Natural Product: NPC488324

Natural Product IDNPC488324
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VEOSVUCNKQEQMB-JOCHJYFZSA-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]

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 VEOSVUCNKQEQMB-JOCHJYFZSA-N
Standard InCHI InChI=1S/C26H26O5/c1-6-25(2,3)19-13-17-12-18-14-22(29-20(18)15-21(17)30-24(19)28)26(4,5)31-23(27)16-10-8-7-9-11-16/h6-13,15,22H,1,14H2,2-5H3/t22-/m1/s1
SMILES C=CC(C)(C)c1cc2cc3C[C@H](C(C)(C)OC(=O)c4ccccc4)Oc3cc2oc1=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   418.18 Volume:   441.613
?
Van der Waals volume.
Dense:   0.947 LogP:   5.695
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.433
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.468
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   24.0
TPSA:   65.74
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   0.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.324 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.483 Fsp3:   0.308
MCE-18:   84.176
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.994 Fluc inhibitor:   0.389
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.899
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.897
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.296 Promiscuous compounds:   0.035

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.976 MDCK Permeability:   -4.777
Pgp-inhibitor:   0.706 Pgp-substrate:   0.0
PAMPA:   0.15
?
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%):   0.833 30% Bioavailability (F30%):   0.736
50% Bioavailability (F50%):   0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   98.436% Volume Distribution (VD):   0.173
Fu: 1.689%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.051
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.931
CYP2C19-inhibitor:   0.875 CYP2C19-substrate:   0.975
CYP2C9-inhibitor:   0.249 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.856
CYP3A4-inhibitor:   0.992 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.012 CYP2C8-inhibitor:   1.0
HLM stability:   0.983
?
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):  5.573 Half-life (T1/2):  0.624

ADMET: Toxicity

hERG Blockers:  0.153 hERG Blockers (10um):  0.611
Human Hepatotoxicity (H-HT):  0.147 Drug-induced Liver Injury (DILI):  0.917
AMES Toxicity:  0.28 Rat Oral Acute Toxicity:  0.482
Maximum Recommended Daily Dose:  0.728 Skin Sensitization:  0.722
Carcinogencity:  0.852 Eye Corrosion:  0.011
Eye Irritation:  0.952 Respiratory Toxicity:  0.428
Drug-induced Neurotoxicity:  0.475 Ototoxicity:  0.159
Hematotoxicity:  0.034 Drug-induced Nephrotoxicity:  0.158
Genotoxicity:  0.621 RPMI-8226 Immunitoxicity:  0.056
A549 Cytotoxicity:  0.129 Hek293 Cytotoxicity:  0.514
BCF:   1.705
?
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:   4.612
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.411
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.996
?
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
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1042/BA20070200]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

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
NPT26641 Cell line P3HR-1 Homo sapiens CC50 = 370400.0 nM PMID[28093914]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 IC50 = 4500.0 nM PMID[28093914]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 = 83.0 n.a. PMID[28093914]

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 NPC488324 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
0.7353 Intermediate Similarity NPC131296
0.7353 Intermediate Similarity NPC326489
0.7353 Intermediate Similarity NPC283331
0.6849 Remote Similarity NPC488325
0.6579 Remote Similarity NPC488332
0.6494 Remote Similarity NPC488333
0.631 Remote Similarity NPC488330
0.6098 Remote Similarity NPC488334
0.6024 Remote Similarity NPC488329
0.6024 Remote Similarity NPC488326
0.6 Remote Similarity NPC488342
0.6 Remote Similarity NPC235682
0.6 Remote Similarity NPC608821
0.593 Remote Similarity NPC488343
0.5862 Remote Similarity NPC488327
0.5862 Remote Similarity NPC488328
0.5493 Remote Similarity NPC611256
0.5205 Remote Similarity NPC109515

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488324 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