Natural Product: NPC182852

Natural Product IDNPC182852
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (-)-(2S)-5,7,2'-Trihydroxy-8,3'-Diprenylflavanone
IUPAC Name (2S)-5,7-dihydroxy-2-[2-hydroxy-3-(3-methylbut-2-enyl)phenyl]-8-(3-methylbut-2-enyl)-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1689202
PubChem CID 51040899
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003642] 8-prenylated flavans
            • [CHEMONTID:0003508] 8-prenylated flavanones

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 SWLGFCRAFOKHQK-QFIPXVFZSA-N
Standard InCHI InChI=1S/C25H28O5/c1-14(2)8-10-16-6-5-7-18(24(16)29)22-13-21(28)23-20(27)12-19(26)17(25(23)30-22)11-9-15(3)4/h5-9,12,22,26-27,29H,10-11,13H2,1-4H3/t22-/m0/s1
SMILES CC(=CCc1cccc(c1O)[C@@H]1CC(=O)c2c(O1)c(CC=C(C)C)c(cc2O)O)C

  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
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. seed n.a. PMID[14640528]
NPO28901 Blighia sapida Species Sapindaceae Eukaryota n.a. fruit n.a. PMID[19653254]
NPO28901 Blighia sapida Species Sapindaceae Eukaryota n.a. fruit n.a. PMID[19653254f]
NPO29014 Dalea boliviana Species Fabaceae Eukaryota n.a. root n.a. PMID[21226489]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29014 Dalea boliviana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28882 Misopates orontium Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28901 Blighia sapida Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28901 Blighia sapida Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29014 Dalea boliviana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28882 Misopates orontium Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28901 Blighia sapida Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29032 Spathiphyllum wallisii Species Araceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = 87.8 % PMID[21226489]
NPT43 Individual protein Tyrosinase Agaricus bisporus IC50 = 68500.0 nM PMID[21226489]

In vitro activity

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

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





 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 NPC182852 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
0.7931 Intermediate Similarity NPC306829
0.7333 Intermediate Similarity NPC324436
0.7333 Intermediate Similarity NPC78
0.7167 Intermediate Similarity NPC76372
0.7167 Intermediate Similarity NPC37496
0.7097 Intermediate Similarity NPC66515
0.6875 Remote Similarity NPC485610
0.6774 Remote Similarity NPC107572
0.6774 Remote Similarity NPC32739
0.6769 Remote Similarity NPC10990
0.6716 Remote Similarity NPC300988
0.6667 Remote Similarity NPC148757
0.6515 Remote Similarity NPC161506
0.6479 Remote Similarity NPC54577
0.6364 Remote Similarity NPC291878
0.6308 Remote Similarity NPC480990
0.6269 Remote Similarity NPC36217
0.597 Remote Similarity NPC285555
0.5857 Remote Similarity NPC81697
0.5857 Remote Similarity NPC485615
0.5775 Remote Similarity NPC166934
0.5758 Remote Similarity NPC91560
0.5758 Remote Similarity NPC236766
0.5652 Remote Similarity NPC608140
0.5634 Remote Similarity NPC24136
0.5571 Remote Similarity NPC485620
0.5522 Remote Similarity NPC150408
0.5484 Remote Similarity NPC4743
0.5455 Remote Similarity NPC218226
0.5417 Remote Similarity NPC278249
0.5417 Remote Similarity NPC223812
0.5342 Remote Similarity NPC131568
0.5286 Remote Similarity NPC166689
0.5217 Remote Similarity NPC187282
0.5217 Remote Similarity NPC265040
0.5217 Remote Similarity NPC250214
0.5211 Remote Similarity NPC278476
0.52 Remote Similarity NPC485617
0.5172 Remote Similarity NPC28918
0.5147 Remote Similarity NPC164980
0.5147 Remote Similarity NPC258630
0.5143 Remote Similarity NPC197252
0.5143 Remote Similarity NPC610133
0.5132 Remote Similarity NPC214774
0.5132 Remote Similarity NPC67805
0.507 Remote Similarity NPC223500
0.5068 Remote Similarity NPC85162
0.5067 Remote Similarity NPC328164

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC182852 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