Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria

Abstract

Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate the structural basis of ribosome-antibiotic interactions, we determined the high-resolution X-ray structures of the 50S ribosomal subunit of the eubacterium Deinococcus radiodurans, complexed with the clinically relevant antibiotics chloramphenicol, clindamycin and the three macrolides erythromycin, clarithromycin and roxithromycin. We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavity and do not involve any interaction of the drugs with ribosomal proteins. Here we report the details of antibiotic interactions with the components of their binding sites. Our results also show the importance of putative Mg+2 ions for the binding of some drugs. This structural analysis should facilitate rational drug design.

Targeting Antibiotic Resistance

“…A number of co‐crystal structures of macrolides bound to the ribosome have been published and they show that the main component in the binding pocket is A2058Ec 54, 55, 56. Key interactions include polar contacts between the functional groups of the C5 desosamine sugar and residues A2058Ec and A2059Ec, as well as hydrogen bonds between the three lactone hydroxy groups and the 50S ribosomal subunit (Figure 10).…”

Synthesis and antibacterial activity of novel 11,12-cyclic carbonate azithromycin 4″-O-carbamate derivatives

“…11 Accordingly, we hoped that a prolonged anchor group at the C-4 00 position might increase the affinity for the new binding sites of the nucleotides in the peptide tunnel, further enhancing antibacterial activity against resistant strains. On the basis of the result Antibacterial activities of 4 00 -O-carbamate derivatives C Ma et al of the high-resolution X-ray co-crystal structure study, 11,19 which showed the overlapping of the macrolide binding structure with clindamycin and chloramphenicol, we designed a series of novel 15-membered AZM derivatives with the C-4 00 prolonged side chains, the length of which was eight or nine atoms distant from oxygen atom at the C-4 00 position to the aromatic ring. These compounds with prolonged side chains showed remarkably improved activity against strains encoded by the erm gene or the erm and mef genes, compared with the corresponding compounds with the C-4 00 short arylalkyl side chain reported by previously by us.…”

“…8 This results in tighter binding to ribosomes and imparts some activity against methylated ribosomes in some species. 9,10 The study of the high-resolution X-ray co-crystal structures has revealed that macrolides bind at the entrance to the peptide tunnel in the 23S rRNA, and the cladinose group in their structures is located at and fits with the cavity formed by G2505, C2610 and C2611 in domain V. 11 On the basis of the results of the X-ray co-crystal structure study, many new derivatives of macrolides for the effective management of erythromycin resistance have been investigated by different research groups. 12 These investigations have led to the discovery of 4 00 -modified macrolide derivatives such as CP-544372 13 and A-60565 14 ( Figure 1).…”

“…11 The overlapping of the macrolide binding structure with clindamycin and chloramphenicol is very informative for the development of new 4 00 -modified macrolide derivatives with the activity against erythromycin-resistant strains. Particularly, the high nucleotide content in the peptide tunnel gives rise to a number of possible interactions such as hydrogen bonding, p-stacking, as well as electrostatic interactions.…”

Identification of Macrolide Antibiotic-binding Human_p8 Protein

“…Macrolide antibiotics, represented by erythromycin A (ERY, 2) and its structural homologues, specifically bind to the bacterial 50S ribosomal subunit resulting in the inhibition of bacterial protein biosynthesis [2]. CLA (1) is also commonly used to target gastric Helicobacter pylori, which is implicated in both gastric ulcers and cancer [3].…”