Natural Product: NPC51824

Natural Product IDNPC51824
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Altersolanol L
IUPAC Name (2R,3R,4R,4aS,9aS,10R)-2,3,4,8,10-pentahydroxy-6-methoxy-3-methyl-1,2,4,4a,9a,10-hexahydroanthracen-9-one
Synonyms Altersolanol L
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL551302
PubChem CID 42639666
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes

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 NDGIDBHYSCKXJM-CBDPYCFPSA-N
Standard InCHI InChI=1S/C16H20O7/c1-16(22)10(18)5-8-12(15(16)21)14(20)7-3-6(23-2)4-9(17)11(7)13(8)19/h3-4,8,10,12,14-15,17-18,20-22H,5H2,1-2H3/t8-,10+,12-,14-,15+,16+/m0/s1
SMILES COc1cc2[C@H](O)[C@@H]3[C@@H](C(=O)c2c(c1)O)C[C@H]([C@@]([C@@H]3O)(C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   324.12 Volume:   310.609
?
Van der Waals volume.
Dense:   1.043 LogP:   1.225
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.596
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.652
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   127.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.481 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.445 Fsp3:   0.562
MCE-18:   78.32
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.22 Fluc inhibitor:   0.052
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.097
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.019
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.215 Promiscuous compounds:   0.385

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.569 MDCK Permeability:   -4.762
Pgp-inhibitor:   0.001 Pgp-substrate:   0.651
PAMPA:   0.962
?
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):   0.34
20% Bioavailability (F20%):   0.743 30% Bioavailability (F30%):   0.6
50% Bioavailability (F50%):   0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.73
Plasma Protein Binding (PPB):   79.57% Volume Distribution (VD):   0.234
Fu: 23.435%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.903
OATP1B3 inhibitor:   0.901 BCRP inhibitor:   0.077
BSEP inhibitor:   0.105

ADMET: Metabolism

CYP1A2-inhibitor:   0.929 CYP1A2-substrate:   0.045
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.02 CYP2C9-substrate:   0.107
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.182
CYP3A4-inhibitor:   0.036 CYP3A4-substrate:   0.145
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.151
HLM stability:   0.118
?
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):  3.735 Half-life (T1/2):  3.066

ADMET: Toxicity

hERG Blockers:  0.017 hERG Blockers (10um):  0.182
Human Hepatotoxicity (H-HT):  0.62 Drug-induced Liver Injury (DILI):  0.54
AMES Toxicity:  0.823 Rat Oral Acute Toxicity:  0.743
Maximum Recommended Daily Dose:  0.548 Skin Sensitization:  0.992
Carcinogencity:  0.783 Eye Corrosion:  0.0
Eye Irritation:  0.571 Respiratory Toxicity:  0.869
Drug-induced Neurotoxicity:  0.127 Ototoxicity:  0.857
Hematotoxicity:  0.856 Drug-induced Nephrotoxicity:  0.927
Genotoxicity:  0.962 RPMI-8226 Immunitoxicity:  0.328
A549 Cytotoxicity:  0.929 Hek293 Cytotoxicity:  0.511
BCF:   0.45
?
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:   3.107
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.429
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.775
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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
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. PMID[15568783]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[18494522]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Mentha pulegium n.a. n.a. PMID[19271717]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[19271717]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. Caribbean sea n.a. PMID[20727745]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[21341726]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. reef slopes on the south side of Cocos Lagoon, Guam n.a. PMID[21550239]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. collected from the plants natural habitat in Tabriz, Northwestern Iran, at an altitude of 1400 m n.a. PMID[21775156]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[22276679]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Stems n.a. n.a. PMID[23664494]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota isolated from fresh Juncus acutus Lake Wadi el Natrun, Egypt 2012-NOV PMID[25010124]
NPO33215 Stemphylium sp. 33231 Species Pleosporaceae Eukaryota n.a. South China Sea n.a. PMID[25136754]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[25265160]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[25760674]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[26841051]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[30794407]
NPO32908 Alternaria sp. Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33215 Stemphylium sp. 33231 Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19321 Notholaena californica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19321 Notholaena californica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19101 Deutzia gracilis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19726 Limnatis nilotica Species Hirudinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15888 Streptogonopus phipsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13444 Centaurea ptosimopappoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18080 Peltophorum ferrugineum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18687 Pterocarpus gracilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14894 Udotea conglutinata Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19382 Corallina elongata Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18944 Vernonia filigera Species Asteraceae 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
NPT1864 Cell line L5178Y Mus musculus Activity = 51.4 % PMID[19271717]
NPT393 Cell line HCT-116 Homo sapiens IC50 > 100000.0 nM PMID[22276679]
NPT306 Cell line PC-3 Homo sapiens IC50 > 100000.0 nM PMID[22276679]
NPT65 Cell line HepG2 Homo sapiens IC50 > 100000.0 nM PMID[22276679]
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[25136754]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[22276679]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[25136754]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC > 10000.0 nM PMID[25136754]
NPT19 Organism Escherichia coli Escherichia coli MIC > 10000.0 nM PMID[25136754]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 10000.0 nM PMID[25136754]
NPT2 Others Unspecified n.a. IC50 > 100000 nM PMID[22276679]
NPT3146 Organism Micrococcus Micrococcus MIC > 10000.0 nM PMID[25136754]
NPT1238 Organism Staphylococcus Staphylococcus MIC > 10000.0 nM PMID[25136754]
NPT314 Organism Bacillus cereus Bacillus cereus MIC > 10000.0 nM PMID[25136754]
NPT3147 Organism Kocuria rhizophila Kocuria rhizophila MIC > 10000.0 nM PMID[25136754]

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 NPC51824 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
0.7018 Intermediate Similarity NPC268992
0.7018 Intermediate Similarity NPC470337
0.7018 Intermediate Similarity NPC113608
0.7018 Intermediate Similarity NPC470338
0.6842 Remote Similarity NPC68727
0.6774 Remote Similarity NPC472055
0.6552 Remote Similarity NPC600297
0.5902 Remote Similarity NPC180944
0.5781 Remote Similarity NPC470339
0.5556 Remote Similarity NPC470340
0.5439 Remote Similarity NPC486434
0.5231 Remote Similarity NPC486426
0.5231 Remote Similarity NPC486427
0.5231 Remote Similarity NPC486428
0.5172 Remote Similarity NPC600511
0.5156 Remote Similarity NPC155302
0.5156 Remote Similarity NPC225854
0.5156 Remote Similarity NPC604497
0.5156 Remote Similarity NPC608598

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC51824 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