The aim of our research is the fight against antibiotic resistance. More specifically, our work focuses on antimicrobial peptides as an alternative to conventional antibiotics.

Context
Since the discovery of penicillin, humans have widely developed and used antibiotics to prevent microbial infections. However, the intensive and sometimes unjustified use of these compounds has led to the emergence of pathogens resistant or multi-resistant to all classes of antibiotics. In 2016, J. O'Neill reported that, if no action is taken, the number of deaths due to antimicrobial resistance could reach 10 million a year by 2050. This major public health threat is prompting scientists to find new molecules, ideally natural ones, with different structures and modes of action to counter resistance phenomena evolutionary developed. A promising alternative is antimicrobial peptides for which some of them are currently in clinical development or have been approved.
In this context, bacteria are a treasure trove of multiple classes of naturally occurring antimicrobial peptides, more commonly known as bacteriocins. One example is the ribosomally synthesized and post-translationally modified peptides (RiPPs). Of peptidic nature, their ribosomal synthesis differentiates them from conventional antibiotics. An advantage of these peptides is that they have an activity spectrum often directed against species in the same ecological niche as the producing bacteria. Numerous studies show that the intestinal microbiome plays a very important role in the health of the host. For example, the barrier effect implemented by commensal bacteria is achieved through the production of antimicrobial molecules including bacteriocins.

Ruminococcine C antimicrobial peptides
Our current work on the antimicrobial peptides focuses on the bacterium Ruminococcus gnavus present in the digestive tract of about 90% of the population. This strain produces five compounds, the Ruminococcins C (RumC1 to C5) belonging to the sactipeptide subgroup of RiPPs. The biosynthesis of these peptides involves a radical-SAM enzyme, called sactisynthase, which in the presence of its cofactor S-adenosylmethionine (SAM), introduces covalent thioether bonds into the substrate. More precisely, the thioether bridge concerns the thiol group of a cysteine and the alpha-carbon of another amino acid. The key results conferring unique properties to RumCs are presented here as highlights. In summary, the post-translational modification step introduces four covalent thioether bonds into the peptides, which create a highly compact double hairpin folding. This structure confers to RumCs a remarkable bactericidal activity at micro-molar concentrations on Gram-positive pathogens including resistant and multi-resistant strains. Moreover, no resistant bacterial clones have emerged following prolonged exposure to RumCs. Added to this efficacy, RumCs are not significantly toxic to a number of human cell lines or intestinal explants. Interestingly, RumC1, the most active peptide, is also effective in vivo to protect mice from Clostridium perfringens infection at a lower dose than the control antibiotic, vancomycin. Finally, RumCs are the only members of the sactipeptide family to display other beneficial properties for the human host, such as anti-inflammatory and wound-healing effects.

Grants
RUMisBAC (ANR-20-CE44-0021), French ANR, 2020-2024
Mode of action and bioengineering of RumC sactipeptides to overcome antibiotic resistance of Gram-positive bacteria

RUMBA (ANR-15-CE21-0020), French ANR, 2016-2020
Biosynthetic, structural and functional characterizations of RumC peptides, a family of bacteriocins as a viable alternative to conventional antibiotics

Publications
Mechanistic and functional aspects of the Ruminococcin C sactipeptide isoforms. Shamseddine L, Roblin C, Veyrier I, Basset C, De Macedo L, Boyeldieu A, Maresca M, Nicoletti C, Brasseur G, Kieffer-Jaquinod S, Courvoisier-Dezord E, Amouric A, Carpentier P, Campo N, Bergé M, Polard P, Perrier P, Duarte V*, Lafond M*. iScience, 2023, 26(19):, 107563

Peptide and Protein Engineering for Biotechnological and Therapeutic Applications. Chapter 3: Antimicrobial Ribosomally Synthesized and Post-Translationally Modified Peptides as a Source of Alternatives to Antibiotics: A Focus on the Sactipeptides and Ranthipeptides Subclasses. Roblin C, Rousselot-Pailley P, Duarte V, Perrier J, Lafond M. World Scientific Publishing Co., 2023, 57-114

The Multifunctional Sactipeptide Ruminococcin C1 Displays Potent Antibacterial Activity In Vivo as Well as Other Beneficial Properties for Human Health. Roblin C, Chiumento S, Jacqueline C, Pinloche E, Nicoletti C, Olleik H, Courvoisier-Dezord E, Amouric A, Basset C, Dru L, Ollivier M, Bogey-Lambert A, Vidal N, Atta M, Maresca M, Devillard E, Duarte V, Perrier J, Lafond M*. International Journal of Molecular Sciences. 2021, 22(6): 3253

The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties. Roblin C, Chiumento S, Bornet O*, Nouailler M, Müller CS, Jeannot K, Basset C, Kieffer-Jaquinod S, Couté Y, Torelli S, Le Pape L, Schünemann V, Olleik H, De La Villeon B, Sockeel P, Di Pasquale E, Nicoletti C, Vidal N, Poljak L, Iranzo O, Giardina T, Fons M, Devillard E, Polard P, Maresca M, Perrier J, Atta M, Guerlesquin F, Lafond M*, Duarte V*. Proc. Natl. Acad. Sci., 2020, 117(32): 19168-19177

Ruminococcin C, a promising antibiotic produced by a human gut symbiont. Chiumento S, Roblin C, Kieffer-Jaquinod S, Tachon S, Leprètre C, Basset C, Aditiyarini D, Olleik H, Nicoletti C, Bornet O, Iranzo O, Maresca M, Hardré R, Fons M, Giardina T, Devillard E, Guerlesquin F, Couté Y, Atta M, Perrier J, Lafond M*, Duarte V*. Science Advances, 2019, 5(9): eaaw9969
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