Natural Product: NPC101458

Natural Product IDNPC101458
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
POKGESLRCWHPFR-GEWRCSBCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14167335
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 POKGESLRCWHPFR-GEWRCSBCSA-N
Standard InCHI InChI=1S/C30H48O2/c1-18(2)19-11-13-27(5)15-16-28(6)20(25(19)27)9-10-22-29(28,7)14-12-21-26(3,4)23(31)17-24(32)30(21,22)8/h19-22,24-25,32H,1,9-17H2,2-8H3/t19-,20+,21-,22-,24+,25+,27+,28+,29+,30-/m0/s1
SMILES C=C(C)[C@@H]1CC[C@]2(C)CC[C@]3(C)[C@H](CC[C@H]4[C@@]3(C)CC[C@H]3C(C)(C)C(=O)C[C@H]([C@]43C)O)[C@@H]12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   440.37 Volume:   496.961
?
Van der Waals volume.
Dense:   0.886 LogP:   5.61
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.691
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -6.339
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   27.0
TPSA:   37.3
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Topological Polar Surface Area.
H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.438 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.945 Fsp3:   0.9
MCE-18:   102.667
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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:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.978 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:   0.557 Promiscuous compounds:   0.41

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.214 MDCK Permeability:   -4.946
Pgp-inhibitor:   0.743 Pgp-substrate:   0.005
PAMPA:   0.09
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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):   0.0
20% Bioavailability (F20%):   0.027 30% Bioavailability (F30%):   0.219
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.811 MRP1:   0.972
Plasma Protein Binding (PPB):   94.611% Volume Distribution (VD):   0.505
Fu: 5.745%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.648
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.799 CYP1A2-substrate:   0.003
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.019
CYP2C9-inhibitor:   0.007 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.014
CYP3A4-inhibitor:   0.973 CYP3A4-substrate:   0.932
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.058
HLM stability:   0.344
?
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):  11.106 Half-life (T1/2):  0.309

ADMET: Toxicity

hERG Blockers:  0.079 hERG Blockers (10um):  0.32
Human Hepatotoxicity (H-HT):  0.699 Drug-induced Liver Injury (DILI):  0.621
AMES Toxicity:  0.352 Rat Oral Acute Toxicity:  0.524
Maximum Recommended Daily Dose:  0.575 Skin Sensitization:  0.936
Carcinogencity:  0.828 Eye Corrosion:  0.169
Eye Irritation:  0.864 Respiratory Toxicity:  0.959
Drug-induced Neurotoxicity:  0.288 Ototoxicity:  0.661
Hematotoxicity:  0.735 Drug-induced Nephrotoxicity:  0.701
Genotoxicity:  0.49 RPMI-8226 Immunitoxicity:  0.071
A549 Cytotoxicity:  0.473 Hek293 Cytotoxicity:  0.452
BCF:   2.55
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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:   4.451
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.325
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.172
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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
NPO26000 Breynia fruticosa Species Phyllanthaceae Eukaryota n.a. root n.a. PMID[21428418]
NPO26000 Breynia fruticosa Species Phyllanthaceae Eukaryota roots Xishuangbanna of Yunnan Province, China n.a. PMID[21428418]
NPO26000 Breynia fruticosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26000 Breynia fruticosa Species Phyllanthaceae 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 NPC101458 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 NPC57469
0.6852 Remote Similarity NPC80297
0.6852 Remote Similarity NPC475727
0.6852 Remote Similarity NPC116119
0.6429 Remote Similarity NPC43300
0.625 Remote Similarity NPC192638
0.625 Remote Similarity NPC25511
0.625 Remote Similarity NPC600137
0.6 Remote Similarity NPC269396
0.5902 Remote Similarity NPC103754
0.5862 Remote Similarity NPC102708
0.5833 Remote Similarity NPC159497
0.5763 Remote Similarity NPC202540
0.5667 Remote Similarity NPC293803
0.5645 Remote Similarity NPC475726
0.5484 Remote Similarity NPC74595
0.5484 Remote Similarity NPC264665
0.541 Remote Similarity NPC248830
0.541 Remote Similarity NPC212241
0.541 Remote Similarity NPC472742
0.5254 Remote Similarity NPC35652
0.5238 Remote Similarity NPC201459
0.5161 Remote Similarity NPC604288
0.5152 Remote Similarity NPC472739
0.5082 Remote Similarity NPC475679
0.5082 Remote Similarity NPC97534
0.5082 Remote Similarity NPC195155
0.5077 Remote Similarity NPC12774
0.5075 Remote Similarity NPC4643

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC101458 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