DS04 - Vie, santé et bien-être

Therapeutic innovations in antibiotics: focus on the targeting of toxin-antitoxin systems using small-molecule RNA binders – InnovAntibio

Submission summary

There is currently an urgent need for new antibiotics in order to overcome the steady emergence of multidrug-resistant bacteria and the associated human and economic cost. For the development of new antimicrobial agents, two major issues must be overcome: the difficulty to permeate bacterial membranes and the toxicity of compounds. Furthermore, the available number of specific targets remains restricted. All these issues led to a strong decrease in the efforts done toward the discovery of new antibiotics both in industry and in academia. In this context, the purpose of this project is the discovery of new antibiotics targeting original and so far unexploited targets: bacterial toxin-antitoxin (TA) systems. TA systems are small genetic elements composed of a toxin gene and its cognate antitoxin both coding for corresponding toxin and antitoxin products. The toxins of all known TA systems are proteins able to inhibit bacterial cell growth or lead to cell death, whereas the antitoxins are either proteins or small regulatory RNAs that neutralize the toxin. Here, we decided to target type I TA systems where the antitoxin is a non-coding RNA that binds to the messenger RNA (mRNA) coding for the toxin thus inhibiting its translation. In order to validate the proposed strategy, we propose to target a particular type I TA system of the major human gastric pathogen Helicobacter pylori which is a gram negative bacterium infecting about 50% of the entire world population. We recently discovered a new family of type I TA systems in H. pylori called AapA/IsoA systems whose regulation relies on a double kissing-loop interaction between the AapA toxin mRNA and the IsoA antitoxin RNA. This TA system is present in multiple copies on the chromosome (multiple loci) of this bacterium. A small molecule that would be able to inhibit the interaction between the antitoxin and the mRNA of the toxin at these multiple loci could turn on the expression of several bacterial toxins thus leading to bacterial cell death. Also, we recently demonstrated that the inhibition of this system by the aminoglycoside neomycin leads to the activation of the toxin synthesis.
Based on our experience about the design and the synthesis of selective RNA ligands, a large library of new compounds constituted of various known RNA binding domains will be prepared using a multicomponent synthetic methodology. The synthesized compounds will be evaluated for their ability to disrupt the loop-loop interaction between the antitoxin and the toxin mRNA using in vitro assays. Their biological evaluation in bacterial cultures will also allow for the study of (i) their ability to induce toxin synthesis, (ii) their antimicrobial activity, (iii) their ability to penetrate inside bacteria and eventually (iv) their toxicity against eukaryotic cells. The most active compounds will be finally optimized thanks to the proposed highly versatile synthetic methodology in order to improve their biological activity and their pharmacodynamic/pharmacokinetic properties toward in vivo studies. It is important to note that compounds bearing activity as inhibitors of toxin-antitoxin systems would be not only interesting therapeutic tools for antimicrobial development, but also biochemical tools toward a better understanding of toxin-antitoxin systems mechanisms that remains still largely unknown.
The expected results of this project are (i) the identification of new RNA ligands targeting loop-loop complexes formation and (ii) the development of an innovative antimicrobial approach by turning on the expression of TA systems toward the eradication of bacterial infection. In conclusion, we present here an original approach toward the validation of TA systems as promising antimicrobial targets and potentially the discovery of new antibacterial compounds against H. pylori infections. The same approach could be further applied to other major pathogens such as Staphylococcus aureus and Mycobacterium tuberculosis.

Project coordination

Maria DUCA (Université Nice Sophia Antipolis - Institut de Chimie de Nice)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

UNS - ICN Université Nice Sophia Antipolis - Institut de Chimie de Nice
INSERM (U1212) Insitut National de la Santé et de la Recherche Médicale (U1212)

Help of the ANR 379,447 euros
Beginning and duration of the scientific project: - 42 Months

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