Natural Product: NPC603719

Natural Product IDNPC603719
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WQXYOCWRQTXKCI-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL5440844
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 WQXYOCWRQTXKCI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H17NO3/c1-20-7-6-11-8-16-19(23-10-22-16)18-12-4-3-5-15(21-2)13(12)9-14(20)17(11)18/h3-5,8-9H,6-7,10H2,1-2H3
SMILES COc1cccc2c1cc1c3c(cc4c(c32)OCO4)CCN1C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   307.12 Volume:   313.31
?
Van der Waals volume.
Dense:   0.98 LogP:   4.446
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.705
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.218
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   24.0
TPSA:   30.93
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.641 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.657 Fsp3:   0.263
MCE-18:   56.25
?
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:   0.841 Fluc inhibitor:   0.099
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.921
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.548
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.007 Promiscuous compounds:   0.445

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.865 MDCK Permeability:   -4.699
Pgp-inhibitor:   0.849 Pgp-substrate:   0.392
PAMPA:   0.016
?
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):   0.096
20% Bioavailability (F20%):   0.113 30% Bioavailability (F30%):   0.091
50% Bioavailability (F50%):   0.598

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.464 MRP1:   0.795
Plasma Protein Binding (PPB):   98.484% Volume Distribution (VD):   0.352
Fu: 1.34%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.764
OATP1B3 inhibitor:   0.805 BCRP inhibitor:   0.486
BSEP inhibitor:   0.965

ADMET: Metabolism

CYP1A2-inhibitor:   0.998 CYP1A2-substrate:   0.935
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.664
CYP2C9-inhibitor:   0.999 CYP2C9-substrate:   0.995
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.998
CYP3A4-inhibitor:   0.068 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.999 CYP2C8-inhibitor:   0.005
HLM stability:   0.622
?
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):  5.762 Half-life (T1/2):  0.546

ADMET: Toxicity

hERG Blockers:  0.572 hERG Blockers (10um):  0.691
Human Hepatotoxicity (H-HT):  0.736 Drug-induced Liver Injury (DILI):  0.917
AMES Toxicity:  0.89 Rat Oral Acute Toxicity:  0.643
Maximum Recommended Daily Dose:  0.764 Skin Sensitization:  0.694
Carcinogencity:  0.926 Eye Corrosion:  0.0
Eye Irritation:  0.525 Respiratory Toxicity:  0.95
Drug-induced Neurotoxicity:  0.902 Ototoxicity:  0.635
Hematotoxicity:  0.764 Drug-induced Nephrotoxicity:  0.824
Genotoxicity:  0.845 RPMI-8226 Immunitoxicity:  0.197
A549 Cytotoxicity:  0.579 Hek293 Cytotoxicity:  0.635
BCF:   2.049
?
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:   4.231
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.139
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.209
?
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
NPO42109 Stephania cepharantha Hayata Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52731 Stephania micrantha H.S.Lo Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO61180 Stephania kwangsiensis H.S.Lo Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO42473 Stephania dielsiana Wu Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48753 Stephania dielsiana Y.C.Wu Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO54698 Stephania epigaea H.S.Lo Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO59858 Stephania micrantha H.S.Lo.et.M.Yang Genus Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22500 Stephania dielsiana Species Menispermaceae 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
NPT67 Individual protein Cholinesterase Equus caballus IC50 = 3260.0 nM PMID[37172474]
NPT66 Individual protein Acetylcholinesterase Electrophorus electricus Ratio IC50 = 4.0 n.a. PMID[37172474]
NPT66 Individual protein Acetylcholinesterase Electrophorus electricus IC50 = 2850.0 nM PMID[37172474]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT34 Cell line BV-2 Mus musculus IC50 = 30200.0 nM PMID[37172474]

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 NPC603719 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
0.7895 Intermediate Similarity NPC611726
0.75 Intermediate Similarity NPC249405
0.7097 Intermediate Similarity NPC142713
0.7 Intermediate Similarity NPC610105
0.6897 Remote Similarity NPC312531
0.6207 Remote Similarity NPC285941
0.6119 Remote Similarity NPC481952
0.6 Remote Similarity NPC481953
0.5522 Remote Similarity NPC296742
0.55 Remote Similarity NPC190461
0.5441 Remote Similarity NPC474904
0.5077 Remote Similarity NPC118332

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC603719 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