Natural Product: NPC146540

Natural Product IDNPC146540
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Melilotoside
IUPAC Name (E)-3-[2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-enoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL374212
PubChem CID 5280759
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic 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 GVRIYIMNJGULCZ-ZMKUSUEASA-N
Standard InCHI InChI=1S/C15H18O8/c16-7-10-12(19)13(20)14(21)15(23-10)22-9-4-2-1-3-8(9)5-6-11(17)18/h1-6,10,12-16,19-21H,7H2,(H,17,18)/b6-5+/t10-,12-,13+,14-,15-/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2ccccc2/C=C/C(=O)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO16949 Aster oharai Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[12193011]
NPO17655 Heliotropium amplexicaule Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30762 Melilotus suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16949 Aster oharai Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14125 Corydalis ochotensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11568 Dendroctonus ponderosae Species Curculionidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14880 Ephydatia syriaca Species Spongillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8527 Holboellia fargesi Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10437 Periploca calophylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17245 Prumnopitys ferruginoides Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6958 Pseudaegle trifoliata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO16735 Sophora tometosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18109 Thorecta marginalis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14125 Corydalis ochotensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17655 Heliotropium amplexicaule Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10437 Periploca calophylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30762 Melilotus suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10437 Periploca calophylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14125 Corydalis ochotensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17655 Heliotropium amplexicaule Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30762 Melilotus suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17245 Prumnopitys ferruginoides Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10437 Periploca calophylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11568 Dendroctonus ponderosae Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14125 Corydalis ochotensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17655 Heliotropium amplexicaule Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16735 Sophora tometosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8527 Holboellia fargesi Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6958 Pseudaegle trifoliata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16949 Aster oharai Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14880 Ephydatia syriaca Species Spongillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18109 Thorecta marginalis Species Thorectidae 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
NPT4667 Protein complex Integrin alpha-V/beta-3 Homo sapiens IC50 = 5.97 ug.mL-1 PMID[17027271]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT81 Cell line A549 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT90 Cell line DU-145 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT139 Cell line HT-29 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT319 Cell line B16 Mus musculus IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT992 Organism Entamoeba histolytica Entamoeba histolytica IC50 = 12.5 ug.mL-1 DOI[10.1007/s00044-011-9767-1]

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 NPC146540 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
0.7069 Intermediate Similarity NPC251102
0.7069 Intermediate Similarity NPC210298
0.6613 Remote Similarity NPC232673
0.6508 Remote Similarity NPC269421
0.6308 Remote Similarity NPC37468
0.6308 Remote Similarity NPC186418
0.6207 Remote Similarity NPC226712
0.6207 Remote Similarity NPC608788
0.589 Remote Similarity NPC294193
0.5873 Remote Similarity NPC164599
0.5614 Remote Similarity NPC212729
0.5614 Remote Similarity NPC604498
0.5455 Remote Similarity NPC228907
0.541 Remote Similarity NPC200092
0.5385 Remote Similarity NPC210478
0.5373 Remote Similarity NPC34456
0.5254 Remote Similarity NPC269242
0.5246 Remote Similarity NPC60589
0.5246 Remote Similarity NPC469708
0.5231 Remote Similarity NPC604356
0.5167 Remote Similarity NPC294470
0.5135 Remote Similarity NPC185103
0.5077 Remote Similarity NPC218685
0.5077 Remote Similarity NPC49074
0.507 Remote Similarity NPC474044

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC146540 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
0.6207 Remote Similarity NPD1091 Pre-clinical

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