Natural Product: NPC28753

Natural Product IDNPC28753
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 2-Hydroxyl-4,6-Dimethoxyldihydrochalcone
IUPAC Name 1-(2-hydroxy-4,6-dimethoxyphenyl)-3-phenylpropan-1-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL492166
PubChem CID 270058
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003473] 2'-Hydroxy-dihydrochalcones

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 JAJFQMZJIQDRSX-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H18O4/c1-20-13-10-15(19)17(16(11-13)21-2)14(18)9-8-12-6-4-3-5-7-12/h3-7,10-11,19H,8-9H2,1-2H3
SMILES COc1cc(c(C(=O)CCc2ccccc2)c(c1)OC)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
NPO12116 Anabasis brevifolia Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17722 Athroisma gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15901 Pentanema indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18174 Rinodina lepida Species Physciaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8708 Vibrio cholerae Species Vibrionaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO8708 Vibrio cholerae Species Vibrionaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12116 Anabasis brevifolia Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18174 Rinodina lepida Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15901 Pentanema indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17722 Athroisma gracile Species Asteraceae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 0.0 % PMID[521818]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 59.0 % PMID[521818]
NPT22906 Protein complex Urease subunit alpha/Urease subunit beta Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacterpylori) IC50 = 1668000.0 nM PMID[23567958]

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 NPC28753 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
0.8372 Intermediate Similarity NPC144051
0.8 Intermediate Similarity NPC18877
0.7273 Intermediate Similarity NPC294593
0.6957 Remote Similarity NPC485643
0.62 Remote Similarity NPC20560
0.6078 Remote Similarity NPC194949
0.6071 Remote Similarity NPC251681
0.5957 Remote Similarity NPC204960
0.5882 Remote Similarity NPC103842
0.5769 Remote Similarity NPC150648
0.5714 Remote Similarity NPC82225
0.5686 Remote Similarity NPC159623
0.5581 Remote Similarity NPC305518
0.5532 Remote Similarity NPC607946
0.549 Remote Similarity NPC286336
0.5439 Remote Similarity NPC183870
0.5424 Remote Similarity NPC243528
0.5424 Remote Similarity NPC26238
0.54 Remote Similarity NPC604715
0.5385 Remote Similarity NPC188646
0.5319 Remote Similarity NPC608363
0.5306 Remote Similarity NPC179494
0.5224 Remote Similarity NPC6985
0.5224 Remote Similarity NPC106625
0.5179 Remote Similarity NPC472368
0.5088 Remote Similarity NPC27139

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC28753 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