Natural Product: NPC190286

Natural Product IDNPC190286
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Withanolide G
IUPAC Name (2R)-2-[(1R)-1-hydroxy-1-[(8R,9S,10R,13R,14R,17S)-14-hydroxy-10,13-dimethyl-1-oxo-7,8,9,11,12,15,16,17-octahydro-4H-cyclopenta[a]phenanthren-17-yl]ethyl]-4,5-dimethyl-2,3-dihydropyran-6-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2333678
PubChem CID 21679023
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001560] Withanolides and derivatives

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 ZRJOVYPUBHQEES-HZRISEJCSA-N
Standard InCHI InChI=1S/C28H38O5/c1-16-15-23(33-24(30)17(16)2)27(5,31)21-12-14-28(32)20-10-9-18-7-6-8-22(29)26(18,4)19(20)11-13-25(21,28)3/h6,8-9,19-21,23,31-32H,7,10-15H2,1-5H3/t19-,20+,21-,23+,25+,26-,27+,28+/m0/s1
SMILES CC1=C(C)C(=O)O[C@H](C1)[C@@](C)([C@H]1CC[C@]2([C@@H]3CC=C4CC=CC(=O)[C@]4(C)[C@H]3CC[C@]12C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   454.27 Volume:   480.831
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Van der Waals volume.
Dense:   0.945 LogP:   1.79
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.203
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.686
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   28.0
TPSA:   83.83
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Topological Polar Surface Area.
H-Bond Acceptor:   5.0
H-Bond Donor:   2.0 Rings:   5.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.476 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.151 Fsp3:   0.714
MCE-18:   93.0
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.521 Fluc inhibitor:   0.122
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.008
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.469 Promiscuous compounds:   0.33

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.751 MDCK Permeability:   -4.679
Pgp-inhibitor:   0.042 Pgp-substrate:   0.105
PAMPA:   0.831
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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):   0.006
20% Bioavailability (F20%):   0.238 30% Bioavailability (F30%):   0.435
50% Bioavailability (F50%):   0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.634 MRP1:   0.87
Plasma Protein Binding (PPB):   96.653% Volume Distribution (VD):   0.151
Fu: 3.137%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.374
BSEP inhibitor:   0.997

ADMET: Metabolism

CYP1A2-inhibitor:   0.999 CYP1A2-substrate:   0.422
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.959 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.866 CYP2D6-substrate:   0.033
CYP3A4-inhibitor:   0.365 CYP3A4-substrate:   0.989
CYP2B6-substrate:   0.002 CYP2C8-inhibitor:   0.999
HLM stability:   0.992
?
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):  6.507 Half-life (T1/2):  2.126

ADMET: Toxicity

hERG Blockers:  0.032 hERG Blockers (10um):  0.133
Human Hepatotoxicity (H-HT):  0.718 Drug-induced Liver Injury (DILI):  0.279
AMES Toxicity:  0.294 Rat Oral Acute Toxicity:  0.337
Maximum Recommended Daily Dose:  0.648 Skin Sensitization:  0.994
Carcinogencity:  0.91 Eye Corrosion:  0.014
Eye Irritation:  0.604 Respiratory Toxicity:  0.425
Drug-induced Neurotoxicity:  0.134 Ototoxicity:  0.306
Hematotoxicity:  0.259 Drug-induced Nephrotoxicity:  0.74
Genotoxicity:  0.873 RPMI-8226 Immunitoxicity:  0.094
A549 Cytotoxicity:  0.186 Hek293 Cytotoxicity:  0.516
BCF:   0.811
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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:   3.473
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.064
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.438
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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
NPO13927 Withania coagulans Species Solanaceae Eukaryota fruits n.a. n.a. PMID[18952419]
NPO13927 Withania coagulans Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23316950]
NPO13927 Withania coagulans Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13927 Withania coagulans Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13927 Withania coagulans Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13927 Withania coagulans Species Solanaceae 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
NPT2601 Individual protein NF-kappaB inhibitor alpha Homo sapiens IC50 > 50000.0 nM PMID[18302334]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus IC50 = 37500.0 nM PMID[23398362]
NPT113 Cell line RAW264.7 Mus musculus Inhibition = 88.5 % PMID[17428663]
NPT2 Others Unspecified n.a. IC50 = 12300.0 nM PMID[16933872]
NPT2 Others Unspecified n.a. Inhibition = 86.9 % PubChem BioAssay data set
NPT2 Others Unspecified n.a. IC50 = 20700.0 nM PMID[20349977]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT71 Cell line HEK293 Homo sapiens Survival = 71.9 % PMID[10560729]
NPT113 Cell line RAW264.7 Mus musculus Survival = 100.0 % PMID[19114678]





 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 NPC190286 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
0.8769 High Similarity NPC46570
0.7246 Intermediate Similarity NPC153440
0.6901 Remote Similarity NPC176840
0.6579 Remote Similarity NPC5292
0.6351 Remote Similarity NPC79579
0.6351 Remote Similarity NPC107493
0.6267 Remote Similarity NPC103045
0.5875 Remote Similarity NPC484717
0.5844 Remote Similarity NPC29133
0.5802 Remote Similarity NPC484718
0.5789 Remote Similarity NPC486565
0.5714 Remote Similarity NPC191620
0.5584 Remote Similarity NPC484742
0.5385 Remote Similarity NPC225826
0.5185 Remote Similarity NPC470961
0.5176 Remote Similarity NPC484725
0.5062 Remote Similarity NPC44428
0.5062 Remote Similarity NPC78691
0.506 Remote Similarity NPC474585

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC190286 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