Natural Product: NPC130581

Natural Product IDNPC130581
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Addisofuran A
IUPAC Name 2-[4-hydroxy-2-methoxy-5-(3-methylbut-2-enyl)phenyl]-1-benzofuran-6-ol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL233142
PubChem CID 44432363
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

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 XQVKBMIVACNFLX-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H20O4/c1-12(2)4-5-13-8-16(19(23-3)11-17(13)22)20-9-14-6-7-15(21)10-18(14)24-20/h4,6-11,21-22H,5H2,1-3H3
SMILES COc1cc(O)c(cc1c1cc2c(o1)cc(cc2)O)CC=C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   324.14 Volume:   342.876
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Van der Waals volume.
Dense:   0.945 LogP:   4.404
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.786
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.748
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   17.0
TPSA:   62.83
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.661 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.569 Fsp3:   0.2
MCE-18:   18.0
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.932 Fluc inhibitor:   0.864
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.993
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.754
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.324 Promiscuous compounds:   0.106

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.783 MDCK Permeability:   -4.726
Pgp-inhibitor:   0.016 Pgp-substrate:   0.352
PAMPA:   0.375
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.036
20% Bioavailability (F20%):   0.98 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.922
Plasma Protein Binding (PPB):   93.476% Volume Distribution (VD):   0.351
Fu: 6.117%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.802
OATP1B3 inhibitor:   0.983 BCRP inhibitor:   0.979
BSEP inhibitor:   0.771

ADMET: Metabolism

CYP1A2-inhibitor:   0.047 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.861 CYP2C9-substrate:   0.8
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.939
CYP3A4-inhibitor:   0.68 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.017 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  8.012 Half-life (T1/2):  1.516

ADMET: Toxicity

hERG Blockers:  0.106 hERG Blockers (10um):  0.572
Human Hepatotoxicity (H-HT):  0.533 Drug-induced Liver Injury (DILI):  0.74
AMES Toxicity:  0.642 Rat Oral Acute Toxicity:  0.645
Maximum Recommended Daily Dose:  0.62 Skin Sensitization:  0.861
Carcinogencity:  0.736 Eye Corrosion:  0.063
Eye Irritation:  0.968 Respiratory Toxicity:  0.866
Drug-induced Neurotoxicity:  0.33 Ototoxicity:  0.209
Hematotoxicity:  0.117 Drug-induced Nephrotoxicity:  0.204
Genotoxicity:  0.905 RPMI-8226 Immunitoxicity:  0.051
A549 Cytotoxicity:  0.277 Hek293 Cytotoxicity:  0.655
BCF:   1.736
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Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.597
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.691
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.225
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96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota Stems; Barks n.a. n.a. PMID[12828487]
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[17517504]
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota Barks n.a. n.a. PMID[18302333]
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20934335]
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23022281]
NPO27387 Erythrina addisoniae Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27387 Erythrina addisoniae Species Fabaceae 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
NPT178 Individual protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 17500.0 nM PMID[19451299]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

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 NPC130581 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
0.6818 Remote Similarity NPC12148
0.6462 Remote Similarity NPC148938
0.6418 Remote Similarity NPC207624
0.5846 Remote Similarity NPC167576
0.5758 Remote Similarity NPC23668
0.5672 Remote Similarity NPC210826
0.5584 Remote Similarity NPC268360
0.5538 Remote Similarity NPC608872
0.5417 Remote Similarity NPC482761
0.527 Remote Similarity NPC213936
0.52 Remote Similarity NPC193976
0.5135 Remote Similarity NPC221868
0.5068 Remote Similarity NPC261227
0.5065 Remote Similarity NPC142308

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC130581 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