Natural Product: NPC33637

Natural Product IDNPC33637
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GGNFRQNGJUKIKW-WTDSWWLTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 71449771
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones
          • [CHEMONTID:0003503] 6-prenylated flavones

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 GGNFRQNGJUKIKW-WTDSWWLTSA-N
Standard InCHI InChI=1S/C20H18O7/c1-10(9-21)2-4-13-15(24)7-18-19(20(13)26)16(25)8-17(27-18)12-5-3-11(22)6-14(12)23/h2-3,5-8,21-24,26H,4,9H2,1H3/b10-2+
SMILES C/C(=CCc1c(cc2c(c(=O)cc(c3ccc(cc3O)O)o2)c1O)O)/CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   370.11 Volume:   366.61
?
Van der Waals volume.
Dense:   1.01 LogP:   1.87
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.015
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.463
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   19.0
TPSA:   131.36
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.446 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.975 Fsp3:   0.15
MCE-18:   20.0
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.791 Fluc inhibitor:   0.573
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.986
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.524
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.245 Promiscuous compounds:   0.293

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.369 MDCK Permeability:   -4.845
Pgp-inhibitor:   0.482 Pgp-substrate:   0.077
PAMPA:   0.133
?
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):   0.022
20% Bioavailability (F20%):   0.821 30% Bioavailability (F30%):   0.959
50% Bioavailability (F50%):   0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.392
Plasma Protein Binding (PPB):   95.199% Volume Distribution (VD):   -0.059
Fu: 6.897%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.973
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.915
BSEP inhibitor:   0.834

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.133
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.977 CYP2C9-substrate:   0.933
CYP2D6-inhibitor:   0.983 CYP2D6-substrate:   0.15
CYP3A4-inhibitor:   0.028 CYP3A4-substrate:   0.497
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.896
HLM stability:   0.192
?
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):  1.466 Half-life (T1/2):  1.775

ADMET: Toxicity

hERG Blockers:  0.02 hERG Blockers (10um):  0.449
Human Hepatotoxicity (H-HT):  0.602 Drug-induced Liver Injury (DILI):  0.666
AMES Toxicity:  0.431 Rat Oral Acute Toxicity:  0.562
Maximum Recommended Daily Dose:  0.829 Skin Sensitization:  0.924
Carcinogencity:  0.365 Eye Corrosion:  0.008
Eye Irritation:  0.988 Respiratory Toxicity:  0.974
Drug-induced Neurotoxicity:  0.044 Ototoxicity:  0.094
Hematotoxicity:  0.05 Drug-induced Nephrotoxicity:  0.087
Genotoxicity:  0.999 RPMI-8226 Immunitoxicity:  0.141
A549 Cytotoxicity:  0.427 Hek293 Cytotoxicity:  0.901
BCF:   1.076
?
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:   3.85
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.982
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.374
?
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
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. root n.a. DOI[10.1016/0031-9422(95)00135-T]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota Wood n.a. n.a. PMID[23113717]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. formosan n.a. PMID[8864236]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17767 Artocarpus heterophyllus Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17767 Artocarpus heterophyllus Species Moraceae 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
NPT2 Others Unspecified n.a. IC50 = 47300.0 nM PMID[23113717]

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 NPC33637 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
0.8667 High Similarity NPC55018
0.7937 Intermediate Similarity NPC189706
0.6769 Remote Similarity NPC284220
0.6286 Remote Similarity NPC303633
0.6176 Remote Similarity NPC3825
0.5915 Remote Similarity NPC59210
0.5857 Remote Similarity NPC486096
0.5811 Remote Similarity NPC602497
0.5625 Remote Similarity NPC274121
0.5352 Remote Similarity NPC24821
0.527 Remote Similarity NPC268204
0.5263 Remote Similarity NPC59739
0.5238 Remote Similarity NPC479643
0.5224 Remote Similarity NPC602367
0.5135 Remote Similarity NPC226644
0.5067 Remote Similarity NPC14871
0.5067 Remote Similarity NPC306488
0.5065 Remote Similarity NPC241100

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC33637 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