“A Broad-Spectrum Lasso Peptide Antibiotic Targeting the Bacterial Ribosome ”

Today, we share an important study published in Nature, which reports for the first time a novel lasso peptide antibiotic named lariocidin (LAR), produced by Paenibacillussp. M2. LAR potently targets the small ribosomal subunit of bacteria, exerting broad-spectrum antibacterial activity by inhibiting protein synthesis and inducing miscoding. Through genomic mining, heterologous expression, structural biology, and animal model validation, the study comprehensively elucidates the unique mechanism of action of LAR, demonstrating its low propensity for resistance development, low toxicity to eukaryotic cells, and significant efficacy in a murine infection model. This work not only identifies the first lasso peptide targeting the ribosome but also provides a new candidate drug framework for combating multidrug-resistant bacterial infections.

01 Research Background

Antibiotic resistance has become a severe global public health crisis, implicated in over 4.5 million deaths in 2019. Drug-resistant pathogens, including Gram-negative bacteria, are listed by the WHO as critical threats, making the development of novel antimicrobials urgent. The ribosome, the core machinery for bacterial protein synthesis, is a major target for existing antibiotics (e.g., aminoglycosides, tetracyclines). However, inhibitors targeting this site often have limited functional binding sites. Their long-term "overuse" and the cross-resistance arising from resistance gene mutations have significantly limited their utility. Against this backdrop, lasso peptides, a unique class of ribosomally synthesized and post-translationally modified peptides (RiPPs), possess a characteristic "lasso" three-dimensional structure (cyclization via an isopeptide bond between the N-terminus and an Asp/Glu side chain, with the C-terminal tail threading through the loop), conferring high stability. Some members (e.g., microcin J25, capistruin) are known to have antibacterial activity, but historically, they were only known to target RNA polymerase; no lasso peptide had been reported to inhibit the ribosome, a core target. Therefore, this study, through long-term cultivation of environmental strains (incubating soil samples for one year), screened and obtained Paenibacillussp. M2, whose metabolites showed strong inhibitory activity against multidrug-resistant Acinetobacter baumannii. Activity-guided isolation ultimately identified the novel antibiotic LAR—the first lasso peptide discovered to target the ribosome. This provides a key paradigm for developing antibacterial drugs acting on novel sites with novel modes of action, offering potential to address the increasingly serious challenge of resistant infections.

02 Innovative Highlights

Structural Innovation:​ The study found that the natural derivative LAR-B possesses a unique "double-loop knot" three-dimensional structure. This structure, formed by a second isopeptide bond (between Lys2 and Arg17), constitutes the first identified Class V lasso peptide. This innovative structure not only enhances the conformational stability of the molecule, allowing it to resist degradation by various proteases like pepsin and trypsin, but more importantly, provides a novel molecular scaffold for structure-based drug optimization, offering a solution to overcome the stability limitations of traditional lasso peptides.

Unique Binding Site:​ LAR exhibits unique target selectivity and a multi-faceted mechanism of action. It binds specifically to the h31 and h34 helix region of the 16S rRNA in the ribosomal 30S small subunit. This site does not overlap with the binding sites of known ribosome-targeting antibiotics like tetracycline (binds at the base of h34) or streptomycin (acts on h44 helix). This unique binding mode allows it to retain potent activity against clinically common resistant strains, with virtually no cross-resistance issues. Crystal structure analysis revealed that the C-terminal extension of LAR directly inserts into the ribosomal A-site, causing steric hindrance with the acceptor stem of the tRNA, thereby effectively inhibiting the EF-G-mediated ribosomal translocation process.

Dual Bactericidal Mechanism:​ On one hand, it stabilizes the ribosome in a pre-translocational state, blocking the relative movement of mRNA-tRNA on the ribosome and inhibiting the elongation step of protein synthesis. On the other hand, its interaction with the decoding center reduces the accuracy of aminoacyl-tRNA selection, leading to an approximately 15-20-fold increase in codon misreading frequency. Notably, LAR crosses the bacterial membrane in a membrane potential-dependent manner, a characteristic that allows it to enter cells without relying on any specific transporter protein. This enables it to exhibit excellent antibacterial activity against Gram-negative bacteria (e.g., A. baumannii) and mycobacteria that lack specific transport systems. 

03 Results and Discussion

3.1 Identification, Biosynthesis, and Structural Characterization of LAR

LAR (molecular weight 1870.06 Da) was purified from Paenibacillussp. M2 through activity-guided fractionation. Genomic analysis identified its biosynthetic gene cluster (lrcBGC), encoding typical elements like the precursor peptide LrcA and the cyclase LrcC. Heterologous expression confirmed this cluster is sufficient to produce LAR and its variants LAR-B (lacking Gly18 and forming a second isopeptide bond) and LAR-C (only lacking Gly18). NMR and crystallography revealed that LAR has a classic lasso structure, while the "double-loop" design of LAR-B likely enhances stability.

Fig. 1 | LAR and its BGC

3.2 Antibacterial Mechanism of LAR: Ribosome Targeting and Dual Inhibition

LAR exhibits bactericidal activity, specifically reducing colony counts by 10^4-fold after 1 hour of treatment at 10× MIC, but does not cause cell lysis, as indicated by no decrease in culture optical density. Membrane permeability assays using propidium iodide staining and membrane potential detection using DiOC2(3) dye showed that LAR does not disrupt membrane integrity. Fluorescently labeled LAR accumulated intracellularly, suggesting an intracellular target. Screening for resistant mutations in a sensitive E. coliSQ110ΔtolC strain revealed mutations concentrated at sites like U1052A and G1207A in the 16S rRNA, located in the h31/h34 helices of the small ribosomal subunit. In vitrotranslation assays showed that LAR significantly inhibited bacterial protein synthesis while having minimal effect on eukaryotic systems.

Fig. 2 | LAR exhibits bactericidal activity and targets bacterial protein synthesis.

3.3 Structural Biology Reveals Binding Site and Molecular Mechanism

By solving the complex structures of LAR and its variant LAR-B bound to the Thermus thermophilus70S ribosome, this study revealed its unique mechanism of action at the atomic level: LAR binds specifically to the head of the small ribosomal subunit, interacting with key residues like G530 and A1492 of the 16S rRNA, and achieves stable binding via a stacking interaction between Phe11 and U531; more importantly, LAR directly contacts the G31 phosphate of the A-site tRNA, structurally explaining its dual function of hindering tRNA-mRNA translocation and inducing codon misreading, a mechanism also independently verified by toeprinting assays; notably, this binding site partially overlaps with that of odilorhabdin but is completely distinct from the binding sites of classic antibiotics like tetracycline and streptomycin. This novel binding mode fundamentally explains the unique advantage of LAR's low propensity for cross-resistance.

Fig. 3 | Structure of LAR in complex with the T. thermophilus 70S ribosome.

3.4 In Vivoand In VitroActivity and Resistance Analysis

LAR is effective against clinically resistant bacteria such as carbapenem-resistant A. baumannii(MIC 8 µg/mL), and its activity is enhanced in the presence of serum. In a mouse neutropenic thigh infection model, the LAR treatment group (4 doses) reduced bacterial loads in the spleen, thigh, and blood by 100-fold at 24 hours and increased survival to 100%. Resistance experiments showed a low spontaneous mutation frequency for LAR (~2×10^-8), and overexpression of common resistance enzymes (e.g., methyltransferases, acetyltransferases) did not affect its activity, indicating a high resistance barrier.

Fig. 4 | Therapeutic efficacy of LAR in a mouse neutropenic thigh infection model

04 Conclusion and Future Perspectives

This study systematically identifies LAR as the first lasso peptide antibiotic targeting the ribosome. By binding to a novel site on the small ribosomal subunit, it simultaneously inhibits translocation and induces codon misreading, exhibiting excellent broad-spectrum antibacterial activity, a low tendency for resistance development, and good in vivotherapeutic efficacy. The unique "double-loop" structure of its natural variant LAR-B expands the structural diversity of the lasso peptide family, and the established heterologous expression platform lays a solid foundation for large-scale production. Future research could focus on discovering more structural analogs through genomic mining, rationally optimizing the pharmacokinetic properties of LAR, and exploring its synergistic effects with existing antibiotics against WHO priority pathogens. In summary, the discovery of LAR not only enriches the molecular arsenal of ribosome inhibitors but also provides an innovative paradigm for developing next-generation anti-resistant bacterial drugs.

Original Article:

Jangra M, Travin DY, Aleksandrova EV, ,et al. A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome. Nature. 2025 Apr;640(8060):1022-1030. doi: 10.1038/s41586-025-08723-7. Epub 2025 Mar 26. Erratum in: Nature. 2025 Sep;645(8082):E11.