PEGylation can improve the pharmacokinetic properties of protein therapeutics via decreasing renal clearance and shielding the protein surface from proteases, antibody neutrailization, and aggregation. Conformational stability enhancement can provide criteria for the identification of optimal sites for PEGylation, but how PEG influence the noncovalent interactions from the surface of proteins has not been well illustrated. Macrocyclization can effectively enhance the conformational stability of small peptides and large proteins. Combination of PEG-based conformational stability enhancement and macrocyclization-based conformational constraint has not been explored. Macrocycliziation has been employed to stabilize protein tertiary structures, but there are no general guidelines for interhelical staple to stabilize coiled-coil motifs of proteins. Chapter 1 is an introduction to peptide stapling and macrocyclization of proteins. Chapter 2 describes our test of the hypothesis that PEG increases the conformational stability of proteins by desolvating nearby salt bridges. In chapter 3, we explore the combination of PEG-based conformational stability enhancement with macrocyclization on WW domain, and find that the most important criteria for PEG stapling is ensuring the side chains cross-linked by PEG are distant in primary sequence but close in tertiary structure. In chapter 4, we further apply this macrocyclization criteria to another -sheet-based protein, SH3 domain of the chicken Src protein, and to a disulfide-bonded parallel coiled-coil heterodimer derived from the yeast transcription factor GCN4. In chapter 5, we explore the determinants of PEG-staple-based stabilization by changing the distance of the staple to the terminal interhelical disulfide bond, varying the length of staple, exploring different solvent exposed positions for stapling and employing heterochiral residues for stapling. We further apply the interhelical PEG staple to a HER-2 affibody, and find that PEG-stapling increases the conformational stability and proteolytic resistance of the stapled affibody relative to its non-stapled counterpart and to the native unmodified affibody.

<p>PEGylation, referring to the covalent attachment of poly(ethylene glycol) or PEG to protein, has become the most established technology for improving pharmacokinetic behavior of native proteins, especially the prolongation of circulation half-life <em>in vivo</em>. This thesis focuses on the synthesis and purification of PEGylated proteins.</p> <p>The conventional way to synthesize PEGylated proteins is in liquid phase batch reaction, which usually causes the formation of significant amount and high diversity of by-products (i.e. di-, tri-, and/or higher-PEGylated forms of a protein). Many chemical and physical ways have been explored to increase the specificity of mono-PEGylated protein. Chemical ways involve manipulation of operating conditions towards site-specific PEGylation. Understanding reaction kinetics is helpful in optimizing conversion and specificity of mono-PEGylation. In this thesis, the PEGylation reaction kinetics between a model protein and PEG NHS ester under various operating conditions was investigated.</p> <p>In the physical perspective, the key point is to gain degree of control on reactant addition instead of one-time addition as in liquid phase batch reaction. Herein, two novel reactor systems were developed. One is solid phase PEGylation bioreactor, bringing free protein to react with immobilized PEG on a membrane surface; the other is Hollow-fiber Membrane Reactor (HMR), distributing PEG into the fiber lumen (where protein is flowing) through the pores on the fiber wall. Greatly improved conversion and specificity of mono-PEGylated protein were observed in both systems, compared to liquid phase batch reactor.</p> <p>An effective and efficient purification technique is very essential because purification step accounts for a significant portion of total cost. In this thesis, the use of hydrophobic interaction chromatography with environment-responsive microporous membranes was examined for the fractionation of different PEGylated proteins. The capability of this technique was demonstrated by obtaining mono-PEGylated protein in a pure form and observing well-resolved chromatographic peaks for different PEGylated proteins.</p> / Doctor of Philosophy (PhD)

Le développement de la thérapie génique dépend des systèmes utilisés pour le transport de gènes vers les cellules eucaryotes. Les systèmes à base de virus sont les plus efficaces. Cependant, il est urgent de trouver une alternative à de tels systèmes viraux pathogènes et oncogènes. Les polymères cationiques sont des vecteurs synthétiques prometteurs ; toutefois, une question cruciale reste en suspens : quelle structure de polymère cationique visée pour une efficacité de transfection élevée et une faible cytotoxicité ? Face à ce questionnement scientifique, de nouveaux polymères cationiques offrant une grande flexibilité en termes de structure et de fonctionnalité sont développés dans cette thèse. Les différents paramètres structuraux pertinents étudiés sont : (i) des entités amines primaire et tertiaire pH-sensibles pour la complexation de l'ADN et pour la libération des polyplexes ADN/polymère, (ii) un groupe alcyne destiné à l’ancragepar chimie click de ligands capables de viser des récepteurs spécifiques de membrane cellulaire pour une reconnaissance efficace des cellules, (iii) des entités polyacrylates à « charge modulable » pour libérer l'ADN et diminuer la cytotoxicité du polymère et (iv) un poly (oxyde d'éthylène) (PEGylation) pour une meilleure stabilité en milieu physiologique et une meilleure biocompatibilté. / The clinical success of gene therapy is really dependent on the development of new efficient gene transfer systems. Viral-based gene transfer systems are remarkably efficient in transfecting body cells. However, viral-based systems raised some concerns in terms of immunogenicity, pathogenicity, and oncogenicity. Cationic polymers are promising candidates as they show low host immunogenicity, are cheaper and easier to produce in a large scale than viral ones. However, a crucial question is still pending: which cationic polymer structures and functionalities give the highest transfection efficiency and the lowest cytotoxicity? In dealing with this scientific issue, new cationic polymers with key structural parameters and functionalities were developped during this PhD thesis. The key structural features studied are : (i) pH sensitive primary and tertiary amine entities for DNA complexation and to ensure the endosomal escape, (ii) an alkyne group to attach ligands capable to target specific cell membrane receptors for an efficient cell recognition and receptor-mediated cellularuptake, (iii) “charge-shifting” amino-based polyacrylates for DNA release and to decrease cytotoxicity and (iv) PEG chains (PEGylation) to achieve high stability, longer circulation in physiological conditions and a better biocompatibility. The synthesis of such multi-structural cationic polymers has been achieved through the combination of RAFT polymerization and thiol-yne click coupling reaction. The structure/complexation and the structure/cells viability relationships have been investigated during this work.

Traumatic spinal cord injury (SCI) is a devastating condition for which there is no effective clinical treatment. Neuroprotective molecules that minimize tissue loss have shown promising results; however systemic delivery may limit in vivo benefits due to short systemic half-life and minimal passage across the blood-spinal cord barrier. To overcome these limitations, an injectable intrathecal delivery vehicle comprised of hyaluronan and methylcellulose (HAMC) was developed, and previously demonstrated to be safe and biocompatible intrathecally. Here, HAMC was determined to persist in the intrathecal space for between 4-7 d in vivo, indicating it as an optimal delivery system for neuroprotective agents to reduce tissue degeneration after SCI. HAMC was then investigated as an in vivo delivery system for two neuroprotective proteins: erythropoietin (EPO) and fibroblast growth factor 2 (FGF2). Both proteins demonstrated a diffusive release profile in vitro and maintained significant bioactivity during release. When EPO was delivered intrathecally with HAMC to the injured spinal cord, reduced cavitation in the tissue and significantly improved neuron counts were observed relative to the conventional delivery strategies of intraperitoneal and intrathecal bolus. When FGF2 was delivered intrathecally from HAMC, therapeutic concentrations penetrated into the injured spinal cord tissue for up to 6 h. Poly(ethylene glycol) modification of FGF2 significantly increased the amount of protein that diffused into the tissue when delivered similarly. Because FGF2 is a known angiogenic agent, dynamic computed tomography was developed for small animal serial assessment of spinal cord hemodynamics. Following SCI and treatment with FGF2 from HAMC, moderate improvement of spinal cord blood flow and a reduction in permeability were observed up to 7 d post-injury, suggesting that early delivery of neuroprotective agents can have lasting effects on tissue recovery. Importantly, the entirety of this work demonstrates that HAMC is an effective short-term delivery system for neuroprotective agents by improving tissue outcomes following traumatic SCI.

Traumatic spinal cord injury (SCI) is a devastating condition for which there is no effective clinical treatment. Neuroprotective molecules that minimize tissue loss have shown promising results; however systemic delivery may limit in vivo benefits due to short systemic half-life and minimal passage across the blood-spinal cord barrier. To overcome these limitations, an injectable intrathecal delivery vehicle comprised of hyaluronan and methylcellulose (HAMC) was developed, and previously demonstrated to be safe and biocompatible intrathecally. Here, HAMC was determined to persist in the intrathecal space for between 4-7 d in vivo, indicating it as an optimal delivery system for neuroprotective agents to reduce tissue degeneration after SCI. HAMC was then investigated as an in vivo delivery system for two neuroprotective proteins: erythropoietin (EPO) and fibroblast growth factor 2 (FGF2). Both proteins demonstrated a diffusive release profile in vitro and maintained significant bioactivity during release. When EPO was delivered intrathecally with HAMC to the injured spinal cord, reduced cavitation in the tissue and significantly improved neuron counts were observed relative to the conventional delivery strategies of intraperitoneal and intrathecal bolus. When FGF2 was delivered intrathecally from HAMC, therapeutic concentrations penetrated into the injured spinal cord tissue for up to 6 h. Poly(ethylene glycol) modification of FGF2 significantly increased the amount of protein that diffused into the tissue when delivered similarly. Because FGF2 is a known angiogenic agent, dynamic computed tomography was developed for small animal serial assessment of spinal cord hemodynamics. Following SCI and treatment with FGF2 from HAMC, moderate improvement of spinal cord blood flow and a reduction in permeability were observed up to 7 d post-injury, suggesting that early delivery of neuroprotective agents can have lasting effects on tissue recovery. Importantly, the entirety of this work demonstrates that HAMC is an effective short-term delivery system for neuroprotective agents by improving tissue outcomes following traumatic SCI.

The success of regenerative cardiac therapy requires reestablishing a capable blood supply via vasculature. The objective of this study was to develop an optimal scaffold formulation for de novo collateral vessel growth of aortic grafts using modified fibrin clots. This ex vivo vascular outgrowth model can be used to interrogate the complex cell or tissue interactions on the angiogenic front as vessels are formed. Based on formulation constraints, the methods used here may provide a clinically applicable option for guided collateral formation. Once understood, the methods and procedures can be tested and modified as necessary for in vivo, in situ regenerative therapy. Aortic segments from wild-type (C57BL/6J) and apolipoprotein-E deficient (ApoE) atherosclerosis-prone mice were cultured in a 3D environment created by various formulations of PEGylated fibrin. Aortic outgrowth was assessed and the optimal formulation was chosen to test the formation of de novo vascular circuits -- the first step necessary for collateral artery formation. The cultures were examined by conventional and confocal microscopy as well as by optical coherence tomography. Experiments testing the relationship between fibrin PEGylation and aortic vascular outgrowth showed that PEGylating fibrinogen prior to clot formation increased outgrowth over non-PEG control (n=6, p<.05) at lower fibrin concentrations. Lowering fibrin concentration to 10, 5, or 2.5mg/ml resulted in significantly higher outgrowth that was 1.92, 2.04, or 2.20 times that of 20mg/ml PEGylated fibrin gels. When multiple aortic segments are cultured in proximity, microvascular outgrowths visually anastamose suggesting that aorta-aorta conduits can be formed in fibrin based hydrogels. Anastomosing circuits appeared between wild-type aortic segments as well as between wild-type and atherosclerotic prone ApoE knockout segments. Fibrin gels, with or without PEGylation, form scaffolds suitable for regenerative vascular outgrowth ex vivo in normal and atherogenic environments. PEGylating fibrin prior to thrombin-initiated polymerization will allow the incorporation of growth factors or other bioactive components, making this a customizable therapy for guided collateral formation. Additionally, the incorporation of PEG itself does not limit and may actually increase the outgrowth from aortic segments in lower density gels. Finally, PEGylated fibrin gels offer an environment that will promote vascular extensions that visually anastamose, making this a viable model for ex vivo collateral formation. / text

Adenovirus-mediated gene therapy is a potential complement to standard cancer treatments. Advantages are that vectors can be used to target tumors and that replicating viruses lead to increased therapeutic dosage. In this thesis, an oncolytic serotype 5 adenovirus (Ad5), Ad[i/PPT-E1A, E3], was developed where viral replication is controlled by the insulator-shielded (i) prostate-specific PPT promoter. The adenoviral E3 region was inserted for its immune regulatory and lysis functions. Ad[i/PPT-E1A, E3] had improved cytotoxic abilities both in vitro and in a prostate cancer xenograft mouse model compared to a virus lacking the E3 region. To further improve adenoviral vectors, the histone deacetylase inhibitor (HDACi) FK228 was studied. FK228 has been proposed to enhance the effect of adenoviral therapy by upregulation of CAR, the primary receptor for Ad5 infection. In the present study, we observed that FK228 promotes transgene expression even better when administered after viral transduction, indicating a post-transductional enhancement of transgene expression. Another interesting finding was that FK228 reduced transgene expression from the PPT promoter in the prostate cancer cell line LNCaP. This is explained by the fact that different HDACi have the ability to provoke a neuroendocrine phenotype of LNCaP. A potential drawback with adenoviral gene therapy is the rapid clearance of the virus from the circulation. Viral particles have been coated with polyethylene glycol (PEG) to evade immune recognition, a strategy that works well in mouse models. However, less is known about the effects of adenoviral PEGylation in human blood. We have studied cell interactions and immune responses to PEGylated and uncoated Ad5 vectors in human whole blood using a blood loop model with constant blood flow. Limited effects of PEGylation were observed in human blood, which were associated with the neutralizing ability of the donor blood. An important finding that donors with high neutralizing ability in whole blood do not necessarily have neutralizing antibodies against the virus strongly implies that neutralization should be measured in whole blood.

Les nanoparticules de Gemcitabine-Squalène (Gem-Sq), synthétisées suivant le concept de " squalénisation ", ont montré des activités anticancéreuses très supérieures à celles obtenues en présence de Gem libre. Néanmoins, leur PEGylation, c'est-à-dire leur décoration par du poly(éthylène glycol)-squalène (PEG-Sq) pour augmenter leur temps de demi-vie plasmatique, s'est avérée infructueuse du fait d'une déstructuration colloïdale. Par ailleurs, aucune stratégie de fonctionnalisation pour effectuer un ciblage actif de cellules cancéreuses, n'est à ce jour disponible. Au cours de cette thèse, nous avons donc cherché à résoudre ces problèmes. Après une étude bibliographique portant sur la conception de nanoparticules de prodrogues lipidiques, dans le but d'établir un constat récent de l'état de l'art dans ce domaine, nous avons proposé une voie de synthèse pour obtenir des nanoparticules multifonctionnelles (i.e., thérapeutique, fluorescentes et ciblées) à base de Gem-Sq, et ce par co-auto-assemblage des composés conjugués de Rhodamine-Sq, Gem-Sq et Biotin-Sq. Ces nanoparticules ont montré une internalisation plus importante dans les cellules cancéreuses et une meilleure efficacité thérapeutique que les nanoparticules de Gem-Sq non-fonctionnalisées. Dans un deuxième temps, nous avons apporté une solution au problème de la PEGylation des nanoparticules de Sq via la synthèse et l'utilisation de composés conjugués de type Gem-poly(méthacrylate de squalène). Ces prodrogues macromoléculaires ont été synthétisées par polymérisation radicalaire contrôlée et plus précisément par la technique RAFT. Les nanoparticules obtenues par auto-assemblage en solution aqueuse sont stables et présentent des activités anticancéreuses importantes sur différentes lignées cellulaires. Leur PEGylation par ajout de Sq-PEG durant la formulation s'est avérée possible et n'a pas conduit à une déstabilisation colloïdale. Enfin, j'ai participé à l'élaboration d'une nouvelle famille de nanoparticules de prodrogues macromoléculaires qui a consisté à faire croitre de courtes chaines de polyisoprène (PI) à partir de la Gem, donnant ainsi des conjugués de type Gem-PI, capables de s'auto-assembler sous la forme de nanoparticules avec une activité anticancéreuse in vitro et in vivo.

In dieser Arbeit wurde geprüft, ob eine sequenzspezifische Hybridisierung von zwei Peptid-PNA-Konjugaten an einem komplementären DNA-Templat die Bildung eines neuen Peptids auslösen kann, welches proapoptotische Eigenschaften besitzt. Dazu binden zwei kurze PNA-Oligomere an einem komplementären DNA-Templat und ermöglichen dadurch den Transfer einer Aminoacylgruppe. In den vorgestellten Untersuchungen trug ein Oligomer einen Alaninrest, welcher C-terminal als Thioester gebunden war. An das zweite PNA-Oligomer war ein Peptid mit N-terminalem Cysteinrest geknüpft. Mittels einer Cystein-vermittelten Transferreaktion wurde die Aminoacyleinheit auf das Akzeptor-Konjugat übertragen und es entstand das freie PNA-Oligomer sowie ein neues Peptid. Die so generierten Peptid-PNA-Konjugate waren so konstruiert, dass sie an BIR3 binden und damit dessen Interaktion mit Caspase-9, einem Schlüsselenzym der Apoptose, entgegenwirken konnten. Es wurde ein Assay entwickelt, bei dem die DNA-gesteuerte Transferreaktion mit der Aktivierung der Caspase-9 aus dem inhibitorischen Komplex mit BIR3 in HEK293-Zelllysat kombiniert wurde. Als Vorbereitung für eine intrazelluläre Anwendung der Nukleinsäuretemplat-katalysierten Peptidsynthese wurde zunächst die Stabilität der Konjugate in Zelllysat untersucht und weiterhin eine Synthesestrategie zur PEGylierung der verwendeten Peptid-PNA-Konjugate entwickelt. Zusammenfassend ist festzustellen, dass mit dem DNA-gesteuerten Aminoacyltransfer zum ersten Mal eine Methode aufgezeigt wurde, welche die in Nukleinsäuren kodierte Information für die Generierung eines Wirkstoffes nutzt, der die Aktivität eines Proteins kontrollieren kann. Die Synthese des aktiven Peptidwirkstoffes gelang in der komplexen Umgebung von Zelllysat, erfolgte sequenzspezifisch und in Gegenwart substöchiometrischer Konzentrationen des Templats. / In this thesis it was investigated, whether the sequence specific hybridisation of two peptide-PNA conjugates could trigger the formation of a new peptide with proapoptotic properties. The method draws upon a nucleic acid-templated reaction, in which two short PNA oligomers bind adjacently on a complementary DNA template enabling the transfer of an amino acyl group. In the presented study one oligomer carried an alanine residue that was C-terminally attached to the PNA sequence via a thioester linkage. The second PNA oligomer conferred a peptide with an N-terminal cysteine residue and served as acceptor. In a cysteine mediated transfer reaction an amino acyl moiety was transferred to the acceptor conjugate yielding a free PNA oligomer and a new peptide. The generated peptide-PNA conjugates were designed to bind BIR3 protein and therefore interrupt its interaction with caspase-9 a key enzyme of apoptosis. In a cell free functional assay, which included recombinant BIR3 protein and HEK293 cell lysate, the peptide-PNA conjugates formed upon the DNA-triggered peptide synthesis acted as BIR3 antagonists and allowed reactivation of inhibited initiator caspase-9 as well as of the executioner caspase-3. Preliminary studies for future intracellular applications of this method included the investigation of the stability of the peptide-PNA conjugates in cell lysate and the development of a synthetic strategy for the PEGylation of the conjugates. With the DNA-triggered peptide synthesis via aminoacyl transfer we introduced a method, which allows for the translation of nucleic acid information into the output of molecules that interfere with disease-related protein-protein interactions. The synthesis of the active peptide drug proceeds sequence specifically and shows turnover in template even in a complex biomolecular environment such as cell lysate.

In der vorliegenden Arbeit wurde gezeigt, dass enzymresponsive Peptid-Poly(ethylenglycol)-Konjugate (Peptid-PEG-Konjugate) effizient biotransformiert und proteinresistente Beschichtungen ausbilden können. Die oberflächenspezifische Haftung eines linearen Biokonjugates auf Basis einer literaturbekannten Adhäsionsdomäne für Titandioxid-Oberflächen wurde durch Verlängerung mit einer proteolytisch spaltbaren Erkennungssequenz und einer Suppressionsdomäne temporär unterbunden. Aus einer Serie unterschiedlich modifizierter Biokonjugate wurde eine anionische Suppressionsdomäne als besonders leistungsfähige haftungsunterdrückende Einheit identifiziert. Die Prozessierung des nicht-bindenden Vorläufers mit einer spezifischen Cysteinprotease hervorgehend aus dem Tabakätzvirus (TEV Protease) bewirkte die Abtrennung der eingeführten Modifikation. Durch die Biotransformation wurden die Haftungseigenschaften der polymergebundenen Adhäsionsdomäne zurückgebildet. Das aktivierte Biokonjugat ermöglichte die nicht-kovalente PEGylierung der Metalloxid-Oberfläche. Das Konzept wurde auf divalente Peptid-PEG-Konjugate unter Verwendung verzweigter Adhäsionsdomänen und verlängerter Suppressionsdomänen übertragen. Die proteolytisch aktivierte Dimer-Beschichtung zeigte eine erhöhte Stabilität im Vergleich zum linearen Biokonjugat und demonstrierte vielversprechende Antifouling-Eigenschaften gegenüber der unspezifischen Adsorption eines Modellproteins für Serumproteine des menschlichen Blutes auf Titandioxid-Oberflächen. / The present thesis has shown that enzyme-responsive peptide-poly(ethylene glycol) (peptide-PEG) conjugates can be efficiently biotransformed to create protein-resistant coatings. The surface-specific adsorption of a linear bioconjugate is temporarily suppressed by extending a titanium dioxide adhesion domain known from literature with a proteolytically cleavable recognition site and a suitable interfering domain. From a series of differently modified bioconjugates, an anionic interfering domain was identified as particularly effective to suppress adhesive functions. The enzymatic processing of the non-binding precursor with a specific cysteine protease derived from tobacco etch virus (TEV protease) resulted in the separation of the introduced modification. The adhesive properties of the polymer-bound binding sequence were reproduced by the biotransformation process. The activated bioconjugate allowed the non-covalent PEGylation of the metal oxide surface. The concept was applied to divalent peptide-PEG conjugates using branched adhesion domains and extended interfering domains. The proteolytically activated dimer coating showed increased stability against dilution compared to the linear bioconjugate and demonstrated promising antifouling properties against the non-specific adsorption of a model protein for human blood serum proteins to titanium dioxide surfaces.