Natural Product: NPC601068

Natural Product IDNPC601068
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WYBOVISLCPAJFV-QLEMLULZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1395109
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 WYBOVISLCPAJFV-QLEMLULZSA-N
Standard InCHI InChI=1S/C22H28O4/c1-13-9-16-11-20(25-5)21(26-6)12-17(16)22(14(13)2)15-7-8-18(23-3)19(10-15)24-4/h7-8,10-14,22H,9H2,1-6H3/t13-,14+,22+/m1/s1
SMILES COc1ccc([C@H]2c3cc(OC)c(OC)cc3C[C@@H](C)[C@@H]2C)cc1OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   356.2 Volume:   382.741
?
Van der Waals volume.
Dense:   0.931 LogP:   3.408
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.331
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.565
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   17.0
TPSA:   36.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.779 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.151 Fsp3:   0.455
MCE-18:   61.75
?
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:   0.138 Fluc inhibitor:   0.604
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.391
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.019
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.34 Promiscuous compounds:   0.247

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.789 MDCK Permeability:   -4.658
Pgp-inhibitor:   0.786 Pgp-substrate:   0.092
PAMPA:   0.0
?
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):   0.001
20% Bioavailability (F20%):   0.082 30% Bioavailability (F30%):   0.041
50% Bioavailability (F50%):   0.818

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.019 MRP1:   0.952
Plasma Protein Binding (PPB):   94.878% Volume Distribution (VD):   0.381
Fu: 4.525%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.979
OATP1B3 inhibitor:   0.984 BCRP inhibitor:   0.312
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.139
CYP2D6-inhibitor:   0.01 CYP2D6-substrate:   0.98
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.931
?
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):  9.427 Half-life (T1/2):  1.168

ADMET: Toxicity

hERG Blockers:  0.239 hERG Blockers (10um):  0.657
Human Hepatotoxicity (H-HT):  0.849 Drug-induced Liver Injury (DILI):  0.449
AMES Toxicity:  0.575 Rat Oral Acute Toxicity:  0.435
Maximum Recommended Daily Dose:  0.615 Skin Sensitization:  0.322
Carcinogencity:  0.661 Eye Corrosion:  0.012
Eye Irritation:  0.707 Respiratory Toxicity:  0.689
Drug-induced Neurotoxicity:  0.795 Ototoxicity:  0.584
Hematotoxicity:  0.427 Drug-induced Nephrotoxicity:  0.661
Genotoxicity:  0.378 RPMI-8226 Immunitoxicity:  0.086
A549 Cytotoxicity:  0.265 Hek293 Cytotoxicity:  0.527
BCF:   2.587
?
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:   4.39
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.774
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.273
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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
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63924 Nectandra puberula Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29258 Virola oleifera Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO42565 Himantandra belgraveana n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2788 Virola surinamensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO29258 Virola oleifera Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2788 Virola surinamensis Species Myristicaceae 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
NPT50 Individual protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 1835.6 nM PubChem BioAssay data set
NPT791 Individual protein Cruzipain Trypanosoma cruzi Potency = 39810.7 nM PubChem BioAssay data set

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 NPC601068 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
0.8636 High Similarity NPC17348
0.7556 Intermediate Similarity NPC177167
0.7292 Intermediate Similarity NPC228771
0.6458 Remote Similarity NPC480480
0.62 Remote Similarity NPC23336
0.5926 Remote Similarity NPC227002
0.5833 Remote Similarity NPC89504
0.5833 Remote Similarity NPC88065
0.5833 Remote Similarity NPC95485
0.5435 Remote Similarity NPC474040
0.5283 Remote Similarity NPC266705
0.5283 Remote Similarity NPC29008
0.5185 Remote Similarity NPC125134

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC601068 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