Natural Product: NPC325732

Natural Product IDNPC325732
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VUPIVOZJYBEXBH-UXXZJWSNSA-N
IUPAC Name n.a.
Synonyms Rel-Trigoheterin E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1926832
PubChem CID 56649424
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003494] Rhamnofolane and daphnane diterpenoids

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 VUPIVOZJYBEXBH-UXXZJWSNSA-N
Standard InCHI InChI=1S/C34H36O9/c1-17(2)32-25(39-28(36)20-12-8-6-9-13-20)19(4)33-22-16-18(3)24(35)31(22,38)29(37)30(5)26(40-30)23(33)27(32)41-34(42-32,43-33)21-14-10-7-11-15-21/h6-15,18-19,22-23,25-27,29,37-38H,1,16H2,2-5H3/t18-,19+,22+,23-,25-,26+,27+,29+,30+,31+,32-,33-,34?/m0/s1
SMILES CC1CC2C34C(C(C5(C(C3C6C(O6)(C(C2(C1=O)O)O)C)OC(O4)(O5)C7=CC=CC=C7)C(=C)C)OC(=O)C8=CC=CC=C8)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   588.24 Volume:   583.552
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Van der Waals volume.
Dense:   1.008 LogP:   3.551
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.457
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.63
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   39.0
TPSA:   124.05
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Topological Polar Surface Area.
H-Bond Acceptor:   9.0
H-Bond Donor:   2.0 Rings:   8.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.315 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.453 Fsp3:   0.529
MCE-18:   184.0
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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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.141 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.593
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.288 Promiscuous compounds:   0.003

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.947 MDCK Permeability:   -4.775
Pgp-inhibitor:   0.292 Pgp-substrate:   0.004
PAMPA:   0.021
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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):   0.0
20% Bioavailability (F20%):   0.001 30% Bioavailability (F30%):   0.036
50% Bioavailability (F50%):   0.899

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.699 MRP1:   1.0
Plasma Protein Binding (PPB):   96.441% Volume Distribution (VD):   0.05
Fu: 2.725%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.005
OATP1B3 inhibitor:   0.738 BCRP inhibitor:   0.011
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.016
CYP2C19-inhibitor:   0.009 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.011 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.026
CYP3A4-inhibitor:   0.58 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.035 CYP2C8-inhibitor:   0.998
HLM stability:   0.75
?
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):  3.891 Half-life (T1/2):  1.193

ADMET: Toxicity

hERG Blockers:  0.111 hERG Blockers (10um):  0.645
Human Hepatotoxicity (H-HT):  0.286 Drug-induced Liver Injury (DILI):  0.457
AMES Toxicity:  0.503 Rat Oral Acute Toxicity:  0.609
Maximum Recommended Daily Dose:  0.239 Skin Sensitization:  0.618
Carcinogencity:  0.081 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.038
Drug-induced Neurotoxicity:  0.794 Ototoxicity:  0.814
Hematotoxicity:  0.037 Drug-induced Nephrotoxicity:  0.048
Genotoxicity:  0.482 RPMI-8226 Immunitoxicity:  0.14
A549 Cytotoxicity:  0.1 Hek293 Cytotoxicity:  0.846
BCF:   1.805
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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:   4.514
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.559
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.917
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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
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. twig n.a. PMID[22122667]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[22122667]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae 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
NPT116 Cell line HL-60 Homo sapiens IC50 = 1800.0 nM PMID[22122667]
NPT81 Cell line A549 Homo sapiens IC50 = 10000.0 nM PMID[22122667]

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 NPC325732 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
1.0 High Similarity NPC324769
0.8667 High Similarity NPC40138
0.7895 Intermediate Similarity NPC323356
0.7317 Intermediate Similarity NPC479347
0.725 Intermediate Similarity NPC322420
0.7037 Intermediate Similarity NPC326328
0.7 Intermediate Similarity NPC154675
0.6296 Remote Similarity NPC322048
0.6279 Remote Similarity NPC61891
0.5843 Remote Similarity NPC326235
0.5682 Remote Similarity NPC481755
0.5682 Remote Similarity NPC66193
0.5444 Remote Similarity NPC471134
0.5275 Remote Similarity NPC12491
0.5217 Remote Similarity NPC323001
0.5106 Remote Similarity NPC481365

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC325732 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