Natural Product: NPC12046

Natural Product IDNPC12046
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
12-O-Deacetyl-12-Epi-Scalarin
IUPAC Name (1R,5aS,5bR,7aS,11aS,11bR,13R,13aS,13bR)-1,13-dihydroxy-5b,8,8,11a,13a-pentamethyl-5,5a,6,7,7a,9,10,11,11b,12,13,13b-dodecahydro-1H-phenanthro[2,1-e][2]benzofuran-3-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL399743
PubChem CID 10960421
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001552] Sesterterpenoids
          • [CHEMONTID:0002883] Scalarane sesterterpenoids

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 ATVQOEWPZTUPDT-PNXXKSHTSA-N
Standard InCHI InChI=1S/C25H38O4/c1-22(2)10-6-11-23(3)15(22)9-12-24(4)16-8-7-14-19(21(28)29-20(14)27)25(16,5)18(26)13-17(23)24/h7,15-19,21,26,28H,6,8-13H2,1-5H3/t15-,16-,17+,18+,19+,21+,23-,24-,25+/m0/s1
SMILES O[C@@H]1OC(=O)C2=CC[C@@H]3[C@]([C@@H]12)(C)[C@H](O)C[C@H]1[C@@]3(C)CC[C@@H]2[C@]1(C)CCCC2(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   402.28 Volume:   428.062
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Van der Waals volume.
Dense:   0.94 LogP:   3.78
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.588
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.044
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The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   26.0
TPSA:   66.76
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Topological Polar Surface Area.
H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.588 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.969 Fsp3:   0.88
MCE-18:   95.319
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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:   0.441 Fluc inhibitor:   0.001
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.021
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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:   0.245 Promiscuous compounds:   0.144

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.186 MDCK Permeability:   -4.855
Pgp-inhibitor:   0.663 Pgp-substrate:   0.003
PAMPA:   0.313
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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):   0.009
20% Bioavailability (F20%):   0.021 30% Bioavailability (F30%):   0.094
50% Bioavailability (F50%):   0.906

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.518 MRP1:   0.516
Plasma Protein Binding (PPB):   97.102% Volume Distribution (VD):   0.217
Fu: 4.321%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.281
BSEP inhibitor:   0.988

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.153
CYP2D6-inhibitor:   0.298 CYP2D6-substrate:   0.06
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.97
HLM stability:   0.448
?
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):  7.07 Half-life (T1/2):  1.641

ADMET: Toxicity

hERG Blockers:  0.105 hERG Blockers (10um):  0.353
Human Hepatotoxicity (H-HT):  0.416 Drug-induced Liver Injury (DILI):  0.296
AMES Toxicity:  0.215 Rat Oral Acute Toxicity:  0.115
Maximum Recommended Daily Dose:  0.777 Skin Sensitization:  0.957
Carcinogencity:  0.719 Eye Corrosion:  0.05
Eye Irritation:  0.707 Respiratory Toxicity:  0.443
Drug-induced Neurotoxicity:  0.07 Ototoxicity:  0.64
Hematotoxicity:  0.204 Drug-induced Nephrotoxicity:  0.744
Genotoxicity:  0.194 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.087 Hek293 Cytotoxicity:  0.407
BCF:   2.047
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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:   4.563
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.995
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.512
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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
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. Tongoa, Vanuatu Islands 1996 PMID[10757711]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[12662110]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[15497946]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. Tong-Yong City in the South Sea, Korea n.a. PMID[16905319]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[17567172]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[17988093]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[18407692]
NPO33376 Spongia sp. Species Spongiidae Eukaryota n.a. Indonesian n.a. PMID[24992702]
NPO33376 Spongia sp. Species Spongiidae 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
NPT540 Individual protein Bile acid receptor FXR Homo sapiens IC50 = 75000.0 nM PMID[23398362]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT137 Cell line L1210 Mus musculus IC50 = 2.3 ug.mL-1 PMID[17070063]
NPT165 Cell line HeLa Homo sapiens IC50 = 15.0 ug.mL-1 PMID[20643902]
NPT81 Cell line A549 Homo sapiens IC50 = 14.8 ug.mL-1 PMID[9213587]
NPT91 Cell line KB Homo sapiens IC50 = 14.3 ug.mL-1 PubChem BioAssay data set

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 NPC12046 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
0.6949 Remote Similarity NPC110496
0.6923 Remote Similarity NPC166346
0.6721 Remote Similarity NPC157441
0.661 Remote Similarity NPC189513
0.6393 Remote Similarity NPC194951
0.6207 Remote Similarity NPC606859
0.6032 Remote Similarity NPC63249
0.5781 Remote Similarity NPC275539
0.5781 Remote Similarity NPC100892
0.5781 Remote Similarity NPC189075
0.5652 Remote Similarity NPC161527
0.5469 Remote Similarity NPC473319
0.5397 Remote Similarity NPC90946
0.5397 Remote Similarity NPC300614
0.5312 Remote Similarity NPC275086
0.5238 Remote Similarity NPC473299
0.5224 Remote Similarity NPC604992
0.5167 Remote Similarity NPC605274
0.5077 Remote Similarity NPC135224
0.5077 Remote Similarity NPC61369
0.5077 Remote Similarity NPC5532
0.5077 Remote Similarity NPC469545
0.5077 Remote Similarity NPC610547
0.5075 Remote Similarity NPC51499
0.5075 Remote Similarity NPC471207
0.5072 Remote Similarity NPC95585

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC12046 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