Natural Product: NPC202595

Natural Product IDNPC202595
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Leptosphaerin E
IUPAC Name 1,3-dihydroxy-8-(hydroxymethyl)-6-methylxanthen-9-one
Synonyms Leptosphaerin E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1095459
PubChem CID 46831409
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

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 ZEQFLUCNLABLNA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H12O5/c1-7-2-8(6-16)13-11(3-7)20-12-5-9(17)4-10(18)14(12)15(13)19/h2-5,16-18H,6H2,1H3
SMILES Cc1cc(CO)c2c(c1)oc1cc(cc(c1c2=O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   272.07 Volume:   267.823
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Van der Waals volume.
Dense:   1.016 LogP:   2.146
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.137
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.833
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
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:   0.59 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.593 Fsp3:   0.133
MCE-18:   18.0
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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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.403 Fluc inhibitor:   0.511
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.828
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.58
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.171 Promiscuous compounds:   0.177

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.078 MDCK Permeability:   -4.785
Pgp-inhibitor:   0.039 Pgp-substrate:   0.431
PAMPA:   0.141
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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):   0.006
20% Bioavailability (F20%):   0.24 30% Bioavailability (F30%):   0.956
50% Bioavailability (F50%):   0.922

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.091 MRP1:   0.793
Plasma Protein Binding (PPB):   96.035% Volume Distribution (VD):   -0.123
Fu: 3.557%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.674
OATP1B3 inhibitor:   0.889 BCRP inhibitor:   0.63
BSEP inhibitor:   0.966

ADMET: Metabolism

CYP1A2-inhibitor:   0.33 CYP1A2-substrate:   0.04
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.014
CYP2C9-inhibitor:   0.736 CYP2C9-substrate:   0.273
CYP2D6-inhibitor:   0.992 CYP2D6-substrate:   0.949
CYP3A4-inhibitor:   0.029 CYP3A4-substrate:   0.013
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.474
?
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):  5.154 Half-life (T1/2):  1.092

ADMET: Toxicity

hERG Blockers:  0.057 hERG Blockers (10um):  0.406
Human Hepatotoxicity (H-HT):  0.355 Drug-induced Liver Injury (DILI):  0.724
AMES Toxicity:  0.618 Rat Oral Acute Toxicity:  0.294
Maximum Recommended Daily Dose:  0.778 Skin Sensitization:  0.451
Carcinogencity:  0.837 Eye Corrosion:  0.426
Eye Irritation:  0.999 Respiratory Toxicity:  0.683
Drug-induced Neurotoxicity:  0.019 Ototoxicity:  0.064
Hematotoxicity:  0.045 Drug-induced Nephrotoxicity:  0.017
Genotoxicity:  0.962 RPMI-8226 Immunitoxicity:  0.035
A549 Cytotoxicity:  0.097 Hek293 Cytotoxicity:  0.475
BCF:   0.692
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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:   3.359
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.652
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.945
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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
NPO32944 leptosphaeria sp. Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[20408555]

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
NPT6578 Organism Microdochium nivale Microdochium nivale IC50 > 150000.0 nM PMID[22079864]
NPT826 Organism Magnaporthe oryzae Magnaporthe oryzae IC50 > 150000.0 nM PMID[22124378]
NPT185 Organism Aspergillus flavus Aspergillus flavus IC50 > 150000.0 nM PMID[22182501]

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 NPC202595 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
0.6923 Remote Similarity NPC71055
0.6078 Remote Similarity NPC275734
0.5849 Remote Similarity NPC202157
0.5357 Remote Similarity NPC151473
0.5185 Remote Similarity NPC239495
0.5167 Remote Similarity NPC487785
0.5079 Remote Similarity NPC329091

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC202595 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