Natural Product: NPC278832

Natural Product IDNPC278832
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
5-Oxo-Isocystofuranoquinol
IUPAC Name (2E,6Z,10E)-1-(2,5-dihydroxy-3-methylphenyl)-3,7,11-trimethyl-12-(4-methylfuran-2-yl)dodeca-2,6,10-trien-5-one
Synonyms 5-Oxo-Isocystofuranoquinol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL461906
PubChem CID 14033288
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 BNCKLSYUMPIDKU-RMYBHBTPSA-N
Standard InCHI InChI=1S/C27H34O4/c1-18(7-6-8-19(2)13-26-14-21(4)17-31-26)11-24(28)12-20(3)9-10-23-16-25(29)15-22(5)27(23)30/h8-9,11,14-17,29-30H,6-7,10,12-13H2,1-5H3/b18-11-,19-8+,20-9+
SMILES C/C(=C/C(=O)C/C(=C/Cc1cc(cc(C)c1O)O)/C)/CC/C=C(C)/Cc1cc(C)co1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   422.25 Volume:   469.868
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Van der Waals volume.
Dense:   0.899 LogP:   6.415
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.312
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.758
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The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   15.0
TPSA:   70.67
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Topological Polar Surface Area.
H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.255 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.465 Fsp3:   0.37
MCE-18:   16.0
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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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.937 Fluc inhibitor:   0.284
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.036
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.291
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.527 Promiscuous compounds:   0.023

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.176 MDCK Permeability:   -4.916
Pgp-inhibitor:   0.912 Pgp-substrate:   0.0
PAMPA:   0.002
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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):   0.0
20% Bioavailability (F20%):   0.337 30% Bioavailability (F30%):   0.585
50% Bioavailability (F50%):   0.498

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.928
Plasma Protein Binding (PPB):   97.638% Volume Distribution (VD):   0.167
Fu: 2.413%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.376 CYP1A2-substrate:   0.882
CYP2C19-inhibitor:   0.985 CYP2C19-substrate:   0.869
CYP2C9-inhibitor:   0.96 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.996 CYP2D6-substrate:   0.387
CYP3A4-inhibitor:   0.49 CYP3A4-substrate:   0.986
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.999
HLM stability:   0.988
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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):  8.572 Half-life (T1/2):  0.782

ADMET: Toxicity

hERG Blockers:  0.256 hERG Blockers (10um):  0.713
Human Hepatotoxicity (H-HT):  0.678 Drug-induced Liver Injury (DILI):  0.065
AMES Toxicity:  0.149 Rat Oral Acute Toxicity:  0.491
Maximum Recommended Daily Dose:  0.904 Skin Sensitization:  0.926
Carcinogencity:  0.501 Eye Corrosion:  0.0
Eye Irritation:  0.285 Respiratory Toxicity:  0.776
Drug-induced Neurotoxicity:  0.216 Ototoxicity:  0.604
Hematotoxicity:  0.229 Drug-induced Nephrotoxicity:  0.653
Genotoxicity:  0.615 RPMI-8226 Immunitoxicity:  0.099
A549 Cytotoxicity:  0.421 Hek293 Cytotoxicity:  0.719
BCF:   2.161
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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:   5.546
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.735
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   6.417
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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
NPO8863 Cystoseira crinita Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[12880316]
NPO8863 Cystoseira crinita Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8863 Cystoseira crinita Species Sargassaceae 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
NPT65 Cell line HepG2 Homo sapiens GI50 = 1.7 ug.mL-1 PMID[18590312]
NPT65 Cell line HepG2 Homo sapiens TGI = 5.0 ug.mL-1 PMID[18590312]
NPT83 Cell line MCF7 Homo sapiens TGI = 1.7 ug.mL-1 DrugMatrix in vitro pharmacology data
NPT83 Cell line MCF7 Homo sapiens GI50 = 0.9 ug.mL-1 DrugMatrix in vitro pharmacology data
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 16.4 % PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 25.2 % PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 38.9 % PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 66.6 % PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 74.6 % PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI50 = 0.9 ug.mL-1 PMID[12880316]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. TGI = 2.0 ug.mL-1 PMID[12880316]
NPT1 Others Radical scavenging activity n.a. Activity = 5.9 % PMID[8450319]
NPT1 Others Radical scavenging activity n.a. Activity = 11.0 % PMID[25871261]
NPT1 Others Radical scavenging activity n.a. Activity = 22.1 % DOI[10.1007/s00044-011-9965-x]
NPT1 Others Radical scavenging activity n.a. Activity = 56.7 % PMID[11929285]
NPT1 Others Radical scavenging activity n.a. Activity = 95.7 % DOI[10.6019/CHEMBL1201861]
NPT1 Others Radical scavenging activity n.a. Activity = 95.8 % PMID[23631483]
NPT35 Others n.a. n.a. Activity = 0.28 mmol/L PMID[16252925]
NPT2 Others Unspecified n.a. Activity = 0.79 mmol/L PMID[18183025]

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 NPC278832 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 NPC64157
0.7031 Intermediate Similarity NPC68260
0.7031 Intermediate Similarity NPC279887
0.6818 Remote Similarity NPC208229
0.6818 Remote Similarity NPC282855
0.6818 Remote Similarity NPC26013
0.6429 Remote Similarity NPC28784
0.6429 Remote Similarity NPC296144
0.6164 Remote Similarity NPC474050
0.6143 Remote Similarity NPC265793
0.5811 Remote Similarity NPC312525
0.5811 Remote Similarity NPC217180
0.5385 Remote Similarity NPC474114
0.5278 Remote Similarity NPC205523

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC278832 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