Natural Product: NPC232454

Natural Product IDNPC232454
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Acerosideviii
IUPAC Name (2R,3R,4S,5S,6R)-2-[(3R)-1,7-bis(4-hydroxyphenyl)heptan-3-yl]oxy-6-[[(2R,3S,4S)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxymethyl]oxane-3,4,5-triol
Synonyms Aceroside VIII
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1087449
PubChem CID 46889081
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002651] Linear diarylheptanoids

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 JLMGCBFIPZDHLZ-RMVWXMGCSA-N
Standard InCHI InChI=1S/C30H42O12/c31-16-30(38)17-40-29(27(30)37)39-15-23-24(34)25(35)26(36)28(42-23)41-22(14-9-19-7-12-21(33)13-8-19)4-2-1-3-18-5-10-20(32)11-6-18/h5-8,10-13,22-29,31-38H,1-4,9,14-17H2/t22-,23-,24-,25+,26-,27-,28-,29-,30+/m1/s1
SMILES OC[C@]1(O)CO[C@H]([C@H]1O)OC[C@H]1O[C@@H](O[C@@H](CCc2ccc(cc2)O)CCCCc2ccc(cc2)O)[C@@H]([C@H]([C@@H]1O)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
NPO4138 Betula platyphylla Species Betulaceae Eukaryota bark n.a. n.a. PMID[20363129]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13983 Acer maximowiczianum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13983 Acer maximowiczianum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13983 Acer maximowiczianum Species Sapindaceae 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
NPT521 Cell line RBL-2H3 Rattus norvegicus Inhibition = 11.7 % PMID[20363129]
NPT521 Cell line RBL-2H3 Rattus norvegicus Inhibition = 22.4 % PMID[20363129]

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 NPC232454 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
1.0 High Similarity NPC470907
1.0 High Similarity NPC178449
0.7971 Intermediate Similarity NPC164172
0.7941 Intermediate Similarity NPC471067
0.791 Intermediate Similarity NPC476448
0.791 Intermediate Similarity NPC469548
0.791 Intermediate Similarity NPC476445
0.7639 Intermediate Similarity NPC469687
0.6866 Remote Similarity NPC201402
0.6351 Remote Similarity NPC471066
0.6154 Remote Similarity NPC469696
0.6133 Remote Similarity NPC471095
0.6111 Remote Similarity NPC282409
0.6111 Remote Similarity NPC469702
0.5867 Remote Similarity NPC90318
0.5753 Remote Similarity NPC264900
0.5652 Remote Similarity NPC472026
0.5541 Remote Similarity NPC94179
0.5479 Remote Similarity NPC17968
0.5479 Remote Similarity NPC469705
0.5432 Remote Similarity NPC470881
0.5333 Remote Similarity NPC469686
0.5325 Remote Similarity NPC473867
0.5303 Remote Similarity NPC219040
0.5301 Remote Similarity NPC184092
0.5135 Remote Similarity NPC158673
0.5135 Remote Similarity NPC264784
0.5067 Remote Similarity NPC160854
0.5067 Remote Similarity NPC469704
0.5067 Remote Similarity NPC469703
0.5062 Remote Similarity NPC473924
0.506 Remote Similarity NPC602810
0.5059 Remote Similarity NPC469549

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC232454 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