Chez les eucaryotes supérieurs, la progression ordonnée du cycle cellulaire est régie par une dizaine de kinases Cdk-cyclines. Les altérations génétiques ou épigénétiques impliquant des oncogènes ou des gènes codant pour des suppresseurs de tumeurs sont souvent associées à l'expression ou l'activation aberrante des Cdks, favorisant ainsi la prolifération cellulaire incontrôlée et notamment le développement de cancers. Malgré la pertinence oncogénique et thérapeutique de ces protéines, leur détection est restée jusqu'à présent limitée à des méthodes indirectes et invasives. Dans ce contexte, mes travaux de thèse ont permis de développer un biosenseur peptidique fluorescent permettant de reconnaître spécifiquement les Cdk-cyclines. Associé à une stratégie de vectorisation non invasive basée sur l'utilisation de peptides vecteurs pénétrants, le biosenseur a été délivré efficacement dans les cellules. La mise au point d'une quantification ratiométrique du signal a par ailleurs permis d'évaluer l'abondance relative des Cdk-cyclines endogènes. Deux variants plus spécifiques de certains complexes ont pu être développés. Enfin, d'autres versions du biosenseur ont quant à elles permis d'évaluer sa biodistribution in vivo et de mettre au point un essai cellulaire en vue d'un criblage de petites molécules ayant un effet sur l'abondance relative des Cdk-cyclines. / Cdk-cyclins represent key regulators of cell cycle progression among superior eukaryotes. Genetic and epigenetic alterations involving oncogenes or tumor suppressor genes are often associated with aberrant expression or activation of Cdks, leading to the sustained proliferation of cells and by the way to the development of cancers. Despite the oncogenic and therapeutic relevance of these proteins, their detection has so far remained limited to indirect and invasive methods. My Ph.D. thesis work aimed in this context at developing peptidic fluorescent biosensors that specifically recognize Cdk-cyclins. Combined to cell-penetrating peptides, the biosensor was efficiently delivered into cells. Following the development of the signal ratiometric quantification, the relative abundance of endogenous Cdk-cyclins was directly evaluated in living cells. Two other variants, that are more specific towards specific Cdk-cyclin complexes, were also designed. Finally, the development of novel versions of the biosensor allowed us to evaluate its biodistribution in vivo and to set up a cell-based assay to screen small molecules having an effect on Cdk-cyclin relative abundance.

<p>Pathogenic bacteria present a critical threat to modern medicine. Therapeutic strategies to target and eliminate resilient bacteria are not advancing at the same rate as the emergence of bacterial resistance. An associated urgent concern regarding antibiotic resistance is the existence and proliferation of intracellular bacteria, which find refuge from bactericidal mechanisms by hiding within mammalian cells. Therefore, many once-successful antibiotics become ineffective through the development of resistance, or through failure to reach intracellular locations in therapeutic concentration. To overcome these challenges, the covalent combination of a conventional antibiotic with an antibiotic, cell-penetrating peptide was explored to develop dual-action antibiotic conjugates. </p> <p>Herein, we utilized a strategy in conjugating the antibiotics by a cleavable linkage to cationic amphiphilic polyproline helices (CAPHs) to improve vancomycin and linezolid antibiotics. This approach enables the conjugate to penetrate cells and deliver two potent monomeric antimicrobial drugs. The vancomycin-CAPH conjugate, <b>VanP14S</b>, showed enhanced mammalian cell uptake compared to vancomycin, a poor mammalian cell-penetrating agent; and <b>VanP14S</b> was capable of cleaving and releasing two antibiotics under mimicked physiological conditions. Enhanced antibacterial activity was observed against a spectrum of Gram-positive and Gram-negative pathogens, including drug-resistant strains. Further investigation revealed that this conjugate’s bactericidal activity was not entirely the result of significant membrane perturbation such as a lytic mode of action. Mammalian cell toxicity and red blood cell lysis were insignificant at relevant bactericidal concentrations below 20 µM. The current results suggest an enhanced binding to the peptidoglycan of bacteria, the target of vancomycin, although more work is needed to justify this claim. Preliminary results on <b>VanP14GAPS</b>, a conjugate with a more rigid CAPH, convey similar activity to <b>VanP14S; </b>however,<b> </b>moderate increases in red blood cell lysis and cytotoxicity were observed. </p> <p>Regarding the <b>LnzP14</b> conjugate, preliminary data reveal that the conjugate has Gram-negative activity against <i>Escherichia coli</i>, whereas linezolid is ineffective in killing Gram-negative bacteria. This conjugate showed significant enhancement in cellular uptake compared to the CAPH, and the release of linezolid and CAPH in physiological conditions was confirmed. Overall, arming a conventional antibiotic with an antimicrobial, cell-penetrating peptide appears to be a powerful strategy in providing novel antibiotic conjugates with the propensity to overcome the limitations in treating challenging pathogens.</p>

Over the years, biological drugs have evolved and have made breakthroughs in diseases associated with extracellular proteins. However, intracellular proteins that cause disease progression are still largely inaccessible. Examples of diseases that are caused by an intracellular aggregation of proteins are neurodegenerative diseases such as Parkinson's disease, Huntington's disease (HD), and Alzheimer's disease (AD). The purpose of the work is to find a strategy to reach the neurons intracellularly. The goal is to be able to design a biological drug that enters the neuron by investigating different uptake mechanisms. A systematic review of 43 published studies was reviewed, and the results could be obtained. All result presents data from different receptors, cell-penetrating peptides, and adeno-associated viruses (AAV) that were examined. It showed that there are advantages and disadvantages with all the uptake mechanisms. There are risks of side effects for each uptake mechanism, and further studies are required to consider the risk. AAV2 and the neuron-specific receptors lack specific information about their mechanism, but there is a high potential to develop these strategies. Both AVV and the neuron-specific receptors provide specific uptake into tissues.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20810号 / 医博第4310号 / 新制||医||1025(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 清水 章, 教授 萩原 正敏, 教授 松原 和夫 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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Viral vectors derived from mouse polyomavirus are a convenient tool for studying the targeted delivery of therapeutical agents into the cells and cellular organelles. Vectors derived from mouse polyomavirus face difficulties similar to other nanoparticles, as they often end up trapped inside an endosome where they are subsequently degraded. This diploma explored the potential of vector modifications, which have the potential to make the transport to the nucleus or cytosol more effective. This work had particularly focused on increasing the transduction efficiency by modifying particle's internally localized VP3 capsid protein with covalently bound membrane-penetrating peptides. Primary covalent genetic modification to the VP3 protein was the polyhistidine peptide KH27K. Its potential of improving the transduction effectivity was compared with two other peptide modifications - LAH4 and R8. The results of the transduction test showed that covalently bound R8 peptide had many-fold improved the transport to the nucleus when compared to the unmodified particles. The modification with LAH4 peptide had been regarded more effective only when was associated with the particles non-covalently. In such scenario the transduction efficiency rose 40-times when compared with unmodified particles. Polyhistidine...

<p>  </p> <p>The access of ring junction functionalized 5,6-hydrindanone systems has been elusive in the realm of synthetic methodology, and the functionalization of a pre-built ring system rarely explored. These 5,6-hydridanone systems are prevalent in a variety of terpenoid ring systems, especially that of steroidal molecules. Previous synthetic methods to reach these systems using a Diels-Alder cycloaddition proved to be difficult and lacked labile functional groups that would be useful for substitution after the cycloaddition. The design of the α-nitrile cyclopentenone dienophile allows for both post-cyclization adduct functionalization, as well as lowering the energy barrier of the cycloaddition itself. In this work, it is shown that the Lewis acid promoted Diels-Alder reaction with α-nitrile β-methyl cyclopentenone dienophile can be performed under standard temperatures and pressures unlike previously established methods.1 This reaction can generate four chiral centers in a single synthetic step when the starting materials are prochiral. After the generation of 5,6-hydrindanone systems, radical cleavage of the nitrile functionality also allowed for electrophile trapping at the ring junction. This radical cleavage and electrophile trapping pathway allows for functionalization of a quaternary carbon at the ring junction, a method that should be fruitful in the generation of difficult to synthesize steroidal and other terpenoid molecules.</p> <p>In the work on synthetic cell penetrating peptides, camptothecin whilst a notably effective topoisomerase I inhibitor, has never quite reached it’s potential as a therapeutic due to its poor solubility in living systems. Previously, cationic amphiphilic polyproline helices (CAPH) molecules from the Chmielewski lab have been hydrophobically functionalized through O-alkylation of hydroxyprolines at specific regions within the peptide to generate a hydrophobic face. The combination of the cationic faces and the hydrophobic face have made the CAPH molecules notably cell penetrant and tunable. With camptothecin’s notable insolubility in water, it may serve as valuable surrogate to the hydrophobic groups on CAPH molecules and allowing it to be delivered intracellularly. Using an endogenously cleavable linker, we have worked towards a CPP that acts as a drug delivery vehicle. Acting as a replacement of the hydrophobic residue of a CAPH molecule, camptothecin will be chaperoned into the cell and should be released through the action of intracellular esterases.</p>

<p dir="ltr">In light of new interest in biomaterials for drug formulation and delivery, coiled-coil assemblies have emerged as promising candidates. Characterized by facile synthesis, low toxicity, and biocompatibility, coiled-coil assemblies hold a significant potential for drug encapsulation and cellular delivery. Herein, I will discuss the development of a novel nanoscale metal-mediated coiled-coil assembly with tunable assembly properties, presenting a compelling platform for drug encapsulation and targeted cell delivery, thereby addressing critical challenges in modern pharmaceutical science.</p><p dir="ltr">Moreover, the rise of antimicrobial resistance has contributed to a global health crisis. Many current antibiotics are announced as unviable, and the addition of bacteria that invade the cell further challenges and limits these current drugs. The Chmielewski group has previously shown that cationic amphiphilic polyproline helices (CAPHs) act as dual agents displaying both cell-penetration and antibiotic activity. To further increase these dual properties, new unnatural amino acids and new CAPH peptides were synthesized with new configurations of hydrophobic and hydrophilic moieties. I will discuss the outcomes of these modifications, including cell penetration, subcellular localization, and antibacterial efficacy.</p>

Genetic mutations can cause a wide range of diseases, e.g. cancer. Gene therapy has the potential to alleviate or even cure these diseases. One of the many gene therapies developed so far is RNA-cleaving deoxyribozymes, short DNA oligonucleotides that specifically bind to and cleave RNA. Since the development of these synthetic catalytic oligonucleotides, the main way of determining their cleavage kinetics has been through the use of a laborious and error prone gel assay to quantify substrate and product at different time-points. We have developed two new methods for this purpose. The first one includes a fluorescent intercalating dye, PicoGreen, which has an increased fluorescence upon binding double-stranded oligonucleotides; during the course of the reaction the fluorescence intensity will decrease as the RNA is cleaved and dissociates from the deoxyribozyme. A second method was developed based on the common denominator of all nucleases, each cleavage event exposes a single phosphate of the oligonucleotide phosphate backbone; the exposed phosphate can simultaneously be released by a phosphatase and directly quantified by a fluorescent phosphate sensor. This method allows for multiple turnover kinetics of diverse types of nucleases, including deoxyribozymes and protein nucleases. The main challenge of gene therapy is often the delivery into the cell. To bypass cellular defenses researchers have used a vast number of methods; one of these are cell-penetrating peptides which can be either covalently coupled to or non-covalently complexed with a cargo to deliver it into a cell. To further evolve cell-penetrating peptides and understand how they work we developed an assay to be able to quickly screen different conditions in a high-throughput manner. A luciferase up- and downregulation experiment was used together with a reduction of the experimental time by 1 day, upscaling from 24- to 96-well plates and the cost was reduced by 95% compared to commercially available assays. In the last paper we evaluated if cell-penetrating peptides could be used to improve the uptake of an LNA oligonucleotide mimic of GRN163L, a telomerase-inhibiting oligonucleotide. The combination of cell-penetrating peptides and our mimic oligonucleotide lead to an IC50 more than 20 times lower than that of GRN163L.

Les peptides pénétrateurs de cellule (CPP) sont des oligopeptides cationiques faisant parti des vecteurs les plus étudiés dans le cadre du développement du transport ciblé de médicament à l’intérieur de l’organisme. Les applications principales sont par exemple le traitement des cancers ou la thérapie génique. Néanmoins, certaines caractéristiques des CPPs rendent leur utilisation médicale compliquée, tels que leur manque de spécificité à l’égard des cellules cibles ou la perte de leurs propriétés pénétrantes lorsqu’un cargo moléculaire leur est greffé. L’une des solutions envisagées pour résoudre ces problèmes est le greffage sur des polypeptides di-blocs auto-assemblés basés sur de l’élastine (ELPBC), des systèmes développés par l’équipe d’Ashutosh Chilkoti à l’Université de Duke (USA). Des travaux précédents ont montré que ces macromolécules, que l’on appelle CPP-ELPBC, retrouvaient les propriétés pénétrantes du CPP même en présence d’un cargo et permettaient également d’induire une spécificité à l’encontre des cellules cancéreuses. En revanche, le mécanisme de pénétration de ces systèmes restait inconnu.Dans cette thèse, je me suis concentré sur l’étude du mécanisme de pénétration des CPP et des CPP-ELPBC au travers de membranes lipidiques modèles, et en particulier sur l’adsorption de ces molécules à la surface de vésicules unilamellaires géantes (GUV). Le développement d’une nouvelle méthode de quantification de la fluorescence en microscopie confocale m’a permis de réaliser des mesures simples de comptage de peptides à la surface des vésicules, ce qui m’a permis par la suite de procéder à des mesures thermodynamiques de l’adsorption des peptides. / Cell-penetrating peptides (CPP) are cationic oligopeptides currently investigated as potential vectors for targeted drug delivery design, for applications in cancer treatment and/or gene therapy. Nevertheless, some drawbacks make the CPP complex for medical applications, such as their lack of specificity toward target cells or the loss of their penetrating properties once they have been grafted with a molecular cargo. One of the solutions studied to overcome these issues is the binding of the CPP unit on a self-assembling elastin-like diblock polypeptide (ELPBC), a macromolecular system designed by the team of Ashutosh Chilkoti from Duke University (USA). While it has already been proven that these molecules, named CPP-ELPBC, recover the penetrating properties of the CPP despite the presence of a cargo and also induce a selectivity toward tumorous cells, the exact mechanism of translocation is still under debate.In this PhD thesis, I focused on the investigation of the translocation mechanism of the CPP and CPP-ELPBC using model lipid membranes, and specifically the adsorption of these molecules at the surface of giant unilamellar vesicles (GUV). The development of a new quantification method of fluorescence in confocal microscopy allowed me to directly count the peptides adsorbed on the surface of the GUVs, which I used to perform thermodynamic measurements on the peptide adsorption.