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Integrins are major adhesion receptors for the extracellular matrix (ECM). This thesis focuses on the motifs and interactions within integrin cytoplasmic tails during integrin-mediated cell adhesion and spreading. The present study investigated the significance of the skelemin-αIIbβ3 interaction using Chinese Hamster Ovary (CHO) cells expressing wild-type or mutant αIIbβ3 receptors defective in skelemin binding. Most mutant cells displayed unimpaired adhesive capacity and spreading on immobilized fibrinogen at the early stages of cell spreading. In addition, they formed normal focal adhesions and stress fibers with no indication of impaired cell spreading. K716A and H722A mutant cells exhibited the greatest cell spreading, which was associated with enhanced p-Src activation. The K716 residue appeared to be the most important for skelemin binding in previous in vitro studies. Here, the protrusions of the leading edge of K716A cells showed strong colocalization of talin with αIIbβ3 which was associated with a loss in skelemin binding. These data suggest that the binding of skelemin to αIIbβ3 is not essential for normal cell spreading, but may act to exert contractile forces on cell spreading and coordinate the binding of talin to the membrane proximal region of integrin tails. The functional mode of peptides corresponding to the central motifs of the αIIb and αV tail, KRNRPPLEED (αIIb peptide) and KRVRPPQEEQ (αV peptide) was also investigated. Both peptides inhibited Mn2+-activated αIIbβ3 binding to soluble fibrinogen as well as the binding of αIIbβ3-expressing CHO cells to immobilized fibrinogen. Breast cancer progression has been linked to tumor cell interaction with ECM. Our αIIb and αV peptides also inhibited adhesion of two breast cancer cell lines (MDA-MB-435 and MCF7) to αV integrin ECM ligand vitronectin. Replacement of RPP with AAA significantly attenuated the inhibitory activity of the αIIb peptide. β-tubulin was identified as a potential αIIb peptide-binding partner, suggesting that microtubule cytoskeleton may participate in the regulation of integrin functions. These results provide insights into the mechanisms by which the central motifs of αIIb and αV tails regulate integrin activation and integrin-mediated cell adhesion

The incorporation of a propargyl group to a natural product target allows for a streamlined approach to the investigation of structure activity relationships (SARs) and target identification in forward chemical genetics programmes using a ‘click’-based approach. To this end, an efficient synthesis of O-propargylated tyrosine derivatives was designed, and these have been used in the construction of peptide motifs both (a) derived from phage display libraries and (b) found in natural products. The L-tyrosine derivative Y* (compound I, X=H, R=H) was incorporated into a peptide sequence, PTTIYY, which is known to prevent the inhibition of p53 by the AG-2 protein. Y* has been included as both the terminal and the internal tyrosine in the peptide sequence. ELISA assays were carried out to determine how the binding of PTTIYY* and PTTIY*Y to AG-2 compared to that of the un-marked PTTIYY sequence. The results of these assays allowed new conclusions to be drawn regarding the important binding features of the peptide and possible sites for further optimisation of the AG-2 binding properties of this peptide through ‘click’ functionalisation of the modified tyrosine. The binding of the peptides incorporating Y* was also assessed using MCF-7 breast cancer cell lysate, known to contain the AG-2 protein. These results confirmed those seen for the purified AG-2 ELISA. The related bromo-D-tyrosine derivative (compound I, X=Br, R=Me) has been prepared and employed towards the synthesis of a bisebromoamide derivative. Bisebromoamide is a newly discovered polypeptide, and a promising anti-cancer agent. The bisebromoamide derivative contains a thiazole unit (Tzl), two N-methylated amino acids, and an oxopropyl pyrrolidine (Opp) moiety, which is unique to bisebromoamide in natural products. The activity of this bisebromoamide derivative will be investigated via ‘click’-based affinity chromatography using a new supported linker recently developed within the Hulme group.

Ce travail concerne la synthèse de courts glycopeptides pouvant adopter une structuration secondaire définie. Les chaînes b-peptidiques peuvent se structurer sur de courtes séquences oligomèriques. C’est pourquoi les b-peptides ont été choisis pour réaliser ce travail, de plus ils sont résistants aux peptidases et aux protéases. Nous nous sommes intéressés à la préparation de ce type d’oligomères artificiels modifiés en les liants à des unités sucres. Nous souhaitons étudier l’influence de la glycosylation de chaînes b-peptidiques, et déterminer si la structuration est conservée lorsque la chaîne est « décorée » par des résidus sucres. Dans ce contexte, nous avons présentés l’homo-oligomérisation de glyco-amino acide artificiel formant une nouvelle classe de carbopeptoïdes. Une analyse conformationnelle par modélisation moléculaire et par des techniques spectroscopiques (RMN, DC, IR) a été menée sur cette première classe d’oligomères. Un second aspect de notre travail à consisté à synthétiser des C-glycosyl-b3-amino acides et des O-glycosyl-b3-amino acides. Ces monomères sont, en effet, des unités centrales dans la formation de glycosyl-b-peptides. Finalement ; nous nous sommes intéressés à la synthèse d’une nouvelle classe d’analogues de glyco-b-amino acide appelée les Na-(C-glycosyl)-hydrazino acides. / The objective of this work was the design and synthesis of short glycopeptides that can fold into well defined and typical secondary structures. b-Peptides frameworks are capable of forming structurally well-defined and predictable structures on short sequences and were therefore chosen for our purpose. In addition, b-peptide backbones are resistant to peptidases and proteases. We were interested in preparing such artificial oligomers modified, like a vaste majority of proteins, by linkage to carbohydrates. The study of carbohydrate-functionalized b-peptides is expected to bring important information concerning the structural stability of such glycoconjugates. In this context, we have presented the homo-oligomerisation of the unnatural glyco-amino acid into a new class of carbopeptoïds. The conformational preference of this first class of oligomers has been assessed by spectroscopic techniques (NMR, IR, CD) and calculations. Another part of this work concerned the synthesis of C-glycosyl-b3-amino acids and O-glycosyl-b3-amino acids as building blocks in the construction of glyco-b-peptides. Finally, we were interested in the synthesis of a new class of glyco-b-amino acids analogues, which are called Na-(C-glycosyl)-hydrazino acids.

Die Aktivität von Biooligomeren wird wesentlich beeinflusst von deren molekularer Struktur bzw. Konformation. Eine Einflussnahme auf die Struktur sollte deswegen auch mit einer Aktivitätsveränderung einhergehen, ein „Schalten“ von Struktur somit ein „Schalten“ von Aktivität nach sich ziehen. Alanyl-PNA ist ein Oligopeptid alternierender Konfiguration mit Nukleobasen in β-Position der Alanyl-Einheiten, das durch Wasserstoffbrückenbildung und π-Stacking mit einem komplementären Strang Paarungsduplexe mit β-faltblattartiger linearer Struktur eingeht. Der Einbau eines Alanyl-PNA-Stranges in ein Peptid oder Protein und Zugabe des korrespondierenden Gegenstranges sollte zu einer lokalen Induktion eines β-Faltblattes führen und strukturelle Veränderungen im Gesamtpeptid hervorrufen. Es kann dann von einem molekularen Schalter gesprochen werden. Im Rahmen dieser Arbeit wurde eine vom cyclischen Peptidantibiotikum Gramicidin S abgeleitete 18mer-Peptid-Alanyl-PNA-Chimäre 20 mit eingebautem Alanyl-PNA-Pentamer dargestellt. Es konnte mittels temperaturabhängiger UV-Spektroskopie gezeigt werden, dass sich bei Zugabe des komplementären Gegenstranges nichtkovalente Duplexe bilden. CD-spektroskopische Untersuchungen dieses Dimers lieferten keine eindeutigen Beweise für das vorliegen eines β-Faltblattes. Es konnte anhand des humanen Interleukins 8 gezeigt werden, dass der Einbau von Alanyl-PNA durch die Technik der native chemical ligation in größere Peptide möglich ist. Hierfür wurde der N-terminale Thioester 31 des humanen Interleukins hIL8(1-55) durch Expression des Fusionsproteines in E.coli und Expressed Protein Ligation dargestellt. Nach Umsetzung des Thioesters 31 mit einem Alanyl-PNA-Peptid-Hybrid 29, das N-terminal mit einem freien Cystein substituiert ist, wurde durch native chemical ligation ein von dem humanen Interleukin 8 abgeleitetes 77 Aminosäuren enthaltendes Peptid 30 mit eingebauter Alanyl-PNA erhalten. Darüber hinaus wurden mit keinem, einem oder zwei Lysinen substituierte Alanyl-PNA-Hexamere dargestellt und Strukturuntersuchungen unterworfen. Es konnte mittels temperaturabhängiger UV-Spektroskopie gezeigt werden, dass der Einbau zweier Lysine sowohl die Löslichkeit als auch die Bildungskinetik verändert, die Stabilität (Tm-Wert) der Duplexe jedoch unverändert lässt. Diese Hexamere wurden Kristallisationsversuchen unterworfen, bisher konnten noch keine Kristalle erhalten werden. Basierend auf den im Rahmen dieser Arbeit erhaltenen Ergebnissen sollte es in Zukunft darüber hinaus möglich sein, genaueren Aufschluss über die Struktur von Alanyl-PNA zu erhalten. Die Erhöhung der Löslichkeit von Alanyl-PNA durch Einbau zweier Lysine ermöglicht nicht nur weitere Kristallisationsversuche, sondern man gelangt auch in Konzentrationsbereiche, in denen NMR-Untersuchungen an Alanyl-PNA möglich werden, die bisher aufgrund zu schlechter Löslichkeit zu keinen zufrieden stellenden Ergebnissen geführt haben. Durch weitere Optimierung der native chemical ligation und Bereitstellung größerer Mengen von Interleukin 8 Derivaten mit eingebauter Alanyl-PNA sollte es in Zukunft möglich sein, den Einfluss des komplementären Alanyl-PNA-Stranges auf die Struktur des Gesamtsystems und dessen biologischer Aktivität zu untersuchen. Durch Variation und Optimierung der Sequenz und des örtlichen Einbaus der Alanyl-PNA kann so vielleicht das Fernziel eines molekularen strukturellen Schalters für Peptide bzw. Proteine erreicht werden. Ebenso ist es denkbar, dass durch den Einbau von Alanyl-PNA in zwei verschiedene Peptide bzw. Proteine nichtkovalente Protein-Protein-Komplexe erhalten werden können. / Activity and properties of biooligomers depend mainly on their molecular structure and conformation. Changing structure causes also a change of activity. Therefore, “switching” structure results in “switching” activity. Alanyl-PNA is an oligopeptide consisting of amino acids with alternating configuration with nucleobases attached to the β-position of an alanyl unit. Addition of a complementary peptide strand induces a β-sheet like conformation in the backbone of the duplex by hydrogen bonding and π-stacking . Incorporation of alanyl-PNA into a peptide or protein and addition of a complementary sequence should induce a β-sheet like structure and produce structural changes in the entire system. For this effect the term molecular switch can be used. In this work a peptide-alanyl-PNA chimera 20 consisting of a sequence of 18 amino acids, which was derived from the cyclic antibiotic Gramicidin S, has been synthesized. It contained a terminal alanyl-PNA pentamere. Using temperature dependent UV-spectroscopy it could be proven that addition of the complementary strand led to noncovalent duplexes. Investigations by CD-spectroscopy did not give clear evidence for the existence of a β-sheet. To accomplish the incorporation of alanyl-PNA into larger peptides the techique native chemical ligation has been applied. Alanyl-PNA has been incorporated into the 77 amino acids containing peptide human interleukine 8 (hIL8). The N-terminal thioester hIL8(1-55) 31 was expressed by a fusion-protein in E.coli and worked up by Expressed Protein Ligation. After reaction of the thioester 31 with an alanyl-PNA-peptide hybrid 29, N-terminally substituted with a free cysteine, a new analogue 30 of hIL-8 could be obtained by native chemical ligation. Furthermore, alanyl-PNA hexamers containing up to two lysines have been synthesized and subjected to structural examinations. Using temperature dependent UV-spectroscopy it could be shown that the incorporation of two lysines not only increased the solubility of the oligomers substantially but also had strong influence on the kinetics of the duplex formation, whereas the stability of the pairing complex (defined by the Tm value) did not change. Attempts to crystallize these hexamers have not been successful up to the present. On the basis of these results it should be possible to obtain in the future more detailed information about the structure of alanyl-PNA. Due to the poor solubility, previous NMR examinations did not give satisfying results. The increase in solubility by addition of a second lysine to alanyl-PNA will allow in future further crystallisation experiments and more promising NMR investigations. By optimization of the native chemical ligation and supply of larger amounts of interleukine 8 derivatives with incorporated alanyl-PNA it should be possible to examine the influence of a complementary alanyl-PNA strand on the structure of the entire system and its biological activity. By variation and optimization of the sequence and the local incorporation of alanyl-PNA moieties the objective of a molecular switch for peptides and proteins might be reached. The incorporation of alanyl-PNA into two different peptides or proteins might also result in the formation of noncovalent protein-protein-complexes mediated by hydrogen bonding.

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Science in Medicine ( Pharmacotherapy) / Species of the genus Plectranthus, a member of the mint family ( Lamiaceae ), have been used in alternative medicines in third world countries dating back to the early Chinese empire. Plectranthus species have been used in the past for coughs and colds (P. ambiguus) and as a mouth-wash for loose and bleeding teeth (P. laxiflorus). The crushed leaves of P. madagascariensis are used by Xhosa as an ointment for scabies P. hadiensis is used orally as a cough mixture. Eight species from the genus were chosen to study the essential oil composition and antimicrobial activity. / IT2018

Thesis advisor: Jianmin Gao / My graduate research has used engineered peptides to perturb the non-covalent interactions in protein folding, protein-protein association and protein-membrane association. We have focused on understanding the fundamental principles of molecular recognition behind protein-protein and protein-membrane interactions, and further using these principles in protein engineering. This thesis includes three projects. I) Towards Small Molecule Receptors for Membrane Lipids: A Case Study on Phosphatidylserine The lipid composition and distribution of cell membranes play important roles in regulating the physiology of the cell. The lipid composition of plasma membranes is one characteristic feature that can be used to identify cell types and functions. Molecules that specifically recognize a particular lipid are useful as imaging probes for targeting cells or tissues of interest. Protein based lipid binding probes have intrinsic limitations due to their large size and poor pharmacokinetic properties such as slow clearance rate and poor in vivo stability. A plausible strategy to achieve a probe with small size and high binding affinity and selectivity is to use a peptide to mimic the protein lipid-binding domains. As a case study, a cyclic peptide that specifically targets phosphatidylserine containing membranes has been developed. This cyclic peptide is potentially capable of imaging apoptosis in vivo, and the strategy of developing this cyclic peptide can be generalized to the design of peptide-based probes for other lipid species. My research has pointed out a challenging but feasible way to design a peptide that achieves specificity and affinity similar to lipid-binding proteins. (II) Study of Apoptotic Cell Membrane (ACM) Permeant Molecules Noninvasive imaging of apoptosis is highly desirable for the diagnosis of a variety of diseases, as well as for the early prognosis of anticancer treatments. One characteristic feature of apoptotic cells that has been targeted for developing specific biomarkers is enhanced membrane permeability compared to that of healthy cells. Several unrelated molecules that are capable of selectively penetrating the apoptotic cell membrane (ACM) have recently been reported. However, the origin of the altered ACM permeability is poorly understood, as is the scope of molecular structures that can permeate through the ACM. Herein, we report a systematic investigation on the altered ACM permeability. Our results show that simple modifications of commonly used dyes (e.g. fluorescein) afford specific entry into cells at the early stages of apoptosis. The ACM appears to be permeable to molecules of various functional groups and charge, but does discriminate against molecules of large size. The new findings reported here greatly expand the pool of small molecules for imaging cell death, thus facilitating the development of noninvasive imaging agents for apoptosis. (III) Study of Aromatic-Fluorinated Aromatic Interactions in Peptide Systems Therapeutic proteins have been through a remarkable expansion in the last two decades. A general problem that they are facing is poor stability. Protein engineering focuses on solving this problem by incorporating unnatural amino acids into protein sequences to purposefully modify protein structures. Fluorinated aliphatic amino acids have been demonstrated to be effective in stabilizing protein structures and functioning as recognition motifs. In contrast, fluorinated aromatic amino acids are less studied. We investigated the effect of perturbation of fluorination on aromatic residues on the stability of protein model systems, as well as the influence on protein-protein association behavior. The results of this study provided a fundamental understanding of aromatic interactions in protein systems, and guidelines for protein engineering with fluorinated aromatics for stabilizing protein structures or directing specific protein-protein interactions. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis advisor: Jianmin Gao / The development of proteins/peptides as therapeutic agents has emerged as a promising area for drug design. Due to increased antibiotic resistance, search for novel antibiotics has become a primary area of interest within the pharmaceutical industry. Antimicrobial peptides have been a significantly desirable model due to their innate cytolytic effects and favorable interaction with the membranes of bacterial cells within the host. Thioxylated analogues of biologically active peptides have shown increased enzymatic stability and increased selectivity and potency. Thioamide linkages have thus been installed in a variety of short peptides, replacing the backbone amide linkage, in order to study the effects on peptide conformation and stability. Several bioanalytical tools were used in the analysis including circular dichroism spectroscopy, NMR, size-exclusion high performance liquid chromatography, and fluorescence. The mutation was well-accommodated within several systems, including Trpzip 4 and gramicidin A, and proved to have comparable, and in several cases, enhanced stability in comparison to the wild-type peptides. / Thesis (MS) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.