Natural Product: NPC480561

Natural Product IDNPC480561
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SKEMYAAMDHTYBL-ONIUZDBUSA-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 SKEMYAAMDHTYBL-ONIUZDBUSA-N
Standard InCHI InChI=1S/C20H30O2/c1-6-14(2)8-10-16-15(3)9-11-17-19(16,4)12-7-13-20(17,5)18(21)22/h6,8-9,16-17H,1,7,10-13H2,2-5H3,(H,21,22)/b14-8+/t16-,17+,19+,20+/m0/s1
SMILES C=C/C(=C/C[C@H]1C(=CC[C@@H]2[C@]1(C)CCC[C@@]2(C)C(=O)O)C)/C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   302.22 Volume:   344.398
?
Van der Waals volume.
Dense:   0.878 LogP:   4.54
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.325
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.905
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   14.0
TPSA:   37.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.559 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.31 Fsp3:   0.65
MCE-18:   42.242
?
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:   0.621 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.968 Promiscuous compounds:   0.11

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.947 MDCK Permeability:   -4.783
Pgp-inhibitor:   0.411 Pgp-substrate:   0.018
PAMPA:   0.818
?
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):   0.002
20% Bioavailability (F20%):   0.575 30% Bioavailability (F30%):   0.152
50% Bioavailability (F50%):   0.901

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.995
Plasma Protein Binding (PPB):   95.719% Volume Distribution (VD):   -0.161
Fu: 4.521%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.557 BCRP inhibitor:   0.023
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.036 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.826 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.754 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.951 CYP3A4-substrate:   0.861
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.091
HLM stability:   0.59
?
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):  3.167 Half-life (T1/2):  1.077

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.047
Human Hepatotoxicity (H-HT):  0.438 Drug-induced Liver Injury (DILI):  0.538
AMES Toxicity:  0.163 Rat Oral Acute Toxicity:  0.367
Maximum Recommended Daily Dose:  0.272 Skin Sensitization:  0.944
Carcinogencity:  0.415 Eye Corrosion:  0.816
Eye Irritation:  0.892 Respiratory Toxicity:  0.809
Drug-induced Neurotoxicity:  0.063 Ototoxicity:  0.328
Hematotoxicity:  0.527 Drug-induced Nephrotoxicity:  0.714
Genotoxicity:  0.531 RPMI-8226 Immunitoxicity:  0.031
A549 Cytotoxicity:  0.042 Hek293 Cytotoxicity:  0.053
BCF:   1.659
?
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:   4.224
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.615
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.062
?
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
NPO40043 Basilicum polystachyon Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31553187]

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
NPT1724 Organism Dengue virus Dengue virus IC50 = 1400.0 nM PMID[31553187]
NPT339 Organism Influenza A virus H3N2 Influenza A virus H3N2 IC50 = 18000.0 nM PMID[31553187]
NPT2 Others Unspecified n.a. IC50 = 1200.0 nM PMID[31553187]
NPT742 Organism Influenza A virus Influenza A virus IC50 = 4100.0 nM PMID[31553187]

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 NPC480561 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
0.7143 Intermediate Similarity NPC237591
0.7143 Intermediate Similarity NPC3753
0.6296 Remote Similarity NPC483605
0.6275 Remote Similarity NPC484817
0.6038 Remote Similarity NPC192540
0.5818 Remote Similarity NPC82979
0.5741 Remote Similarity NPC59436
0.5556 Remote Similarity NPC198240
0.5517 Remote Similarity NPC72397
0.5455 Remote Similarity NPC109854
0.5424 Remote Similarity NPC24816
0.537 Remote Similarity NPC610518
0.5357 Remote Similarity NPC102197
0.5263 Remote Similarity NPC606858
0.5246 Remote Similarity NPC479388
0.5161 Remote Similarity NPC479389
0.5088 Remote Similarity NPC471159
0.5088 Remote Similarity NPC123880
0.5088 Remote Similarity NPC302661

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480561 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