Structure Elucidation of Helical Aromatic Foldamer–Protein Complexes with Large Contact Surface Areas

Abstract

The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions.H erein,w ep resent long helical aromatic oligoamide foldamersb earing proteinogenic side chainst hat cover up to 450 2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a9 -a nd a1 4-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 wounda round ar od of stacked foldamers. Solution studies confirmt he positioning of the foldamer at the protein surface as well as ad imerization of the complexes.Aromatic foldamers [1] emerge as an ew class of folded oligomers that may be decorated with proteinogenic side chains to interactw ith proteins [2,3] and nucleic acids, [4,5] ande ventually serve as inhibitors of nucleic acid-protein andp rotein-protein interactions. Amphipathic structures have also been shown to interactw ith, or to insert themselves in,m embranes. [6, 7] Some possess antibiotic activity. [6] Both linear [2,5, 6] and helical [3, 4, 7] foldamers have been developed and varied targets have been identified, including hDM2 and B-cell lymphoma-2 (Bcl-2)r egulator proteins, [2a,d,e] protein precursors of amyloids, [2c, 3a-e] G-quadruplex DNA [4] and some DNA-binding enzymes. [3f] Advantages of aromatic foldamersi nclude their ease of synthesis, for example through solid-phasem ethodologies, [8] and the predictability and stability of their folded conformations in both protica nd aprotics olvents. [9] Becauser elativelyl arge and welldefined folded objects can be produced using aromatic amide backbones, [10] it mayb ee nvisaged to cover large surfacea reas of proteins and nucleic acids. For example, we recently reported protein binding using a9 .2 kDa foldamer mimicking a 16 base-pair DNA duplex. [3f] Nevertheless, designing objects that can recognize large surfacea reas of proteins is difficult: whichs ide chains are to be selecteda nd where should they be located?S ome of the published work concerned mimetics of a-helices, [2] B-DNA, [3f] or natural products. [5] Other approachesuse screening through directed evolution methods. [11] It remains that no general approache xists for the ab initio designo fl arge ligands for ap roteins urface. Structurali nformationa bout aromatic foldamer-protein interactions would constitute af irm stepping-stonef or further design,b ut it can hardlyb eo btained without having reasonable binding affinity in the first place.To overcomet his sort of deadlock, we endeavoredt oi nvestigate foldamer-protein interfaces by confining foldamers at the surface of ap rotein. [12, 13] For example, helical oligoamides based on 8-aminoqu...

Aromatic Foldamer Helices as α‐Helix Extended Surface Mimetics

“…Oligoamideso fd-peptidic 8-amino-2-quinolinecarboxylic acid Qa dopt helical conformations with 2.5 units per turn (Figure 1a,b). [16] Q n helicesh ave until now been built with low side chain density,m ainly in position 4, [13,14,16] occasionally in position 5, [15,17] and not in position6 .U ponc areful examination of the Q n helix ( Figure S1), we realized that as imple side chain arrangementi nvolving4 -a nd 6-functionalized quinoline rings potentially matches with that of the face of an a-helix. The actualc urvature of a-helices may vary between the ideal 3.66 13 a-helix, with 3t urns for 11 residues ( Figure 1d), and the more classical 3.6 13 a-helix with 5t urns for 18 units (Figure 1e,F igure S2).…”

“…[12] These helicesf eature ap itch of 3.5 and ad iameter of at least 1.3 nm that do not relate to those of an a-helix. They can be decorated with proteinogenics ide chains and may interactw ithp rotein surfaces [13] but, at first sight, they appeart ob eu nsuitable for ahelix mimicry( see Figure 1i nr ef. [14]).…”

Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins

“…A recent perspective paper highlighted synthetic host molecules interacting with proteins and available structural data, and the modulation of protein function typical of supramolecular chemistry [73]. Crystal structures are particularly important in this field, because they are used as starting point for "retrostructural" analysis in order to improve further design of a specific nanomolecule interacting with a protein [74].…”

NMR Spectroscopy of supramolecular chemistry on protein surfaces

“…Cucurbiturils (bottom right, [47][48][49][50][51]) recognize methylated lysines and arginines by binding their methylated head groups inside the macrocycle. carbonylpyrrole (GCP) ligands [41][42][43][44][45][46], cucurbiturils [47][48][49][50][51], porphyrins [52][53][54][55][56][57][58][59][60], metal complexes [61][62][63], foldamers [64][65][66][67], nanoparticles [34,68], imprinted polymers [69][70][71][72], and dendrimers [73,74].…”

“…Supramolecular chemistry is ideally suited to address these challenges because it merges the knowledge of non-covalent molecular recognition with the possibility to combine multiple recognition units into one molecule for improved selectivity and affinity. Examples for supramolecular ligands designed to recognize protein surfaces include tweezers [ 5 – 18 ], calixarenes [ 19 – 40 ], guanidiniocarbonylpyrrole (GCP) ligands [ 41 – 46 ], cucurbiturils [ 47 – 51 ], porphyrins [ 52 – 60 ], metal complexes [ 61 – 63 ], foldamers [ 64 – 67 ], nanoparticles [ 34 , 68 ], imprinted polymers [ 69 – 72 ], and dendrimers [ 73 – 74 ].…”