The identification of metabolites from gut microbiota in coronary heart disease via network pharmacology

Figures & data

Figure 1. The workflow of this study.

Figure 2. (A) The number of overlapping 726 targets between SEA and STP database. (B) The number of overlapping 98 targets between the 726 targets and CHD-related targets. (C) The number of the final overlapping 12 targets between the 98 targets and targets of gut microbiota. (D) The PPI network (10 nodes and 38 edges).

Figure 3. GO (A) and KEGG (B) enrichment analysis.

Figure 4. MMTS network (79 nodes and 118 edges). Green diamond: gut microbiota; pink triangle: gut microbial metabolites; yellow circle: targets; red quadrilateral: signalling pathways. The size of the node represents the number of relationships to the target.

Table 1. Metabolites and core targets of major signalling pathways.

Signalling pathways	Targets	Metabolites
hsa04625: C-type lectin receptor signalling pathway	IL-6, MAPK1, IL-2, AKT1, PTGS2	Glycocholic acid, levodopa, enterodiol, colibactin, palmitic acid, p-cresol sulphate, phenylacetylglutamine, acifran, 5-hydroxyindole-3-acetic acid
hsa04620: Toll-like receptor signalling pathway	IL-6, MAPK1, CXCL8, AKT1	Glycocholic acid, phenylacetylglutamine, enterodiol, colibactin, palmitic acid
hsa04151: PI3K–Akt signalling pathway	IL-6, MAPK1, AKT1, IL-2, EGFR	Glycocholic acid, levodopa, phenylalanine, (R)-3-(4-hydroxyphenyl)lactate, serotonin, indole-3-acrylic acid, 5-hydroxyindole-3-acetic acid, 3-methyloxindole, enterodiol, colibactin, palmitic acid

Figure 5. The molecular docking test on core targets-metabolites pairs. (A) Glycocholic acid-AKT1. (B) Colibactin-MAPK1. (C) Indole-3-acrylic acid-EGFR. (D) Phenylacetylglutamine-PTGS2.

Table 2. Molecular docking results of metabolites and core targets.

Protein	PDB ID	Metabolites	PubChem ID	Binding energy (kcal mol^–1)	Grid box centre			Hydrogen bond interactions amino acid residue
					X	Y	Z
IL6	4O9H	Enterodiol	115089	−6.1	−15.877	9.362	37.115	Arg179(A), Gln183(A), Arg30(A), Asp55(L), Ser52(L)
MAPK1	4FV5	Enterodiol	115089	−6.6	−5.35	2.77	18.381	Asp289(A), Lys268(A), Ser244(A), Gly243(A), Leu242(A)
		Colibactin	138805674	−7.8	−4.488	−3.205	17.963	Lys342(A), Phe57(A), Gly35(A), Gly32(A), Gln15(A)
		Palmitic acid	985	−4.6	−0.687	2.045	21.787	Asp334(A), Arg68(A)
CXCL8	1ICW	Phenylacetylglutamine	92258	−5.7	−3.614	26.384	26.384	Glu48(B), Lys11(B), Ile10(B)
EGFR	5UG9	Dopamine	681	−5.9	−3.566	18.964	−21.519	Met793(A)
		Dihydrocaffeic acid	348154	−6.7	−4.32	21.413	−24.316	Lys745(A), Thr854(A), Met793(A)
		Levodopa	6047	−6.5	−5.66	18.092	−27.47	Met793(A), Lys745(A), Thr854(A)
		Phenylalanine	6140	−6.4	−5.02	17.062	−28.418	Lys745(A)
		(R)-3-(4-Hydroxyphenyl)lactate	9548632	−6.7	−5.744	17.171	−23.515	Met793(A), Lys745(A)
		Serotonin	5202	−6.5	−1.629	19.701	−24.352	Lys745(A)
		Indole-3-acrylic acid	5375048	−7.4	−7.337	18.866	−25.661	Met793(A), Lys745(A)
		5-Hydroxyindole-3-acetic acid	1826	−6.7	−5.75	20.147	−23.962	Lys745(A)
		3-Methyloxindole	150923	−6.5	−3.426	19.27	19.27	–
PTGS2	5F19	p-Cresol sulphate	4615423	−5.0	19.208	36.492	35.78	Lys511(B), Glu520(B)
		Phenylacetylglutamine	92258	−7	22.93	41.378	39.713	Gln372(A), Lys532(A), His122(A)
		Enterodiol	115089	−6.6	22.674	39.852	45.928	Arg376(B), Gly225(A), Arg376(A)
		Acifran	51576	−5.3	5.821	3.434	10.66	Arg44(A), Gly45(A), Gln461(A), His39(A),Gly45(A)
		5-Hydroxyindole-3-acetic acid	1826	−7.1	17.615	34.459	45.696	Asn382(A), His388(A), Ala199(A)
IL2	1M48	Levodopa	6047	−5.3	5.821	3.434	10.66	Arg83(B), Gln74(B), Met23(B)
AKT1	3O96	Glycocholic acid	10140	−10.1	6.633	−12.725	18.381	Gln79(A), Cys296(A), Thr82(A), Trp80(A)

Table 3. The physicochemical properties of the metabolites from gut microbiota.

No.	Metabolites	Lipinski rules				Lipinski’s violations ≤1	Bioavailability score >0.1	TPSA <140 Å^2
		MW ≤500	HBA ≤10	HBD ≤5	MlogP ≤ 5
1	Enterodiol	302.36	4	4	2.2	0	0.55	80.92
2	Colibactin	770.88	11	4	−2.54	2	0.17	274.59
3	Palmitic acid	256.42	2	1	4.19	0	0.85	37.30
4	Phenylacetylglutamine	264.28	4	3	0.4	0	0.56	109.49
5	Dihydrocaffeic acid	182.17	4	3	0.79	0	0.56	77.76
6	Dopamine	153.18	3	3	0.6	0	0.55	153.18
7	Levodopa	197.19	5	4	−2.26	0	0.55	103.78
8	Phenylalanine	165.19	3	2	−1.11	0	0.55	63.32
9	(R)-3-(4-Hydroxyphenyl)lactate	181.17	4	2	0.52	0	0.56	80.59
10	Serotonin	176.22	2	3	0.65	0	0.55	62.04
11	Indole-3-acrylic acid	187.19	2	2	1.32	0	0.85	53.09
12	5-Hydroxyindole-3-acetic acid	191.18	3	3	0.53	0	0.85	73.32
13	3-Methyloxindole	147.17	1	1	1.45	0	0.55	29.10
14	p-Cresol sulphate	188.2	4	1	1	0	0.85	71.98
15	Acifran	218.21	4	1	0.57	0	0.85	63.60
16	Glycocholic acid	465.62	6	5	2.15	0	0.26	127.09

Figure 6. The chemical structures of phenylacetylglutamine (A) and glycocholic acid (B).

Table 4. Toxicological properties of the metabolites from the gut microbiota.

No.	Metabolites	hERG blockers	Human hepatotoxicity (H-HT)	Respiratory toxicity	Rat oral acute toxicity	Carcinogenicity	Drug induced liver injury (DILI)	Skin sensitization, (r) LLNA	LD50 of acute toxicity (mg/kg)
1	Enterodiol	Non-blockers	Negative	Negative	Negative	Negative	Negative	Sensitizer	4.804
2	Palmitic acid	Non-blockers	Negative	Positive	Negative	Negative	Negative	Sensitizer	4.357
3	Phenylacetylglutamine	Non-blockers	Negative	Negative	Negative	Negative	Negative	Non-sensitizer	3.038
4	Dihydrocaffeic acid	Non-blockers	Negative	Negative	Negative	Negative	Negative	Sensitizer	4.153
5	Dopamine	Non-blockers	Negative	Negative	Positive	Negative	Negative	Sensitizer	4.602
6	Levodopa	Non-blockers	Negative	Negative	Negative	Negative	Negative	Sensitizer	3.971
7	Phenylalanine	Non-blockers	Negative	Negative	Positive	Negative	Negative	Non-sensitizer	3.394
8	(R)-3-(4-Hydroxyphenyl)lactate	Non-blockers	Negative	Negative	Positive	Negative	Positive	Sensitizer	2.871
9	Serotonin	Non-blockers	Negative	Positive	Positive	Negative	Negative	Sensitizer	5.738
10	Indole-3-acrylic acid	Non-blockers	Positive	Positive	Positive	Negative	Positive	Sensitizer	4.725
11	5-Hydroxyindole-3-acetic acid	Non-blockers	Negative	Negative	Positive	Negative	Positive	Sensitizer	4.158
12	3-Methyloxindole	Non-blockers	Negative	Positive	Positive	Positive	Positive	Non-sensitizer	5.208
13	p-Cresol sulphate	Non-blockers	Positive	Negative	Negative	Positive	Negative	Sensitizer	3.567
14	Acifran	Non-blockers	Positive	Negative	Negative	Negative	Positive	Sensitizer	3.666
15	Glycocholic acid	Non-blockers	Negative	Negative	Negative	Negative	Negative	Non-sensitizer	5.173

Data availability statement

All data generated or analysed during this study are included in this published article (and its Supplementary Information Files).