Natural Product: NPC104861

Natural Product IDNPC104861
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Quassin
IUPAC Name n.a.
Synonyms Quassin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL517016
PubChem CID 65571
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0002119] Quassinoids

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 IOSXSVZRTUWBHC-LBTVDEKVSA-N
Standard InCHI InChI=1S/C22H28O6/c1-10-7-14(26-5)20(25)22(4)12(10)8-15-21(3)13(9-16(23)28-15)11(2)18(27-6)17(24)19(21)22/h7,10,12-13,15,19H,8-9H2,1-6H3/t10-,12+,13+,15-,19+,21-,22+/m1/s1
SMILES C[C@@H]1C=C(C(=O)[C@@]2(C)[C@H]1C[C@@H]1[C@@]3(C)[C@@H](CC(=O)O1)C(=C(C(=O)[C@H]23)OC)C)OC

  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
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. leaf n.a. PMID[16730421]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[19586051]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota stems n.a. n.a. PMID[20095629]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[25506718]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[27494664]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[30917277]
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO704 Quassia amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8372 Picrasma quassioides Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2349 Picrasma excelsa Species Simaroubaceae 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
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 100.46 % PMID[23571415]
NPT67 Individual protein Cholinesterase Equus caballus Inhibition = 4.69 % PMID[23062825]
NPT66 Individual protein Acetylcholinesterase Electrophorus electricus Inhibition = 24.69 % PMID[23062825]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT91 Cell line KB Homo sapiens IC50 = 911000.0 nM PMID[14640524]
NPT165 Cell line HeLa Homo sapiens IC50 > 2000.0 nM PMID[19199792]
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 73.1 % PMID[30917277]
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 10.7 % PMID[30917277]
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 13.7 % PMID[30917277]
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 2.45 % PMID[30917277]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 1000000.0 nM PMID[14640524]
NPT992 Organism Entamoeba histolytica Entamoeba histolytica IC50 = 0.5 ug.mL-1 DOI[10.1007/s00044-011-9767-1]

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 NPC104861 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
0.7818 Intermediate Similarity NPC484811
0.6909 Remote Similarity NPC277746
0.6897 Remote Similarity NPC602806
0.6034 Remote Similarity NPC484773
0.6 Remote Similarity NPC202524
0.5857 Remote Similarity NPC176005
0.5806 Remote Similarity NPC484810
0.5763 Remote Similarity NPC484771
0.5738 Remote Similarity NPC485624
0.5645 Remote Similarity NPC27814
0.5574 Remote Similarity NPC484769
0.5484 Remote Similarity NPC484770

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC104861 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