Natural Product: NPC146554

Natural Product IDNPC146554
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Rosacea Acid B
IUPAC Name (E,6R)-6-[(3R,8R,9R,10S,13R,14S,17R)-3-hydroxy-4,4,9,13,14-pentamethyl-2,3,7,8,10,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methylhept-2-enoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL487001
PubChem CID 44559230
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001686] Cucurbitacins

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 JMOPTHLWCJXLBX-IJAJUTMCSA-N
Standard InCHI InChI=1S/C30H48O3/c1-19(9-8-10-20(2)26(32)33)21-15-16-30(7)24-13-11-22-23(12-14-25(31)27(22,3)4)28(24,5)17-18-29(21,30)6/h10-11,19,21,23-25,31H,8-9,12-18H2,1-7H3,(H,32,33)/b20-10+/t19-,21-,23-,24-,25-,28+,29-,30+/m1/s1
SMILES C[C@H](CC/C=C(C)/C(=O)O)[C@H]1CC[C@@]2(C)[C@@H]3CC=C4[C@@H](CC[C@H](C4(C)C)O)[C@]3(C)CC[C@]12C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   456.36 Volume:   511.671
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Van der Waals volume.
Dense:   0.892 LogP:   5.698
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.173
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.288
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   22.0
TPSA:   57.53
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Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.335 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.735 Fsp3:   0.833
MCE-18:   81.455
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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:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.76 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:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.576 Promiscuous compounds:   0.205

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.46 MDCK Permeability:   -5.02
Pgp-inhibitor:   0.046 Pgp-substrate:   0.004
PAMPA:   0.93
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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):   0.001
20% Bioavailability (F20%):   0.613 30% Bioavailability (F30%):   0.495
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.901
Plasma Protein Binding (PPB):   90.95% Volume Distribution (VD):   -0.43
Fu: 7.825%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.498
BSEP inhibitor:   0.763

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.995 CYP2C19-substrate:   0.192
CYP2C9-inhibitor:   0.01 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.966
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.922
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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):  8.302 Half-life (T1/2):  0.745

ADMET: Toxicity

hERG Blockers:  0.024 hERG Blockers (10um):  0.052
Human Hepatotoxicity (H-HT):  0.649 Drug-induced Liver Injury (DILI):  0.421
AMES Toxicity:  0.1 Rat Oral Acute Toxicity:  0.164
Maximum Recommended Daily Dose:  0.495 Skin Sensitization:  0.757
Carcinogencity:  0.366 Eye Corrosion:  0.005
Eye Irritation:  0.488 Respiratory Toxicity:  0.844
Drug-induced Neurotoxicity:  0.013 Ototoxicity:  0.724
Hematotoxicity:  0.391 Drug-induced Nephrotoxicity:  0.714
Genotoxicity:  0.416 RPMI-8226 Immunitoxicity:  0.054
A549 Cytotoxicity:  0.092 Hek293 Cytotoxicity:  0.154
BCF:   1.482
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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:   4.25
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.67
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.09
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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
NPO33367 Alnus acuminata Species Betulaceae Eukaryota whole?plant Ttankarpata, Peru n.a. PMID[16124770]
NPO1370 Russula rosacea Species Russulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1370 Russula rosacea Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1370 Russula rosacea Species Russulaceae 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
NPT1794 Individual protein LXR-alpha Homo sapiens EC50 > 50000.0 nM PMID[16124770]
NPT1746 Individual protein LXR-beta Homo sapiens EC50 > 50000.0 nM PMID[16124770]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

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 NPC146554 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
0.7458 Intermediate Similarity NPC300324
0.6618 Remote Similarity NPC472240
0.6618 Remote Similarity NPC262858
0.5902 Remote Similarity NPC602278
0.5694 Remote Similarity NPC472239
0.5625 Remote Similarity NPC106364
0.5588 Remote Similarity NPC110923
0.5588 Remote Similarity NPC74296
0.527 Remote Similarity NPC480720
0.5135 Remote Similarity NPC212948
0.5135 Remote Similarity NPC479293
0.5135 Remote Similarity NPC479294

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC146554 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