Promoteur de thèse: Professeur Pascal Gerbaux

Résumé de la dissertation:

Peptoids are polymers of N-substituted glycines. Peptoids differ from peptides by the position of the side chain, located on the nitrogen atom rather than the α-carbon. This difference leads to the achirality of the backbone as well as the loss of the backbone hydrogen-bond donor. The conformation of peptoids is then primary dictated by the sequence and the functionalities of the side chains. In addition, ternary amides are particularly sensitive to the cis/trans isomerization which enlarges the conformational space that can be explored by peptoids. Hence, CD and more particularly NMR data are often complexed to analyze. This project thesis aims to envisage mass spectrometry (MS) for the structural investigation of peptoids. The first part of this project involves the synthesis of the peptoid compounds. A traineeship in the group of Prof. Zuckermann (Berkeley – USA), pioneer of the current peptoid solid-phase synthesis, allowed to bring this synthetic knowledge in our laboratory. Mass spectrometry-based methods have then been used for the structural characterization of gaseous peptoid ions with a special attention paid both to the primary and secondary structure determination. The possibility to determine the primary structures, say the sequence, of peptoid ions by collision-induced dissociation experiments (CID) was first envisaged. Mechanistic studies revealed that peptoid ions mostly dissociate following B/Y and side chain loss (SCL) reactions. Based on extensive CID studies, powered by the synthesis of a new class of biomimetic synthetic polymers with tunable secondary structurestailored made peptoids, we monitored the internal energy dependence of the SCL allowing us to propose competitive cleavage and rearrangement pathways. In addition, we also demonstrated the importance of the side chain structure in the fragmentation process. In a second discussion, we tackled the backbone dissociation processes undergone by collisional activated peptoid ions and we ended up with the proposal of competitive B/Y and A/Y mechanisms. Based on our studies, the CID reactions of protonated peptoids is now fully rationalized and involve B/Y, A/Y and the SCL processes. These studies will now pave the way to the development of sequencing methods for original peptoids. The second part of this project concerns the analysis of the secondary structure of peptoid ions using ion mobility MS experiments. First, in-solution analyses (NMR, CD) were performed and confirmed the helical structure of (S)-phenylethyl peptoids in solution. However, we demonstrated that the structure of helical (S)-phenylethyl peptoids is not conserved in the gas phase. Based on Molecular Dynamic simulations, we proposed that protonated peptoids adopt a loop conformation in the gas phase due to a charge solvatation effect since the weak interactions, responsible for the secondary structures of peptoids in solution, cannot compete with the necessity to stabilize the naked charge in the gas phase ions. Nevertheless, we showed that the helical structure can be conserved by acetylation of the terminal amine function that relocates the charge on the carbonyl function. We also demonstrated that more rigid or basic side chains do not help to conserve the helical structure in the gas phase due to the high flexibility of peptoid main chain as well as the lack of stabilizing hydrogen bond.