Peptide Antibiotics Targeting the Small Ribosomal Subunit

In recent years, the overuse of antibiotics and the increasing problem of antibiotic pollution from major environmental sources such as purines and tetracyclines have resulted in the growing issue of bacterial resistance in the medical field. Therefore, the development of new antibiotics has become a common area of focus for researchers. Among them, peptide antibiotics targeting ribosomal small subunits have received much attention. There are currently five classes of peptide antibiotics known to target ribosomal small subunits, with edeine and GE81112 targeting translation initiation, while dityromycin/GE82832, tuberactinomycin (viomycin and capreomycin) and the odilorhabdin family inhibit translocation or decoding steps.

Fig.1 Small-molecular antibiotics on the bacterial ribosome.¹

Edeine Inhibits Initiation Complex Formation

Edeine (EDE) antibiotics are pentapeptide amide antibiotics produced by Bacillus brevis Vm4 bacteria, which are active against Gram-positive, Gram-negative bacteria, and mycoplasma. EDE has a single binding site on the small 30S subunit, which is associated with the binding of initiator tRNA and can indirectly affect the binding of P-site tRNA by blocking the mRNA pathway. EDE induces the formation of base pairs at positions h23 and h24, obstructing the pathway of mRNA. EDE inhibits the formation of 30S pre-initiation complexes by blocking the binding of initiator tRNA to the 30S subunit, thereby preventing the formation of an effective 70S initiation complex.

GE81112 Targets Translation Initiation

GE81112 is a tetrapeptide antibiotic synthesized by certain Streptomyces species through a series of non-ribosomal peptide synthetases and non-ribosomal peptide hydrolases. Besides uS13, little interaction between GE81112 and other components of the 30S subunit has been observed, indicating that the major determinant for GE81112 binding is the tRNA present at the P site. Chemical probing experiments have shown that GE81112 binding causes conformational changes in the h44/h45/h24a interface of the 30S subunit, which is believed to promote initiation tRNA while preventing formation of the "locked" 30S-PIC, thereby inhibiting the joining of the 50S subunit.

GE82832/Dityromycin Targets Translation Elongation

GE82832 is a peptide antibiotic produced by the strain Streptosporangium cinnabarinum, which inhibits tRNA translocation and 30S subunit interactions through mutual interactions. The crystal structure of the 70S ribosome complexed with both erythromycin and GE82832 indicates that these antibiotics are unique in that they bind only to the ribosomal protein (uS12) and not rRNA. uS12 is located at the shoulder of the 30S subunit and serves as a control element in tRNA selection and tRNA-mRNA translocation through the ribosome. Erythromycin binding to protein uS12 captures EF-G in a compact conformation on the ribosome, inhibiting EF-G-mediated tRNA translocation.

Tuberactinomycins Viomycin and Capreomycin Inhibit Translocation

Viomycin and capreomycin are cyclic pentapeptide antibiotics containing non-classical amino acids, produced by non-ribosomal peptide synthase (NRPS) found in various Streptomyces species. Tuberculin has a single binding site on the ribosome, spanning the ribosome interface between h44 of the 30S small subunit and H69 of the 50S large subunit. Biophysical studies have shown that viomycin stabilizes the rotational conformation of the ribosome by mixing A/P- and P/E-tRNA. Viomycin is considered a translocation inhibitor as it stabilizes the rotational conformation of the ribosome by mixing A/P and P/E-tRNA to inhibit translation. This has been confirmed by cryo-electron microscopy.

Odilorhabdins Cause Miscoding by Tethering tRNA to the Ribosome

Odilorhabdins (ODLs) are similar to tuberactinomycins, produced by NRPS, but they are derived from the gram-negative bacteria Xenorhabdus nematophila, which is symbiotic with soil nematodes. ODLs bind to the decoding center of the 30S subunit and promote misreading. At the binding site, ODL interacts with both the 16S rRNA and the anticodon loop of A-site tRNA. The direct interaction between ODL and the anticodon of tRNA not only promotes misreading, but also potentially inhibits the transition of tRNA from the A site to the P site, thereby inhibiting translocation at high antibiotic concentrations.

Research on peptide antibiotics targeting small subunits of the ribosome is still ongoing and promises to be a major tool in addressing the challenge of drug resistance. Creative Biolabs has assembled a professional team dedicated to ribosome research, providing customized services for global customers, including but not limited to Ribosomal Transcriptome service and Ribosomal Proteomics service. If you are interested in our ribosome services, please contact us immediately to obtain more information for free.

Reference

1. Polikanov, Yury S., et al. "The mechanisms of action of ribosome-targeting peptide antibiotics." Frontiers in molecular biosciences 5 (2018): 48.