Natural Product: NPC98813

Natural Product IDNPC98813
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Verrucarin J
IUPAC Name n.a.
Synonyms Verrucarin J
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL507752
PubChem CID 12444784
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0001789] Trichothecenes

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 GXCGYHWSYNQVHU-GYDJLPFWSA-N
Standard InCHI InChI=1S/C27H32O8/c1-17-8-10-26-15-32-24(30)13-18(2)9-11-31-22(28)6-4-5-7-23(29)35-19-14-21(34-20(26)12-17)27(16-33-27)25(19,26)3/h4-7,12-13,19-21H,8-11,14-16H2,1-3H3/b6-4+,7-5-,18-13+/t19-,20-,21-,25-,26-,27+/m1/s1
SMILES CC1=C[C@@H]2[C@@]3(CC1)COC(=O)/C=C(C)/CCOC(=O)/C=C/C=CC(=O)O[C@@H]1C[C@H]([C@@]4(CO4)[C@@]31C)O2

  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
NPO30443 Myrothecium verrucaria Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[10075777]
NPO29965 Myrothecium roridum Species Stachybotryaceae Eukaryota n.a. Palau n.a. PMID[11277768]
NPO29965 Myrothecium roridum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[12027756]
NPO30443 Myrothecium verrucaria Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[13678412]
NPO30443 Myrothecium verrucaria Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[21539317]
NPO29965 Myrothecium roridum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30443 Myrothecium verrucaria Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29965 Myrothecium roridum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30443 Myrothecium verrucaria Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[HerDing]

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
NPT168 Cell line P388 Mus musculus Dose = 0.8 n.a. PMID[7411550]
NPT168 Cell line P388 Mus musculus T/C = 150.0 n.a. PMID[6694172]
NPT168 Cell line P388 Mus musculus T/C = 150.0 survivors/total PMID[6694172]
NPT116 Cell line HL-60 Homo sapiens IC50 = 0.0025 ug.mL-1 PMID[8691213]
NPT137 Cell line L1210 Mus musculus IC50 = 0.0025 ug.mL-1 PMID[21546135]
NPT91 Cell line KB Homo sapiens EC50 = 0.0039 ug.mL-1 PMID[24063567]
NPT189 Cell line Vero Chlorocebus aethiops EC50 = 0.0012 ug.mL-1 PMID[18302334]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 0.014 ug.mL-1 PMID[10075777]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 150.0 % PMID[19586689]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 2.176 n.a. PMID[19586689]
NPT485 Organism Plasmodium falciparum (isolate K1 / Thailand) Plasmodium falciparum K1 EC50 = 0.0002 ug.mL-1 PMID[18293903]

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 NPC98813 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 NPC600365
0.8594 High Similarity NPC484152
0.8235 Intermediate Similarity NPC13743
0.8116 Intermediate Similarity NPC29389
0.8116 Intermediate Similarity NPC112316
0.726 Intermediate Similarity NPC108682
0.72 Intermediate Similarity NPC484149
0.7083 Intermediate Similarity NPC469959
0.7083 Intermediate Similarity NPC469957
0.7083 Intermediate Similarity NPC98038
0.7083 Intermediate Similarity NPC313921
0.7067 Intermediate Similarity NPC484923
0.7067 Intermediate Similarity NPC484922
0.6857 Remote Similarity NPC265502
0.68 Remote Similarity NPC472263
0.675 Remote Similarity NPC484153
0.675 Remote Similarity NPC484925
0.6456 Remote Similarity NPC474286
0.6456 Remote Similarity NPC484150
0.6456 Remote Similarity NPC484155
0.6316 Remote Similarity NPC9579
0.622 Remote Similarity NPC475130
0.622 Remote Similarity NPC484145
0.622 Remote Similarity NPC484151
0.619 Remote Similarity NPC484154
0.6125 Remote Similarity NPC101965
0.6125 Remote Similarity NPC101400
0.5897 Remote Similarity NPC469960
0.5897 Remote Similarity NPC93026
0.5846 Remote Similarity NPC234293
0.5783 Remote Similarity NPC484144
0.5625 Remote Similarity NPC484920
0.557 Remote Similarity NPC65700
0.5488 Remote Similarity NPC484924
0.5231 Remote Similarity NPC94915

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC98813 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