Networks can be used to view global drug-targets-pathway-disease relationships between nodes[29,30]. Network pharmacology approach have been applied in drug discovery[31-35]. In this research, we utilized the network pharmacology method to illustrate SR-CR inter-reinforcement mechanism by mapping compound combinations into SR-CR chemical space.
Target-Pathway association profile of Common compounds for the herb pair
The herb-pair shared 2 common compounds and they have 24 targets from four public databases. We obtained 24 targets associated 15 KEGG pathways and 22 REACTOME pathways in total and the inter-reinforcement mechanisms of herb-pair were mapped to the target-pathway network according to their targets information (Fig. 4, see Supplementary Table S2 for further details of these pathways). The degree of PIK3CG among the 24 targets is the largest one. We also obtained 27 targets associated 87 diseases in total and an average degree of 14 targets per compound (Fig. 5a, see Supplementary Table S3 for further details of these 87 diseases).
Table 2 Physical and chemical properties of the common compounds
Common compound
|
LogP
|
OB(%)[36]
|
pKa
|
alexandrin
|
8.615
|
20.63
|
12.91±0.70
|
hederagenin
|
7.065
|
36.91
|
4.63±0.70
|
The two common compounds were connected to multiple targets and they have 6 common targets, namely PTGS2, PGR, NCOA2, ADH1C, PTGS1, LYZ. The 6 targets associated 35 diseases and the maximum degree of 32 diseases is PTGS2 in Fig. 5b. (See SupplementaryTable S4 for further details of these 35 diseases)
Compound-Target-Pathway Associations (CTPAs) network
To understand the complex interaction of herb-pair’s targets at system level, we constructed a Compound-Target-Pathway Associations (CTPAs) network. The CTPAs network embodied 327 nodes (100 compounds, 104 targets, and 128 pathways) (Fig. 6, see Supplementary Table S5 for further details of these pathways associated targets). The mean degree value (the number of associated common targets) of candidate compounds was 1.08, and 24 compounds had a degree value >10, indicating that most of the compounds regulated multiple targets to exert various therapeutic effects in the herb-pair’s chemical space. The top 5 degree of Compound-Target-Pathway network were Neuroactive ligand-receptor interaction, Morphine addiction, Retrograde endocannabinoid signaling, Calcium signaling pathway, Nicotine addiction.
Compound-Target-Disease interactions (CTDIs) network
The Compound-Target-Disease interactions (CTDIs) network was built by targets and diseases [37-41]. Node size was proportional to its degree. The light green (green) ellipses indicated Sparganii Rhizoma (Curcumae Rhizoma) compounds, the pink ellipses indicates the targets of herb-pair’s compounds, and the cyan ellipses indicated the disease types (Fig. 7, see SupplementaryTable S6 for further details of these diseases). The involved diseases were type 2 diabetes, hypercholesterolemia, hypertension, cardiovascular diseases, etc.
All of these targets were shown by the gene name. All of the targets and diseases were selected to construct the Compound-Target-Disease interactions (CTDIs) network by linking the targets to the corresponding diseases. All visualized network graphs were constructed by Cytoscape 3.2.1 (http://www.cytoscape.org/), an open software package project for visualizing, integrating, modeling and analyzing the interaction networks[42,43].
Target-Pathway Association Interactions (TPAs)
We analyzed Target-Pathway Association Interactions (TPAs) and screened the combinatorial compounds which their targets were in the same pathway[21]. Then we combined the two compounds which one from Sparganii Rhizoma and the other from Curcumae Rhizoma. Finally, 14370 pairs of pathway-guided combination compounds, including 1267 pairs of compound combinations (Supplementary Table S7) were obtained. After setting compounds similarity to 0.7 in each compound combinations (Fig. 8), 497 pairs of compound combinations associated 128 pathways (SupplementaryTable S8) were obtained.
Pathway guided compound combinations
The pathway of platelet activation is one of 128 pathways, and platelets play a key role in preventing blood loss in response to injury, thrombosis, atherosclerosis, inflammation and metastasis, but they are also responsible for the formation of pathogenic thrombi that cause acute manifestations of vascular atherothrombotic disease[44-46]. In this research, four compound combinations and their associated targets in platelet activation pathway (Fig 9.) were obtained. The compound combination (S039, E063) acted on Akt pathway, and the compound combinations ((S039, E085), (S039, E074), (S039, E005)) targeted on the PTGS1 (the numbered chemical ingredients see the supplementary Table S1). The mechanism of compound combinations is alike drug combinations. As we knew, drug combinations can improve over single therapeutic agents in two ways[47]. In additionally, drug combinations have been used for treating diseases and reducing suffering in Chinese herbal medicine[48].
Synergy between two drugs may result in a better response than the two drugs independently[47]. In this research, we picked out another two pathways (Calcium signaling pathway, vascular smooth muscle contraction) closely related to cardiovascular diseases (CVDs) and the 3 pathways were consolidated into a “CVDs pathway” under the pathological and clinical data[49]. In order to illustrate the material basis of herb-pair inter-reinforcement mechanism, we mapped compound combinations to pathways associated compounds’ targets (supplementary Table S9).
Across all kingdoms in the tree of life, Calcium (Ca2+) is an essential element used by cells to respond and adapt to constantly changing environments[50]. Signaling occurs when the cell is stimulated to release calcium ions (Ca2+) from intracellular stores, and/or when calcium enters the cell through plasma could induce the development of atherosclerosis[49].
This strategy of studying herb-pair inter-reinforcement membrane ion channels[51]. Many diseases, such as cardiovascular diseases, type 2 diabetes, malignant hyperthermia, central core disease, associated with calcium signaling pathway[50,52]. Vascular smooth muscle contraction also plays an important role in the regulation of CVDs, there is due mechanism mapping on chemical space will lead to the development of many today’s drug discovery from Chinese herb-pairs. Future research in our group will focus on investigating compound combinations’ pathological effect on specific diseases, such as, CVDs.