Natural Product: NPC484742

Natural Product IDNPC484742
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZPQINAJJLUVHTB-NDBONZKESA-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]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001560] Withanolides and derivatives

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 ZPQINAJJLUVHTB-NDBONZKESA-N
Standard InCHI InChI=1S/C28H38O7/c1-15-13-21(35-23(31)16(15)2)26(5,32)28(34)12-11-27(33)22-18(9-10-24(27,28)3)25(4)17(14-19(22)29)7-6-8-20(25)30/h6,8,14,18-19,21-22,29,32-34H,7,9-13H2,1-5H3/t18-,19-,21+,22-,24-,25-,26-,27+,28-/m0/s1
SMILES CC1=C(C)C(=O)O[C@H](C1)[C@@](C)([C@@]1(CC[C@]2([C@H]3[C@H](CC[C@]12C)[C@]1(C)C(=C[C@@H]3O)CC=CC1=O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   486.26 Volume:   498.411
?
Van der Waals volume.
Dense:   0.976 LogP:   1.278
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.774
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.593
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   28.0
TPSA:   124.29
?
Topological Polar Surface Area.
H-Bond Acceptor:   7.0
H-Bond Donor:   4.0 Rings:   5.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.349 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.535 Fsp3:   0.714
MCE-18:   100.75
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.44 Fluc inhibitor:   0.157
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.026
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.009
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.223 Promiscuous compounds:   0.379

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.434 MDCK Permeability:   -4.963
Pgp-inhibitor:   0.0 Pgp-substrate:   0.984
PAMPA:   0.998
?
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):   0.025
20% Bioavailability (F20%):   0.878 30% Bioavailability (F30%):   0.891
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.114 MRP1:   0.992
Plasma Protein Binding (PPB):   73.187% Volume Distribution (VD):   -0.199
Fu: 28.37%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.993 BCRP inhibitor:   0.006
BSEP inhibitor:   0.899

ADMET: Metabolism

CYP1A2-inhibitor:   0.944 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.968 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.045 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.048 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.023 CYP3A4-substrate:   0.225
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.994
HLM stability:   0.285
?
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):  4.548 Half-life (T1/2):  3.039

ADMET: Toxicity

hERG Blockers:  0.031 hERG Blockers (10um):  0.129
Human Hepatotoxicity (H-HT):  0.769 Drug-induced Liver Injury (DILI):  0.285
AMES Toxicity:  0.396 Rat Oral Acute Toxicity:  0.306
Maximum Recommended Daily Dose:  0.758 Skin Sensitization:  0.985
Carcinogencity:  0.892 Eye Corrosion:  0.001
Eye Irritation:  0.363 Respiratory Toxicity:  0.612
Drug-induced Neurotoxicity:  0.168 Ototoxicity:  0.647
Hematotoxicity:  0.224 Drug-induced Nephrotoxicity:  0.873
Genotoxicity:  0.986 RPMI-8226 Immunitoxicity:  0.114
A549 Cytotoxicity:  0.2 Hek293 Cytotoxicity:  0.39
BCF:   0.492
?
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:   3.127
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.575
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.794
?
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
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[28617598]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[30649869]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota Whole Fruits n.a. n.a. PMID[32159343]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28734 Physalis peruviana Species Solanaceae 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
NPT858 Cell line LNCaP Homo sapiens IC50 = 330.0 nM PMID[28617598]
NPT1629 Cell line CWR22R Homo sapiens IC50 = 560.0 nM PMID[28617598]
NPT369 Cell line ACHN Homo sapiens IC50 > 2000.0 nM PMID[28617598]
NPT387 Cell line M14 Homo sapiens IC50 > 2000.0 nM PMID[28617598]
NPT170 Cell line SK-MEL-28 Homo sapiens IC50 > 2000.0 nM PMID[28617598]
NPT859 Cell line HFF Homo sapiens IC50 > 2000.0 nM PMID[28617598]

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 NPC484742 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
0.75 Intermediate Similarity NPC153440
0.7042 Intermediate Similarity NPC484743
0.6575 Remote Similarity NPC107493
0.6486 Remote Similarity NPC103045
0.64 Remote Similarity NPC285729
0.6351 Remote Similarity NPC79579
0.6216 Remote Similarity NPC225826
0.6154 Remote Similarity NPC5292
0.6133 Remote Similarity NPC158285
0.6 Remote Similarity NPC486565
0.5844 Remote Similarity NPC125794
0.5844 Remote Similarity NPC171401
0.5679 Remote Similarity NPC484717
0.5584 Remote Similarity NPC270850
0.5584 Remote Similarity NPC190286
0.5584 Remote Similarity NPC305260
0.5432 Remote Similarity NPC484745
0.5422 Remote Similarity NPC484718
0.5385 Remote Similarity NPC176840
0.5316 Remote Similarity NPC191620
0.5122 Remote Similarity NPC5073
0.506 Remote Similarity NPC488108
0.5059 Remote Similarity NPC55621

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484742 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