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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-12 20:17:34 UTC
Update Date2022-03-07 02:49:18 UTC
HMDB IDHMDB0003409
Secondary Accession Numbers
  • HMDB03409
Metabolite Identification
Common NameBerberine
DescriptionBerberine is a quaternary ammonium salt that belongs to the protoberberine group of benzylisoquinoline alkaloids. Chemically, berberine is classified as an isoquinoline alkaloid. More specifically, berberine is a plant alkaloid derived from tyrosine through a complex 8 step biosynthetic process. Berberine is found in plants such as Berberis vulgaris (barberry), Berberis aristata (tree turmeric), Mahonia aquifolium (Oregon grape) and Hydrastis canadensis (goldenseal). Two other known berberine-containing plants are Phellodendron chinense and Phellodendron amurense. Berberine is usually found in the roots, rhizomes, stems, and bark of Berberis plants. Due to berberine's intense yellow color, plants that contain berberine were traditionally used to dye wool, leather, and wood. Under ultraviolet light, berberine shows a strong yellow fluorescence, making it useful in histology for staining heparin in mast cells. Berberine is a bioactive plant compound that has been frequently used in traditional medicine. Among the known physiological effects or bioactivities are: 1) Antimicrobial action against bacteria, fungi, protozoa, viruses, helminthes, and Chlamydia; 2) Antagonism against the effects of cholera and E coli heat-stable enterotoxin; 3) Inhibition of intestinal ion secretion and of smooth muscle contraction; 4) Reduction of inflammation and 5) Stimulation of bile secretion and bilirubin discharge (PMID:32335802 ). Berberine can inhibit bacterial growth in the gut, including Helicobacter pylori, protect the intestinal epithelial barrier from injury, and ameliorate liver injury. Currently, berberine is sold as an Over-the-Counter (OTC) drug for treating gastrointestinal infections in China (PMID:18442638 ). Berberine also inhibits the proliferation of various types of cancer cells and impedes invasion and metastasis (PMID:32335802 ). Recent evidence has also confirmed that berberine improves the efficacy and safety of both chemo and radiotherapies for cancer treatment (PMID:32335802 ). Berberine has also been shown to regulate glucose and lipid metabolism in vitro and in vivo (PMID:18442638 ). In fact, berberine is the main active component of an ancient Chinese herb Coptis chinensis French, which has been used to treat diabetes for thousands of years. As an anti-diabetic, berberine increases glucose uptake by muscle fibers independent of insulin levels. It triggers AMPK activation and increases glycolysis, leading to decreased insulin resistance and decreased oxygen respiration. The same mechanism leads to a reduction in gluconeogenesis in the liver. AMPK activation by berberine also leads to an antiatherosclerotic effect in mice. Berberine's AMPK activation may also underlie berberines' anti-obesity effects and favorable influence on weight loss (PMID:18442638 ). While its use as a medication is widely touted, it is important to remember that berberine inhibits CYP2D6 and CYP3A4 enzymes, both of which are involved in the metabolism of many endogenous substances and xenobiotics, including a number of prescription drugs.
Structure
Data?1582752275
Synonyms
ValueSource
7,8,13,13a-Tetradehydro-9,10-dimethoxy-2,3-[methylenebis(oxy)]berbiniumChEBI
9,10-Dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbiniumChEBI
BerberinChEBI
Coptis rhizomeHMDB
Chemical FormulaC20H18NO4
Average Molecular Weight336.3612
Monoisotopic Molecular Weight336.123583069
IUPAC Name16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium
Traditional Name16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium
CAS Registry Number2086-83-1
SMILES
COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC
InChI Identifier
InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChI KeyYBHILYKTIRIUTE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as protoberberine alkaloids and derivatives. These are alkaloids with a structure based on a protoberberine moiety, which consists of a 5,6-dihydrodibenzene moiety fused to a quinolizinium and forming 5,6-Dihydrodibenzo(a,g)quinolizinium skeleton.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassProtoberberine alkaloids and derivatives
Sub ClassNot Available
Direct ParentProtoberberine alkaloids and derivatives
Alternative Parents
Substituents
  • Protoberberine skeleton
  • Isoquinoline
  • Benzodioxole
  • Anisole
  • Alkyl aryl ether
  • Pyridine
  • Pyridinium
  • Benzenoid
  • Heteroaromatic compound
  • Acetal
  • Ether
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point145 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility9.62 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.990 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available175.882http://allccs.zhulab.cn/database/detail?ID=AllCCS00001369
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00035 g/LALOGPS
logP-0.18ALOGPS
logP-1.3ChemAxon
logS-6ALOGPS
pKa (Strongest Basic)-4.4ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.8 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity93.52 m³·mol⁻¹ChemAxon
Polarizability36.92 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+185.89330932474
DeepCCS[M-H]-182.91830932474
DeepCCS[M-2H]-218.27430932474
DeepCCS[M+Na]+194.56430932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
BerberineCOC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC4258.7Standard polar33892256
BerberineCOC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC2841.7Standard non polar33892256
BerberineCOC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC3266.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Berberine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4l-0059000000-2d03f2d248021273bb662017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Berberine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-000i-0009000000-19928d40d547cbbc26dc2012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-00di-0029000000-42f72c3da8025ad70c4d2012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0103-0089000000-dbcf680bd232ed620a002012-07-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive-QTOFsplash10-000i-0009000000-2993f75f22b9532dc39f2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive-QTOFsplash10-000i-0009000000-1d4cdb20920f8c9003202012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive-QTOFsplash10-0079-0019000000-4995338b7526764bbad32012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive-QTOFsplash10-00dl-0059000000-ab35b8a7ec73f1063bb22012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive-QTOFsplash10-00fu-0089000000-09273e18fcd3186156f02012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOFsplash10-00di-0039000000-3a3f7eba3883c388e58c2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOFsplash10-0006-0092000000-6f10979e1ecdd29611b12012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOFsplash10-0006-0090000000-bacf940c54361560b64b2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-ITTOF (Shimadzu LC20A-IT-TOFMS) , Positive-QTOFsplash10-000i-0009000000-3d6d1928f5797f4633e42012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-ITTOF (LCMS-IT-TOF) , Positive-QTOFsplash10-000i-0009000000-6337ae6880e36d106adf2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ , positive-QTOFsplash10-00dl-0039000000-5d1ff6b7636484db90d12017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QQ , positive-QTOFsplash10-00dl-0059000000-131055c16d28a84b61302017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOFsplash10-000i-0009000000-9d8986d4bd9f3b6d634d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOFsplash10-000i-0009000000-4459c8c8f7b607ad7b492017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOFsplash10-00dr-0019000000-a0c1c55261d223b092562017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOFsplash10-00dl-0069000000-437bdc5509b367efef252017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 10V, Positive-QTOFsplash10-000i-0009000000-41bc0e7901cbc892051c2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 20V, Positive-QTOFsplash10-000i-0009000000-b2e1ddadd60e4f52d2dd2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 40V, Positive-QTOFsplash10-0iki-0179000000-85594d2e5f4b265077ab2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 10V, Negative-QTOFsplash10-000i-0009000000-604df9f348201c3c531e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 20V, Negative-QTOFsplash10-000i-0009000000-34b3c7d90696ff1943952017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberine 40V, Negative-QTOFsplash10-0nnc-3095000000-2e76003cd5b376964ba82017-07-26Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, Methanol, experimental)2021-10-10Wishart LabView Spectrum
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, Methanol, experimental)2021-10-10Wishart LabView Spectrum
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, Methanol, experimental)2021-10-10Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CD3OD, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
Tissue Locations
  • Fibroblasts
  • Intestine
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0013 +/- 0.0012 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04115
Phenol Explorer Compound IDNot Available
FooDB IDFDB023165
KNApSAcK IDC00001819
Chemspider ID2263
KEGG Compound IDC00757
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBerberine
METLIN ID3471
PubChem Compound2353
PDB IDNot Available
ChEBI ID16118
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1070241
References
Synthesis ReferenceDominguez, Xorge A.; Garcia Delgado, Jesus; Reeves, Wylie P.; Gardner, Pete D. Photochemical formation of berberine alkaloids from protopine alkaloids. Tetrahedron Letters (1967), (26), 2493-5.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Pan GY, Wang GJ, Sun JG, Huang ZJ, Zhao XC, Gu Y, Liu XD: [Inhibitory action of berberine on glucose absorption]. Yao Xue Xue Bao. 2003 Dec;38(12):911-4. [PubMed:15040083 ]
  2. Yu HH, Kim KJ, Cha JD, Kim HK, Lee YE, Choi NY, You YO: Antimicrobial activity of berberine alone and in combination with ampicillin or oxacillin against methicillin-resistant Staphylococcus aureus. J Med Food. 2005 Winter;8(4):454-61. [PubMed:16379555 ]
  3. Zhao CC, Zheng WF, Li MQ: [The interaction of berberine and human serum albumin]. Guang Pu Xue Yu Guang Pu Fen Xi. 2004 Jan;24(1):111-3. [PubMed:15768991 ]
  4. Pan JF, Yu C, Zhu DY, Zhang H, Zeng JF, Jiang SH, Ren JY: Identification of three sulfate-conjugated metabolites of berberine chloride in healthy volunteers' urine after oral administration. Acta Pharmacol Sin. 2002 Jan;23(1):77-82. [PubMed:11860742 ]
  5. Zhang H, Shao Z, Sun Y: [Determination of berberine in human serum by reversed-phase high performance liquid chromatography]. Se Pu. 1997 Sep;15(5):454-5. [PubMed:15739507 ]
  6. Liu Y, Huang CZ, Li YF: Fluorescence assay based on preconcentration by a self-ordered ring using berberine as a model analyte. Anal Chem. 2002 Nov 1;74(21):5564-8. [PubMed:12433089 ]
  7. Mantena SK, Sharma SD, Katiyar SK: Berberine, a natural product, induces G1-phase cell cycle arrest and caspase-3-dependent apoptosis in human prostate carcinoma cells. Mol Cancer Ther. 2006 Feb;5(2):296-308. [PubMed:16505103 ]
  8. Song D, Hao J, Fan D: Biological properties and clinical applications of berberine. Front Med. 2020 Oct;14(5):564-582. doi: 10.1007/s11684-019-0724-6. Epub 2020 Apr 25. [PubMed:32335802 ]
  9. Yin J, Xing H, Ye J: Efficacy of berberine in patients with type 2 diabetes mellitus. Metabolism. 2008 May;57(5):712-7. doi: 10.1016/j.metabol.2008.01.013. [PubMed:18442638 ]