Review Article

Interaction of Herbal Compounds with Biological Targets: A Case Study with Berberine

Table 1

Potential targets of berberine.

Target namesTarget gene symbolCellsEffectsPossible clinical applicationsReferences

72 kDa type IV collagenaseMMP2HUVECs, tongue cancer SCC-4 cells, gastric carcinoma SNU-5 cells, lung cancer A549 cells, and U-87 glioma cellsDownregulation of MMP2 mRNA and protein expression, reduced MMP-2 levelsAntimetastatic [18, 6972]

Acetyl-Coenzyme A carboxylase-αACACAHepG2 hepatoma cellsPhosphorylationAntihyperlipidemic[73]

α-FetoproteinAFPHepG2 hepatoma cellsReduced secretion of alpha fetoproteinApoptosis[74]

Amyloid-β (A4) precursor protein (peptidase nexin-II, Alzheimer disease)APPNeuroglioma H4 cellsReduces amyloid-β peptide (Aβ) levels via modulation of APPAlzheimer disease[75]

Bcl-XBCL2L1Colonic carcinoma cells, HepG2 cells/A549 cells, prostate carcinoma cells (DU145 and PC-3, LNCaP), Jurkat cellsJNK/p38 pathway and induction of ROS production. Decreased expression Cell apoptosis, anticancer, and anti-inflammatory[1921, 30, 76, 77]

Arylamine -acetyltransferase 1NATLeukemia HL-60 cells, colon tumour cells, brain tumour cells (G95/VGH and GBM 8401)Decrease in -acetyltransferase (NAT) protein and expression of mRNA Anticancer (leukemia, colon cancer, brain tumour, etc.)[7880]

ATP-binding cassette subfamily G member 2ABCG2MCF-7 breast cancer cellsDecrease in ABCG2 expressionBreast cancer[81]

Baculoviral IAP repeat-containing protein 2 (antiapoptosis factor c-IPA-1)BIRC2Jurkat cells, colonic carcinoma cells (SW620)Suppresses expression of antiapoptosis factor IAP1Anticancer [19, 77]

Baculoviral IAP repeat-containing protein 3BIRC3Jurkat cellsSuppresses expression of antiapoptosis factor IAP2Anticancer [77]

Baculoviral IAP repeat-containing protein 5 (Survivin)BIRC5Jurkat cellsSuppresses expression of survivinAnticancer and anti-inflammatory agent[77]

B-cell CLL/lymphoma 2BCL2HepG2 cells, oral squamous cell carcinoma, tongue cancer SCC-4 cells, colonic carcinoma cells, lung cancer cells, breast cancer MCF-7 (estrogen receptor+) cells, prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Bcl-2 DownregulationCell apoptosis, cancer, and ER antagonist adjuvant therapy [1923, 30, 34, 82, 83]

B-cell lymphoma 3-encoded proteinBcl-3Gastric carcinoma SNU-5 cells Downregulation of Bcl-3Gastric cancer[24]

Bcl2 antagonist of cell deathBADHuman oral squamous cell carcinomaIncreased expression of proapoptotic BAD proteinAntitumour [23]

BCL2-associated X proteinBAXGastric carcinoma SNU-5 cells, prostate carcinoma cells (DU145, PC-3, LNCaP and PWR-1E), leukemia HL-60, tongue cancer SCC-4 cells, lung cancer cells, activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs) Upregulation of Bax, increased expression. G2/M phase arrestCell apoptosis, gastric cancer[18, 20, 21, 24, 29, 30, 83, 84]

BH3-interacting domain death agonist p11BIDColonic carcinoma cells/HepG2 cellsJNK/p38 pathway and induction of ROS productionInduction of apoptosis [19, 76]

C/EBP homologous protein (CHOP) or growth arrest- and DNA damage-inducible gene 153 (GADD153) or DNA damage-inducible transcript 3GADD153/DDIT3Cervical cancer
Ca Ski cells
Induced expression of GADD153 Cervical cancer [85]

CASP8 and FADD-like apoptosis regulator subunit p12CFLAR/cFLIPJurkat cellsSuppresses expression of cFLIPAnticancer and anti-inflammatory [77]

Caspase 3CASP3Tongue cancer SCC-4 cells, neuroblastoma (SK-N-SH), glioblastoma T98G cells, gastric carcinoma SNU-5 cells, HL-60 cells, prostate carcinoma cells (DU145, PWR-1E, PC-3 and LNCaP), colonic carcinoma cells, hepatoma cells, oral squamous cell carcinoma, promonocytic U937 cells, lung cancer A549, H1301 cells, activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs), BIU-87 and T24 bladder cancer cellsActivation of caspase-3, G2/M phase arrestAnticancer[1821, 2325, 30, 33, 76, 83, 8689]

Caspase 8CASP8Tongue cancer SCC-4 cells, colonic carcinoma cells, hepatoma cells, oral squamous cell carcinomaActivated caspase 8 Anticancer[18, 19, 23, 76]

Caspase 9CASP9Tongue cancer SCC-4 cells, glioblastoma T98G, oral squamous carcinoma, promonocytic U937 cells, prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs), BIU-87 and T24 bladder cancer cellsActivation of caspase 9Cell apoptosis, anticancer[18, 21, 23, 30, 33, 83, 86, 87, 89, 90]

Cdc42 effector protein 1CDC42EP1Nasopharyngeal carcinoma (HONE1) cellsSuppression of Rho GTPases activation (Cdc42)Cancer metastasis inhibition[91]

Cell division protein kinase 6CDK6Prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in Cdk6Cell apoptosis, cancer[21, 30, 83]

Cellular tumor antigen p53TP53Gastric carcinoma SNU-5 cells, osteosarcomaIncreased expression of p53 protein, cell cycle arrest at G1G2/M phase arrestAnticancer (gastric cancer, osteosarcoma)[24, 92]

Chemokine (C-C motif) ligand 2 (monocyte chemotactic protein-1)CCL2Retinal pigment epithelial cell lineInhibits CCL2 (MCP-1) expressionAnti-inflammatory[93]

Cyclic AMP-dependent transcription factor ATF-3ATF3Colorectal cancer cellsInduces ATF3 expressionColorectal cancer [94]

Cyclin-dependant kinase 1/cell division control protein 2 homologCDK1/CDC2HL-60 cell, gastric carcinoma SNU-5 cells Inactivation of Cdc2 (CDK1) or decreased protein expression Antiproliferative and proapoptotic[24, 95]

Cyclin E1CCNE1Neuroblastoma (SK-N-SK), glioblastoma T98G cells, activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in cyclin EAnticancer [25, 83, 90]

Cyclin-dependent kinase 2CDK2Neuroblastoma (SK-N-SK), glioblastoma T98G cells, prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in Cdk2Cell apoptosis, anticancer[21, 25, 30, 83, 90]

Cyclin-dependent kinase 4CDK4Neuroblastoma (SK-N-SK), glioblastoma T98G cells, prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in Cdk4Cell apoptosis, anticancer[21, 25, 30, 83, 90]

Cyclin-dependent kinase inhibitor 1 (p21)CDKN1ABrest cancer MCF-7 (estrogen receptor+) cells, epidermoid carcinoma A431 cells, activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Increased expression of p21Breast cancer, ER antagonist adjuvant therapy [21, 30, 82, 83]

Cyclin-dependent kinase inhibitor 1B (P27/KIP1)CDKN1BEpidermoid carcinoma A431 cells, activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Increased expression of Cdki proteins Cell apoptosis, cancer[21, 30, 83]

Cytochrome c-1CYC1Tongue cancer SCC-4 cells, colonic carcinoma cells, promyelocytic leukemia HL-60 cellsRelease of cytochrome c-1Anticancer[18, 19, 84, 86]

CYP2C9CYP2C9Recombinant CYPInhibition of CYP2C9Drug interactions[96]

CYP2D6CYP2D6Recombinant CYPInhibition of CYP2D6Drug interactions[96]

CYP3A4CYP3A4Caco-2 cells, patientsCYP3A4 Downregulation and inhibition Drug interactions[97, 98]

Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2)DPP4Recombinant DPP4Inhibition of DPP4[99]

Early activation antigen CD69CD69Human peripheral lymphocytes Reduced expression of CD69 Immunosuppressive agent[100]

Epidermal growth factor receptorEGFRBrest cancer MCF-7 (estrogen receptor+) cellsEGFRdownregulatedBreast cancer, ER antagonist adjuvant therapy [82]

EzrinEZRNasopharyngeal carcinoma 5–8F cellsEzrin inhibitionAnticancer [26]

G1/S-specific cyclin-D1CCND1Giant cell carcinoma cell line, HL-60 cell, prostate carcinoma cells (DU145 and PC-3, LNCaP), Jurkat cells, neuroblastoma (SK-N-SK), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Inhibits expression of cyclin D1Antiproliferative and proapoptotic, anticancer, anti-inflammatory [21, 25, 30, 32, 77, 83, 95]

G1/S-specific cyclin-D2CCND2Prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in cyclin D2Cell apoptosis, cancer[21, 30, 83]

G1/S-specific cyclin-E1CCNE1Prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Decrease in cyclin ECell apoptosis, cancer[21, 30, 83]

G2/mitotic-specific cyclin-B1CCNB1Gastric carcinoma SNU-5 cells Decreased cyclin B, G2/M phase arrestCell apoptosis, anticancer[24]

Glucagon-like peptide (GCG/GLP-1/GLP-2)GCGNCI-H716 cellsEnhanced glucagon-like peptide (GLP)-1 Antidiabetic agent[42]

Growth/differentiation factor 15 (NAG-1)GDF15Colorectal cancer cellsInduces NAG-1 expressionColorectal cancer [94]

Hypoxia-inducible factor 1αHIF1AHUVECs, HepG2 cellsPrevention and reduction of HIF-1 alpha expressionTumour angiogenesis[101, 102]

Induced myeloid leukemia cell differentiation protein Mcl-1MCL1Oral cancer cellsInhibition of Mcl-1 expressionInduced apoptosis[103]

Inhibitor of NF-κB kinase subunit alpha (IκB kinase)CHUK(IKK)Jurkat cellsInhibition of IκB kinase (IKK)Anticancer and anti-inflammatory agent[77]

Interferon-γIFNB1Brest cancer MCF-7 (estrogen receptor+) cellsIFN-beta upregulated Breast cancer, ER antagonist adjuvant therapy [82]

Interleukin 8IL8Retinal pigment epithelial cell lineInhibits IL-8 expressionAnti-inflammatory[93]

Interleukin-1βIL1BFibroblasts (HFL1)Induces IL-1B productionsPulmonary inflammation[104]

Interleukin-2 receptor α-chainIL2RA/CD25Human peripheral lymphocytes Reduced expression of CD25Immunosuppressive agent[100]

Interleukin-6IL6KeratinocytesReduces and IL-6 expressionAntiskin ageing agent[105]

Low-density lipoprotein receptor (familial hypercholesterolemia)LDLRHepG2 cellsIncreased mRNA and protein expressionHyperlipidemia [106108]

Matrix metallopeptidase 1 (27 kDa interstitial collagenase)MMP1Dermal fibroblasts, U-87 glioma cellsMMP-1 expression decreased Antiskin ageing agent, anticancer [70, 109]

Matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)MMP9Tongue cancer SCC-4 cells, keratinocytes, gastric carcinoma SNU-5InhibitionAnticancer[34, 70, 105]

Matrix metalloproteinase-16MMP16Jurkat cellsSuppresses expression of MMP-16Anticancer and anti-inflammatory agent[77]

Mitogen-activated protein kinase 3ERK1/MAPK3Peripheral blood monocytes (PBMC) ERK1 protein expression inhibitionAntiatherosclerotic effects[110]

Mitogen-activated protein kinase 4ERK2/MAPK4Peripheral blood monocytes (PBMC) ERK2 protein expression inhibitionAntiatherosclerotic effects[110]

Mitogen-activated protein kinase 8 (JNK)MAPK8Peripheral blood monocytes (PBMC) Jun N-terminal kinase (JNK) protein expression inhibited at high levels of BBRAntiatherosclerotic effects[19, 110]

M-phase inducer phosphatase 1CDC25AHL-60 cell Phosphorylation and degradation of Cdc25AAntiproliferative and proapoptotic[95]

Multidrug resistance protein 1 (P-gp, P-gp-170)ABCB1Tumour cell lines Significant inhibited P-gp multidrug resistance (MDR) activity MDR activity reversal[111]

Hepatoma
HepG2 cells
Upregulated multidrug resistance transporter (P-gp-170) expressionReduced retention of chemotherapeutic agents[112]

Myc proto-oncogene proteinMYCU-87 glioma cellsMyc level decreasedMalignant glioma and cancer development [71]

NF-κB inhibitor-αNFKBIALung epithelial cells (A-549)Inhibition of κB-α phosphorylation and degradation Pulmonary inflammation[104]

Nuclear factor NF-κB p50 subunit (NF-κB)NFKB1Jurkat cells, osteoblastic cells, HepG2 cellsInhibit NF-κB production and suppress NF-κB Anticancer and anti-inflammatory agent, alcohol liver disease, osteoclast formation [77, 113115]

Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)NR3C1HepG2 cellsReduced GR levelsCell growth arrest [74]

Nucleophosmin (nucleolar phosphoprotein B23) and telomeraseNPM1Leukemia HL-60 cells Downregulation of nucleophosmin/B23 and telomerase activity Cancer [116]

Peroxisome proliferator-activated receptor-γPPARGFree-fatty-acid-induced insulin resistance muscle cells-L6 myotubes, 3T3-L1 preadipocytesDecreased expressionAntidiabetic [37, 117]

Platelet glycoprotein 4CD36/FATFree-fatty-acid-induced insulin resistance muscle cells-L6 myotubesDecreased expressionAntidiabetic [37]

Poly (ADP-ribose) polymerase family, member 1PARPHepG2 cells/hepatoma cells, colonic carcinoma cells, prostate cancer cells (PC-3), prostate carcinoma cells (DU145 and PC-3, LNCaP), activated rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs)Cleavage of poly (ADP-ribose) polymerase. Activation of PARPCell apoptosis, Anticancer [19, 21, 22, 30, 76, 83, 87]

Potassium voltage-gated channel subfamily H member 2KCNH2/HERG1Leukemic stem cells (LSCs)Inhibits HERG1 K (+) channels of leukemic cells Inhibits AML cell migration [35]

Processed sterol regulatory element-binding protein 2SREBP2HepG2 cellsReduction of SREBP2Hyperlipidemia[101]

Proprotein convertase subtilisin/kexin type 9PCSK9HepG2 cells Suppression of PCSK9 mRNA and protein levelsHyperlipidemia [101, 107]

Prostaglandin G/H synthase 2PTGS2/COX2Peripheral blood monocytes (PBMC), oral cancer cell lines OC2 and KB cells, breast cancer MCF-7 (estrogen receptor+) cells, Jurkat cells, colon cancer cellsDecrease of Cox-2 mRNA and protein expressionAntiatherosclerotic effects, anti-inflammatory, anticancer, breast cancer ER antagonist adjuvant therapy, Anticancer[27, 77, 82, 103, 110, 118]

Proto-oncogene tyrosine-protein kinase ROSROS1HUVECsInhibition of ROS generationProtects LDL oxidation and prevents ox-LDL-induced cellular dysfunction[19, 119]

Ras-related C3 botulinum toxin substrate 1RAC1Nasopharyngeal carcinoma (HONE1) cellsSuppression of Rho GTPases activation (Rac1)Cancer metastasis inhibition[91]

Receptor tyrosine-protein kinase erbB-2 ERBB2/HER2Brest cancer MCF-7 (estrogen receptor+) cellsHER2 downregulatedBreast cancer, ER antagonist adjuvant therapy [82]

Rho-associated protein kinase 1ROCK1/RHONasopharyngeal carcinoma 5–8F cellsSuppression of Rho kinase activity Anticancer [91]

Runt-related transcription factor 2RUNX2Osteoblast cellsPromotes transcriptional activity of Runx2Osteoblast differentiation and bone formation in osteoporosis[120]

SDF-1-α (3–67) (SDF-1)CXCL12Acute myeloid leukemia (AML)Reduces SDF-1 chemokine Inhibits AML cell migration [35]

Sucrase-isomaltase (α-glucosidase)SICaco-2 cellsInhibit alpha-glucosidaseAntihyperglycaemic[39]

Topoisomerase (DNA) ITop1Recombinant human topoisomerase ITop1 inhibitionAnticancer[121]

Transcription factor AP-1AP-1Hepatoma cells, MDA-MB-231 breast cancer cells, giant cell carcinoma cell line, colon cancer cells, U-87 glioma cells, HeLa cellsInhibition of AP-1 activity, AP-1 DNA suppression Antitumor activity, Anticancer[27, 32, 71, 115, 118, 122124]

Transforming protein RhoARHOANasopharyngeal carcinoma (HONE1) cellsSuppression of Rho GTPases activation (RhoA)Cancer metastasis inhibition[91]

Tumor necrosis factor-αTNFAMacrophages, fibroblasts (HFL1)Inhibition of TNF-αAnti-inflammatory[104, 125]

Urokinase-plasminogen activatorPLAULung cancer A549 cells, tongue cancer SCC-4 cells Reduced urokinase-plasminogen activator (u-PA)Antimetastatic, Anticancer[34, 72]

Vascular endothelial growth factor AVEGFAHUVECsPrevention of VEGF expressionTumour angiogenesis[102]

Wee1-like protein kinaseWee1Gastric carcinoma SNU-5 cells Increased expression of Wee1protein, G2/M phase arrestGastric cancer[24]