Natural Product: NPC477566

Natural Product IDNPC477566
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Ilicicolinic acid C
IUPAC Name 5-chloro-2,4-dihydroxy-3-[(2E)-7-hydroxy-3,7,11-trimethyldodeca-2,10-dienyl]-6-methylbenzoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101910507
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 UPKGCCJDPUMZAM-XNTDXEJSSA-N
Standard InCHI InChI=1S/C23H33ClO5/c1-14(2)8-6-12-23(5,29)13-7-9-15(3)10-11-17-20(25)18(22(27)28)16(4)19(24)21(17)26/h8,10,25-26,29H,6-7,9,11-13H2,1-5H3,(H,27,28)/b15-10+
SMILES CC1=C(C(=C(C(=C1Cl)O)C/C=C(\C)/CCCC(C)(CCC=C(C)C)O)O)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   424.2 Volume:   441.151
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Van der Waals volume.
Dense:   0.962 LogP:   6.506
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.197
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.338
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The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   9.0
TPSA:   97.99
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Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.35 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.629 Fsp3:   0.522
MCE-18:   30.0
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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:   1 PAINS Alert:   0
Colloidal aggregators:   0.414 Fluc inhibitor:   0.061
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.308
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.328
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.457 Promiscuous compounds:   0.17

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.181 MDCK Permeability:   -4.79
Pgp-inhibitor:   0.003 Pgp-substrate:   0.001
PAMPA:   0.962
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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):   0.008
20% Bioavailability (F20%):   0.016 30% Bioavailability (F30%):   0.035
50% Bioavailability (F50%):   0.658

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.976
Plasma Protein Binding (PPB):   98.118% Volume Distribution (VD):   -0.443
Fu: 1.639%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.995
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.049
BSEP inhibitor:   0.181

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.14
CYP2C19-inhibitor:   0.048 CYP2C19-substrate:   0.474
CYP2C9-inhibitor:   0.852 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.006 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.026 CYP3A4-substrate:   0.742
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
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):  2.819 Half-life (T1/2):  1.094

ADMET: Toxicity

hERG Blockers:  0.045 hERG Blockers (10um):  0.203
Human Hepatotoxicity (H-HT):  0.72 Drug-induced Liver Injury (DILI):  0.483
AMES Toxicity:  0.064 Rat Oral Acute Toxicity:  0.196
Maximum Recommended Daily Dose:  0.265 Skin Sensitization:  0.954
Carcinogencity:  0.084 Eye Corrosion:  0.025
Eye Irritation:  0.932 Respiratory Toxicity:  0.965
Drug-induced Neurotoxicity:  0.139 Ototoxicity:  0.809
Hematotoxicity:  0.381 Drug-induced Nephrotoxicity:  0.907
Genotoxicity:  0.098 RPMI-8226 Immunitoxicity:  0.05
A549 Cytotoxicity:  0.044 Hek293 Cytotoxicity:  0.045
BCF:   1.36
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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:   4.419
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.807
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.994
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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
NPO33613 Neonectria discophora Species Nectriaceae Eukaryota n.a. Rmire-Montjoly, French Guiana 2011-JUL PMID[25478997]

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
NPT171 Cell line MRC5 Homo sapiens IC50 = 13700 nM PMID[25478997]
NPT91 Cell line KB Homo sapiens IC50 = 28400 nM PMID[25478997]
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 32 ug/ml PMID[25478997]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC = 32 ug/ml PMID[25478997]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MIC = 4 ug/ml PMID[25478997]
NPT20 Organism Candida albicans Candida albicans MIC = 32 ug/ml PMID[25478997]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 32 ug/ml PMID[25478997]
NPT19 Organism Escherichia coli Escherichia coli MIC = 8 ug/ml PMID[25478997]
NPT2 Others Unspecified n.a. IC50 = 4900 nM PMID[25478997]

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 NPC477566 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
0.8305 Intermediate Similarity NPC477567
0.7895 Intermediate Similarity NPC477569
0.7031 Intermediate Similarity NPC611110
0.5625 Remote Similarity NPC600345
0.5625 Remote Similarity NPC610690
0.5455 Remote Similarity NPC180261
0.5217 Remote Similarity NPC37299
0.5156 Remote Similarity NPC208891

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC477566 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