AURKB, CHEK1 and NEK2 as the Potential Target Proteins of Scutellaria barbata on Hepatocellular Carcinoma: An Integrated Bioinformatics Analysis

Figures & data

Figure 1 Workflow for exploring the molecular mechanisms of Scutellaria barbata against Hepatocellular carcinoma.

Table 1 Detail Information of 16 Compounds of Scutellaria barbata

No.	Components	PubChemCID	CAS	Molecular ID	OB%	DL
1	5,7,4ʹ-trihydroxy-6-methoxyflavanone	5322074	94942-49-1	MOL012245	36.63	0.27
2	5-hydroxy-7,8-dimethoxy-2-(4-methoxyphenyl)chromone	14353376	57096-03-4	MOL012248	65.82	0.33
3	7-hydroxy-5,8-dimethoxy-2-phenyl-chromone	14825644	N/A	MOL012250	43.72	0.25
4	Baicalin	64982	21967-41-9	MOL002776	40.12	0.75
5	CLR	5997	57-88-5	MOL000953	37.87	0.68
6	Beta-sitosterol	222284	83-46-5	MOL000358	36.91	0.75
7	Rivularin	13889022	70028-59-0	MOL012266	37.94	0.37
8	Sitosteryl acetate	5354503	915-05-9	MOL001973	40.39	0.85
9	Stigmasterol	5280794	83-48-7	MOL000449	43.83	0.76
10	Dinatin	5281628	1447-88-7	MOL001735	30.97	0.27
11	24-Ethylcholest-4-en-3-one	5484202	67392-96-5	MOL001755	36.08	0.76
12	Salvigenin	161271	19103-54-9	MOL002915	49.07	0.33
13	Rhamnazin	5320945	552-54-5	MOL000351	47.14	0.34
14	Sitosterol	12303645	83-46-5	MOL000359	36.91	0.75
15	Moslosooflavone	188316	3570-62-5	MOL008206	44.09	0.25
16	Quercetin	5280343	117-39-5	MOL000098	46.43	0.28

Figure 2 Identification of hub targets of HCC. (A) Volcano plot of DEGs, (B) Heatmap of the top 50 up-regulated and down-regulated DEGs, (C)Analysis of the scale-free network coefficient R-squared for the soft threshold, (D) A cluster dendrogram was built based on the dissimilarity of the topological overlap, (E) Module-trait relationships.

Figure 3 Venn diagram. (A) Venn diagram of turquoise module and up-regulated DEGs, (B) Venn diagram of black module and down-regulated DEGs, (C) Venn diagram of up-regulated overlapping genes, down-regulated overlapping genes and SwisstargetPrediction targets.

Table 2 Cross Verification of the 10 Critical Target Genes and Compounds of Scutellaria barbata

No.	Components in Scutellaria barbata	Critical Targets Predicted in Swiss Target Prediction Database
1	5,7,4ʹ-trihydroxy-6-methoxyflavanone	AURKA, CHEK1, CHEK1
2	5-hydroxy-7,8-dimethoxy-2-(4-methoxyphenyl)chromone	AURKB, CDK1
3	7-hydroxy-5,8-dimethoxy-2-phenyl-chromone	NEK2, AURKB, FEN1, CDK1, TOP2A
4	Baicalin	TYMS, POLA1
5	CLR	TOP2A
6	Beta-sitosterol	TOP2A
7	Rivularin	NEK2, TOP2A
8	Sitosteryl acetate	AURKB, POLA1
9	Stigmasterol	TOP2A
10	Dinatin	NEK2, AURKB, CDK1
11	24-Ethylcholest-4-en-3-one	/
12	Salvigenin	AURKB, CDK1
13	Rhamnazin	NEK2, AURKB, CDK1, TOP2A
14	Sitosterol	TOP2A
15	Moslosooflavone	AURKB, CDK1
16	Quercetin	NEK2, AURKB, CDK1, TOP2A

Figure 4 PPI analysis. (A) PPI network of the 19 up-regulated targets without disconnected nodes. (B) 10up-regulated targets that were screened according to the MCC and DC.

Figure 5 Active component-anti-hepatoma target-pathway network of Scutellaria barbata.

Figure 6 The results of GO enrichment analysis. (A) The barplot of GO enrichment analysis, (B) The bubble plot of GO enrichment analysis. “Gene ratio” means the percentage of the genes that enriched in corresponding pathway in all the genes that annotated in GO dataset.

Figure 7 The results of KEGG pathways enrichment analysis. (A) The barplot of KEGG analysis, (B) The bubble plot of KEGG analysis. “Gene ratio” means the percentage of the genes that enriched in corresponding pathway in all the genes that annotated in GO dataset.

Table 3 Information of Proteins Involved in Molecular Docking

No.	Target Protiens	PDB-ID	Ligand-ID
1	CDK1	3LFS	A07
2	AURKB	4AF3	VX6
3	TOP2A	1ZXN	ADP
4	CHEK1	4QYE	3DL
5	AURKA	5DR6	5E1
6	KIF11	3L9H	EMQ
7	FEN1	6CVR	AMP
8	TYMS	5X66	MTX
9	NEK2	2XK8	5R1
10	POLA1	4Q5V	2ZE

Figure 8 The results of molecular docking. (A) Heatmap of binding energy between active components and target proteins, (B) Visualization of molecular docking between MOL000449 and AURKB, (C) Visualization of molecular docking between MOL002776 and CHEK1, (D) Visualization of molecular docking between MOL002776 and NEK2, (E) Visualization of molecular docking between MOL000098 and CHEK1.

Figure 9 The results of Prognostic value of AURKB, CHEK1 and NEK2. (A) Overall Survival Kaplan-Meier curve of AURKB, (B) Disease Free Survival Kaplan-Meier curve of AURKB, (C) Overall Survival Kaplan-Meier curve of CHEK1, (D) Disease Free Survival Kaplan-Meier curve of CHEK1, (E) Overall Survival Kaplan-Meier curve of NEK2, (F) Disease Free Survival Kaplan-Meier curve of NEK2.