The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics

Abstract

Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by Streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. Biochemical and functional studies verified this finding and showed interference with peptide bond formation. Chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. These two antibiotics can bind to the ribosome simultaneously and display synergy in inhibiting bacterial growth. The binding site of lankacidin and lankamycin partially overlap with the binding site of another pair of synergistic antibiotics, the streptogramins. Thus, at least two pairs of structurally dissimilar compounds have been selected in the course of evolution to act synergistically by targeting neighboring sites in the ribosome. These results underscore the importance of the corresponding ribosomal sites for development of clinically relevant synergistic antibiotics and demonstrate the utility of structural analysis for providing new directions for drug discovery.lankamycin | ribosomes | synergism | resistance | rRNA

Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit

“…The [IC 50 ] of LM (Table 1) shows that compared to Ery it exerts a weaker inhibition of ribosomes by a few orders of magnitude (11). A comparison of the structures of LM-D50S complex with the Ery-50S complex (Fig.…”

“…However, as these differences are rather modest, it was assumed that LM should bind to the ribosome at the nascent protein exit tunnel in similar position and mode as erythromycin. Interestingly, although LM and LC are able to bind simultaneously, erythromycin disrupts the binding of LC (11).…”

“…This ribosome was shown to serve as an excellent model for eubacterial ribosomes, including bacterial pathogens, and compared them to the structure of the (LC-D50S) complex that has been recently reported (11).…”

“…LC, a 17-membered conjugated macrocycle, bridged by a 6-membered lactone, binds in the peptidyl transferase center (PTC) in the 50S subunit (11). LM, a member of the macrolide family, differs from erythromycin in its substituent groups on the macrolactone ring, as well as the two deoxysugars at the C-3 and C-5 positions.…”

Giant linear plasmids in Streptomyces: a treasure trove of antibiotic biosynthetic clusters

“…2 This idea proved to be true by a collaborative work with Drs Yonath and Mankin. 54 Furthermore, crystallographic analysis and chemical probing showed that two antibiotics were bound to a different ribosome site, lankacidin to the peptidyl transferase center and lankamycin to the nascent peptide exit tunnel, leading to a synergistic inhibition of peptide formation. A similar super-cluster for cephamycin and clavulanic acid was found in S. clavuligerus, 55 where the two metabolites function synergistically as an antibiotic and a b-lactamase inhibitor, respectively, and their biosynthesis is regulated by the SARP gene ccaR.…”