Page last updated: 2024-12-06

columbamine

Columbamine is a protoberberine alkaloid found in plants of the Berberidaceae family. It exhibits a wide range of biological activities, including anti-inflammatory, anticancer, and neuroprotective effects. It is being investigated for its potential therapeutic use in various diseases, including cancer, Alzheimer's disease, and Parkinson's disease. Research suggests that columbamine may exert its effects through multiple mechanisms, such as inhibiting inflammation, regulating cell growth and differentiation, and protecting neurons from damage. The compound's complex structure poses a challenge for its synthetic production, with current methods often involving multi-step reactions and low yields. Further research is needed to optimize columbamine's synthesis and explore its potential clinical applications.'

FloraRankFlora DefinitionFamilyFamily Definition
Enantia chloranthaspecies[no description available]AnnonaceaeThe custard-apple plant family of the order Magnoliales, subclass Magnoliidae, class Magnoliopsida. Some members provide large pulpy fruits and commercial timber. Leaves and wood are often fragrant. Leaves are simple, with smooth margins, and alternately arranged in two rows along the stems.[MeSH]

Cross-References

ID SourceID
PubMed CID72310
CHEMBL ID400345
CHEBI ID15920
SCHEMBL ID422073
MeSH IDM0156846

Synonyms (31)

Synonym
2-hydroxy-3,9,10-trimethoxy-5,6-dihydroisoquino[3,2-a]isoquinolinium
5,6-dihydro-2-hydroxy-3,9,10-trimethoxydibenzo[a,g]quinolizinium
CHEBI:15920 ,
5,6-dihydro-2-hydroxy-3,9,10-trimethoxydibenzo[a,g]quinolizinium iodide
dibenzo[a,g]quinolizinium, 5,6-dihydro-2-hydroxy-3,9,10-trimethoxy-
dehydroisocorypalmine
3,9,10-trimethoxy-5,6-dihydroisoquinolino[3,2-a]isoquinolin-7-ium-2-ol
C01795
columbamine ,
3621-36-1
dibenzo(a,g)quinolizinium, 5,6-dihydro-2-hydroxy-3,9,10-trimethoxy-
bdbm50226664
CHEMBL400345 ,
3,9,10-trimethoxy-5,6-dihydroisoquinolino[2,1-b]isoquinolin-7-ium-2-ol
7t4808fejw ,
unii-7t4808fejw
7,8,13,13.alpha.-tetradehydro-2-hydroxy-3,9,10-trimethoxyberbinium
columbamine [mi]
5,6-dihydro-2-hydroxy-3,9,10-trimethoxydibenzo(a,g)quinolizinium
SCHEMBL422073
CS-4254
AC-34218
HY-N0926
DTXSID80189766
AKOS030526792
YYFOFDHQVIODOQ-UHFFFAOYSA-O
FT-0723334
columbamin;dehydroisocorypalmine
Q27098298
2-hydroxy-3,9,10-trimethoxy-5,6-dihydroisoquinolino[3,2-a]isoquinolin-7-ium
columbamin

Research Excerpts

Pharmacokinetics

ExcerptReferenceRelevance
" The results showed that the pharmacokinetic behaviors of the alkaloids were different although their chemical structures were similar."( Pharmacochemistry and integrated pharmacokinetics of six alkaloids after oral administration of huang-lian-jie-du-tang decoction.
Liu, JX; Ma, ZT; Yang, XW; Zhang, Y, 2014
)
0.4

Compound-Compound Interactions

ExcerptReferenceRelevance
" In this work, we constructed an optimized method for quality evaluation and species discrimination of CR by ion-pairing high performance liquid chromatography (IP-HPLC) combined with response surface methodology (RSM)."( Construction of an optimized method for quality evaluation and species discrimination of Coptidis Rhizoma by ion-pair high performance liquid chromatography combined with response surface methodology.
Jiang, Y; Li, HJ; Li, P; Lu, J; Ni, H; Wu, TJ, 2018
)
0.48
"In order to develop a direct and reliable method for discovering lead compounds from traditional Chinese medicines (TCMs), a comparative online ligand fishing platform was developed using immobilized capillary enzyme reactors (ICERs) in combination with liquid chromatography-mass spectrometry (LC-MS)."( Online screening of acetylcholinesterase inhibitors in natural products using monolith-based immobilized capillary enzyme reactors combined with liquid chromatography-mass spectrometry.
Jiang, Z; Kool, J; Somsen, GW; Wang, L; Wang, Q; Zhang, T; Zhang, Y; Zhao, Y, 2018
)
0.48

Bioavailability

ExcerptReferenceRelevance
" However, the plasma concentration of BBR is very low after oral administration for the reason that BBR is poorly absorbed and rapidly metabolized."( Berberine metabolites could induce low density lipoprotein receptor up-regulation to exert lipid-lowering effects in human hepatoma cells.
Bin, W; Cao, S; Kang, N; Qiu, F; Wang, Y; Xu, P; Yan, J; Zhou, Y, 2014
)
0.4
[information is derived through text-mining from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Drug Classes (2)

ClassDescription
berberine alkaloid
organic heterotetracyclic compound
[compound class information is derived from Chemical Entities of Biological Interest (ChEBI), Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res]

Protein Targets (2)

Inhibition Measurements

ProteinTaxonomyMeasurementAverageMin (ref.)Avg (ref.)Max (ref.)Bioassay(s)
Lysine-specific histone demethylase 1AHomo sapiens (human)IC50 (µMol)0.47000.00312.16029.6000AID1845962; AID1872433
Cytochrome P450 3A4Homo sapiens (human)IC50 (µMol)30.60000.00011.753610.0000AID311859
[prepared from compound, protein, and bioassay information from National Library of Medicine (NLM), extracted Dec-2023]

Biological Processes (51)

Processvia Protein(s)Taxonomy
regulation of double-strand break repair via homologous recombinationLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of protein ubiquitinationLysine-specific histone demethylase 1AHomo sapiens (human)
regulation of protein localizationLysine-specific histone demethylase 1AHomo sapiens (human)
cellular response to UVLysine-specific histone demethylase 1AHomo sapiens (human)
cellular response to gamma radiationLysine-specific histone demethylase 1AHomo sapiens (human)
DNA repair-dependent chromatin remodelingLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of transcription by RNA polymerase IILysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of neuroblast proliferationLysine-specific histone demethylase 1AHomo sapiens (human)
regulation of transcription by RNA polymerase IILysine-specific histone demethylase 1AHomo sapiens (human)
protein demethylationLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of epithelial to mesenchymal transitionLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of neuron projection developmentLysine-specific histone demethylase 1AHomo sapiens (human)
cerebral cortex developmentLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of protein bindingLysine-specific histone demethylase 1AHomo sapiens (human)
neuron maturationLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of DNA bindingLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of DNA-binding transcription factor activityLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of DNA damage response, signal transduction by p53 class mediatorLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of cell sizeLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of DNA-templated transcriptionLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of transcription by RNA polymerase IILysine-specific histone demethylase 1AHomo sapiens (human)
guanine metabolic processLysine-specific histone demethylase 1AHomo sapiens (human)
muscle cell developmentLysine-specific histone demethylase 1AHomo sapiens (human)
regulation of androgen receptor signaling pathwayLysine-specific histone demethylase 1AHomo sapiens (human)
response to fungicideLysine-specific histone demethylase 1AHomo sapiens (human)
cellular response to cAMPLysine-specific histone demethylase 1AHomo sapiens (human)
regulation of DNA methylation-dependent heterochromatin formationLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of cold-induced thermogenesisLysine-specific histone demethylase 1AHomo sapiens (human)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediatorLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of neural precursor cell proliferationLysine-specific histone demethylase 1AHomo sapiens (human)
positive regulation of stem cell proliferationLysine-specific histone demethylase 1AHomo sapiens (human)
chromatin remodelingLysine-specific histone demethylase 1AHomo sapiens (human)
lipid hydroxylationCytochrome P450 3A4Homo sapiens (human)
lipid metabolic processCytochrome P450 3A4Homo sapiens (human)
steroid catabolic processCytochrome P450 3A4Homo sapiens (human)
xenobiotic metabolic processCytochrome P450 3A4Homo sapiens (human)
steroid metabolic processCytochrome P450 3A4Homo sapiens (human)
cholesterol metabolic processCytochrome P450 3A4Homo sapiens (human)
androgen metabolic processCytochrome P450 3A4Homo sapiens (human)
estrogen metabolic processCytochrome P450 3A4Homo sapiens (human)
alkaloid catabolic processCytochrome P450 3A4Homo sapiens (human)
monoterpenoid metabolic processCytochrome P450 3A4Homo sapiens (human)
calcitriol biosynthetic process from calciolCytochrome P450 3A4Homo sapiens (human)
xenobiotic catabolic processCytochrome P450 3A4Homo sapiens (human)
vitamin D metabolic processCytochrome P450 3A4Homo sapiens (human)
vitamin D catabolic processCytochrome P450 3A4Homo sapiens (human)
retinol metabolic processCytochrome P450 3A4Homo sapiens (human)
retinoic acid metabolic processCytochrome P450 3A4Homo sapiens (human)
long-chain fatty acid biosynthetic processCytochrome P450 3A4Homo sapiens (human)
aflatoxin metabolic processCytochrome P450 3A4Homo sapiens (human)
oxidative demethylationCytochrome P450 3A4Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Molecular Functions (42)

Processvia Protein(s)Taxonomy
telomeric DNA bindingLysine-specific histone demethylase 1AHomo sapiens (human)
p53 bindingLysine-specific histone demethylase 1AHomo sapiens (human)
chromatin bindingLysine-specific histone demethylase 1AHomo sapiens (human)
transcription coactivator activityLysine-specific histone demethylase 1AHomo sapiens (human)
protein bindingLysine-specific histone demethylase 1AHomo sapiens (human)
oxidoreductase activityLysine-specific histone demethylase 1AHomo sapiens (human)
enzyme bindingLysine-specific histone demethylase 1AHomo sapiens (human)
nuclear receptor coactivator activityLysine-specific histone demethylase 1AHomo sapiens (human)
demethylase activityLysine-specific histone demethylase 1AHomo sapiens (human)
histone demethylase activityLysine-specific histone demethylase 1AHomo sapiens (human)
histone H3K4 demethylase activityLysine-specific histone demethylase 1AHomo sapiens (human)
histone H3K9 demethylase activityLysine-specific histone demethylase 1AHomo sapiens (human)
identical protein bindingLysine-specific histone demethylase 1AHomo sapiens (human)
MRF bindingLysine-specific histone demethylase 1AHomo sapiens (human)
flavin adenine dinucleotide bindingLysine-specific histone demethylase 1AHomo sapiens (human)
nuclear androgen receptor bindingLysine-specific histone demethylase 1AHomo sapiens (human)
RNA polymerase II-specific DNA-binding transcription factor bindingLysine-specific histone demethylase 1AHomo sapiens (human)
telomeric repeat-containing RNA bindingLysine-specific histone demethylase 1AHomo sapiens (human)
DNA-binding transcription factor bindingLysine-specific histone demethylase 1AHomo sapiens (human)
FAD-dependent H3K4me/H3K4me3 demethylase activityLysine-specific histone demethylase 1AHomo sapiens (human)
promoter-specific chromatin bindingLysine-specific histone demethylase 1AHomo sapiens (human)
transcription factor bindingLysine-specific histone demethylase 1AHomo sapiens (human)
monooxygenase activityCytochrome P450 3A4Homo sapiens (human)
steroid bindingCytochrome P450 3A4Homo sapiens (human)
iron ion bindingCytochrome P450 3A4Homo sapiens (human)
protein bindingCytochrome P450 3A4Homo sapiens (human)
steroid hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
retinoic acid 4-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
oxidoreductase activityCytochrome P450 3A4Homo sapiens (human)
oxygen bindingCytochrome P450 3A4Homo sapiens (human)
enzyme bindingCytochrome P450 3A4Homo sapiens (human)
heme bindingCytochrome P450 3A4Homo sapiens (human)
vitamin D3 25-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
caffeine oxidase activityCytochrome P450 3A4Homo sapiens (human)
quinine 3-monooxygenase activityCytochrome P450 3A4Homo sapiens (human)
testosterone 6-beta-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
anandamide 8,9 epoxidase activityCytochrome P450 3A4Homo sapiens (human)
anandamide 11,12 epoxidase activityCytochrome P450 3A4Homo sapiens (human)
anandamide 14,15 epoxidase activityCytochrome P450 3A4Homo sapiens (human)
aromatase activityCytochrome P450 3A4Homo sapiens (human)
vitamin D 24-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
estrogen 16-alpha-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
estrogen 2-hydroxylase activityCytochrome P450 3A4Homo sapiens (human)
1,8-cineole 2-exo-monooxygenase activityCytochrome P450 3A4Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Ceullar Components (10)

Processvia Protein(s)Taxonomy
chromatinLysine-specific histone demethylase 1AHomo sapiens (human)
nucleusLysine-specific histone demethylase 1AHomo sapiens (human)
chromosome, telomeric regionLysine-specific histone demethylase 1AHomo sapiens (human)
nucleusLysine-specific histone demethylase 1AHomo sapiens (human)
nucleoplasmLysine-specific histone demethylase 1AHomo sapiens (human)
transcription regulator complexLysine-specific histone demethylase 1AHomo sapiens (human)
protein-containing complexLysine-specific histone demethylase 1AHomo sapiens (human)
DNA repair complexLysine-specific histone demethylase 1AHomo sapiens (human)
cytoplasmCytochrome P450 3A4Homo sapiens (human)
endoplasmic reticulum membraneCytochrome P450 3A4Homo sapiens (human)
intracellular membrane-bounded organelleCytochrome P450 3A4Homo sapiens (human)
[Information is prepared from geneontology information from the June-17-2024 release]

Bioassays (5)

Assay IDTitleYearJournalArticle
AID311859Inhibition of human CYP3A4 expressed in Escherichia coli assessed as inhibition of nifedipine oxidation2007Journal of natural products, Dec, Volume: 70, Issue:12
Cytochrome P3A4 inhibitors and other constituents of Fibraurea tinctoria.
AID1845962Inhibition of recombinant LSD1 (unknown origin) expressed in Escherichia coli BL21 using H3K4me2 as substrate preincubated for 10 mins followed by substrate addition and measured after 30 mins by fluorescence based analysis2021European journal of medicinal chemistry, Mar-15, Volume: 214Annual review of LSD1/KDM1A inhibitors in 2020.
AID1653955Inhibition of TNF-alpha/IFN-gamma-induced apoptosis in human HaCaT cells after 24 hrs by Annexin V-FITC/propidium iodide double staining-based flow cytometry
AID1872433Inhibition of recombinant KDM1A (unknown origin) expressed in Escherichia coli BL21 using H3K4Me2 peptide as substrate preincubated for 10 mins followed by substrate addition measured after 30 mins by fluorescence based assay2022European journal of medicinal chemistry, Mar-05, Volume: 231Drug discovery of histone lysine demethylases (KDMs) inhibitors (progress from 2018 to present).
AID1653971Cytotoxicity against human HaCaT cells assessed as reduction in cell viability after 24 hrs by MTT assay
[information is prepared from bioassay data collected from National Library of Medicine (NLM), extracted Dec-2023]

Research

Studies (29)

TimeframeStudies, This Drug (%)All Drugs %
pre-19902 (6.90)18.7374
1990's1 (3.45)18.2507
2000's4 (13.79)29.6817
2010's16 (55.17)24.3611
2020's6 (20.69)2.80
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]

Market Indicators

Research Demand Index: 25.25

According to the monthly volume, diversity, and competition of internet searches for this compound, as well the volume and growth of publications, there is estimated to be moderate demand-to-supply ratio for research on this compound.

MetricThis Compound (vs All)
Research Demand Index25.25 (24.57)
Research Supply Index3.40 (2.92)
Research Growth Index5.31 (4.65)
Search Engine Demand Index26.67 (26.88)
Search Engine Supply Index2.00 (0.95)

This Compound (25.25)

All Compounds (24.57)

Study Types

Publication TypeThis drug (%)All Drugs (%)
Trials0 (0.00%)5.53%
Reviews2 (6.90%)6.00%
Case Studies0 (0.00%)4.05%
Observational0 (0.00%)0.25%
Other27 (93.10%)84.16%
[information is prepared from research data collected from National Library of Medicine (NLM), extracted Dec-2023]
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