Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition

Abstract

With bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (AMPs) have become a promising area of focus in antibiotic research. AMPs are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. Proline-rich antimicrobial peptides (PrAMPs) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. Recently, it was reported that some PrAMPs, such as Bac71–35, oncocins and apidaecins, bind and inactivate the bacterial ribosome. Here we report the crystal structures of Bac71–35, Pyrrhocoricin, Metalnikowin and two oncocin derivatives, bound to the Thermus thermophilus 70S ribosome. Each of the PrAMPs blocks the peptide exit tunnel of the ribosome by simultaneously occupying three well characterized antibiotic-binding sites and interferes with the initiation step of translation, thereby revealing a common mechanism of action used by these PrAMPs to inactivate protein synthesis. Our study expands the repertoire of PrAMPs and provides a framework for designing new-generation therapeutics.

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1

“…First, these factors might test-drive the tunnel as a form of quality control. Second, the presence of their C termini along the entire path of the tunnel might help prevent potential translation inhibitors—for example, the tunnel-targeting antimicrobial peptides produced by insects and mammals 41,42 —from accessing the tunnel.…”

Host defense antimicrobial peptides as antibiotics: design and application strategies

“…Proline-rich AMPs (PrAMPs) have recently been shown to bind either the 70S or 50S subunit of ribosomes of Gram-negative bacteria [18,19,36]. Gagnon et al [37] confirmed this mechanism by determining the crystal structures of several PrAMPs, such as Bac7 1–35 and pyrrhocoricin (Table 1) in complex with a ribosome. The N-terminal twelve residues of Onc112 are critical for partially occluding the ribosomal exit tunnel and simultaneously overlapping the aminoacyl (A) site, preventing elongation after initiation [38,39].…”

First Total Synthesis and Biological Screening of a Proline-Rich Cyclopeptide from a Caribbean Marine Sponge

“…The possible mechanism of action for the antimicrobial effect of heptacyclopeptide stylissamide G might involve the active transport inside the bacterial cell where it binds and inactivates specific targets such as the bacterial ribosome and thereby inhibits protein synthesis like other proline-rich antimicrobial peptides (PRAPs) [66]. This implies that PRAPs can be used as molecular hooks to identify the intracellular or membrane proteins that are involved in their mechanism of action and that may be subsequently used as targets for the design of novel antibiotics with mechanisms different from those now in use.…”