CN105868518A - Network pharmacology analysis method for chemical components of over-the-counter species in traditional Chinese medicine preparation - Google Patents
Network pharmacology analysis method for chemical components of over-the-counter species in traditional Chinese medicine preparation Download PDFInfo
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Abstract
The invention discloses a network pharmacology analysis method for chemical components of an over-the-counter species in a traditional Chinese medicine preparation. The method comprises the following steps of obtaining components of a biological species in a to-be-analyzed traditional Chinese medicine preparation, wherein the biological species includes a prescription species and the over-the-counter species; obtaining the chemical components of the over-the-counter species, and performing standardization processing on different format files of the chemical components; establishing a relationship between the chemical components of the over-the-counter species and human proteins by utilizing an STITCH database to obtain an interaction relationship file of the chemical components of the over-the-counter species in the to-be-analyzed traditional Chinese medicine preparation and the proteins; establishing an interaction relationship between the obtained human proteins to obtain a human protein interaction relationship file; and constructing a network of ''the chemical components of the over-the-counter species in the traditional Chinese medicine preparation, the human proteins and diseases''. According to the method, the chemical components, as research objects, of the over-the-counter species in the traditional Chinese medicine preparation are researched by utilizing a network analysis technology based on a system biology thought.
Description
Technical field
The invention belongs to Chinese medicine preparation network pharmacology research field, a kind of based on system biological
The network pharmacology analysis method of the Chinese medicine preparation OTC species chemical composition learned.
Background technology
Chinese medicine preparation is under instruction of Chinese Medicine theory, and according to the principles of formulating prescriptions of " monarch ", it is suitable to select
Flavour of a drug and dosage, the ready-made medicine using rational preparation process to make at any time can to take.Chinese medicine preparation
Often containing multiple animals and plants composition, its drug effect is the embodiment of multiple flavour of a drug mass action, be Multiple components,
The result of number of mechanisms comprehensive function.But, owing to traditional Chinese medicinal material raw materials is adulterated, mistake is identified, and plantation,
Processing and the introducing of preparation technical process impurity so that some OTC species (medicines in Chinese medicine preparation, may be contained
The species that in allusion quotation, this Chinese medicine preparation prescription is not recorded).Although the shared ratio of these OTC species is the least, but
Its contained chemical composition is likely to reduce clinical efficacy, even produces or increases toxic and side effect, jeopardizing
Patient health and life security.
First genome research method based on high throughput sequencing technologies is current understanding, analyzes biological mixed system
One of 26S Proteasome Structure and Function method most effective, most important.The method is utilized can more comprehensively to detect Chinese medicine system
Species composition in agent, so that we can easier obtain the OTC species information of Chinese medicine preparation
(Cheng, Su et al.2014), and then evaluate its potential toxic and side effect.
In recent years, along with modern genetic group, proteomics, metabolism group etc. " group is learned " theoretical sending out
Exhibition, the introducing at systems biology visual angle and the application of bioinformatics, network pharmacology (Network
Pharmacology) concept is arisen at the historic moment, and it is on the basis of systems biology Yu computer technology high speed development
On grow up, on the basis of " disease---gene---target spot---medicine " interactive network, pass through
Network analysis, system synthesis ground is observed medicine to the intervention of disease network and impact, is disclosed multimolecular drug association
Same-action is in the secret of human body, and this goes the theory of diagnosis and treatment disease with traditional Chinese medicine from overall angle, Chinese medicine and multiple
The multicomponent of side, multipath, the synergistic principle of Mutiple Targets are reached the same goal by different routes.The research strategy of Chinese medicine preparation
Also predictive research is being transferred to from descriptive research.One of them important symbol is exactly from " biomolecule network "
Structure and function recognize disease molecules mechanism and mechanism of drug action.It is considered as that " medicine of future generation grinds
Study carefully pattern " network pharmacology bring the major transformation of drug research, also the research for Chinese medicine preparation brings
New opportunity, maximum of which opportunity is to understand by the thought of network Yu system and process Chinese medicine system
Agent chemical system and the complexity of body biosystem.The network pharmacology of Chinese medicine preparation prescription species chemical composition
Analyze current research report more (Li, Zhang et al.2010, Zhao, Jiang et al.2010, Liang, Li et
Al.2014), the network pharmacology analysis of its OTC species chemical composition is had no report.The non-place of Chinese medicine preparation
Square object kind chemical composition has very important impact to human health, is therefore highly desirable to use system biological
The method learned is by network pharmacology analyses and prediction Chinese medicine preparation OTC species chemical composition and human therapeutic target
Interaction relationship, thus disclose the harmful effect that health may be produced by they.
Summary of the invention
For above-mentioned weak point present in prior art, the technical problem to be solved in the present invention is to provide one
Plant the network pharmacology analysis method of Chinese medicine preparation OTC species chemical composition.
The present invention be the technical scheme is that a kind of Chinese medicine preparation OTC is speciated for achieving the above object
The network pharmacology analysis method studied point, comprises the following steps:
Step 1: according to Pharmacopoeia of People's Republic of China with to the experimental result of biochemical component in Chinese medicine preparation
Obtain the living species composition of Chinese medicine preparation to be analyzed, including prescription species and OTC species；
Step 2: obtain the chemical composition of above-mentioned OTC species, the different-format file to described chemical composition
It is standardized processing；
Step 3: chemical composition in STITCH database is carried out same standard process, utilizes STITCH
Database above-mentioned OTC species chemical composition contacts with people's albumen, obtains Chinese medicine preparation to be analyzed non-
Prescription species chemical composition and protein-interacting relational file；Then in STRING database, set up institute
Obtain the interaction relationship between people's albumen, obtain interaction relationship file between people's albumen；
Step 4: obtain No. OMIM and gene relationship respective file according to omim database, utilizes
Gene Name is converted to the id information of " ENSG " form by Clone/Gene IDconverter instrument, simultaneously
The protein information obtained in STRING database is carried out the process of same nature, makes the ID after conversion unite
Can be obtained by No. OMIM and people's protein interaction file through screening coupling after one change, then utilize step
The Chinese medicine preparation OTC species chemical composition to be analyzed obtained in rapid 3 and protein-interacting file and
Interaction relationship file between people's albumen, totally three files build " Chinese medicine preparation in Cytoscape software
OTC species chemical composition---people's albumen---disease " network.
Described prescription species are the living species composition of Chinese medicine preparation to be analyzed, and this living species composition in
In China's people's republic pharmacopeia on the books.
Described OTC species are the living species composition of Chinese medicine preparation to be analyzed, and this living species composition exists
Pharmacopoeia of People's Republic of China is not recorded.
The chemical composition of described OTC species obtains from Traditional Chinese Medicine in Taiwan medicine data bank and traditional Chinese medical science integrated database
?.
Described standardization comprises the following steps:
By Open Babel software, the different-format file of chemical composition is converted to Canonical SMILES
Format form；
Result after conversion is removed in form " H ,@, [,] ,/, ", and then generate a can
Formatted file.
Processing particularly as follows: utilize the protein Alias information literary composition in STRING database of described same nature
Part, carries out protein conversion process and makes its title be converted to the id information of " ENSG " form equally.
Described step 4 also includes: utilize Clone/Gene IDconverter instrument in omim database
No. OMIM corresponding gene carries out title conversion processing, it is simple to protein data and omim database
Docking.
The present invention is so that in Chinese medicine preparation, the chemical composition of OTC species is as research object, based on system biological
Learn thinking, utilize network analysis technique that it is studied.For comparing conventional method, the method has following
Advantage:
(1) cycle is shorter.
(2) database used in the method has authority and generality in its art: in Taiwan
Medicine data bank and traditional Chinese medical science integrated database are used by tens of the scientific research institutions in the whole world, and citation times all reaches
To hundreds of times (sing on web of Science data).
(3) that be converted to chemical composition to simplify, without repeating, unambiguous can formatted file, thus increase
Add Chinese medicine preparation OTC species chemical composition matching rate in STITCH database.
(4) bioinformatics method can be utilized to predict Chinese medicine preparation OTC species chemical composition in theory
Harm that may be present.
Accompanying drawing explanation
Fig. 1 is that Chinese medicine preparation OTC species chemical composition joins with STITCH and STRING database sharing
The schematic diagram of system；
Fig. 2 is Chinese medicine preparation OTC species chemical composition and disease network struction schematic diagram；
Fig. 3 is the network of embodiment Liuwei Dihuang Wan OTC species and relevant disease；
Wherein, triangle represents six Dihuang Wan OTC species chemical small molecule, circular representative's albumen,
Square represents disease, and dotted line represents the interaction of chemical small molecule and people's albumen, solid line representative's albumen
Between interaction, contacting between parallel lines representative's albumen and disease.
Detailed description of the invention
Below in conjunction with the accompanying drawings and embodiment the present invention is described in further detail.
The technical solution used in the present invention is:
1) the living species composition of Chinese medicine preparation is obtained according to Pharmacopoeia of People's Republic of China and experimental result, i.e.
Prescription species and OTC species.Described experiment includes extracting the DNA of biotic component in Chinese medicine preparation,
After amplification and high-flux sequence, sequencing data is analyzed, and then Chinese medicine preparation contained place square object can be learnt
Plant and OTC Species composition.
2) comprehensive from Traditional Chinese Medicine in Taiwan medicine data bank (Chen 2011) (chemical composition is mol2 form) and the traditional Chinese medical science
In database, (Xue, Fang et al.2013) (chemical composition is SMILES form) obtains above-mentioned gained Chinese medicine
The chemical composition of preparation OTC species.Then it is standardized locating to the data obtained with Open Babel software
Reason, and after being converted to Canonical SMILES format, result is carried out artificial treatment, remove form
In " H ,@, [,] ,/, ", thus be simplified, without repeat, unambiguous can formatted file,
Acquired results is the research object of the present invention.
Under described Traditional Chinese Medicine in Taiwan medicine data bank (http://tcm.cmu.edu.tw) provides for current whole world maximum
Carry the database of Chinese herbal medicine compound.
Described traditional Chinese medical science integrated database (http://www.megabionet.org/tcmid/) is for providing traditional Chinese medicine letter
Breath and the integrated database with modern life science thereof.
3) by the chemistry of SMILES form in STITCH database (Kuhn, Szklarczyk et al.2014)
Component equally be processed as simplify, without repeat, unambiguous can formatted file, then by non-for Chinese medicine preparation place
The chemical composition of square object kind is mated with this database, obtains chemical constituent corresponding after duplicate removal is screened
CID numbers；Then the connection of Chinese medicine preparation OTC species chemical composition and people's albumen is set up according to CID numbering
System (see Fig. 1).
Described STITCH database (http://stitch.embl.de/) is for exploring chemical small molecule and protein phase
The database of interaction relation.
4) STRING database (Szklarczyk, Franceschini et al.2011) is utilized to obtain in above-mentioned institute
Obtain the interaction relationship (Fig. 1) between people's albumen.
Described STRING database (http://string-db.org/) is for characterizing protein interaction relationship
Database.
5) No. OMIM (disease can be obtained according to omim database (Hamosh, Scott et al.2005)
Relevant) and gene relationship respective file, utilize this instrument of Clone/Gene IDconverter by Gene Name
Be converted to be easier to identification " ENSG " form id information, simultaneously by STRING database
Protein information carries out " another name conversion " and processes, and i.e. utilizes the protein another name letter in STRING database
Breath file, is converted to the ID of " ENSG " form equally by protein title, and the ID after both conversions is unified
After form, No. OMIM and people's protein interaction file can be obtained through screening coupling；By above
The analyzing and processing of step, can respectively obtain from STITCH Yu STRING database Chinese medicine preparation non-from
Interaction file between square object kind chemical composition and the interaction file of people's albumen and people's albumen；Can
With utilize these three file build in Cytoscape software " Chinese medicine preparation OTC species chemical composition---
People's albumen---disease " network, and utilize morbid-map (the gene-disease relation in omim database
File, the information that this document comprises: disease name, No. OMIM, disease related gene and place dyeing thereof
Position on body) resolving this Network finding as auxiliary may can with Chinese medicine preparation OTC species chemical composition
The disease (see Fig. 2) that can cause.
Described omim database (http://www.omim.org/) is about human gene and genetic disease
Database.
Embodiment is as a example by Liuwei Dihuang Wan
1) according to pharmacopeia and high-flux sequence result of study, (implementing step is: the genome of Liuwei Dihuang Wan
The fragment that DNA extracts---DNA molecular is carried out PCR amplification---obtains amplification carries out high pass measurement
Sequence also builds library, and---utilizing Species Structure to resolve software to be analyzed sequencing data---determines Liuwei Dihuang Wan
Prescription species and OTC species) must obtain Liuwei Dihuang Wan prescription species (glutinous rehmannia, wine cornus, male
The root bark of tree peony, Chinese yam, Poria cocos and rhizoma alismatis) and OTC species (windproof genus, Polygonum, Rumex, Cassia,
Vigna and Dandelion) (Cheng, Su et al.2014).
2) from Traditional Chinese Medicine in Taiwan medicine data bank (chemical constituent form is mol2) and traditional Chinese medical science integrated database (TCMID)
In (chemical constituent form is SMILES) obtain the chemical constituent (116) contained by above-mentioned OTC species,
It is standardized processing to the data obtained with Open Babel software, will gained chemical constituent be converted to
Canonical SMILES format, then carries out artificial treatment by result, remove in form " H ,@,
[,] ,/, ", obtain one simplify, without repeat, unambiguous can formatted file.
3) meanwhile, the chemical constituent of SMILES form in STITCH database is processed as letter equally
That change, without repetition, unambiguous can formatted file, then by Liuwei Dihuang Wan OTC species chemical composition
Mate with this database, after duplicate removal, obtain the CID that Liuwei Dihuang Wan OTC species chemical composition is corresponding
Numbering 58, and then little molecule and people's albumen (about 2200) can be set up according to numbering and database information
Contact.
4) in STRING database, the interaction relationship between above-mentioned obtained people's albumen is obtained.
5) No. OMIM and gene relationship respective file can be obtained according to omim database, utilize
Gene Name is converted to be easier to the id information of identification by this instrument of Clone/Gene IDconverter, simultaneously
The protein information obtained in STRING database carries out " another name conversion " process, after both conversions
After ID Unified Form, No. OMIM and people's protein interaction file can be obtained through screening coupling, so
After therefrom search with Liuwei Dihuang Wan OTC speciated study split-phase close people's albumen, through screening coupling can
To obtain No. OMIM and people's protein interaction file；Through the analyzing and processing of preceding step, obtain
STITCH with STRING database respectively obtains the phase interaction of OTC species chemical composition and people's albumen
With the interaction file between file and people's albumen；Utilize these three file structure in Cytoscape software
Build " Liuwei Dihuang Wan OTC species chemical composition---people's albumen---disease " network, and utilize this network and
Morbid-map result obtains the relevant disease information such as table 1 (portion of Liuwei Dihuang Wan OTC species chemical composition
Divide result).These data can be at some extent as the theoretical foundation of experimental verification.
The partial results of disease corresponding to table 1 Liuwei Dihuang Wan OTC species chemical composition
The overall network figure built manually is resolved, finds little molecule contained by Liuwei Dihuang Wan OTC species
Rheum emodin (emodin) and PUD D target spot ERBB2 and TGFB (Orho, Buist et al.1998, Pittet,
Griffiths et al.2001), and hepatopathy target spot GYS2 (Orho, Buist et al.1998) have interaction (figure
3, the artificial analysis result of part), prompting rheum emodin is probably the reason causing PUD D to occur, therefore net
Network analysis result contributes to the little molecule of systematic screening and the interactively of target protein and action pathway, thus
Premise and foundation is provided for next step experimental verification.For another one angle, pertinent literature is also had to study
Show that the rheum emodin (emodin) in Cassia can produce toxic action (S.M.Yagi, Tigani to liver, kidney and lung
Et al.1998, Maiga, Diallo et al.2005), predict with the network analysis of this embodiment and match.This knot
Fruit demonstrates this network analysis method to a certain extent and causes in prediction Chinese medicine preparation OTC species chemical composition
Characteristic of disease affects feasibility and the reasonability of aspect.
Claims (7)
1. the network pharmacology analysis method of a Chinese medicine preparation OTC species chemical composition, it is characterised in that
Comprise the following steps:
Step 1: according to Pharmacopoeia of People's Republic of China with to the experimental result of biochemical component in Chinese medicine preparation
Obtain the living species composition of Chinese medicine preparation to be analyzed, including prescription species and OTC species；
Step 2: obtain the chemical composition of above-mentioned OTC species, the different-format file to described chemical composition
It is standardized processing；
Step 3: chemical composition in STITCH database is carried out same standard process, utilizes STITCH
Database above-mentioned OTC species chemical composition contacts with people's albumen, obtains Chinese medicine preparation to be analyzed non-
Prescription species chemical composition and protein-interacting relational file；Then in STRING database, set up institute
Obtain the interaction relationship between people's albumen, obtain interaction relationship file between people's albumen；
Step 4: obtain No. OMIM and gene relationship respective file according to omim database, utilizes
Gene Name is converted to the id information of " ENSG " form by Clone/Gene IDconverter instrument, simultaneously
The protein information obtained in STRING database is carried out the process of same nature, makes the ID after conversion unite
Can be obtained by No. OMIM and people's protein interaction file through screening coupling after one change, then utilize step
The Chinese medicine preparation OTC species chemical composition to be analyzed obtained in rapid 3 and protein-interacting file and
Interaction relationship file between people's albumen, totally three files build " Chinese medicine preparation in Cytoscape software
OTC species chemical composition---people's albumen---disease " network.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that described prescription species are the living species composition of Chinese medicine preparation to be analyzed, and should
Living species composition is on the books in Pharmacopoeia of People's Republic of China.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that described OTC species are the living species composition of Chinese medicine preparation to be analyzed, and
This living species composition is not recorded in Pharmacopoeia of People's Republic of China.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that the chemical composition of described OTC species is from Traditional Chinese Medicine in Taiwan medicine data bank and the traditional Chinese medical science
Integrated database obtains.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that described standardization comprises the following steps:
By Open Babel software, the different-format file of chemical composition is converted to Canonical SMILES
Format form；
Result after conversion is removed in form " H ,@, [,] ,/, ", and then generate a can
Formatted file.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that processing particularly as follows: utilize in STRING database of described same nature
Protein Alias information file, carries out protein conversion process and makes its title be converted to " ENSG " shape equally
The id information of formula.
The network pharmacology of a kind of Chinese medicine preparation OTC species chemical composition the most according to claim 1 is divided
Analysis method, it is characterised in that described step 4 also includes: utilize Clone/Gene IDconverter instrument pair
In omim database, No. OMIM corresponding gene carries out title conversion processing, it is simple to protein data with
The docking of omim database.
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Cited By (5)
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| CN107680692A (en) * | 2017-09-13 | 2018-02-09 | 华中科技大学鄂州工业技术研究院 | The network pharmacology analysis method and system of Chinese medicine and Chinese medicine preparation |
| 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 |
| CN110890136A (en) * | 2019-11-13 | 2020-03-17 | 安徽中医药大学 | Traditional Chinese medicine pharmacological analysis method |
| CN112927766A (en) * | 2021-03-29 | 2021-06-08 | 天士力国际基因网络药物创新中心有限公司 | Method for screening disease combination drug |
| CN113567639A (en) * | 2021-07-13 | 2021-10-29 | 中国食品药品检定研究院 | Comprehensive evaluation method for quality of traditional Chinese medicinal materials |
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| CN112927766A (en) * | 2021-03-29 | 2021-06-08 | 天士力国际基因网络药物创新中心有限公司 | Method for screening disease combination drug |
| CN113567639A (en) * | 2021-07-13 | 2021-10-29 | 中国食品药品检定研究院 | Comprehensive evaluation method for quality of traditional Chinese medicinal materials |
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Application publication date: 20160817 |