Titre de la dissertation: “On the structural modifications experienced by (poly)peptoids when transferred from the solution to the gas phase: an ion mobility-mass spectrometry investigation”

Promoteur: Monsieur Julien De Winter et Olivier Coulembier

Résumé de la dissertation: Peptoids or polymers of N-substituted glycine constitute an emergent class of peptidomimetic foldamers, i.e., macromolecules adopting specific secondary structures in solution offering a large panel of potential applications. The establishment of any structure/activity relationship, say the interplay between the structures of the active molecules in the context of targeted applications, clearly relies on the elucidation of the conformational dynamics within active conditions. Nuclear magnetic resonance and circular dichroism (for chiral molecules) are most of the time considered as the privileged characterization methods to track the macromolecule structures in solution, although these methods require extensive purification and provide averaged information on the solution phase conformations.  Mass spectrometry (MS) is increasingly reported and developed as an efficient method to decipher the primary and secondary structures of macromolecules, even in complex mixtures.  The combination between Ion Mobility Spectrometry MS and computational chemistry is nowadays largely demonstrated to be able to afford reliable structural data on macromolecules and macromolecules assemblies whose secondary structures is expected to remain mostly unchanged from the solution to the gas phase upon ionization and desolvation. However, numerous counter examples are reported demonstrating that significant secondary structures modifications may occur between both states questioning the pertinence of using MS-based methods to study solution phase structures. The intrinsic reasons of the structure modifications upon ionization/desolvation are clearly dominated by the requirement of charge stabilization in a solvent free environment, leading to the so-called charge solvation effect in which the stabilization of the charge finds its origin in an intramolecular folding. Such a structure modification can be of course counter balanced by strong intramolecular secondary interactions, such as H-bonds, if present. Facing the huge benefit from the MS-based analysis in the peptide/protein research, we recently endeavored to expose sequence-defined peptoids to ion mobility experiments since such studies remain scarcely reported in the literature.   In the first part of the present thesis, we designed and synthetized tailor-made peptoids possessing targeted structural specificities in terms of nature of the residues and the sequence and length of the peptoids. Short peptoids were efficiently prepared using a stepwise solid-phase approach allowing the fine tuning of their sequence by the addition of different side chains at defined positions on the way to sequence-defined oligomers. Longer chain peptoids were obtained based on ring-opening polymerization of original N-substituted N-carboxyanhydride monomers. The great advantage of such a procedure is the obtention in a single reaction of a distribution of chains with different degrees of polymerization (DP), specifically named as « poly(N – substituted glycines) » or « polypeptoids ». The main drawback of such a procedure is that the production of copolymers remains largely unexplored and probably difficult. By associating both synthesis methods, we created and characterized a library of different original peptoids with targeted sequence and lengths.In the second part of the study, the Electrospray-generated peptoid ions were subjected to ion mobility spectrometry experiments in order to monitor the influence of the charge (position), the sequence and the length on the solvent-free gas phase ion conformations. Most of our peptoids were built around the incorporation of chiral side chains able to create helical structures as demonstrated for the solution phase macromolecules. A typical side chain is the so-called (s)-phenylethyl (spe) group whose accumulation all along the peptoid backbone is clearly demonstrated to stabilize helical structures in methanol or acetonitrile. As a consequence, most of our structures incorporated spe or spe derivatives. Firstly, we focused our attention on homopolypeptoids bearing methyl, benzyl and (S)-phenylethyl groups. Although characterized by different conformations in solution, with only the Nspe peptoids being characterized by helical structures in solution, the corresponding peptoids were shown to adopt loop-like conformations in the gas phase due to the charge solvation effect. Globally, this indicates that the secondary interactions responsible for the solution phase structures are no stronger enough to compensate for the charge stabilization. Twarting such a denaturating effect then became the cornerstone of the second part of the thesis.Inspired by the peptide chemistry, we developed a strategy based on the incorporation of H-bond donor/acceptor moieties all along the peptoid backbone at defined positions to create a H-bond network able to prevent the folding effect. We demonstrated that the helical structure of Nter (N-terminal extremity) protonated peptoids bearing (S)-N-(1-carboxy-2-phenylethyl) bulky side chains (Nscp) is largely preserved in the gas phase by the creation of a hydrogen bond network, induced by the presence of carboxylic moieties, that compensates for the charge solvation process.  We further demonstrated, using a less bulky side chain such as (R)-N-(1-carboxy-2-ethyl) that the presence of H-bond donor/acceptor is necessary but no sufficient to conserve the helical structures and that the association between H-bonds and steric hindrance is mandatory.Also inspired by the peptide chemistry and especially the possibility to stabilize gas phase helical structures by positioning the protonation site at the negative side of the helix macrodipole, we finally considered negatively charged peptoids and positioned the negative charge carrier at the positive side of the helical peptoid macrodipole. N-(S)-(1-carboxy-2-phenylethyl) (Nscp) and N-(S)-phenylethyl (Nspe) were then selected as the negative charge carrier and as the helix inductor, respectively. We demonstrated that the structures adopted by the anions, whatever the tested sequences and lengths, remain compactly folded in the gas phase for chains containing up to 10 residues, and no evidence of the presence of a helical structure was obtained, even if, for selected sequences and lengths, different gas phase conformations are detected.