Natural Product: NPC116711

Natural Product IDNPC116711
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VDYACOATPFOZIO-DYXDTQHNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10915273
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 VDYACOATPFOZIO-DYXDTQHNSA-N
Standard InCHI InChI=1S/C21H24O5/c1-6-7-15-12-21(25-5)13(2)20(26-19(21)11-16(15)22)14-8-9-17(23-3)18(10-14)24-4/h6,8-13,20H,1,7H2,2-5H3/t13-,20+,21-/m0/s1
SMILES C=CCC1=C[C@@]2([C@@H](C)[C@H](c3ccc(c(c3)OC)OC)OC2=CC1=O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   356.16 Volume:   371.599
?
Van der Waals volume.
Dense:   0.958 LogP:   3.123
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.15
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.005
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   18.0
TPSA:   53.99
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.727 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.064 Fsp3:   0.381
MCE-18:   64.138
?
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:   0.31 Fluc inhibitor:   0.402
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.075
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.22
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.364 Promiscuous compounds:   0.184

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.66 MDCK Permeability:   -4.575
Pgp-inhibitor:   0.782 Pgp-substrate:   0.014
PAMPA:   0.017
?
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):   0.008
20% Bioavailability (F20%):   0.313 30% Bioavailability (F30%):   0.801
50% Bioavailability (F50%):   0.937

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.189 MRP1:   0.357
Plasma Protein Binding (PPB):   86.223% Volume Distribution (VD):   0.22
Fu: 14.881%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.91
BSEP inhibitor:   0.845

ADMET: Metabolism

CYP1A2-inhibitor:   0.976 CYP1A2-substrate:   0.766
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.594
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.049
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.803
CYP3A4-inhibitor:   0.818 CYP3A4-substrate:   0.985
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.911
?
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):  7.191 Half-life (T1/2):  2.215

ADMET: Toxicity

hERG Blockers:  0.13 hERG Blockers (10um):  0.504
Human Hepatotoxicity (H-HT):  0.425 Drug-induced Liver Injury (DILI):  0.837
AMES Toxicity:  0.517 Rat Oral Acute Toxicity:  0.667
Maximum Recommended Daily Dose:  0.623 Skin Sensitization:  0.868
Carcinogencity:  0.673 Eye Corrosion:  0.061
Eye Irritation:  0.899 Respiratory Toxicity:  0.933
Drug-induced Neurotoxicity:  0.728 Ototoxicity:  0.367
Hematotoxicity:  0.311 Drug-induced Nephrotoxicity:  0.506
Genotoxicity:  0.842 RPMI-8226 Immunitoxicity:  0.14
A549 Cytotoxicity:  0.104 Hek293 Cytotoxicity:  0.317
BCF:   1.633
?
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:   4.044
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.259
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.244
?
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
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11040054]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16724856]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. leaf n.a. PMID[17999353]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota Roots; Tubers n.a. n.a. PMID[19639966]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[19900811]
NPO9925 Rhododendron latoucheae Species Ericaceae Eukaryota Twigs; Leaves n.a. n.a. PMID[30106288]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. aerial part n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8368081]
NPO313 Castilleja sulphurea Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19174 Anoplophora chinensis Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7522 Streptomyces amakusaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9301 Dioscorea sativa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1155 Forsythia japonica Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6475 Gymnosporia trigyna Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9571 Pseudobrickellia brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9925 Rhododendron latoucheae Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6475 Gymnosporia trigyna Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1155 Forsythia japonica Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19174 Anoplophora chinensis Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9925 Rhododendron latoucheae Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9301 Dioscorea sativa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9571 Pseudobrickellia brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7522 Streptomyces amakusaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO313 Castilleja sulphurea Species Orobanchaceae 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 NPC116711 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
1.0 High Similarity NPC280399
1.0 High Similarity NPC339621
0.8448 Intermediate Similarity NPC166184
0.8214 Intermediate Similarity NPC145769
0.5735 Remote Similarity NPC64948
0.5672 Remote Similarity NPC51681
0.5606 Remote Similarity NPC268317

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC116711 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