Natural Product: NPC472640

Natural Product IDNPC472640
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GIBGTMIKVMTTHM-BYTXZFODSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3581364
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001772] Eudesmanolides, secoeudesmanolides, and derivatives

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 GIBGTMIKVMTTHM-BYTXZFODSA-N
Standard InCHI InChI=1S/C17H24O6/c1-8-11-5-12-9(2)15(20)23-17(12,21)7-16(11,4)14(19)6-13(8)22-10(3)18/h8,11,13-14,19,21H,5-7H2,1-4H3/t8-,11-,13+,14-,16+,17-/m1/s1
SMILES C[C@@H]1[C@H]2CC3=C(C)C(=O)O[C@@]3(C[C@]2(C)[C@@H](C[C@@H]1OC(=O)C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   324.16 Volume:   321.751
?
Van der Waals volume.
Dense:   1.007 LogP:   0.807
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.228
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.546
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   17.0
TPSA:   93.06
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.706 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.821 Fsp3:   0.765
MCE-18:   59.8
?
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.401 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.024
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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:   0.378 Promiscuous compounds:   0.624

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.187 MDCK Permeability:   -4.832
Pgp-inhibitor:   0.984 Pgp-substrate:   0.808
PAMPA:   0.952
?
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):   0.36
20% Bioavailability (F20%):   0.933 30% Bioavailability (F30%):   0.992
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.899
Plasma Protein Binding (PPB):   39.409% Volume Distribution (VD):   -0.127
Fu: 62.456%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.981 BCRP inhibitor:   0.037
BSEP inhibitor:   0.975

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.002
CYP2C19-inhibitor:   0.03 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.002 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.151 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.382
HLM stability:   0.598
?
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):  5.938 Half-life (T1/2):  2.007

ADMET: Toxicity

hERG Blockers:  0.009 hERG Blockers (10um):  0.047
Human Hepatotoxicity (H-HT):  0.518 Drug-induced Liver Injury (DILI):  0.132
AMES Toxicity:  0.422 Rat Oral Acute Toxicity:  0.058
Maximum Recommended Daily Dose:  0.499 Skin Sensitization:  0.911
Carcinogencity:  0.559 Eye Corrosion:  0.037
Eye Irritation:  0.824 Respiratory Toxicity:  0.028
Drug-induced Neurotoxicity:  0.013 Ototoxicity:  0.638
Hematotoxicity:  0.278 Drug-induced Nephrotoxicity:  0.715
Genotoxicity:  0.444 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.019 Hek293 Cytotoxicity:  0.081
BCF:   0.31
?
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:   2.943
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.427
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.625
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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
NPO1371 Teucrium viscidum Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[23337296]
NPO1371 Teucrium viscidum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24484201]
NPO1371 Teucrium viscidum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25739048]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27933899]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28960981]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1371 Teucrium viscidum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1371 Teucrium viscidum Species Lamiaceae 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
NPT65 Cell line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[15497936]
NPT393 Cell line HCT-116 Homo sapiens IC50 > 10000.0 nM PMID[25856683]
NPT165 Cell line HeLa Homo sapiens IC50 > 10000.0 nM PMID[18343122]
NPT113 Cell line RAW264.7 Mus musculus IC50 > 100000.0 nM PMID[28960981]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[25739048]
NPT30060 Protein-protein interaction PCSK9/LDLR Homo sapiens Inhibition n.a. n.a. % PMID[33567826]
NPT2 Others Unspecified n.a. IC50 > 1000000.0 nM PMID[2509636]

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 NPC472640 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
0.6415 Remote Similarity NPC485367
0.62 Remote Similarity NPC472642
0.6038 Remote Similarity NPC472641
0.5849 Remote Similarity NPC606843
0.5345 Remote Similarity NPC485366
0.5273 Remote Similarity NPC78594
0.5085 Remote Similarity NPC600091

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC472640 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