Curcumin for gastric cancer: Mechanism prediction via network pharmacology, docking, and in vitro experiments

Table 1 Primer sequences

Genes	Primers (5' to 3')
ESR1	F: AGTGCCTTGTTGGATGCT
	R: TGCCAGGTTGGTCAGTAAG
EGFR	F: GGGTGCAGGAGAGGAGAA
	R: CTGGTTGTGGCAGCAGTC
CYP3A4	F: ATGGCACCGTAAGTGGAG
	R: TGGTGTTCTCAGGCACAG
MAPK14	F: AATACTGGGGAGGGGACA
	R: GGCTTCATTCGTTTTCGTT
CYP1A2	F: AGAATGCCCTCAACACCTT
	R: CCTTGCTCACATGCTCCT
CYP2B6	F: GTCTTCCCCAGTCCTCATT
	R: AGTGCAGAATCCCACAGC
GAPDH	F: TGTGTCCGTCGTGGATCTGA
	R: TTGCTGTTGAAGTCGCAGGAG

ESR1: Estrogen receptor 1; EGFR: Epidermal growth factor receptor; CYP3A4: Cytochrome P450 family 3 subfamily A member 4; MAPK14: Mitogen-activated protein kinase 14; CYP1A2: Cytochrome P450 family 1 subfamily A member 2; CYP2B6: Cytochrome P450 family 2 subfamily B member 6.

Table 2 Databases and online tools

Database/tool	Use/version	Database website/version
SwissADME	Drug similarity prediction	http://www.swissadme.ch
PharmMapper database	Molecular target prediction	http://www.lilab-ecust.cn/pharmmapper/
Swiss TargetPrediction database		http://www.swisstargetprediction.ch/
Drugbank database		www.drugbank.ca
GeneCard database	Disease target prediction	https://www.genecards.org/
OMIM database		https://omim.org/
TTD database		http://db.idrblab.net/ttd/
Drugbank database		www.drugbank.ca
String database	Protein InterNetNetwork	https://string-db.org/
Cytoscape tool		Cytoscape_v3.7.2
cythubba tool	Hub target filtering	Cytoscape_v3.7.2
DAVID database	KEGG and GO Analysis	https://david.ncifcrf.gov/
Kaplan-Meier tool	Survival analysis	https://kmplot.com/analysis/
AutoDock Vina	Molecular docking	AutoDock Vina1.1.2
Bioinformatics tool	Visualization drawing	http://www.bioinformatics.com.cn/
Ualcan	TCGA	http://ualcan.path.uab.edu/

Table 3 Molecular properties of curcumin

Property	Value
Molecular weight	368.38 g/mol
PSA	93.06 A²
XLogP3	3.20
Rotatable bonds	8
H-bond donor	2
H-bond acceptor	6
Molar refractivity	102.80
Bioavailability score	0.55

PSA: Polar surface area.

Table 4 Top 10 representative pathways according to gene count

Pathway ID	Pathway	Corrected P value	Gene count	Annotated genes
KEGG: hsa04068	FoxO signaling pathway	7.66E-07	8	MAPK10, MAPK8, PLK1, CDK2, EP300, MAPK14, EGFR, TGFBR1
KEGG: hsa05200	Pathways in cancer	1.19E-04	9	MAPK10, MAPK8, RXRA, GSTP1, CDK2, EP300, PPARG, EGFR, TGFBR1
KEGG: hsa00982	Drug metabolism - cytochrome P450	1.50E-04	5	CYP2B6, CYP2D6, GSTP1, CYP1A2, CYP3A4
KEGG: hsa00980	Metabolism of xenobiotics by cytochrome P450	2.08E-04	5	CYP2B6, CYP2D6, GSTP1, CYP1A2, CYP3A4
KEGG: hsa05120	Epithelial cell signaling in Helicobacter pylori infection	0.002430862	4	MAPK10, MAPK8, MAPK14, EGFR
KEGG: hsa04912	GnRH signaling pathway	0.00577562	4	MAPK10, MAPK8, MAPK14, EGFR
KEGG: hsa04620	Toll-like receptor signaling pathway	0.008806272	4	MAPK10, MAPK8, TLR9, MAPK14
KEGG: hsa04071	Sphingolipid signaling pathway	0.012342719	4	MAPK10, MAPK8, MAPK14, CTSD
KEGG: hsa05169	Epstein-Barr virus infection	0.012905562	4	MAPK10, MAPK8, CDK2, MAPK14
KEGG: hsa04110	Cell cycle	0.013483025	4	PLK1, CHEK1, CDK2, EP300

ESR1: Estrogen receptor 1; EGFR: Epidermal growth factor receptor; CYP3A4: Cytochrome P450 family 3 subfamily A member 4; MAPK14: Mitogen-activated protein kinase 14; CYP1A2: Cytochrome P450 family 1 subfamily A member 2; CYP2B6: Cytochrome P450 family 2 subfamily B member 6.

Table 5 Binding information for curcumin and docking of the hub target molecules

Hub targets	Binding energy (kcal/mol)	Hydrogen bonds				Hydrogen bonds, lengths
ESR1	-6.3	Ala307 (A)	Gly366 (A)		Ser305 (A)	2.82Å	3.06Å	2.95Å	3.47Å
EGFR	-7.8	Lys745 (A)				3.31Å
CYP3A4	-8.4	-				-
MAPK14	-7.9	Lys53 (A)				3.22Å
CYP1A2	-9.5	Arg108 (A)		Arg456 (A)		3.15Å		3.15Å
CYP2B6	-9.3	Arg98 (A)				2.95Å		2.96Å

ESR1: Estrogen receptor 1; EGFR: Epidermal growth factor receptor; CYP3A4: Cytochrome P450 family 3 subfamily A member 4; MAPK14: Mitogen-activated protein kinase 14; CYP1A2: Cytochrome P450 family 1 subfamily A member 2; CYP2B6: Cytochrome P450 family 2 subfamily B member 6.