Natural Product: NPC127218

Natural Product IDNPC127218
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 R-Coluteol
IUPAC Name 2,4-dimethoxy-5-[(3R)-7-methoxy-3,4-dihydro-2H-chromen-3-yl]benzene-1,3-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL517357
PubChem CID 10336847
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002586] O-methylated isoflavonoids
          • [CHEMONTID:0002606] 4'-O-methylated isoflavonoids
            • [CHEMONTID:0003651] 3'-hydroxy,4'-methoxyisoflavonoids

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 LXTMXFSTGUINPR-NSHDSACASA-N
Standard InCHI InChI=1S/C18H20O6/c1-21-12-5-4-10-6-11(9-24-15(10)7-12)13-8-14(19)18(23-3)16(20)17(13)22-2/h4-5,7-8,11,19-20H,6,9H2,1-3H3/t11-/m0/s1
SMILES COc1ccc2C[C@@H](COc2c1)c1cc(c(c(c1OC)O)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   332.13 Volume:   331.137
?
Van der Waals volume.
Dense:   1.003 LogP:   2.663
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.764
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.138
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   17.0
TPSA:   77.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.896 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.045 Fsp3:   0.333
MCE-18:   58.5
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.469 Fluc inhibitor:   0.79
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.086
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.23
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.311 Promiscuous compounds:   0.47

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.175 MDCK Permeability:   -4.792
Pgp-inhibitor:   0.709 Pgp-substrate:   0.257
PAMPA:   0.029
?
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):   0.0
20% Bioavailability (F20%):   0.016 30% Bioavailability (F30%):   0.005
50% Bioavailability (F50%):   0.606

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.884 MRP1:   0.95
Plasma Protein Binding (PPB):   91.194% Volume Distribution (VD):   -0.602
Fu: 7.848%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.855
BSEP inhibitor:   0.947

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.942
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.425
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.253
CYP2D6-inhibitor:   0.998 CYP2D6-substrate:   0.424
CYP3A4-inhibitor:   0.997 CYP3A4-substrate:   0.754
CYP2B6-substrate:   0.04 CYP2C8-inhibitor:   0.538
HLM stability:   0.994
?
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):  4.708 Half-life (T1/2):  1.456

ADMET: Toxicity

hERG Blockers:  0.213 hERG Blockers (10um):  0.58
Human Hepatotoxicity (H-HT):  0.713 Drug-induced Liver Injury (DILI):  0.563
AMES Toxicity:  0.55 Rat Oral Acute Toxicity:  0.491
Maximum Recommended Daily Dose:  0.718 Skin Sensitization:  0.628
Carcinogencity:  0.715 Eye Corrosion:  0.027
Eye Irritation:  0.952 Respiratory Toxicity:  0.618
Drug-induced Neurotoxicity:  0.707 Ototoxicity:  0.488
Hematotoxicity:  0.326 Drug-induced Nephrotoxicity:  0.593
Genotoxicity:  0.253 RPMI-8226 Immunitoxicity:  0.136
A549 Cytotoxicity:  0.383 Hek293 Cytotoxicity:  0.39
BCF:   1.196
?
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:   3.612
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.348
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.371
?
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
NPO21208 Solanum chrysotrichum Species Solanaceae Eukaryota Leaves n.a. n.a. PMID[12502320]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[19006373]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. stem n.a. PMID[19006373]
NPO20922 Colutea arborescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9548836]
NPO21208 Solanum chrysotrichum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20922 Colutea arborescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18585 Sphaerostephanos arbuscula Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21208 Solanum chrysotrichum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18585 Sphaerostephanos arbuscula Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20922 Colutea arborescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20467 Macaranga barteri Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16870 Athanasia linifolia 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC < 100.0 ug.mL-1 PMID[9548836]

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 NPC127218 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
0.6296 Remote Similarity NPC283049
0.6296 Remote Similarity NPC479544
0.5333 Remote Similarity NPC265433
0.5333 Remote Similarity NPC270456
0.5333 Remote Similarity NPC162659

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC127218 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