Yanshuang Zhuang‡
a,
Kunming Qin‡bcd,
Bing Yang‡a,
Xiao Liu‡a,
Baochang Cai‡*ab and
Hao Cai‡*a
aEngineering Center of State Ministry of Education for Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing 210023, China. E-mail: haocai_98@126.com; 295331981@qq.com; bingbingyang_2012@163.com; 1498223254@qq.com; Fax: +86-25-68193500; Tel: +86 13770500190 Tel: +86 13585148874
bNanjing Haichang Chinese Medicine Group Co., Ltd., Nanjing 210061, China. E-mail: qinkm123@126.com; baochangcai_2012@126.com
cNanjing Haiyuan Prepared Slices of Chinese Crude Drugs Co., Ltd., Nanjing 210061, China
dHuaihai Institute of Technology, Lianyu Gang 222005, China
First published on 27th February 2018
Xanthii Fructus (XF), a famous traditional Chinese medicine (TCM), has been widely used in the treatment of rhinitis and other diseases. However, the targets of the main XF components found in the blood after oral administration of XF extract are still unclear. In the current study, a feasible systems pharmacology method was developed to predict these targets. In accordance with our previous research, XF components were selected including cleomiscosin A, myristic acid, succinic acid, xanthosine, sitostenone, emodin, apigenin, and chrysophanol. Three components, namely emodin, apigenin, and chrysophanol, failed to be detected with target proteins, thus the other five components, namely cleomiscosin A, myristic acid, succinic acid, xanthosine and sitostenone, were eventually chosen for further systematic analysis. Ninety-nine target proteins and fifty-two pathways were found after a series of analyses. The frequency of some target proteins was much higher than that of others; high frequencies were obtained for P15086, P07360, P07195, MAOM_HUMAN (P23368), P35558, P35520, ACE_HUMAN (P12821), C1S_HUMAN (P09871), PH4H_HUMAN (P00439), FPPS_HUMAN (P14324), P50613, P12724, IMPA1_HUMAN (P29218), HXK1_HUMAN (P19367), P14061, and MCR_HUMAN (P08235). The frequency of eight pathways was also high, including Generic Transcription Pathway, RNA Polymerase II Transcription, Metabolism, Metabolism of steroids, Gene expression (Transcription), Cellular responses to stress, Platelet activation, signaling and aggregation, Signaling by Receptor Tyrosine Kinases, and Cellular Senescence. This study identified a common pathway – the Metabolism pathway – for all five XF components. We successfully developed a network pharmacology method to predict the potential targets of the main XF components absorbed in serum after oral administration of XF extract.
Network pharmacology, based on the network of “disease-gene-target-drug” interactions, is a way of revealing the synergistic effects of complex drugs on the human system and finding efficient and low toxicity multi-target new drugs at the network level by observing the intervention of drugs and their impact on disease. With information databases such as gene network libraries, protein network libraries, disease network libraries, and drug network libraries, and systematic spectrogram data analysis, network pharmacology is able to reveal mysterious disease–disease, disease phenotype-target protein, target protein–drug and drug–drug linkages.1–7
Uncovering the material basis of TCM is the key and precondition for TCM quality control, which puts it at the core of TCM modernization. In a network pharmacology study, drug–drug networks can be constructed based on the similarities in the structures and efficacies of different drugs. In the process of TCM modernization, some researchers have achieved good initial results in exploring the essential properties of TCMs and revealing their comprehensive overall effects on multi-pathways, multi-targets and multi-components via the research ideas of network pharmacology.8–11
Xanthii Fructus (XF) is the ripe fruit of Xanthium sibiricum Patr. XF is used for the treatment of cramping, numbness of the limbs, ulcers, sinusitis, catarrhs, and pruritus, for its function in smoothing nasal orifices and eliminating wind-dampness.12 In modern clinic application, XF is commonly used for the treatment of rhinitis. Particularly when combined with Magnoliae flos, mint and other Chinese medicines, XF has enhanced effects in curing chronic rhinitis, allergic rhinitis and other rhinitis.13
No. | Compound | Protein code | Protein name | Frequency |
---|---|---|---|---|
1 | Cleomiscosin A | P06276 | CHLE_HUMAN | 3 |
2 | Cleomiscosin A | P23141 | EST1_HUMAN | 3 |
3 | Cleomiscosin A | P62937 | P62937 | 3 |
4 | Cleomiscosin A | P00918 | CAH2_HUMAN | 3 |
5 | Cleomiscosin A | P24941 | P24941 | 3 |
6 | Cleomiscosin A | P07339 | CATD_HUMAN | 3 |
7 | Cleomiscosin A | P03372 | ESR1_HUMAN | 3 |
8 | Cleomiscosin A | Q15078 | CD5R1_HUMAN | 3 |
9 | Cleomiscosin A | P00915 | CAH1_HUMAN | 3 |
10 | Cleomiscosin A | P04062 | GLCM_HUMAN | 3 |
11 | Cleomiscosin A | P11309 | PIM1_HUMAN | 3 |
12 | Cleomiscosin A | P00491 | PNPH_HUMAN | 3 |
13 | Cleomiscosin A | Q9NP99 | Q9NP99 | 3 |
14 | Cleomiscosin A | O14965 | STK6_HUMAN | 3 |
15 | Cleomiscosin A | Q16539 | Q16539 | 4 |
16 | Cleomiscosin A | Q92731 | ESR2_HUMAN | 3 |
17 | Cleomiscosin A | Q07343 | PDE4B_HUMAN | 4 |
18 | Cleomiscosin A | O14757 | CHK1_HUMAN | 4 |
19 | Cleomiscosin A | P45983 | MK08_HUMAN | 4 |
20 | Cleomiscosin A | P08758 | ANXA5_HUMAN | 4 |
21 | Myristic acid | P12643 | BMP2_HUMAN | 3 |
22 | Myristic acid | P28482 | MK01_HUMAN | 3 |
23 | Myristic acid | P09211 | GSTP1_HUMAN | 3 |
24 | Myristic acid | P15121 | ALDR_HUMAN | 3 |
25 | Myristic acid | P49137 | P49137 | 3 |
26 | Myristic acid | P10828 | P10828 | 3 |
27 | Myristic acid | P11309 | P11309 | 3 |
28 | Myristic acid | P27338 | AOFB_HUMAN | 3 |
29 | Myristic acid | P62937 | P62937 | 3 |
30 | Myristic acid | P02774 | VTDB_HUMAN | 4 |
31 | Myristic acid | P02768 | ALBU_HUMAN | 3 |
32 | Myristic acid | P52732 | KIF11_HUMAN | 4 |
33 | Myristic acid | P02652 | APOA2_HUMAN | 3 |
34 | Myristic acid | P00918 | CAH2_HUMAN | 3 |
35 | Myristic acid | P08842 | STS_HUMAN | 3 |
36 | Myristic acid | P02766 | TTHY_HUMAN | 3 |
37 | Myristic acid | Q14994 | NR1I3_HUMAN | 3 |
38 | Myristic acid | P37231 | PPARG_HUMAN | 3 |
39 | Myristic acid | P30044 | PRDX5_HUMAN | 3 |
40 | Succinic acid | P09012 | P09012 | 3 |
41 | Succinic acid | P02743 | P02743 | 4 |
42 | Succinic acid | P12931 | SRC_HUMAN | 4 |
43 | Succinic acid | O15382 | O15382 | 4 |
44 | Succinic acid | P18031 | PTN1_HUMAN | 4 |
45 | Succinic acid | P15086 | P15086 | 5 |
46 | Succinic acid | P07360 | P07360 | 5 |
47 | Succinic acid | P02788 | TRFL_HUMAN | 4 |
48 | Succinic acid | P03950 | ANGI_HUMAN | 4 |
49 | Succinic acid | P07195 | P07195 | 5 |
50 | Succinic acid | P23368 | MAOM_HUMAN | 5 |
51 | Succinic acid | Q9P2W7 | B3GA1_HUMAN | 4 |
52 | Succinic acid | P35558 | P35558 | 6 |
53 | Succinic acid | P35520 | P35520 | 7 |
54 | Succinic acid | P12821 | ACE_HUMAN | 7 |
55 | Succinic acid | P09871 | C1S_HUMAN | 6 |
56 | Succinic acid | P00439 | PH4H_HUMAN | 5 |
57 | Succinic acid | P14324 | FPPS_HUMAN | 8 |
58 | Succinic acid | P50613 | P50613 | 8 |
59 | Succinic acid | P12724 | P12724 | 6 |
60 | Xanthosine | Q9BW91 | Q9BW91 | 3 |
61 | Xanthosine | P37173 | TGFR2_HUMAN | 3 |
62 | Xanthosine | P04062 | GLCM_HUMAN | 3 |
63 | Xanthosine | O14965 | STK6_HUMAN | 3 |
64 | Xanthosine | Q13126 | Q13126 | 3 |
65 | Xanthosine | P00533 | EGFR_HUMAN | 3 |
66 | Xanthosine | P24941 | P24941 | 4 |
67 | Xanthosine | Q07343 | PDE4B_HUMAN | 3 |
68 | Xanthosine | P00915 | CAH1_HUMAN | 3 |
69 | Xanthosine | Q12884 | SEPR_HUMAN | 3 |
70 | Xanthosine | O14757 | CHK1_HUMAN | 3 |
71 | Xanthosine | Q05315 | LPPL_HUMAN | 3 |
72 | Xanthosine | P04745 | P04745 | 3 |
73 | Xanthosine | P18075 | BMP7_HUMAN | 4 |
74 | Xanthosine | P03950 | ANGI_HUMAN | 4 |
75 | Xanthosine | P00491 | PNPH_HUMAN | 4 |
76 | Xanthosine | P29218 | IMPA1_HUMAN | 5 |
77 | Xanthosine | Q99933 | BAG1_HUMAN | 4 |
78 | Xanthosine | P19367 | HXK1_HUMAN | 5 |
79 | Xanthosine | P17707 | DCAM_HUMAN | 4 |
80 | Sitostenone | P52895 | AK1C2_HUMAN | 3 |
81 | Sitostenone | P49137 | P49137 | 3 |
82 | Sitostenone | P55210 | CASP7_HUMAN | 3 |
83 | Sitostenone | P12643 | BMP2_HUMAN | 3 |
84 | Sitostenone | P08842 | STS_HUMAN | 3 |
85 | Sitostenone | P27338 | AOFB_HUMAN | 3 |
86 | Sitostenone | P02774 | VTDB_HUMAN | 4 |
87 | Sitostenone | P11309 | P11309 | 3 |
88 | Sitostenone | P02768 | ALBU_HUMAN | 3 |
89 | Sitostenone | P28482 | MK01_HUMAN | 3 |
90 | Sitostenone | P45452 | MMP13_HUMAN | 4 |
91 | Sitostenone | P10828 | P10828 | 3 |
92 | Sitostenone | P52732 | KIF11_HUMAN | 3 |
93 | Sitostenone | P00918 | CAH2_HUMAN | 3 |
94 | Sitostenone | P14061 | P14061 | 5 |
95 | Sitostenone | P02652 | APOA2_HUMAN | 3 |
96 | Sitostenone | P08235 | MCR_HUMAN | 5 |
97 | Sitostenone | P06401 | PRGR_HUMAN | 4 |
98 | Sitostenone | P10275 | ANDR_HUMAN | 3 |
99 | Sitostenone | P02766 | TTHY_HUMAN | 3 |
No. of pathway | Pathway name | Frequency |
---|---|---|
Pw1 | Nuclear receptor transcription pathway | 1 |
Pw2 | Activation of the AP-1 family of transcription factors | 3 |
Pw3 | MAPK targets/nuclear events mediated by MAP kinases | 10 |
Pw4 | p38MAPK events | 3 |
Pw5 | Generic Transcription Pathway | 42 |
Pw6 | Transcriptional regulation by RUNX2 | 10 |
Pw7 | Signalling to RAS | 3 |
Pw8 | RNA polymerase II transcription | 73 |
Pw9 | Regulation of TP53 Activity through phosphorylation | 5 |
Pw10 | Metabolism | 68 |
Pw11 | Nuclear events (kinase and transcription factor activation) | 7 |
Pw12 | RUNX2 regulates osteoblast differentiation | 5 |
Pw13 | Metabolism of steroids | 23 |
Pw14 | MAP kinase activation in TLR cascade | 15 |
Pw15 | Erythrocytes take up oxygen and release carbon dioxide | 1 |
Pw16 | RUNX2 regulates bone development | 5 |
Pw17 | Signalling to ERKs | 3 |
Pw18 | Gene expression (transcription) | 80 |
Pw19 | Interleukin-17 signaling | 15 |
Pw20 | Digestion of dietary carbohydrate | 2 |
Pw21 | Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | 3 |
Pw22 | DSCAM interactions | 2 |
Pw23 | NGF signalling via TRKA from the plasma membrane | 10 |
Pw24 | Reversible hydration of carbon dioxide | 2 |
Pw25 | O2/CO2 exchange in erythrocytes | 2 |
Pw26 | Erythrocytes take up carbon dioxide and release oxygen | 1 |
Pw27 | Cellular responses to stress | 27 |
Pw28 | MyD88 cascade initiated on plasma membrane | 15 |
Pw29 | Toll like receptor 10 (TLR10) cascade | 15 |
Pw30 | Toll like receptor 5 (TLR5) cascade | 15 |
Pw31 | TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation | 15 |
Pw32 | Platelet activation, signaling and aggregation | 32 |
Pw33 | Oxidative stress induced senescence | 12 |
Pw34 | MyD88 dependent cascade initiated on endosome | 15 |
Pw35 | Toll like receptor 7/8 (TLR7/8) cascade | 15 |
Pw36 | MyD88:Mal cascade initiated on plasma membrane | 15 |
Pw37 | Toll like receptor TLR6:TLR2 cascade | 15 |
Pw38 | Spry regulation of FGF signaling | 2 |
Pw39 | Netrin-1 signaling | 12 |
Pw40 | Toll like receptor 9 (TLR9) cascade | 15 |
Pw41 | Toll like receptor 3 (TLR3) cascade | 15 |
Pw42 | Toll like receptor TLR1:TLR2 cascade | 15 |
Pw43 | Toll like receptor 2 (TLR2) cascade | 15 |
Pw44 | TRIF(TICAM1)-mediated TLR4 signaling | 15 |
Pw45 | MyD88-independent TLR4 cascade | 15 |
Pw46 | Defective HK1 causes hexokinase deficiency (HK deficiency) | 1 |
Pw47 | Metabolism of angiotensinogen to angiotensins | 4 |
Pw48 | Regulation of TP53 Activity | 6 |
Pw49 | Signaling by receptor tyrosine kinases | 81 |
Pw50 | Cellular senescence | 21 |
Pw51 | HSP90 chaperone cycle for steroid hormone receptors (SHR) | 3 |
Pw52 | Interleukin-12 family signaling | 3 |
Cleomiscosin A was related to the following pathways: nuclear receptor transcription pathway (Pw1), activation of the AP-1 family of transcription factors (Pw2), MAPK targets/nuclear events mediated by MAP kinases (Pw3), p38MAPK events (Pw4), Generic Transcription Pathway (Pw5), Transcriptional regulation by RUNX2 (Pw6), Signalling to RAS (Pw7), RNA Polymerase II Transcription (Pw8), Regulation of TP53 Activity through Phosphorylation (Pw9), Metabolism (Pw10), Nuclear Events (kinase and transcription factor activation) (Pw11), MAP kinase activation in TLR cascade (Pw14), erythrocytes take up oxygen and release carbon dioxide (Pw15), Signalling to ERKs (Pw17), Gene expression (Transcription) (Pw18), Interleukin-17 signaling (Pw19), Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation (Pw21), DSCAM interactions (Pw22), NGF signalling via TRKA from the plasma membrane (Pw23), Reversible hydration of carbon dioxide (Pw24), O2/CO2 exchange in erythrocytes (Pw25), erythrocytes take up carbon dioxide and release oxygen (Pw26), cellular responses to stress (Pw27), MyD88 cascade initiated on plasma membrane (Pw28), Toll Like Receptor 10 (TLR10) Cascade (Pw29), Toll Like Receptor 5 (TLR5) Cascade (Pw30), TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation (Pw31), platelet activation, signaling and aggregation (Pw32), oxidative stress induced senescence (Pw33), MyD88 dependent cascade initiated on endosome (Pw34), Toll Like Receptor 7/8 (TLR7/8) Cascade (Pw35), MyD88:Mal cascade initiated on plasma membrane (Pw36), Toll Like Receptor TLR6:TLR2 Cascade (Pw37), Netrin-1 signaling (Pw39), Toll Like Receptor 9 (TLR9) Cascade (Pw40), Toll Like Receptor 3 (TLR3) Cascade (Pw41), Toll Like Receptor TLR1:TLR2 Cascade (Pw42), Toll Like Receptor 2 (TLR2) Cascade (Pw43), TRIF(TICAM1)-mediated TLR4 signaling (Pw44), MyD88-independent TLR4 cascade (Pw45), Regulation of TP53 Activity (Pw48), Signaling by Receptor Tyrosine Kinases (Pw49), Cellular Senescence (Pw50) and Interleukin-12 family signaling (Pw52).
Myristic acid was related to the following pathways: nuclear receptor transcription pathway (Pw1), Activation of the AP-1 family of transcription factors (Pw2), MAPK targets/nuclear events mediated by MAP kinases (Pw3), p38MAPK events (Pw4), Generic Transcription Pathway (Pw5), Transcriptional regulation by RUNX2 (Pw6), Signalling to RAS (Pw7), RNA Polymerase II Transcription (Pw8), Metabolism (Pw10), Nuclear Events (kinase and transcription factor activation) (Pw11), RUNX2 regulates osteoblast differentiation (Pw12), Metabolism of steroids (Pw13), MAP kinase activation in TLR cascade (Pw14), RUNX2 regulates bone development (Pw16), Signalling to ERKs (Pw17), Gene expression (Transcription) (Pw18), Interleukin-17 signaling (Pw19), NGF signalling via TRKA from the plasma membrane (Pw23), Cellular responses to stress (Pw27), MyD88 cascade initiated on plasma membrane (Pw28), Toll Like Receptor 10 (TLR10) Cascade (Pw29), Toll Like Receptor 5 (TLR5) Cascade (Pw30), TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation (Pw31), Platelet activation, signaling and aggregation (Pw32), Oxidative Stress Induced Senescence (Pw33), MyD88 dependent cascade initiated on endosome (Pw34), Toll Like Receptor 7/8 (TLR7/8) Cascade (Pw35), MyD88:Mal cascade initiated on plasma membrane (Pw36), Toll Like Receptor TLR6:TLR2 Cascade (Pw37), Spry regulation of FGF signaling (Pw38), Toll Like Receptor 9 (TLR9) Cascade (Pw40), Toll Like Receptor 3 (TLR3) Cascade (Pw41), Toll Like Receptor TLR1:TLR2 Cascade (Pw42), Toll Like Receptor 2 (TLR2) Cascade (Pw43), TRIF(TICAM1)-mediated TLR4 signaling (Pw44), MyD88-independent TLR4 cascade (Pw45), Signaling by Receptor Tyrosine Kinases (Pw49) and Cellular Senescence (Pw50).
Succinic acid was related to the following pathways: p38MAPK events (Pw4), Generic Transcription Pathway (Pw5), Transcriptional regulation by RUNX2 (Pw6), Signalling to RAS (Pw7), RNA Polymerase II Transcription (Pw8), Metabolism (Pw10), RUNX2 regulates osteoblast differentiation (Pw12), Metabolism of steroids (Pw13), RUNX2 regulates bone development (Pw16), Signalling to ERKs (Pw17), Gene expression (Transcription) (Pw18), NGF signalling via TRKA from the plasma membrane (Pw23), Platelet activation, signaling and aggregation (Pw32), Spry regulation of FGF signaling (Pw38), Netrin-1 signaling (Pw39), Metabolism of Angiotensinogen to Angiotensins (Pw47) and Signaling by Receptor Tyrosine Kinases (Pw49).
Xanthosine was related to the following pathways: Metabolism (Pw10), Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation (Pw21), Defective HK1 causes hexokinase deficiency (HK deficiency) (Pw46) and Interleukin-12 family signaling (Pw52).
Sitostenone was related to the following pathways: nuclear receptor transcription pathway (Pw1), Generic Transcription Pathway (Pw5), transcriptional regulation by RUNX2 (Pw6), Signalling to RAS (Pw7), RNA Polymerase II Transcription (Pw8), Metabolism (Pw10), Nuclear Events (kinase and transcription factor activation) (Pw11), RUNX2 regulates osteoblast differentiation (Pw12), Metabolism of steroids (Pw13), RUNX2 regulates bone development (Pw16), Gene expression (Transcription) (Pw18), Interleukin-17 signaling (Pw19), Cellular responses to stress (Pw27), Signaling by Receptor Tyrosine Kinases (Pw49) and HSP90 chaperone cycle for steroid hormone receptors (SHR) (Pw51).
We were surprised to find that the five components have one common pathway – the Metabolism pathway (Pw10). Nine other pathways occurred frequently including Generic Transcription Pathway (Pw5), RNA Polymerase II Transcription (Pw8), Metabolism (Pw10), Metabolism of steroids (Pw13), Gene expression (Transcription) (Pw18), Cellular responses to stress (Pw27), Platelet activation, signaling and aggregation (Pw32), Signaling by Receptor Tyrosine Kinases (Pw49) and Cellular Senescence (Pw50).
According to the network pharmacological prediction of the five components in XF, all five components can be connected with the same pathway via the same target, and also can be connected with the same pathways with different targets. Different components can produce the same effect through different ways, and also can offer multi-target synergy.
Interestingly, this predicted common pathway is consistent with the result we got from the metabolic pathway analysis experiment (unpublished), which indicates that this result is reliable although it still requires further verification.
Footnotes |
† Electronic supplementary information (ESI) available. See DOI: 10.1039/c8ra00186c |
‡ Dr Baochang Cai and Dr Hao Cai are responsible for the idea behind this paper. Dr Yanshuang Zhuang is the main implementer of this paper. The remaining authors helped with this paper. |
This journal is © The Royal Society of Chemistry 2018 |