Compounds in EXD
Eight hundred and ninety-five phytochemicals were collected from the six herbs in
EXD. From the TCM Database@Taiwan, 203 compounds were identified, comprising 29 in
HE, 44 in RC, 38 in RMO, 56 in RAS, seven in CPC, and 29 in RA. From the TCMSP database,
646 compounds were identified, comprising 130 in HE, 78 in RC, 174 in RMO, 125 in
RAS, 58 in CPC, and 81 in RA. 46 phytochemicals from previous studies in the literature
26]–30], 35], 45], 46], comprising 15 in HE, one in RC, five in ROM, five in RAS, 14 in CPC, 5 in RA, and
one in EXD (specific herbs unknown). Finally, a total of 721 phytochemicals were identified
in EXD after removing overlapping/duplicate compounds from the database
s and the literature (Additional file 1).
Identifying druggable compounds by LR, OB, and DL predictions
Of the 150 compounds from HE, 75 (50%) compounds were identified based on LR, 23 (15.3%)
had OB ?30% and DL index ?0.18, and only 17 (11.3%) satisfied all criteria. Of the
104 compounds from RC, 29 (27.9%) passed LR, seven (6.7%) had OB ?30% and DL index
?0.18, and only four (3.8%) satisfied all criteria. Of the 189 compounds from RMO,
125 (66.1%) passed LR, 20 (10.6%) had OB ?30% and DL index ?0.18, and only 12 (6.3%)
satisfied all criteria. Of the 173 compounds from RAS, 131 (75.7%) passed LR, five
(2.9%) had OB ?30% and DL index ?0.18, and only three (1.7%) satisfied all criteria.
Of the 63 compounds from CPC, 43 (68.3%) passed LR, 28 (44.4%) had OB ?30% and DL
index ?0.18, and only 19 (30.2%) satisfied all criteria. Of the 81 compounds from
RA, 45 (55.6%) passed LR, 15 (18.5%) had OB ?30% and DL index ?0.18, and only 11 (13.6%)
satisfied all criteria (Table 1). The physicochemical properties of anemarsaponin BII from EXD reported in the literature
(specific herbs unknown) did not pass LR. Overall, 66 compounds passed LR and had
OB ?30% and DL index ?0.18. A total of 63 compounds were obtained after removing the
duplicate compounds (Table 2).
Table 1. Compounds in EXD satisfying LR, OB ?30% and DL ?0.18
Table 2. The 63 bioactive compounds from HE, RC, RMO, RAS, CPC, and RA herbs and their corresponding
molecular properties, OB and DL (20 of 63 bioactive compounds related to 34 significant
pathway- or 12 gene- associated with menopause)
Revealing the significant pathways and gene-associated diseases
Overall, 155 of the 721 compounds from EXD were found to have 2,656 chemical–protein
interactions. After removing the overlapping/duplicate information, 1,963 associated
proteins were obtained (Additional file 2). 1,824 of 1,963 proteins with a confidence score exceeding 0.5 were obtained. After
enrichment analysis of 1,824 associated proteins, XD-scores and q values of pathways
have been obtained. The XD-score is relative to the average distance to all pathways
and represents a deviation from the average distance 43]. A larger positive XD-score indicates a stronger association between the inputted
associated proteins and molecular interaction network of pathways. The q value determines
the significance of the overlap (Fisher’s exact test) between the input information
and the pathways. The enrichment algorithm analysis (graph-based statistic) of XD-score
and q-value revealed that the threshold value of XD-score in this study was 0.67,
therefore there are 34 pathways significantly associated with input set of proteins
(Table 3).
Table 3. The 34 significant pathways found by JEPETTO (Cytoscape plugin) with KEGG database
In total, 210 of the 721 compounds from EXD were found to have 14,893 compound–gene
interactions with 8,536 associated genes in the CTD (Additional file 3). Subsequently, the 8,536 genes were ranked according to their frequency of occurrence.
The number of genes fell abruptly when the frequency of occurrence was small (gene
frequency ?8; Figure 2). Subsequently, the number of genes became stabilized for gene frequencies between
10 and 19. However, the number of genes with gene frequencies ?20 was quite small.
Genes with gene frequencies below the average of 1.74 were removed to reduce the number
of redundant genes. After that, the remaining 2,183 genes were used to conduct the
gene enrichment analysis by the DAVID platform. The “GENETIC_ASSOCIATION_DB_DISEASE_CLASSâ€
was selected as the annotation category to search for the significant diseases associated
with the input genes, which was statistically verified by Fisher’s exact test using
the DAVID platform 47]. P ? 0.01 indicated significant association or enrichment with the related items. After
removing nonspecific diseases, 12 classes of diseases were found to be highly associated
with the input genes (Tables 4 and 5). Most of these diseases were related to menopause, such as aging, reproduction,
cancer, cardiovascular diseases, and neurological diseases 55]–58].
Figure 2. Gene frequency of the associated genes of 210 compounds.
Table 4. Chemical–protein interactions and related significant signaling pathways
Table 5. The 12 disease classes highly associated with input genes
Identifying twenty bioactive compounds related to menopause with following the druggability
prediction
Eighteen of the 155 compounds that have 2,656 chemical–protein interaction, followed
the Lipinski’s Rule with OB ?30% and DL index ?0.18. Thirteen of the 210 compounds
that have compound–gene interactions interaction, followed the Lipinski’s Rule with
OB ?30% and DL index ?0.18. Finally, 11 compounds has been identified related to both
chemical–gene and chemical–protein interaction and followed the druglikeness prediction.
Moreover, 20 compounds related to 34 significant pathway- or 12 gene- associated with
menopause have been identified (Table 3).