Natural Product: NPC70230

Natural Product IDNPC70230
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
FAFUWLJMHOPRJO-DPAIGORZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101337437
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 FAFUWLJMHOPRJO-DPAIGORZSA-N
Standard InCHI InChI=1S/C50H82O22/c1-20(19-64-44-39(60)37(58)34(55)29(16-51)67-44)8-13-50(63)21(2)32-28(72-50)15-27-25-7-6-23-14-24(9-11-48(23,4)26(25)10-12-49(27,32)5)66-47-43(71-45-40(61)36(57)33(54)22(3)65-45)41(62)42(31(18-53)69-47)70-46-38(59)35(56)30(17-52)68-46/h6,20-22,24-47,51-63H,7-19H2,1-5H3/t20-,21-,22-,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?/m0/s1
SMILES C[C@@H](CCC1([C@@H](C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@H]([C@H](CO)O2)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1034.53 Volume:   987.096
?
Van der Waals volume.
Dense:   1.048 LogP:   0.641
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.55
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.222
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The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   47.0
TPSA:   346.06
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Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   13.0 Rings:   9.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.076 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.719 Fsp3:   0.96
MCE-18:   175.02
?
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:   0.599 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:   0.002
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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:   0.319 Promiscuous compounds:   0.038

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.926 MDCK Permeability:   -4.915
Pgp-inhibitor:   0.0 Pgp-substrate:   0.89
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):   0.676
20% Bioavailability (F20%):   0.24 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.003
Plasma Protein Binding (PPB):   48.846% Volume Distribution (VD):   -0.357
Fu: 33.221%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.023
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:   0.985 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.714
HLM stability:   0.105
?
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):  -0.233 Half-life (T1/2):  3.326

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.022
Human Hepatotoxicity (H-HT):  0.48 Drug-induced Liver Injury (DILI):  0.918
AMES Toxicity:  0.95 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.012 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.371 Drug-induced Nephrotoxicity:  0.777
Genotoxicity:  0.011 RPMI-8226 Immunitoxicity:  0.235
A549 Cytotoxicity:  0.872 Hek293 Cytotoxicity:  0.432
BCF:   1.367
?
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:   3.439
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.764
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.845
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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
NPO27472 Daiswa polyphylla Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27472 Daiswa polyphylla Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27472 Daiswa polyphylla Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27472 Daiswa polyphylla Species Melanthiaceae 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 NPC70230 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
1.0 High Similarity NPC247037
0.9785 High Similarity NPC73243
0.9785 High Similarity NPC244086
0.9785 High Similarity NPC84956
0.9388 High Similarity NPC23808
0.9388 High Similarity NPC87998
0.9286 High Similarity NPC249265
0.8454 Intermediate Similarity NPC98696
0.8218 Intermediate Similarity NPC102016
0.8218 Intermediate Similarity NPC95051
0.783 Intermediate Similarity NPC218571
0.783 Intermediate Similarity NPC487615
0.7767 Intermediate Similarity NPC475182
0.757 Intermediate Similarity NPC194207
0.757 Intermediate Similarity NPC22779
0.757 Intermediate Similarity NPC254255
0.7383 Intermediate Similarity NPC486386
0.7297 Intermediate Similarity NPC308140
0.7264 Intermediate Similarity NPC480555
0.7264 Intermediate Similarity NPC150372
0.7232 Intermediate Similarity NPC232054
0.7157 Intermediate Similarity NPC94272
0.6981 Remote Similarity NPC470433
0.6981 Remote Similarity NPC46190
0.6981 Remote Similarity NPC171073
0.6847 Remote Similarity NPC475333
0.6847 Remote Similarity NPC224098
0.6847 Remote Similarity NPC208383
0.6757 Remote Similarity NPC269297
0.6757 Remote Similarity NPC222202
0.6754 Remote Similarity NPC480553
0.6606 Remote Similarity NPC248746
0.6606 Remote Similarity NPC122819
0.6579 Remote Similarity NPC480554
0.6538 Remote Similarity NPC476538
0.6538 Remote Similarity NPC476539
0.6471 Remote Similarity NPC480556
0.6415 Remote Similarity NPC485601
0.6396 Remote Similarity NPC42171
0.6311 Remote Similarity NPC291203
0.6311 Remote Similarity NPC217205
0.6281 Remote Similarity NPC224314
0.6271 Remote Similarity NPC287885
0.6261 Remote Similarity NPC13193
0.6261 Remote Similarity NPC309278
0.625 Remote Similarity NPC6806
0.6214 Remote Similarity NPC485602
0.6176 Remote Similarity NPC165439
0.6091 Remote Similarity NPC113044
0.6091 Remote Similarity NPC283829
0.6091 Remote Similarity NPC161676
0.5982 Remote Similarity NPC486388
0.5965 Remote Similarity NPC300557
0.5965 Remote Similarity NPC124677
0.5909 Remote Similarity NPC470432
0.5909 Remote Similarity NPC230507
0.5909 Remote Similarity NPC306991
0.5877 Remote Similarity NPC477809
0.5862 Remote Similarity NPC98018
0.5862 Remote Similarity NPC284104
0.5862 Remote Similarity NPC103616
0.5847 Remote Similarity NPC32361
0.5825 Remote Similarity NPC485600
0.5804 Remote Similarity NPC305423
0.5789 Remote Similarity NPC265275
0.5789 Remote Similarity NPC602423
0.5763 Remote Similarity NPC470863
0.5714 Remote Similarity NPC477808
0.5688 Remote Similarity NPC476540
0.5688 Remote Similarity NPC476541
0.5641 Remote Similarity NPC150057
0.5641 Remote Similarity NPC147753
0.5625 Remote Similarity NPC15249
0.5625 Remote Similarity NPC25455
0.5625 Remote Similarity NPC6295
0.5528 Remote Similarity NPC84111
0.5528 Remote Similarity NPC287483
0.5528 Remote Similarity NPC470865
0.5514 Remote Similarity NPC181845
0.5417 Remote Similarity NPC51520
0.5417 Remote Similarity NPC303069
0.5391 Remote Similarity NPC470748
0.5391 Remote Similarity NPC14704
0.5372 Remote Similarity NPC475550
0.5357 Remote Similarity NPC19400
0.5328 Remote Similarity NPC470861
0.528 Remote Similarity NPC477811
0.5217 Remote Similarity NPC485595
0.52 Remote Similarity NPC486384
0.5185 Remote Similarity NPC486114
0.5169 Remote Similarity NPC40440
0.5159 Remote Similarity NPC92297
0.513 Remote Similarity NPC295980
0.5045 Remote Similarity NPC272015
0.5043 Remote Similarity NPC195297
0.5041 Remote Similarity NPC249553

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC70230 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
0.6606 Remote Similarity NPD8449 Approved
0.5641 Remote Similarity NPD8450 Suspended

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