CN114822722B - Method for screening Chinese medicinal effective substances for treating hepatitis - Google Patents

Method for screening Chinese medicinal effective substances for treating hepatitis Download PDF

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CN114822722B
CN114822722B CN202210453778.2A CN202210453778A CN114822722B CN 114822722 B CN114822722 B CN 114822722B CN 202210453778 A CN202210453778 A CN 202210453778A CN 114822722 B CN114822722 B CN 114822722B
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吴嘉瑞
段小霞
沈亮亮
刘鑫馗
张景媛
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Abstract

The invention discloses a method for screening a traditional Chinese medicine drug effect substance for treating hepatitis, which is based on an association map and a molecular fingerprint similarity technology, provides a method capable of verifying a possible drug effect mechanism and a material basis of traditional Chinese medicine for treating hepatitis and screening out corresponding key effective components; aiming at the difference genes of the hepatitis, a candidate micromolecule drug with the potential of treating the hepatitis is obtained by screening from a CMAP database based on a correlation map technology; a system method system capable of screening small molecular compounds and verifying the effectiveness of related medicaments by utilizing a target-based similarity reasoning and molecular fingerprint similarity analysis method aiming at different hepatitis patient omics and clinical big data is formed, so that technical support and methodological guidance are provided for solving the problem of researching the pharmacodynamic substances of the anti-hepatitis traditional Chinese medicine with the potential of treating different hepatitis patients, and more effective traditional Chinese medicine treatment schemes are provided for clinical hepatitis treatment.

Description

Method for screening drug effect substance of traditional Chinese medicine for treating hepatitis
Technical Field
The invention relates to the technical field of traditional Chinese medicine and biology, in particular to a screening method of a traditional Chinese medicine effective substance for treating hepatitis.
Background
The number of Chronic Hepatitis B (CHB) patients in China is 2000-3000 ten thousand, the incidence rate of non-alcoholic fatty liver disease (NAFLD) is increased year by year, and the total incidence rate in Asia is 29.62%. There is an increasing incidence of both CHB and NAFLD disease in the same individual, with NAFLD occurring in nearly 1/3 of CHB patients. Research shows that virological response rate of CHB combined NAFLD patients is obviously lower than that of CHB patients; and accelerating hepatic steatosis and hepatic fibrosis progression, increasing the risk of cirrhosis and hepatocellular carcinoma, is one of the factors leading to the increase of mortality rate. Therefore, CHB combined with NAFLD becomes a new research hotspot, and the traditional Chinese medicine has certain curative effect on the disease.
At present, the research on the drugs for treating various hepatitis at home and abroad is correspondingly progressed. The traditional Chinese medicine plays a unique curative effect in the aspect of treating viral hepatitis and the like, and mechanism research and material basis exploration on treating hepatitis by the traditional Chinese medicine are also reported in recent years, western medicine plays a curative effect mechanism of resisting hepatitis mainly by precise intervention of small molecular monomer compounds on target points and molecular action research, while traditional Chinese medicine has been seen to play a pharmacodynamic action by 'multiple components, multiple target points and multiple ways', and material basis research for clearly playing a key pharmacodynamic action is particularly important for deeply analyzing mechanism research such as target point paths and the like of disease treatment.
Disclosure of Invention
Therefore, the invention provides a method for screening the drug effect substances of the traditional Chinese medicine for treating hepatitis, so as to provide an effective scheme for screening the drugs with the potential of treating certain types of hepatitis.
In order to achieve the above purpose, the invention provides the following technical scheme: a screening method of a traditional Chinese medicine drug effect substance for treating hepatitis comprises the following steps:
the method comprises the following steps: downloading and acquiring hepatocyte gene expression profile data of a hepatitis patient from a database, and screening differential genes by using R language to obtain hepatocyte differential expression genes;
step two: classifying the obtained differential genes to obtain an up-regulation gene group and a down-regulation gene group in the liver cells of the hepatitis patient;
step three: respectively inputting the gene id of the up-regulated gene and the down-regulated gene into a correlation map database, and obtaining a candidate small molecule compound with the potential of treating hepatitis by screening by using a gene-disease-drug correlation method;
step four: the key active ingredients of the traditional Chinese medicine with the anti-hepatitis effect are selected, the key active ingredients of the traditional Chinese medicine and the obtained candidate micromolecular compound are subjected to molecular fingerprint similarity analysis, and the key active ingredients of the traditional Chinese medicine with similarity to the candidate micromolecular compound are found and used as key pharmacodynamic substances of the traditional Chinese medicine with anti-hepatitis potential.
Further, the up-regulated gene group and the down-regulated gene group in the second step are both significant difference gene groups in liver cells of hepatitis patients.
Further, in the first step, the gene information of mRNA expression level in the liver cells of the hepatitis patients and the gene information of differential expression compared with normal liver cells are obtained by using the R language program packet diffExp as a differential gene screening tool.
Further, in the third step, the CMAP database used is a "ConnectivityMap" association map database, and the function module used is "CLUE QUERY".
Further, in the third step, the gene ids of the up-regulated gene and the down-regulated gene are respectively input into the text boxes corresponding to the CMAP database, the invalid and valid but unused gene ids are deleted, after the sub button is clicked, the system generates a HEAT MAP HEAT MAP result through calculation and comparison, the query _ result is clicked, the anti-hepatitis candidate molecule screening result based on the association MAP is obtained, the small molecule compounds which enable the 'obviously down-regulated gene' and the 'obviously up-regulated gene' in the liver cells of the hepatitis patient to be down-regulated are further screened from the result, and the small molecule compounds are determined to be candidate small molecules with the potential for treating the hepatitis. A compound is provided.
Furthermore, the three-dimensional structures of key active ingredients of traditional Chinese medicines with the effect of treating hepatitis, which are reported in the literature at present, are downloaded and collected one by one, and then the three-dimensional structures and the screened small molecular compounds are subjected to molecular fingerprint similarity analysis one by one.
Further, in the fourth step, the database Analysis in DS 2.5 software is used to perform the "Find similarity molecules by Fingerprints" module under "Library Analysis" for molecular fingerprint similarity Analysis.
The invention has the following advantages:
the invention provides a screening method of a traditional Chinese medicine drug effect substance for treating hepatitis, which selects different hepatitis patient groups as research objects, adopts a R language difference gene screening method to perform significant difference analysis on hepatic cell gene expression of hepatitis patients, adopts a correlation map method to screen out candidate micromolecule compound correlation medicines for treating the hepatitis, and adopts a molecular fingerprint similarity analysis method to perform similarity analysis of key effective components of traditional Chinese medicines and micromolecule compound correlation medicines. The method can provide more accurate individual anti-hepatitis traditional Chinese medicine screening for different hepatitis patients through analyzing the expression states of the differential genes, thereby promoting the effective and wide application of the traditional Chinese medicine in the aspects of hepatitis adjuvant therapy and the like.
Drawings
In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below. It should be apparent that the drawings in the following description are merely exemplary, and that other embodiments can be derived from the drawings provided by those of ordinary skill in the art without inventive effort.
FIG. 1 is a schematic flow chart of the screening method of the drug effective substance of Chinese traditional medicine for treating hepatitis according to the present invention;
FIG. 2 is a graph showing the results of screening for candidate anti-hepatitis B small molecule compounds based on a CMAP association profile in an alternative embodiment of the invention;
FIG. 3 is a block diagram of an anti-hepatitis B candidate small molecule compound according to an alternative embodiment of the present invention;
FIG. 4 is a structural diagram of key effective components of a Chinese medicine having anti-hepatitis B potential in an alternative embodiment of the present invention.
Detailed Description
The present invention is described in terms of specific embodiments, and other advantages and benefits of the present invention will become apparent to those skilled in the art from the following disclosure. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
In order to provide a method for researching an anti-hepatitis drug effect substance of a traditional Chinese medicine suitable for hepatitis patients, the embodiment selects hepatitis b patients as research objects, utilizes gene expression profile data of hepatocytes of the hepatitis b patients to screen differential expression genes, and utilizes R language to screen 263 differential expression genes closely related to hepatitis b, wherein 180 up-regulated genes are provided, and 83 down-regulated genes are provided. A method for screening Chinese medicinal effective substance for treating hepatitis is shown in figure 1.
Example 1
Based on the above research results, this example proposes a method for screening anti-hepatitis b small molecule compounds based on a correlation map, which comprises:
and inquiring the gene expression profile data of the hepatitis B patient in the NCBI database to determine that the data source of the hepatitis gene set is GSE83148. 263 differentially expressed genes closely related to hepatitis B were screened by using the R language program package diffExp, of which 180 genes were up-regulated and 83 genes were down-regulated, as shown in Table 1.
TABLE 1
Figure BDA0003619887920000041
Figure BDA0003619887920000051
Inputting the screened up-down gene id into a CMAP database website respectively, clicking a submit button, calculating and comparing by a system to generate a HEAT MAP result, clicking query _ result, obtaining an anti-hepatitis B candidate molecule screening result based on a correlation MAP, as shown in figure 2, further screening 4 candidate micromolecule compounds which are ranked at the top and have related research reports, and the related description is shown in table 2. By using the method, more accurate individual anti-hepatitis small molecule drug screening can be provided for different types of hepatitis patients.
TABLE 2
name cell dose time sample
palbociclib MCF7 10μM 24h 2
BMS-777607 ASC 10μM 24h 3
prostaglandin VCAP 10μM 24h 5
BX-795 ASC 10μM 24h 2
The screening result shows that 4 candidate small molecule compounds with anti-hepatitis B potential are palbociclib (palbociclib), BMS-777607, prostaglandin (prostaglandin) and BX-795 respectively, wherein the prostaglandin has been proved to have the anti-hepatitis B pharmaceutical activity by related researches; the palbociclib is a marketed anti-breast cancer drug, and no relevant research report on anti-hepatitis B exists; the other 2 small molecular compounds BMS-777607 and BX-795 have not been studied about the activity of anti-hepatitis B drugs.
Example 2
In a preferred embodiment of the present invention, a method for researching a drug-effect substance of a traditional Chinese medicine for resisting hepatitis b based on molecular fingerprint similarity analysis is provided, the research method comprises:
according to literature reports, a small molecule active ingredient three-dimensional structure mol file of artemisia capillaris is downloaded and collected from a Traditional Chinese Medicine System Pharmacology (TCMSP) database and an analysis platform, 53 key small molecule compounds are contained, and as shown in a table 3, the small molecule active ingredient mol file is introduced into Discovery Studio 2.5 (DS 2.5) software to prepare screening of key active ingredients of anti-hepatitis B traditional Chinese medicines based on molecular fingerprint similarity analysis.
TABLE 3
MOL000036 MOL000040 MOL000098 MOL000118
MOL000126 MOL000172 MOL000207 MOL000251
MOL000254 MOL000339 MOL000354 MOL000358
MOL000415 MOL000437 MOL000635 MOL000908
MOL000916 MOL000918 MOL001314 MOL001801
MOL001880 MOL001955 MOL001999 MOL002818
MOL004609 MOL004617 MOL004734 MOL005109
MOL005573 MOL006589 MOL007260 MOL007274
MOL007405 MOL008039 MOL008040 MOL008041
MOL008042 MOL008043 MOL008044 MOL008045
MOL008046 MOL008047 MOL008048 MOL008049
MOL008050 MOL008051 MOL008052 MOL008053
MOL008054 MOL008055 MOL008056 MOL008057
MOL008058
The screened small molecule compounds palbociclib (Palbociclib), BMS-777607, prostaglandin (prostaglandin) and BX-795 are taken as centers, a database in DS 2.5 software is utilized to analyze a 'Find Simiarmolecules by Fingerprints' module under 'Libraryanalysis' to carry out molecular similarity search on key active ingredients of artemisia capillaris, and the similarity between the key active ingredients in the artemisia capillaris and the 4 small molecule compounds with anti-hepatitis B potential is investigated from the aspect of molecular fingerprint.
The two-dimensional molecular structure of the small molecule compounds palbociclib (Pabociclib), BMS-777607, prostaglandin (prostaglandin) and BX-795 is shown in FIG. 3.
According to the screening result of key active ingredients of the anti-hepatitis B traditional Chinese medicine based on molecular fingerprint similarity analysis, the artemisia capillaries contain 9 small molecular active ingredients similar to palbociclib, 16 small molecular active ingredients similar to BMS-777607, 7 small molecular active ingredients similar to prostaglandin and 9 small molecular active ingredients similar to BX-795, which are shown in Table 4.
TABLE 4
Figure BDA0003619887920000071
Among the key small molecule active ingredients of artemisia capillaries, the ingredients with the largest similarity values with palbociclib (palbociclib), BMS-777607, prostaglandin (prostaglandin) and BX-795 are MOL008047, MOL008045, MOL000358 and MOL007260, respectively, and the names of the corresponding compounds are artepilina (artemisianin a), 4 '-methycaplarisin (4' -methyl capillaristolone), beta-sitosterol (beta-sitosterol) and isorhamnetin-3-mono-beta-D-glucoside (isorhamnetin-3-O-glucoside), respectively, and the two-dimensional diagram of the chemical structure is shown in fig. 4.
According to the research results, the Chinese medicinal artemisia capillaries are rich in a series of key effective components which are high in similarity with micromolecular compounds with anti-hepatitis B potential, namely palbociclib (palbociclib), BMS-777607, prostaglandin (prostaglandin) and BX-795, represented by artepilin A (capillarin A), 4'-methylcapillaris (4' -methylcapillarin), beta-sitosterol (beta-sitosterol) and isorhamnetin-3-mono-beta-D-glucoside, so that a certain theoretical basis is provided for the anti-hepatitis B curative effect of the artemisia capillaries, and a methodological guidance is provided for discovery and research of pharmacodynamic substances which play a key anti-hepatitis role.
Although the invention has been described in detail with respect to the general description and the specific embodiments, it will be apparent to those skilled in the art that modifications and improvements may be made based on the invention. Accordingly, such modifications and improvements are intended to be within the scope of the invention as claimed.

Claims (5)

1. A method for screening a traditional Chinese medicine drug effect substance for treating hepatitis is characterized by comprising the following steps:
the method comprises the following steps: downloading and acquiring hepatocyte gene expression profile data of a hepatitis patient from a database, and screening differential genes by using R language to obtain hepatocyte differential expression genes;
step two: classifying the obtained differential genes to obtain an up-regulated gene group and a down-regulated gene group in the liver cells of the hepatitis patients;
step three: respectively inputting the gene id of the up-regulated gene and the down-regulated gene into a correlation map database, and obtaining a candidate small molecule compound with the potential of treating hepatitis by screening by using a gene-disease-drug correlation method; in the third step, the adopted database is a ConnectivityMap correlation map database, the differential expression genes are compared with reference gene expression profiles in the database one by one, the similarity of the gene profiles is taken as a reference, the small molecular compounds in the database are scored, the small molecular compounds with the scores ranked in the first several places are screened out, and the small molecular compounds are correlated with corresponding medicines;
step four: selecting anti-hepatitis traditional Chinese medicine, determining key active ingredients of the anti-hepatitis traditional Chinese medicine, and performing molecular fingerprint similarity analysis on the key active ingredients of the traditional Chinese medicine and the obtained candidate micromolecule compound, thereby finding out the key active ingredients of the traditional Chinese medicine with similarity to the candidate micromolecule compound as key drug effect substances of the traditional Chinese medicine with anti-hepatitis potential.
2. The method for screening a drug effective substance of a Chinese medicine for treating hepatitis as claimed in claim 1, wherein in said step one, the database used is NCBI database, and the data source of the hepatitis gene set is determined to be GSE83148.
3. The method for screening a drug effect substance of a traditional Chinese medicine for treating hepatitis according to claim 1, wherein in the first step, mRNA expression level in hepatocytes of a hepatitis patient and gene information differentially expressed compared with normal hepatocytes are obtained by using a language R program packet diffExp as a differential gene screening tool.
4. The method for screening pharmacodynamic substances of a traditional Chinese medicine for treating hepatitis according to claim 1, wherein in the fourth step, molecular fingerprint similarity analysis is performed on the key active ingredients of the traditional Chinese medicine and the obtained candidate small molecule compound by using Discovery Studio 2.5 software.
5. The method for screening pharmacodynamic substances of a traditional Chinese medicine for treating hepatitis of claim 4, wherein in the fourth step, the three-dimensional structure of key active ingredients of the selected traditional Chinese medicine is downloaded and collected from TCMSP database, and introduced into Discovery Studio 2.5 software for molecular fingerprint similarity analysis.
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