Natural Product: NPC163846

Natural Product IDNPC163846
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Amorfrutin A
IUPAC Name 2-hydroxy-4-methoxy-3-(3-methylbut-2-enyl)-6-(2-phenylethyl)benzoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL491820
PubChem CID 17950432
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey CTNFTPUIYFUXBE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C21H24O4/c1-14(2)9-12-17-18(25-3)13-16(19(20(17)22)21(23)24)11-10-15-7-5-4-6-8-15/h4-9,13,22H,10-12H2,1-3H3,(H,23,24)
SMILES COc1cc(CCc2ccccc2)c(c(c1CC=C(C)C)O)C(=O)O

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18841906]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota Fruits n.a. n.a. PMID[28075580]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8326318]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8350086]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16886 Amorpha fruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT152 Individual protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 20596.2 nM PMID[9677271]
NPT154 Individual protein Mothers against decapentaplegic homolog 3 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT10 Individual protein Geminin Homo sapiens Potency n.a. 10322.5 nM PMID[20452770]
NPT1474 Individual protein ATP-dependent Clp protease proteolytic subunit Bacillus subtilis (strain 168) Potency n.a. 25118.9 nM PMID[3172136]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens Potency n.a. 10000.0 nM PMID[16933872]
NPT159 Individual protein Aberrant vpr protein Human immunodeficiency virus 1 Potency n.a. 63095.7 nM PMID[18070962]
NPT106 Individual protein Peroxisome proliferator-activated receptor delta Homo sapiens Kd = 27000.0 nM DOI[10.1016/S0960-894X(00)80225-5]
NPT161 Individual protein Rap guanine nucleotide exchange factor 4 Homo sapiens Potency n.a. 35481.3 nM PMID[26067904]
NPT11 Individual protein Guanine nucleotide-binding protein G(s), subunit alpha Homo sapiens Potency n.a. 19952.6 nM PMID[15568778]
NPT803 Individual protein Flap endonuclease 1 Homo sapiens Potency n.a. 19952.6 nM PMID[19778089]
NPT866 Individual protein Peroxisome proliferator-activated receptor alpha Homo sapiens Kd = 27000.0 nM PMID[23819826]
NPT866 Individual protein Peroxisome proliferator-activated receptor alpha Homo sapiens FC = 5.0 n.a. PMID[37940359]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Activity = 39.0 % PMID[20064677]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens EC50 = 458.0 nM Open TG-GATES in vivo data: Biochemistry
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Kd = 236.0 nM PMID[24211635]
NPT831 Individual protein Serine/threonine-protein kinase PLK1 Homo sapiens Potency n.a. 26679.5 nM PMID[1791475]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens %max = 39.0 % PMID[25734377]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens FC > 20.0 n.a. PMID[37940359]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Activity n.a. n.a. n.a. PMID[37940359]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Activity = 39.0 % PMID[33992930]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Ki = 236.0 nM PMID[33992930]
NPT535 Individual protein Parathyroid hormone receptor Homo sapiens Potency n.a. 70794.6 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT139 Cell line HT-29 Homo sapiens IC50 = 50800.0 nM PMID[18610999]
NPT1970 Cell line THP-1 Homo sapiens IC50 = 50000.0 nM PMID[28075580]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC > 50000.0 nM PMID[28075580]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 50000.0 nM PMID[28075580]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 6300.0 nM PMID[28075580]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 100000.0 nM PMID[28075580]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 25000.0 nM PMID[28075580]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Activity = -31.3 % PMID[30444360]
NPT2 Others Unspecified n.a. IC50 = 840.0 nM DrugMatrix in vivo data: Pathology
NPT2 Others Unspecified n.a. IC50 = 4170.0 nM PMID[18829331]
NPT2 Others Unspecified n.a. IC50 n.a. 12100.0 nM PMID[15043426]
NPT2 Others Unspecified n.a. Potency n.a. 50118.7 nM PMID[16610794]
NPT2 Others Unspecified n.a. Potency n.a. 39810.7 nM PMID[22546674]
NPT2 Others Unspecified n.a. Potency n.a. 8912.5 nM PMID[22290833]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC = 50000.0 nM PMID[28075580]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC = 25000.0 nM PMID[28075580]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC > 50000.0 nM PMID[28075580]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference
Mus musculus n.a. T1/2 = 2.0 hr PMID[33992930]
Mus musculus n.a. Cmax = 124552.02 nM PMID[33992930]





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC163846 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8276 Intermediate Similarity NPC488442
0.7719 Intermediate Similarity NPC600248
0.7241 Intermediate Similarity NPC600562
0.7 Intermediate Similarity NPC610386
0.6949 Remote Similarity NPC603552
0.678 Remote Similarity NPC225173
0.678 Remote Similarity NPC45931
0.6552 Remote Similarity NPC609283
0.6452 Remote Similarity NPC600705
0.6071 Remote Similarity NPC609982
0.5882 Remote Similarity NPC125801
0.5538 Remote Similarity NPC268157
0.5373 Remote Similarity NPC118919
0.5373 Remote Similarity NPC230334
0.5091 Remote Similarity NPC601095

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC163846 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data