Natural Product: NPC485015

Natural Product IDNPC485015
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UAMFJPWONGDZLS-LHHJGKSTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and 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 UAMFJPWONGDZLS-LHHJGKSTSA-N
Standard InCHI InChI=1S/C20H24O5/c1-13(2)11-19(22)24-12-14(3)5-8-16-17(23-4)9-6-15-7-10-18(21)25-20(15)16/h5-7,9-10,13H,8,11-12H2,1-4H3/b14-5+
SMILES CC(C)CC(=O)OC/C(=C/Cc1c(ccc2ccc(=O)oc12)OC)/C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   344.16 Volume:   362.859
?
Van der Waals volume.
Dense:   0.948 LogP:   4.41
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.797
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.932
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   14.0
TPSA:   65.74
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.433 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.634 Fsp3:   0.4
MCE-18:   14.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.862 Fluc inhibitor:   0.059
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.993
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.69
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.192 Promiscuous compounds:   0.021

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.641 MDCK Permeability:   -4.531
Pgp-inhibitor:   0.001 Pgp-substrate:   0.0
PAMPA:   0.264
?
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):   0.014
20% Bioavailability (F20%):   0.722 30% Bioavailability (F30%):   0.423
50% Bioavailability (F50%):   0.917

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.99
Plasma Protein Binding (PPB):   96.966% Volume Distribution (VD):   0.082
Fu: 2.55%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.984

ADMET: Metabolism

CYP1A2-inhibitor:   0.082 CYP1A2-substrate:   0.997
CYP2C19-inhibitor:   0.998 CYP2C19-substrate:   0.954
CYP2C9-inhibitor:   0.108 CYP2C9-substrate:   0.092
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.79
CYP3A4-inhibitor:   0.971 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.09 CYP2C8-inhibitor:   1.0
HLM stability:   0.999
?
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):  6.537 Half-life (T1/2):  0.455

ADMET: Toxicity

hERG Blockers:  0.231 hERG Blockers (10um):  0.453
Human Hepatotoxicity (H-HT):  0.708 Drug-induced Liver Injury (DILI):  0.828
AMES Toxicity:  0.494 Rat Oral Acute Toxicity:  0.649
Maximum Recommended Daily Dose:  0.813 Skin Sensitization:  0.612
Carcinogencity:  0.69 Eye Corrosion:  0.001
Eye Irritation:  0.243 Respiratory Toxicity:  0.818
Drug-induced Neurotoxicity:  0.464 Ototoxicity:  0.533
Hematotoxicity:  0.409 Drug-induced Nephrotoxicity:  0.653
Genotoxicity:  0.96 RPMI-8226 Immunitoxicity:  0.149
A549 Cytotoxicity:  0.137 Hek293 Cytotoxicity:  0.37
BCF:   1.741
?
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:   4.476
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.13
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.705
?
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
NPO40301 Prangos haussknechtii Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[28885836]
NPO40301 Prangos haussknechtii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT324 Individual protein Cyclooxygenase-1 Ovis aries IC50 = 47700.0 nM PMID[28885836]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens IC50 = 56400.0 nM PMID[28885836]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT35 Others n.a. n.a. IC50 = 128200.0 nM PMID[28885836]
NPT2 Others Unspecified n.a. IC50 = 86100.0 nM PMID[28885836]

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 NPC485015 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
0.7937 Intermediate Similarity NPC485014
0.6949 Remote Similarity NPC96286
0.5625 Remote Similarity NPC80170
0.5625 Remote Similarity NPC55147
0.5493 Remote Similarity NPC484112
0.5455 Remote Similarity NPC185066
0.5441 Remote Similarity NPC605506
0.5342 Remote Similarity NPC129572
0.5342 Remote Similarity NPC484113
0.5278 Remote Similarity NPC479311
0.527 Remote Similarity NPC479308
0.5224 Remote Similarity NPC62366
0.5217 Remote Similarity NPC168710
0.5135 Remote Similarity NPC479310
0.5075 Remote Similarity NPC73413
0.5075 Remote Similarity NPC122259
0.5075 Remote Similarity NPC601793

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485015 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