2.1 Screening of active ingredients and related targets
43 chemical components of Gastrodiae Rhizoma (Herb), 188 chemical components of Lycii Fructus (TCMSP), and 33 chemical components of Ziziphi Spinosae Semen (TCMSP) were preliminarily extracted. After screening by TCMSP (OB ≥ 30%, DL ≥ 0.18) and SwissADME, 25(Gastrodiae Rhizoma), 45 (Lycii Fructus) and 9 (Ziziphi Spinosae Semen) active components were obtained, including quercetin, dauricine, cyanin, and sanjoinenine (Tables 1 and 2). At the same time, four active ingredients, Betaine (Lycii Fructus), jujuboside A (Ziziphi Spinosae Semen), Spinosin (Ziziphi Spinosae Semen), and Gastrodin (Gastrodiae Rhizoma), which are not screened by the above conditions but have been reported to have sedative and sedative effects, are added to the table.
After predicting the active ingredient targets, it was found that there were 389 active ingredient targets in Lycii Fructus, 47 active ingredient targets in Ziziphi Spinosae Semen, and 173 active ingredient targets in Gastrodiae Rhizoma. After merging, a total of 303 active ingredient targets were obtained by deleting duplicate values.
Table 1
Main active ingredients in Gastrodiae Rhizoma
Drug
|
Ingredient ID
|
Mark
|
Ingredient name
|
GI absorption
|
Druglikeness
(yes༞3)
|
Gastrodiae Rhizoma
|
HBIN009937
|
TM1
|
4,4'-dihydroxy dibenzyl ether
|
High
|
4
|
HBIN009938
|
TM2
|
4,4'-dihydroxy diphenyl methane
|
High
|
5
|
HBIN009959
|
TM3
|
4-(4'-hydroxybenzyloxy)benzyl methyl ether
|
High
|
5
|
HBIN009960
|
TM4
|
4-(4'-hydroxybenzyloxy)benzyl nethyl ether
|
High
|
5
|
HBIN010380
|
TM5
|
4-ethoxymethylphenyl-4'-hydroxybenzylether
|
High
|
5
|
HBIN010513
|
TM6
|
4-hydroxybenzylamine
|
High
|
3
|
HBIN010518
|
TM7
|
4-hydroxybenzyl mathyl ether
|
High
|
3
|
HBIN010519
|
TM8
|
4-hydroxybenzyl methyl ether
|
High
|
3
|
HBIN018559
|
TM9
|
bis(4-hydroxybenzyl)ether
|
High
|
5
|
HBIN018560
|
TM10
|
bis(4-hydroxybenzyl)ether mono-beta-d-glucopyranoside
|
High
|
5
|
HBIN020993
|
TM11
|
citronellal
|
High
|
3
|
HBIN022781
|
TM12
|
dauricine
|
High
|
3
|
HBIN025849
|
TM13
|
ethoxysanguinarine
|
High
|
5
|
HBIN027383
|
TM14
|
gastrodamine
|
High
|
5
|
HBIN027384
|
TM15
|
Gastrodin
|
High
|
4
|
HBIN029268
|
TM16
|
hexadecanoic acid
|
High
|
3
|
HBIN035490
|
TM17
|
m-hydroxybenzoicacid
|
High
|
3
|
HBIN039671
|
TM18
|
p-hydroxybenzaldehyde
|
High
|
3
|
HBIN039681
|
TM19
|
p-hydroxybenzyl alcohol
|
High
|
3
|
HBIN039682
|
TM20
|
p-hydroxy benzyl ethylether
|
High
|
3
|
HBIN040911
|
TM21
|
protocatechuic aldehyde
|
High
|
3
|
HBIN045062
|
TM22
|
succinic acid
|
High
|
3
|
HBIN045071
|
TM23
|
suchilactone
|
High
|
5
|
HBIN047744
|
TM24
|
vanillin
|
High
|
3
|
HBIN047745
|
TM25
|
vanillin acetate
|
High
|
5
|
HBIN047752
|
TM26
|
Vanillyl alcohol
|
High
|
3
|
Table 2
Main active ingredients in Lycii Fructus, and Ziziphi Spinosae Semen
Drug
|
Ingredient ID
|
Mark
|
Ingredient name
|
OB(%)
|
DL
|
Lycii Fructus
|
MOL001323
|
GQZ1
|
Sitosterol alpha1
|
43.28
|
0.78
|
MOL003578
|
GQZ2
|
Cycloartenol
|
38.69
|
0.78
|
MOL001494
|
GQZ3
|
Mandenol
|
42
|
0.19
|
MOL001495
|
GQZ4
|
Ethyl linolenate
|
46.1
|
0.2
|
MOL001979
|
GQZ5
|
LAN
|
42.12
|
0.75
|
MOL000449
|
GQZ6
|
Stigmasterol
|
43.83
|
0.76
|
MOL000358
|
GQZ7
|
beta-sitosterol
|
36.91
|
0.75
|
MOL005406
|
GQZ8
|
atropine
|
45.97
|
0.19
|
MOL005438
|
GQZ9
|
campesterol
|
37.58
|
0.71
|
MOL006209
|
GQZ10
|
cyanin
|
47.42
|
0.76
|
MOL007449
|
GQZ11
|
24-methylidenelophenol
|
44.19
|
0.75
|
MOL008173
|
GQZ12
|
daucosterol_qt
|
36.91
|
0.75
|
MOL008400
|
GQZ13
|
glycitein
|
50.48
|
0.24
|
MOL010234
|
GQZ14
|
delta-Carotene
|
31.8
|
0.55
|
MOL000953
|
GQZ15
|
CLR
|
37.87
|
0.68
|
MOL009604
|
GQZ16
|
14b-pregnane
|
34.78
|
0.34
|
MOL009612
|
GQZ17
|
(24R)-4alpha-Methyl-24-ethylcholesta-7,25-dien-3beta-ylacetate
|
46.36
|
0.84
|
MOL009615
|
GQZ18
|
24-Methylenecycloartan-3beta,21-diol
|
37.32
|
0.8
|
MOL009617
|
GQZ19
|
24-ethylcholest-22-enol
|
37.09
|
0.75
|
MOL009618
|
GQZ20
|
24-ethylcholesta-5,22-dienol
|
43.83
|
0.76
|
MOL009620
|
GQZ21
|
24-methyl-31-norlanost-9(11)-enol
|
38
|
0.75
|
MOL009621
|
GQZ22
|
24-methylenelanost-8-enol
|
42.37
|
0.77
|
MOL009622
|
GQZ23
|
Fucosterol
|
43.78
|
0.76
|
MOL009631
|
GQZ24
|
31-Norcyclolaudenol
|
38.68
|
0.81
|
MOL009633
|
GQZ25
|
31-norlanost-9(11)-enol
|
38.35
|
0.72
|
MOL009634
|
GQZ26
|
31-norlanosterol
|
42.2
|
0.73
|
MOL009635
|
GQZ27
|
4,24-methyllophenol
|
37.83
|
0.75
|
MOL009639
|
GQZ28
|
Lophenol
|
38.13
|
0.71
|
MOL009640
|
GQZ29
|
4alpha,14alpha,24-trimethylcholesta-8,24-dienol
|
38.91
|
0.76
|
MOL009641
|
GQZ30
|
4alpha,24-dimethylcholesta-7,24-dienol
|
42.65
|
0.75
|
MOL009642
|
GQZ31
|
4alpha-methyl-24-ethylcholesta-7,24-dienol
|
42.3
|
0.78
|
MOL009644
|
GQZ32
|
6-Fluoroindole-7-Dehydrocholesterol
|
43.73
|
0.72
|
MOL009646
|
GQZ33
|
7-O-Methylluteolin-6-C-beta-glucoside_qt
|
40.77
|
0.3
|
MOL009650
|
GQZ34
|
Atropine
|
42.16
|
0.19
|
MOL009651
|
GQZ35
|
Cryptoxanthin monoepoxide
|
46.95
|
0.56
|
MOL009653
|
GQZ36
|
Cycloeucalenol
|
39.73
|
0.79
|
MOL009656
|
GQZ37
|
(E,E)-1-ethyl octadeca-3,13-dienoate
|
42
|
0.19
|
MOL009660
|
GQZ38
|
methyl (1R,4aS,7R,7aS)-4a,7-dihydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,5,6,7a-tetrahydrocyclopenta[d]pyran-4-carboxylate
|
39.43
|
0.47
|
MOL009662
|
GQZ39
|
Lantadene A
|
38.68
|
0.57
|
MOL009664
|
GQZ40
|
Physalin A
|
91.71
|
0.27
|
MOL009665
|
GQZ41
|
Physcion-8-O-beta-D-gentiobioside
|
43.9
|
0.62
|
MOL009677
|
GQZ42
|
lanost-8-en-3beta-ol
|
34.23
|
0.74
|
MOL009678
|
GQZ43
|
lanost-8-enol
|
34.23
|
0.74
|
MOL009681
|
GQZ44
|
Obtusifoliol
|
42.55
|
0.76
|
MOL000098
|
GQZ45
|
quercetin
|
46.43
|
0.28
|
MOL000430
|
GQZ46
|
Betaine
|
40.92
|
0.01
|
Ziziphi Spinosae Semen
|
MOL001521
|
SZR1
|
ceanothic acid
|
33.41
|
0.77
|
MOL001522
|
SZR2
|
(S)-Coclaurine
|
42.35
|
0.24
|
MOL001525
|
SZR3
|
Daucosterol
|
36.91
|
0.75
|
MOL001527
|
SZR4
|
jujuboside A_qt
|
34.96
|
0.62
|
MOL001532
|
SZR5
|
phytosterol
|
36.91
|
0.75
|
MOL001539
|
SZR6
|
sanjoinenine
|
67.28
|
0.79
|
MOL001542
|
SZR7
|
swertisin
|
31.83
|
0.75
|
MOL001546
|
SZR8
|
zizyphusine
|
41.53
|
0.55
|
MOL000211
|
SZR9
|
Mairin
|
55.38
|
0.78
|
MOL001526
|
SZR10
|
jujuboside A
|
8.04
|
0.02
|
MOL001540
|
SZR11
|
Spinosin
|
6.31
|
0.72
|
2.2 Screening of disease targets related to sedation and tranquilizing mind
In the GeneCards database target information, target targets with a Score > 1.5 are identified as potential targets for insomnia, while target targets with a Score > 7.0 are identified as potential targets for any entity. Combining the target information related to sedation and tranquilizing mind in GeneCards, OMIM, and Drugbank databases, the duplicate values were deleted after merging, and finally, 492 related targets were obtained.
2.3 Construction of active ingredient-disease target PPI network
A total of 81 common targets were obtained for both component targets and disease targets (Fig. 1). Furthermore, the target was submitted to the STRING11.5 platform to obtain a PPI network (Fig. 2). To analyze the mechanism of action of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen more accurately, the PPI network was obtained and its intrinsic modules were further identified. After obtaining the PPI network, the MCODE plugin in Cytoscape 3.9.1 was used to analyze the interaction relationship through the molecular complex detection algorithm, and the module was obtained (Fig. 3). According to the P-value, the biological processes with the three best scores in the PPI network and Module were retained for functional description (Table 2).
Table 3
Description of PPI network functions for three modules
MCODE1
|
biologic function
|
GO ID
|
Description
|
P value
|
0.0159
|
Biological processes
|
GO:0060559
|
Positive regulation of calcidiol 1-monooxygenase activity
|
GO:0002874
|
regulation of chronic inflammatory response to antigenic stimulus
|
GO:0030730
|
sequestering of triglyceride
|
Molecular function
|
GO:0070851
|
growth factor receptor binding
|
GO:0005125
|
cytokine activity
|
GO:0005126
|
cytokine receptor binding
|
MCODE2
|
Biological processes
|
GO:0051932
|
synaptic transmission, GABAergic
|
1.88e-10
|
GO:1904862
|
inhibitory synapse assembly
|
GO:0007214
|
gamma-aminobutyric acid signaling pathway
|
Molecular function
|
GO:0008503
|
benzodiazepine receptor activity
|
GO:0022851
|
GABA-gated chloride ion channel activity
|
GO:0005237
|
inhibitory extracellular ligand-gated monoatomic ion channel activity
|
MCODE3
|
Biological processes
|
GO:0001993
|
regulation of systemic arterial blood pressure by norepinephrine-epinephrine
|
9.39e-10
|
GO:0071880
|
adenylate cyclase-activating adrenergic receptor signaling pathway
|
GO:0007200
|
phospholipase C-activating G protein-coupled receptor signaling pathway
|
Molecular function
|
GO:0004935
|
adrenergic receptor activity
|
GO:0008227
|
G protein-coupled amine receptor activity
|
GO:0004993
|
G protein-coupled serotonin receptor activity
|
2.4 Enrichment analysis of intersection target functions and pathways
The functions of multiple targets were closely related to their sedation and tranquilizing mind effects. The main biological processes involved in the Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen: cellular response to organic cyclic compound, regulation of tube diameter, and response to xenobiotic stimulus, the main cellular components were postsynaptic membrane, membrane raft, GABA-ergic synapse, the main molecular functions included G protein-coupled amine receptor activity, neurotransmitter receptor activity, catecholamine binding (Fig. 4). The main pathways were neuroactive ligand-receptor interaction, chemical carcinogenesis-receptor activation, serotonergic synapse, and Lipid and atherosclerosis (Fig. 5). The enrichment results of the target pathway (Table 4) indicated that Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen significantly acted on the neuroactive ligand-receptor interaction to exert sedation and tranquilizing mind effects.
![](https://myfiles.space/user_files/122228_c8a1650c59388082/122228_custom_files/img1688475131.png)
![](https://myfiles.space/user_files/122228_c8a1650c59388082/122228_custom_files/img1688475145.png)
2.5 Construction of component target network diagram
Active ingredient sedation and tranquilizing mind network were constructed using Cytoscape 3.9.1 (Fig. 6). By analyzing the network Topology parameters that play a calming role through the built-in Network Analyzer of CytoScape 3.9.1, the core components and core action targets were obtained. Cytoscape network analysis showed that GQZ45 (Quercetin) had a connectivity degree of 34, betweenness centrality of 0.4017, and a closeness centrality of 0.4232. It was predicted that Quercetin was the main component of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen which played a calming role. Secondly, GQZ34 (Atropine) (connectivity: 27, betweenness: 0.1314, compactness: 0.4021), SZR2 (mydrine) in Ziziphi Spinosae Semen was the main component (connectivity: 14, betweenness: 0.0494, compactness: 0.3610), and TM12 (Dauricine) in Gastrodiae Rhizoma was the main component (connectivity: 8, betweenness: 0.0723, compactness: 0.3029) (Table 5). The connectivity of PTGS2 in the network was 16, the mediation was 0.1250, and the tightness was 0.4232. It was predicted that PTGS2 was the main target for the calming effect of Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen. PTGS1, MAOB, GABRA1, SLC6A2, ADRB2, CHRM1, HTR2A, and ADRA1A were also relatively important targets (Table 6).
Table 5
Main active ingredient network node characteristic parameters
Mark ID
|
Compound name
|
Connectivity
|
Betweenness
|
Compactness
|
GQZ45
|
quercetin
|
34
|
0.401702098
|
0.423220974
|
GQZ34
|
Atropine
|
27
|
0.131435047
|
0.402135231
|
GQZ7
|
beta-sitosterol
|
23
|
0.133755168
|
0.385665529
|
TM12
|
dauricine
|
8
|
0.072296565
|
0.302949062
|
TM5
|
4-ethoxymethylphenyl-4'-hydroxybenzylether
|
6
|
0.042675336
|
0.372937294
|
TM3
|
4-(4'-hydroxybenzyloxy)benzyl methyl ether
|
5
|
0.027101405
|
0.370491803
|
SZR2
|
(S)-Coclaurine
|
14
|
0.049455498
|
0.361022364
|
SZR8
|
zizyphusine
|
6
|
0.012606377
|
0.331378299
|
SZR6
|
sanjoinenine
|
3
|
0.003918413
|
0.325648415
|
Table 6
Main active ingredient target network node characteristic parameters
Mark ID
|
Compound name
|
Connectivity
|
Betweenness
|
Compactness
|
PTGS2
|
Prostaglandin G/H synthase 2
|
16
|
0.12501423
|
0.423220974
|
PTGS1
|
Prostaglandin G/H synthase 1
|
12
|
0.086957031
|
0.410909091
|
MAOB
|
Amine oxidase
|
9
|
0.066102002
|
0.388316151
|
GABRA1
|
Gamma-aminobutyric acid receptor subunit alpha-1
|
7
|
0.0491451
|
0.385665529
|
SLC6A2
|
Sodium-dependent noradrenaline transporter
|
6
|
0.020399725
|
0.331378299
|
ADRB2
|
Beta-2 adrenergic receptor
|
6
|
0.041484238
|
0.383050847
|
CHRM1
|
Muscarinic acetylcholine receptor M1
|
6
|
0.00886712
|
0.320113314
|
HTR2A
|
5-hydroxytryptamine receptor 2A
|
6
|
0.018837197
|
0.345565749
|
ADRA1A
|
Alpha-1A adrenergic receptor
|
6
|
0.028127314
|
0.352024922
|
2.6 Molecular docking verification
The active ingredients (quercetin, dauricine, (S) - Coclaurine) ranking first in each main drug in Table 5 were used as ligand compounds, and the core target (PTGS2) ranking first in Table 6 was used as receptor protein for molecular docking. The Binding energy of PTGS2 with quercetin, dauricine, and (S) - Coclaurine was − 9.8 kcal/mol, -10.0 kcal/mol, and − 8.9 kcal/mol, respectively. The smaller the binding energy of ligand and receptor, the more stable the molecular binding conformation. It was generally believed that the ligand and receptor could bind at Binding energy<-5 kcal/mol. Among them, quercetin bound to PTGS2 through four hydrogen bonds formed by HIS-39, TYR-130, ARG-44, ASP-125, dauricine bound to PTGS2 through one hydrogen bond formed by APG-376, and (S) - Coclaurine bound to PTGS2 through two hydrogen bonds formed by GLY-45 and HIS-39. Therefore, it could be concluded that Gastrodiae Rhizoma, Lycii Fructus, and Ziziphi Spinosae Semen could effectively exert sedation and tranquilizing mind effects.