Natural Product: NPC262359

Natural Product IDNPC262359
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (E)-1-(2,4-Dihydroxyphenyl)-3-(4-Methoxyphenyl)Prop-2-En-1-One
IUPAC Name (E)-1-(2,4-dihydroxyphenyl)-3-(4-methoxyphenyl)prop-2-en-1-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL182653
PubChem CID 5711223
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003472] 2'-Hydroxychalcones

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 ADRQFDIWPRFKSP-RUDMXATFSA-N
Standard InCHI InChI=1S/C16H14O4/c1-20-13-6-2-11(3-7-13)4-9-15(18)14-8-5-12(17)10-16(14)19/h2-10,17,19H,1H3/b9-4+
SMILES COc1ccc(cc1)/C=C/C(=O)c1ccc(cc1O)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
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. seed n.a. PMID[10661881]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. leaf n.a. PMID[17124632]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. fruit n.a. PMID[17124632]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[17125236]
NPO15741 Embelia ribes Species Primulaceae Eukaryota roots n.a. n.a. PMID[17125236]
NPO10682 Cystoseira mediterranea Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[2045820]
NPO10682 Cystoseira mediterranea Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15553 Barringtonia acutangula Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16182 Desmodium canadense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1281 Schleichera trijuga Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16096 Astragalus adsurgens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5457 Dalbergia congestiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12581 Corydalis densiflora Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15206 Mabea fistulifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15553 Barringtonia acutangula Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13520 Craibiodendron yunnanense Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13641 Napoleonaea vogelii Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5457 Dalbergia congestiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7887 Schultesia guianensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10447 Triclisia subcordata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10947 Aspilia parvifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1281 Schleichera trijuga Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16096 Astragalus adsurgens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10682 Cystoseira mediterranea Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16182 Desmodium canadense 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
NPT12 Individual protein Human immunodeficiency virus type 1 integrase Human immunodeficiency virus 1 IC50 > 100000.0 nM PMID[17502148]
NPT12 Individual protein Human immunodeficiency virus type 1 integrase Human immunodeficiency virus 1 IC50 = 39000.0 nM PMID[17502148]
NPT178 Individual protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 > 60000.0 nM PMID[17125223]
NPT149 Individual protein Endoplasmic reticulum-associated amyloid beta-peptide-binding protein Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT282 Individual protein MAP kinase ERK2 Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT151 Individual protein 15-hydroxyprostaglandin dehydrogenase [NAD+] Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens Potency = 2511.9 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT1422 Individual protein ATP-binding cassette sub-family G member 2 Homo sapiens IC50 = 33320.0 nM PMID[22112540]
NPT1422 Individual protein ATP-binding cassette sub-family G member 2 Homo sapiens IC50 = 12050.0 nM PMID[22112540]
NPT483 Individual protein Prelamin-A/C Homo sapiens Potency = 35481.3 nM PubChem BioAssay data set
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 354.8 nM PubChem BioAssay data set
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 39.8 nM PubChem BioAssay data set
NPT540 Individual protein Bile acid receptor FXR Homo sapiens Inhibition = 34.39 % PMID[28235703]
NPT540 Individual protein Bile acid receptor FXR Homo sapiens Activity = 3.97 % PMID[28235703]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens FC = 1.8 n.a. PMID[19807106]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens FC = 2.6 n.a. PMID[19807106]
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT444 Individual protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 56234.1 nM PubChem BioAssay data set
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 = 930.0 nM DOI[10.1007/s00044-012-0367-5]
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 15848.9 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 11220.2 nM PubChem BioAssay data set
NPT792 Individual protein Arachidonate 15-lipoxygenase Homo sapiens Potency = 19952.6 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT539 Individual protein Cellular tumor antigen p53 Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT539 Individual protein Cellular tumor antigen p53 Homo sapiens Potency = 19952.6 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 4466.8 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT520 Cell line 3T3-L1 Mus musculus Activity = 248.0 mg/dl PMID[22608392]
NPT633 Organism Leishmania donovani Leishmania donovani Inhibition = 15.0 % PMID[15225696]
NPT633 Organism Leishmania donovani Leishmania donovani Inhibition = 60.0 % PMID[15225696]
NPT2 Others Unspecified n.a. Potency = 20.0 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 10000.0 nM PubChem BioAssay data set
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv GI = 58.0 % PMID[25977095]
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 101.0 % PMID[30852084]
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 76.0 % PMID[30852084]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Inhibition = 51.41 % DOI[10.1007/s00044-009-9202-z]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 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 NPC262359 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
0.7609 Intermediate Similarity NPC144281
0.7561 Intermediate Similarity NPC19174
0.7561 Intermediate Similarity NPC115159
0.7442 Intermediate Similarity NPC139813
0.7333 Intermediate Similarity NPC205468
0.7209 Intermediate Similarity NPC297186
0.7174 Intermediate Similarity NPC605344
0.7083 Intermediate Similarity NPC254659
0.6731 Remote Similarity NPC131039
0.6667 Remote Similarity NPC267552
0.6667 Remote Similarity NPC26697
0.6667 Remote Similarity NPC56031
0.6522 Remote Similarity NPC13238
0.6429 Remote Similarity NPC190487
0.6383 Remote Similarity NPC64359
0.6316 Remote Similarity NPC484050
0.6182 Remote Similarity NPC185526
0.6122 Remote Similarity NPC284556
0.6087 Remote Similarity NPC224273
0.6078 Remote Similarity NPC190043
0.6 Remote Similarity NPC259767
0.6 Remote Similarity NPC129132
0.5918 Remote Similarity NPC242294
0.5893 Remote Similarity NPC235239
0.5849 Remote Similarity NPC169250
0.5849 Remote Similarity NPC44960
0.58 Remote Similarity NPC312318
0.58 Remote Similarity NPC265045
0.5769 Remote Similarity NPC472365
0.5763 Remote Similarity NPC188967
0.5741 Remote Similarity NPC188879
0.5714 Remote Similarity NPC336114
0.5686 Remote Similarity NPC263670
0.5652 Remote Similarity NPC73532
0.5636 Remote Similarity NPC65005
0.5614 Remote Similarity NPC11056
0.551 Remote Similarity NPC192304
0.551 Remote Similarity NPC213603
0.551 Remote Similarity NPC602737
0.549 Remote Similarity NPC142165
0.5417 Remote Similarity NPC122793
0.541 Remote Similarity NPC608873
0.541 Remote Similarity NPC609853
0.54 Remote Similarity NPC257756
0.54 Remote Similarity NPC201959
0.5385 Remote Similarity NPC119660
0.5385 Remote Similarity NPC87231
0.5357 Remote Similarity NPC269694
0.5357 Remote Similarity NPC482939
0.5345 Remote Similarity NPC154304
0.5319 Remote Similarity NPC211120
0.5319 Remote Similarity NPC158222
0.5306 Remote Similarity NPC167205
0.5306 Remote Similarity NPC212631
0.5306 Remote Similarity NPC608685
0.5208 Remote Similarity NPC176930
0.5208 Remote Similarity NPC485640
0.5208 Remote Similarity NPC602047
0.5192 Remote Similarity NPC308037
0.5192 Remote Similarity NPC477243
0.5192 Remote Similarity NPC607239
0.5111 Remote Similarity NPC17525
0.5088 Remote Similarity NPC168105

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC262359 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