Natural Product: NPC471853

Natural Product IDNPC471853
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Cyrtophyllone B
IUPAC Name (4aS,10aS)-5,6-dihydroxy-7-(1-hydroxypropan-2-yl)-1,1,4a-trimethyl-3,4,10,10a-tetrahydro-2H-phenanthren-9-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3261316
PubChem CID 90675931
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] 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 YNCLENYSOZNFFY-YNSNGZELSA-N
Standard InCHI InChI=1S/C20H28O4/c1-11(10-21)12-8-13-14(22)9-15-19(2,3)6-5-7-20(15,4)16(13)18(24)17(12)23/h8,11,15,21,23-24H,5-7,9-10H2,1-4H3/t11?,15-,20-/m0/s1
SMILES OCC(c1cc2C(=O)C[C@@H]3[C@](c2c(c1O)O)(C)CCCC3(C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   332.2 Volume:   353.422
?
Van der Waals volume.
Dense:   0.94 LogP:   2.542
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.358
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.992
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   17.0
TPSA:   77.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.719 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.049 Fsp3:   0.65
MCE-18:   78.758
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.147 Fluc inhibitor:   0.18
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.323
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.026
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.122 Promiscuous compounds:   0.026

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.128 MDCK Permeability:   -4.83
Pgp-inhibitor:   0.054 Pgp-substrate:   0.01
PAMPA:   0.607
?
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):   0.003
20% Bioavailability (F20%):   0.112 30% Bioavailability (F30%):   0.17
50% Bioavailability (F50%):   0.871

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.149 MRP1:   0.985
Plasma Protein Binding (PPB):   82.139% Volume Distribution (VD):   0.228
Fu: 24.562%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.988
OATP1B3 inhibitor:   0.981 BCRP inhibitor:   0.098
BSEP inhibitor:   0.568

ADMET: Metabolism

CYP1A2-inhibitor:   0.646 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.027 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.78 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.221 CYP2D6-substrate:   0.177
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.111
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.046
HLM stability:   0.771
?
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):  12.794 Half-life (T1/2):  1.297

ADMET: Toxicity

hERG Blockers:  0.027 hERG Blockers (10um):  0.26
Human Hepatotoxicity (H-HT):  0.608 Drug-induced Liver Injury (DILI):  0.207
AMES Toxicity:  0.404 Rat Oral Acute Toxicity:  0.367
Maximum Recommended Daily Dose:  0.666 Skin Sensitization:  0.962
Carcinogencity:  0.743 Eye Corrosion:  0.009
Eye Irritation:  0.922 Respiratory Toxicity:  0.845
Drug-induced Neurotoxicity:  0.14 Ototoxicity:  0.829
Hematotoxicity:  0.533 Drug-induced Nephrotoxicity:  0.828
Genotoxicity:  0.254 RPMI-8226 Immunitoxicity:  0.084
A549 Cytotoxicity:  0.438 Hek293 Cytotoxicity:  0.37
BCF:   1.413
?
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:   4.119
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.675
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.034
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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
NPO17762 Crossopetalum gaumeri Species Celastraceae Eukaryota Roots Yucatan Peninsula n.a. PMID[24709561]
NPO17762 Crossopetalum gaumeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17762 Crossopetalum gaumeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17762 Crossopetalum gaumeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17762 Crossopetalum gaumeri Species Celastraceae 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
NPT165 Cell line HeLa Homo sapiens IC50 > 70000.0 nM PMID[24709561]
NPT189 Cell line Vero Chlorocebus aethiops IC50 > 70000.0 nM PMID[19067555]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 70000.0 nM PMID[24709561]

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 NPC471853 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 NPC478653
0.84 Intermediate Similarity NPC111845
0.7018 Intermediate Similarity NPC471851
0.6842 Remote Similarity NPC478646
0.6034 Remote Similarity NPC176130
0.5902 Remote Similarity NPC196941
0.5763 Remote Similarity NPC606689
0.569 Remote Similarity NPC92079
0.5667 Remote Similarity NPC248068
0.5667 Remote Similarity NPC600435
0.5645 Remote Similarity NPC309169
0.55 Remote Similarity NPC80443
0.55 Remote Similarity NPC303910
0.5439 Remote Similarity NPC605496
0.5345 Remote Similarity NPC219573
0.5333 Remote Similarity NPC69424
0.5224 Remote Similarity NPC474991
0.5079 Remote Similarity NPC273248

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471853 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