Natural Product: NPC135369

Natural Product IDNPC135369
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
QOGHAXHWJGZEST-XEUUVMKCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3357161
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 QOGHAXHWJGZEST-XEUUVMKCSA-N
Standard InCHI InChI=1S/C58H96O24/c1-10-12-36(62)74-24-31-40(65)43(68)47(72)51(78-31)81-49-45(70)39(64)30(23-60)77-53(49)80-35-16-18-55(6)33(54(35,4)5)15-20-56(7)34(55)21-28(61)37-27(14-19-57(37,56)8)58(9,17-11-13-26(2)3)82-52-48(73)44(69)41(66)32(79-52)25-75-50-46(71)42(67)38(63)29(22-59)76-50/h10,12-13,27-35,37-53,59-61,63-73H,11,14-25H2,1-9H3/b12-10+/t27-,28+,29+,30+,31+,32+,33-,34+,35-,37-,38+,39+,40+,41+,42-,43-,44-,45-,46+,47+,48+,49+,50+,51-,52-,53-,55-,56+,57+,58-/m0/s1
SMILES C/C=C/C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O[C@H]1O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2C[C@H]([C@@H]2[C@H](CC[C@@]32C)[C@](C)(CCC=C(C)C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O2)O)O)O)O)C1(C)C)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1176.63 Volume:   1146.328
?
Van der Waals volume.
Dense:   1.026 LogP:   1.522
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.285
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.065
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   19.0 Rigid Bonds:   47.0
TPSA:   383.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   14.0 Rings:   8.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.034 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.077 Fsp3:   0.914
MCE-18:   178.667
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.791 Fluc inhibitor:   0.017
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.007
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.296 Promiscuous compounds:   0.165

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.399 MDCK Permeability:   -5.219
Pgp-inhibitor:   0.0 Pgp-substrate:   0.121
PAMPA:   0.999
?
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):   0.999
20% Bioavailability (F20%):   0.207 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.001
Plasma Protein Binding (PPB):   58.199% Volume Distribution (VD):   -0.381
Fu: 24.145%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.602
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.037
?
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):  -0.66 Half-life (T1/2):  4.074

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.005
Human Hepatotoxicity (H-HT):  0.482 Drug-induced Liver Injury (DILI):  0.971
AMES Toxicity:  0.924 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.008 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.168 Drug-induced Nephrotoxicity:  0.996
Genotoxicity:  0.03 RPMI-8226 Immunitoxicity:  0.298
A549 Cytotoxicity:  0.663 Hek293 Cytotoxicity:  0.346
BCF:   0.854
?
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:   3.718
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.511
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.344
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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
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[ 12877918]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota leaves and stems n.a. n.a. PMID[25442304]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20712 Panax quinquefolius Species Araliaceae 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
NPT380 Cell line U-251 Homo sapiens Activity = 97.22 % PMID[25442304]
NPT76 Cell line C6 Rattus norvegicus Activity = 99.37 % PMID[25304895]

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 NPC135369 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
0.9111 High Similarity NPC208650
0.8913 High Similarity NPC220427
0.8438 Intermediate Similarity NPC14946
0.8438 Intermediate Similarity NPC159005
0.8438 Intermediate Similarity NPC63368
0.8416 Intermediate Similarity NPC146868
0.8222 Intermediate Similarity NPC208477
0.8218 Intermediate Similarity NPC241381
0.8155 Intermediate Similarity NPC488294
0.8132 Intermediate Similarity NPC69737
0.7545 Intermediate Similarity NPC488291
0.7451 Intermediate Similarity NPC246124
0.74 Intermediate Similarity NPC65167
0.7216 Intermediate Similarity NPC269627
0.7188 Intermediate Similarity NPC181467
0.7143 Intermediate Similarity NPC31907
0.6983 Remote Similarity NPC488293
0.6961 Remote Similarity NPC472988
0.6961 Remote Similarity NPC38217
0.6909 Remote Similarity NPC488292
0.6765 Remote Similarity NPC234160
0.6574 Remote Similarity NPC472718
0.6364 Remote Similarity NPC312553
0.6364 Remote Similarity NPC180183
0.6316 Remote Similarity NPC146652
0.6224 Remote Similarity NPC157659
0.6216 Remote Similarity NPC6931
0.62 Remote Similarity NPC8039
0.62 Remote Similarity NPC120123
0.6161 Remote Similarity NPC472716
0.6154 Remote Similarity NPC152584
0.6 Remote Similarity NPC159036
0.6 Remote Similarity NPC127801
0.5962 Remote Similarity NPC213190
0.5938 Remote Similarity NPC66654
0.5909 Remote Similarity NPC160816
0.5849 Remote Similarity NPC194842
0.578 Remote Similarity NPC208594
0.5727 Remote Similarity NPC476360
0.5727 Remote Similarity NPC476361
0.5673 Remote Similarity NPC472987
0.5631 Remote Similarity NPC472897
0.5631 Remote Similarity NPC472896
0.5607 Remote Similarity NPC472719
0.5556 Remote Similarity NPC472715
0.5524 Remote Similarity NPC16573
0.54 Remote Similarity NPC234287
0.5392 Remote Similarity NPC160734
0.5377 Remote Similarity NPC165033
0.5377 Remote Similarity NPC273879
0.537 Remote Similarity NPC131479
0.5288 Remote Similarity NPC114874
0.5248 Remote Similarity NPC88000
0.5248 Remote Similarity NPC4831
0.5248 Remote Similarity NPC472023
0.5225 Remote Similarity NPC472717
0.5138 Remote Similarity NPC139271
0.5135 Remote Similarity NPC304011
0.5094 Remote Similarity NPC611039
0.505 Remote Similarity NPC280825
0.505 Remote Similarity NPC473198
0.5047 Remote Similarity NPC252253

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC135369 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