Natural Product: NPC198325

Natural Product IDNPC198325
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
HZKLFYZYQUFAMX-IJFIWZGTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL508270
PubChem CID 44567201
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 HZKLFYZYQUFAMX-IJFIWZGTSA-N
Standard InCHI InChI=1S/C55H82O25/c1-20-17-70-55(48(67)42(20)77-50-41(66)39(64)37(62)22(3)71-50)21(2)36-34(80-55)16-31-29-11-10-27-14-28(59)15-35(54(27,9)30(29)12-13-53(31,36)8)76-51-46(44(33(61)19-69-51)78-49-40(65)38(63)32(60)18-68-49)79-52-47(75-26(7)58)45(74-25(6)57)43(23(4)72-52)73-24(5)56/h10,21-23,28-52,59-67H,1,11-19H2,2-9H3/t21-,22+,23-,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-/m0/s1
SMILES CC(=O)O[C@H]1[C@H](O[C@H]2[C@@H](OC[C@@H]([C@@H]2O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)O)O[C@@H]2C[C@H](O)CC3=CC[C@@H]4[C@@H]([C@@]23C)CC[C@]2([C@H]4C[C@H]3[C@@H]2[C@H](C)[C@@]2(O3)OCC(=C)[C@@H]([C@@H]2O)O[C@@H]2O[C@H](C)[C@@H]([C@@H]([C@H]2O)O)O)C)O[C@H]([C@@H]([C@H]1OC(=O)C)OC(=O)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1142.51 Volume:   1080.844
?
Van der Waals volume.
Dense:   1.057 LogP:   1.51
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.238
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.964
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   58.0
TPSA:   353.27
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   9.0 Rings:   10.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.067 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.652 Fsp3:   0.873
MCE-18:   271.922
?
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:   0.799 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
?
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:   0.343 Promiscuous compounds:   0.298

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.8 MDCK Permeability:   -5.445
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
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):   0.001
20% Bioavailability (F20%):   0.04 30% Bioavailability (F30%):   0.985
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.154
Plasma Protein Binding (PPB):   35.222% Volume Distribution (VD):   -0.602
Fu: 47.27%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.199
BSEP inhibitor:   0.016

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:   0.001
CYP3A4-inhibitor:   0.855 CYP3A4-substrate:   0.986
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.922
HLM stability:   0.087
?
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):  -0.148 Half-life (T1/2):  3.189

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.015
Human Hepatotoxicity (H-HT):  0.533 Drug-induced Liver Injury (DILI):  0.988
AMES Toxicity:  0.891 Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.029 Skin Sensitization:  1.0
Carcinogencity:  0.001 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.002
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.735 Drug-induced Nephrotoxicity:  0.965
Genotoxicity:  0.024 RPMI-8226 Immunitoxicity:  0.658
A549 Cytotoxicity:  0.495 Hek293 Cytotoxicity:  0.537
BCF:   0.328
?
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:   3.456
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.475
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.292
?
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
NPO8452 Dracaena angustifolia Species Asparagaceae Eukaryota roots and rhizomes n.a. n.a. PMID[11575942]
NPO8452 Dracaena angustifolia Species Asparagaceae Eukaryota stems Xishuangbanna, Yunnan, China 2005-JUL PMID[20718450]
NPO8452 Dracaena angustifolia Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8452 Dracaena angustifolia 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
NPT453 Cell line HT-1080 Homo sapiens IC50 = 600.0 nM PMID[23398362]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 22100.0 nM PMID[11575942]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 11900.0 nM PMID[11575942]

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 NPC198325 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
0.8919 High Similarity NPC207243
0.8839 High Similarity NPC233391
0.844 Intermediate Similarity NPC229962
0.8036 Intermediate Similarity NPC50689
0.768 Intermediate Similarity NPC202261
0.75 Intermediate Similarity NPC479532
0.7478 Intermediate Similarity NPC195560
0.7431 Intermediate Similarity NPC11548
0.7209 Intermediate Similarity NPC106589
0.6957 Remote Similarity NPC475247
0.6957 Remote Similarity NPC294129
0.6694 Remote Similarity NPC43842
0.6667 Remote Similarity NPC295133
0.6325 Remote Similarity NPC476085
0.6212 Remote Similarity NPC257207
0.6154 Remote Similarity NPC51154
0.5882 Remote Similarity NPC112274
0.5772 Remote Similarity NPC160888
0.5714 Remote Similarity NPC70204
0.5714 Remote Similarity NPC475670
0.5691 Remote Similarity NPC473633
0.5614 Remote Similarity NPC13190
0.5528 Remote Similarity NPC475403
0.525 Remote Similarity NPC306131
0.525 Remote Similarity NPC200802
0.5167 Remote Similarity NPC476540
0.5167 Remote Similarity NPC476541
0.5124 Remote Similarity NPC475431
0.5115 Remote Similarity NPC475487
0.5111 Remote Similarity NPC475357

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC198325 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