Bioinspired Selective Surface Deposition of Fragrance Delivery Systems

The perception of pleasantness in many of the consumer goods is provided by volatile chemical compounds called fragrances. While the volatility of fragrances is essential to provide a pleasant olfactory response, it presents at the same time a technological problem, such that their premature evaporation and degradation may occur prior to the application during the storage. Another crucial aspect that affects the performance of the consumer goods is the deposition of these delivery systems to the target of interest. The potential strategies to improve the deposition of fragrance delivery systems are much less explored compared to their preparation and predominantly based on the physiochemical optimization of the surface/interface properties, such as hydrophobicity and charge of the existing delivery systems. However, the extent of depositions achieved using these strategies are typically modest. Phage display is an in vitro evolutionary selection technique that is widely used to identify substrate selective short peptide ligands. Although it has been predominantly used to isolate biomolecule binding ligands, its scope has been expanded in the last decade and it has also found use to identify hard and soft material binders. From this aspect, phage display may also provide short peptide ligands that can bind to i. e. cotton and hair surfaces under laundry and hair wash conditions. These ligands can be considered as a tool to improve the deposition of any fragrance delivery system upon their chemical incorporation via orthogonal functional groups. This Thesis aims to explore the feasibility of phage display identified peptides to selectively deposit fragrance delivery systems on cotton fabric and human hair surfaces and it can be subdivided into 4 Chapters. Chapter 1 provides a summary for the identification and characterization of soft matter binding peptides via phage display. Herein, soft matter will be subdivided into three general classes: synthetic polymers, small organic molecules and natural polymers. Chapter 2 proposes a general synthetic method for the preparation of water soluble peptide-polymer conjugates that proceeds at mild conditions without the requirement of peptide protecting groups. Chapter 3 describes the preparation of fragrance delivery systems that can selectively deposit onto cotton fabric under laundry wash conditions. The Chapter will first show the identification of cotton fabric binding peptides via phage display experiments. In the next steps, the strongest cotton binding peptide will be incorporated into two different model fragrance delivery systems that are based on linear polymers and nanoparticles. Chapter 4 applies the general strategy described in Chapter 3 to a more challenging task: Selectively depositing fragrance delivery systems onto hair under shampoo conditions. First, the feasibility of phage display to identify hair binding peptides under shampoo conditions will be demonstrated. Subsequently, two of the peptide-polymer conjugates described in Chapter 2 will be used as a model for hair targeting fragrance delivery systems. In the final section, the influence of the stringency of the shampoo conditions as well as the steric hindrance in the peptide terminal domains to the deposition of these peptides onto hair will be assessed.

New methods for developing (bi)cyclic peptides by phage display

Camille Villequey

Cyclic peptide ligands are a promising molecular format for the development of therapeutics. They combine some of the advantages of large protein therapeutics (high affinity and specificity) and of small molecule drugs (accessibility to chemical synthesis and low immunogenicity). With phage display, large combinatorial libraries of more than one billion mono- and polycyclic peptides can be developed and screened against virtually any target. During phage affinity selections, the physical link between phenotype (encoded peptide) and genotype (phage DNA) allows the identification of enriched peptide binders by sequencing of the phage vector DNA. Based on these concepts, our laboratory has established a robust chemistry in which phage displayed peptides containing two or three cysteines are cyclized or bi-cyclized with thiol-reactive linkers. This procedure has been generally applied for the isolation of potent and selective (bi)cyclic peptide ligands with therapeutic potential. The isolation of binders with optimal properties is highly dependent on the possibility to generate (bi)cyclic peptide libraries with high structural diversity and on the ability to thoroughly decode the phage selection output. In my PhD work, I developed new methods to generate large and structurally diverse libraries and to decode more efficiently phage selected peptides. In my first project, I explore the cyclization of peptides with two chemical bridges as a method to provide rapid access to phage-encoded libraries with high scaffold diversity. To this end, a range of twelve structurally diverse chemicals were tested for thiol-reactivity and phage compatibility. Subsequently, peptide libraries of the format XCXnCXnCX (X = random amino acid, C = cysteine, n = 3 or 4) were cyclized with six of these chemical linkers and panned against the protease plasma kallikrein. The selection yielded inhibitors with remarkable affinity (sub-nM KI), target selectivity (>1000-fold) and proteolytic stability (t1/2 in plasma > 3 days) despite a relatively small molecular mass (~ 1200 Da). In the second project, I developed phage-encoded libraries of small cyclic peptides in order to identify ligands that have the potential to be orally absorbed. A major challenge for the generation of such library is the usually low diversity of compounds due to the limited number of amino acids. In this work, we addressed this limitation by taking advantage of a recently discovered peptide cyclization reaction in which the thiol of a cysteine is ligated with the N-terminal amino group using a chemical reagent. We applied this strategies to two phage-encoded peptide libraries of four and five amino acids (XXXC and XXXXC) that were cyclized with eight chemical linkers yielding a collection of more than 1.3 million compounds. Panning the libraries against the two disease targets plasma kallikrein and coagulation factor XIa yielded ligands with single-digit micromolar affinity. In a third project, I developed a strategy to bypass the bacterial infection step in phage display. Bacterial infection is usually crucial for the propagation and identification of enriched clones by DNA sequencing. However, mutations or chemical modifications of the phage coat proteins, sometimes lead to decreased infection rates and therefore compromise the entire procedure. Consequently, there is an interest for developing methods in which this step could be completely omitted.

EPFL2017

Le concept switch-peptides

Karine Murat

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.

EPFL2006

Functional polymer brushes via surface-initiated controlled radical polymerizations

Stefano Tugulu

The term polymer brush refers to a well defined arrangement of polymer chains, which are tethered with one end to an interface and usually the surface of a solid substrate. Due to steric repulsion the polymer chains furthermore adopt a defined, stretched chain conformation, which significantly differs from the random walk conformation of free polymer chains in solution or in conventionally solution casted polymer coatings. From a structural point of view polymer brushes can therefore be regarded as the most defined type of polymer coating that can currently be realized. Especially the combination of surface-initiated polymerizations (SIP) with modern, controlled polymerization methods thereby allows tailoring the structure of the polymer brushes almost on the molecular level. Specifically precise control over the thickness, composition, chain architecture, grafting density and via the use of lithographic techniques also over the topography of the brushes can be achieved. This high degree of control over the structural and implicated (physico-)chemical properties of the brush allows at the same time tailoring and fine tuning the interfacial properties of the brush. This thesis describes the systematic exploitation of well-defined polymer brushes as functional coatings with fine-tuned physicochemical properties to direct and control the interaction with and the response of specific biological, bioanalytical and even reactive chemical environments. In detail the use of surface-initiated atom transfer radical polymerization (SI-ATRP) for the fabrication of functional polymer brushes will be presented. These brushes were used as highly defined coatings in various applications ranging from biomedical and bioanalytical applications to biomimetic materials fabrication (Figure 1). Figure 1 Numerous synthetic approaches for the preparation of polymer brushes have been described in the literature. Chapter 2 will therefore present a summary of the most important types of surface-initiated polymerizations, focusing especially on controlled SIP methods and SI-ATRP. Chapter 3 describes a chemoselective and specific immobilization strategy to decorate intrinsically bioinert polymer brushes with proteins of interest in a defined orientation and density. Specifically the resulting substrates represent attractive candidates for the realization of protein microarrays. In view of this application protein-small molecule and protein-protein interactions as well as posttranslational modifications were analyzed within a feasibility study. Due to their well-defined structure polymer brushes represent also attractive candidates for the realization of molecularly defined cell adhesion substrates for tissue engineering or as highly defined biophysical model system to analyze cell adhesion and mechanics. Chapter 4 describes the decoration of intrinsically bioinert polymer brushes with small peptide ligands with defined density to induce integrin specific cell adhesion on the brushes. Peptide functionalized polymer brushes could be readily endothelialized and adhering cell layers have shown to preserve their homeostatic ability to respond to an applied mechanical stimulus in a physiological manner. In Chapter 5 the limitations of high density polymer brushes in biomedical applications were assessed by analyzing their stability under in vitro cell culture conditions. Intrinsically bioinert high density polymer brushes were found to degraft from glass or silicon substrates upon swelling in good solvents, which lead to deterioration of the bioinert properties of the substrate. The degrafting of the brushes might be connected to swelling induced mechanical activation of chemical bonds, which link the brushes to the substrate. Chapter 6 describes the transfer of the developed SIP approach onto flexible PDMS substrates by exploiting the formation of interpenetrating networks of ATRP-initiator siloxane and PDMS. The modification of the PDMS substrates with hydrophilic brushes effectively reduces the unspecific protein adsorption on the substrates. This approach might therefore represent an attractive and facile route for the surface modification of miniaturized PDMS devices for biomedical or bioanalytical applications. In Chapter 7 the systematic development of a reliable and robust protocol for the aqueous SI-ATRP of sodium methacrylate is presented, which gives access to poly(methacrylic acid) (PMAA) brushes with defined molecular weight and grafting density. The resulting brushes were assessed for their ability to direct the mineralization of calcium carbonate. Chapter 8 describes the use of photolithographically patterned poly(methacrylic acid) brushes as biomimetic, acidic macromolecular matrix to fabricate microstructured calcite thin films that are an exact 3D replica of the PMAA brush. The presented strategy relies on three key elements: (i) the use of photolithographic techniques to prepare microstructured PMAA brushes; (ii) the ability of PMAA brushes to stabilize amorphous calcium carbonate (ACC) and (iii) the possibility to convert the metastable ACC phase into a polycrystalline calcite film via a thermal treatment.

EPFL2007