New insight into gut microbiota-derived metabolites to enhance liver regeneration via network pharmacology study

Figures & data

Figure 1. (A) A workflow of this study. (B) The number of 668 overlapping targets between SEA (1256) and STP (947). (C) The number of 61 targets between 668 targets and liver regeneration-related targets (365). (D) The identification of 13 core targets between 61 targets and Gut human targets (223 targets) from gutMGene database. SEA: Similarity Ensemble Approach; STP: SwissTargetPrediction; PPI: protein–protein interaction; GO: gene ontology; MSTM: microbiota-signalling pathways-targets-metabolite.

Table 1. The degree value of core targets.

No.	Target	Degree of value
1	AKT1	12
2	EGFR	11
3	IL6	11
4	PPARG	11
5	CASP3	10
6	MAPK8	10
7	HDAC1	9
8	MAPK14	9
9	NFE2L2	9
10	TLR4	9
11	MAPK1	7
12	HDAC3	4
13	NR1H4	4

Table 2. The number of 36 signalling pathways and targets related to LR.

KEGG ID & description	Targets	False discovery rate
hsa04933: AGE-RAGE signalling pathway in diabetic complications	AKT1, CASP3, MAPK1, MAPK8, MAPK14, IL6	0.00000000197
hsa04664: Fc epsilon RI signalling pathway	AKT1, MAPK1, MAPK8, MAPK14	0.00000110000
hsa04620: Toll-like receptor signalling pathway	AKT1, IL6, TLR4, MAPK1, MAPK8, MAPK14	0.00000000197
hsa04917: Prolactin signalling pathway	AKT1, MAPK1, MAPK8, MAPK14	0.00000122000
hsa04657: IL-17 signalling pathway	CASP3, IL6, MAPK1, MAPK8, MAPK14	0.00000005640
hsa04668: TNF signalling pathway	AKT1, CASP3, IL6, MAPK1, MAPK8, MAPK14	0.00000000235
hsa04370: VEGF signalling pathway	AKT1, MAPK1, MAPK14	0.00004220000
hsa04625: C-type lectin receptor signalling pathway	AKT1, IL6, MAPK1, MAPK8, MAPK14	0.00000007720
hsa04012: ErbB signalling pathway	AKT1, MAPK1, MAPK8, EGFR	0.00000229000
hsa04068: FoxO signalling pathway	AKT1, MAPK1, MAPK8, MAPK14, IL6, EGFR	0.00000000405
hsa04066: HIF-1 signalling pathway	AKT1, MAPK1, IL6, EGFR, TLR4	0.00000008920
hsa04912: GnRH signalling pathway	MAPK1, MAPK8, MAPK14, EGFR	0.00000292000
hsa04660: T cell receptor signalling pathway	AKT1, MAPK1, MAPK8, MAPK14	0.00000441000
hsa04926: Relaxin signalling pathway	AKT1, MAPK1, MAPK8, MAPK14, EGFR	0.00000020600
hsa04722: Neurotrophin signalling pathway	AKT1, MAPK1, MAPK8, MAPK14	0.00000656000
hsa04071: Sphingolipid signalling pathway	AKT1, MAPK1, MAPK8, MAPK14	0.00000686000
hsa04919: Thyroid hormone signalling pathway	AKT1, MAPK1, HDAC1, HDAC3	0.00000726000
hsa04920: Adipocytokine signalling pathway	AKT1, MAPK8	0.00320000000
hsa04621: NOD-like receptor signalling pathway	MAPK1, MAPK8, MAPK14, IL6, TLR4	0.00000079400
hsa04622: RIG-I-like receptor signalling pathway	MAPK8, MAPK14	0.00320000000
hsa04662: B cell receptor signalling pathway	AKT1, MAPK1	0.00390000000
hsa04915: Oestrogen signalling pathway	AKT1, MAPK1, EGFR	0.00037000000
hsa04910: Insulin signalling pathway	AKT1, MAPK1, MAPK8	0.00037000000
hsa04010: MAPK signalling pathway	AKT1, MAPK1, MAPK8, MAPK14, CASP3, EGFR	0.00000020600
hsa04072: Phospholipase D signalling pathway	AKT1, MAPK1, EGFR	0.00045000000
hsa04015: Rap1 signalling pathway	AKT1, MAPK1, MAPK14, EGFR	0.00004220000
hsa04630: JAK-STAT signalling pathway	AKT1, IL6, EGFR	0.00057000000
hsa04014: Ras signalling pathway	AKT1, MAPK1, MAPK8, EGFR	0.00006310000
hsa04152: AMPK signalling pathway	AKT1, PPARG	0.00820000000
hsa04371: Apelin signalling pathway	AKT1, MAPK1	0.00950000000
hsa04024: cAMP signalling pathway	AKT1, MAPK1, MAPK8	0.00120000000
hsa04151: PI3K-Akt signalling pathway	AKT1, MAPK1, IL6, EGFR, TLR4	0.00001430000
hsa04921: Oxytocin signalling pathway	MAPK1, EGFR	0.01190000000
hsa04150: mTOR signalling pathway	AKT1, MAPK1	0.01200000000
hsa04022: cGMP-PKG signalling pathway	AKT1, MAPK1	0.01350000000
hsa04062: Chemokine signalling pathway	AKT1, MAPK1	0.01740000000

Table 3. The evaluation of drug-likeness properties on two key metabolites.

No.	Compounds	Lipinski Rules				Lipinski’s violations	Bioavailability score	TPSA (Å^2)
		MW	HBA	HBD	MLog P
		< 500	< 10	≤ 5	≤ 4.15	≤1	> 0.1	<140
1	Myricetin	318.24	8	6	−1.08	1	0.55	151.59
2	Compound K	653.80	8	4	1.72	1	0.55	131.17

Note: MW: molecular weight; HBA: hydrogen bond acceptor; HBD: hydrogen bond donor; MLog P: Moriguchi octanol-water partition coefficient; TPSA: topological polar surface area.

Figure 2. (A) The protein–protein interaction (PPI) networks (13 nodes and 58 edges). (B) Bubble plot of 36 signalling pathways related to liver regeneration (LR). (C) Gene ontology (GO) enrichment analysis.

Figure 3. (A) The docking result of myricetin-AKT1. (B) The docking result of Compound K-MAPK1. (C) Microbiota-signalling pathways-targets-metabolite (MSTM) networks (144 nodes, 499 edges).

Table 4. The evaluation of toxicity on two key metabolites.

Parameter	Compound K	Myricetin
1) hERG blockers	Non-blockers	Non-blockers
2) H-HT	Negative	Negative
3) Ames Mutagenicity	Negative	Negative
4) SkinSen (skin sensitization, (r)LLNA)	Negative	Negative
5) LD50	3.403 mg/kg	2.691 mg/kg
6) DILI	Negative	Negative

Notes: 1) Human ether-a-go-go-related gene (hERG): encoding potassium ion (K+) channel; 2) Human Hepatotoxicity (H-HT): Chemical-driven liver damage; 3) Ames Mutagenicity: Salmonella mutagenicity assay; 4) Local Lymph Node Assay (LLNA or (r) LLNA): A murine model to verify the skin sensitization risk of compounds; 5) Lethal Dose for 50% kill (LD50): The amount of a toxic chemical to kill 50% population; 6) Drug Induced Liver Injury (DILI): A liver injury induced from various drugs.

Data availability statement

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