Natural Product: NPC225221

Natural Product IDNPC225221
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WXQYRBLGGSLJHA-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 3083613
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives

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 WXQYRBLGGSLJHA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C12H10/c1-2-3-4-6-9-12-10-7-5-8-11-12/h5,7-8,10-11H,9H2,1H3
SMILES CC#CC#CCc1ccccc1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   154.08 Volume:   189.097
?
Van der Waals volume.
Dense:   0.815 LogP:   3.981
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.35
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.052
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   8.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.544 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.532 Fsp3:   0.167
MCE-18:   4.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.003 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.031
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.036

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.481 MDCK Permeability:   -4.519
Pgp-inhibitor:   0.973 Pgp-substrate:   0.0
PAMPA:   0.853
?
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):   0.139
20% Bioavailability (F20%):   0.134 30% Bioavailability (F30%):   0.262
50% Bioavailability (F50%):   0.945

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.015
Plasma Protein Binding (PPB):   98.162% Volume Distribution (VD):   0.025
Fu: 0.904%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.04
OATP1B3 inhibitor:   0.569 BCRP inhibitor:   0.997
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.899 CYP1A2-substrate:   0.851
CYP2C19-inhibitor:   0.221 CYP2C19-substrate:   0.995
CYP2C9-inhibitor:   0.137 CYP2C9-substrate:   0.283
CYP2D6-inhibitor:   0.366 CYP2D6-substrate:   0.983
CYP3A4-inhibitor:   0.408 CYP3A4-substrate:   0.009
CYP2B6-substrate:   0.806 CYP2C8-inhibitor:   0.945
HLM stability:   0.048
?
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):  6.955 Half-life (T1/2):  1.767

ADMET: Toxicity

hERG Blockers:  0.155 hERG Blockers (10um):  0.695
Human Hepatotoxicity (H-HT):  0.378 Drug-induced Liver Injury (DILI):  0.856
AMES Toxicity:  0.531 Rat Oral Acute Toxicity:  0.577
Maximum Recommended Daily Dose:  0.637 Skin Sensitization:  0.578
Carcinogencity:  0.292 Eye Corrosion:  0.916
Eye Irritation:  0.984 Respiratory Toxicity:  0.988
Drug-induced Neurotoxicity:  0.267 Ototoxicity:  0.193
Hematotoxicity:  0.041 Drug-induced Nephrotoxicity:  0.051
Genotoxicity:  0.075 RPMI-8226 Immunitoxicity:  0.04
A549 Cytotoxicity:  0.05 Hek293 Cytotoxicity:  0.45
BCF:   1.793
?
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:   4.232
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.772
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.013
?
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
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s10646-011-0728-8]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0032-9592(02)00165-6]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.2174/1573413711309030012]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO40427 Ailanthus altissima Species Simaroubaceae Eukaryota Roots n.a. n.a. PMID[30106297]
NPO40427 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[36671701]
NPO47426 Erigeron canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36671701]
NPO60360 Erigeron bonariensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36671701]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36983962]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37420038]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37666615]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38008924]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38538562]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38538562]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38542997]
NPO40427 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[38672940]
NPO40427 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[6619885]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO59040 Artemisia annua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40427 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31579 Artemisia capillaries Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31579 Artemisia capillaries Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18681 Artemisia scoparia 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
NPO18681 Artemisia scoparia Oil n.a. 22.8 ± 0.9 n.a. n.a. % PMID[38542997]
NPO18681 Artemisia scoparia Oil n.a. 9.6 ± 0.3 n.a. n.a. % PMID[38542997]
NPO18681 Artemisia scoparia Oil n.a. 18.1 ± 0.5 n.a. n.a. % PMID[38542997]
NPO18681 Artemisia scoparia Oil n.a. 31.8 ± 0.7 n.a. n.a. % PMID[38542997]
NPO18681 Artemisia scoparia Oil n.a. 24.6 ± 0.5 n.a. n.a. % PMID[38542997]
NPO18681 Artemisia scoparia Oil n.a. 18.3 n.a. n.a. % PMID[38538562]
NPO40427 Ailanthus altissima Oil n.a. 23.7 n.a. n.a. % PMID[36671701]
NPO47426 Erigeron canadensis Oil n.a. 0.6 n.a. n.a. % PMID[36671701]
NPO59040 Artemisia annua Oil n.a. 0.491 n.a. n.a. % PMID[37666615]
NPO60360 Erigeron bonariensis Oil n.a. 3.7 n.a. n.a. % PMID[36671701]

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 NPC225221 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
0.5455 Remote Similarity NPC65873
0.5152 Remote Similarity NPC488290

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC225221 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