Natural Product: NPC171598

Natural Product IDNPC171598
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Casearlucin B
IUPAC Name [(1R,3S,5R,6aR,7S,8S,10R,10aR)-1,3-diacetyloxy-10-methoxy-7,8-dimethyl-7-(3-methylidenepent-4-enyl)-1,3,5,6,6a,8,9,10-octahydrobenzo[d][2]benzofuran-5-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2419877
PubChem CID 73352260
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001757] Colensane and clerodane diterpenoids

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 BZVDIOLNPIHYMD-FIHQBSKBSA-N
Standard InCHI InChI=1S/C27H38O8/c1-9-15(2)10-11-26(7)16(3)12-23(31-8)27-21(13-20(14-22(26)27)32-17(4)28)24(33-18(5)29)35-25(27)34-19(6)30/h9,13,16,20,22-25H,1-2,10-12,14H2,3-8H3/t16-,20-,22+,23+,24+,25-,26-,27-/m0/s1
SMILES C=CC(=C)CC[C@@]1(C)[C@@H](C)C[C@H]([C@]23C(=C[C@@H](C[C@H]12)OC(=O)C)[C@H](OC(=O)C)O[C@@H]3OC(=O)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
NPO32459 casearia balansae Species Salicaceae Eukaryota leaves and twigs n.a. n.a. PMID[24033131]
NPO32459 casearia balansae Species Salicaceae Eukaryota twigs n.a. n.a. PMID[25286284]
NPO32459 casearia balansae Species Salicaceae Eukaryota Leaves n.a. n.a. PMID[26699618]
NPO32459 casearia balansae Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT1374 Cell line WI-38 Homo sapiens IC50 = 13300.0 nM PMID[15646539]
NPT81 Cell line A549 Homo sapiens IC50 = 7100.0 nM Open TG-GATES in vivo data: Hematology
NPT146 Cell line SK-OV-3 Homo sapiens IC50 = 6200.0 nM DrugMatrix in vitro pharmacology data
NPT90 Cell line DU-145 Homo sapiens IC50 = 4300.0 nM DOI[10.6019/CHEMBL1201861]
NPT306 Cell line PC-3 Homo sapiens IC50 = 4700.0 nM PMID[21481593]

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 NPC171598 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
0.9434 High Similarity NPC472189
0.9273 High Similarity NPC318917
0.9273 High Similarity NPC481019
0.8947 High Similarity NPC471366
0.8947 High Similarity NPC476800
0.8947 High Similarity NPC488649
0.8947 High Similarity NPC488237
0.8929 High Similarity NPC471362
0.8929 High Similarity NPC471372
0.8909 High Similarity NPC481018
0.8772 High Similarity NPC472186
0.875 High Similarity NPC481020
0.8475 Intermediate Similarity NPC481017
0.8448 Intermediate Similarity NPC472188
0.8136 Intermediate Similarity NPC488236
0.8065 Intermediate Similarity NPC472187
0.7742 Intermediate Similarity NPC473545
0.7627 Intermediate Similarity NPC606965
0.7213 Intermediate Similarity NPC132395
0.7213 Intermediate Similarity NPC471364
0.7213 Intermediate Similarity NPC600724
0.7 Intermediate Similarity NPC603601
0.6875 Remote Similarity NPC473204
0.6667 Remote Similarity NPC488651
0.6667 Remote Similarity NPC488648
0.6567 Remote Similarity NPC48548
0.6515 Remote Similarity NPC471365
0.6406 Remote Similarity NPC479934
0.6308 Remote Similarity NPC479935
0.6308 Remote Similarity NPC479936
0.6308 Remote Similarity NPC488235
0.6212 Remote Similarity NPC479943
0.6154 Remote Similarity NPC488962
0.6061 Remote Similarity NPC479939
0.6029 Remote Similarity NPC479940
0.6029 Remote Similarity NPC7644
0.6 Remote Similarity NPC488219
0.597 Remote Similarity NPC479937
0.5915 Remote Similarity NPC488221
0.5915 Remote Similarity NPC488220
0.5915 Remote Similarity NPC488216
0.5882 Remote Similarity NPC479938
0.5857 Remote Similarity NPC488963
0.5781 Remote Similarity NPC488650
0.5781 Remote Similarity NPC481022
0.5714 Remote Similarity NPC217921
0.5714 Remote Similarity NPC88013
0.5714 Remote Similarity NPC475889
0.5714 Remote Similarity NPC7613
0.5714 Remote Similarity NPC479942
0.5714 Remote Similarity NPC135015
0.5634 Remote Similarity NPC479941
0.56 Remote Similarity NPC486752
0.5571 Remote Similarity NPC128795
0.5493 Remote Similarity NPC238397
0.5385 Remote Similarity NPC162569
0.5385 Remote Similarity NPC35160
0.5316 Remote Similarity NPC486759
0.5316 Remote Similarity NPC488217
0.5316 Remote Similarity NPC488218
0.5256 Remote Similarity NPC473399
0.5256 Remote Similarity NPC473216
0.52 Remote Similarity NPC127933
0.5135 Remote Similarity NPC471363

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC171598 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