Natural Product: NPC485411

Natural Product IDNPC485411
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CIVOMJGWQZOGDF-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0002042] Terphenyls
          • [CHEMONTID:0002126] P-terphenyls

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 CIVOMJGWQZOGDF-UHFFFAOYSA-N
Standard InCHI InChI=1S/C26H28O5/c1-16(2)11-12-18-13-19(14-22(30-4)24(18)27)23-21(29-3)15-20(26(31-5)25(23)28)17-9-7-6-8-10-17/h6-11,13-15,27-28H,12H2,1-5H3
SMILES CC(=CCc1cc(cc(c1O)OC)c1c(cc(c2ccccc2)c(c1O)OC)OC)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   420.19 Volume:   450.169
?
Van der Waals volume.
Dense:   0.933 LogP:   5.463
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.141
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.512
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   19.0
TPSA:   68.15
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Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.461 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.545 Fsp3:   0.231
MCE-18:   20.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.965 Fluc inhibitor:   0.2
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.551
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.748
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.351 Promiscuous compounds:   0.11

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.054 MDCK Permeability:   -4.727
Pgp-inhibitor:   0.739 Pgp-substrate:   0.021
PAMPA:   0.672
?
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):   0.186
20% Bioavailability (F20%):   0.599 30% Bioavailability (F30%):   0.569
50% Bioavailability (F50%):   0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.913
Plasma Protein Binding (PPB):   98.409% Volume Distribution (VD):   0.085
Fu: 1.539%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.854
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.984
BSEP inhibitor:   0.95

ADMET: Metabolism

CYP1A2-inhibitor:   0.899 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.999 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   0.978 CYP2C9-substrate:   0.262
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.469
CYP3A4-inhibitor:   0.082 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.242 CYP2C8-inhibitor:   0.999
HLM stability:   0.999
?
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):  6.389 Half-life (T1/2):  1.042

ADMET: Toxicity

hERG Blockers:  0.144 hERG Blockers (10um):  0.665
Human Hepatotoxicity (H-HT):  0.657 Drug-induced Liver Injury (DILI):  0.666
AMES Toxicity:  0.461 Rat Oral Acute Toxicity:  0.687
Maximum Recommended Daily Dose:  0.635 Skin Sensitization:  0.662
Carcinogencity:  0.505 Eye Corrosion:  0.0
Eye Irritation:  0.436 Respiratory Toxicity:  0.863
Drug-induced Neurotoxicity:  0.744 Ototoxicity:  0.552
Hematotoxicity:  0.429 Drug-induced Nephrotoxicity:  0.678
Genotoxicity:  0.552 RPMI-8226 Immunitoxicity:  0.117
A549 Cytotoxicity:  0.562 Hek293 Cytotoxicity:  0.572
BCF:   1.99
?
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:   4.787
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.123
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.568
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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
NPO40443 Aspergillus candidus LDJ-5 Strain Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31904949]
NPO40443 Aspergillus candidus LDJ-5 Strain Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT116 Cell line HL-60 Homo sapiens IC50 > 50000.0 nM PMID[31904949]
NPT111 Cell line K562 Homo sapiens IC50 > 50000.0 nM PMID[31904949]
NPT1535 Cell line U-87 MG Homo sapiens IC50 > 50000.0 nM PMID[31904949]
NPT165 Cell line HeLa Homo sapiens IC50 = 11400.0 nM PMID[31904949]
NPT519 Cell line SH-SY5Y Homo sapiens IC50 = 16700.0 nM PMID[31904949]
NPT81 Cell line A549 Homo sapiens IC50 = 14800.0 nM PMID[31904949]
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 11100.0 nM PMID[31904949]
NPT393 Cell line HCT-116 Homo sapiens IC50 = 14700.0 nM PMID[31904949]
NPT3140 Cell line MGC-803 Homo sapiens IC50 = 14500.0 nM PMID[31904949]
NPT21742 Cell line L02 Homo sapiens IC50 = 24400.0 nM PMID[31904949]

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 NPC485411 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
0.661 Remote Similarity NPC295719
0.6393 Remote Similarity NPC165026
0.6333 Remote Similarity NPC73505
0.6129 Remote Similarity NPC34431
0.5873 Remote Similarity NPC485408
0.5846 Remote Similarity NPC485412
0.5636 Remote Similarity NPC25111
0.5439 Remote Similarity NPC73535

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485411 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