Natural Product: NPC102015

Natural Product IDNPC102015
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
[(3S,8S,9R,10R,12R,13S,14R,17S)-17-Acetyl-8,14,17-Trihydroxy-3-[(2R,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,4R,5R,6R)-5-[(2S,3R,4S,5R,6R)-3-Hydroxy-4-Methoxy-6-Methyl-5-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyoxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-10,13-Dimethyl-1,2,3,4,7,9,11,12,15,16-Decahydrocyclopenta[A]Phenanthren-12-Yl] Acetate
IUPAC Name [(3S,8S,9R,10R,12R,13S,14R,17S)-17-acetyl-8,14,17-trihydroxy-3-[(2R,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,4R,5R,6R)-5-[(2S,3R,4S,5R,6R)-3-hydroxy-4-methoxy-6-methyl-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-10,13-dimethyl-1,2,3,4,7,9,11,12,15,16-decahydrocyclopenta[a]phenanthren-12-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL444397
PubChem CID 44566882
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides

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 ILIYDXHSTQCKOH-XRVJZQCTSA-N
Standard InCHI InChI=1S/C57H92O25/c1-25-46(33(68-9)20-39(72-25)77-32-14-15-53(7)31(19-32)13-16-56(66)37(53)23-38(76-30(6)60)54(8)55(65,29(5)59)17-18-57(54,56)67)79-40-21-34(69-10)47(26(2)73-40)80-41-22-35(70-11)48(27(3)74-41)81-52-45(64)50(71-12)49(28(4)75-52)82-51-44(63)43(62)42(61)36(24-58)78-51/h13,25-28,32-52,58,61-67H,14-24H2,1-12H3/t25-,26-,27-,28-,32+,33+,34+,35-,36-,37-,38-,39+,40+,41+,42-,43+,44-,45-,46-,47-,48-,49-,50+,51+,52+,53+,54-,55-,56+,57-/m1/s1
SMILES CO[C@H]1C[C@@H](O[C@@H]([C@H]1O[C@H]1C[C@@H](OC)[C@@H]([C@H](O1)C)O[C@@H]1O[C@H](C)[C@H]([C@H]([C@H]1O)OC)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)C)O[C@H]1[C@@H](OC)C[C@@H](O[C@@H]1C)O[C@H]1CC[C@]2(C(=CC[C@@]3([C@@H]2C[C@@H](OC(=O)C)[C@]2([C@]3(O)CC[C@@]2(O)C(=O)C)C)O)C1)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1176.59 Volume:   1129.266
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Van der Waals volume.
Dense:   1.042 LogP:   1.318
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.931
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.466
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The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   52.0
TPSA:   334.43
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Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   8.0 Rings:   9.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.072 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.248 Fsp3:   0.93
MCE-18:   190.909
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.592 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:   0.001
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.005
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.496 Promiscuous compounds:   0.715

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.95 MDCK Permeability:   -5.482
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
PAMPA:   1.0
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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):   0.008
20% Bioavailability (F20%):   0.324 30% Bioavailability (F30%):   0.771
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.968
Plasma Protein Binding (PPB):   41.256% Volume Distribution (VD):   -0.574
Fu: 59.388%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.993 BCRP inhibitor:   0.025
BSEP inhibitor:   0.034

ADMET: Metabolism

CYP1A2-inhibitor:   0.065 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.036 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   0.028
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.008
HLM stability:   0.989
?
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):  0.371 Half-life (T1/2):  5.624

ADMET: Toxicity

hERG Blockers:  0.017 hERG Blockers (10um):  0.052
Human Hepatotoxicity (H-HT):  0.438 Drug-induced Liver Injury (DILI):  0.992
AMES Toxicity:  0.992 Rat Oral Acute Toxicity:  0.362
Maximum Recommended Daily Dose:  0.318 Skin Sensitization:  1.0
Carcinogencity:  0.189 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.015
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.999
Hematotoxicity:  0.776 Drug-induced Nephrotoxicity:  0.934
Genotoxicity:  0.93 RPMI-8226 Immunitoxicity:  0.519
A549 Cytotoxicity:  0.959 Hek293 Cytotoxicity:  0.865
BCF:   0.49
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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:   3.363
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.13
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.105
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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
NPO33108 leptadenia hastata Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7623046]
NPO33108 leptadenia hastata Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[8786361]

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
NPT80 Cell line Raji Homo sapiens Activity = 98.0 % DrugMatrix in vitro pharmacology data
NPT80 Cell line Raji Homo sapiens Activity = 87.0 % DrugMatrix in vitro pharmacology data
NPT80 Cell line Raji Homo sapiens Activity = 69.0 % DrugMatrix in vitro pharmacology data
NPT80 Cell line Raji Homo sapiens Activity = 30.0 % DrugMatrix in vitro pharmacology data
NPT80 Cell line Raji Homo sapiens Activity = 28.0 % DrugMatrix in vitro pharmacology data
NPT80 Cell line Raji Homo sapiens Activity = 26.0 % DrugMatrix in vitro pharmacology data

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 NPC102015 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
0.8889 High Similarity NPC475358
0.8889 High Similarity NPC473566
0.828 Intermediate Similarity NPC481661
0.828 Intermediate Similarity NPC481655
0.8137 Intermediate Similarity NPC473641
0.8137 Intermediate Similarity NPC475300
0.7717 Intermediate Similarity NPC473519
0.7615 Intermediate Similarity NPC473797
0.75 Intermediate Similarity NPC481657
0.7423 Intermediate Similarity NPC473805
0.7333 Intermediate Similarity NPC475613
0.729 Intermediate Similarity NPC70236
0.7156 Intermediate Similarity NPC475437
0.7156 Intermediate Similarity NPC475464
0.687 Remote Similarity NPC475175
0.6842 Remote Similarity NPC475447
0.6724 Remote Similarity NPC475531
0.6724 Remote Similarity NPC475198
0.67 Remote Similarity NPC481658
0.67 Remote Similarity NPC79250
0.67 Remote Similarity NPC290746
0.6422 Remote Similarity NPC475536
0.6404 Remote Similarity NPC476092
0.624 Remote Similarity NPC476090
0.6147 Remote Similarity NPC165234
0.6147 Remote Similarity NPC481659
0.6147 Remote Similarity NPC271687
0.614 Remote Similarity NPC475218
0.5873 Remote Similarity NPC481650
0.5702 Remote Similarity NPC474564
0.5619 Remote Similarity NPC479287
0.5545 Remote Similarity NPC481656
0.5526 Remote Similarity NPC473468
0.5417 Remote Similarity NPC473557
0.541 Remote Similarity NPC475567
0.5167 Remote Similarity NPC481654

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC102015 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