Natural Product: NPC237281

Natural Product IDNPC237281
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CWFOGDITMOXAQC-PNENFHPVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101612558
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 CWFOGDITMOXAQC-PNENFHPVSA-N
Standard InCHI InChI=1S/C19H20O3/c1-4-5-13-10-16-12(2)18(14-6-8-15(20)9-7-14)22-19(16)17(11-13)21-3/h4-12,18,20H,1-3H3/b5-4+/t12-,18-/m1/s1
SMILES C/C=C/c1cc2[C@@H](C)[C@H](c3ccc(cc3)O)Oc2c(c1)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   296.14 Volume:   319.426
?
Van der Waals volume.
Dense:   0.927 LogP:   3.632
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.327
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.791
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   17.0
TPSA:   38.69
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.894 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.227 Fsp3:   0.263
MCE-18:   53.833
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.906 Fluc inhibitor:   0.719
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.171
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.53
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.513 Promiscuous compounds:   0.17

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.123 MDCK Permeability:   -4.871
Pgp-inhibitor:   0.911 Pgp-substrate:   0.24
PAMPA:   0.034
?
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%):   0.356 30% Bioavailability (F30%):   0.349
50% Bioavailability (F50%):   0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.916
Plasma Protein Binding (PPB):   98.518% Volume Distribution (VD):   0.058
Fu: 1.944%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.842
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.977 CYP1A2-substrate:   0.032
CYP2C19-inhibitor:   0.985 CYP2C19-substrate:   0.916
CYP2C9-inhibitor:   0.496 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.851 CYP2D6-substrate:   0.124
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.367
?
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):  9.982 Half-life (T1/2):  0.875

ADMET: Toxicity

hERG Blockers:  0.279 hERG Blockers (10um):  0.598
Human Hepatotoxicity (H-HT):  0.857 Drug-induced Liver Injury (DILI):  0.542
AMES Toxicity:  0.362 Rat Oral Acute Toxicity:  0.449
Maximum Recommended Daily Dose:  0.574 Skin Sensitization:  0.906
Carcinogencity:  0.42 Eye Corrosion:  0.152
Eye Irritation:  0.931 Respiratory Toxicity:  0.825
Drug-induced Neurotoxicity:  0.794 Ototoxicity:  0.499
Hematotoxicity:  0.316 Drug-induced Nephrotoxicity:  0.44
Genotoxicity:  0.598 RPMI-8226 Immunitoxicity:  0.126
A549 Cytotoxicity:  0.497 Hek293 Cytotoxicity:  0.618
BCF:   2.061
?
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:   4.314
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.88
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.106
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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
NPO315 Krameria interior Species Krameriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO315 Krameria interior Species Krameriaceae 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

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 NPC237281 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
0.8039 Intermediate Similarity NPC187616
0.8039 Intermediate Similarity NPC193026
0.8039 Intermediate Similarity NPC49603
0.7647 Intermediate Similarity NPC154258
0.7115 Intermediate Similarity NPC98745
0.7115 Intermediate Similarity NPC115663
0.6491 Remote Similarity NPC170779
0.6491 Remote Similarity NPC90083
0.6415 Remote Similarity NPC150026
0.5484 Remote Similarity NPC156502
0.5484 Remote Similarity NPC10737
0.5312 Remote Similarity NPC284881
0.5312 Remote Similarity NPC93433
0.5312 Remote Similarity NPC474444
0.5254 Remote Similarity NPC81641
0.5246 Remote Similarity NPC87725
0.5246 Remote Similarity NPC263261
0.5211 Remote Similarity NPC180768
0.5167 Remote Similarity NPC131121
0.5152 Remote Similarity NPC253878
0.5152 Remote Similarity NPC206413
0.5152 Remote Similarity NPC482649
0.5152 Remote Similarity NPC149003
0.5152 Remote Similarity NPC471414
0.5152 Remote Similarity NPC482647
0.5152 Remote Similarity NPC482648
0.5152 Remote Similarity NPC482651
0.5152 Remote Similarity NPC194244
0.5152 Remote Similarity NPC482650
0.5147 Remote Similarity NPC131971
0.5147 Remote Similarity NPC15189
0.5147 Remote Similarity NPC480707
0.5139 Remote Similarity NPC45943
0.5139 Remote Similarity NPC469889

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC237281 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