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JKM > Volume 44(2); 2023 > Article
Kweon, Ryu, Kim, Oh, Jang, Park, and Bae: Network pharmacology-based prediction of efficacy and mechanism of Chongmyunggongjin-dan acting on Alzheimer’s disease

Abstract

Objectives

Network pharmacology is a method of constructing and analyzing a drug-compound-target network to predict potential efficacy and mechanisms related to drug targets. In that large-scale analysis can be performed in a short time, it is considered a suitable tool to explore the function and role of herbal medicine. Thus, we investigated the potential functions and pathways of Chongmyunggongjin-dan (CMGJD) on Alzheimer’s disease (AD) via network pharmacology analysis.

Methods

Using public databases and PubChem database, compounds of CMGJD and their target genes were collected. The putative target genes of CMGJD and known target genes of AD were compared and found the correlation. Then, the network was constructed using Cytoscape 3.9.1. and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms.

Results

The result showed that total 104 compounds and 1157 related genes were gathered from CMGJD. The network consisted of 1157nodes and 10034 edges. 859 genes were interacted with AD gene set, suggesting that the effects of CMGJD are closely related to AD. Target genes of CMGJD are considerably associated with various pathways including ‘Positive regulation of chemokine production’, ‘Cellular response to toxic substance’, ‘Arachidonic acid metabolic process’, ‘PI3K-Akt signaling pathway’, ‘Metabolic pathways’, ‘IL-17 signaling pathway’ and ‘Neuroactive ligand-receptor interaction’.

Conclusion

Through a network pharmacological method, CMGJD was predicted to have high relevance with AD by regulating inflammation. This study could be used as a basis for effects of CMGJD on AD.

Supplementary Information

Supplementary Fig. 1
Veen diagram of intersection targets between components of CMGJD and the gene sets of Alzheimer’s disease
jkm-44-2-106-Supplementary-Fig-1.pdf
Supplementary table. 1
List of the common genes of herbs of Chongmyunggongjin-dan and Alzheimer’s disease gene sets.
jkm-44-2-106-Supplementary-table-1.pdf

Fig. 1
(A) Network of CMGJD with 1157nodes and 10034edges. (B) Veen diagram of intersection targets between CMGJD and the gene sets of Alzheimer’s disease. (C) Network of common genes of CMGJD and Alzheimer’s disease.
jkm-44-2-106f1.gif
Fig. 2
Biological processes related to targets of CMGJD using GO Biological process database.
jkm-44-2-106f2.gif
Fig. 3
Biological processes related to targets of CMGJD using KEGG Pathways database.
jkm-44-2-106f3.gif
Table 1
List of the compounds from Chongmyunggongjin-dan with the Pubchem ID
Compound Pubchem ID Origin
Poricoic acid A 5471851 P.cocos Wolf
Poricoic acid B 5471852 P.cocos Wolf
Pachymic acid 5484385 P.cocos Wolf
Polyporenic acid C 9805290 P.cocos Wolf
Eburicoic acid 10004946 P.cocos Wolf
Tumulosic acid 12314446 P.cocos Wolf
Dehydrotumulosic acid 15225964 P.cocos Wolf
Dehydropachymic acid 15226717 P.cocos Wolf
Dehydroeburicoic acid 15250826 P.cocos Wolf
15R-hydroxydehydrotumulosic acid 16736459 P.cocos Wolf
Dehydrotrametenonic acid 44424826 P.cocos Wolf
Poricoic acid D 44424827 P.cocos Wolf
Poricoic acid C 56668247 P.cocos Wolf
Androsterone 5879 Moschus
Cholesterol 5997 Moschus
Cholestanol 6665 Moschus
5β-androstane-3α,17β-diol 134494 Moschus
Androstanedione 222865 Moschus
5β-androstane-3,17-dione 440114 Moschus
5α-androstane-3β,17α-diol 446934 Moschus
5α-cholestane 2723895 Moschus
2-methoxy-4-vinylphenol 332 P.tenuifolia
2-hydroxybenzoic acid 338 P.tenuifolia
Sucrose 5988 P.tenuifolia
A.gigas
1-(3,4-dimethoxyphenyl)ethan-1-one 14328 P.tenuifolia
Propyl benzoate 16846 P.tenuifolia
Phenyl acetate 31229 P.tenuifolia
3,4-dimethoxycinnamic acid 717531 P.tenuifolia
3,4,5-trimethoxycinnamic acid 735755 P.tenuifolia
Gentisin 5281636 P.tenuifolia
Mangiferin 5281647 P.tenuifolia
Sibiricose A6 6326021 P.tenuifolia
Tenuifoliside B 10055215 P.tenuifolia
Onjisaponin F 10701737 P.tenuifolia
Polygalaxanthone III 11169063 P.tenuifolia
3,6′-di-O-sinapoyl sucrose 11968389 P.tenuifolia
Tenuifoliside C 11968391 P.tenuifolia
Senegin III 21669942 P.tenuifolia
Tenuifoliside A 46933844 P.tenuifolia
β-asarone 5281758 A.gramineus
α-asarone 636822 A.gramineus
Eugenol 3314 A.gramineus
p-hydroxybenzaldehyde 126 Cervi Parvum cornu
Uracil 1174 Cervi Parvum cornu
Progesterone 5994 Cervi Parvum cornu
Testosterone 6013 Cervi Parvum cornu
Uridine 6029 Cervi Parvum cornu
3′-cytidine monophosphate 66535 Cervi Parvum cornu
3′-uridine monophosphate 101543 Cervi Parvum cornu
2′-cytidine monophosphate 101544 Cervi Parvum cornu
Gallic acid 370 C.officinalis
Oleanolic acid 10494 C.officinalis
Ursolic acid 64945 C.officinalis
(−)-epicatechin-3-O-gallate 65056 C.officinalis
Loganic acid 89640 C.officinalis
Cornuside 131348 C.officinalis
Sweroside 161036 C.officinalis
Secoxyloganin 162868 C.officinalis
β-sitosterol 222284 C.officinalis
5-hydroxymethylfurfural 237332 C.officinalis
Tellimagrandin II 442679 C.officinalis
p-coumaric acid 637542 C.officinalis
Caffeic acid 689043 C.officinalis
Quercetin 3-O-β-D-glucuronide 5274585 C.officinalis
Quercetin 5280343 C.officinalis
Kaempferol 5280863 C.officinalis
Hyperoside 5281643 C.officinalis
Kaempferide 5281666 C.officinalis
Caftaric acid 6440397 C.officinalis
Morronisde 11304302 C.officinalis
Tachioside 11962143 C.officinalis
Quercetin-3-O-β-D-glucopyranoside 15959354 C.officinalis
7-O-Galloyl-D-sedoheptulose 42636959 C.officinalis
Butoxysuccinic acid 71722049 C.officinalis
Acetate 176 A.gigas
Formate 284 A.gigas
Choline 305 A.gigas
Citrate 311 A.gigas
Malate 525 A.gigas
Histamine 774 A.gigas
Succinate 1110 A.gigas
Xanthotoxin 4114 A.gigas
Glucose 5793 A.gigas
Alanine 5950 A.gigas
Histidine 6274 A.gigas
Valine 6287 A.gigas
Arginine 6322 A.gigas
Nodakenin 26305 A.gigas
Isoimperatorin 68081 A.gigas
N-acetylglutamate 70914 A.gigas
Lactose 84571 A.gigas
Marmesin 334704 A.gigas
Decursin 442126 A.gigas
Decursinol 442127 A.gigas
Fumarate 444972 A.gigas
Ferulic acid 445858 A.gigas
Decursinol angelate 776123 A.gigas
Chlorogenic acid 1794427 A.gigas
Demethylsuberosin 5316525 A.gigas
Peucedanone 5324562 A.gigas
Coniferylferulate 6441913 A.gigas
Columbianetin O-β-D-glucopyranoside 6453269 A.gigas
Table 2
List of the common genes of Chongmyunggongjin-dan and Alzheimer’s disease gene sets.
859 Common Genes of CMGJD and Alzheimer’s disease
ABAT, ABCA1, ABCB1, ABCC2, ABCD2, ABCG1, ABCG2, ABCG5, ABCG8, ABI1, ABL1, ACACB, ACAT1, ACE, ACE2, ACHE, ACLY, ACO2, ACSBG1, ADA, ADAM8, ADH1A, ADH5, ADH6, ADIPOQ, ADORA2A, ADRB3, AGER, AGPAT4, AGT, AGTR1, AHR, AICDA, AIF1, AIMP2, AK8, AKR1B1, AKR1B10, AKT1, ALB, ALDH2, ALDH5A1, ALDOA, ALOX12, ALOX15, ALOX5, ALPK2, ALPL, AMBP, ANG, ANO2, ANXA5, APAF1, APMAP, APOA1, APOA2, APOA5, APOB, APOBEC3A, APOBEC3F, APOBEC3G, APOBEC3H, APOC2, APOC3, APOD, APOE, AR, ARC, ARG1, ARG2, ARRB2, ARTN, ASL, ASS1, ATF1, ATF2, ATF4, ATF6, ATG13, ATG16L1, ATG5, ATG7, ATP12A, ATP1B1, ATP2B1, AVP, AVPI1, AXL, AZIN2, BACE1, BAK1, BAX, BCHE, BCL2, BCL2A1, BCL2L1, BDNF, BECN1, BGLAP, BIRC5, BMF, BMI1, BMP2, BMP3, BNIP3, BRCA1, BTK, C3, C5, C5AR1, CA1, CA2, CACNA1E, CAD, CALCA, CALCR, CALCRL, CALR, CAMK2G, CAMKK2, CAPN1, CARM1, CASP1, CASP14, CASP3, CASP7, CASP8, CASP9, CAT, CAV1, CBR1, CCK, CCL11, CCL2, CCL3, CCL4, CCL5, CCL7, CCNB1, CCND1, CCR2, CCR3, CCS, CD14, CD19, CD1A, CD248, CD28, CD36, CD4, CD40LG, CD44, CD46, CD55, CD63, CD68, CD79A, CD80, CDC20, CDC25A, CDC25C, CDH1, CDH2, CDK1, CDK13, CDK16, CDK2, CDK2AP1, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CEBPA, CETP, CGA, CGB5, CHAT, CHEK1, CHEK2, CHL1, CHMP2B, CHUK, CKMT1B, CLDN2, CLDN5, CLYBL, CNP, CNTF, COG2, COL1A1, COMT, COX4I1, COX7A1, CP, CPS1, CPT1A, CPVL, CREBBP, CRH, CRP, CRTC1, CS, CSF1, CSF2, CSF3, CSTB, CTNNB1, CTRL, CTSB, CTSD, CTSK, CXCL10, CXCL12, CXCL8, CXCR4, CYBB, CYP17A1, CYP19A1, CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP2J2, CYP3A4, CYP51A1, CYSLTR2, DAG1, DAPK1, DAPK2, DBH, DCLRE1A, DCTN4, DDAH1, DDAH2, DDC, DEGS1, DES, DHCR7, DHFR, DHRS9, DIABLO, DKK1, DLD, DLG4, DLL1, DMD, DNAJB6, DNAJB9, DNASE1, DNTT, DPP4, DPYD, DPYS, DRD2, DUT, DYNC1H1, ECHDC2, EDN1, EEF1A2, EGF, EGFR, EIF2AK1, EIF2AK2, EIF2AK3, EIF4A1, ELANE, ELAVL1, ENO2, EPHA2, EPHB2, EPO, ERBB2, ERCC4, ERN1, ERVW-1, ESR1, ESR2, F2, F2R, F3, F7, FAAH, FAM20C, FASLG, FASN, FCGR2A, FDFT1, FDPS, FEN1, FGF21, FGFR1, FGFR3, FH, FHIT, FIS1, FKBP2, FLNB, FLNC, FMR1, FNDC5, FOS, FOSB, FOXO1, FOXO3, FPR1, FSHR, FST, FURIN, FXN, FZD10, G6PD, GAA, GABPA, GAD1, GAD2, GALNT12, GAP43, GAPDH, GAR1, GAS6, GAST, GATA3, GATM, GCG, GCK, GCLC, GCLM, GDF5, GDNF, GFAP, GGPS1, GH1, GHRH, GHRL, GJA1, GLB1, GLIPR1, GLO1, GLP1R, GLS, GLUD1, GLUL, GNAS, GNPNAT1, GNRH1, GNRHR, GOT1L1, GPBAR1, GPER1, GPIHBP1, GPT, GPX1, GPX4, GRB2, GRIA1, GRIA2, GRIK4, GRIN2A, GRIN2B, GRIN2D, GRM1, GRM2, GRM6, GSDMD, GSR, GSTM1, GSTO1, GSTP1, GUSB, HAS2, HAVCR2, HBA1, HCRT, HDC, HGF, HIF1A, HK1, HLA-B, HLA-DRB1, HMGB1, HMGCR, HMGCS1, HMOX1, HNRNPA2B1, HNRNPH1, HP, HPRT1, HPSE, HRG, HRH1, HRH2, HRH3, HRH4, HSD3B1, HSP90AA1, HSP90B1, HSPA5, HSPA8, HSPB1, HTR2A, HTR2C, HTR3A, HTT, HYAL1, HYAL2, IAH1, IAPP, IBSP, ICAM1, ICAM5, IFNA1, IFNG, IFNLR1, IGF1, IGF2, IGFBP1, IGFBP3, IL10, IL13, IL17A, IL18, IL1B, IL2, IL23A, IL3, IL4, IL6, IL9, ILK, INS, INSR, IRS1, ISG20, ISYNA1, ITGAM, ITPR3, IVNS1ABP, JAK2, JPH3, JUN, JUND, KAT8, KCNA3, KCNMA1, KDM1A, KDR, KEAP1, KISS1, KISS1R, KL, KLK3, KNG1, LATS1, LCAT, LCK, LCMT1, LDHA, LDHB, LDLR, LDLRAP1, LEF1, LEP, LGALS3, LGALS4, LHCGR, LIN28B, LIPA, LIPC, LIPE, LMNA, LMNB1, LPA, LPL, LPO, LRRC7, LY96, LYZ, MAOA, MAOB, MAP1A, MAP1LC3A, MAP2K1, MAP2K4, MAP2K7, MAP3K5, MAP3K7, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK14, MAPK3, MAPK8, MAPK9, MAPT, MARK2, MB, MBP, MC1R, MCL1, MDH1, MDH2, MDM2, ME2, MEF2D, MIPEP, MITF, MKI67, MLN, MME, MMP1, MMP13, MMP2, MMP3, MMP7, MMP9, MPO, MRC1, MST1, MSTN, MT-CYB, MTHFR, MT-ND2, MTOR, MTR, MTRNR2L8, MX1, MYC, MYD88, MYLK, MYO9A, NAALADL1, NFATC1, NFATC2, NFE2L2, NFKB1, NFKBIA, NFKBIB, NGB, NGF, NIM1K, NIT2, NLRP1, NLRP3, NME1, NOLC1, NOS1, NOS2, NOS3, NOTCH1, NOX4, NPC1, NPC1L1, NPC2, NPM1, NPPA, NPPB, NPY, NQO1, NR1H2, NR1H3, NR1H4, NR1I2, NR3C1, NR3C2, NT5C2, NT5C3A, NTRK2, NTS, OAT, OCLN, ODC1, OGG1, OPRD1, OPRM1, OTC, OXSR1, OXTR, P2RY2, P2RY4, P2RY6, P4HB, PADI3, PADI4, PAEP, PAPSS1, PARP1, PAX6, PCK1, PCNA, PCSK9, PDE3B, PDK1, PDK2, PDK4, PDPK1, PDX1, PDYN, PFKFB3, PFKL, PGR, PGRMC1, PIK3AP1, PIK3C3, PIK3CA, PIKFYVE, PIN1, PINK1, PKD1, PKM, PKN1, PLA2G12A, PLA2G1B, PLA2G7, PLAT, PLAU, PLBD2, PLD1, PLD2, PLD5, PLG, PLTP, PMEL, PNLIP, POLB, POLR3C, POMC, PON1, PON2, PON3, POR, POU2F1, POU5F1, PPARA, PPARD, PPARG, PPARGC1A, PPIB, PPIF, PPME1, PPP1R12A, PPP1R13B, PPP2CA, PREP, PRG2, PRKAA2, PRKACA, PRKCE, PRKCQ, PRL, PRMT5, PRNP, PROKR1, PRPF19, PRPF4B, PRPF6, PRTN3, PSEN1, PTEN, PTGER2, PTGES, PTGS1, PTGS2, PTH, PTK2, PTPN1, PTPRF, PYCARD, PYGB, RAC2, RAD1, RAD18, RB1, RBMS3, RELA, REN, RETN, RGN, RGS1, RHOA, RNASE2, ROCK1, ROCK2, RPAIN, RPP38, RPS2, RPS6KB1, RUNX2, RYR2, S100B, SAMHD1, SCARB1, SCD5, SCGB1A1, SCN2A, SCT, SELE, SELP, SERPINA6, SERPINB1, SERPINF1, SETD2, SGMS1, SHBG, SIRT1, SIRT3, SLC10A2, SLC12A2, SLC12A9, SLC13A3, SLC18A3, SLC1A1, SLC1A2, SLC1A5, SLC22A1, SLC22A2, SLC22A5, SLC22A6, SLC22A8, SLC25A11, SLC25A13, SLC28A1, SLC29A1, SLC29A2, SLC2A1, SLC2A2, SLC2A4, SLC38A5, SLC3A2, SLC5A1, SLC5A2, SLC6A3, SLC6A4, SLC7A1, SLC7A11, SLCO2B1, SMAD2, SMAD3, SMAD5, SMAD7, SNAI1, SNCA, SOAT1, SOAT2, SOD1, SOD2, SORD, SP1, SPANXC, SPG7, SPP1, SREBF1, SREBF2, SRM, SRPK1, SRSF1, SST, STAR, STAT1, STAT3, STK11, STK24, STK3, STK39, STT3A, STX8, SUCNR1, SUGCT, SUGT1, SYK, SYN1, SYP, SYT1, TAC1, TBC1D9, TCF4, TDG, TET1, TF, TFEB, TGFB1, TGFBR1, TGIF1, TGM1, TH, THBS1, TIMP1, TIMP2, TIPARP, TJP1, TJP2, TK1, TLR2, TLR4, TLR7, TLR8, TMC1, TMPRSS15, TNF, TNFRSF10B, TNFRSF11A, TNFRSF11B, TNFSF11, TNK1, TOP1, TOP2B, TP53, TPH1, TPM3, TRAF2, TREM1, TRH, TRPM1, TSC1, TSLP, TTBK1, TUFM, TXN, TXNIP, TXNRD3, TYR, TYRP1, U2AF2, UBAC1, UCP1, UGT1A1, UGT1A8, UGT1A9, UMPS, UPP1, USP9X, VCAM1, VEGFA, VIM, VIP, VPS4A, VWF, WEE1, WNK1, WNT1, WNT10B, WNT3A, WNT7A, XAF1, XBP1, XDH, XIAP, XRCC1, YAP1, YARS2, ZFP36, ZMYND8, ZNF346

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