CN107680692A - The network pharmacology analysis method and system of Chinese medicine and Chinese medicine preparation - Google Patents
The network pharmacology analysis method and system of Chinese medicine and Chinese medicine preparation Download PDFInfo
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- CN107680692A CN107680692A CN201710820809.2A CN201710820809A CN107680692A CN 107680692 A CN107680692 A CN 107680692A CN 201710820809 A CN201710820809 A CN 201710820809A CN 107680692 A CN107680692 A CN 107680692A
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- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/30—Prediction of properties of chemical compounds, compositions or mixtures
Abstract
The network pharmacology analysis method of a kind of Chinese medicine and Chinese medicine preparation, it comprises the following steps：Each source file information of S1, acquisition Chinese medicine and Chinese medicine preparation network pharmacology analysis；S2, the inner link relation according to each source file, " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica people albumen/genopathy " database is established, " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica people albumen/genopathy " database includes the toxic side effect of compound；S3, network built in Cytoscape softwares according to " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica people albumen/genopathy " path in " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica people albumen/genopathy " database of foundation.
Description
Technical field
The present invention relates to field of computer technology, method of testing and device on more particularly to a kind of charging pile complete machine line.
Background technology
Traditional Chinese medicine is that the relation of life, disease and medicine is held with overall, dynamic, dialectical viewpoint, and its characteristic is " dialectical
By controlling " and " organic conception ".Traditional Chinese medicine have accumulated rich experience after the clinical practice of 1,100.Chinese medicine and its preparation tool
There is the features such as multicomponent, multipath and Mutiple Targets act synergistically, with the characteristic and excellent of its own in terms of complex disease prevent and treat
Gesture.However, due to lacking the research method for being suitable for analyzing disease and the aspect complexity of Chinese medicine two, Chinese medicine study still face at present
Face some difficult points.For example, bioactive components and mechanism of action are indefinite, differentiation of tcm, herbal nature and prescription
The scientific basic of the traditional theories such as compatibility is unintelligible, lacks scientific and reasonable drug effect and safety assessment system etc..Therefore, establish
The research new strategy and new method of traditional Chinese medicine entirety characteristic can be reflected, turn into the task of top priority of TCM Modernization.
And in recent years, with the development that modern genetic group, proteomics, metabolism group etc. " group is learned " are theoretical, system
The introducing at biology visual angle and the application of bioinformatics, network pharmacology (Network pharmacology) concept meet the tendency of
And give birth to, it grows up on the basis of systems biology with computer technology high speed development, based on " disease --- base
On the basis of cause --- target spot --- medicine " interactive network, by network analysis, system synthetically observes medicine to disease net
The intervention and influence of network, the secret that multimolecular drug acts synergistically on human body is disclosed, this and traditional Chinese medicine go to examine from overall angle
Control the theory of disease, the multicomponent of Chinese medicine and its compound, multipath, the principle of Mutiple Targets synergy are reached the same goal by different routes.Chinese medicine system
The research strategy of agent is also switching to predictive research from descriptive research.One of important symbol is exactly from " biomolecule net
The structure of network " recognizes disease molecules mechanism and mechanism of drug action with function.It is considered as " drug research pattern of future generation "
Network pharmacology bring the major transformation of drug research, also new opportunity is brought for the research of Chinese medicine preparation, wherein maximum
Opportunity be to understand and handle Chinese medicine preparation chemical system and body biosystem with the thought of network and system
Complexity.Therefore, it is highly desirable to probe into Chinese medicine by establishing network pharmacology analysis system with the method for systems biology
And its preparation is to the interactively of human therapeutic target, so as to further disclose Chinese medicine and its preparation to the mechanism of action of disease and its
Issuable adverse reaction.
The content of the invention
In view of this, the present invention propose it is a kind of can predict Chinese medicine and Chinese medicine preparation to the Chinese medicine of the effect path of disease and
The network pharmacology analysis method and system of Chinese medicine preparation.
The network pharmacology analysis method of a kind of Chinese medicine and Chinese medicine preparation, it comprises the following steps：
Each source file information of S1, acquisition Chinese medicine and Chinese medicine preparation network pharmacology analysis；
S2, the inner link relation according to each source file, establish " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica ---
People's albumen/gene --- disease " database, " the Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene ---
Disease " database includes the toxic side effect of compound；
S3, " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " data according to foundation
" Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " path is in Cytoscape softwares in storehouse
Build network.
In the network pharmacology analysis method of Chinese medicine of the present invention and Chinese medicine preparation, the Chinese medicine and Chinese medicine preparation
Each source file information of network pharmacology analysis includes；
The chemical composition of Chinese medicine and Chinese medicine preparation, compound and people's protein-interacting file, compound side-effects information
Interaction relationship file, people's albumen text corresponding with gene relationship between file, toxicity of compound message file, people's albumen
Part, gene and disease association file.
In the network pharmacology analysis method of Chinese medicine of the present invention and Chinese medicine preparation,
Described Chinese medicine and the chemical composition of Chinese medicine preparation are from Chinese Traditional Chinese Medicine in Taiwan medicine data bank and traditional Chinese medical science integrated database
Middle acquisition；
Described compound obtains with people's protein-interacting file from STITCH databases；
Described compound side-effects information file obtains from SIDER databases；
Described toxicity of compound message file obtains from TOXNET databases；
Interaction relationship file obtains from STRING databases between described people's albumen；
Described people's albumen obtains with gene relationship respective file from omim database；
Described gene obtains with disease association file from omim database and GAD databases.
In the network pharmacology analysis method of Chinese medicine of the present invention and Chinese medicine preparation,
" Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " data in the step S2
Storehouse based on MySQL by being established.
In the network pharmacology analysis method of Chinese medicine of the present invention and Chinese medicine preparation,
When the compound is ginseng compound, small molecule ginsenoside Rg1 and tumor necrosis factor contained by ginseng compound
Sub- TNF has interaction, and TNF is the target spot of diabetes, Alzheimer's disease, hypertension and atherosclerosis；Equally, ginseng
Saponin(e Re and alzheimer target spot NOS3 interacts；Ginsenoside Rb1 interacts with diabetes target spot AKT1.
The present invention also provides the network pharmacology analysis system of a kind of Chinese medicine and Chinese medicine preparation, and it includes such as lower unit：
Source file information acquisition unit, each source file letter of the network pharmacology analysis for obtaining Chinese medicine and Chinese medicine preparation
Breath；
Database unit, for the inner link relation according to each source file, establish " Chinese medicine preparation chemistry into
Point/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " database, it is described " Chinese medicine preparation chemical composition/Chemistry for Chinese Traditional Medicine into
Point --- people's albumen/gene --- disease " database includes the toxic side effect of compound；
Network construction unit, for " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's egg according to foundation
In vain/gene --- disease " in database " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease "
Path builds network in Cytoscape softwares.
In the network pharmacology analysis system of Chinese medicine of the present invention and Chinese medicine preparation, the Chinese medicine and Chinese medicine preparation
Each source file information of network pharmacology analysis includes；
The chemical composition of Chinese medicine and Chinese medicine preparation, compound and people's protein-interacting file, compound side-effects information
Interaction relationship file, people's albumen text corresponding with gene relationship between file, toxicity of compound message file, people's albumen
Part, gene and disease association file.
In the network pharmacology analysis system of Chinese medicine of the present invention and Chinese medicine preparation,
Described Chinese medicine and the chemical composition of Chinese medicine preparation are from Chinese Traditional Chinese Medicine in Taiwan medicine data bank and traditional Chinese medical science integrated database
Middle acquisition；
Described compound obtains with people's protein-interacting file from STITCH databases；
Described compound side-effects information file obtains from SIDER databases；
Described toxicity of compound message file obtains from TOXNET databases；
Interaction relationship file obtains from STRING databases between described people's albumen；
Described people's albumen obtains with gene relationship respective file from omim database；
Described gene obtains with disease association file from omim database and GAD databases.
In the network pharmacology analysis system of Chinese medicine of the present invention and Chinese medicine preparation,
" Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease in the Database unit
Disease " database based on MySQL by being established.
In the network pharmacology analysis system of Chinese medicine of the present invention and Chinese medicine preparation,
When the compound is ginseng compound, small molecule ginsenoside Rg1 and tumor necrosis factor contained by ginseng compound
Sub- TNF has interaction, and TNF is the target spot of diabetes, Alzheimer's disease, hypertension and atherosclerosis；Equally, ginseng
Saponin(e Re and alzheimer target spot NOS3 interacts；Ginsenoside Rb1 interacts with diabetes target spot AKT1.
Implement the network pharmacology analysis method and system and prior art phase of Chinese medicine and Chinese medicine preparation provided by the invention
Than having the advantages that：Based on systems biology thinking, it is studied using network analysis technique, had following excellent
Point：(1) cycle is shorter；(2) data source used in this method has authoritative and generality in its art；(3)
The effect path of Chinese medicine and Chinese medicine preparation to disease can be predicted in theory.
Brief description of the drawings
Fig. 1 is the overall schematic of the database sharing contact of the embodiment of the present invention；
Fig. 2 is the ginseng compound of the embodiment of the present invention and the network of relevant disease；
Wherein, square represents the compound small molecule of ginseng, circular representative's albumen/gene, and triangle represents disease,
Solid line represents chemical combination and people's albumen/gene, people's albumen/contacting between gene and disease and people's protein-interacting relation.
Embodiment
As shown in Figure 1, 2, below in conjunction with the accompanying drawings and embodiment the present invention is described in further detail.
The technical solution adopted by the present invention is：
(1) (Xue, the Fang et from Chinese Traditional Chinese Medicine in Taiwan medicine data bank (Chen 2011) and traditional Chinese medical science integrated database
Al.2013 the compound information that Chinese medicine or Chinese medicine preparation are included) is obtained.
The TaiWan, China traditional Chinese medicine data bank (http://tcm.cmu.edu.tw) provided down for the current whole world is maximum
Carry the database of medium-height grass drug compound.
Traditional Chinese medical science integrated database (the http://www.megabionet.org/tcmid/) it is that traditional Chinese medicine information is provided
And its integrated database with modern life science.
(2) No. CID is obtained corresponding to compound from STITCH databases (Kuhn, Szklarczyk et al.2014),
Then by people's albumen associated corresponding to No. CID acquisition, so as to obtain compound and people's protein-interacting file
(Fig. 1).
STITCH databases (the http://stitch.embl.de/) it is mutual to explore chemical small molecule and protein
The database of interactively.
(3) compound side-effects information file (figure is obtained from SIDER databases (Kuhn and Letunic 2016)
1)。
SIDER databases (the http://sideeffects.embl.de/) it is to explore compound and its adverse reaction
Database.
(4) toxicity of compound message file (Fig. 1) is obtained from TOXNET databases (Wexler 2001).
TOXNET databases (the https://toxnet.nlm.nih.gov/) it is the number for exploring compound and its toxicity
According to storehouse.
(5) using between STRING databases (Szklarczyk, Franceschini et al.2015) acquisition people's albumen
Interaction relationship (Fig. 1).
STRING databases (the http://string-db.org/) it is the data for characterizing protein interaction relationship
Storehouse.
(6) people's albumen text corresponding with gene relationship is obtained using omim database (Hamosh, Scott et al.2002)
Part, while obtain gene and disease respective file (Fig. 1) using omim database.
Omim database (the http://www.omim.org/) for database on human gene and genetic disease.
(7) gene and disease association file (figure are obtained using GAD databases (Becker, Barnes et al.2004)
1)。
GAD databases (the https://geneticassociationdb.nih.gov/) be on complex disease and
The database of the genetic association data of disease.
(8) inner link of file is obtained using above-mentioned steps, based on MySQL, establish " Chinese medicine preparation chemical composition/in
Medicine chemical composition --- people's albumen/gene --- disease " database (toxic side effect of inclusion compound) (Fig. 1).
(9) obtained using database command from the database built up " Chinese medicine preparation chemical composition/Chemistry for Chinese Traditional Medicine into
Divide --- people's albumen/gene --- disease " network information.
(10) " the Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- generated by database
Disease " path builds network in Cytoscape softwares.
Embodiment is by taking ginseng as an example
(1) (TCMID) obtains people from Chinese Traditional Chinese Medicine in Taiwan medicine data bank (TCM Taiwan) and traditional Chinese medical science integrated database
The included compound information (125) of ginseng.
(2) the ginseng micromolecular compound information of above-mentioned acquisition is imported in well-established database, obtains ginseng
Compound --- people's albumen contacts (5183).
(3) above-claimed cpd information is retrieved in database, obtains side-effects information 0, toxicity information 1.
(4) above-mentioned acquisition people albumen is retrieved in database, obtains the interaction relationship between people's albumen and people
Join compound --- the contact of gene (people's albumen).
(5) obtained gene is retrieved in database, obtains ginseng compound --- gene (people's albumen) --- disease
Sick network.And can to the progress of " ginseng compound --- gene (people's albumen) --- disease " network using Cytoscape softwares
Depending on change.
The network of structure is manually parsed, finds small molecule ginsenoside Rg1 and tumor necrosis factor contained by ginseng
Sub (TNF) has interaction, and TNF is diabetes (Grauballe, Ostergaard et al.2015), Alzheimer's disease
(Hao and Friedman 2016), hypertension (Nepal, Malik et al. 2012) and atherosclerosis (Jin
And Kim 2016, Tocci, Goletti et al.2016) target spot；Equally, ginsenoside Re and alzheimer target spot
NOS3 (de la Monte, Jhaveri et al.2007) interacts；Ginsenoside Rb1 and diabetes target spot AKT1
(Albury-Warren, Pandey et al.2016) interacts.Network analysis prediction and the document report knot of the embodiment
Fruit matches, demonstrate to a certain extent the network analysis system parsing Mechanism of TCM on feasibility with rationally
Property.
It is understood that for the person of ordinary skill of the art, it can be conceived with the technique according to the invention and done
Go out other various corresponding changes and deformation, and all these changes and deformation should all belong to the protection model of the claims in the present invention
Enclose.
Claims (10)
1. a kind of network pharmacology analysis method of Chinese medicine and Chinese medicine preparation, it is characterised in that it comprises the following steps：
Each source file information of S1, acquisition Chinese medicine and Chinese medicine preparation network pharmacology analysis；
S2, the inner link relation according to each source file, establish " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's egg
In vain/gene --- disease " database, described " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease
Disease " database includes the toxic side effect of compound；
In S3, " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " database according to foundation
" Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " path is built in Cytoscape softwares
Network.
2. the network pharmacology analysis method of Chinese medicine as claimed in claim 1 and Chinese medicine preparation, it is characterised in that the Chinese medicine and
Each source file information of the network pharmacology analysis of Chinese medicine preparation includes；
The chemical composition of Chinese medicine and Chinese medicine preparation, compound and people's protein-interacting file, compound side-effects information file,
Interaction relationship file, people's albumen and gene relationship respective file, gene between toxicity of compound message file, people's albumen
With disease association file.
3. the network pharmacology analysis method of Chinese medicine as claimed in claim 1 and Chinese medicine preparation, it is characterised in that
Described Chinese medicine and the chemical composition of Chinese medicine preparation obtains from Chinese Traditional Chinese Medicine in Taiwan medicine data bank and traditional Chinese medical science integrated database
；
Described compound obtains with people's protein-interacting file from STITCH databases；
Described compound side-effects information file obtains from SIDER databases；
Described toxicity of compound message file obtains from TOXNET databases；
Interaction relationship file obtains from STRING databases between described people's albumen；
Described people's albumen obtains with gene relationship respective file from omim database；
Described gene obtains with disease association file from omim database and GAD databases.
4. the network pharmacology analysis method of Chinese medicine as claimed in claim 3 and Chinese medicine preparation, it is characterised in that
" Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " database leads in the step S2
Cross and established based on MySQL.
5. the network pharmacology analysis method of Chinese medicine as claimed in claim 1 and Chinese medicine preparation, it is characterised in that
When the compound is ginseng compound, small molecule ginsenoside Rg1 and TNF contained by ginseng compound
There is interaction, TNF is the target spot of diabetes, Alzheimer's disease, hypertension and atherosclerosis；Equally, ginsenoside
Re and alzheimer target spot NOS3 interacts；Ginsenoside Rb1 interacts with diabetes target spot AKT1.
6. the network pharmacology analysis system of a kind of Chinese medicine and Chinese medicine preparation, it is characterised in that it includes such as lower unit：
Source file information acquisition unit, each source file information of the network pharmacology analysis for obtaining Chinese medicine and Chinese medicine preparation；
Database unit, for the inner link relation according to each source file, establish " Chinese medicine preparation chemical composition/in
Medicine chemical composition --- people's albumen/gene --- disease " database, described " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica ---
People's albumen/gene --- disease " database includes the toxic side effect of compound；
Network construction unit, for " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/base according to foundation
Cause --- disease " " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease " path exists in database
Network is built in Cytoscape softwares.
7. the network pharmacology analysis system of Chinese medicine as claimed in claim 6 and Chinese medicine preparation, it is characterised in that the Chinese medicine and
Each source file information of the network pharmacology analysis of Chinese medicine preparation includes；
The chemical composition of Chinese medicine and Chinese medicine preparation, compound and people's protein-interacting file, compound side-effects information file,
Interaction relationship file, people's albumen and gene relationship respective file, gene between toxicity of compound message file, people's albumen
With disease association file.
8. the network pharmacology analysis system of Chinese medicine as claimed in claim 7 and Chinese medicine preparation, it is characterised in that
Described Chinese medicine and the chemical composition of Chinese medicine preparation obtains from Chinese Traditional Chinese Medicine in Taiwan medicine data bank and traditional Chinese medical science integrated database
；
Described compound obtains with people's protein-interacting file from STITCH databases；
Described compound side-effects information file obtains from SIDER databases；
Described toxicity of compound message file obtains from TOXNET databases；
Interaction relationship file obtains from STRING databases between described people's albumen；
Described people's albumen obtains with gene relationship respective file from omim database；
Described gene obtains with disease association file from omim database and GAD databases.
9. the network pharmacology analysis system of Chinese medicine as claimed in claim 8 and Chinese medicine preparation, it is characterised in that
In the Database unit " Chinese medicine preparation chemical composition/chemical composition of Chinese materia medica --- people's albumen/gene --- disease "
Database based on MySQL by being established.
10. the network pharmacology analysis system of Chinese medicine as claimed in claim 9 and Chinese medicine preparation, it is characterised in that
When the compound is ginseng compound, small molecule ginsenoside Rg1 and TNF contained by ginseng compound
There is interaction, TNF is the target spot of diabetes, Alzheimer's disease, hypertension and atherosclerosis；Equally, ginsenoside
Re and alzheimer target spot NOS3 interacts；Ginsenoside Rb1 interacts with diabetes target spot AKT1.
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN109637594A (en) * | 2018-10-25 | 2019-04-16 | 华中科技大学鄂州工业技术研究院 | Chinese materia medica preparation over the counter species chemical component pathogenic analysis method and equipment |
| CN109738552A (en) * | 2019-03-06 | 2019-05-10 | 湖南中医药大学第一附属医院((中医临床研究所)) | A method of screening Fructus Corni hypoglycemic activity ingredient |
| CN110277143A (en) * | 2019-06-21 | 2019-09-24 | 沈阳药科大学 | A kind of important target spot evaluation method of drug based on weighted network |
| CN110751981A (en) * | 2019-10-15 | 2020-02-04 | 中国人民解放军第四军医大学 | Analysis method for explaining essence of traditional Chinese medicine syndrome based on system biology |
| CN110827916A (en) * | 2019-10-24 | 2020-02-21 | 南方医科大学南方医院 | Schizophrenia gene-gene interaction network and construction method thereof |
| CN111241164A (en) * | 2020-01-18 | 2020-06-05 | 湖北理工学院 | Traditional Chinese medicine system pharmacology analysis platform and analysis method |
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Application publication date: 20180209 |