| 1. |
- Cerrato, Carmine Pasquale
(författare)
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Cell-penetrating peptide targeting mitochondria : Design, synthesis, characterization, and biological effects
- 2015
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- More than twenty years after the discovery of the first cell-penetrating peptide (CPP), a large number of both naturally occurring as well as engineered CPPs have been discovered. Generally, CPPs are short polycationic sequences of less than 30 amino acids that are able to translocate different cargoes into cells. They are amphipathic and net positively charged at physiological pH. The cargo can be covalently attached to the CPP, which can be achieved by expression as a fusion construct or by chemical coupling; or the cargo and carrier could bind each other non-covalently mainly through ionic interactions.A series of CPPs targeting mitochondria (mtCPPs) were studied in an effort to optimize their applications for the reduction of reactive oxygen species targeting this therapeutically important organelle. Mitochondria have evolved to play a vital role in both life and death of eukaryotic cells, through involvement in numerous cellular functions, such as the proficient production of energy from ATP biosynthesis and the regulation of programmed cell death. As a result, dysfunction in the biochemical processes housed within this organelle is implicated in diverse diseases, including cancer, diabetes, and neurodegenerative disorders. Advancing mitochondrial medicine by probing the subcellular biochemistry or targeting therapeutics into this organelle has motivated the development of effective mitochondrial delivery vectors. A fluorescent probe was covalently attached at the N-terminus of the analog peptides to determine the cellular internalization and the possibility to be transported to mitochondria by mtCPPs. The results report the development of a novel cationic peptides (mtCPP-1), which is readily cell permeable and preferentially localize into the mitochondria of living mammalian cells. By substitutions with both natural and synthetic amino acids, and monitoring the intracellular localization by fluorescence microscopy, the mitochondrial accumulation with a cationic peptide was achieved. The biological and chemical characterization of mtCPP-1 revealed the importance of balancing the opposing characteristics of positive charge and lipophilicity to attain preferential sequestration into mitochondria, as well as provide evidence that this antioxidant peptide will be suitable as mitochondrial delivery vector.
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| 2. |
- Cerrato, Carmine Pasquale, 1987-
(författare)
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Cell-Penetrating Peptides for Mitochondrial Targeting
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mitochondria have simply been known as the cell’s powerhouse for a long time, with its vital function of producing ATP. However, substantially more attention was directed towards these organelles once they were recognized to perform several essential functions having an impact in cell biology, pharmaceutics and medicine. Dysfunctions of these organelles have been linked to several diseases such as diabetes, cancer, neurodegenerative diseases and cardiovascular disorders. Mitochondrial medicine emerged once the relationship of reactive oxygen species and mutations of the mitochondrial DNA linked to diseases was shown, referred to as mitochondrial dysfunction. This has led to the need to deliver therapeutic molecules in their active form not only to the target cells but more importantly into the targeted organelles.In this thesis, cell-penetrating peptides (CPPs) used as mitochondrial drug delivery system and the pathways involved in the uptake mechanisms of a CPP are described. In particular, Paper I describes a novel cell-penetrating peptide targeting mitochondria with intrinsic antioxidant properties. Paper II expands upon this first finding and show that the same peptide can carry a glutathione analogue peptide with improved radical scavenging ability into cytoplasm and mitochondria. Paper III introduces mitochondrial targeting peptides for delivery of therapeutic biomolecules to modify mitochondrial gene expression. In Paper IV, the uptake mechanisms of the CPP delivery strategy has been investigated to gain a better understanding of the used transfection system.Overall, this thesis summarizes our current effort regarding cell-penetrating peptides delivery system to target mitochondria and the progress made towards a potential gene therapy. It contributes to the field of CPPs and drug delivery with a set of peptides with radical scavenging ability, a strategy to deliver oligonucleotides to mitochondria as proof-of-concept for mitochondrial gene therapy, and to help understanding the pathways involved in CPPs uptake.
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| 3. |
- Dowaidar, Moataz, 1984-
(författare)
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Chimeric gene delivery vectors : Design, synthesis, and mechanisms from transcriptomics analysis
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Delivery of nucleic acid is a promising approach for genetic diseases/disorders. However, gene therapy using oligonucleotides (ONs) suffers from low transfection efficacy due to negative charges, weak cellular permeability, and enzymatic degradation. Thus, cell-penetrating peptide (CPP), is a short cationic peptide, is used to improve the cell transfection. In this thesis, new strategies for gene transfection using the CPP vectors in complex with ONs without and with nanoparticles, such as magnetic nanoparticles (MNPs, Fe3O4), and graphene oxide (GO), are investigated. Furthermore, the possible CPP uptake signalling pathways are also discussed.A fragment quantitative structure-activity relationship (FQSAR) model is applied to predict new effective peptides for plasmid DNA transfection. The best-predicted peptides were able to transfect plasmids with significant enhancement compared to the other peptides. CPPs (PeptFect220 (denoted PF220), PF221, PF222, PF223, PF224) generated from the FQSAR, and standard PF14 were able to form self-assembled complexes with MNPs and GO. The formed new hybrid vectors improved the cell transfection for plasmid (pGL3), splicing correcting oligonucleotides (SCO), and small interfering RNA (siRNA). These vectors showed high cell biocompatibility and offered high transfection efficiency (> 4-fold for MNPs, 10–25-fold for GO) compared to PF14/SCO complex, which was before reported with a higher efficacy compared to the commercial lipid-based transfection vector Lipofectamine™2000. The high transfection efficiency of the novel complexes (CPP/ON/MNPs and CPP/ON/GO) may be due to their low cytotoxicity, and the synergistic effect of MNPs, GO, and CPPs. In vivo gene delivery using PF14/pDNA/MNPs was also reported. The assembly of CPPs/ON with MNPs or GO is promising and may open new venues for potent and selective gene therapy using external stimuli. The uptake signaling pathways using CPPs vectors, the RNA expression profile for PF14, with and without ON were investigated using RNA sequencing and qPCR analysis. Data showed that the signaling pathways are due to the regulation of autophagy-related genes. Our study revealed that the autophagy regulating proteins are concentration-dependent. Confocal microscopy and transmission electron microscopy have demonstrated the autophagy initiation and colocalization of ON with autophagosomes. Results showed that the cellular uptake of CPP-based transfection activates the autophagy signaling pathway. These findings may open new opportunities to use autophagy modifiers in gene therapy.
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| 4. |
- Eiríksdóttir, Emelía, 1976-
(författare)
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Structures, toxicity and internalization of cell-penetrating peptides
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cellular internalization is a highly regulated process controlled by proteins in the plasma membrane. Large and hydrophilic compounds, in particular, face difficulties conquering the plasma membrane barrier in order to gain access to intracellular environment. This puts serious constrains on the drug industry since many drugs are hydrophilic. Several methods aiming at aiding the cellular internalization of otherwise impermeable compounds have therefore been developed. One such class, so-called cell-penetrating peptides (CPPs), emerged around twenty years ago. This group constitutes hundreds of peptides that have shown a remarkable ability in translocating diverse molecules, ranging from small molecules to large proteins, over the cell membrane. The internalization mechanism of CPPs has been questioned ever since the first peptides were discovered. Initially, the consensus in the field was direct translocation but endocytosis has gradually gained ground. The confusion and the disunity within this research field through the years proceeds from divergent results between research groups that hamper comparison of the peptides.This thesis aims at characterizing several well-established CPPs with comprehensive studies on cellular toxicity, secondary structure and cellular internalization kinetics.The results demonstrate that CPPs act in general in a low or non-toxic way, but the apparent toxicity is both peptide- and cell line-dependent. Structural studies show that the CPPs have a diverse polymorphic behavior ranging from random coil to structured β-sheet or α-helix, depending on the environment. The ability to change secondary structure could be the key to the internalization property of the CPPs. Internalization kinetic studies of CPP conjugates reveal two sorts of internalization profiles, either fast curves that cease in few minutes or slow curves that peak in tens of minutes. Furthermore, improved synthesis of CPP conjugates is demonstrated.In conclusion, the studies in this thesis provide useful information about cytotoxicity and structural diversity of CPPs, and emphasize the importance of kinetic measurements over end-point studies in order to give better insights into the internalization mechanisms of CPPs.
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| 5. |
- EL Andaloussi, Samir
(författare)
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Vectorization of oligonucleotides with cell-penetrating peptides : Characterization of uptake mechanisms and cytotoxicity
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The hydrophobic plasma membrane constitutes an indispensable barrier for cells in living animals. Albeit being pivotal for the maintenance of cells, the inability to cross the plasma membrane is still one of the major obstacles to overcome in order to progress current drug development. A group of substances, with restricted access to the interior of cells, which has shown great promise for future clinical use is oligonucleotides that are exploited to interfere with gene expression. Short interfering RNAs that are utilized to confer gene silencing and splice correcting oligonucleotides, applied for the manipulation of splicing patterns, are two classes of oligonucleotides that have been explored in this thesis. Cell-penetrating peptides (CPPs) are a class of peptides that has gained increasing focus in last years. This ensues as a result of their remarkable ability to convey various, otherwise impermeable, macromolecules across the plasma membrane of cells in a relatively non-toxic fashion. This thesis aims at further characterizing well-established, and newly designed, CPPs in terms of toxicity, delivery efficacy, and internalization mechanism. Our results demonstrate that different CPPs display different toxic profiles and that cargo conjugation alters the toxicity and uptake levels. Furthermore, we confirm the involvement of endocytosis in translocation of CPPs, and in particular the importance of macropinocytosis. All tested peptides facilitate the delivery of splice correcting oligonucleotides with varying efficacy, the newly designed CPP, M918, being the most potent. Finally we conclude that by promoting endosomolysis, by exploring new CPPs with improved endosomolytic properties, the biological response increases significantly. In conclusion, we believe that these results will facilitate the development of new CPPs with improved delivery properties that could be used for transportation of oligonucleotides in clinical settings.
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| 6. |
- Eriksson, Jonas, 1986-
(författare)
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Gene therapy tools: oligonucleotides and peptides
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 7. |
- Eriksson Sollenberg, Ulla, 1977-
(författare)
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Characterization of galanin receptors using chimeric peptides and site-directed mutagenesis
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Galanin, a 29 (30) amino acid neuropeptide, is found throughout both the central and peripheral nervous systems. It signals via three receptors, GalR1-3, all belonging to the rhodopsin-like G-protein coupled receptors. Galanin and its receptors have been implicated in a vast variety of biological processes. To facilitate further characterization of the physiological/pathological roles of galanin, subtype selective ligands targeting the three receptors individually would be of great aid. In this thesis the main objective was to provide more information about galanin receptor-ligand interactions, primarily concerning GalR2 and 3. By using information gained from previously developed chimeric peptides, we designed and synthesized a novel peptide selective towards GalR2 (Paper I). This peptide, M871, binds GalR2 in an inhibitory manner, likely due to its truncated N-terminus and bulky character. In Paper II and IV we performed L-alanine mutagenesis assays of GalR2 and 3 respectively. By point substituting amino acid residues in the receptor sequence, we identified crucial pharmacophores for ligand binding, primarily in transmembrane regions 6 and 7. The targeted residues were selected based on knowledge concerning GalR1 and on conservation between the three receptors. For GalR3 we also conducted a computational docking assay. A homology model was first constructed using three crystallized structures of other receptors also belonging to the Rhodopsin family. Ligands galanin(2-6) and SNAP398299 were then docked to GalR3 in flexible mode. The docking resulted in characterization of GalR3-ligand interactions and conclude that this receptor display a relatively deep and narrow binding pocket. As a result of this, it was hypothesized that the C-terminus of ligands is of importance for GalR3 affinity. An L-alanine scan of ligand was performed (paper III), which confirmed this theory. In conclusion, our results give insights into galanin receptor-ligand interactions, information that is relevant for ligand design and drug development.
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| 8. |
- Ezzat, Kariem
(författare)
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CELL PENETRATING PEPTIDES : CHEMICAL MODIFICATION AND FORMULATION DEVELOPMENT
- 2011
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cell penetrating peptides (CPPs) have been extensively studied and exploited as drug delivery vectors for a wide variety of therapeu-tic cargos. However, several issues remain to be addressed regarding the enhancement of their efficiency and stability. In addition, to be available for patients, CPP-based therapeutics have to be formulated into suitable pharmaceutical forms that can be readily manufactured, transported, stored and conveniently used.In this thesis, three chemically modified CPPs are developed having superior delivery properties for several nucleic acid-based the-rapeutic cargoes including: plasmids, small interfering RNA (siRNA) and splice switching oligonucleutides (SSOs), in different in-vitro and in-vivo models. In Paper I, we show that an N-terminally stearic acid-modified version of transportan-10 (TP10) can form stable nanopar-ticles with plasmids that efficiently transfect different cell types and can mediate efficient gene delivery in-vivo when administrated intra muscularly (i.m.) or intradermaly (i.d.). In paper II, stearyl-TP10 is further modified with pH titratable trifluoromethylquinoline moieties to facilitate endosomal release. The new peptide, denoted PepFect 6 (PF6), elicited robust RNAi responses when complexed with siRNA in several cell models and promoted strong RNAi responses in differ-ent organs following systemic delivery in mice without any associated toxicity. In paper III , a new peptide with ornithine modification, PF14, is shown to efficiently deliver SSOs in different cell models including HeLa pLuc705 and mdx mouse myotubes; a cell culture model of Duchenne‟s muscular dystrophy (DMD). Additionally, we have developed a method for incorporating this delivery system into solid formulation that could be suitable for several therapeutic appli-cations. Solid dispersion technique is utilized and the formed solid formulations are as active as the freshly prepared nanocparticles in solution even when stored at elevated temperatures for several weeks.Taken together, these results demonstrate that certain chemical modifications could drastically enhance the activity and stability of CPPs in-vitro and in-vivo. Moreover, we show that CPP-based thera-peutics could be formulated into convenient and manufacturable do-sage forms.
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| 9. |
- Ezzat, Kariem, 1983-
(författare)
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Cell-penetrating peptides; chemical modification, mechanism of uptake and formulation development
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gene therapy holds the promise of revolutionizing the way we treat diseases. By using recombinant DNA and oligonucleotides (ONs), gene functions can be restored, altered or silenced according to the therapeutic need. However, gene therapy approaches require the delivery of large and charged nucleic acid-based molecules to their intracellular targets across the plasma membrane, which is inherently impermeable to such molecules. In this thesis, two chemically modified cell-penetrating peptides (CPPs) that have superior delivery properties for several nucleic acid-based therapeutics are developed. These CPPs can spontaneously form nanoparticles upon non-covalent complexation with the nucleic acid cargo, and the formed nanoparticles mediate efficient cellular transfection. In paper I, we show that an N-terminally stearic acid-modified version of transportan-10 (PF3) can efficiently transfect different cell types with plasmid DNA and mediates efficient gene delivery in-vivo when administrated intra muscularly (i.m.) or intradermaly (i.d.). In paper II, a new peptide with ornithine modification, PF14, is shown to efficiently deliver splice-switching oligonucleotides (SSOs) in different cell models including mdx mouse myotubes; a cell culture model of Duchenne’s muscular dystrophy (DMD). Additionally, we describe a method for incorporating the PF14-SSO nanoparticles into a solid formulation that is active and stable even when stored at elevated temperatures for several weeks. In paper III, we demonstrate the involvement of class-A scavenger receptor subtypes (SCARA3 & SCARA5) in the uptake of PF14-SSO nanoparticles, which possess negative surface charge, and suggest for the first time that some CPP-based systems function through scavenger receptors. In paper IV, the ability of PF14 to deliver siRNA to different cell lines is shown and their stability in simulated gastric acidic conditions is highlighted. Taken together, these results demonstrate that certain chemical modifications can drastically enhance the activity and stability of CPPs for delivering nucleic acids after spontaneous nanoparticle formation upon non-covalent complexation. Moreover, we show that CPP-based nanoparticles can be formulated into convenient and stable solid formulations that can be suitable for several therapeutic applications. Importantly, the involvement of scavenger receptors in the uptake of such nanoparticles is presented, which could yield novel possibilities to understand and improve the transfection by CPPs and other gene therapy nanoparticles.
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| 10. |
- Ferreira Vasconcelos, Luis Daniel, 1979-
(författare)
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Complexes of cell-penetrating peptides with oligonucleotides : Structure, binding and translocation in lipid membranes
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The fundamental element of life known to man is the gene. The information contained in genes regulates all cellular functions, in health and disease. The ability to selectively alter genes or their transcript intermediates with designed molecular tools, as synthetic oligonucleotides, represents a paradigm shift in human medicine.The full potential of oligonucleotide therapeutics is however dependent on the development of efficient delivery vectors, due to their intrinsic characteristics, as size, charge and low bioavailability. Cell-penetrating peptides are short sequences of amino acids that are capable of mediating the transport of most types of oligonucleotide therapeutics to the cell interior. It is the interaction of cell-penetrating peptides with oligonucleotides and the transport of their non-covalently formed complexes across the cellular membrane, that constitutes the main subject of this thesis.In Paper I we studied the effects of different types of oligonucleotide cargo in the capacity of cationic and amphipathic peptides to interact with lipid membranes. We found that indeed the cargo sequesters some of the peptide’s capacity to interact with membranes. In Paper II we revealed the simultaneous interaction of different molecular and supramolecular peptide and peptide/oligonucleotide species in equilibrium, with the cellular membrane. In Paper III we developed a series of peptides with improved affinity for oligonucleotide cargo as well as enhanced endosomal release and consequently better delivery capacity. In Paper IV we investigated the effect of saturated fatty acid modifications to a cationic cell-penetrating peptide. The varying amphipathicity of the peptide correlated with the complex physicochemical properties and with its delivery efficiency.This thesis contributes to the field with a set of characterized mechanisms and physicochemical properties for the components of the ternary system – cell-penetrating peptide, oligonucleotide and cell membrane – that should be considered for the future development of gene therapy.
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