Natural Product: NPC471157

Natural Product IDNPC471157
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Idesolidine
IUPAC Name [(2R,3R,4R,5R,6R)-4-acetyloxy-5-hydroxy-6-[(1S,2S)-2-hydroxycyclohexyl]oxy-2-(hydroxymethyl)oxan-3-yl] (Z)-3-(4-hydroxyphenyl)prop-2-enoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2385170
PubChem CID 73350447
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives
          • [CHEMONTID:0003002] Hydroxycinnamic acid esters
            • [CHEMONTID:0000465] Coumaric acid esters

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 QNQHICGWQNOHBT-JFQZHESASA-N
Standard InCHI InChI=1S/C23H30O10/c1-13(25)30-22-20(29)23(31-17-5-3-2-4-16(17)27)32-18(12-24)21(22)33-19(28)11-8-14-6-9-15(26)10-7-14/h6-11,16-18,20-24,26-27,29H,2-5,12H2,1H3/b11-8-/t16-,17-,18+,20+,21+,22+,23+/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@H]2CCCC[C@@H]2O)[C@@H]([C@H]([C@@H]1OC(=O)/C=Cc1ccc(cc1)O)OC(=O)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   466.18 Volume:   452.778
?
Van der Waals volume.
Dense:   1.03 LogP:   0.915
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.471
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.111
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   21.0
TPSA:   151.98
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.333 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.127 Fsp3:   0.565
MCE-18:   72.222
?
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:   0.9 Fluc inhibitor:   0.987
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.158
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.202
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.118 Promiscuous compounds:   0.555

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.018 MDCK Permeability:   -5.181
Pgp-inhibitor:   0.042 Pgp-substrate:   0.223
PAMPA:   0.983
?
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):   0.507
20% Bioavailability (F20%):   0.787 30% Bioavailability (F30%):   0.989
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.118
Plasma Protein Binding (PPB):   61.422% Volume Distribution (VD):   -0.136
Fu: 38.716%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.01
BSEP inhibitor:   0.336

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.004
CYP2C9-inhibitor:   0.002 CYP2C9-substrate:   0.05
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.039
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.168
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.364
?
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):  4.87 Half-life (T1/2):  2.288

ADMET: Toxicity

hERG Blockers:  0.075 hERG Blockers (10um):  0.272
Human Hepatotoxicity (H-HT):  0.598 Drug-induced Liver Injury (DILI):  0.174
AMES Toxicity:  0.856 Rat Oral Acute Toxicity:  0.039
Maximum Recommended Daily Dose:  0.082 Skin Sensitization:  1.0
Carcinogencity:  0.041 Eye Corrosion:  0.006
Eye Irritation:  0.582 Respiratory Toxicity:  0.045
Drug-induced Neurotoxicity:  0.094 Ototoxicity:  0.633
Hematotoxicity:  0.07 Drug-induced Nephrotoxicity:  0.409
Genotoxicity:  0.014 RPMI-8226 Immunitoxicity:  0.068
A549 Cytotoxicity:  0.904 Hek293 Cytotoxicity:  0.683
BCF:   0.524
?
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:   3.227
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.795
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.019
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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
NPO27632 Idesia polycarpa Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[23628332]
NPO27632 Idesia polycarpa Species Salicaceae 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
NPT520 Cell line 3T3-L1 Mus musculus IC50 > 150000.0 nM DOI[10.1039/C4MD00211C]

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 NPC471157 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
0.6232 Remote Similarity NPC253668
0.6232 Remote Similarity NPC57039
0.6232 Remote Similarity NPC83218
0.6232 Remote Similarity NPC479471
0.6232 Remote Similarity NPC126991
0.6232 Remote Similarity NPC479467
0.6232 Remote Similarity NPC201249
0.6232 Remote Similarity NPC479470
0.6232 Remote Similarity NPC479472
0.5802 Remote Similarity NPC46137
0.5467 Remote Similarity NPC479473
0.5467 Remote Similarity NPC275721
0.5467 Remote Similarity NPC479468
0.5467 Remote Similarity NPC479474
0.5402 Remote Similarity NPC263829
0.5402 Remote Similarity NPC106677
0.5238 Remote Similarity NPC173150

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471157 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