Targeting colorectal cancer with Herba Patriniae and Coix seed: Network pharmacology, molecular docking, and in vitro validation

Table 1 Basic information of the 19 active ingredients in Herba Patriniae-Coix seed

Herb	Mol ID	Molecule name	Oral bioavailability (%)	Drug-likeness	Target amount
BJC1	MOL001676	Vilmorrianine C	33.96	0.22	59
BJC2	MOL001677	Asperglaucide	58.02	0.52	100
BJC3	MOL001678	Bolusanthol B	39.94	0.41	100
BJC4	MOL001689	Acacetin	34.97	0.24	100
BJC5	MOL002322	Isovitexin	31.29	0.72	3
BJC6	MOL001697	Sinoacutine	63.39	0.53	100
BJC7	MOL000358	Beta-sitosterol	36.91	0.75	44
BJC8	MOL000359	Sitosterol	36.91	0.75	44
BJC9	MOL000422	Kaempferol	41.88	0.24	3
BJC10	MOL000449	Stigmasterol	43.83	0.76	41
BJC11	MOL000006	Luteolin	36.16	0.25	100
BJC12	MOL000098	Quercetin	46.43	0.28	100
YYR1	MOL001323	Sitosterol alpha 1	43.28	0.78	60
YYR2	MOL001494	Mandenol	42.00	0.19	100
YYR3	MOL002882	[(2R)-2,3-dihydroxypropyl](Z)-octadec-9-enoate	34.13	0.30	41
YYR4	MOL000359	Sitosterol	36.91	0.75	44
YYR5	MOL000449	Stigmasterol	43.83	0.76	41
YYR6	MOL008121	2-Monoolein	34.23	0.29	52
YYR7	MOL000953	CLR	37.87	0.68	46

Table 2 Top 10 core targets in the protein-protein interaction network between Herba Patriniae-Coix seed and colorectal cancer

Rank	Target	Degree
1	EGFR	122
2	AKT1	122
3	TNF	109
4	HSP90AA1	105
5	SRC	102
6	HIF1A	99
7	ESR1	97
8	HSP90AB1	94
9	MMP9	90
10	MAPK3	87

Table 3 Top five active ingredients in the herbal ingredient-target-pathway-disease network

Molecule name	Degree	CC	BC
Acacetin	56	0.433	0.107
Luteolin	54	0.430	0.089
Quercetin	53	0.428	0.090
Bolusanthol B	49	0.419	0.148
Sinoacutine	45	0.414	0.127

CC: Closeness centrality; BC: Betweenness centrality.

Table 4 Top five Kyoto Encyclopedia of Genes and Genomes pathways in the herbal ingredient-target-pathway-disease network

KEGG pathway name	Degree	CC	BC
Pathways in cancer	70	0.457	0.163
PI3K-Akt signaling pathway	47	0.404	0.052
Proteoglycans in cancer	34	0.393	0.030
Chemical carcinogenesis-receptor activation	33	0.391	0.038
MicroRNAs in cancer	32	0.388	0.035

CC: Closeness centrality; BC: Betweenness centrality; KEGG: Kyoto Encyclopedia of Genes and Genomes; PI3K: Phosphoinositide 3-kinase.

Table 5 Top five core targets in the herbal-ingredient-target-pathway-disease network

Target gene	Degree	CC	BC
AR	16	0.452	0.028
CYP19A1	15	0.444	0.030
ESR2	13	0.433	0.019
PIK3R1	12	0.413	0.010
PTPN1	12	0.380	0.011

CC: Closeness centrality; BC: Betweenness centrality.

Table 6 Binding energy of the molecular docking

Target	PDB ID	Ingredient	Binding energy (kcal/mol)	Hydrogen bond number	Action of amino acid residues
AKT1	6HHG	Acacetin	-9.2	1	THR-211
AKT1	6HHG	Bolusanthol B	-10.2	2	ASP-274/THR-81
AKT1	6HHG	Luteolin	-9.5	3	THR-211/TYR-272/GLN-79
AKT1	6HHG	Quercetin	-9.1	3	THR-211/TYR-272/GLN-79

Note: Binding energy function.