Natural Product: NPC478823

Natural Product IDNPC478823
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CMUZWAVAVWWGFJ-VCDQTMHGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44445350
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 CMUZWAVAVWWGFJ-VCDQTMHGSA-N
Standard InCHI InChI=1S/C64H102O33/c1-23-34(70)40(76)49(95-53-45(81)41(77)47(24(2)89-53)93-52-46(82)48(94-51-42(78)35(71)28(69)20-86-51)31(21-87-52)92-54-43(79)38(74)36(72)29(18-65)90-54)56(88-23)97-58(85)63-13-12-59(3,4)16-26(63)25-8-9-32-60(5)17-27(68)50(96-55-44(80)39(75)37(73)30(19-66)91-55)62(7,57(83)84)33(60)10-11-61(32,6)64(25,22-67)15-14-63/h8,23-24,26-56,65-82H,9-22H2,1-7H3,(H,83,84)/t23-,24+,26?,27-,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+,60+,61+,62-,63-,64-/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)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 NPC478823 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 NPC478822
0.7937 Intermediate Similarity NPC478825
0.7778 Intermediate Similarity NPC478824
0.736 Intermediate Similarity NPC484943
0.7244 Intermediate Similarity NPC484942
0.6535 Remote Similarity NPC300419
0.597 Remote Similarity NPC191827
0.5797 Remote Similarity NPC473645
0.5778 Remote Similarity NPC257211
0.5766 Remote Similarity NPC487505
0.5649 Remote Similarity NPC481079
0.5634 Remote Similarity NPC33068
0.5522 Remote Similarity NPC815
0.55 Remote Similarity NPC57484
0.5486 Remote Similarity NPC70809
0.5481 Remote Similarity NPC213952
0.5448 Remote Similarity NPC224381
0.5352 Remote Similarity NPC473452
0.5303 Remote Similarity NPC609763
0.5294 Remote Similarity NPC75287
0.5285 Remote Similarity NPC209894
0.5263 Remote Similarity NPC475368
0.5245 Remote Similarity NPC286457
0.5221 Remote Similarity NPC104137
0.5221 Remote Similarity NPC26626
0.5208 Remote Similarity NPC470876
0.5185 Remote Similarity NPC301449
0.5185 Remote Similarity NPC601290
0.5141 Remote Similarity NPC471577
0.5106 Remote Similarity NPC480419
0.5105 Remote Similarity NPC85154
0.5103 Remote Similarity NPC258617
0.5102 Remote Similarity NPC309223
0.5101 Remote Similarity NPC250247
0.5069 Remote Similarity NPC237191
0.5069 Remote Similarity NPC473386
0.5038 Remote Similarity NPC469946
0.5036 Remote Similarity NPC241909
0.5035 Remote Similarity NPC475899
0.5034 Remote Similarity NPC135849
0.5034 Remote Similarity NPC480418

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478823 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