Natural Product: NPC107811

Natural Product IDNPC107811
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
LTOOLRVQEJDNFR-DLMAKPSPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968863
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal 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 LTOOLRVQEJDNFR-DLMAKPSPSA-N
Standard InCHI InChI=1S/C50H84O23/c1-20(66-44-39(61)36(58)34(56)29(16-51)68-44)8-13-50(64-5)21(2)32-28(73-50)15-26-24-7-6-22-14-23(9-11-48(22,3)25(24)10-12-49(26,32)4)67-45-41(63)38(60)42(31(18-53)70-45)71-47-43(33(55)27(54)19-65-47)72-46-40(62)37(59)35(57)30(17-52)69-46/h20-47,51-63H,6-19H2,1-5H3/t20?,21?,22?,23?,24?,25?,26?,27-,28?,29-,30-,31-,32?,33+,34-,35-,36+,37+,38-,39-,40-,41-,42-,43-,44-,45-,46+,47+,48?,49?,50?/m1/s1
SMILES CC(CCC1(C(C)C2C(CC3C4CCC5CC(CCC5(C)C4CCC23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)O)O1)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1052.54 Volume:   998.523
?
Van der Waals volume.
Dense:   1.054 LogP:   0.22
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.964
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.381
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   48.0
TPSA:   355.29
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   13.0 Rings:   9.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.073 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.806 Fsp3:   1.0
MCE-18:   177.92
?
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:   0.411 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.009
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.299 Promiscuous compounds:   0.003

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.508 MDCK Permeability:   -4.984
Pgp-inhibitor:   0.0 Pgp-substrate:   0.22
PAMPA:   0.987
?
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):   0.873
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.984
50% Bioavailability (F50%):   0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.606 MRP1:   0.72
Plasma Protein Binding (PPB):   34.006% Volume Distribution (VD):   -0.473
Fu: 51.746%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.911
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.003 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:   0.003
HLM stability:   0.039
?
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):  -0.28 Half-life (T1/2):  5.207

ADMET: Toxicity

hERG Blockers:  0.006 hERG Blockers (10um):  0.009
Human Hepatotoxicity (H-HT):  0.798 Drug-induced Liver Injury (DILI):  0.908
AMES Toxicity:  0.977 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.006 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.296 Drug-induced Nephrotoxicity:  0.743
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.26
A549 Cytotoxicity:  0.938 Hek293 Cytotoxicity:  0.656
BCF:   1.717
?
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:   3.899
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.285
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.345
?
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
NPO6867 Asparagus curillus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6867 Asparagus curillus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6867 Asparagus curillus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6867 Asparagus curillus Species Asparagaceae 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

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 NPC107811 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
0.7396 Intermediate Similarity NPC107962
0.7204 Intermediate Similarity NPC325828
0.7143 Intermediate Similarity NPC116756
0.7009 Intermediate Similarity NPC470864
0.7 Intermediate Similarity NPC470866
0.6857 Remote Similarity NPC97700
0.6857 Remote Similarity NPC30856
0.6822 Remote Similarity NPC475625
0.6804 Remote Similarity NPC250393
0.6727 Remote Similarity NPC132080
0.6698 Remote Similarity NPC184617
0.6495 Remote Similarity NPC297348
0.6495 Remote Similarity NPC249204
0.6495 Remote Similarity NPC48339
0.6495 Remote Similarity NPC141769
0.6495 Remote Similarity NPC477547
0.6455 Remote Similarity NPC232037
0.6337 Remote Similarity NPC211354
0.6337 Remote Similarity NPC107188
0.6321 Remote Similarity NPC475643
0.6311 Remote Similarity NPC6295
0.6263 Remote Similarity NPC234352
0.6262 Remote Similarity NPC92890
0.62 Remote Similarity NPC477451
0.6132 Remote Similarity NPC475351
0.6078 Remote Similarity NPC206003
0.6078 Remote Similarity NPC473610
0.6038 Remote Similarity NPC160426
0.6019 Remote Similarity NPC19400
0.6018 Remote Similarity NPC232611
0.6 Remote Similarity NPC128572
0.6 Remote Similarity NPC177834
0.5913 Remote Similarity NPC470862
0.5909 Remote Similarity NPC51172
0.5909 Remote Similarity NPC49032
0.5862 Remote Similarity NPC233433
0.5849 Remote Similarity NPC125324
0.5818 Remote Similarity NPC477809
0.5785 Remote Similarity NPC220836
0.5766 Remote Similarity NPC471464
0.5752 Remote Similarity NPC115165
0.5714 Remote Similarity NPC470867
0.5641 Remote Similarity NPC476112
0.5641 Remote Similarity NPC307534
0.5537 Remote Similarity NPC94086
0.5537 Remote Similarity NPC473817
0.5526 Remote Similarity NPC98018
0.5526 Remote Similarity NPC284104
0.5526 Remote Similarity NPC103616
0.5508 Remote Similarity NPC83137
0.5481 Remote Similarity NPC294686
0.5462 Remote Similarity NPC84111
0.5462 Remote Similarity NPC287483
0.5462 Remote Similarity NPC470865
0.5431 Remote Similarity NPC470863
0.5372 Remote Similarity NPC232054
0.5364 Remote Similarity NPC195297
0.5351 Remote Similarity NPC6806
0.534 Remote Similarity NPC485594
0.5339 Remote Similarity NPC194207
0.5339 Remote Similarity NPC22779
0.5328 Remote Similarity NPC262050
0.5299 Remote Similarity NPC475550
0.5278 Remote Similarity NPC54619
0.5273 Remote Similarity NPC470432
0.5273 Remote Similarity NPC230507
0.5273 Remote Similarity NPC485595
0.5254 Remote Similarity NPC473518
0.5234 Remote Similarity NPC263359
0.5234 Remote Similarity NPC222731
0.5221 Remote Similarity NPC473601
0.5214 Remote Similarity NPC475319
0.5189 Remote Similarity NPC291203
0.5189 Remote Similarity NPC217205
0.5185 Remote Similarity NPC121453
0.5089 Remote Similarity NPC70204
0.5082 Remote Similarity NPC477811
0.5045 Remote Similarity NPC215408
0.5043 Remote Similarity NPC480555
0.5043 Remote Similarity NPC151134
0.5043 Remote Similarity NPC150372
0.5041 Remote Similarity NPC108072
0.5041 Remote Similarity NPC31896
0.5037 Remote Similarity NPC329807
0.5036 Remote Similarity NPC481189

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC107811 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
0.7204 Intermediate Similarity NPD8171 Phase 2
0.6154 Remote Similarity NPD8170 Phase 2

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