Natural Product: NPC478824

Natural Product IDNPC478824
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YWHKEVIZIAGDJH-IEJCCLIMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44445351
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 YWHKEVIZIAGDJH-IEJCCLIMSA-N
Standard InCHI InChI=1S/C64H102O33/c1-24-34(70)40(76)47(95-50-44(80)41(77)45(25(2)89-50)93-53-46(94-51-42(78)38(74)35(71)29(18-65)90-51)37(73)31(20-86-53)92-55-48(81)64(85,22-68)23-87-55)54(88-24)97-57(84)62-13-12-58(3,4)16-27(62)26-8-9-32-59(5)17-28(69)49(96-52-43(79)39(75)36(72)30(19-66)91-52)61(7,56(82)83)33(59)10-11-60(32,6)63(26,21-67)15-14-62/h8,24-25,27-55,65-81,85H,9-23H2,1-7H3,(H,82,83)/t24-,25+,27?,28-,29-,30+,31+,32?,33+,34+,35+,36+,37-,38+,39-,40+,41+,42-,43+,44-,45+,46+,47-,48-,49-,50+,51+,52-,53-,54+,55-,59+,60+,61-,62-,63-,64+/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)OC(=O)[C@@]12CCC(C)(C)CC2C2=CCC3[C@@]4(C)C[C@@H]([C@@H]([C@](C)([C@@H]4CC[C@@]3(C)[C@@]2(CC1)CO)C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O[C@@H]1[C@H]([C@H]([C@@H]([C@@H](C)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O[C@H]1[C@@H]([C@@](CO)(CO1)O)O)O)O[C@@H]1[C@H]([C@@H]([C@@H]([C@H](CO)O1)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1398.63 Volume:   1303.547
?
Van der Waals volume.
Dense:   1.073 LogP:   -1.072
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.195
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.193
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The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   63.0
TPSA:   529.27
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Topological Polar Surface Area.
H-Bond Acceptor:   33.0
H-Bond Donor:   19.0 Rings:   11.0
Heavy Atoms:   33.0

MedChem Properties

QED Drug-Likeness Score:   0.037 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.933 Fsp3:   0.938
MCE-18:   245.548
?
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:   0.647 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.043
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.368 Promiscuous compounds:   0.357

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.743 MDCK Permeability:   -4.693
Pgp-inhibitor:   0.0 Pgp-substrate:   0.829
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):   0.998
20% Bioavailability (F20%):   0.654 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.071
Plasma Protein Binding (PPB):   64.331% Volume Distribution (VD):   -0.329
Fu: 22.523%
?
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:   0.082
HLM stability:   0.002
?
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):  -1.582 Half-life (T1/2):  5.313

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.818 Drug-induced Liver Injury (DILI):  0.917
AMES Toxicity:  0.977 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.01 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.55 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.317 RPMI-8226 Immunitoxicity:  0.376
A549 Cytotoxicity:  0.953 Hek293 Cytotoxicity:  0.291
BCF:   0.472
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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:   3.435
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.297
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.007
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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
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota Roots n.a. n.a. PMID[17927264]
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7712 Nylandtia spinosa Species Polygalaceae 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
NPT393 Cell line HCT-116 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17927264]
NPT139 Cell line HT-29 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17927264]

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 NPC478824 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
0.8374 Intermediate Similarity NPC478825
0.7778 Intermediate Similarity NPC478823
0.7769 Intermediate Similarity NPC478822
0.6977 Remote Similarity NPC484942
0.6615 Remote Similarity NPC487505
0.6565 Remote Similarity NPC484943
0.5852 Remote Similarity NPC191827
0.5789 Remote Similarity NPC300419
0.5758 Remote Similarity NPC75287
0.5683 Remote Similarity NPC473645
0.5563 Remote Similarity NPC135849
0.5373 Remote Similarity NPC488564
0.5368 Remote Similarity NPC213952
0.5303 Remote Similarity NPC609763
0.5285 Remote Similarity NPC209894
0.5252 Remote Similarity NPC475899
0.5214 Remote Similarity NPC257211
0.5172 Remote Similarity NPC65105
0.5102 Remote Similarity NPC144644
0.5102 Remote Similarity NPC37860
0.5102 Remote Similarity NPC170407
0.5074 Remote Similarity NPC481079
0.5069 Remote Similarity NPC57484
0.5068 Remote Similarity NPC43550
0.5067 Remote Similarity NPC68767
0.5067 Remote Similarity NPC293031
0.5034 Remote Similarity NPC480418
0.5034 Remote Similarity NPC51564

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478824 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