Natural Product: NPC471526

Natural Product IDNPC471526
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Oscillapeptin E
IUPAC Name [(2R)-3-[[(2R)-1-[[(2S,5S,8S,11R,12S,15S,18S,21R)-5-benzyl-8-[(2R)-butan-2-yl]-2-[(2S)-butan-2-yl]-21-hydroxy-15-[2-(4-hydroxyphenyl)ethyl]-4,11-dimethyl-3,6,9,13,16,22-hexaoxo-10-oxa-1,4,7,14,17-pentazabicyclo[16.3.1]docosan-12-yl]amino]-4-(4-hydroxyphenyl)-1-oxobutan-2-yl]amino]-2-methoxy-3-oxopropyl] hydrogen sulfate
Synonyms Oscillapeptin E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL254782
PubChem CID 44448153
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

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 IPSPUQFSLMOERD-FESXDSMZSA-N
Standard InCHI InChI=1S/C55H75N7O17S/c1-8-31(3)45-55(73)79-33(5)46(60-49(67)40(26-20-35-17-23-38(64)24-18-35)56-51(69)43(77-7)30-78-80(74,75)76)52(70)57-39(25-19-34-15-21-37(63)22-16-34)48(66)58-41-27-28-44(65)62(53(41)71)47(32(4)9-2)54(72)61(6)42(50(68)59-45)29-36-13-11-10-12-14-36/h10-18,21-24,31-33,39-47,63-65H,8-9,19-20,25-30H2,1-7H3,(H,56,69)(H,57,70)(H,58,66)(H,59,68)(H,60,67)(H,74,75,76)/t31-,32+,33-,39+,40-,41+,42+,43-,44-,45+,46+,47+/m1/s1
SMILES CC[C@H]([C@@H]1N=C(O)[C@H](Cc2ccccc2)N(C)C(=O)[C@H]([C@H](CC)C)N2[C@H](O)CC[C@@H](C2=O)N=C([C@@H](N=C([C@H]([C@H](OC1=O)C)N=C([C@H](N=C([C@@H](COS(=O)(=O)O)OC)O)CCc1ccc(cc1)O)O)O)CCc1ccc(cc1)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1137.49 Volume:   1117.154
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Van der Waals volume.
Dense:   1.018 LogP:   0.592
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.158
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.122
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The logarithm of aqueous solubility value.
Rotatable Bonds:   20.0 Rigid Bonds:   48.0
TPSA:   363.39
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Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   9.0 Rings:   5.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.029 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.837 Fsp3:   0.527
MCE-18:   145.714
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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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.877 Fluc inhibitor:   0.032
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.105
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.846
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.006 Promiscuous compounds:   0.019

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.684 MDCK Permeability:   -5.15
Pgp-inhibitor:   0.999 Pgp-substrate:   0.995
PAMPA:   0.445
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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):   0.97
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.03
Plasma Protein Binding (PPB):   83.901% Volume Distribution (VD):   -0.503
Fu: 14.844%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.006
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.045 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.009
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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):  -0.032 Half-life (T1/2):  2.592

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  1.0 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.086 Rat Oral Acute Toxicity:  0.098
Maximum Recommended Daily Dose:  0.558 Skin Sensitization:  1.0
Carcinogencity:  0.531 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.242
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.321 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.009
BCF:   0.441
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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:   3.562
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.128
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.486
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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
NPO32547.2 oscillatoria agardhii Under-species n.a. n.a. n.a. n.a. n.a. Database[Title]

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
NPT2 Others Unspecified n.a. IC50 = 2640.0 nM Open TG-GATES in vivo data: Hematology

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 NPC471526 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
0.9135 High Similarity NPC473407
0.7328 Intermediate Similarity NPC60516
0.7069 Intermediate Similarity NPC63040
0.681 Remote Similarity NPC489102
0.6752 Remote Similarity NPC22883
0.6667 Remote Similarity NPC5719
0.664 Remote Similarity NPC489835
0.664 Remote Similarity NPC489836
0.664 Remote Similarity NPC489837
0.6555 Remote Similarity NPC45037
0.648 Remote Similarity NPC163961
0.6417 Remote Similarity NPC471053
0.6417 Remote Similarity NPC471051
0.6406 Remote Similarity NPC489838
0.632 Remote Similarity NPC61332
0.6293 Remote Similarity NPC62104
0.621 Remote Similarity NPC302715
0.621 Remote Similarity NPC471048
0.6154 Remote Similarity NPC306804
0.6129 Remote Similarity NPC230611
0.6124 Remote Similarity NPC240130
0.6094 Remote Similarity NPC220060
0.6083 Remote Similarity NPC50016
0.608 Remote Similarity NPC476227
0.605 Remote Similarity NPC273755
0.6048 Remote Similarity NPC294951
0.6048 Remote Similarity NPC15068
0.6047 Remote Similarity NPC25539
0.6033 Remote Similarity NPC471052
0.5923 Remote Similarity NPC489834
0.5906 Remote Similarity NPC102959
0.5887 Remote Similarity NPC217804
0.5854 Remote Similarity NPC137627
0.5846 Remote Similarity NPC277306
0.584 Remote Similarity NPC471050
0.576 Remote Similarity NPC210377
0.5703 Remote Similarity NPC159767
0.5662 Remote Similarity NPC473305
0.5659 Remote Similarity NPC155506
0.5478 Remote Similarity NPC163392
0.5462 Remote Similarity NPC40234
0.5462 Remote Similarity NPC487289
0.5424 Remote Similarity NPC239762
0.5403 Remote Similarity NPC1390
0.5391 Remote Similarity NPC194671
0.5308 Remote Similarity NPC269750
0.5308 Remote Similarity NPC107938
0.5303 Remote Similarity NPC46009
0.5267 Remote Similarity NPC294516
0.5259 Remote Similarity NPC473404
0.5224 Remote Similarity NPC488263
0.5197 Remote Similarity NPC248670
0.5159 Remote Similarity NPC471165
0.5149 Remote Similarity NPC65714
0.5149 Remote Similarity NPC473371
0.5116 Remote Similarity NPC279871
0.5115 Remote Similarity NPC248822
0.5115 Remote Similarity NPC194699

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471526 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