Natural Product: NPC54065

Natural Product IDNPC54065
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 4Beta-Acetoxy-6Alpha-Hydroxy-1Alpha,10Betah-Pseudoguaia-11(13)-En-12,8Alpha-Olide
IUPAC Name [(3aS,5R,5aS,8S,8aR,9S,9aS)-9-hydroxy-5,8a-dimethyl-1-methylidene-2-oxo-4,5,5a,6,7,8,9,9a-octahydro-3aH-azuleno[6,7-b]furan-8-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1912048
PubChem CID 14414379
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

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 YVHZSHLHIUHLCM-ASINEMROSA-N
Standard InCHI InChI=1S/C17H24O5/c1-8-7-12-14(9(2)16(20)22-12)15(19)17(4)11(8)5-6-13(17)21-10(3)18/h8,11-15,19H,2,5-7H2,1,3-4H3/t8-,11+,12+,13+,14-,15+,17+/m1/s1
SMILES CC(=O)O[C@H]1CC[C@@H]2[C@]1(C)[C@@H](O)[C@H]1[C@H](C[C@H]2C)OC(=O)C1=C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   308.16 Volume:   312.961
?
Van der Waals volume.
Dense:   0.985 LogP:   1.445
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.562
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.77
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   72.83
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.591 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.538 Fsp3:   0.765
MCE-18:   56.0
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.47 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.035
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.418 Promiscuous compounds:   0.592

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.376 MDCK Permeability:   -4.965
Pgp-inhibitor:   0.992 Pgp-substrate:   0.186
PAMPA:   0.678
?
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):   0.453
20% Bioavailability (F20%):   0.932 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.833
Plasma Protein Binding (PPB):   52.918% Volume Distribution (VD):   -0.087
Fu: 50.203%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.02
BSEP inhibitor:   0.923

ADMET: Metabolism

CYP1A2-inhibitor:   0.024 CYP1A2-substrate:   0.03
CYP2C19-inhibitor:   0.393 CYP2C19-substrate:   0.013
CYP2C9-inhibitor:   0.002 CYP2C9-substrate:   0.002
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.042
CYP3A4-inhibitor:   0.422 CYP3A4-substrate:   0.249
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.897
HLM stability:   0.61
?
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):  4.531 Half-life (T1/2):  1.605

ADMET: Toxicity

hERG Blockers:  0.016 hERG Blockers (10um):  0.161
Human Hepatotoxicity (H-HT):  0.727 Drug-induced Liver Injury (DILI):  0.913
AMES Toxicity:  0.569 Rat Oral Acute Toxicity:  0.231
Maximum Recommended Daily Dose:  0.553 Skin Sensitization:  0.965
Carcinogencity:  0.626 Eye Corrosion:  0.293
Eye Irritation:  0.874 Respiratory Toxicity:  0.46
Drug-induced Neurotoxicity:  0.269 Ototoxicity:  0.698
Hematotoxicity:  0.519 Drug-induced Nephrotoxicity:  0.831
Genotoxicity:  0.492 RPMI-8226 Immunitoxicity:  0.094
A549 Cytotoxicity:  0.109 Hek293 Cytotoxicity:  0.102
BCF:   0.528
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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:   3.271
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.803
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.123
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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
NPO22238 Inula falconeri Species Asteraceae Eukaryota aerial parts Tibet, China n.a. PMID[21924800]
NPO22238 Inula falconeri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2402 Valeriana chionophila Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2106 Elephantopus carolinianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2106 Elephantopus carolinianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2106 Elephantopus carolinianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15457 Bunodophoron patagonicum Species Sphaerophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4106 Pyrola alpina Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2402 Valeriana chionophila Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22449 Ulnaria acus Species Fragilariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5581 Psammaplysilla arabica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3738 Achillea stepposa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3551 Thymus collinus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2106 Elephantopus carolinianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18658 Dolichospermum flos-aquae Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22238 Inula falconeri 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 2050.0 nM PMID[21924800]

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 NPC54065 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
0.6471 Remote Similarity NPC29821
0.6471 Remote Similarity NPC43777
0.64 Remote Similarity NPC155935
0.6111 Remote Similarity NPC63193
0.5962 Remote Similarity NPC168679
0.566 Remote Similarity NPC483168
0.566 Remote Similarity NPC35959
0.5577 Remote Similarity NPC606717
0.5536 Remote Similarity NPC24956
0.5455 Remote Similarity NPC297474
0.537 Remote Similarity NPC193645
0.537 Remote Similarity NPC48803
0.537 Remote Similarity NPC275960
0.5091 Remote Similarity NPC56593

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC54065 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
0.537 Remote Similarity NPD1698 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