Natural Product: NPC26626

Natural Product IDNPC26626
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Asterlingulatoside C
IUPAC Name [(2S,3R,4S,5S)-3-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxyoxan-2-yl] (4aR,5R,6aR,6aS,6bR,8aR,10S,12aR,14bS)-5-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-10-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms asterlingulatoside C
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL450513
PubChem CID 44566668
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 CBKUPIHIUWBHCR-WJOMFMDUSA-N
Standard InCHI InChI=1S/C52H84O21/c1-22-40(71-42-37(62)32(57)25(54)20-66-42)36(61)39(64)43(68-22)72-41-33(58)26(55)21-67-45(41)73-46(65)52-16-15-47(2,3)17-24(52)23-9-10-29-49(6)13-12-31(70-44-38(63)35(60)34(59)27(19-53)69-44)48(4,5)28(49)11-14-50(29,7)51(23,8)18-30(52)56/h9,22,24-45,53-64H,10-21H2,1-8H3/t22-,24-,25+,26-,27+,28-,29+,30+,31-,32-,33-,34+,35-,36-,37+,38+,39+,40-,41+,42-,43-,44-,45-,49-,50+,51+,52+/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](CO[C@H]1OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1044.55 Volume:   1010.261
?
Van der Waals volume.
Dense:   1.034 LogP:   1.6
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.368
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.198
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   51.0
TPSA:   333.67
?
Topological Polar Surface Area.
H-Bond Acceptor:   21.0
H-Bond Donor:   12.0 Rings:   9.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.077 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.74 Fsp3:   0.942
MCE-18:   195.446
?
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:   0.756 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.199 Promiscuous compounds:   0.101

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.307 MDCK Permeability:   -5.07
Pgp-inhibitor:   0.0 Pgp-substrate:   0.819
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):   0.576
20% Bioavailability (F20%):   0.537 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.034
Plasma Protein Binding (PPB):   68.093% Volume Distribution (VD):   -0.392
Fu: 20.352%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.003
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.941
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.134
HLM stability:   0.139
?
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):  -0.184 Half-life (T1/2):  3.458

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.007
Human Hepatotoxicity (H-HT):  0.798 Drug-induced Liver Injury (DILI):  0.942
AMES Toxicity:  0.951 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.047 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.002
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.515 Drug-induced Nephrotoxicity:  0.997
Genotoxicity:  0.128 RPMI-8226 Immunitoxicity:  0.316
A549 Cytotoxicity:  0.874 Hek293 Cytotoxicity:  0.306
BCF:   1.427
?
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:   3.656
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.183
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.285
?
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
NPO26359 Aster lingulatus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9249983]
NPO26359 Aster lingulatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26359 Aster lingulatus 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
NPT116 Cell line HL-60 Homo sapiens IC50 = 8800.0 nM PMID[19128055]

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 NPC26626 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 NPC104137
0.9135 High Similarity NPC85154
0.8962 High Similarity NPC286457
0.8485 Intermediate Similarity NPC164389
0.8365 Intermediate Similarity NPC815
0.8273 Intermediate Similarity NPC473452
0.8108 Intermediate Similarity NPC13998
0.8036 Intermediate Similarity NPC470876
0.7938 Intermediate Similarity NPC1046
0.7647 Intermediate Similarity NPC489209
0.7636 Intermediate Similarity NPC123522
0.7589 Intermediate Similarity NPC283417
0.7589 Intermediate Similarity NPC200049
0.7429 Intermediate Similarity NPC488526
0.7417 Intermediate Similarity NPC102505
0.7417 Intermediate Similarity NPC488514
0.7391 Intermediate Similarity NPC57484
0.7377 Intermediate Similarity NPC33012
0.7304 Intermediate Similarity NPC4749
0.7295 Intermediate Similarity NPC8524
0.728 Intermediate Similarity NPC489208
0.7227 Intermediate Similarity NPC309223
0.713 Intermediate Similarity NPC480423
0.7107 Intermediate Similarity NPC220160
0.7083 Intermediate Similarity NPC144644
0.7083 Intermediate Similarity NPC37860
0.7083 Intermediate Similarity NPC170407
0.6949 Remote Similarity NPC21691
0.6909 Remote Similarity NPC64715
0.6885 Remote Similarity NPC70809
0.6855 Remote Similarity NPC68767
0.6855 Remote Similarity NPC293031
0.6852 Remote Similarity NPC117714
0.6754 Remote Similarity NPC11242
0.6697 Remote Similarity NPC30289
0.6667 Remote Similarity NPC237191
0.6667 Remote Similarity NPC302543
0.6636 Remote Similarity NPC232237
0.6514 Remote Similarity NPC263756
0.6514 Remote Similarity NPC469946
0.6491 Remote Similarity NPC481079
0.6475 Remote Similarity NPC23020
0.6455 Remote Similarity NPC112352
0.6449 Remote Similarity NPC485563
0.6429 Remote Similarity NPC63159
0.6429 Remote Similarity NPC482010
0.6379 Remote Similarity NPC207738
0.6379 Remote Similarity NPC481078
0.6364 Remote Similarity NPC213674
0.6338 Remote Similarity NPC472270
0.6338 Remote Similarity NPC112492
0.6333 Remote Similarity NPC135904
0.6299 Remote Similarity NPC224381
0.6299 Remote Similarity NPC142151
0.6299 Remote Similarity NPC267694
0.629 Remote Similarity NPC475514
0.6279 Remote Similarity NPC110385
0.6279 Remote Similarity NPC153673
0.626 Remote Similarity NPC473386
0.6228 Remote Similarity NPC297263
0.6218 Remote Similarity NPC475287
0.6216 Remote Similarity NPC76497
0.621 Remote Similarity NPC265841
0.6183 Remote Similarity NPC485562
0.6182 Remote Similarity NPC480420
0.6176 Remote Similarity NPC329893
0.6154 Remote Similarity NPC51099
0.614 Remote Similarity NPC105800
0.6136 Remote Similarity NPC275225
0.6102 Remote Similarity NPC31838
0.6102 Remote Similarity NPC187290
0.6098 Remote Similarity NPC471577
0.6083 Remote Similarity NPC60557
0.6083 Remote Similarity NPC67857
0.6068 Remote Similarity NPC301449
0.6068 Remote Similarity NPC601290
0.6066 Remote Similarity NPC480419
0.6066 Remote Similarity NPC123199
0.6053 Remote Similarity NPC305267
0.6032 Remote Similarity NPC41061
0.6032 Remote Similarity NPC227551
0.6017 Remote Similarity NPC295823
0.6017 Remote Similarity NPC174720
0.6017 Remote Similarity NPC475467
0.6015 Remote Similarity NPC480421
0.6 Remote Similarity NPC185466
0.5985 Remote Similarity NPC484831
0.5985 Remote Similarity NPC484830
0.5952 Remote Similarity NPC488308
0.595 Remote Similarity NPC610204
0.5946 Remote Similarity NPC235405
0.5942 Remote Similarity NPC472268
0.5938 Remote Similarity NPC236638
0.5938 Remote Similarity NPC294453
0.5938 Remote Similarity NPC305981
0.592 Remote Similarity NPC481080
0.5909 Remote Similarity NPC475208
0.5909 Remote Similarity NPC48499
0.5906 Remote Similarity NPC471580
0.5906 Remote Similarity NPC271610
0.5906 Remote Similarity NPC312650
0.5902 Remote Similarity NPC79643
0.5893 Remote Similarity NPC249848
0.5893 Remote Similarity NPC107966
0.5891 Remote Similarity NPC261506
0.5891 Remote Similarity NPC4328
0.5882 Remote Similarity NPC475177
0.5874 Remote Similarity NPC311178
0.5872 Remote Similarity NPC90856
0.587 Remote Similarity NPC297950
0.5862 Remote Similarity NPC235438
0.5857 Remote Similarity NPC475394
0.582 Remote Similarity NPC300419
0.5816 Remote Similarity NPC233223
0.5816 Remote Similarity NPC183816
0.5816 Remote Similarity NPC43589
0.5814 Remote Similarity NPC481081
0.5811 Remote Similarity NPC322904
0.5806 Remote Similarity NPC475209
0.5806 Remote Similarity NPC603137
0.5793 Remote Similarity NPC488619
0.5789 Remote Similarity NPC80843
0.5785 Remote Similarity NPC210729
0.5785 Remote Similarity NPC82931
0.5776 Remote Similarity NPC44716
0.5776 Remote Similarity NPC46665
0.5776 Remote Similarity NPC2370
0.5776 Remote Similarity NPC480475
0.5775 Remote Similarity NPC475584
0.5775 Remote Similarity NPC475152
0.5763 Remote Similarity NPC302887
0.5762 Remote Similarity NPC488204
0.5758 Remote Similarity NPC250247
0.575 Remote Similarity NPC160452
0.575 Remote Similarity NPC69811
0.5746 Remote Similarity NPC480422
0.5745 Remote Similarity NPC484829
0.5741 Remote Similarity NPC128925
0.5738 Remote Similarity NPC288205
0.5738 Remote Similarity NPC51465
0.5727 Remote Similarity NPC214484
0.5726 Remote Similarity NPC284449
0.5724 Remote Similarity NPC222951
0.5703 Remote Similarity NPC480418
0.5702 Remote Similarity NPC295371
0.5702 Remote Similarity NPC39211
0.569 Remote Similarity NPC30735
0.5682 Remote Similarity NPC488309
0.5678 Remote Similarity NPC222580
0.5678 Remote Similarity NPC488517
0.5664 Remote Similarity NPC300655
0.5664 Remote Similarity NPC13989
0.5664 Remote Similarity NPC196874
0.5664 Remote Similarity NPC475516
0.5655 Remote Similarity NPC478559
0.5655 Remote Similarity NPC478560
0.5646 Remote Similarity NPC472269
0.5641 Remote Similarity NPC251768
0.5635 Remote Similarity NPC602995
0.563 Remote Similarity NPC488515
0.5621 Remote Similarity NPC488201
0.5616 Remote Similarity NPC488618
0.5615 Remote Similarity NPC476779
0.5614 Remote Similarity NPC127056
0.561 Remote Similarity NPC475119
0.5593 Remote Similarity NPC475591
0.5593 Remote Similarity NPC236870
0.5591 Remote Similarity NPC488560
0.5586 Remote Similarity NPC204458
0.5586 Remote Similarity NPC238935
0.5578 Remote Similarity NPC475444
0.5578 Remote Similarity NPC473679
0.5565 Remote Similarity NPC76972
0.5565 Remote Similarity NPC469782
0.5565 Remote Similarity NPC204414
0.5565 Remote Similarity NPC607904
0.5565 Remote Similarity NPC610461
0.5563 Remote Similarity NPC324933
0.5556 Remote Similarity NPC160415
0.5546 Remote Similarity NPC475504
0.5537 Remote Similarity NPC606145
0.5524 Remote Similarity NPC329878
0.5512 Remote Similarity NPC475160
0.5512 Remote Similarity NPC473714
0.5508 Remote Similarity NPC10607
0.55 Remote Similarity NPC471435
0.55 Remote Similarity NPC471434
0.5492 Remote Similarity NPC488564
0.5492 Remote Similarity NPC241909
0.5492 Remote Similarity NPC80986
0.547 Remote Similarity NPC192791
0.547 Remote Similarity NPC223301
0.547 Remote Similarity NPC171544
0.5462 Remote Similarity NPC476774
0.5462 Remote Similarity NPC476780
0.5455 Remote Similarity NPC202828
0.5455 Remote Similarity NPC119592
0.5455 Remote Similarity NPC104372
0.5448 Remote Similarity NPC482011

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC26626 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