Natural Product: NPC303942

Natural Product IDNPC303942
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RZUCCKARTVHQBW-ZFDNOKKTSA-N
IUPAC Name n.a.
Synonyms 9Alpha-Hydroxyparthenolide
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL464587
PubChem CID 14466187
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001771] Germacranolides and 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 RZUCCKARTVHQBW-ZFDNOKKTSA-N
Standard InCHI InChI=1S/C15H20O4/c1-8-5-4-6-15(3)13(19-15)12-10(7-11(8)16)9(2)14(17)18-12/h5,10-13,16H,2,4,6-7H2,1,3H3/b8-5+/t10-,11+,12-,13-,15+/m0/s1
SMILES C/C/1=CCC[C@]2(C)[C@H]([C@@H]3[C@@H](C[C@H]1O)C(=C)C(=O)O3)O2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   264.14 Volume:   269.578
?
Van der Waals volume.
Dense:   0.98 LogP:   1.401
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.488
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.679
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The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   18.0
TPSA:   59.06
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.313 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.034 Fsp3:   0.667
MCE-18:   50.16
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.51 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.026
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.008
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.485 Promiscuous compounds:   0.402

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.296 MDCK Permeability:   -4.853
Pgp-inhibitor:   0.726 Pgp-substrate:   0.082
PAMPA:   0.765
?
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):   0.212
20% Bioavailability (F20%):   0.84 30% Bioavailability (F30%):   0.961
50% Bioavailability (F50%):   0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.014 MRP1:   0.603
Plasma Protein Binding (PPB):   61.429% Volume Distribution (VD):   0.118
Fu: 36.603%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.223
BSEP inhibitor:   0.986

ADMET: Metabolism

CYP1A2-inhibitor:   0.039 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.319 CYP2C19-substrate:   0.008
CYP2C9-inhibitor:   0.139 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.057 CYP2D6-substrate:   0.109
CYP3A4-inhibitor:   0.904 CYP3A4-substrate:   0.011
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.028
HLM stability:   0.79
?
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):  12.288 Half-life (T1/2):  1.854

ADMET: Toxicity

hERG Blockers:  0.024 hERG Blockers (10um):  0.101
Human Hepatotoxicity (H-HT):  0.737 Drug-induced Liver Injury (DILI):  0.845
AMES Toxicity:  0.534 Rat Oral Acute Toxicity:  0.229
Maximum Recommended Daily Dose:  0.497 Skin Sensitization:  0.98
Carcinogencity:  0.543 Eye Corrosion:  0.146
Eye Irritation:  0.963 Respiratory Toxicity:  0.083
Drug-induced Neurotoxicity:  0.309 Ototoxicity:  0.748
Hematotoxicity:  0.427 Drug-induced Nephrotoxicity:  0.85
Genotoxicity:  0.205 RPMI-8226 Immunitoxicity:  0.085
A549 Cytotoxicity:  0.066 Hek293 Cytotoxicity:  0.148
BCF:   0.633
?
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:   3.281
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.869
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.157
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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
NPO24419 Anvillea garcinii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11087618]
NPO8670 Chloranthus multistachys Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[20392109]
NPO24419 Anvillea garcinii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[8699183]
NPO24419 Anvillea garcinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8670 Chloranthus multistachys Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20991 Commiphora pyracanthoides Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22958 Cyclamen hederifolium Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18725 Senecio tournefortii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8670 Chloranthus multistachys Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22958 Cyclamen hederifolium Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24419 Anvillea garcinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20991 Commiphora pyracanthoides Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18725 Senecio tournefortii 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

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
NPT404 Cell line CCRF-CEM Homo sapiens ED50 = 0.84 ug ml-1 PMID[8699183]
NPT112 Cell line MOLT-4 Homo sapiens ED50 = 0.94 ug ml-1 PMID[8699183]
NPT379 Cell line HOP-62 Homo sapiens ED50 = 1.32 ug ml-1 PMID[8699183]
NPT455 Cell line NCI-H522 Homo sapiens ED50 = 0.5 ug ml-1 PMID[8699183]
NPT393 Cell line HCT-116 Homo sapiens ED50 = 1.66 ug ml-1 PMID[8699183]
NPT323 Cell line SW-620 Homo sapiens ED50 = 1.08 ug ml-1 PMID[8699183]
NPT395 Cell line SF-268 Homo sapiens ED50 = 10.3 ug ml-1 PMID[8699183]
NPT390 Cell line LOX IMVI Homo sapiens ED50 = 1.66 ug ml-1 PMID[8699183]
NPT375 Cell line Malme-3M Homo sapiens ED50 = 1.07 ug ml-1 PMID[8699183]
NPT458 Cell line IGROV-1 Homo sapiens ED50 = 8.63 ug ml-1 PMID[8699183]
NPT381 Cell line OVCAR-8 Homo sapiens ED50 = 4.07 ug ml-1 PMID[8699183]
NPT369 Cell line ACHN Homo sapiens ED50 = 1.91 ug ml-1 PMID[8699183]
NPT371 Cell line UO-31 Homo sapiens ED50 = 7.63 ug ml-1 PMID[8699183]
NPT306 Cell line PC-3 Homo sapiens ED50 = 11.62 ug ml-1 PMID[8699183]
NPT90 Cell line DU-145 Homo sapiens ED50 = 6.73 ug ml-1 PMID[8699183]
NPT82 Cell line MDA-MB-231 Homo sapiens ED50 = 4.49 ug ml-1 PMID[8699183]
NPT457 Cell line BT-549 Homo sapiens ED50 = 2.77 ug ml-1 PMID[8699183]
NPT396 Cell line T47D Homo sapiens ED50 = 1.54 ug ml-1 PMID[8699183]
NPT5027 Cell line Hs 683 Homo sapiens IC50 = 7000.0 nM PMID[24998377]
NPT81 Cell line A549 Homo sapiens IC50 = 7000.0 nM PMID[24998377]
NPT83 Cell line MCF7 Homo sapiens IC50 = 6000.0 nM PMID[24998377]
NPT170 Cell line SK-MEL-28 Homo sapiens IC50 = 9000.0 nM PMID[24998377]
NPT1125 Cell line T98G Homo sapiens IC50 = 11000.0 nM PMID[24998377]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 4000.0 nM PMID[24998377]

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 NPC303942 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 NPC57405
0.6604 Remote Similarity NPC608845
0.6346 Remote Similarity NPC38468
0.6346 Remote Similarity NPC192678
0.6346 Remote Similarity NPC319795
0.6346 Remote Similarity NPC50362
0.6346 Remote Similarity NPC488056
0.6346 Remote Similarity NPC605079
0.6226 Remote Similarity NPC49342
0.6226 Remote Similarity NPC251385
0.6207 Remote Similarity NPC473859
0.6034 Remote Similarity NPC475659
0.6 Remote Similarity NPC70251
0.6 Remote Similarity NPC475881
0.5932 Remote Similarity NPC487572
0.569 Remote Similarity NPC471147
0.5424 Remote Similarity NPC481908
0.5424 Remote Similarity NPC481993
0.5263 Remote Similarity NPC151770
0.5161 Remote Similarity NPC474035
0.5161 Remote Similarity NPC81386

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC303942 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
0.6346 Remote Similarity NPD1733 Clinical (unspecified phase)

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