Peptide Antibiotics Targeting the Large Ribosomal Subunit

The large ribosomal subunit is an important component of the ribosome and a potential target for new antibiotics. Peptide antibiotics targeting the large ribosomal subunit have become a hot topic in the development of the next generation of antibiotics. Unlike traditional antibiotics, peptide antibiotics are small molecules composed of amino acids that can target specific molecular structures with precision. This is one of the reasons why peptide antibiotics are attracting widespread attention. It has been reported that several research laboratories have conducted related studies on peptide antibiotics targeting the large ribosomal subunit. These antibiotics can bind to specific positions on the large subunit, thereby preventing the normal function of the ribosome, leading to bacterial death. Most of the binding sites for peptide antibiotics targeting the 50S subunit are clustered around the peptidyl transferase center (PTC) formed by peptide bonds and the exit tunnel for nascent peptides, such as streptogramins A, streptogramins B, and klebsazolicin. In contrast, sulfide-containing antibiotics, such as thiostrepton, bind at the translation factor binding site within the large subunit, away from the PTC and exit tunnel.

Streptogramin Antibiotics Act Synergistically on the Large Ribosomal Subunit

Streptogramin antibiotics are produced by several species of Streptomyces, including two structurally different subclasses. Streptogramin A contains a 23- membered macrocyclic polyketide/nonribosomal peptide hybrids. The binding site of streptogramins A spans the A-site cleft and also encroaches on the P-site of the bacterial ribosome. For example, the SA antibiotic virginiamycin M binds in the PTC, causing rearrangement of nucleotides A2062 and U2585. The oxazole ring also extends into the A-site cleft and establishes hydrophobic interactions, inhibiting the binding of A- and P-site substrates. Another subclass of streptogramins, streptogramins B, contains a 19-membered macrocyclic depsipeptides, targeting the exit tunnel of the ribosome for nascent peptides.

Proline-Rich Antimicrobial Peptides Exhibit Distinct Mechanisms of Action

Unlike most antimicrobial peptides (AMPs) that kill bacteria by disrupting the bacterial membrane, proline-rich antimicrobial peptides (PrAMPs) can penetrate the bacterial membrane and inhibit bacterial growth by targeting intracellular processes such as protein synthesis. PrAMPs are products of the innate immune system that are rich in proline and have been shown to bind to the ribosome and inhibit protein synthesis in vivo and in vitro. Two different modes of action have been identified for PrAMPs: Type I PrAMPs allow translation initiation but block the transition to the elongation phase, while Type II PrAMPs allow translation initiation and elongation but block the translation termination phase.

Klebsazolicin Obstructs the Ribosomal Exit Tunnel

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are among the most diverse classes of antibacterial agents synthesized by bacteria, including those in the human microbiome. Klebsazolicin (KLB) is the first linearly azole-containing RiPP, derived from the human pathogen Klebsiella pneumonia. Structural analysis shows that KLB overlaps with the binding sites of macrocyclic lactones, streptogramins B, and PrAMPs in the exit tunnel for nascent peptides and blocks the tunnel. This inhibition suppresses synthesis of proteins by blocking the elongation of nascent peptides.

Thiopeptide Antibiotics That Interfere with Translation Factor Binding

Thiopeptide antibiotics, such as thiostrepton, nosiheptide, and micrococcin, inhibit translation by interacting with translation factor EF-Tu or by directly binding to the ribosome. These antibiotics are synthesized by the ribosome as precursor peptides, which are then translated and modified post-translationally to produce bioactive compounds. Thiopeptide antibiotics are effective against Gram-positive bacteria and Plasmodium falciparum, but cannot be used in large quantities due to disadvantages such as low water solubility and poor bioavailability.

Fig. 1 Binding site of GE81112 on the 30S subunit.¹

Peptide antibiotics targeting the large ribosomal subunit can interact with the ribosome and interfere with translation in diverse ways. Modified peptides can be developed to improve the characteristics of peptide antibiotics by targeting additional sites of interaction with the ribosome. Creative Biolabs has assembled an experienced professional team dedicated to ribosome research, providing customized services for global clients, including but not limited to Ribosome Separation and Extraction service and Ribosome Analysis 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.