Natural Product: NPC13083

Natural Product IDNPC13083
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AVUGPESHBVLBAI-IBGZPJMESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10092034
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0001612] Isoflavans
          • [CHEMONTID:0001828] Isoflavanols

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 AVUGPESHBVLBAI-IBGZPJMESA-N
Standard InCHI InChI=1S/C25H30O4/c1-15(2)5-7-17-11-18-12-19(21-10-8-20(26)13-23(21)27)14-29-25(18)22(24(17)28)9-6-16(3)4/h5-6,8,10-11,13,19,26-28H,7,9,12,14H2,1-4H3/t19-/m0/s1
SMILES CC(=CCc1cc2C[C@@H](COc2c(CC=C(C)C)c1O)c1ccc(cc1O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   394.21 Volume:   429.356
?
Van der Waals volume.
Dense:   0.918 LogP:   5.941
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.164
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.025
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   19.0
TPSA:   69.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.582 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.564 Fsp3:   0.36
MCE-18:   63.529
?
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:   0.987 Fluc inhibitor:   0.701
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.143
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.174
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.576 Promiscuous compounds:   0.137

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.064 MDCK Permeability:   -4.762
Pgp-inhibitor:   0.051 Pgp-substrate:   0.074
PAMPA:   0.193
?
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%):   0.997 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.96
Plasma Protein Binding (PPB):   94.2% Volume Distribution (VD):   0.592
Fu: 6.123%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.995
OATP1B3 inhibitor:   0.961 BCRP inhibitor:   0.996
BSEP inhibitor:   0.189

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.467 CYP2C9-substrate:   0.681
CYP2D6-inhibitor:   0.998 CYP2D6-substrate:   0.36
CYP3A4-inhibitor:   0.147 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.001 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):  4.099 Half-life (T1/2):  1.862

ADMET: Toxicity

hERG Blockers:  0.084 hERG Blockers (10um):  0.627
Human Hepatotoxicity (H-HT):  0.923 Drug-induced Liver Injury (DILI):  0.114
AMES Toxicity:  0.709 Rat Oral Acute Toxicity:  0.877
Maximum Recommended Daily Dose:  0.925 Skin Sensitization:  0.985
Carcinogencity:  0.345 Eye Corrosion:  0.0
Eye Irritation:  0.827 Respiratory Toxicity:  0.811
Drug-induced Neurotoxicity:  0.778 Ototoxicity:  0.685
Hematotoxicity:  0.162 Drug-induced Nephrotoxicity:  0.94
Genotoxicity:  0.987 RPMI-8226 Immunitoxicity:  0.074
A549 Cytotoxicity:  0.705 Hek293 Cytotoxicity:  0.844
BCF:   2.183
?
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:   5.467
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.935
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.482
?
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
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. root n.a. PMID[15597305]
NPO17390 Dysidea robusta Species Dysideidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13146 Pertusaria albescens Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16356 Crocynia membranacea Species Crocyniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14662 Lomatia longifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5160 Pandanus veitchi Species Pandanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17390 Dysidea robusta Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16070 Indigofera oblongifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13146 Pertusaria albescens Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3710 Erythrina zeyheri 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT28438 Unchecked Unchecked n.a. GI50 = 3650.0 nM PMID[36938984]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[36938984]
NPT21798 Cell line ARPE-19 Homo sapiens GI50 > 100000.0 nM PMID[36938984]

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 NPC13083 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
0.6452 Remote Similarity NPC609848
0.6393 Remote Similarity NPC77027
0.6349 Remote Similarity NPC53986
0.6129 Remote Similarity NPC38664
0.5938 Remote Similarity NPC601714
0.5522 Remote Similarity NPC482698
0.5303 Remote Similarity NPC482760
0.5205 Remote Similarity NPC482702
0.5075 Remote Similarity NPC259519
0.5072 Remote Similarity NPC70682
0.5072 Remote Similarity NPC164804
0.5072 Remote Similarity NPC118683
0.5072 Remote Similarity NPC93962
0.5072 Remote Similarity NPC120083

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC13083 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