Natural Product: NPC172337

Natural Product IDNPC172337
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HKODIGSRFALUTA-GMWZVWMNSA-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:0000147] Macrolides and analogues

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 HKODIGSRFALUTA-GMWZVWMNSA-N
Standard InCHI InChI=1S/C18H25NO5/c1-4-12-9-11(2)18(3,22)17(21)23-10-13-5-7-19-8-6-14(15(13)19)24-16(12)20/h4-5,11,14-15,22H,6-10H2,1-3H3/b12-4-/t11?,14-,15?,18-/m1/s1
SMILES C/C=C1/CC(C)[C@](C)(C(=O)OCC2=CCN3CC[C@H](C23)OC1=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   335.17 Volume:   338.617
?
Van der Waals volume.
Dense:   0.99 LogP:   0.542
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.903
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.687
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   22.0
TPSA:   76.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.407 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.044 Fsp3:   0.667
MCE-18:   52.0
?
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:   0.037 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.056
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.005 Promiscuous compounds:   0.087

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.158 MDCK Permeability:   -4.84
Pgp-inhibitor:   0.054 Pgp-substrate:   0.777
PAMPA:   0.939
?
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):   0.007
20% Bioavailability (F20%):   0.504 30% Bioavailability (F30%):   0.821
50% Bioavailability (F50%):   0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.041 MRP1:   0.997
Plasma Protein Binding (PPB):   62.298% Volume Distribution (VD):   0.209
Fu: 39.648%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.961
OATP1B3 inhibitor:   0.926 BCRP inhibitor:   0.146
BSEP inhibitor:   0.973

ADMET: Metabolism

CYP1A2-inhibitor:   0.844 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.19 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.003
CYP3A4-inhibitor:   0.577 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.007
HLM stability:   0.116
?
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):  4.385 Half-life (T1/2):  2.939

ADMET: Toxicity

hERG Blockers:  0.023 hERG Blockers (10um):  0.157
Human Hepatotoxicity (H-HT):  0.825 Drug-induced Liver Injury (DILI):  0.333
AMES Toxicity:  0.479 Rat Oral Acute Toxicity:  0.624
Maximum Recommended Daily Dose:  0.934 Skin Sensitization:  0.998
Carcinogencity:  0.9 Eye Corrosion:  0.004
Eye Irritation:  0.066 Respiratory Toxicity:  0.071
Drug-induced Neurotoxicity:  0.134 Ototoxicity:  0.585
Hematotoxicity:  0.309 Drug-induced Nephrotoxicity:  0.905
Genotoxicity:  0.997 RPMI-8226 Immunitoxicity:  0.133
A549 Cytotoxicity:  0.012 Hek293 Cytotoxicity:  0.293
BCF:   0.395
?
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:   3.039
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.398
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.727
?
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
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29999 Senecio jacobaea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26898 Jacobaea vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29999 Senecio jacobaea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26898 Jacobaea vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29999 Senecio jacobaea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26898 Jacobaea vulgaris Species Asteraceae 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

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 NPC172337 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
1.0 High Similarity NPC130124
1.0 High Similarity NPC193471
0.8421 Intermediate Similarity NPC201889
0.8421 Intermediate Similarity NPC106791
0.8421 Intermediate Similarity NPC607716
0.7931 Intermediate Similarity NPC47857
0.7931 Intermediate Similarity NPC181510
0.7931 Intermediate Similarity NPC168758
0.7931 Intermediate Similarity NPC602310
0.7586 Intermediate Similarity NPC608663
0.75 Intermediate Similarity NPC23963
0.7167 Intermediate Similarity NPC608751
0.7049 Intermediate Similarity NPC609037
0.6667 Remote Similarity NPC608959
0.6557 Remote Similarity NPC30911
0.6557 Remote Similarity NPC608092
0.6406 Remote Similarity NPC316984
0.6364 Remote Similarity NPC600980
0.6 Remote Similarity NPC235625
0.5522 Remote Similarity NPC195435
0.5522 Remote Similarity NPC196073
0.5224 Remote Similarity NPC610562

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC172337 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
0.6557 Remote Similarity NPD2204 Approved

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