Natural Product: NPC471740

Natural Product IDNPC471740
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (8E)-4Alpha-Acetoxy-12Alpha,13Alpha-Epoxycembra-1(15),8-Diene
IUPAC Name [(1S,6S,10E,14R)-6,10,14-trimethyl-2-oxo-3-propan-2-ylidene-15-oxabicyclo[12.1.0]pentadec-10-en-6-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3109419
PubChem CID 76335689
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 QRIAHPSWAQTBHB-ZUBFFHLMSA-N
Standard InCHI InChI=1S/C22H34O4/c1-15(2)18-11-14-21(5,25-17(4)23)12-7-9-16(3)10-8-13-22(6)20(26-22)19(18)24/h10,20H,7-9,11-14H2,1-6H3/b16-10+/t20-,21+,22-/m1/s1
SMILES CC1=CCCC2(C(O2)C(=O)C(=C(C)C)CCC(CCC1)(C)OC(=O)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   362.25 Volume:   396.57
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Van der Waals volume.
Dense:   0.913 LogP:   4.197
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.754
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.101
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   19.0
TPSA:   55.9
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Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.283 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.764 Fsp3:   0.727
MCE-18:   45.474
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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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.269 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.167
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.811 Promiscuous compounds:   0.021

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.574 MDCK Permeability:   -4.754
Pgp-inhibitor:   0.976 Pgp-substrate:   0.019
PAMPA:   0.041
?
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):   0.002
20% Bioavailability (F20%):   0.011 30% Bioavailability (F30%):   0.076
50% Bioavailability (F50%):   0.639

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.474 MRP1:   0.993
Plasma Protein Binding (PPB):   91.403% Volume Distribution (VD):   0.202
Fu: 8.77%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.964
OATP1B3 inhibitor:   0.965 BCRP inhibitor:   0.017
BSEP inhibitor:   0.996

ADMET: Metabolism

CYP1A2-inhibitor:   0.012 CYP1A2-substrate:   0.369
CYP2C19-inhibitor:   0.996 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.004 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.002
CYP3A4-inhibitor:   0.918 CYP3A4-substrate:   0.003
CYP2B6-substrate:   0.672 CYP2C8-inhibitor:   0.151
HLM stability:   0.77
?
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):  8.116 Half-life (T1/2):  0.415

ADMET: Toxicity

hERG Blockers:  0.027 hERG Blockers (10um):  0.345
Human Hepatotoxicity (H-HT):  0.328 Drug-induced Liver Injury (DILI):  0.195
AMES Toxicity:  0.146 Rat Oral Acute Toxicity:  0.095
Maximum Recommended Daily Dose:  0.169 Skin Sensitization:  0.974
Carcinogencity:  0.732 Eye Corrosion:  0.859
Eye Irritation:  0.937 Respiratory Toxicity:  0.158
Drug-induced Neurotoxicity:  0.381 Ototoxicity:  0.161
Hematotoxicity:  0.336 Drug-induced Nephrotoxicity:  0.089
Genotoxicity:  0.011 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.061 Hek293 Cytotoxicity:  0.031
BCF:   1.699
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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:   4.01
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.432
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.976
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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
NPO32786 chandonanthus birmensis Species Anastrophyllaceae Eukaryota n.a. Chinese liverworts n.a. PMID[24491225]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. Chinese liverworts n.a. PMID[24491225]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae 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
NPT2410 Cell line NCI-H1299 Homo sapiens IC50 = 41600.0 nM PMID[16472241]
NPT2452 Cell line NCI-H292 n.a. IC50 > 50000.0 nM PMID[14987072]
NPT81 Cell line A549 Homo sapiens IC50 > 50000.0 nM PMID[22394155]
NPT306 Cell line PC-3 Homo sapiens IC50 > 50000.0 nM DOI[10.6019/CHEMBL1201861]
NPT90 Cell line DU-145 Homo sapiens IC50 > 50000.0 nM PMID[17685651]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[24491225]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 47100.0 nM PMID[24491225]

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 NPC471740 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
0.72 Intermediate Similarity NPC286229
0.6923 Remote Similarity NPC471738
0.5818 Remote Similarity NPC622
0.5818 Remote Similarity NPC276647

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471740 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