A series of foldamer libraries were designed and synthesized in such a way that these have linkers at N-terminus to anchor to the protein surface and include proteinogenic side chains on quinoline units to interact with the protein surface. These complexes/adducts were prepared by a convergent procedure.
The interactions of the foldamers with the protein surfaces were assessed in solution by induced circular dichroism (ICD), LCMS analysis, NMR spectroscopy and in the solid state by X-ray crystal structure analysis.
The results showed that two long foldamer sequences bearing proteinogenic side chains could cover up to 800 Ų of the human carbonic anhydrase II (HCA) surface. These foldamers are composed of amino-quinolinecarboxylic acids units bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids units that enhance helix handedness dynamics. Crystal structures of those HCA-foldamer complexes were obtained with a 9-mer and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Same complexes were also studied in solution by using NMR.
The concept was extended to therapeutically relevant proteins such as cyclophilin (CypA), interleukin-4 (IL4) and human ubiquitin (Ub) involved in PPIs. Since these proteins do not possess active sites or known small molecule ligands, tethering consisted of covalently ligating foldamers at a cysteine residue introduced via site-directed mutagenesis using either short or long linkers. We have used appended active disulfides at the N- terminus of aromatic oligoamide foldamers on solid phase, optimized conditions under which foldamer-protein disulfide bridges form, and developed methods to purify these adducts and characterize them by NMR and mass spectrometry. ICD and solution NMR results indicating selective foldamer-protein interactions. In the case of CypA, the experiments were also carried without any tether. Altogether, our results constitute an important milestone toward the identification of aromatic foldamer-protein interactions and toward the structure elucidation of foldamer-protein interfaces in the contexts of IL4, CypA and Ub.
One paper has been published in Eur. J. Org. Chem. Describing the results obtained in WPs 1 and 2. Recently another paper has been submitted describing the results obtained in WPs 1, 2 and 3. During his stay, the researcher has had a chance to present the preliminary work on several occasions.
