J]. Nucleic Acids Res,2010,38(Web Server issue): W609-W614.
XU J,CHEN H B,LI S L. Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota[J]. Med Res Rev,2017,37(5): 1140-1185.
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