Natural Product: NPC25663

Natural Product IDNPC25663
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Dianversicoside A
IUPAC Name (3S)-5-[[(2R,3S,4S,5R,6R)-6-[[(2R,3S,4S,5R,6S)-6-[(4aR,5R,6aR,6aS,6bR,8aR,9S,10S,12aR,14bS)-5,10-dihydroxy-2,2,6a,6b,9,12a-hexamethyl-9-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxycarbonyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carbonyl]oxy-3,4,5-trihydroxyoxan-2-yl]methoxy]-3,4-dihydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]methoxy]-3-hydroxy-3-methyl-5-oxopentanoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL554394
PubChem CID 42639817
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 IJSZPFMPQUDYPI-FYIVALIFSA-N
Standard InCHI InChI=1S/C60H94O30/c1-54(2)14-15-60(25(16-54)24-8-9-30-56(4)12-11-32(63)59(7,31(56)10-13-57(30,5)58(24,6)17-33(60)64)52(79)89-49-45(77)41(73)37(69)27(21-62)85-49)53(80)90-50-46(78)42(74)38(70)29(86-50)23-83-51-47(88-48-44(76)40(72)36(68)26(20-61)84-48)43(75)39(71)28(87-51)22-82-35(67)19-55(3,81)18-34(65)66/h8,25-33,36-51,61-64,68-78,81H,9-23H2,1-7H3,(H,65,66)/t25-,26+,27+,28+,29+,30+,31+,32-,33+,36+,37+,38+,39+,40-,41-,42-,43-,44+,45+,46+,47+,48-,49-,50-,51+,55-,56+,57+,58+,59-,60+/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@H]2[C@H](OC[C@H]3O[C@@H](OC(=O)[C@@]45CCC(C[C@H]5C5=CC[C@H]6[C@@]([C@@]5(C[C@H]4O)C)(C)CC[C@@H]4[C@]6(C)CC[C@@H]([C@@]4(C)C(=O)O[C@@H]4O[C@H](CO)[C@H]([C@@H]([C@H]4O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]3O)O)O)O[C@@H]([C@H]([C@@H]2O)O)COC(=O)C[C@](CC(=O)O)(O)C)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1294.58 Volume:   1219.832
?
Van der Waals volume.
Dense:   1.061 LogP:   -1.298
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.396
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.141
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The logarithm of aqueous solubility value.
Rotatable Bonds:   20.0 Rigid Bonds:   54.0
TPSA:   495.26
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Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   17.0 Rings:   9.0
Heavy Atoms:   30.0

MedChem Properties

QED Drug-Likeness Score:   0.037 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.405 Fsp3:   0.9
MCE-18:   210.737
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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:   0.666 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.165 Promiscuous compounds:   0.615

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.673 MDCK Permeability:   -5.088
Pgp-inhibitor:   0.0 Pgp-substrate:   0.007
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):   0.994
20% Bioavailability (F20%):   0.998 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.214 MRP1:   0.001
Plasma Protein Binding (PPB):   62.807% Volume Distribution (VD):   -0.309
Fu: 25.959%
?
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:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.002
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):  -0.691 Half-life (T1/2):  5.093

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.956 Drug-induced Liver Injury (DILI):  0.845
AMES Toxicity:  0.936 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.098 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.781 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.971 RPMI-8226 Immunitoxicity:  0.309
A549 Cytotoxicity:  0.519 Hek293 Cytotoxicity:  0.045
BCF:   0.409
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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:   3.21
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.96
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.766
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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
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. whole plant n.a. PMID[19290648]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota aerial parts Changqing, Shangdong Province, China 2004-JUN PMID[19290648]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27907 Dianthus versicolor Species Caryophyllaceae 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
NPT1855 Cell line HFL1 Homo sapiens IC50 = 2800.0 nM PMID[19290648]
NPT83 Cell line MCF7 Homo sapiens IC50 > 10000.0 nM PMID[19290648]
NPT65 Cell line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[19290648]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 6200.0 nM PMID[19290648]

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 NPC25663 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
0.9189 High Similarity NPC476991
0.819 Intermediate Similarity NPC305267
0.7623 Intermediate Similarity NPC51564
0.7434 Intermediate Similarity NPC69811
0.6562 Remote Similarity NPC135849
0.6303 Remote Similarity NPC64715
0.6129 Remote Similarity NPC476992
0.6016 Remote Similarity NPC283417
0.6016 Remote Similarity NPC200049
0.5878 Remote Similarity NPC21691
0.5802 Remote Similarity NPC4749
0.5776 Remote Similarity NPC475208
0.569 Remote Similarity NPC1046
0.5656 Remote Similarity NPC164389
0.563 Remote Similarity NPC480420
0.5591 Remote Similarity NPC207738
0.558 Remote Similarity NPC220160
0.5556 Remote Similarity NPC29069
0.5547 Remote Similarity NPC11242
0.5528 Remote Similarity NPC488526
0.536 Remote Similarity NPC63159
0.5351 Remote Similarity NPC48249
0.5349 Remote Similarity NPC104137
0.5349 Remote Similarity NPC26626
0.5328 Remote Similarity NPC475514
0.5324 Remote Similarity NPC302543
0.5308 Remote Similarity NPC75287
0.5299 Remote Similarity NPC470218
0.5278 Remote Similarity NPC33012
0.525 Remote Similarity NPC48499
0.5238 Remote Similarity NPC105800
0.521 Remote Similarity NPC238935
0.5208 Remote Similarity NPC8524
0.5191 Remote Similarity NPC815
0.5188 Remote Similarity NPC123522
0.5185 Remote Similarity NPC475140
0.5161 Remote Similarity NPC485563
0.5159 Remote Similarity NPC251768
0.5159 Remote Similarity NPC473459
0.5152 Remote Similarity NPC288205
0.5152 Remote Similarity NPC51465
0.5135 Remote Similarity NPC489208
0.5133 Remote Similarity NPC167383
0.5113 Remote Similarity NPC473824
0.5108 Remote Similarity NPC258617
0.5106 Remote Similarity NPC309223
0.5096 Remote Similarity NPC23020
0.5081 Remote Similarity NPC295371
0.5077 Remote Similarity NPC301449
0.5077 Remote Similarity NPC481079
0.5077 Remote Similarity NPC601290
0.5074 Remote Similarity NPC191827
0.5072 Remote Similarity NPC473386
0.5069 Remote Similarity NPC102505
0.5069 Remote Similarity NPC488514
0.5043 Remote Similarity NPC237503
0.5039 Remote Similarity NPC232237
0.5038 Remote Similarity NPC160452
0.5038 Remote Similarity NPC213952
0.5038 Remote Similarity NPC185466
0.5035 Remote Similarity NPC482010

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC25663 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