Natural Product: NPC478822

Natural Product IDNPC478822
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VYNXOOKMMMDMJH-XFNHPOKCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44445349
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 VYNXOOKMMMDMJH-XFNHPOKCSA-N
Standard InCHI InChI=1S/C69H110O37/c1-25-36(76)42(82)51(104-58-47(87)50(103-60-52(88)69(92,23-73)24-95-60)48(26(2)97-58)101-55-46(86)49(102-54-43(83)37(77)30(75)20-93-54)33(21-94-55)100-56-44(84)40(80)38(78)31(18-70)98-56)59(96-25)106-62(91)67-13-12-63(3,4)16-28(67)27-8-9-34-64(5)17-29(74)53(105-57-45(85)41(81)39(79)32(19-71)99-57)66(7,61(89)90)35(64)10-11-65(34,6)68(27,22-72)15-14-67/h8,25-26,28-60,70-88,92H,9-24H2,1-7H3,(H,89,90)/t25-,26+,28?,29-,30-,31+,32+,33+,34?,35+,36+,37-,38-,39+,40-,41-,42+,43+,44+,45+,46+,47-,48+,49-,50+,51-,52-,53-,54-,55-,56-,57-,58+,59+,60-,64+,65+,66-,67-,68-,69+/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)OC(=O)[C@@]12CCC(C)(C)CC2C2=CCC3[C@@]4(C)C[C@@H]([C@@H]([C@](C)([C@@H]4CC[C@@]3(C)[C@@]2(CC1)CO)C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O[C@@H]1[C@H]([C@H]([C@@H]([C@@H](C)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)O)O[C@H]1[C@@H]([C@@](CO)(CO1)O)O)O)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
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota Roots n.a. n.a. PMID[17927264]
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7712 Nylandtia spinosa Species Polygalaceae 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
NPT393 Cell line HCT-116 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17927264]
NPT139 Cell line HT-29 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17927264]

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 NPC478822 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
0.878 High Similarity NPC478823
0.7923 Intermediate Similarity NPC478825
0.7769 Intermediate Similarity NPC478824
0.6791 Remote Similarity NPC473645
0.6519 Remote Similarity NPC487505
0.6496 Remote Similarity NPC484942
0.6471 Remote Similarity NPC484943
0.5957 Remote Similarity NPC480418
0.5743 Remote Similarity NPC480417
0.5725 Remote Similarity NPC300419
0.5674 Remote Similarity NPC191827
0.5643 Remote Similarity NPC475899
0.5603 Remote Similarity NPC257211
0.5563 Remote Similarity NPC480422
0.5473 Remote Similarity NPC33068
0.5362 Remote Similarity NPC481079
0.5319 Remote Similarity NPC213952
0.5298 Remote Similarity NPC142151
0.5298 Remote Similarity NPC267694
0.5195 Remote Similarity NPC51099
0.5192 Remote Similarity NPC480421
0.5066 Remote Similarity NPC144644
0.5066 Remote Similarity NPC37860
0.5066 Remote Similarity NPC170407
0.5036 Remote Similarity NPC609763
0.5035 Remote Similarity NPC301449
0.5035 Remote Similarity NPC75287
0.5035 Remote Similarity NPC601290
0.5031 Remote Similarity NPC475368

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478822 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