Natural Product: NPC473256

Natural Product IDNPC473256
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
IFECWTDQYRRRPG-SQURXFQPSA-N
IUPAC Name n.a.
Synonyms 17-Alpha-Hydroxywithanolide D
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL388053
PubChem CID 44423097
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003569] Pregnane steroids

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 IFECWTDQYRRRPG-SQURXFQPSA-N
Standard InCHI InChI=1S/C28H40O7/c1-14-12-21(34-23(31)15(14)2)26(5,32)27(33)11-9-17-16-13-22-28(35-22)20(30)7-6-19(29)25(28,4)18(16)8-10-24(17,27)3/h6-7,16-18,20-23,30-33H,8-13H2,1-5H3/t16-,17-,18-,20-,21+,22+,23?,24-,25-,26-,27+,28+/m0/s1
SMILES CC1=C(C(OC(C1)C(C)(C2(CCC3C2(CCC4C3CC5C6(C4(C(=O)C=CC6O)C)O5)C)O)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   488.28 Volume:   495.128
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Van der Waals volume.
Dense:   0.986 LogP:   1.861
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.431
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.626
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   29.0
TPSA:   119.75
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Topological Polar Surface Area.
H-Bond Acceptor:   7.0
H-Bond Donor:   4.0 Rings:   6.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.348 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.113 Fsp3:   0.821
MCE-18:   157.667
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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:   0.041 Fluc inhibitor:   0.037
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.013
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.234
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.149 Promiscuous compounds:   0.003

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.901 MDCK Permeability:   -4.683
Pgp-inhibitor:   0.001 Pgp-substrate:   0.741
PAMPA:   0.958
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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):   0.142
20% Bioavailability (F20%):   0.168 30% Bioavailability (F30%):   0.454
50% Bioavailability (F50%):   0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.923 MRP1:   0.994
Plasma Protein Binding (PPB):   90.806% Volume Distribution (VD):   0.144
Fu: 8.799%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.004
OATP1B3 inhibitor:   0.414 BCRP inhibitor:   0.007
BSEP inhibitor:   0.752

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.929 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.358 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.175 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.118 CYP2C8-inhibitor:   0.007
HLM stability:   0.248
?
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):  5.423 Half-life (T1/2):  2.872

ADMET: Toxicity

hERG Blockers:  0.12 hERG Blockers (10um):  0.343
Human Hepatotoxicity (H-HT):  0.663 Drug-induced Liver Injury (DILI):  0.235
AMES Toxicity:  0.537 Rat Oral Acute Toxicity:  0.574
Maximum Recommended Daily Dose:  0.838 Skin Sensitization:  0.274
Carcinogencity:  0.441 Eye Corrosion:  0.0
Eye Irritation:  0.003 Respiratory Toxicity:  0.664
Drug-induced Neurotoxicity:  0.381 Ototoxicity:  0.893
Hematotoxicity:  0.13 Drug-induced Nephrotoxicity:  0.085
Genotoxicity:  0.847 RPMI-8226 Immunitoxicity:  0.113
A549 Cytotoxicity:  0.157 Hek293 Cytotoxicity:  0.547
BCF:   0.853
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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:   3.885
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.747
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.515
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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
NPO28641 Tubocapsicum anomalum Species Solanaceae Eukaryota stems, roots, and leaves Da-Han Mountain, Kaohsiung, Taiwan 2004-OCT PMID[17417907]
NPO28641 Tubocapsicum anomalum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17417907]
NPO28641 Tubocapsicum anomalum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28641 Tubocapsicum anomalum 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens IC50 = 0.49 ug.mL-1 PMID[18077363]
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.45 ug.mL-1 PMID[8786363]
NPT81 Cell line A549 Homo sapiens IC50 = 0.72 ug.mL-1 PubChem BioAssay data set
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 0.71 ug.mL-1 DOI[10.1039/C1MD00022E]
NPT171 Cell line MRC5 Homo sapiens IC50 = 1.89 ug.mL-1 PMID[11000021]

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 NPC473256 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
0.7397 Intermediate Similarity NPC470878
0.7162 Intermediate Similarity NPC329736
0.7162 Intermediate Similarity NPC599946
0.7027 Intermediate Similarity NPC473274
0.6125 Remote Similarity NPC264954
0.5802 Remote Similarity NPC473253
0.575 Remote Similarity NPC125794
0.575 Remote Similarity NPC171401
0.575 Remote Similarity NPC609580
0.561 Remote Similarity NPC153700
0.5542 Remote Similarity NPC67569
0.5422 Remote Similarity NPC329671
0.5375 Remote Similarity NPC286528
0.5349 Remote Similarity NPC23786
0.5244 Remote Similarity NPC140055
0.5244 Remote Similarity NPC167606
0.5233 Remote Similarity NPC470880
0.5119 Remote Similarity NPC88326
0.5119 Remote Similarity NPC183580
0.5119 Remote Similarity NPC474370
0.506 Remote Similarity NPC270929
0.5057 Remote Similarity NPC470494

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473256 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
0.5244 Remote Similarity NPD7115 Discovery

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