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Interactions between Macromolecules and their Ligands in Solution State

Objectives

  • to compare the free and bound structures of several macrolides possessing a variety of biological activities
  • to identify areas of the macrolide which are the closest to the E. coli ribosome surface and are most likely involved in binding to the active site

Comparison of free and bound structures of macrolides

  • Analysis of trNOESY experiments showed that macrolide conformation does not change significantly upon binding to the E. coli ribosome


Comparison of STD signal enhancements and distances from ribosome taken from X-ray structure of co-crystallized azithromycin with H. Marismortui  (*peak overlap)

STD NMR as a tool

  • Competition experiment has proved the examined macrolide binds to the active site
  • STD enhancements observed for azithromycin and distances between azithromycin and ribosome (determined in X-ray co-crystallized structure of azithromycin and H. marismortui) showed a good correlation
  • STD NMR can be used as a tool to monitor the interactions between macrolides and ribosome

Epitope mapping

Macrolides have three distinct areas which are the closest to the ribosome:
  • methyl group 15 (macrocyclic ring)
  • 3”Me and 3”OMe (cladinose)
  • dimethylamino group (desosamine)

References

  • P. Novak, J. Barber, A. Čikoš, B. Arsic, J. Plavec, G. Lazarevski, P. Tepeš and N. Košutić-Hulita,
    Free and bound state structures of 6-O-methyl homoerythromycins and epitope mapping of their interactions with ribosomes
    Bioorg Med Chem 2009, 17, 5857-5867

 
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