Natural Product: NPC244364

Natural Product IDNPC244364
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3,4,5-Trimethoxy-6'',6''-Dimethylpyran[2'',3'':3',4']Stilbene
IUPAC Name 2,2-dimethyl-7-[(E)-2-(3,4,5-trimethoxyphenyl)ethenyl]chromene
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL463011
PubChem CID 10689330
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

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 WPVCFJCNTJKNBK-VOTSOKGWSA-N
Standard InCHI InChI=1S/C22H24O4/c1-22(2)11-10-17-9-8-15(12-18(17)26-22)6-7-16-13-19(23-3)21(25-5)20(14-16)24-4/h6-14H,1-5H3/b7-6+
SMILES CC1(C)C=Cc2ccc(/C=C/c3cc(c(c(c3)OC)OC)OC)cc2O1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   352.17 Volume:   377.468
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Van der Waals volume.
Dense:   0.933 LogP:   5.08
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.355
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.049
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   18.0
TPSA:   36.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.704 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.525 Fsp3:   0.273
MCE-18:   39.357
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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:   0.993 Fluc inhibitor:   0.997
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.283
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.638
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.447 Promiscuous compounds:   0.235

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.812 MDCK Permeability:   -4.696
Pgp-inhibitor:   0.909 Pgp-substrate:   0.004
PAMPA:   0.071
?
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):   0.001
20% Bioavailability (F20%):   0.67 30% Bioavailability (F30%):   0.55
50% Bioavailability (F50%):   0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.875 MRP1:   0.943
Plasma Protein Binding (PPB):   93.621% Volume Distribution (VD):   0.113
Fu: 5.77%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.988
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.933
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.389
CYP2C19-inhibitor:   0.034 CYP2C19-substrate:   0.059
CYP2C9-inhibitor:   0.841 CYP2C9-substrate:   0.023
CYP2D6-inhibitor:   0.854 CYP2D6-substrate:   0.033
CYP3A4-inhibitor:   0.804 CYP3A4-substrate:   0.994
CYP2B6-substrate:   0.091 CYP2C8-inhibitor:   1.0
HLM stability:   0.989
?
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):  7.527 Half-life (T1/2):  0.797

ADMET: Toxicity

hERG Blockers:  0.437 hERG Blockers (10um):  0.658
Human Hepatotoxicity (H-HT):  0.685 Drug-induced Liver Injury (DILI):  0.606
AMES Toxicity:  0.704 Rat Oral Acute Toxicity:  0.626
Maximum Recommended Daily Dose:  0.822 Skin Sensitization:  0.225
Carcinogencity:  0.771 Eye Corrosion:  0.0
Eye Irritation:  0.558 Respiratory Toxicity:  0.821
Drug-induced Neurotoxicity:  0.763 Ototoxicity:  0.541
Hematotoxicity:  0.349 Drug-induced Nephrotoxicity:  0.622
Genotoxicity:  0.361 RPMI-8226 Immunitoxicity:  0.188
A549 Cytotoxicity:  0.45 Hek293 Cytotoxicity:  0.586
BCF:   2.495
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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:   4.337
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.168
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.691
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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
NPO5368 Achillea cretica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36408972]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2671 Pedicularis semitorta Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12750 Cordia americana Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5368 Achillea cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12750 Cordia americana Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2671 Pedicularis semitorta Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5368 Achillea cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6147 Eupatorium riparium Species Asteraceae 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
NPT2680 Individual protein Ornithine decarboxylase Homo sapiens IC50 = 3900.0 nM PMID[10075742]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell line MCF7 Homo sapiens IC50 = 24000.0 nM PMID[10075742]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 7000.0 nM PMID[10075742]
NPT2 Others Unspecified n.a. IC50 = 4900.0 nM PMID[10075742]

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 NPC244364 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
0.5435 Remote Similarity NPC194626
0.5319 Remote Similarity NPC106141
0.5283 Remote Similarity NPC270030
0.5273 Remote Similarity NPC36661

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC244364 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