1 GHz NMR investigation of the binding of peptidyl transferase inhibitor antibiotics to conserved secondary structural motifs of 23S ribosomal RNAs. .

1 GHz NMR investigation of the binding of peptidyl transferase inhibitor antibiotics to conserved secondary structural motifs of 23S ribosomal RNAs. Vasudevan RameshSchool of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess Street, Manchester, M1 7DN, U.K. *E-mail: [email protected] growing challenge of antibiotic resistance being witnessed in recent times has prompted intense efforts to elucidate the mechanism of action of antibiotics at the molecular level. Blocking protein synthesis is an effective way of combating bacterial infection and many antibiotics function in just this manner. The most important functional site on the ribosome is the 'peptidyl transferase centre' and previous resistance studies using a number of antibiotics have located this within 23S like rRNAs in the highly conserved central circle of domain V. We have successfully determined the NMR structures of the RNA binding, peptidyl tranferase inhibitor antibiotics Amicetin, Blasticidin S and Gougerotin and the structures all exhibit a stable conformation, stabilised by intramolecular hydrogen bonds.1 Amicetin was observed to be folded, distinctly different from the linear, extended conformation previously determined by X-ray crystallography.2 All the NMR structures revealed a similar conformation in the analogous regions of their chemical structure, suggesting that hybrid antibiotics could be generated. The NMR structures of the amicetin binding E. coli. 29-mer, H. h. 29- and 37-mers and B. subtilis 27-mer RNA motifs have been determined using ultra high field 1 GHz spectroscopy and all the motifs form stable, well folded A-form RNA conformations.1 Addition of Amicetin to the RNA samples were accompanied by discrete changes to the spectra which can be interpreted to changes induced in the local conformation of the RNA motifs and the Amicetin, arising from the formation of a complex, between the Amicetin and the bulge region of the particular motif.1,3References (1) John King, PhD Thesis (2011), University of Manchester, Manchester, U.K.(2) C. Shammas, J. Donarski, and V. Ramesh (2007) Magn Res. Chem. 45, 133-141(3) J. Donarski, C. Shammas, R. Banks and V. Ramesh (2006) J. Antibiotics, 59(3) 177-183Acknowledgement We thank the EU Bio-NMR consortium for the valuable support and Dr Moreno Lelli, RALF-NMR Facility, Lyon (France) for his expert technical assistance with the 1 GHz NMR experiments.