Natural Product: NPC48156

Natural Product IDNPC48156
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
HUBUCUOTSSVULF-WPWLPRNLSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 42608006
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 HUBUCUOTSSVULF-WPWLPRNLSA-N
Standard InCHI InChI=1S/C32H40O19/c1-44-19-4-13(2-3-15(19)35)18-7-17(37)22-16(36)5-14(6-20(22)49-18)48-28-25(24(39)23(38)21(8-33)50-28)51-30-27(41)32(43,12-47-30)11-46-29-26(40)31(42,9-34)10-45-29/h2-6,18,21,23-30,33-36,38-43H,7-12H2,1H3/t18-,21?,23?,24?,25?,26?,27?,28?,29?,30?,31?,32?/m0/s1
SMILES COc1cc(ccc1O)[C@@H]1CC(=O)c2c(cc(cc2O1)OC1C(C(C(C(CO)O1)O)O)OC1C(C(COC2C(C(CO)(CO2)O)O)(CO1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   728.22 Volume:   659.248
?
Van der Waals volume.
Dense:   1.105 LogP:   -0.883
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.094
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.545
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   34.0
TPSA:   293.21
?
Topological Polar Surface Area.
H-Bond Acceptor:   19.0
H-Bond Donor:   10.0 Rings:   6.0
Heavy Atoms:   19.0

MedChem Properties

QED Drug-Likeness Score:   0.11 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.489 Fsp3:   0.594
MCE-18:   150.706
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.049 Fluc inhibitor:   0.051
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.051
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.475
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.206 Promiscuous compounds:   0.334

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.926 MDCK Permeability:   -5.01
Pgp-inhibitor:   0.0 Pgp-substrate:   0.847
PAMPA:   1.0
?
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):   0.997
20% Bioavailability (F20%):   0.953 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.952
Plasma Protein Binding (PPB):   75.586% Volume Distribution (VD):   -0.353
Fu: 23.763%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.007
OATP1B3 inhibitor:   0.991 BCRP inhibitor:   0.843
BSEP inhibitor:   0.002

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.847 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.0
?
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):  1.071 Half-life (T1/2):  3.485

ADMET: Toxicity

hERG Blockers:  0.02 hERG Blockers (10um):  0.116
Human Hepatotoxicity (H-HT):  0.735 Drug-induced Liver Injury (DILI):  0.836
AMES Toxicity:  0.978 Rat Oral Acute Toxicity:  0.324
Maximum Recommended Daily Dose:  0.203 Skin Sensitization:  0.932
Carcinogencity:  0.255 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.052
Drug-induced Neurotoxicity:  0.405 Ototoxicity:  0.993
Hematotoxicity:  0.047 Drug-induced Nephrotoxicity:  0.552
Genotoxicity:  0.966 RPMI-8226 Immunitoxicity:  0.351
A549 Cytotoxicity:  0.435 Hek293 Cytotoxicity:  0.891
BCF:   0.404
?
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:   2.738
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.742
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.534
?
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
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[2082684]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[21922656]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3254039]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3256207]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23218 Viscum coloratum Species Viscaceae 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 NPC48156 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 NPC241196
0.9405 High Similarity NPC261254
0.6827 Remote Similarity NPC469371
0.6304 Remote Similarity NPC236934
0.625 Remote Similarity NPC200708
0.625 Remote Similarity NPC604887
0.6162 Remote Similarity NPC105095
0.6162 Remote Similarity NPC177731
0.6162 Remote Similarity NPC725
0.6146 Remote Similarity NPC105283
0.602 Remote Similarity NPC97285
0.602 Remote Similarity NPC142860
0.602 Remote Similarity NPC152538
0.602 Remote Similarity NPC246469
0.602 Remote Similarity NPC89088
0.59 Remote Similarity NPC291124
0.59 Remote Similarity NPC131157
0.5577 Remote Similarity NPC47140
0.5158 Remote Similarity NPC183536
0.5104 Remote Similarity NPC219163
0.5104 Remote Similarity NPC39351
0.5098 Remote Similarity NPC265480
0.5056 Remote Similarity NPC601998

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC48156 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