GO terms and KEGG pathway enrichment analyses
Next, the 73 common targets were imported to the g: Profiler for GO and KEGG analysis. GO terms and KEGG pathways with a p-value < 0.05 were considered to be notably enriched. The top 20 elements were then visualized using OmicShare tools (Fig. 2).
As shown in Fig. 2, the top five items of biological processes (each with a p value < 0.05) included organonitrogen compound metabolic process, cell population proliferation, protein metabolic process, regulation of response to stress, and response to chemicals. The top five items for the cellular components category included cyclin-dependent protein kinase holoenzyme complex, serine/threonine protein kinase complex, protein kinase complex, extracellular region, and extracellular space. The top five items for the molecular functions category included catalytic activity, catalytic activity, acting on a protein, protein kinase activity, metalloendopeptidase activity, and serine-type endopeptidase activity.
KEGG analysis further showed that 54 of the 73 common targets (74.0%) were notably enriched in 51 pathways (Table S3). Among the enriched pathways, we identified abnormalities in terms of the PI3K-AKT signaling pathway in OP. The predicted targets that refer to the PI3K-AKT signaling pathway are indicated in red in Fig. 3.
Molecular Docking
Ten select key targets, VEGFA, IL6, EGFR, MAPK1, HRAS, CCND1, FGF2, IL2, MCL1 and CDK4, were obtained because they were not only the key targets of PPI network, but also played a major role in the PI3K-AKT signaling pathway. These genes were subjected to OG for molecular docking. As summarized in Table 3, the binding energies were computed to evaluate the binding affinities of the ten targets with OG. A binding affinity < − 7 showed strong binding activity [26].
Table 3
Molecular docking results between orcinol glucoside and key targets
Targets | PDB ID | Binding Energy (ΔG)/kcal·moL− 1 |
VEGFA | 3QTK | -7.3 |
IL6 | 4O9H | -6.7 |
EGFR | 3IKA | -7.0 |
MAPK1 | 4FV4 | -7.2 |
HRAS | 6ZL3 | -7.4 |
CCND1 | 6P8E | -7.0 |
FGF2 | 5 × 1O | -7.9 |
IL2 | 4NEM | -6.1 |
MCL1 | 4WMR | -7.2 |
CDK4 | 2W99 | -7.8 |
The mode of action for OG with VEGFA is shown in Fig. 4A; the hydroxyl group of OG is able to form two hydrogen bonds with the amino acid Asn55 (2.82 Å) and Asp56 (3.00 Å) within the active pocket. In addition, Cys53, Cys54, Phe29, Arg98, Lys101, Ile39, and Glu57, can all form hydrophobic interactions; these help to stabilize the entire region that is used for interaction. In addition, the results in Fig. 4B show that OG binds to IL6 by forming several hydrophobic interactions with the surrounding residues: Lys46, Arg104, Leu39, Leu101, and Ala112.
As shown in Fig. 4C, we observed hydrophobic interactions between OG and seven residues in 3IKA ( Leu718, Ala743, Leu844, Leu792, Gly796, Val726, and Met790). Two hydrogen bonds, Met793 (3.10 Å) and Lys745 (2.92 Å), further enhanced the interaction between OG and the 3IKA protein.
Figure 4D shows that OG binds to MAPK1 by forming several hydrophobic interaction with several surrounding residues: Cys164, Ala50, Leu154, Val37, Ile29, and Leu105. Analysis also showed that OG forms three H-bonds with Met106 (3.05 Å), Gln103 (3.17 Å) and Lys52 (3.34 Å).
The interplay between OG and HRAS is shown in Fig. 4E; three H-bonds were observed with Lys117 (2.80 Å), Ala146 (3.02 Å), and Lys147 (3.02 Å), in the binding pocket of HRAS. In addition, hydrophobic interactions with five residues in HRAS (Phe28, Gly15, Ala18, Asn116, and Asp30), along with pi-pi stacking with Phe28, further facilitated the binding of OG to HRAS.
As shown in Fig. 4F, OG interacted with CCND1 by Asn221, Pro220, Arg218, Leu217, Ile177, and Gly214. Furthermore, OG can form H-bonds with Asn174 (3.22 Å), His181 (3.00 Å), and Asn222 (3.16 Å).
Figure 4G shows that OG binds to a pocket in FGF2 which consists of Pro36, His50, Ile51, Val40, Lys66, Tyr73, and Ala84. Furthermore, OG can form two H-Bonds with Leu74 (2.94 Å), and Gly67 (3.14 Å).
The data shown in Fig. 4H further shows that OG can form hydrophobic interactions with four residues in IL2 (Pro34, Ile28, Ile24, and Gln74) and one H-Bond ( Asn30 (3.33 Å)).
Figure 4I show the binding ability between OG and MCL1 (Fig. 4I) which involves hydrophobic interactions with Phe254, Val253, Thr266, Leu267, Gly271, Ile294, Leu290, Met250, and Val249. In addition, one H-Bond with Arg263 (3.30 Å), along with pi-pi stacking with Phe270, further facilitated the binding of OG to MCL1.
The docking results between OG and CDK4 are shown in Fig. 4J. OG binds to a pocket in CDK4 which consists of Ile12, Glu144, Val20, Asn145, Phe93, Ala157, Leu147, Val72, and Ala33. Four H-Bonds (Asp158 (3.11 Å), Lys35 (3.02 Å), Val96 (3.17 Å), and His95 (3.28 Å)) further enhance the interaction between OG and the CDK4 protein.