Natural Product: NPC482576

Natural Product IDNPC482576
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
KQONYAOLNHWUPY-KBKYTNSVSA-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 KQONYAOLNHWUPY-KBKYTNSVSA-N
Standard InCHI InChI=1S/C30H44O3/c1-18-8-10-23(33-26(18)32)19(2)20-12-16-30(7)22-9-11-24-27(3,4)25(31)14-15-28(24,5)21(22)13-17-29(20,30)6/h8,19-20,23-24H,9-17H2,1-7H3/t19-,20+,23-,24-,28+,29+,30-/m0/s1
SMILES CC1=CC[C@@H]([C@@H](C)[C@H]2CC[C@@]3(C)C4=C(CC[C@]23C)[C@@]2(C)CCC(=O)C(C)(C)[C@@H]2CC4)OC1=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   452.33 Volume:   500.479
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Van der Waals volume.
Dense:   0.904 LogP:   3.557
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.442
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.507
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   28.0
TPSA:   43.37
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Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.328 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.876 Fsp3:   0.8
MCE-18:   93.333
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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:   0.982 Fluc inhibitor:   0.112
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.015
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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:   0.506 Promiscuous compounds:   0.265

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.033 MDCK Permeability:   -4.806
Pgp-inhibitor:   0.988 Pgp-substrate:   0.001
PAMPA:   0.161
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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):   0.0
20% Bioavailability (F20%):   0.059 30% Bioavailability (F30%):   0.241
50% Bioavailability (F50%):   0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.902
Plasma Protein Binding (PPB):   94.826% Volume Distribution (VD):   0.403
Fu: 5.815%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.214
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.002
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.018 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.998
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.971
CYP2B6-substrate:   0.008 CYP2C8-inhibitor:   1.0
HLM stability:   0.984
?
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):  10.256 Half-life (T1/2):  0.336

ADMET: Toxicity

hERG Blockers:  0.02 hERG Blockers (10um):  0.121
Human Hepatotoxicity (H-HT):  0.642 Drug-induced Liver Injury (DILI):  0.381
AMES Toxicity:  0.181 Rat Oral Acute Toxicity:  0.124
Maximum Recommended Daily Dose:  0.513 Skin Sensitization:  0.983
Carcinogencity:  0.937 Eye Corrosion:  0.423
Eye Irritation:  0.909 Respiratory Toxicity:  0.736
Drug-induced Neurotoxicity:  0.064 Ototoxicity:  0.449
Hematotoxicity:  0.825 Drug-induced Nephrotoxicity:  0.908
Genotoxicity:  0.451 RPMI-8226 Immunitoxicity:  0.051
A549 Cytotoxicity:  0.157 Hek293 Cytotoxicity:  0.343
BCF:   1.859
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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:   4.346
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.594
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.193
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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
NPO40139 Ganoderma colossus Species Polyporaceae Eukaryota n.a. n.a. n.a. PMID[32639735]
NPO40139 Ganoderma colossus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT189 Cell line Vero Chlorocebus aethiops IC50 > 50.0 ug.mL-1 PMID[32639735]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 3.6 ug.mL-1 PMID[32639735]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC > 50.0 ug.mL-1 PMID[32639735]

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 NPC482576 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
0.7619 Intermediate Similarity NPC486186
0.7213 Intermediate Similarity NPC109512
0.7121 Intermediate Similarity NPC69982
0.6984 Remote Similarity NPC486193
0.6462 Remote Similarity NPC219495
0.6308 Remote Similarity NPC482575
0.6308 Remote Similarity NPC486198
0.6269 Remote Similarity NPC479662
0.6119 Remote Similarity NPC486197
0.6 Remote Similarity NPC474083
0.5775 Remote Similarity NPC11903
0.5541 Remote Similarity NPC478297
0.5522 Remote Similarity NPC606148
0.5507 Remote Similarity NPC142253
0.5507 Remote Similarity NPC3511
0.5417 Remote Similarity NPC479661
0.5395 Remote Similarity NPC478299
0.5325 Remote Similarity NPC478311
0.5278 Remote Similarity NPC489792
0.5256 Remote Similarity NPC478309
0.5256 Remote Similarity NPC162033
0.5211 Remote Similarity NPC486187
0.5211 Remote Similarity NPC486191
0.52 Remote Similarity NPC95779
0.52 Remote Similarity NPC475320
0.5143 Remote Similarity NPC201912
0.5143 Remote Similarity NPC38350
0.5143 Remote Similarity NPC601139
0.5063 Remote Similarity NPC482572

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC482576 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