Development of new antibiotics targeting the bacterial DNA sliding clamp

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Development of new antibiotics targeting the bacterial DNA sliding clamp

The multimeric DNA sliding clamps (also known as β rings) confer high processivity to replicative DNA polymerases. They are also molecular hubs on which many proteins involved in DNA metabolism interact through their binding, via a conserved peptidic sequence, into a universally conserved pocket (figure).

E. coli Processivity Ring — Structure of a co-crystal of the E.coli β clamp and the binding peptide (yellow) of the cognate DNA polymerase IV. Only one monomer of the clamp is bound.

Peptide interaction in the bipartite pocket of E. coli — Detail of the peptide interaction within the bipartite pocket at 1.65 Å resolution (Burnouf, JMB, 2004 ; Wolff, J Med Chem, 2011).

In bacteria, the interacting pocket is a new potential target for the development of new antibacterial compounds, which are urgently needed to control and overcome the expanding bacterial resistance to antibiotics.

We use a structure-based approach to design peptides that bind into the interacting pocket with high affinity, compete with the DNA polymerases and trigger cell death. This project is conducted through a multidisciplinary and integrated strategy resulting from a close collaboration between seven different laboratories, thus combining chemical synthesis, molecular modeling, structural, biophysical and biochemical analyses and in vivo assessment of ligand efficiency to inhibit bacterial growth and infectious processes.

Within the frame of this collaboration, our task is to produce β rings from different bacterial origin and to analyze the interaction of newly designed peptides with these rings, using biophysical techniques such as ITC, X-ray crystallography and mass spectrometry.

Bibliography

Burnouf D., Olieric V., Wagner J., Fujii S., Reinbolt J., Fuchs R.P. and Dumas P. (2004). Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. J Mol Biol, 335(5):1187-1197.
Wolff P., Olieric V., Briand J.P., Chaloin O., Dejaegere A., Dumas P., Ennifar E., Guichard G., Wagner J., Burnouf D. (2011). Structure-based design of short peptide ligands binding onto the E. coli processivity ring. J Med Chem, 54(13):4627-37.
Wolff P., Amal I., Oliéric V., Chaloin O., Gygli G., Ennifar E., Lorber B., Guichard G., Wagner J., Dejaegere A. and Burnouf D. (2014). Differential modes of peptide binding onto replicative sliding clamps from various bacterial origins. J Med Chem., 57(18):7565-7576.
Wolff P., Ennifar E., Guichard G., Burnouf D. and Dumas P. Native ESI mass spectroscopy can help avoiding wrong interpretations from isothermal titration calorimetry in difficult situations. Soumis à American Journal of Mass Spectrometry

Collaborations

Prof Annick Dejaegere (IGBMC, Illkirch, France), Dr Gilles Guichard (IECB, Pessac, France), Dr Gaetan Mislin (ESBS, Illkirch, France), Dr Vincent Oliéric ( SLS, Villigen, Suisse), Prof Jean Marc Reichardt (IBMC, Strasbourg, France), Dr Jérôme Wagner (ESBS, Illkirch, France).

Funding

Inserm, AstraZeneca

Patents

Structure cristalline de la protéine du facteur de processivité de l’ADN polymérase et un ligand et cet usage. EP 1639509, 29 mars 2003 – WO2004EP06942 20040625. Burnouf D, Wagner J, Dumas P, Fujii S, Fuchs R, Olieric V.
Compounds binding to the bacterial beta ring. EP11162733.7, dépôt EPO le 15 avril 2011, délivré le 7 septembre 2012. Burnouf D, Dejaegere A, Guichard G, Oliéric V, Wagner J.

Group leader

Eric ENNIFAR