Natural Product: NPC248310

Natural Product IDNPC248310
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LRUIASUJJNMESX-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10359254
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

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 LRUIASUJJNMESX-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O7/c1-22-12-5-8(3-4-9(12)18)11-6-10(19)15-13(24-11)7-14(23-2)16(20)17(15)21/h3-7,18,20-21H,1-2H3
SMILES COc1cc(ccc1O)c1cc(=O)c2c(cc(c(c2O)O)OC)o1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   330.07 Volume:   317.359
?
Van der Waals volume.
Dense:   1.04 LogP:   2.211
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.141
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.179
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   109.36
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.633 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.4 Fsp3:   0.118
MCE-18:   19.0
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.637 Fluc inhibitor:   0.824
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.926
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.693
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.458 Promiscuous compounds:   0.881

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.109 MDCK Permeability:   -4.788
Pgp-inhibitor:   0.356 Pgp-substrate:   0.115
PAMPA:   0.189
?
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):   0.114
20% Bioavailability (F20%):   0.52 30% Bioavailability (F30%):   0.669
50% Bioavailability (F50%):   0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.983
Plasma Protein Binding (PPB):   96.098% Volume Distribution (VD):   -0.474
Fu: 4.287%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.999
BSEP inhibitor:   0.914

ADMET: Metabolism

CYP1A2-inhibitor:   0.011 CYP1A2-substrate:   0.576
CYP2C19-inhibitor:   0.009 CYP2C19-substrate:   0.023
CYP2C9-inhibitor:   0.671 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.998 CYP2D6-substrate:   0.953
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.034
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.992
HLM stability:   0.166
?
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):  7.454 Half-life (T1/2):  1.696

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.497
Human Hepatotoxicity (H-HT):  0.383 Drug-induced Liver Injury (DILI):  0.735
AMES Toxicity:  0.569 Rat Oral Acute Toxicity:  0.419
Maximum Recommended Daily Dose:  0.646 Skin Sensitization:  0.762
Carcinogencity:  0.674 Eye Corrosion:  0.36
Eye Irritation:  0.989 Respiratory Toxicity:  0.773
Drug-induced Neurotoxicity:  0.086 Ototoxicity:  0.152
Hematotoxicity:  0.168 Drug-induced Nephrotoxicity:  0.097
Genotoxicity:  0.75 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.353 Hek293 Cytotoxicity:  0.504
BCF:   0.917
?
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:   3.429
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.251
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.837
?
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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38754641]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28276 Artemisia argyi 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 NPC248310 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
0.7925 Intermediate Similarity NPC198826
0.7778 Intermediate Similarity NPC162313
0.75 Intermediate Similarity NPC283600
0.7407 Intermediate Similarity NPC275722
0.7368 Intermediate Similarity NPC47781
0.7368 Intermediate Similarity NPC137062
0.7321 Intermediate Similarity NPC212678
0.7273 Intermediate Similarity NPC57030
0.7193 Intermediate Similarity NPC18607
0.7193 Intermediate Similarity NPC128863
0.7119 Intermediate Similarity NPC485299
0.7018 Intermediate Similarity NPC83508
0.678 Remote Similarity NPC183950
0.6724 Remote Similarity NPC20830
0.6552 Remote Similarity NPC312924
0.65 Remote Similarity NPC606105
0.6441 Remote Similarity NPC280339
0.6333 Remote Similarity NPC4455
0.6333 Remote Similarity NPC115323
0.623 Remote Similarity NPC227325
0.5902 Remote Similarity NPC167815
0.5882 Remote Similarity NPC602497
0.5738 Remote Similarity NPC305663
0.5574 Remote Similarity NPC48479
0.5574 Remote Similarity NPC234133
0.5574 Remote Similarity NPC120163
0.5574 Remote Similarity NPC276409
0.5484 Remote Similarity NPC108406
0.5484 Remote Similarity NPC78913
0.5484 Remote Similarity NPC25270
0.5469 Remote Similarity NPC261004
0.5469 Remote Similarity NPC252933
0.5469 Remote Similarity NPC78326
0.5455 Remote Similarity NPC311830
0.5455 Remote Similarity NPC602805
0.541 Remote Similarity NPC71334
0.541 Remote Similarity NPC43243
0.541 Remote Similarity NPC241498
0.541 Remote Similarity NPC284552
0.5397 Remote Similarity NPC300943
0.5397 Remote Similarity NPC69394
0.5385 Remote Similarity NPC227192
0.5323 Remote Similarity NPC100887
0.5312 Remote Similarity NPC160951
0.5312 Remote Similarity NPC195202
0.5312 Remote Similarity NPC223579
0.5263 Remote Similarity NPC475942
0.5246 Remote Similarity NPC75279
0.52 Remote Similarity NPC146792
0.5172 Remote Similarity NPC61871
0.5161 Remote Similarity NPC127447
0.5161 Remote Similarity NPC239128
0.5161 Remote Similarity NPC29353
0.5156 Remote Similarity NPC255350
0.5132 Remote Similarity NPC58716
0.5128 Remote Similarity NPC43211
0.5079 Remote Similarity NPC33265
0.5079 Remote Similarity NPC184136
0.5079 Remote Similarity NPC18260
0.5079 Remote Similarity NPC145379
0.5079 Remote Similarity NPC120464
0.5077 Remote Similarity NPC179126
0.5077 Remote Similarity NPC177298
0.5063 Remote Similarity NPC111249

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC248310 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
0.5156 Remote Similarity NPD2801 Pre-clinical

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