Structural elucidation of protein kinase-ligand complexes

Environment – The candidate will join an exciting and multidisciplinary scientific environment with on-site access to cutting-edge facilities in cryo-EM, X-Ray crystallography, NMR, Biochemistry, Biophysics, molecular biology and cell biology

Remuneration: 580€ net/month; Duration: 6 months between January and July 2025

Mission –We are looking for a highly motivated master-level student with training in biochemistry and structural biochemistry to elucidate the structures of brain penetrant drug candidates in complex with the protein kinase IRE1.

Scientific background – Signaling by the Inositol Requiring Enzyme 1 (IRE1) plays an instrumental role in glioblastoma (GB), a deadly brain tumor. We showed in the past that IRE1 pharmacological inhibition results in reduced tumor aggressiveness and increased sensitivity to the standard of care in mouse models, confirming the therapeutic potential of targeting IRE1 as an adjuvant strategy.^[1,2] Using an in-house drug discovery pipeline^[3] we have identified novel IRE1 kinase inhibitors that are able to access the brain and are effective in GB in vivo models^[4] and we have since prepared more than 80 analogs in the context of a structure-activity relationship study. In order to better understand their mode of action and in particular their binding interactions with the protein, your goal will be to elucidate the atomic structures of the best hit compounds in complex with the protein kinase IRE1.

The project involves a close collaboration between the group of Dr Pierre Maisonneuve at the European Institute of Chemistry and Biology (IECB, Bordeaux, France), which investigate the structural basis of protein kinases and pseudokinases in human signaling by using cryo-EM, and a research consortium of biologists and chemists from the Université de Rennes (Inserm U1242 & CNRS UMR 6226) which develops these molecules. The student will be hosted in Dr Maisonneuve’s lab in Bordeaux, France, with potential visits of Dr. Guillory’s lab in Rennes.

Main activities –

• Protein expression (in insect cells) and protein purification (affinity & SEC).

• Screening and optimization of protein crystallization conditions and cryo-EM grids preparation.

• X-Ray and/or cryo-EM data acquisition (in house or in national facilities).

• Data processing on an in-house high computing server equipped with last generation GPUs.

• Structural characterization by X-ray protein crystallography and/or cryo-EM.

• Functional and biophysical characterization in vitro of enzymatic activities (kinase & RNase), protein-protein interactions (biophysical assays).

[1] P-J. Le Reste et al., Cancer Letters, 2020. doi: 10.1016/j.canlet.2020.08.028

[2] D. P. Raymundo et al., Trends in Cancer, 2020. doi: 10.1016/j.trecan.2020.07.006

[3] D. Doultsinos et al., The FEBS Journal, 2020. doi: 10.1111/febs.15372

[4] D. Pelizarri et al., iScience, 2023. doi: 10.1016/j.isci.2023.106687

Profile desired –Master 2 or 5^th year engineer student with a background in protein biochemistry, protein expression and protein purification.