Natural Product: NPC131104

Natural Product IDNPC131104
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(4As,4Br,6S,6As,7S,8S,9S,10As,10Br,12As)-8-Acetyl-7-Formyl-9-Hydroxy-1,1,4A,6A,10B-Pentamethyloctadecahydrochrysen-6-Yl Acetate
IUPAC Name [(4aS,4bR,6S,6aS,7S,8S,9S,10aS,10bR,12aS)-8-acetyl-7-formyl-9-hydroxy-1,1,4a,6a,10b-pentamethyl-2,3,4,4b,5,6,7,8,9,10,10a,11,12,12a-tetradecahydrochrysen-6-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL517640
PubChem CID 637470
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 UFBZWPSQIJARTK-QMHVTLFBSA-N
Standard InCHI InChI=1S/C28H44O5/c1-16(30)24-18(15-29)28(7)22(13-19(24)32)27(6)12-9-20-25(3,4)10-8-11-26(20,5)21(27)14-23(28)33-17(2)31/h15,18-24,32H,8-14H2,1-7H3/t18-,19-,20-,21+,22-,23-,24-,26-,27+,28+/m0/s1
SMILES CC(=O)[C@H]1[C@H](C=O)[C@]2(C)[C@@H](C[C@@H]1O)[C@]1(C)CC[C@H]3C(C)(C)CCC[C@]3(C)[C@H]1C[C@@H]2OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   460.32 Volume:   494.66
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Van der Waals volume.
Dense:   0.931 LogP:   3.676
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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:   -4.531
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   80.67
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Topological Polar Surface Area.
H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.475 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.994 Fsp3:   0.893
MCE-18:   88.415
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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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.71 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:   0.005
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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:   0.191 Promiscuous compounds:   0.412

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.386 MDCK Permeability:   -5.073
Pgp-inhibitor:   0.995 Pgp-substrate:   0.002
PAMPA:   0.533
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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%):   0.031 30% Bioavailability (F30%):   0.046
50% Bioavailability (F50%):   0.736

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.2 MRP1:   0.627
Plasma Protein Binding (PPB):   85.252% Volume Distribution (VD):   -0.032
Fu: 10.924%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.162
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.161
CYP2C19-inhibitor:   0.967 CYP2C19-substrate:   0.028
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.002
CYP3A4-inhibitor:   0.184 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.312
HLM stability:   0.683
?
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):  6.291 Half-life (T1/2):  0.795

ADMET: Toxicity

hERG Blockers:  0.016 hERG Blockers (10um):  0.047
Human Hepatotoxicity (H-HT):  0.447 Drug-induced Liver Injury (DILI):  0.738
AMES Toxicity:  0.749 Rat Oral Acute Toxicity:  0.297
Maximum Recommended Daily Dose:  0.546 Skin Sensitization:  0.986
Carcinogencity:  0.916 Eye Corrosion:  0.229
Eye Irritation:  0.808 Respiratory Toxicity:  0.764
Drug-induced Neurotoxicity:  0.065 Ototoxicity:  0.359
Hematotoxicity:  0.863 Drug-induced Nephrotoxicity:  0.971
Genotoxicity:  0.894 RPMI-8226 Immunitoxicity:  0.08
A549 Cytotoxicity:  0.405 Hek293 Cytotoxicity:  0.291
BCF:   1.226
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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:   4.072
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.593
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.038
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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 % PMID[11473412]

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 NPC131104 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
0.8333 Intermediate Similarity NPC3032
0.6842 Remote Similarity NPC181871
0.6667 Remote Similarity NPC208912
0.6667 Remote Similarity NPC83242
0.6552 Remote Similarity NPC219535
0.6094 Remote Similarity NPC474253
0.6094 Remote Similarity NPC474346
0.6 Remote Similarity NPC213737
0.5909 Remote Similarity NPC67653
0.5902 Remote Similarity NPC269729
0.5902 Remote Similarity NPC606340
0.5758 Remote Similarity NPC88337
0.5714 Remote Similarity NPC95899
0.5714 Remote Similarity NPC473319
0.5645 Remote Similarity NPC9060
0.5625 Remote Similarity NPC194951
0.5625 Remote Similarity NPC608115
0.5625 Remote Similarity NPC611248
0.5538 Remote Similarity NPC325229
0.5538 Remote Similarity NPC2096
0.5507 Remote Similarity NPC475211
0.5397 Remote Similarity NPC237938
0.5385 Remote Similarity NPC474572
0.5373 Remote Similarity NPC228251
0.5373 Remote Similarity NPC477972
0.5303 Remote Similarity NPC606805
0.5303 Remote Similarity NPC607360
0.5147 Remote Similarity NPC282233
0.5072 Remote Similarity NPC474284
0.5065 Remote Similarity NPC473677
0.5065 Remote Similarity NPC475404

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC131104 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