Natural Product: NPC273462

Natural Product IDNPC273462
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 4-[(2E)-3,7-Dimethylocta-2,6-Dienyl]-1,3,5-Trihydroxyxanthen-9-One
IUPAC Name 4-[(2E)-3,7-dimethylocta-2,6-dienyl]-1,3,5-trihydroxyxanthen-9-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL482023
PubChem CID 15127379
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones
                • [CHEMONTID:0003518] 4-prenylated xanthones

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 PCKHKINJZFNYEO-GXDHUFHOSA-N
Standard InCHI InChI=1S/C23H24O5/c1-13(2)6-4-7-14(3)10-11-15-18(25)12-19(26)20-21(27)16-8-5-9-17(24)22(16)28-23(15)20/h5-6,8-10,12,24-26H,4,7,11H2,1-3H3/b14-10+
SMILES C/C(=CCc1c(O)cc(c2c1oc1c(O)cccc1c2=O)O)/CCC=C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   380.16 Volume:   400.918
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Van der Waals volume.
Dense:   0.948 LogP:   5.801
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.184
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.552
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   19.0
TPSA:   90.9
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Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.413 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.982 Fsp3:   0.261
MCE-18:   20.0
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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:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.948 Fluc inhibitor:   0.377
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.967
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.764
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.198 Promiscuous compounds:   0.105

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.965 MDCK Permeability:   -4.653
Pgp-inhibitor:   0.967 Pgp-substrate:   0.037
PAMPA:   0.028
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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):   0.029
20% Bioavailability (F20%):   0.431 30% Bioavailability (F30%):   0.956
50% Bioavailability (F50%):   0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.902
Plasma Protein Binding (PPB):   97.159% Volume Distribution (VD):   0.062
Fu: 2.443%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.981 BCRP inhibitor:   0.768
BSEP inhibitor:   0.968

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.999
CYP2C19-inhibitor:   0.83 CYP2C19-substrate:   0.98
CYP2C9-inhibitor:   0.914 CYP2C9-substrate:   0.192
CYP2D6-inhibitor:   0.989 CYP2D6-substrate:   0.94
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.994
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
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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):  3.482 Half-life (T1/2):  1.274

ADMET: Toxicity

hERG Blockers:  0.042 hERG Blockers (10um):  0.515
Human Hepatotoxicity (H-HT):  0.675 Drug-induced Liver Injury (DILI):  0.929
AMES Toxicity:  0.411 Rat Oral Acute Toxicity:  0.668
Maximum Recommended Daily Dose:  0.377 Skin Sensitization:  0.947
Carcinogencity:  0.518 Eye Corrosion:  0.001
Eye Irritation:  0.84 Respiratory Toxicity:  0.975
Drug-induced Neurotoxicity:  0.085 Ototoxicity:  0.252
Hematotoxicity:  0.248 Drug-induced Nephrotoxicity:  0.156
Genotoxicity:  0.961 RPMI-8226 Immunitoxicity:  0.086
A549 Cytotoxicity:  0.256 Hek293 Cytotoxicity:  0.373
BCF:   2.022
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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:   5.199
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.576
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.165
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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
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4020(01)89039-6]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota root bark n.a. n.a. PMID[16562837]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. PMID[21028890]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5638 Garcinia livingstonei Species Clusiaceae 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
NPT171 Cell line MRC5 Homo sapiens IC50 > 64000.0 nM PMID[20185316]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 59000.0 nM PMID[20185316]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 5700.0 nM PMID[17256988]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 > 64000.0 nM PMID[22916954]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 = 2000.0 nM PMID[20681570]

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 NPC273462 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
0.8197 Intermediate Similarity NPC70433
0.6667 Remote Similarity NPC227337
0.6 Remote Similarity NPC33051
0.575 Remote Similarity NPC206153
0.575 Remote Similarity NPC271629
0.5493 Remote Similarity NPC75069
0.5412 Remote Similarity NPC479158
0.5395 Remote Similarity NPC68093
0.5342 Remote Similarity NPC170333
0.5309 Remote Similarity NPC77856
0.5256 Remote Similarity NPC483042
0.5244 Remote Similarity NPC273843
0.5122 Remote Similarity NPC474681
0.5065 Remote Similarity NPC168247
0.5062 Remote Similarity NPC223988

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC273462 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