Natural Product: NPC208912

Natural Product IDNPC208912
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(1R,3S,3As,4S,5As,5Br,7As,11As,11Br,13S,13As,13Bs)-1,4-Dihydroxy-3,5B,8,8,11A,13A-Hexamethylicosahydrochryseno[2,1-C]Furan-13-Yl Acetate
IUPAC Name [(1R,3S,3aS,4S,5aS,5bR,7aS,11aS,11bR,13S,13aS,13bS)-1,4-dihydroxy-3,5b,8,8,11a,13a-hexamethyl-1,3,3a,4,5,5a,6,7,7a,9,10,11,11b,12,13,13b-hexadecahydrophenanthro[2,1-e][2]benzofuran-13-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL464295
PubChem CID 11005073
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 YXMVZNUXPZBMJR-KCEWOJSZSA-N
Standard InCHI InChI=1S/C28H46O5/c1-15-22-17(30)13-20-27(6)12-9-18-25(3,4)10-8-11-26(18,5)19(27)14-21(33-16(2)29)28(20,7)23(22)24(31)32-15/h15,17-24,30-31H,8-14H2,1-7H3/t15-,17-,18-,19+,20-,21-,22+,23+,24+,26-,27+,28+/m0/s1
SMILES CC(=O)O[C@H]1C[C@H]2[C@@]([C@H]3[C@@]1(C)[C@H]1[C@H](O)O[C@H]([C@@H]1[C@H](C3)O)C)(C)CC[C@@H]1[C@]2(C)CCCC1(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   462.33 Volume:   491.376
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Van der Waals volume.
Dense:   0.941 LogP:   3.61
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.633
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.388
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   26.0
TPSA:   75.99
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Topological Polar Surface Area.
H-Bond Acceptor:   5.0
H-Bond Donor:   2.0 Rings:   5.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.541 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.159 Fsp3:   0.964
MCE-18:   100.909
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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:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.638 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:   0.008
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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:   0.142 Promiscuous compounds:   0.342

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.574 MDCK Permeability:   -5.288
Pgp-inhibitor:   0.408 Pgp-substrate:   0.011
PAMPA:   0.971
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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%):   0.068 30% Bioavailability (F30%):   0.053
50% Bioavailability (F50%):   0.923

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.279 MRP1:   0.792
Plasma Protein Binding (PPB):   90.26% Volume Distribution (VD):   -0.39
Fu: 7.441%
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The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.985 BCRP inhibitor:   0.278
BSEP inhibitor:   0.971

ADMET: Metabolism

CYP1A2-inhibitor:   0.107 CYP1A2-substrate:   0.882
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.393
CYP2C9-inhibitor:   0.055 CYP2C9-substrate:   0.508
CYP2D6-inhibitor:   0.089 CYP2D6-substrate:   0.201
CYP3A4-inhibitor:   0.477 CYP3A4-substrate:   0.981
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.864
HLM stability:   0.919
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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):  5.602 Half-life (T1/2):  1.184

ADMET: Toxicity

hERG Blockers:  0.021 hERG Blockers (10um):  0.093
Human Hepatotoxicity (H-HT):  0.414 Drug-induced Liver Injury (DILI):  0.788
AMES Toxicity:  0.857 Rat Oral Acute Toxicity:  0.464
Maximum Recommended Daily Dose:  0.455 Skin Sensitization:  0.998
Carcinogencity:  0.892 Eye Corrosion:  0.506
Eye Irritation:  0.824 Respiratory Toxicity:  0.913
Drug-induced Neurotoxicity:  0.073 Ototoxicity:  0.55
Hematotoxicity:  0.914 Drug-induced Nephrotoxicity:  0.952
Genotoxicity:  0.388 RPMI-8226 Immunitoxicity:  0.085
A549 Cytotoxicity:  0.851 Hek293 Cytotoxicity:  0.363
BCF:   1.617
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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:   3.986
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.537
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.903
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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
NPO33404 phyllospongia sp. Species Thorectidae Eukaryota n.a. Indonesian n.a. PMID[12502324]

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
NPT91 Cell line KB Homo sapiens Inhibition = 30.0 % 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 NPC208912 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
0.8393 Intermediate Similarity NPC2096
0.6935 Remote Similarity NPC474253
0.6935 Remote Similarity NPC474346
0.6667 Remote Similarity NPC131104
0.6061 Remote Similarity NPC213737
0.5902 Remote Similarity NPC83242
0.5821 Remote Similarity NPC474284
0.5806 Remote Similarity NPC219535
0.5692 Remote Similarity NPC194951
0.5692 Remote Similarity NPC608115
0.5692 Remote Similarity NPC611248
0.5538 Remote Similarity NPC3032
0.5441 Remote Similarity NPC228251
0.5441 Remote Similarity NPC477972
0.5312 Remote Similarity NPC181871
0.5303 Remote Similarity NPC95899
0.5217 Remote Similarity NPC94905
0.5217 Remote Similarity NPC163902
0.5217 Remote Similarity NPC112457
0.5217 Remote Similarity NPC8954
0.5147 Remote Similarity NPC325229
0.5147 Remote Similarity NPC475456
0.5077 Remote Similarity NPC473299
0.5072 Remote Similarity NPC325054
0.5072 Remote Similarity NPC31522
0.5072 Remote Similarity NPC607359

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC208912 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