Natural Product: NPC476860

Natural Product IDNPC476860
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (1R,2R,4S,7S,8S,10S,15R,16R,19R)-7-(furan-3-yl)-16-(2-hydroxypropan-2-yl)-1,8,15-trimethyl-3,6,11-trioxapentacyclo[8.8.1.02,4.02,8.015,19]nonadec-13-ene-5,12,18-trione
IUPAC Name (1R,2R,4S,7S,8S,10S,15R,16R,19R)-7-(furan-3-yl)-16-(2-hydroxypropan-2-yl)-1,8,15-trimethyl-3,6,11-trioxapentacyclo[8.8.1.02,4.02,8.015,19]nonadec-13-ene-5,12,18-trione
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 90670774
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001640] Naphthopyrans

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 JDBBJFOPZDNBDA-CHALWBKJSA-N
Standard InCHI InChI=1S/C26H30O8/c1-22(2,30)15-10-16(27)25(5)18-14(32-17(28)6-8-23(15,18)3)11-24(4)19(13-7-9-31-12-13)33-21(29)20-26(24,25)34-20/h6-9,12,14-15,18-20,30H,10-11H2,1-5H3/t14-,15-,18+,19-,20+,23-,24-,25+,26+/m0/s1
SMILES C[C@@]12C[C@H]3[C@@H]4[C@@](C=CC(=O)O3)([C@@H](CC(=O)[C@]4([C@@]15[C@H](O5)C(=O)O[C@H]2C6=COC=C6)C)C(C)(C)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   470.19 Volume:   461.416
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Van der Waals volume.
Dense:   1.019 LogP:   1.274
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.592
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.83
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   31.0
TPSA:   115.57
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Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   1.0 Rings:   6.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.518 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.894 Fsp3:   0.654
MCE-18:   189.488
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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:   0.331 Fluc inhibitor:   0.029
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.018
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.018
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.092 Promiscuous compounds:   0.421

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.161 MDCK Permeability:   -4.834
Pgp-inhibitor:   0.494 Pgp-substrate:   0.053
PAMPA:   0.954
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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):   0.011
20% Bioavailability (F20%):   0.018 30% Bioavailability (F30%):   0.033
50% Bioavailability (F50%):   0.116

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.058 MRP1:   0.917
Plasma Protein Binding (PPB):   77.591% Volume Distribution (VD):   -0.204
Fu: 21.302%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.975
OATP1B3 inhibitor:   0.973 BCRP inhibitor:   0.002
BSEP inhibitor:   0.974

ADMET: Metabolism

CYP1A2-inhibitor:   0.674 CYP1A2-substrate:   0.008
CYP2C19-inhibitor:   0.728 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.013 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.065
CYP3A4-inhibitor:   0.473 CYP3A4-substrate:   0.368
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.703
HLM stability:   0.077
?
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):  5.57 Half-life (T1/2):  1.59

ADMET: Toxicity

hERG Blockers:  0.034 hERG Blockers (10um):  0.226
Human Hepatotoxicity (H-HT):  0.438 Drug-induced Liver Injury (DILI):  0.867
AMES Toxicity:  0.862 Rat Oral Acute Toxicity:  0.956
Maximum Recommended Daily Dose:  0.983 Skin Sensitization:  0.998
Carcinogencity:  0.86 Eye Corrosion:  0.025
Eye Irritation:  0.948 Respiratory Toxicity:  0.976
Drug-induced Neurotoxicity:  0.412 Ototoxicity:  0.387
Hematotoxicity:  0.632 Drug-induced Nephrotoxicity:  0.968
Genotoxicity:  0.999 RPMI-8226 Immunitoxicity:  0.374
A549 Cytotoxicity:  0.024 Hek293 Cytotoxicity:  0.114
BCF:   0.768
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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:   3.428
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.291
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.688
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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
NPO33678 Clausena emarginata Species Rutaceae Eukaryota stems Xishuangbanna, Yunnan Province, China 2010-AUG PMID[24593150]

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
NPT393 Cell line HCT-116 Homo sapiens IC50 > 10000 nM PMID[24593150]
NPT65 Cell line HepG2 Homo sapiens IC50 > 10000 nM PMID[24593150]
NPT1820 Cell line NCI-H1650 Homo sapiens IC50 > 10000 nM PMID[24593150]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 > 10000 nM PMID[24593150]
NPT2 Others Unspecified n.a. IC50 > 10000 nM PMID[24593150]

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 NPC476860 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
0.6047 Remote Similarity NPC23387
0.6 Remote Similarity NPC263265
0.5977 Remote Similarity NPC611267
0.5909 Remote Similarity NPC193798
0.5568 Remote Similarity NPC476857
0.5568 Remote Similarity NPC609366
0.5556 Remote Similarity NPC476856
0.5529 Remote Similarity NPC60973
0.5529 Remote Similarity NPC605384
0.5506 Remote Similarity NPC473473
0.5506 Remote Similarity NPC475295
0.5495 Remote Similarity NPC476858
0.5435 Remote Similarity NPC25255
0.5116 Remote Similarity NPC604270
0.5056 Remote Similarity NPC470939

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC476860 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