borrelidin   Click here for help

GtoPdb Ligand ID: 11306

Synonyms: (-)-borrelidin
Antimalarial Ligand
Compound class: Natural product or derivative
Comment: Borrelidin is a macrolide antibacterial originally isolated from Streptomyces. It is a noncompetitive inhibitor of both bacterial and eukaryotic threonyl-tRNA synthetases (also known as threonine--tRNA ligase), exhibiting antibacterial, antimalarial and antiangiogenic activities.

The Malaria tab on this ligand page provides additional curator comments of relevance to the Guide to MALARIA PHARMACOLOGY
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 7
Hydrogen bond donors 3
Rotatable bonds 2
Topological polar surface area 127.85
Molecular weight 489.31
XLogP 4.67
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

✖
Canonical SMILES N#C/C/1=C/C=C/C[C@H](OC(=O)C[C@@H]([C@H](C[C@H](C[C@H](C[C@@H]([C@H]1O)C)C)C)C)O)[C@@H]1CCC[C@H]1C(=O)O
Isomeric SMILES N#C/C/1=C/C=C/C[C@H](OC(=O)C[C@@H]([C@H](C[C@H](C[C@H](C[C@@H]([C@H]1O)C)C)C)C)O)[C@@H]1CCC[C@H]1C(=O)O
InChI InChI=1S/C28H43NO6/c1-17-12-18(2)14-20(4)27(32)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(33)34)35-26(31)15-24(30)19(3)13-17/h5-6,8,17-20,22-25,27,30,32H,7,9-15H2,1-4H3,(H,33,34)/b6-5+,21-8-/t17-,18+,19-,20-,22+,23+,24-,25-,27+/m0/s1
InChI Key OJCKRNPLOZHAOU-UGKRXNSESA-N
Bioactivity Comments
Borrelidin is toxic at low concentrations in human cell culture (HEK293 cells, IC50 of 345 nM), and it thought to inhibit human threonyl-tRNA synthetase 1 (TARS1)[1].
In P. falciparum, borrelidin acts rapidly and has potent asexual blood stage activity against both drug-sensitive and drug-resistant strains of the parasite.
Whole organism assay data
Key to terms and symbols Click on species/strain names for details Click column headers to sort
MOA/likely target Sp. Assay description Type Action Value Parameter Concentration range (M) Reference
Plasmodium falciparum threonyl-tRNA synthetase Pf3D7

Plasmodium falciparum 3D7

P. falciparum strain 3D7 (Pf3D7) was derived from isolate NF54 by limiting dilution. The complete genome of Pf3D7 has been sequenced (GenBank: LN999946.1).
Pf3D7 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is sensitive to a panel of antimalarial compounds including chloroquine and pyrimethamine.
✖
 Parasite growth inhibition assay - - 8.9 – 9.0 pIC50 - 1
⤷ pIC50 9.0 (IC50 9.7x10-10 M) Parasite lactate dehydrogenase (pLDH ) assay following 96 hours in culture [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
pIC50 8.9 (IC50 1.24x10-9 M) Parasite lactate dehydrogenase (pLDH ) assay following 48 hours in culture [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
Plasmodium falciparum threonyl-tRNA synthetase PfFCR3

Plasmodium falciparum FCR3

P. falciparum strain FCR3 (PfFCR3) was originally isolated from a patient in The Gambia, West Africa in 1976.
PfFCR3 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4). Differences in sensitivity of PfFCR3 clones to chloroquine have been reported, with the original isolate that was chloroquine sensitive rapidly acquiring resistance in culture (PMID: 7031656, PMID: 51801).
✖
 Parasite growth inhibition assay - - 8.7 pIC50 - 2
⤷ pIC50 8.7 (IC50 1.8x10-9 M) Parasite lactate dehydrogenase (pLDH ) assay [2]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
Plasmodium falciparum threonyl-tRNA synthetase PfK1

Plasmodium falciparum K1

P. falciparum strain K1 (PfK1) was isolated in Kanchanaburi, Thailand in 1979.
PfK1 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is reported to be a multidrug-resistant strain.
✖
 Parasite growth inhibition assay - - 8.7 pIC50 - 2
⤷ pIC50 8.7 (IC50 1.9x10-9 M) Parasite lactate dehydrogenase (pLDH ) assay. [2]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)