Natural Product: NPC253561

Natural Product IDNPC253561
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Canangaterpene Iii
IUPAC Name (4aS,5R,8S,8aR)-5-hydroxy-5-methyl-8-propan-2-yl-4,4a,6,7,8,8a-hexahydro-3H-naphthalene-2-carbaldehyde
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3262198
PubChem CID 90676284
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 FHFKLFYRFFKTRP-ZQDZILKHSA-N
Standard InCHI InChI=1S/C15H24O2/c1-10(2)12-6-7-15(3,17)14-5-4-11(9-16)8-13(12)14/h8-10,12-14,17H,4-7H2,1-3H3/t12-,13-,14-,15+/m0/s1
SMILES O=CC1=C[C@@H]2[C@H](CC1)[C@](C)(O)CC[C@H]2C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   236.18 Volume:   263.191
?
Van der Waals volume.
Dense:   0.897 LogP:   3.162
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.059
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.915
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   12.0
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:   0.748 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.35 Fsp3:   0.8
MCE-18:   36.296
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.263 Fluc inhibitor:   0.259
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.012
?
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:   0.681 Promiscuous compounds:   0.433

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.739 MDCK Permeability:   -4.714
Pgp-inhibitor:   0.79 Pgp-substrate:   0.077
PAMPA:   0.294
?
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):   0.011
20% Bioavailability (F20%):   0.244 30% Bioavailability (F30%):   0.525
50% Bioavailability (F50%):   0.854

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.006 MRP1:   0.187
Plasma Protein Binding (PPB):   87.65% Volume Distribution (VD):   0.322
Fu: 10.349%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.99
OATP1B3 inhibitor:   0.789 BCRP inhibitor:   0.285
BSEP inhibitor:   0.93

ADMET: Metabolism

CYP1A2-inhibitor:   0.133 CYP1A2-substrate:   0.065
CYP2C19-inhibitor:   0.05 CYP2C19-substrate:   0.116
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.012
CYP3A4-inhibitor:   0.113 CYP3A4-substrate:   0.355
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.376
HLM stability:   0.076
?
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):  10.123 Half-life (T1/2):  1.066

ADMET: Toxicity

hERG Blockers:  0.039 hERG Blockers (10um):  0.242
Human Hepatotoxicity (H-HT):  0.452 Drug-induced Liver Injury (DILI):  0.184
AMES Toxicity:  0.463 Rat Oral Acute Toxicity:  0.247
Maximum Recommended Daily Dose:  0.305 Skin Sensitization:  0.717
Carcinogencity:  0.782 Eye Corrosion:  0.904
Eye Irritation:  0.987 Respiratory Toxicity:  0.648
Drug-induced Neurotoxicity:  0.094 Ototoxicity:  0.292
Hematotoxicity:  0.427 Drug-induced Nephrotoxicity:  0.538
Genotoxicity:  0.126 RPMI-8226 Immunitoxicity:  0.058
A549 Cytotoxicity:  0.104 Hek293 Cytotoxicity:  0.244
BCF:   0.658
?
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:   3.257
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.669
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.132
?
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
NPO9348 Cananga odorata Species Annonaceae Eukaryota fruits n.a. n.a. PMID[11374955]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO9348 Cananga odorata Species Annonaceae Eukaryota flower buds Thailand n.a. PMID[24601675]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[39459015]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9348 Cananga odorata Species Annonaceae 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
NPT2 Others Unspecified n.a. Inhibition = 19.2 % PubChem BioAssay data set
NPT2 Others Unspecified n.a. Inhibition = 29.9 % PMID[21733601]
NPT2 Others Unspecified n.a. Inhibition = 35.8 % PMID[23501116]
NPT2 Others Unspecified n.a. Inhibition = 50.8 % PMID[9358640]
NPT2 Others Unspecified n.a. Inhibition = 66.3 % PMID[18443129]
NPT2 Others Unspecified n.a. Inhibition = 26.2 % PMID[11421732]

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 NPC253561 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 NPC80088
0.7222 Intermediate Similarity NPC79576
0.7222 Intermediate Similarity NPC473728
0.7222 Intermediate Similarity NPC282694
0.7222 Intermediate Similarity NPC194208
0.7222 Intermediate Similarity NPC12845
0.641 Remote Similarity NPC605908
0.6098 Remote Similarity NPC76966
0.6098 Remote Similarity NPC186554
0.6098 Remote Similarity NPC610509
0.5238 Remote Similarity NPC23954
0.5238 Remote Similarity NPC603450
0.5238 Remote Similarity NPC605037

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC253561 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