Natural Product: NPC191158

Natural Product IDNPC191158
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2S,3S)-2-(5-Methoxy-3,4-Methylenedioxybenzyl)-3-(3,4-Methylenedioxybenzyl)Butyrolactone
IUPAC Name (3S,4S)-4-(1,3-benzodioxol-5-ylmethyl)-3-[(7-methoxy-1,3-benzodioxol-5-yl)methyl]oxolan-2-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL493854
PubChem CID 11509246
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans
        • [CHEMONTID:0001604] Tetrahydrofuran lignans
          • [CHEMONTID:0003424] 9,9'-epoxylignans
            • [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

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 GDOAQHHMFNQXLJ-CABCVRRESA-N
Standard InCHI InChI=1S/C21H20O7/c1-23-18-7-13(8-19-20(18)28-11-27-19)5-15-14(9-24-21(15)22)4-12-2-3-16-17(6-12)26-10-25-16/h2-3,6-8,14-15H,4-5,9-11H2,1H3/t14-,15+/m1/s1
SMILES COc1cc(C[C@@H]2C(=O)OC[C@H]2Cc2ccc3c(c2)OCO3)cc2c1OCO2

  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
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16499322]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[17358082]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[17547458]
NPO16915 Callyspongia aerizusa Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[26213786]
NPO17517 Artemisia arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38592817]
NPO15369 Tabernaemontana rupicola Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2913 Tabebuia pentaphylla Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15893 Solandra guttata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16447 Potato virus n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO16048 Euphorbia serrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15734 Euchresta horsfeldii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21786 Culcitium serratifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17297 Caragana pygmaea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16915 Callyspongia aerizusa Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17517 Artemisia arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14795 Vitis coignetiae Species Vitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18069 Streptomyces coelicoflavus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14795 Vitis coignetiae Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17517 Artemisia arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15893 Solandra guttata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17297 Caragana pygmaea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15734 Euchresta horsfeldii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21786 Culcitium serratifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16048 Euphorbia serrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17040 Peperomia duclouxii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18069 Streptomyces coelicoflavus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2913 Tabebuia pentaphylla Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16447 Potato virus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14795 Vitis coignetiae Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16915 Callyspongia aerizusa Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15369 Tabernaemontana rupicola Species Apocynaceae 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
NPT1475 Cell line WI-38 VA13 Homo sapiens IC50 = 23200.0 nM PMID[16499322]
NPT65 Cell line HepG2 Homo sapiens IC50 = 26400.0 nM PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 80.0 % PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 90.0 % PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 109.0 % PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 103.0 % PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 124.0 % PMID[16499322]
NPT2 Others Unspecified n.a. Activity = 86.0 % PMID[16499322]

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 NPC191158 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 NPC177644
0.9388 High Similarity NPC176586
0.9388 High Similarity NPC210354
0.875 High Similarity NPC92693
0.86 High Similarity NPC205915
0.8571 High Similarity NPC40237
0.8542 High Similarity NPC110958
0.8542 High Similarity NPC19890
0.7857 Intermediate Similarity NPC145569
0.7647 Intermediate Similarity NPC211386
0.75 Intermediate Similarity NPC293757
0.75 Intermediate Similarity NPC143895
0.75 Intermediate Similarity NPC668
0.7458 Intermediate Similarity NPC216223
0.7451 Intermediate Similarity NPC474288
0.7288 Intermediate Similarity NPC282291
0.7288 Intermediate Similarity NPC166137
0.72 Intermediate Similarity NPC223807
0.7143 Intermediate Similarity NPC72796
0.7059 Intermediate Similarity NPC11453
0.6885 Remote Similarity NPC174512
0.6792 Remote Similarity NPC192255
0.6667 Remote Similarity NPC476748
0.6557 Remote Similarity NPC56184
0.6167 Remote Similarity NPC106920
0.6167 Remote Similarity NPC15811
0.6 Remote Similarity NPC185908
0.6 Remote Similarity NPC482891
0.5962 Remote Similarity NPC600801
0.5902 Remote Similarity NPC5310
0.5902 Remote Similarity NPC300776
0.5902 Remote Similarity NPC176814
0.5902 Remote Similarity NPC3982
0.5902 Remote Similarity NPC4982
0.5902 Remote Similarity NPC606629
0.5781 Remote Similarity NPC76687
0.569 Remote Similarity NPC158737
0.5606 Remote Similarity NPC136757
0.5538 Remote Similarity NPC487679
0.5538 Remote Similarity NPC487678
0.5538 Remote Similarity NPC482889
0.5536 Remote Similarity NPC196937
0.5469 Remote Similarity NPC262455
0.5469 Remote Similarity NPC177476
0.5469 Remote Similarity NPC474158
0.5441 Remote Similarity NPC478705
0.5424 Remote Similarity NPC68779
0.5424 Remote Similarity NPC108598
0.5323 Remote Similarity NPC273657
0.5254 Remote Similarity NPC171550
0.5254 Remote Similarity NPC134764
0.5192 Remote Similarity NPC81067
0.5192 Remote Similarity NPC602945
0.5185 Remote Similarity NPC344161
0.5167 Remote Similarity NPC283949
0.5152 Remote Similarity NPC480477
0.5143 Remote Similarity NPC478703
0.5143 Remote Similarity NPC478704
0.5077 Remote Similarity NPC80230
0.5077 Remote Similarity NPC104024
0.5077 Remote Similarity NPC101755
0.5077 Remote Similarity NPC304687
0.5077 Remote Similarity NPC65574

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC191158 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