Academic literature on the topic 'Foldamer-Protein interaction'

A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.

Foldamers are complex molecular scaffolds that mimic the form and function of biological molecules and are composed of simple repeating units.[1] Their potential applications include stereoselective and efficient organic catalysis mimicking the properties of enzymes, as well as bioreceptor mimics for new foldamer-protein interactions which could provide interesting possibilities for the medical industry.[2] In our previous studies we have investigated the folding properties of two oligoamides.[3] As the next step we prepared a series of aromatic oligoamide foldamers with several folding units and a hinge group between the units. The length of the hinge group is an important feature of the foldamer and understanding the properties the varying lengths is an integral step towards the preparation of foldamers with versatile conformational and functional properties. The prepared foldamers adopt a helical structure with multiple hydrogen bonds to single carboxyl oxygen. The structure is very compact and unlike many other aromatic foldamers, there is no void in the center of the structure resembling many of the biological helices formed in proteins. The diameter of the fold is roughly 11 Å, fairly close to the diameter of the biological alpha-helix (12 Å). The structure also has vast potential for a specific functionalization because of the aromatic rings, and desired properties can be produced with minimal variation in the secondary structure of the foldamer.

Current methods for proteomimetic engineering rely on structure‐based design. Here we describe a design strategy that allows the construction of proteomimetics against challenging targets without a priori characterization of the target surface. Our approach relies on (i) a 100‐membered photoreactive foldamer library, the members of which act as local surface mimetics, and (ii) the subsequent affinity maturation of the primary hits using systems chemistry. Two surface‐oriented proteinogenic side chains drove the interactions between the short helical foldamer fragments and the proteins. Diazirine‐based photo‐crosslinking was applied to sensitively detected and localize binding even to shallow and dynamic patches on representatively difficult targets. Photo‐foldamers identified functionally relevant protein interfaces, allosteric and previously unexplored targetable regions on the surface of STAT3 and an oncogenic K‐Ras variant. Target‐templated dynamic linking of foldamer hits resulted in two orders of magnitude affinity improvement in a single step. The dimeric K‐Ras ligand mimicked protein‐like catalytic functions. The photo‐foldamer approach thus enables the highly efficient mapping of protein‐protein interaction sites and provides a viable starting point for proteomimetic ligand development without a priori structural hypotheses.

Current methods for proteomimetic engineering rely on structure‐based design. Here we describe a design strategy that allows the construction of proteomimetics against challenging targets without a priori characterization of the target surface. Our approach relies on (i) a 100‐membered photoreactive foldamer library, the members of which act as local surface mimetics, and (ii) the subsequent affinity maturation of the primary hits using systems chemistry. Two surface‐oriented proteinogenic side chains drove the interactions between the short helical foldamer fragments and the proteins. Diazirine‐based photo‐crosslinking was applied to sensitively detected and localize binding even to shallow and dynamic patches on representatively difficult targets. Photo‐foldamers identified functionally relevant protein interfaces, allosteric and previously unexplored targetable regions on the surface of STAT3 and an oncogenic K‐Ras variant. Target‐templated dynamic linking of foldamer hits resulted in two orders of magnitude affinity improvement in a single step. The dimeric K‐Ras ligand mimicked protein‐like catalytic functions. The photo‐foldamer approach thus enables the highly efficient mapping of protein‐protein interaction sites and provides a viable starting point for proteomimetic ligand development without a priori structural hypotheses.

Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential at binding biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A helical aromatic foldamer was identified that undergoes flexizyme‐mediated tRNA acylation and is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer‐peptide hybrids. A hybrid macrocyle nanomolar binder to the C‐lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.

Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential at binding biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A helical aromatic foldamer was identified that undergoes flexizyme‐mediated tRNA acylation and is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer‐peptide hybrids. A hybrid macrocyle nanomolar binder to the C‐lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.

Le terme foldamère désigne tout oligomère capable de se replier en une structure conformationnellement stable en solution. Parmi eux, les foldamères peptidiques semblent particulièrement intéressants pour répondre à plusieurs défis rencontrés avec les peptides en chimie médicinale, tels que leur trop grande flexibilité et leur faible stabilité in vivo. Le caractère structuré des foldamères peut ainsi s’avérer être un atout dans le développement de nouveaux peptides d’intérêt biologique interagissant avec des protéines ou des membranes (Peptides de Pénétration Cellulaire, CPPs ou Peptides AntiMicrobiens, AMPs). En particulier, les foldamères de type hélice polyproline II (PPII), bien que constituant l’une des structures secondaires les plus répandues, sont encore peu étudiés en comparaison des hélices α et des feuillets β, même si des exemples de la littérature montrent déjà leur potentiel dans la conception de foldamères CPPs et AMPs efficaces. En parallèle, l’intégration d’atomes de fluor dans des molécules biologiquement actives est devenue une approche courante en chimie médicinale. Cette stratégie est motivée par les propriétés uniques de l’atome de fluor, qui peuvent stabiliser certaines conformations, moduler l’hydrophobie ou encore être utilisé comme sonde RMN 19F par exemple.L’objectif de ces travaux de thèse est de combiner ces deux domaines prometteurs de la chimie médicinale en développant des foldamères fluorées de type PPII, qui restent encore largement sous-exploités pour des applications biologiques. Plusieurs séries de foldamères fluorés ont ainsi été obtenues. Une première série de composés entièrement hydrophobes a permis de démontrer, grâce à des analyses RMN, CD et de diffraction aux rayons X, que l’incorporation de pseudoprolines trifluorométhylées, CF3ΨPro, au sein d’oligomères de proline ne perturbait pas la structuration en hélice PPII. Ces foldamères fluorés se sont avérés plus hydrophobes que leurs analogues non fluorés, tout en étant aussi stables vis-à-vis de la dégradation enzymatique et non-cytotoxiques, permettant ainsi d’envisager leur utilisation pour des applications biologiques. Des charges cationiques ont ensuite été introduites conduisant à trois nouvelles séries de foldamères amphipathiques. Des techniques de DSC et de RMN 19F ont révélé, pour l’une d’entre elles, la capacité à interagir avec des mimes de membranes. Enfin, la conception de dix foldamères fluorés candidats inhibiteurs de l’agrégation de la protéine amyloïde α-synucléine a été réalisée. Pour ce faire, les oligomères de proline ont été fonctionnalisés de façon rationnelle afin d’optimiser les interactions peptides-protéines
The term foldamer refers to any oligomer with the ability to fold into a conformationally stable structure in solution. Among them, peptide-based foldamers appear to be particularly interesting as a response to several issues raised by peptides in medicinal chemistry, such as their high flexibility and low in vivo stability. The structured nature of foldamers can therefore prove to be an asset in the development of new peptides of biological interest, able to interact with proteins or membranes (Cell Penetrating Peptides, CPPs or AntiMicrobial Peptides, AMPs). In particular, polyproline helix II (PPII) foldamers, although one of the most widespread secondary structures, are still less studied than α-helices and β-sheets, despite examples in the literature already showing their potential in the design of efficient CPPs and AMPs foldamers. In parallel, the integration of fluorine atoms into biologically active molecules has become a common approach in medicinal chemistry. This strategy is motivated by the unique properties of the fluorine atom, which can stabilize certain conformations, modulate hydrophobicity or be used as a 19F NMR probe, for example.The aim of this thesis work is to combine these two promising areas of medicinal chemistry by developing PPII-type fluorinated foldamers, which are still largely under-exploited for biological applications. Several series of fluorinated foldamers have been obtained. A first series of fully hydrophobic compounds demonstrated, through NMR, CD and X-ray diffraction analyses, that the incorporation of trifluoromethylated pseudoprolines, CF3ΨPro, within proline oligomers did not disrupt PPII helix structure. These fluorinated foldamers were found to be more hydrophobic than their non-fluorinated analogues, yet equally stable against enzymatic degradation and non-cytotoxic, enabling them to be considered for biological applications. Cationic charges were then introduced, leading to three new series of amphipathic foldamers. DSC and 19F NMR techniques revealed the ability of one series to interact with membrane mimetics. Finally, the design of ten fluorinated foldamers inhibiting the aggregation of the amyloid protein α-synuclein was carried out. To this end, proline oligomers were functionalized in a rational manner to optimize peptide-protein interactions

Avec 8,8 millions de décès dénombrés en 2015, le cancer est l’une des plus grandes causes de mortalité dans le monde. De nouvelles stratégies thérapeutiques ont émergé et l’identification de nouvelles cibles biologiques comme notamment la protéine Asf1, un chaperon d’histone H3-H4 surexprimée dans les cellules cancéreuses et en particulier le cancer du sein. Cette protéine possède différentes fonctions dans la cellule et agit à plusieurs endroits par des interactions protéine-protéines. Au cours de cette thèse de doctorat, nous avons développé une stratégie originale de design d’inhibiteurs d’interactions protéine-protéine avec des foldamères peptidomimes à base d’urées. Ces foldamères ont 1) la capacité de se replier en hélice 2,5, rappelant les hélices α des peptides et 2) d’être hautement tolérés et initiateurs d’hélicité lorsqu’ils sont conjugués à des fragments peptidiques. Nous avons développé des oligomères mixtes comprenant une alternance de segment(s) peptidique(s) et multi-urée, appelées chimères, ayant l’avantage de combiner la reconnaissance naturelle de peptides et la forte propension des oligourées à former des hélices stables. Après une étude structurale montrant qu’avec l’insertion d’un court segment à base d’urées dans un peptide hydrosoluble adoptant une conformation en hélice  la conformation hélicoïdale pour une majorité des chimères est conservée, des composés mimant la partie hélicoïdale C-terminale de l’histone H3 ont été élaborés. Une interaction de l’ordre du micromolaire avec Asf1 a été observée en solution puis validée à l’état solide par cristallographie aux rayons X. En vue d’optimiser la reconnaissance de ces chimères avec la surface d’Asf1 et leur sélectivité, un panel de modifications a été réalisée (i.e. séquence primaire, longueur du segment urée). Nous avons ainsi conçu des chimères α/urée possédant des affinités de liaison pour Asf1 comprises entre le nano- et micromolaire. Le composé le plus prometteur a été internalisé avec succès dans des cellules cancéreuses après conjugaison bioreductible avec un peptide vecteur et pourrait conduire à la mort cellulaire de la lignée tumorale étudiée
In 2015, 8.8 million of death were due to cancer making it an important cause of death in the world. The necessity to develop new anticancer treatments led to the search and discovery of new biological targets, such as Asf1, a histone chaperone protein of H3-H4 which is overexpressed in cancer cells, in particular in breast cancer. This protein plays a role in different biological processes in cells through protein-protein interactions (PPIs). During this thesis, we developed an original strategy to design inhibitors of PPIs with urea-based peptidomimetics. These foldamers are able to fold into stable 2.5-helix reminiscent to the natural α-helix. Designed urea-based foldamers have been synthesized as hybrid oligomers consisting of α-peptide and oligourea segments. With a combination of the two backbones, these compounds named “chimeras” presents advantages of both species with the natural recognition of α-peptides and the innate helical stability of oligourea. First, a model study was performed to evaluate the impact of the introduction of short urea segments into a long water-soluble peptide. Circular dichroism experiments confirmed that the helical conformation was conserved. New series of compounds that mimic a helical part of H3 were synthesized and their interaction with Asf1 was studied in solution and in solid state using a range of biophysical methods. Several modifications into the sequence were performed (side chain substitution, size of the urea segment or compound) in order to improve the recognition of Asf1 surface as well as their selectivity. We conceived oligourea-peptide chimeras with affinity for Asf1 in the micromolar range. Our best compound linked to a cell penetrating peptide was shown to enter into cells and to induce cell death

Les interactions protéine - protéine sont au centre de nombreux processus biologiques, et représentent des cibles thérapeutiques pertinentes pour le traitement de certaines maladies. La conception de molécules antagonistes visant à inhiber ces interactions requiert la reconnaissance spécifique d’une des surfaces protéiques impliquées. Les foldamères de type oligoamides de quinoline constituent de bons candidats. Leur production et leur fonctionnalisation sont relativement aisées. Ils adoptent des structures hélicoïdales semblables à celles rencontrées dans les protéines. Grâce à différentes techniques biophysiques (CD, SPR, diffraction des rayons X), nous montrons que ces molécules sont aptes à reconnaître une surface protéique. Deux protéines cibles ont été choisies : l’interleukine 4 et l’anhydrase carbonique humaine II.La stratégie retenue dans ce travail (ancrage du foldamère à la protéine via un bras espaceur) nous a permis d’obtenir des informations structurales sur les interactions foldamère – protéine avant toute optimisation de ces interactions. La première structure 3D d’un complexe foldamère de quinoline complexée à une protéine est décrite
Protein-protein interactions are a central issue in biological processes and represent relevant therapeutic targets for the treatment of diseases. The design of antagonistic molecules directed towards the disruption of these interactions requires the specific recognition of protein surfaces. Quinoline oligoamide foldamers present all the properties to reach that point. They are easily synthesized and fold into helices (similar to α helices) which can be decorated. Thanks to biophysical studies (CD, SPR, RX diffraction), we demonstrate that these molecules are able to recognize protein surfaces. Two proteins have been studied: the human interleukin 4 and the human carbonic anhydrase II.The applied strategy (keeping the foldamer close to the protein surface via a linker) allowed us to gather structural information about foldamer protein interactions before any strong binding is established. The first crystal structure between a protein and an aromatic amide foldamer is reported