<p>This thesis investigates three different surface modifications, and the route to design and synthesize them. The thesis is therefore divided into three sub- projects. (i.) Design and synthesis of a peptide which secondary structure could be controlled by a negatively charged surface. (ii.) Design and synthesis of a cyclic peptide, that would self-organize prior to surface interaction, using the type I anti-freeze protein of a winter flounder as template. (iii.) The use of solid-phase synthesis to make the synthesis of SAM-molecules easier.</p>

In 1908, H. Emil Fisher attempted to prepare glycinal, an unprotected amino aldehyde, which he found to be inherently unstable and prone to polymerization. This instability arises from the propensity of amines to condense with aldehydes. Accordingly, amino aldehydes require protection of the amine functional group. On the contrary, aziridines do not condense with aldehydes; the aziridine ring-strain precludes the formation of an iminium ion. Predicated upon this orthogonal reactivity, a stable class of unprotected amino aldehydes has been prepared, and an in-depth investigation into their chemical reactivity has been undertaken. Reactions designed to utilize both their nucleophilic (amine) and electrophilic (aldehyde) centres have demonstrated their capacity to forge multiple bonds in a single transformation, and have been implemented in the synthesis of complex heterocycles and cyclic peptides.

This thesis investigates three different surface modifications, and the route to design and synthesize them. The thesis is therefore divided into three sub- projects. (i.) Design and synthesis of a peptide which secondary structure could be controlled by a negatively charged surface. (ii.) Design and synthesis of a cyclic peptide, that would self-organize prior to surface interaction, using the type I anti-freeze protein of a winter flounder as template. (iii.) The use of solid-phase synthesis to make the synthesis of SAM-molecules easier.

In 1908, H. Emil Fisher attempted to prepare glycinal, an unprotected amino aldehyde, which he found to be inherently unstable and prone to polymerization. This instability arises from the propensity of amines to condense with aldehydes. Accordingly, amino aldehydes require protection of the amine functional group. On the contrary, aziridines do not condense with aldehydes; the aziridine ring-strain precludes the formation of an iminium ion. Predicated upon this orthogonal reactivity, a stable class of unprotected amino aldehydes has been prepared, and an in-depth investigation into their chemical reactivity has been undertaken. Reactions designed to utilize both their nucleophilic (amine) and electrophilic (aldehyde) centres have demonstrated their capacity to forge multiple bonds in a single transformation, and have been implemented in the synthesis of complex heterocycles and cyclic peptides.

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京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第21050号 / 薬科博第93号 / 新制||薬科||10(附属図書館) / 京都大学大学院薬学研究科医薬創成情報科学専攻 / (主査)教授 大野 浩章, 教授 竹本 佳司, 教授 二木 史朗 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

Les interactions multivalentes sucre/protéine sont impliquées dans de nombreux processus biologiques tels que l'adhésion hôte-pathogène, la communication cellulaire ou les réponses immunitaires. La conception de glycoconjugués capables de présenter des motifs osidiques en cluster est essentielle, non seulement pour étudier ces phénomènes de reconnaissance complexes mais aussi pour développer des agents biologiquement actifs. Dans ce contexte, l'objectif de ma thèse a été de synthétiser de nouveaux glycoclusters et d'évaluer leurs propriétés biologiques. Ces glycoclusters ont été obtenus en conjuguant des sucres sur des cyclopeptides par des méthodes chimiosélectives (cycloaddition de Huisgen et ligation oxime). Des composés tetravalents, hexavalents et hexadécavalents d'architectures et de compositions variables ont été synthétisés, entièrement caractérisés puis évalués au laboratoire ou dans le cadre de collaborations avec différentes cibles. Un glycocluster hexadécavalent fucosylé a ainsi pu être identifié comme puissant inhibiteur de l'interaction de la lectine PA-IIL de la bactérie Pseudomonas aeruginosa à une concentration subnanomolaire. Une autre famille de composés associant des sucres et des peptides a montré des propriétés immunologiques uniques, notamment pour activer les cellules NK contre des cellules cancéreuses sans déclencher de phénomène d'autoapoptose. Mots clés : chimie des sucres, chimie des peptides, glycoclusters, ligations chimiosélectives, interactions sucre-protéine, lectine, cellule NK. / Multivalent carbohydrates-protein interactions are involved in a large variety of biological processes such as host-pathogen adhesions, cell communication or immune responses. The design of glycoconjugates displaying multiple copies of sugars as cluster is essential, not only to study these complex recognition processes but also to develop bioactive agents. In this context, the objective of my PhD was to synthesize new glycoclusters and evaluate their biological properties. These glycoclusters were obtained by conjugating carbohydrate moieties and peptides using chemoselective ligations (Huisgen cycloaddition and oxime ligation). Tetravalent, hexavalent and hexadecavalent glycoclusters with variable structures and compositions were synthesized, fully characterized and biologically evaluated with different targets in our laboratory or in collaborations. A hexadecavalent fucosylated glycocluster was thus identified as a strong inhibitor of the lectin PA-IIL from Pseudomonas aeruginosa at subnanomolar concentration. Another type of molecule containing carbohydrate and peptides has showed unique immunological properties, in particular for the activation of NK cells against tumors without inducing apoptotic effect Key words: carbohydrate chemistry, peptide chemistry, chimioselective ligations, glycoclusters, carbohydrate-protein interactions, lectin, NK cell.

Title: Raman optical activity and conformational flexibility of peptides in solution Author: Jana Hrudíková Department: Institute of Physics of Charles University Supervisor: Doc. RNDr. Vladimír Baumruk, DrSc. Supervisor's e-mail address: baumruk@karlov.mff.cuni.cz Abstract: Molecular flexibility can significantly modify Raman and ROA spectral intensities, band positions and the ROA signs. Taking into account dynamic aspects of behavior of studied molecules in solution via conformational averaging therefore seems to be crucial for spectral interpretation. The first of studied models, histidine, plays an important role in metallo-enzymatic reactions and peptide folding, due to its imidazole ring. ROA spectra of His at different pH, His complexed with Cu2+ and dipeptides His- Gly and Gly-His were recorded on the spectrometer built at the Institute of Physics of the Charles University as a first step of the subsequent study. The second studied system, a cyclic hexapeptide c-(Phe-D-Pro-Gly-Arg-Gly-Asp), serves as a convenient model for β- hairpin and anti-parallel β-sheet. It was previously studied by means of VCD and IR. From molecular dynamics simulations 10 peptide geometries were selected for spectral modeling. The Raman and ROA spectra were calculated ab initio. For a model fragment Phe-D-Pro, which...

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The human TAR DNA-binding protein 43 (TDP-43) is crucial for regulating cellular processes such as transcription, RNA splicing, and mRNA transport and translation. However, its abnormal cytoplasmic aggregation disrupts these functions and contributes to the development of many neurodegenerative diseases. The aim of this study is to design and evaluate cyclic peptide binders capable of modulating the TDP-43 aggregation. Using the AfDesign tool, we generated 84 cyclic peptide binders of varying lengths (10 to 13 amino acids). Analysis revealed 17 binders with pLDDT scores above 70, indicating stable conformation, and 43 binders with pAE scores below 10, suggesting strong binding affinity to the target protein. Further binding affinity analysis with PRODIGY confirmed these results, identifying binders with low dissociation constant. Molecular dynamics (MD) simulations indicated that peptide binders effectively delayed TDP-43 aggregation. However, permeability studies using Steered Molecular Dynamics (SMD) simulation showed that the designed binders had a low permeability coefficient (2.18x10-15 cm/sec), significantly lower than the benchmark for effective permeability. This highlights the need for further optimization to enhance the binders’ permeability. Future work will involve scaling up the design process, improving screening techniques, and employing advanced simulation methods to achieve better insights and more effective peptide binders.