cyclothialidine   Click here for help

GtoPdb Ligand ID: 10988

Synonyms: Ro 09-1437
Compound class: Natural product
Comment: Cyclothialidine is a potent DNA gyrase inhibitor, isolated from Streptomyces filipinensis following microbial broth screening [4]. It belongs to a novel class of antibacterial compounds, containing a unique 12-membered lactone ring that is partly integrated into a pentapeptide chain, that exhibit broad-spectrum in vitro activity against Gram-positive bacteria. Further development of cyclothialidine has been precluded due to low growth-inhibitory activity against intact bacterial cells but analogues with improved in vivo efficacy have been synthesized [1].
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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.

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View interactive charts of activity data across species
2D Structure
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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.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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.

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Hydrogen bond acceptors 15
Hydrogen bond donors 9
Rotatable bonds 10
Topological polar surface area 303.45
Molecular weight 641.2
XLogP -4.34
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES OCC(C(=O)N1CC[C@H]([C@H]1C(=O)N[C@H]1COC(=O)c2c(C)c(O)cc(c2CSC[C@H](NC1=O)C(=O)N[C@H](C(=O)O)C)O)O)N
Isomeric SMILES OCC(C(=O)N1CC[C@H]([C@H]1C(=O)N[C@H]1COC(=O)c2c(C)c(O)cc(c2CSC[C@H](NC1=O)C(=O)N[C@H](C(=O)O)C)O)O)N
InChI InChI=1S/C26H35N5O12S/c1-10-17(34)5-18(35)12-8-44-9-15(22(37)28-11(2)25(40)41)30-21(36)14(7-43-26(42)19(10)12)29-23(38)20-16(33)3-4-31(20)24(39)13(27)6-32/h5,11,13-16,20,32-35H,3-4,6-9,27H2,1-2H3,(H,28,37)(H,29,38)(H,30,36)(H,40,41)/t11-,13?,14-,15-,16+,20-/m0/s1
InChI Key HMHQWJDFNVJCHA-ZPGBQQFCSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Bioactivity Comments
Cyclothialidine inhibits Escherichia coli DNA gyrase in vitro, with an IC50 of 30 ng/ml [4] and competitively inhibits the ATPase activity of DNA gyrase with a Ki of 6nM [3].
However, the compound has low growth-inhibitory activity against intact bacterial cells, presumably due to poor penetration across the bacterial cytoplasmic membrane [2].
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
DNA gyrase subunit B E.coli Inhibitor Competitive 8.2 pKi - 3
⤷ pKi 8.2 (Ki 6x10-9 M) Cyclothialidine competitively inhibits the ATPase activity of DNA gyrase [3]
Whole organism assay data
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MOA/likely target Sp. Assay description Type Action Value Parameter Concentration range (M) Reference
DNA gyrase subunit B E.coli - Inhibition - - - 2
⤷ MIC >128 μg/ml [2]