Natural Product: NPC87448

Natural Product IDNPC87448
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Reissantin E
IUPAC Name n.a.
Synonyms Reissantin E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL467201
PubChem CID 10323282
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002051] Agarofurans

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 VDMRSWTYKXKIDN-SWHFUDTGSA-N
Standard InCHI InChI=1S/C26H34O9/c1-14(27)32-17-12-13-24(5,31)26-20(29)18(23(3,4)35-26)19(33-15(2)28)21(25(17,26)6)34-22(30)16-10-8-7-9-11-16/h7-11,17-21,29,31H,12-13H2,1-6H3/t17-,18+,19-,20+,21-,24-,25-,26-/m0/s1
SMILES CC(=O)O[C@H]1CC[C@@](C)([C@@]23[C@@H]([C@@H]([C@@H]([C@@H]([C@]12C)OC(=O)c1ccccc1)OC(=O)C)C(C)(C)O3)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   490.22 Volume:   487.32
?
Van der Waals volume.
Dense:   1.006 LogP:   1.726
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.031
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.462
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The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   23.0
TPSA:   128.59
?
Topological Polar Surface Area.
H-Bond Acceptor:   9.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.482 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.662 Fsp3:   0.654
MCE-18:   148.884
?
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:   0.288 Fluc inhibitor:   0.012
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.012
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.008
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.069 Promiscuous compounds:   0.313

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.633 MDCK Permeability:   -4.851
Pgp-inhibitor:   0.999 Pgp-substrate:   0.472
PAMPA:   0.73
?
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):   0.005
20% Bioavailability (F20%):   0.847 30% Bioavailability (F30%):   0.961
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.999
Plasma Protein Binding (PPB):   66.084% Volume Distribution (VD):   -0.42
Fu: 31.885%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.96 BCRP inhibitor:   0.054
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.003 CYP1A2-substrate:   0.149
CYP2C19-inhibitor:   0.054 CYP2C19-substrate:   0.006
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.064
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.138
CYP3A4-inhibitor:   0.566 CYP3A4-substrate:   0.019
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.881
HLM stability:   0.829
?
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):  5.502 Half-life (T1/2):  1.329

ADMET: Toxicity

hERG Blockers:  0.026 hERG Blockers (10um):  0.507
Human Hepatotoxicity (H-HT):  0.142 Drug-induced Liver Injury (DILI):  0.148
AMES Toxicity:  0.18 Rat Oral Acute Toxicity:  0.55
Maximum Recommended Daily Dose:  0.675 Skin Sensitization:  0.913
Carcinogencity:  0.171 Eye Corrosion:  0.012
Eye Irritation:  0.661 Respiratory Toxicity:  0.581
Drug-induced Neurotoxicity:  0.026 Ototoxicity:  0.488
Hematotoxicity:  0.076 Drug-induced Nephrotoxicity:  0.347
Genotoxicity:  0.707 RPMI-8226 Immunitoxicity:  0.052
A549 Cytotoxicity:  0.008 Hek293 Cytotoxicity:  0.049
BCF:   0.495
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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:   3.263
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.016
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.283
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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
NPO28607 Reissantia buchananii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[14640511]
NPO28607 Reissantia buchananii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28607 Reissantia buchananii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

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
NPT81 Cell line A549 Homo sapiens ED50 > 20.0 ug ml-1 PMID[22276679]
NPT83 Cell line MCF7 Homo sapiens ED50 > 20.0 ug ml-1 PMID[26821820]
NPT180 Cell line HCT-8 Homo sapiens ED50 > 20.0 ug ml-1 PMID[26821820]
NPT91 Cell line KB Homo sapiens ED50 = 14.4 ug ml-1 PMID[24617303]
NPT306 Cell line PC-3 Homo sapiens ED50 > 20.0 ug ml-1 PMID[24387703]
NPT309 Cell line 1A9 Homo sapiens ED50 > 20.0 ug ml-1 PMID[23092389]
NPT310 Cell line 1A9/ptx-10 Homo sapiens ED50 > 20.0 ug ml-1 PMID[12444694]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 = 16.5 ug ml-1 PMID[14640511]

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 NPC87448 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
0.8485 Intermediate Similarity NPC470153
0.8116 Intermediate Similarity NPC70403
0.8116 Intermediate Similarity NPC177940
0.7231 Intermediate Similarity NPC118080
0.7121 Intermediate Similarity NPC97947
0.6667 Remote Similarity NPC163719
0.6667 Remote Similarity NPC95810
0.6429 Remote Similarity NPC291599
0.6316 Remote Similarity NPC470159
0.6111 Remote Similarity NPC483846
0.6104 Remote Similarity NPC472571
0.6087 Remote Similarity NPC483863
0.5974 Remote Similarity NPC29704
0.5974 Remote Similarity NPC470157
0.5942 Remote Similarity NPC301556
0.5921 Remote Similarity NPC481490
0.5753 Remote Similarity NPC200471
0.5753 Remote Similarity NPC472575
0.5679 Remote Similarity NPC301368
0.5679 Remote Similarity NPC84815
0.5556 Remote Similarity NPC125106
0.5556 Remote Similarity NPC472573
0.5513 Remote Similarity NPC147340
0.5493 Remote Similarity NPC100913
0.5479 Remote Similarity NPC483847
0.5479 Remote Similarity NPC470152
0.5476 Remote Similarity NPC253738
0.5455 Remote Similarity NPC57628
0.5417 Remote Similarity NPC66761
0.5417 Remote Similarity NPC483843
0.5263 Remote Similarity NPC471101
0.5222 Remote Similarity NPC294579
0.5222 Remote Similarity NPC144779
0.5205 Remote Similarity NPC211137
0.52 Remote Similarity NPC483886
0.5181 Remote Similarity NPC611111
0.5067 Remote Similarity NPC152440
0.5067 Remote Similarity NPC475759
0.5067 Remote Similarity NPC483888

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC87448 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