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Conformational transitions have found broad interest due to their impact on protein misfolding and self-assembly as key events leading to the development of neurodegenerative diseases. However, investigation of these dynamic events has been limited so far mainly due to the intrinsic tendency of the involved polypeptides for self-association and aggregation. Consequently, the elucidation of β-sheet and fibril-forming processes related to degenerative diseases remains a difficult task, often giving contradictory results. In order to overcome these difficulties and to investigate early steps of misfolding and subsequent fibril and plaque formation, a new concept termed "Switch-peptides" is presented in this thesis, opening new perspectives for the rational design of drugs preventing Alzheimer's disease. Figure. Elaboration of the "Switch-peptides" concept via S to N acyl migration. As shown in the Figure, the switch-peptides represent stable, self-contained folding precursors, in which folding and self-assembly is blocked by the presence of the Ser-, Thr-, Cys- derived switch elements S dissecting the regular peptide backbone by an (thio)ester and a flexible C-C bond (Soff). Removal of the protecting group Y by enzymatic cleavage or by change of pH, triggers X,N acyl migration restoring the native peptide backbone in situ, and setting off the folding process in the nascent state ("in statu nascendi", ISN) of the parent molecule. These resulting conformational changes i.e. from a random coil to a folded state, can be used to study the onset of biological activity (A) onset (B) and disruption (C) of secondary and tertiary structures. The work described in the present thesis elaborates the structural and chemical foundations of the concept, notably in the induction of structural and conformational properties of peptides. Special attention is focused on the S to N acyl migration in elaborating an in situ ligation methodology. For potential applications in vitro and in vivo, we explore a new thioester solubilizing group to realize efficient native chemical ligations at physiological conditions (Figure). Besides the synthetic access of switch-peptides thioesters via solid-phase techniques, the impact of internal (steric hindrance) and external pH factors on the kinetics of the intramolecular acyl migration is evaluated by analytical HPLC. The major applications of the switch-peptides concept are explored via three main axis : In order to settle the foundations of strategy B, our study was based on the possibility of inducing in situ the formation of secondary and tertiary structures. For this purpose, an amphiphilic model peptide is designed to mimic conformational transitions relevant in degenerative disease, i.e. transitions of type random coil to β sheet. The role of the switch element S in the disruption of secondary structures due to the conformational decoupling of σ on P (Soff), is demonstrated by CD.The induced conformational transition to β sheet conformations is accompanied by a significant decrease in peptide solubility. Moreover, the controlled release of nucleophile within the S element can modulate the rate of structure transition over a broad time scale, as demonstrated by kinetic studies. The use of orthogonal protecting groups Y allows the sequential and individual triggering of multiple elements S, localized in strategic positions in more complex polypeptides. With this objective in mind, the concept is expanded to the induction of ββα supersecondary structures such as the Zinc finger domain (Zif). Actually, the simultaneous introduction of a chemically (pH) and enzymatically (DPPIV) cleavable group at the N- and C-terminus in a sequence derived of Zif1 268 permited the consecutive onset of secondary and tertiary structure by a hierarchical triggering of acyl migrations. The second part of the thesis is devoted to the elaboration of a new generation of β breaking switch-peptides (Figure, strategy C). For the design of such inhibitors, the concept of "separating" recognition (σ inactivated) and functional (σ activated) states appears essential. To construct molecules able to switch between recognition and functional state, we assemble different pseudoproline (ψ Pro)-containing building blocks as induction units σ for β-sheet breaking and a target peptide P. The impact of the ψ Pro-moiety is decoupled from the peptide chain via a flexible thioester bond (Soff) and set off after acyl migration (Son). As a consequence, the insertion and association into existing β-sheet templates should be promoted. Preliminary results by EM studies indicate that a controlled enzyme-induced acyl migration results in a significant improvement of the β-sheet breaking potential. For example, one of the designed switch-peptides slowed down the fibrillogenesis of an amyloid model, representing a significant step in the developement of therapeutically relevant compounds in Alzheimer's disease. The third part focuses on the in situ creation of structure and function of potentially bioactive peptide ligands (Figure, strategy A) via a novel ligation method ("Switch-ligation"). For the example of an angiotensin II-derived analogue, we explore the potential of chemoselective ligations for the onset of biological function under physiologically relevant conditions. Receptor (AT1) binding studies of [Cys5]Ang II in collaboration with PD. Dr. E. Grouzmann, CHUV reveal a fast and efficient ligation without the need of additives (IC50= 25 nM). As an alternative example, the covalent self-assembling of two precursors results in the in situ creation of an efficient peptide deformylase inhibitor. The perspective to extend these methodologies for in vivo applications has been tentatively explored as a new concept in prodrug design. In conclusion, the results of this thesis contribute substantially to the proof of concept of switch-peptides, opening new perspectives in drug design as well as in the study of peptide and protein misfolding relevant in degenerative diseases.

Switch peptides

Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of degenerative diseases including Alzheimer's disease and late onset diabetes. Amyloid forming proteins are believed to be mainly α-helical in their native conformation, but undergo an α-helical to β-sheet conversion paralleled by fibril and plaque formation. As a most challenging experimental hurdle, the transition from helical / rc conformations to β-sheeted structures is followed by dramatic changes in the physicochemical properties, such as self association and insolubility, thus strongly limiting the experimental access of this molecular key process in neurodegenerative diseases. In 2000, M. Mutter and his group proposed a new concept for resolving some of these intrinsic problems of peptide self-assembly. As a basic idea, peptides with a high potential for β-sheet formation, considered as early event in fibrillogenesis, are prepared as 'folding precursors', in which the folding process is blocked by the insertion of a non native bond (see Figure). These modular switch peptides comprise three distinct elements: A conformational induction unit (σ), a switch element (S), and a target peptide (P). A central feature of the concept of switch-peptides, the switch element S dissects the native polyamide backbone of the peptide P by an ester and a flexible C-C bond, thereby preventing the peptide from folding and separating the conformational impact of σ. The triggering of the switch element by removing the protecting group Y reestablishes the native polyamide backbone via a spontaneous O to N acyl migration reaction, whereupon peptide folding can proceed. The present Ph.D. thesis aims to elaborate this concept in putting conformational transitions from helical or random coil to β-sheet structures in focus. This idea is developed using first potentially β-sheet forming model peptides, and is extended in a second step to amyloid-derived sequences. To this end, a series of model peptides exhibiting high β-sheet potential have been synthesized by SPPS synthesis and the critical chain length for β-sheet formation of oligopeptide (Leu-Ser)n was determined by CD studies. The insertion of a pH inducible S-element allowed for the delineation of the in situ transition from rc (Soff) to β-sheet structure (Son). The kinetic evaluation of these conformational transitions as a function of concentration, pH and temperature served as a base for the host-guest peptides according to the switch concept. Host-guest techniques allow to mimic the structural environment of the peptide segments 'excised' from their polypeptide. Typically, peptide segments (guest sequence) regarded as nucleation centers ('hot spots') for β-sheet and fibril formation are incorporated into a host oligopeptide of high β-sheet potential, e.g. (Leu-Ser)n. The incorporation of S-elements at the C- and N-terminal end of the guest segment results in a rc structure (Soff-state), as monitored by CD and TEM studies. By adjusting the pH to physiological conditions, O,N-acyl migration is triggered (Son) and a well defined rc to β-sheet transition is observed by CD, paralleled by the formation of amyloid-like fibrils. For example, after insertion into the β-sheet promoting host peptide (Leu-Ser)n, the amyloid β (14-24) and amylin derived peptide NFGAIL undergo upon pH induced acyl migration a conformational transition from rc to β-sheet , paralleled by the onset of fibril formation. For evaluating the impact of β-breaking compounds upon the kinetics of β-sheet formation, the potential of the developed host-guest switch peptides to serve as a diagnostic tool is elaborated. As the folding is set off in the moment of creating the bioactive molecule ("in statu nascendi", ISN), the present concept allows for the first time to investigate early steps of protein misfolding as relevant in neurodegenerative diseases, opening new perspectives for the rational design of compounds of therapeutic interest. This is demonstrated for the design and synthesis of a reference host-guest system ('molecular kit for screening amyloid β inhibitors'), in which the kinetics of rc to β-sheet transitions is determined under a variety of experimental conditions, including physiological pH. Finally, as a most challenging goal, the disruption or even reversion of β-sheet formation and aggregation is addressed by applying the concept of switch peptides. To accomplish this formidable task, a series of switch-peptides containing various induction systems are investigated. Preliminary results by CD and TEM studies confirm the potential of host-guest switch-peptides for obtaining quantitative data on the impact of β-breaking compounds. A critical evaluation of known β-breaking peptides point to the need for a reliable screening system as developed in the present thesis. The results obtained firmly establish the capability of employing the concept of switch peptides as a tool to study folding/misfolding events during the dynamic process of structure onset and evolution. Keywords: Switch peptides ; host-guest switch peptides ; screening ; inhibitors ; Aβ ; amylin.

EPFL2006

Amyloid ß-derived switch-peptides as tool to study conformational changes relevant in degenerative diseases

Marie-Stéphanie Camus

The rapid growing number of patients diagnosed with a neurodegenerative disease and more particularly with Alzheimer's disease (AD) has stimulated intensive research in determining and understanding biological phenomena causing such devastating diseases and hence allowing for the elaboration of adapted therapeutic treatments. These diseases are also commonly called "conformational" diseases because they result from the misfolding of a protein leading to the formation of self-associated β-sheets, which in turn give rise to the formation of oligomers, protofibrils as well as insoluble fibrils characterizing the plaques found in the brain of affected patients. Consequently, the investigation of such proteins, in particular of Amyloid β (Aβ) in the case of AD, is a limited and difficult task to achieve, which often leads to contradictory results. To overcome these difficulties and to be able to study the key steps of conformational transitions and misfolding of such peptides and proteins, our research group has developed a new tool, called switch-peptides, enabling to block (Soff state) and trigger (Son state) peptide folding at will (Figure). The introduction of a switch element S built from Ser, Thr or Cys residues disrupts the regular polypeptide chain by the insertion of an ester and a flexible C-C bond resulting in a conformational disconnection of P1 and P2 (Figure), i.e. in an unordered (random coil), non-folded conformation. Each S element is protected by a protecting group Y (Soff state) that can be cleaved independently by adding a base, an enzyme or by light, depending on the chemical nature of Y. The cleavage of the different protecting groups Y triggers a spontaneous O to N acyl migration, re-establishing the regular amide backbone of the peptide chain, hence enabling the peptide to fold "in statu nascendi" and to adopt a well-defined secondary structure. The present thesis explores the potential of this novel concept for the example of conformational transitions relevant in amyloid β misfolding. In the first part we investigate the chemical stability of the S element in aqueous media, exposing a number of switch-peptides to various experimental conditions. Most notably, the ester bond proved to be stable at acidic as well as physiological conditions for several hours, opening a broad range of biological applications. The second part of the work is dedicated to the study of conformational transitions of switch-peptides derived from Aβ(1-42). By incorporating one or several switch elements disposing orthogonal protecting groups Y, the impact of different fragments of the peptide as nucleation site for the process of β-sheet formation, self-assembly and aggregation has been revealed as monitored by CD, TEM studies and ThT (pathway B, Figure). For the first time, the orthogonal triggering of the two switch elements, i.e. S26 and S37 allowed to delineate the important role of the C-terminal part of Aβ in the early step of misfolding. Subsequently, one of the nucleation sites for aggregation, i.e. segment Aβ(14-24) was excised from the native sequence and transformed to a switch-peptide applying the host-guest technique. Detailed CD studies were applied for investigating conformational transitions of type random-coil (Soff) to β-sheet structure (Son), serving as proof of concept for the use of Aβ-derived nucleation sites as guest sequence in combination with β-sheet promoting host peptides for the screening of potential inhibitors of fibril formation as early molecular event in the context of AD. This has been demonstrated in applying the elaborated host-guest peptides to evaluate the β-sheet breaking potential of pseudo-proline (ψPro)-containing switch-peptides derived from Aβ (pathway C, Figure). Preliminary results indicate that the in situ formation of kink-conformations may exert a β-sheet destabilizing effect, confirming previous observations from the Soto group. Finally, the use of switch-peptides as β-sheet and fibril breaking molecules by in situ α-helix nucleation (pathway A, Figure) has been explored. To this end, the potentially β-sheet forming segment Aβ(14-24) was linked via S element to a helix nucleating peptidomimetic ("N-Cap"). In the Soff state (pH ≤ 4), CD and TEM studies point to the onset of a β-sheet, fibril forming structure. In triggering O,N-acyl migration (pH ≈ 7), a so far unprecedented transition of type β-sheet to α-helix is observed, paralleled by a drastic increase in solubility and a complete disappearance of fibrils. The reversibility of β-sheet and fibril formation by α-helix nucleation in situ represents a most interesting observation and deserves further exploration as potential tool in the study of folding processes. In conclusion, the concept of "switch-peptides" has been successfully applied to biologically relevant molecular events of utmost therapeutic interest.

EPFL2008

Switch-peptides: controlling biological function and self-assembly of amyloid ß-derived peptides using enzyme-triggered acyl migrations

Sonia Dos Santos

Conformational transitions of peptides and proteins have recently moved to the center of interest in various domains of research at the interface of chemistry, biology, and medicine due to their implication in an increasing number of diseases in which the pathogenesis is causally linked to the misfolding of a protein. For example, the amyloid β protein linked to Alzheimer's disease undergoes various conformational transitions, eventually leading to the formation of self-associating β-sheets, which in turn give rise to insoluble, fibrillar aggregates. Consequently, studies of such proteins are hampered by problems of solubility and often yield contradictory results. With the aim of surmounting these difficulties in the study of conformational transitions of peptides and proteins, a novel tool based on the concept of "Switch-Peptides" enabling the in situ induction of peptide folding will be elaborated in the present thesis. As shown in the Scheme, N(Y)-protected switch-peptides serve as stable, self-contained precursor molecules, in which folding and self-assembly is blocked by the presence of Ser or Thr derived switch-elements S, dissecting the regular peptide backbone by an ester and a flexible C-C bond. Removal of the protecting group Y triggers a spontaneous acyl migration that restores the native polypeptide chain ("statu nascendi") setting off the folding process. The body of work presented herein consists of two main themes: With the goal of developing a system amenable to physiological conditions, the introduction and evaluation of different, enzymatically cleavable Y groups was conceived. For proof of concept, the biologically active peptides angiotensin and neuropeptide Y were used, allowing the study of the impact of the S-element on their biological activities. Investigations of the analogue [Thr]5-Ang II containing a pH-triggered switch (Y = H+) reveal that the acyl migrations are very fast, exhibiting half-lives of less than one minute. With the introduction of enzymatically labile Y groups, specifically an Arg-Pro dipeptide (cleavable by dipeptidyl aminopeptidase) or the amino acid pGlu (cleavable by pyroglutamate aminopeptidase), rates of conversion ranging from minutes to hours are observed as monitored by HPLC, NMR and CD. Problems of steric interference associated with the action of enzymes such as esterases and penicillin amidase were overcome by developing linkers of different structural features. D-aminopeptidase (Y = D-Ala) was shown to extend the rates of enzymatic cleavage to half-lives of several days. The enzymes studied display high specificity for the switch-peptide substrates and a quantitative conversion from the Soff to the Son state. We took advantage of the affinity of Ang II and NPY for their respective receptors (AT2 and Y1) to show that their switch-peptide analogs are inactive in the Soff state where as after enzymatically triggered acyl migration, the peptides display high receptor affinity (IC50 = 45 nM for Ang II and IC50 = 5 nM for NPY). In the case of NPY, a conformational transition from a random coil to an α-helix as bioactive conformation is observed by CD. The second part of the work is dedicated to conformational transitions of type random coil → β-sheet in different model peptides or peptides derived from Aβ(1-42). All peptides studied show high potential for self-association and subsequent precipitation. However, in the Soff state, the switch-peptides display a high degree of stability and strongly enhanced aqueous solubility. After enzymatic triggering of the acyl migration, a conformational transition to a β-sheet accompanied by the formation of fibrils and spontaneous precipitation are observed by CD and EM studies. Based on the elaborated systems, the introduction of several orthogonal S-elements in Aβ derived peptides was realized. The incorporation of two different S-elements into the Aβ(1-42) sequence was found to greatly facilitate the normally difficult synthesis, and enabled the study of the influence of the individual peptide segments on the overall folding process. It was shown for the first time that the hexamer Aβ(37-42) is essential for the formation of β-sheets and subsequent fibrillization. As a final aspect, the elaboration of switch-peptides exhibiting β-breaking properties was investigated. Preliminary results indicate that one of the designed switch-peptides substantially slows down the formation of fibrils, representing a significant step in the development of therapeutically relevant compounds for the treatment of Alzheimer's disease. In conclusion, the elaborated methodologies allow for a general application of the switch concept as diagnostic tool in the study of fibrillogenesis.

EPFL2005