Natural Product: NPC176329

Natural Product IDNPC176329
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Isolinderanolide
IUPAC Name (3E,4S)-3-hexadecylidene-4-hydroxy-5-methylideneoxolan-2-one
Synonyms Isolinderanolide
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL450686
PubChem CID 44576045
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001967] Oxolanes

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 HFEZVKMFKXUREP-LFNFIXQYSA-N
Standard InCHI InChI=1S/C21H36O3/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-19-20(22)18(2)24-21(19)23/h17,20,22H,2-16H2,1H3/b19-17+/t20-/m1/s1
SMILES CCCCCCCCCCCCCCC/C=C/1[C@@H](C(=C)OC1=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
NPO5141 Lindera benzoin Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[1602301]
NPO5141 Lindera benzoin Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5141 Lindera benzoin Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5141 Lindera benzoin Species Lauraceae 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
NPT81 Cell line A549 Homo sapiens ED50 = 4.57 ug ml-1 PMID[11520232]
NPT83 Cell line MCF7 Homo sapiens ED50 = 3.12 ug ml-1 PMID[19289528]
NPT139 Cell line HT-29 Homo sapiens ED50 = 3.07 ug ml-1 PMID[24689881]
NPT141 Organism Agrobacterium tumefaciens Agrobacterium tumefaciens Inhibition = 44.9 % PMID[14987059]
NPT3062 Organism Spodoptera eridania Spodoptera eridania Activity = 0.0 % DOI[10.6019/CHEMBL1201861]
NPT350 Organism Tetranychus urticae Tetranychus urticae Activity = 0.0 % DOI[10.6019/CHEMBL1201861]
NPT3061 Organism Diabrotica undecimpunctata Diabrotica undecimpunctata Activity = 20.0 % PMID[20738103]
NPT3063 Organism Aphis gossypii Aphis gossypii Activity = 0.0 % PMID[18177007]

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
- Artemia salina LC50 = 0.96 ppm DrugMatrix in vitro pharmacology data

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 NPC176329 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 NPC125365
1.0 High Similarity NPC51809
1.0 High Similarity NPC301207
1.0 High Similarity NPC221095
1.0 High Similarity NPC279214
1.0 High Similarity NPC474818
1.0 High Similarity NPC49302
0.9118 High Similarity NPC473471
0.8485 Intermediate Similarity NPC209113
0.8485 Intermediate Similarity NPC127118
0.6053 Remote Similarity NPC47148
0.6053 Remote Similarity NPC603790
0.5897 Remote Similarity NPC256640
0.5897 Remote Similarity NPC16279
0.5897 Remote Similarity NPC205615
0.561 Remote Similarity NPC229799
0.561 Remote Similarity NPC284472
0.561 Remote Similarity NPC474959
0.561 Remote Similarity NPC310450
0.561 Remote Similarity NPC286770
0.561 Remote Similarity NPC11383
0.55 Remote Similarity NPC605151

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC176329 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