Natural Product: NPC16701

Natural Product IDNPC16701
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
KWAUEUQHUYWWTO-CBFFWNJESA-N
IUPAC Name n.a.
Synonyms 6Alpha-Hydroxycinobufagin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL515220
PubChem CID 10939450
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001557] Bufanolides 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 KWAUEUQHUYWWTO-CBFFWNJESA-N
Standard InCHI InChI=1S/C26H34O7/c1-13(27)32-22-21(14-4-5-20(30)31-12-14)25(3)9-7-16-17(26(25)23(22)33-26)11-19(29)18-10-15(28)6-8-24(16,18)2/h4-5,12,15-19,21-23,28-29H,6-11H2,1-3H3/t15-,16-,17+,18-,19-,21-,22+,23+,24+,25+,26+/m0/s1
SMILES O[C@H]1CC[C@]2([C@@H](C1)[C@@H](O)C[C@@H]1[C@@H]2CC[C@]2([C@]31O[C@@H]3[C@@H]([C@@H]2c1ccc(=O)oc1)OC(=O)C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   458.23 Volume:   457.899
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Van der Waals volume.
Dense:   1.001 LogP:   2.247
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.599
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.44
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The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   30.0
TPSA:   109.5
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Topological Polar Surface Area.
H-Bond Acceptor:   7.0
H-Bond Donor:   2.0 Rings:   6.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.518 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.393 Fsp3:   0.769
MCE-18:   180.087
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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:   0.876 Fluc inhibitor:   0.001
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.407
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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:   0.046 Promiscuous compounds:   0.48

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.632 MDCK Permeability:   -5.136
Pgp-inhibitor:   0.068 Pgp-substrate:   0.006
PAMPA:   0.712
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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):   0.002
20% Bioavailability (F20%):   0.895 30% Bioavailability (F30%):   0.904
50% Bioavailability (F50%):   0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.006 MRP1:   0.989
Plasma Protein Binding (PPB):   59.626% Volume Distribution (VD):   -0.316
Fu: 42.358%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.967

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.016 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.002
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.021 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.319
HLM stability:   0.192
?
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):  10.779 Half-life (T1/2):  1.831

ADMET: Toxicity

hERG Blockers:  0.018 hERG Blockers (10um):  0.078
Human Hepatotoxicity (H-HT):  0.432 Drug-induced Liver Injury (DILI):  0.422
AMES Toxicity:  0.742 Rat Oral Acute Toxicity:  0.561
Maximum Recommended Daily Dose:  0.871 Skin Sensitization:  0.97
Carcinogencity:  0.845 Eye Corrosion:  0.004
Eye Irritation:  0.466 Respiratory Toxicity:  0.514
Drug-induced Neurotoxicity:  0.129 Ototoxicity:  0.342
Hematotoxicity:  0.591 Drug-induced Nephrotoxicity:  0.834
Genotoxicity:  0.997 RPMI-8226 Immunitoxicity:  0.229
A549 Cytotoxicity:  0.487 Hek293 Cytotoxicity:  0.658
BCF:   0.498
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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:   3.219
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.788
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.07
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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
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. PMID[11575946]
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. PMID[12141860]
NPO11981 Bufo gargarizans Species Bufonidae Eukaryota venom n.a. n.a. PMID[24050254]
NPO11981 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. PMID[28256122]
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8733 Duttaphrynus melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8733 Duttaphrynus melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11981 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11981 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8733 Duttaphrynus melanostictus Species Bufonidae 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
NPT91 Cell line KB Homo sapiens IC50 = 0.87 ug.mL-1 PMID[11575946]
NPT116 Cell line HL-60 Homo sapiens IC50 = 0.038 ug.mL-1 PMID[11575946]
NPT1366 Cell line MH60 Mus musculus IC50 > 25.0 ug.mL-1 PMID[11575946]
NPT1081 Cell line BXPC-3 Homo sapiens IC50 = 0.46 ug.mL-1 PMID[11575946]
NPT83 Cell line MCF7 Homo sapiens IC50 = 0.36 ug.mL-1 PMID[11575946]
NPT395 Cell line SF-268 Homo sapiens IC50 = 0.32 ug.mL-1 PMID[11575946]
NPT397 Cell line NCI-H460 Homo sapiens IC50 = 0.74 ug.mL-1 PMID[11575946]
NPT575 Cell line KM-20L2 Homo sapiens IC50 = 0.28 ug.mL-1 PMID[11575946]
NPT90 Cell line DU-145 Homo sapiens IC50 = 0.21 ug.mL-1 PMID[11575946]

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 NPC16701 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
0.8133 Intermediate Similarity NPC157380
0.7436 Intermediate Similarity NPC485877
0.6829 Remote Similarity NPC213761
0.6627 Remote Similarity NPC35171
0.5843 Remote Similarity NPC485878
0.5529 Remote Similarity NPC185287
0.5529 Remote Similarity NPC43063
0.5529 Remote Similarity NPC79298
0.5474 Remote Similarity NPC312481
0.5393 Remote Similarity NPC485880
0.5341 Remote Similarity NPC75389
0.5149 Remote Similarity NPC6193
0.5055 Remote Similarity NPC485879
0.5055 Remote Similarity NPC221414

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC16701 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