Ribosomal stalling by short peptides targeting conserved sites in the ribosome: a new class of novel ribosomal antibiotics.

Tareq Tarabeih, from Noam Adir’s group, Schulich Faculty of Chemistry, Technion.

In light of the power of genomics and computational biology, our group developed a new strategy of proteomic analysis called Reverse Bioinformatics, a computational method able to detect short peptide sequences that are rarely present or are totally excluded from the cell proteome, revealing the existence of Under-represented sequences (for short we called them URS). The URS’s effect was examined in vivo in genetically modified E. coli able to express proteins with embedded URSs in a controlled manner. The expression of URS-protein led to a significant reduction in ribosomal activity, followed by cell damage and death, exhibiting irreversible inhibition of protein synthesis. Thus it can be suggested that Peptidyl compounds based on these sequences are potential ribosomal inhibitors [1]. Recently, we have developed novel ribosomal antibiotics based on the URSs for pathogenic bacteria by using synthetic short peptides containing the URSs. Bacterial growth was strongly inhibited when the bacterial cultures were exposed to the URSs. This study will also show the biochemical challenges we faced and provide insights on optimizing peptidyl compounds for antibiotic use. To learn more about the inhibition mechanisms caused by these peptides in the atomic resolution, we have determined the structures of 70S Ribosomes from E.coli and Salmonella by high-resolution Cryo-Electron Microscopy to 2.83Å, revealing the binding site of the URS peptide in the ribosome. The peptide was found within the ribosome exit tunnel, close to the peptidyl transfer center. More importantly, it can be suggested that peptide binding interferes with the functions of the highly conserved nucleotides A2602 and U2585 in the 23S rRNA [2]. So, we believe that the URS antibiotic development method can be a new approach that, within this research, will allow us to develop a significant number of peptidyl antibiotics able to target highly conserved sites on the ribosome, customized for specific organisms, which can provide a new way to fight against bacterial resistance.

References

1) Navon, Sharon et al (2016). Proceedings of the National Academy of Sciences113(26), 7166-7170.‏

2) Polacek, Norbert et al (2003). Molecular cell11(1), 103-112.‏