Natural Product: NPC131684

Natural Product IDNPC131684
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Triptophenolide
IUPAC Name (3bR,9bS)-6-hydroxy-9b-methyl-7-propan-2-yl-3,3b,4,5,10,11-hexahydronaphtho[2,1-e][2]benzofuran-1-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3039217
PubChem CID 173273
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001194] Oxosteroids

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 KPXIBWGPZSPABK-FXAWDEMLSA-N
Standard InCHI InChI=1S/C20H24O3/c1-11(2)12-4-6-16-14(18(12)21)5-7-17-15-10-23-19(22)13(15)8-9-20(16,17)3/h4,6,11,17,21H,5,7-10H2,1-3H3/t17-,20+/m0/s1
SMILES O=C1OCC2=C1CC[C@]1([C@H]2CCc2c1ccc(c2O)C(C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   312.17 Volume:   333.439
?
Van der Waals volume.
Dense:   0.936 LogP:   3.376
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.077
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.257
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   21.0
TPSA:   46.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.798 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.871 Fsp3:   0.55
MCE-18:   82.839
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.281 Fluc inhibitor:   0.103
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.146
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.021
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.406 Promiscuous compounds:   0.006

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.059 MDCK Permeability:   -4.716
Pgp-inhibitor:   0.968 Pgp-substrate:   0.106
PAMPA:   0.022
?
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):   0.002
20% Bioavailability (F20%):   0.389 30% Bioavailability (F30%):   0.667
50% Bioavailability (F50%):   0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.05 MRP1:   0.94
Plasma Protein Binding (PPB):   98.329% Volume Distribution (VD):   0.218
Fu: 2.022%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.316
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.989 CYP1A2-substrate:   0.134
CYP2C19-inhibitor:   0.992 CYP2C19-substrate:   0.117
CYP2C9-inhibitor:   0.981 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.101 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   0.563
CYP2B6-substrate:   0.963 CYP2C8-inhibitor:   0.853
HLM stability:   0.998
?
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):  6.775 Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.074 hERG Blockers (10um):  0.443
Human Hepatotoxicity (H-HT):  0.89 Drug-induced Liver Injury (DILI):  0.442
AMES Toxicity:  0.789 Rat Oral Acute Toxicity:  0.797
Maximum Recommended Daily Dose:  0.954 Skin Sensitization:  0.985
Carcinogencity:  0.961 Eye Corrosion:  0.0
Eye Irritation:  0.268 Respiratory Toxicity:  0.625
Drug-induced Neurotoxicity:  0.111 Ototoxicity:  0.853
Hematotoxicity:  0.777 Drug-induced Nephrotoxicity:  0.944
Genotoxicity:  0.835 RPMI-8226 Immunitoxicity:  0.268
A549 Cytotoxicity:  0.671 Hek293 Cytotoxicity:  0.746
BCF:   2.141
?
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:   4.795
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.176
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.779
?
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
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(90)85349-K]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. DOI[10.1016/S0040-4039(99)00339-1]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. DOI[10.1186/1471-2202-6-1]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[10579865]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. leaf n.a. PMID[10716597]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. PMID[10746886]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. PMID[10757718]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[10757718]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota root bark Kunming, Yunnan, China n.a. PMID[10757718]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[10757718]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11374948]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11561442]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[12579877]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[1375626]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[1375626]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[1602302]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[1602302]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[16864458]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota roots n.a. n.a. PMID[16989518]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[17250858]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[17265278]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. leaf n.a. PMID[1823717]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[1823717]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[18554602]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. bark n.a. PMID[18996177]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. bark n.a. PMID[20167482]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[21486005]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota root n.a. n.a. PMID[21486005]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[21514608]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota dried roots purchased from Sichuan Neautus Traditional Chinese Medicine Co. Ltd. (Chengdu, P.R. China) n.a. PMID[22148431]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. PMID[22256754]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[22256754]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. PMID[23252270]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota leaves n.a. n.a. PMID[23268606]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[23852638]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[24549173]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[24963543]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[25237706]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. bark n.a. PMID[2534610]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[2534610]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. stem n.a. PMID[27113553]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. root n.a. PMID[2801129]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. PMID[2816380]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota Leaves n.a. n.a. PMID[29355322]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota Leaves n.a. n.a. PMID[31556299]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Europe PMC[535601]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[7102323]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[7304185]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[8328267]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[8699928]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[8722541]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. root n.a. Database[Article]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. root n.a. Database[Article]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. leaf n.a. Database[Article]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[Phytochemistry, 2000, 53, 715-722.]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota root bark Kunming, Yunnan, China n.a. Database[Title]
NPO1152 Tripterygium hypoglaucum Species Celastraceae Eukaryota root bark n.a. n.a. Database[Title]
NPO2348 Tripterygium regelii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13661 Tripterygium wilfordii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1152 Tripterygium hypoglaucum Species Celastraceae 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
NPT153 Individual protein Androgen Receptor Homo sapiens FC = 3.0 n.a. PMID[27994731]
NPT299 Individual protein Androgen Receptor Rattus norvegicus IC50 = 467.0 nM PMID[27994731]
NPT153 Individual protein Androgen Receptor Homo sapiens IC50 = 260.0 nM PMID[27994731]
NPT153 Individual protein Androgen Receptor Homo sapiens IC50 = 388.0 nM PMID[27994731]
NPT153 Individual protein Androgen Receptor Homo sapiens IC50 = 480.0 nM PMID[27994731]
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 110.8 % PMID[23571415]
NPT73 Individual protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 120.27 % PMID[23571415]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1872 Cell line Bcap37 Homo sapiens IC50 = 22400.0 nM PMID[27133593]
NPT65 Cell line HepG2 Homo sapiens IC50 = 17010.0 nM PMID[27133593]
NPT380 Cell line U-251 Homo sapiens IC50 > 100000.0 nM PMID[27133593]
NPT83 Cell line MCF7 Homo sapiens IC50 > 100000.0 nM PMID[27133593]
NPT81 Cell line A549 Homo sapiens IC50 = 42880.0 nM PMID[27133593]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 > 100000.0 nM PMID[28011223]
NPT306 Cell line PC-3 Homo sapiens IC50 > 100000.0 nM PMID[28011223]
NPT81 Cell line A549 Homo sapiens IC50 > 100000.0 nM PMID[28011223]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 22210.0 nM PMID[27133593]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 50.0 ug.mL-1 PMID[29153424]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 75.0 ug.mL-1 PMID[29153424]
NPT19 Organism Escherichia coli Escherichia coli MIC = 100.0 ug.mL-1 PMID[29153424]
NPT1209 Organism Pseudomonas fluorescens Pseudomonas fluorescens MIC = 75.0 ug.mL-1 PMID[29153424]

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 NPC131684 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
0.6154 Remote Similarity NPC481013
0.6061 Remote Similarity NPC481014
0.6 Remote Similarity NPC481012

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC131684 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