Natural Product: NPC251118

Natural Product IDNPC251118
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Cordiachrome C
IUPAC Name (6S,7R)-7-ethenyl-7-methyl-6-prop-1-en-2-yl-6,8-dihydro-5H-naphthalene-1,4-dione
Synonyms Cordiachrome C
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL401583
PubChem CID 44448135
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones

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 KZWBZRSKUWXBGO-BBRMVZONSA-N
Standard InCHI InChI=1S/C16H18O2/c1-5-16(4)9-12-11(8-13(16)10(2)3)14(17)6-7-15(12)18/h5-7,13H,1-2,8-9H2,3-4H3/t13-,16-/m0/s1
SMILES C=C[C@@]1(C)CC2=C(C[C@H]1C(=C)C)C(=O)C=CC2=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   242.13 Volume:   269.941
?
Van der Waals volume.
Dense:   0.897 LogP:   2.948
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.941
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.084
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   15.0
TPSA:   34.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.55 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.328 Fsp3:   0.375
MCE-18:   35.455
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   1
Colloidal aggregators:   0.672 Fluc inhibitor:   0.338
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.313
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.01
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.993 Promiscuous compounds:   0.328

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.662 MDCK Permeability:   -4.494
Pgp-inhibitor:   0.096 Pgp-substrate:   0.0
PAMPA:   0.652
?
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%):   0.002 30% Bioavailability (F30%):   0.022
50% Bioavailability (F50%):   0.684

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.764 MRP1:   0.453
Plasma Protein Binding (PPB):   96.703% Volume Distribution (VD):   0.418
Fu: 3.49%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.952
OATP1B3 inhibitor:   0.98 BCRP inhibitor:   0.558
BSEP inhibitor:   0.729

ADMET: Metabolism

CYP1A2-inhibitor:   0.068 CYP1A2-substrate:   0.973
CYP2C19-inhibitor:   0.035 CYP2C19-substrate:   0.117
CYP2C9-inhibitor:   0.022 CYP2C9-substrate:   0.88
CYP2D6-inhibitor:   0.005 CYP2D6-substrate:   0.992
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.996
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   1.0
HLM stability:   0.997
?
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):  8.1 Half-life (T1/2):  1.058

ADMET: Toxicity

hERG Blockers:  0.035 hERG Blockers (10um):  0.59
Human Hepatotoxicity (H-HT):  0.661 Drug-induced Liver Injury (DILI):  0.197
AMES Toxicity:  0.26 Rat Oral Acute Toxicity:  0.872
Maximum Recommended Daily Dose:  0.978 Skin Sensitization:  0.996
Carcinogencity:  0.918 Eye Corrosion:  1.0
Eye Irritation:  1.0 Respiratory Toxicity:  0.962
Drug-induced Neurotoxicity:  0.742 Ototoxicity:  0.143
Hematotoxicity:  0.603 Drug-induced Nephrotoxicity:  0.008
Genotoxicity:  0.956 RPMI-8226 Immunitoxicity:  0.02
A549 Cytotoxicity:  0.012 Hek293 Cytotoxicity:  0.75
BCF:   1.595
?
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:   5.151
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.709
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.482
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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
NPO6865 Cordia fragrantissima Species Cordiaceae Eukaryota n.a. Myanmar n.a. PMID[18088097]
NPO22854 Cordia globifera Species Cordiaceae Eukaryota n.a. n.a. n.a. PMID[19368377]
NPO22854 Cordia globifera Species Cordiaceae Eukaryota n.a. n.a. n.a. PMID[20384317]
NPO6865 Cordia fragrantissima Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22854 Cordia globifera Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6865 Cordia fragrantissima Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22854 Cordia globifera Species Cordiaceae 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
NPT189 Cell line Vero Chlorocebus aethiops IC50 = 1.4 ug.mL-1 PMID[17877337]
NPT91 Cell line KB Homo sapiens IC50 = 1.5 ug.mL-1 PMID[12828469]
NPT639 Cell line NCI-H187 Homo sapiens IC50 = 0.2 ug.mL-1 PubChem BioAssay data set
NPT3632 Organism Leishmania panamensis Leishmania panamensis IC50 = 5.5 ug.mL-1 PMID[25747550]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 1.5 ug.mL-1 PMID[23792351]
NPT20 Organism Candida albicans Candida albicans IC50 = 4.6 ug.mL-1 PMID[10560729]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 1.8 ug.mL-1 PMID[19368377]
NPT3631 Organism Leishmania guyanensis Leishmania guyanensis IC50 = 6.0 ug.mL-1 PMID[25316316]
NPT841 Organism Leishmania major Leishmania major IC50 = 21.1 ug.mL-1 PMID[23265253]
NPT485 Organism Plasmodium falciparum (isolate K1 / Thailand) Plasmodium falciparum K1 IC50 = 0.2 ug.mL-1 PMID[22545792]

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 NPC251118 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
0.5641 Remote Similarity NPC188292
0.525 Remote Similarity NPC87141

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC251118 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