Natural Product: NPC150893

Natural Product IDNPC150893
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Symplocososide J
IUPAC Name (2S,3S,4S,5R,6R)-6-[[(3S,4aR,6aR,6bS,7R,8S,8aR,9R,10R,12aS,14aR,14bR)-9-benzoyloxy-10-[(2Z)-3,7-dimethylocta-2,6-dienoyl]oxy-7,8-dihydroxy-8a-(hydroxymethyl)-4,4,6a,6b,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-4-acetyloxy-3-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
Synonyms symplocososide J
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL502506
PubChem CID 44566493
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 FCZPZIOLLOUAGS-TYFCTVMQSA-N
Standard InCHI InChI=1S/C66H96O24/c1-31(2)16-15-17-32(3)26-42(71)86-54-55(90-57(81)34-18-13-12-14-19-34)66(30-69)36(27-61(54,5)6)35-20-21-40-63(9)24-23-41(62(7,8)39(63)22-25-64(40,10)65(35,11)52(77)53(66)78)85-60-51(89-59-47(76)45(74)43(72)37(28-67)83-59)49(82-33(4)70)48(50(88-60)56(79)80)87-58-46(75)44(73)38(29-68)84-58/h12-14,16,18-20,26,36-41,43-55,58-60,67-69,72-78H,15,17,21-25,27-30H2,1-11H3,(H,79,80)/b32-26-/t36-,37+,38-,39-,40+,41-,43+,44-,45-,46+,47+,48-,49-,50-,51+,52-,53+,54-,55-,58-,59-,60+,63-,64+,65-,66-/m0/s1
SMILES CC(=CCC/C(=CC(=O)O[C@H]1[C@@H]([C@@]2(CO)[C@@H](CC1(C)C)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)[C@H]([C@H]2O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O)OC(=O)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC(=O)c1ccccc1)/C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1272.63 Volume:   1257.684
?
Van der Waals volume.
Dense:   1.012 LogP:   2.94
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.373
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.696
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   21.0 Rigid Bonds:   55.0
TPSA:   373.88
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   11.0 Rings:   9.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.033 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.234 Fsp3:   0.758
MCE-18:   268.966
?
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:   0.971 Fluc inhibitor:   0.023
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.003
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.084 Promiscuous compounds:   0.194

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.382 MDCK Permeability:   -5.278
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):   0.013
20% Bioavailability (F20%):   0.071 30% Bioavailability (F30%):   0.933
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.122 MRP1:   0.98
Plasma Protein Binding (PPB):   74.499% Volume Distribution (VD):   -0.502
Fu: 12.928%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.005

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:   0.467 CYP3A4-substrate:   0.953
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.806
HLM stability:   0.058
?
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):  -0.142 Half-life (T1/2):  4.127

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.013
Human Hepatotoxicity (H-HT):  0.285 Drug-induced Liver Injury (DILI):  0.978
AMES Toxicity:  0.647 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.014 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.003
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.996
Hematotoxicity:  0.564 Drug-induced Nephrotoxicity:  0.985
Genotoxicity:  0.182 RPMI-8226 Immunitoxicity:  0.097
A549 Cytotoxicity:  0.931 Hek293 Cytotoxicity:  0.385
BCF:   0.14
?
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:   4.058
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.379
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.926
?
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
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota roots n.a. n.a. PMID[15620235]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota roots Nanning City, Guangxi Province, People's Republic of China 1997-Jan PMID[17190442]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8121 Symplocos chinensis Species Symplocaceae 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
NPT180 Cell line HCT-8 Homo sapiens IC50 = 2100.0 nM PMID[22440015]
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 1700.0 nM PMID[24904961]
NPT547 Cell line BGC-823 Homo sapiens IC50 = 1800.0 nM PMID[23398362]
NPT81 Cell line A549 Homo sapiens IC50 = 3000.0 nM PMID[26087936]
NPT179 Cell line A2780 Homo sapiens IC50 = 1400.0 nM PMID[26702644]

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 NPC150893 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
0.8468 Intermediate Similarity NPC329960
0.8374 Intermediate Similarity NPC475377
0.8374 Intermediate Similarity NPC476074
0.8361 Intermediate Similarity NPC262796
0.8361 Intermediate Similarity NPC45346
0.8175 Intermediate Similarity NPC295408
0.7805 Intermediate Similarity NPC264566
0.7045 Intermediate Similarity NPC484833
0.687 Remote Similarity NPC329923
0.687 Remote Similarity NPC475281
0.6742 Remote Similarity NPC475167
0.6444 Remote Similarity NPC473755
0.6434 Remote Similarity NPC329976
0.6377 Remote Similarity NPC329657
0.6107 Remote Similarity NPC477078
0.6087 Remote Similarity NPC134914
0.6 Remote Similarity NPC329993
0.5874 Remote Similarity NPC173435
0.5874 Remote Similarity NPC172374
0.5874 Remote Similarity NPC478064
0.5857 Remote Similarity NPC178264
0.5827 Remote Similarity NPC46823
0.5786 Remote Similarity NPC192765
0.5775 Remote Similarity NPC475513
0.5662 Remote Similarity NPC605294
0.563 Remote Similarity NPC477077
0.5597 Remote Similarity NPC470914
0.557 Remote Similarity NPC69425
0.5563 Remote Similarity NPC301639
0.5563 Remote Similarity NPC478065
0.5507 Remote Similarity NPC25998
0.5493 Remote Similarity NPC473918
0.5462 Remote Similarity NPC603026
0.5441 Remote Similarity NPC477075
0.5396 Remote Similarity NPC478152
0.5396 Remote Similarity NPC478151
0.5385 Remote Similarity NPC277212
0.5385 Remote Similarity NPC470912
0.5385 Remote Similarity NPC30279
0.5347 Remote Similarity NPC71391
0.5342 Remote Similarity NPC225791
0.5333 Remote Similarity NPC470913
0.5245 Remote Similarity NPC478150
0.5241 Remote Similarity NPC329828
0.5214 Remote Similarity NPC606553
0.5208 Remote Similarity NPC602995
0.5135 Remote Similarity NPC312650
0.5068 Remote Similarity NPC488308
0.5035 Remote Similarity NPC609119
0.5034 Remote Similarity NPC271610

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC150893 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