2.1 Screening of active ingredients.
By consulting the relevant literature, 79 compounds were obtained, 79 compounds were screened, the ADME parameters (OB-20% and DL-0.15) were used as the criteria, or the activity of the compound was reported in the existing literature, a total of 6 active compounds were screened, the results are seen in Table 1.
Table 1 Number of serum gallblader active compounds and targets.
MolId
|
MolName
|
OB(%)
|
DL
|
Target numbers
|
MOL000098
|
quercetin
|
46.43
|
0.28
|
135
|
MOL000498
|
isoorientin
|
23.30
|
0.76
|
26
|
MOL000006
|
luteolin
|
36.16
|
0.25
|
53
|
MOL000449
|
Stigmasterol[13]
|
43.83
|
0.76
|
24
|
MOL000114
|
vanillic acid[14]
|
35.47
|
0.04
|
8
|
MOL000511
|
ursolic acid
|
16.77
|
0.75
|
80
|
2.2 Predictive results of the potential target for the treatment of pneumonia by serum dragon bile.
In the Genecards and OMIM databases, using "Pneumonia" as the key word, a total of 3980 genes related to pneumonia were retrieved, the pneumonia gene was matched with the target associated with serum dragon bile, and the results were shown in Figure 1. A total of 158 common targets were obtained, indicating that the 158 targets (PTGS1, AR, PPARG, PTGS2, ADRB2, etc.) were involved in the common system of serum gallbladler active ingredient pneumonia, and these 158 targets were common targets.
2.3 PPI network analysis.
The network diagram of the 158 interaction relationship obtained in the String database was imported into the string database, the species was set to "human" and the confidence level was 0.950, as shown in Figure 2. Export the results in TSV format and import the TSV files into the Cytoscape 3.6.1 software. Using the plug-in Network Analytics to get topological parameters Foregree, Betweenness Centrality, Closeness Centrality for each target, where number of nodes=158, number of edges=272, average node=degree=3.44, PPI enrichment p-value <1.0e-16, calculate the median of the three topology parameters are 27, 0.0021, 0.5259, filter Degree, Betweenness centrality are greater than 2 times the median, Closeness centrality is greater than the median target.
A total of 30 key targets were obtained from the screening results. The results are shown in Table 2. The interaction between proteins shows that these targets are interconnected and play an anti-pneumonia effect through multi-channel and multi-faceted coordination. By counting the number of occurrences of each target, that is, the number of gene connection nodes, the more the number of connection nodes, the more important the role of the target in the treatment of pneumonia, indicating that these targets are important in the PPI network The effect suggests that these targets have important significance in the effect of safflower gen.
Table 2. Related topological parameters of the targets of the anti-pneumonia active ingredients of Gentiana
UniprotID
|
Protein names
|
name
|
Degree
|
Betweenness
Centrality
|
Closeness
Centrality
|
P31749
|
RAC-alpha serine/threonine-protein kinase
|
AKT1
|
107
|
0.0598
|
0.7548
|
P02768
|
Serum albumin
|
ALB
|
101
|
0.0718
|
0.7371
|
P05231
|
Interleukin-6
|
IL6
|
99
|
0.0423
|
0.7202
|
P15692
|
Vascular endothelial growth factor A
|
VEGFA
|
94
|
0.0262
|
0.7040
|
P35354
|
Prostaglandin G/H synthase 2
|
PTGS2
|
88
|
0.0334
|
0.6856
|
P42574
|
Caspase-3, CASP-3,
|
CASP3
|
87
|
0.0280
|
0.6886
|
P00533
|
Epidermal growth factor receptor
|
EGFR
|
85
|
0.0302
|
0.6767
|
P05412
|
Transcription factor AP-1
|
JUN
|
83
|
0.0191
|
0.6709
|
P01133
|
Pro-epidermal growth factor
|
EGF
|
82
|
0.0265
|
0.6653
|
P28482
|
Mitogen-activated protein kinase 1
|
MAPK1
|
82
|
0.0292
|
0.6681
|
P01106
|
Myc proto-oncogene protein
|
MYC
|
81
|
0.0183
|
0.6653
|
P10145
|
Interleukin-8, IL-8
|
CXCL8
|
80
|
0.0162
|
0.6624
|
P14780
|
Matrix metalloproteinase-9, MMP-9
|
MMP9
|
80
|
0.0186
|
0.6624
|
P01584
|
Interleukin-1 beta, IL-1 beta
|
IL1B
|
75
|
0.0114
|
0.6488
|
P03372
|
Estrogen receptor, ER
|
ESR1
|
75
|
0.0186
|
0.6488
|
P24385
|
G1/S-specific cyclin-D1
|
CCND1
|
73
|
0.0155
|
0.6382
|
P01100
|
Proto-oncogene c-Fos
|
FOS
|
72
|
0.0198
|
0.6408
|
P13500
|
C-C motif chemokine 2
|
CCL2
|
71
|
0.0096
|
0.6356
|
P22301
|
Interleukin-10, IL-10
|
IL10
|
66
|
0.0069
|
0.6181
|
P08253
|
72 kDa type IV collagenase
|
MMP2
|
66
|
0.0109
|
0.6206
|
P04626
|
Receptor tyrosine-protein kinase erbB-2
|
ERBB2
|
63
|
0.0110
|
0.6157
|
Q04206
|
Transcription factor p65
|
RELA
|
62
|
0.0130
|
0.6038
|
P37231
|
Peroxisome proliferator-activated receptor gamma, PPAR-gamma
|
PPARG
|
61
|
0.0105
|
0.6157
|
O15519
|
CASP8 and FADD-like apoptosis regulator
|
CASP8
|
57
|
0.0087
|
0.6015
|
Q07817
|
Bcl-2-like protein 1, Bcl2-L-1
|
BCL2L1
|
56
|
0.0059
|
0.6015
|
P09601
|
Heme oxygenase 1
|
HMOX1
|
56
|
0.0099
|
0.6015
|
P05362
|
Intercellular adhesion molecule 1, ICAM-1
|
ICAM1
|
56
|
0.0028
|
0.5970
|
P05067
|
Amyloid-beta precursor protein, APP
|
APP
|
56
|
0.0320
|
0.5992
|
P05121
|
Plasminogen activator inhibitor 1, PAI, PAI-1
|
SERPINE1
|
55
|
0.0113
|
0.6015
|
P05112
|
Interleukin-4, IL-4
|
IL4
|
55
|
0.0073
|
0.5925
|
2.4 GO Biology Feature Rich Analysis
A total of 158 common targets of the serum dragon bile compound target and pneumonia-related target were analyzed for GO richness, and the top 5 riching processes include response to drug, signal transduction, positive regulation of response to lipopolysaccharide, negative regulation of apoptotic process and inflammatory response. The rich results were all associated with the top 30 genes, such as IL-6, IL-10 and FOS, and the top 20 biological processes were presented in the form of bubble charts, as shown in Figure 3. Quick Go's interpretation of response to drug refers to any process that causes changes in the body's state or activity (movement, secretion, enzyme production, gene expression, etc.) caused by lipid polysaccharose stimulation. Inflammatory response refers to the immediate defensive response of vertebrate tissue to infection or injury caused by chemical or physical substances, characterized by local vascular dilation, plasma seepage into cell gaps, and white blood cells and macrophages, which are similar to inflammatory reactions. The Cytoscape 3.6.1 software plug-in "Bingo" was imported into the Serum Dragon Bile Composite Target, and the species was set as "human", and P<1.0×10-11 was taken for visual analysis of biological processes. The yellow circle represents the biological process of the adjusted P<1.0×10-11, and the size of the circle indicates how much of the relevant target is well-connected in the path, as shown in Figure 4. The darker the color of the circle represents the stronger the concentration effect, reflecting that the mechanism of action of seroclon bile against pneumonia involves multiple biological processes in the body, and the various biological processes are related to each other, and also indicates that the active ingredient of serococcal bile may play an anti-pneumonia role by regulating these biological processes.
2.5 KEGG path analysis
The 158 potential targets were mapped to the database for KEGG path agglus rich analysis, and a total of 113 signal paths were obtained. By screening KEGG rich analysis P≤0.000001, FRD<0.001 screened out a total of 29 signal pathways of major richness of key targets, which are closely related to the mechanism of the role of red dragon bile against pneumonia, including Pathways In cancer, Bradder cancer, Hepatitis B, TNF signaling pathway, Prostate cancer and Non-small cell lung cancer, etc., are associated with treatments such as bladder cancer, liver cancer, prostate cancer, etc., and the first 20 pathways with significant differences are output in the form of bar charts, as shown in Figure 5.
Using Cytoscape 3.6.1 software, 158 common genes, diseases and 6 active ingredients were visualized and analyzed to create an interactive network of serum gallblades against pneumonia. After screening out the corresponding interactive proteins and visualizing them with different color and shape graphs, the network relationship between the active chemical composition and the target can be seen intuitively. The results can be seen in Figure 6.