Natural Product: NPC227062

Natural Product IDNPC227062
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Thunberginol E
IUPAC Name (3R)-6,8-dihydroxy-3-(3-hydroxy-4-methoxyphenyl)-3,4-dihydroisochromen-1-one
Synonyms thunberginol E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL421486
PubChem CID 10040569
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0001248] Hydroxybenzoic acid derivatives

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 MZKMQBPFGDJUFV-CQSZACIVSA-N
Standard InCHI InChI=1S/C16H14O6/c1-21-13-3-2-8(5-11(13)18)14-6-9-4-10(17)7-12(19)15(9)16(20)22-14/h2-5,7,14,17-19H,6H2,1H3/t14-/m1/s1
SMILES COc1ccc(cc1O)[C@@H]1OC(=O)c2c(C1)cc(cc2O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   302.08 Volume:   293.909
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Van der Waals volume.
Dense:   1.028 LogP:   1.782
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.996
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.789
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   96.22
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Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.736 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.943 Fsp3:   0.188
MCE-18:   57.789
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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:   1 PAINS Alert:   0
Colloidal aggregators:   0.643 Fluc inhibitor:   0.884
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.208
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.423
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.397 Promiscuous compounds:   0.618

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.12 MDCK Permeability:   -4.832
Pgp-inhibitor:   0.179 Pgp-substrate:   0.192
PAMPA:   0.324
?
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):   0.048
20% Bioavailability (F20%):   0.524 30% Bioavailability (F30%):   0.95
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.017 MRP1:   0.81
Plasma Protein Binding (PPB):   97.27% Volume Distribution (VD):   -0.461
Fu: 2.437%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.99
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.867
BSEP inhibitor:   0.201

ADMET: Metabolism

CYP1A2-inhibitor:   0.915 CYP1A2-substrate:   0.963
CYP2C19-inhibitor:   0.075 CYP2C19-substrate:   0.692
CYP2C9-inhibitor:   0.721 CYP2C9-substrate:   0.938
CYP2D6-inhibitor:   0.14 CYP2D6-substrate:   0.984
CYP3A4-inhibitor:   0.012 CYP3A4-substrate:   0.959
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.968
?
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):  4.538 Half-life (T1/2):  1.6

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.573
Human Hepatotoxicity (H-HT):  0.408 Drug-induced Liver Injury (DILI):  0.556
AMES Toxicity:  0.596 Rat Oral Acute Toxicity:  0.2
Maximum Recommended Daily Dose:  0.735 Skin Sensitization:  0.933
Carcinogencity:  0.531 Eye Corrosion:  0.182
Eye Irritation:  0.995 Respiratory Toxicity:  0.321
Drug-induced Neurotoxicity:  0.177 Ototoxicity:  0.181
Hematotoxicity:  0.045 Drug-induced Nephrotoxicity:  0.344
Genotoxicity:  0.955 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.269 Hek293 Cytotoxicity:  0.482
BCF:   1.077
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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:   3.854
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.826
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.226
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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
NPO33513 hydrangeae dulcis folium Species n.a. n.a. n.a. n.a. n.a. PMID[11549443]
NPO9360.1 Hydrangea macrophylla var. thunbergii Varieties Hydrangeaceae Eukaryota Leaves n.a. n.a. PMID[17609121]
NPO33513 hydrangeae dulcis folium Species n.a. n.a. n.a. n.a. n.a. PMID[9871657]
NPO9360.1 Hydrangea macrophylla var. thunbergii Varieties Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33513 hydrangeae dulcis folium Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO9360.1 Hydrangea macrophylla var. thunbergii Varieties Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9360.1 Hydrangea macrophylla var. thunbergii Varieties Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

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
NPT10 Individual protein Geminin Homo sapiens Potency n.a. 18.4 nM PMID[21028898]
NPT157 Individual protein Breast cancer type 1 susceptibility protein Homo sapiens Potency n.a. 10000.0 nM PMID[18809936]
NPT8 Individual protein DNA polymerase iota Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT535 Individual protein Parathyroid hormone receptor Homo sapiens Potency n.a. 3981.1 nM PMID[16309311]
NPT64 Individual protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 5171.4 nM DOI[10.6019/CHEMBL1201861]
NPT84 Individual protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A Rattus norvegicus AC50 = 8431.0 nM PMID[13678412]
NPT64 Individual protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 11174.9 nM PMID[19708637]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT520 Cell line 3T3-L1 Mus musculus Activity = -6.3 % PMID[15165138]
NPT520 Cell line 3T3-L1 Mus musculus Activity = -8.0 % PMID[17988094]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 3.4 % PMID[21314138]
NPT520 Cell line 3T3-L1 Mus musculus Activity = -4.0 % PMID[17672504]
NPT520 Cell line 3T3-L1 Mus musculus Activity = -7.5 % PMID[24224843]
NPT2 Others Unspecified n.a. Potency n.a. 707.9 nM PMID[20444528]

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 NPC227062 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
0.7358 Intermediate Similarity NPC295646
0.7 Intermediate Similarity NPC155205
0.6923 Remote Similarity NPC476463
0.6863 Remote Similarity NPC245234

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC227062 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