FGF2 (Fibroblast Growth Factor 2), o fundador da família FGF, tem funções regulatórias na mitogênese, diferenciação, morfogênese e reparo tecidual. Diversas espécies moleculares de FGF2 compartilham uma seqüência C-terminal comum de 155 aminoácidos, pois se originam de diferentes sítios de iniciação de leitura de um único mRNA. O menor, o FGF2-18kDa, é liberado extracelularmente para se ligar a receptores específicos (FGFRs) para disparar as funções parácrinas e autócrinas pelas quais este fator é conhecido. Por outro lado, as espécies maiores (FGF2-21, 22, 22,5 e 34kDa) são intracelulares se ligam a parceiros moleculares desconhecidos para exercer funções intrácrinas ainda indefinidas. O objetivo desta tese foi produzir espécies recombinantes do FGF2-18 e FGF2-22,5, na forma de proteínas de fusão, para analisar funções biológicas e mecanismos de sinalização. Nas células malignas Y1 de camundongo, os recombinantes de FGF2-18kDa (FGF2-18, His-FGF2-18 e His-FGF2-18-ProA) dispararam uma resposta antagônica estimulando as vias de sinalização mitogênica, mas bloqueando o ciclo celular. Nos fibroblastos não tumorigênicos Balb3T3, estes mesmos recombinantes de FGF2-18kDa dispararam apenas a resposta mitogênica clássica. Todos os efeitos biológicos destes recombinantes de FGF2-18kDa foram bloqueados pelo inibidor específico da proteína quinase de tirosina dos FGFRs, PD173074, demonstrando que são respostas intermediadas pelos FGFRs. Portanto, os domínios estruturais adicionados aos recombinantes de FGF2-18kDa não impediram que estas proteínas se ligassem e ativassem os FGFRs. Por outro lado, o recombinante His-FGF2-22,5 dispara apenas as vias de sinalização mitogênica em ambas as células Y1 e 3T3, mas este efeito biológico não é inibido por PD173074. Estes resultados sugerem que a seqüência N-terminal de 55 resíduos, rica em aminoácidos básicos, impede que o FGF2-22,5kDa se ligue e/ou ative os FGFRs. Entretanto, o recombinante His-FGF2-22,5ProA dispara a resposta antagônica característica do FGF2-18kDa. As implicações destes últimos resultados é que o domínio de ProA adicionado ao C-terminal torna o FGF2-22,5kDa um bom ligante dos FGFRs. A interação física entre ligante e receptor das formas recombinantes His-FGF2-18kDa (ou His-FGF2-18ProA) e FGF2-22,5kDa com os putativos FGFRs foi analisada através da técnica de SPR e os resultados mostram KDs aproximados (Kd18=21, 488.10-9 e Kd22,5=20,70393.10-9), enquanto que o número de sítios ligantes em vesículas microssomais das células é significantemente inferior para o FGF2-22,5kDa. Estes resultados são compatíveis com a existência de receptores diferentes para FGF2-18kDa e FGF2-22,5kDa, uma hipótese ainda a ser definitivamente corroborada. Em conclusão, o FGF2-18kDa, mesmo em formas recombinantes como proteína de fusão, dispara todos os efeitos biológicos descritos para FGF2, através dos FGFRs. Diferentemente, o FGF2-22,5kDa, como fator parácrino, só desencadeou a resposta mitogênica clássica de FGF2, provavelmente através de receptores diferentes dos FGFRs. Os resultados e conclusões desta tese têm um potencial indiscutivelmente relevante para a biologia molecular do câncer, com implicações possíveis em terapia oncológica / FGF2 (Fibroblast Growth Factor 2), the founder of the FGF family, has regulatory functions in mitogenesis, differentiation, morphogenesis and tissue repair. Multiple FGF2 molecular species, sharing a C-terminal sequence of 155 amino acids, are translated from different iniciation sites of the same mRNA. The smaller, the FGF2-18kD, is extracellularly released to bind to specific membrane receptors (FGFRs), performing paracrine and autocrine functions. On the other hand, the larger FGF2s (21, 22, 22.5 and 34kDa) are intracellular species that bind to unknown partners to play still undefined intracrine roles. The aim of this thesis was to produce recombinant species of FGF2-18kDa and FGF2-22,5kDa, in the form of fusion proteins, to analyze functions and signaling mechanisms. In mouse Y1 malignant cells, FGF2-18kD recombinants (FGF2-18kDa and His-FGF2-18kDaProA) triggered an antagonistic response activating mitogenic signaling pathways, but blocking the cell cycle. However, in non tumorigenic Balb3T3 fibroblasts, these same FGF2-18kD recombinants only elicited the classical mitogenic response. All biological effects of these FGF2-18kD recombinants were blocked by the specific inhibitor of FGFR-protein-tyrosine-kinases, PD173074, demonstrating that these responses are mediated by FGFRs. Therefore, the new peptide domains added to FGF2-18kD did not prevent these recombinant fusion proteins to bind and activate FGFRs. Conversely, the recombinant His-FGF2-22,5kDa triggered only mitogenic signaling pathways in both Y1 and Balb3T3 cells, a biological effect not inhibited by PD173074. These results suggested that the additional basic-rich N-terminal sequence of 55 amino acid residues, found in FGF2-22,5kDa, prevents this FGF2 species from binding and / or activate FGFRs. However, surprisingly, the recombinant His-FGF2-22kDaProA triggered the antagonistic response characteristic of FGF2-18kDa. These results imply that the ProA-domain added to the C-terminal end rendered the FGF2-22,5kDaProA a good ligand of FGFRs. The physical interaction between recombinants of both His-FGF2-18kD and His-FGF2-22kDa with putative FGFRs, analyzed by SPR, yielded close KD values (KD18=21, 5.10-9 e K D22,5=20,7.10-9), while the number of binding sites in cell microsomal vesicles were significantly lower for the His-FGF2-22,5kDa. These results are consistent with the existence of different receptors for FGF2 and FGF2-18kD-22,5kDa, a hypothesis that has yet to be definitively confirmed. In conclusion, FGF2-18kD, even as recombinant fusion proteins, triggered all biological effects of FGF2, through FGFRs. Conversely, the FGF2-22, 5kDa only triggered the classical mitogenic response, probably via receptors other than FGFRs. The results and conclusions of this thesis are potentially of great interest in cancer molecular biology, with implications in oncologic therapy.

<p>In this study the formation of supported membranes onto planar solid supports has been investigated. The stability and activity of reconstituted membrane receptors has been studied. The potential use of such preparations in biosensor applications is discussed.</p><p>The lipid films were made by the Langmuir Blodgett and by the liposome fusion techniques. These supported films were characterised by ellipsometry, atomic force microscopy, surface plasmon resonance (SPR) and resonant mirror techniques. The thickness of the films was in agreement with that of a cell membrane. The kinetics of formation of the lipid films was studied and discussed.</p><p>The proteins, bacteriorhodopsin, cytochrome oxidase, acetylcholinesterase and the nicotinic acetylcholine receptor were reconstituted into the supported membrane. The subsequent analysis showed that the proteins were individually distributed and that the activity was retained, in some cases for several weeks after immobilisation.</p><p>The glycolipids, GM1, GM2, GD1b, asialo-GM1, globotriaosylceramide, lactosylceramide and galactosylceramide, were also reconstituted into the supported membranes. Their specific interaction with the toxin ricin or with its B-chain was examined using SPR. The affinity of intact toxin and of its B-chain differed markedly and was pH dependent. The carbohydrate chain length and charge density of the glycolipids also influenced the affinity.</p>

My doctoral research has focused on the development of surface plasmon resonance (SPR) reflectance imaging technique to detect near-field transport properties such as concentration, temperature, and salinity in micro/nano fluidic phenomena in label-free, real-time, and full-field manner. A label-free visualization technique based on surface plasmon resonance (SPR) reflectance sensing is presented for real-time and full-field mapping of microscale concentration and temperature fields. The key idea is that the SPR reflectance sensitivity varies with the refractive index of the near-wall region of the test mixture fluid. The Fresnel equation, based on Kretschmann’s theory, correlates the SPR reflectance with the refractive index of the test medium, and then, the refractive index correlates with the mixture concentration or temperature. The basic operation principle is summarized and the laboratory-developed SPR imaging/analyzing system is described with the measurement sensitivity, uncertainties and detection limitations of the implemented SPR reflectance imaging. Total five proposed uses of SPR reflectance imaging technique are presented: (1) micromixing concentration field development of ethanol penetrating into water contained in a micro-channel, (2) full-field detection of the near-wall salinity profiles for convective/diffusion of saline droplet into water, (3) full-field and real-time surface plasmon resonance imaging thermometry, (4) correlation of near-field refractive index of nanofluids with surface plasmon resonance reflectance, and (5) unveiling hidden complex cavities formed during nanocrystalline self-assembly.

In this study the formation of supported membranes onto planar solid supports has been investigated. The stability and activity of reconstituted membrane receptors has been studied. The potential use of such preparations in biosensor applications is discussed. The lipid films were made by the Langmuir Blodgett and by the liposome fusion techniques. These supported films were characterised by ellipsometry, atomic force microscopy, surface plasmon resonance (SPR) and resonant mirror techniques. The thickness of the films was in agreement with that of a cell membrane. The kinetics of formation of the lipid films was studied and discussed. The proteins, bacteriorhodopsin, cytochrome oxidase, acetylcholinesterase and the nicotinic acetylcholine receptor were reconstituted into the supported membrane. The subsequent analysis showed that the proteins were individually distributed and that the activity was retained, in some cases for several weeks after immobilisation. The glycolipids, GM1, GM2, GD1b, asialo-GM1, globotriaosylceramide, lactosylceramide and galactosylceramide, were also reconstituted into the supported membranes. Their specific interaction with the toxin ricin or with its B-chain was examined using SPR. The affinity of intact toxin and of its B-chain differed markedly and was pH dependent. The carbohydrate chain length and charge density of the glycolipids also influenced the affinity.

Dans un avenir proche, les dispositifs de détection médicaux miniaturisés en temps réels (lab-on-chip) seront au centre de la révolution des méthodes de diagnostics médicaux et d’identification des processus biologiques et cela, autant au niveau clinique qu’au niveau de la recherche. Pour y arriver, il est important de développer des chimies de surface stables et spécifiques, ce qui demande une compréhension des interactions intermoléculaires à l’interface liquide/solide. Pour bien comprendre ces interactions, il est important de développer des instruments adaptés à la mesure près de l’interface liquide/solide des différentes caractéristiques à identifier. Ce projet de recherche présente la conception, la fabrication et les expériences tests d’un capteur multimodal pour l’identification de processus biologiques à l’interface basés sur des technologies de résonance des plasmons de surface (SPR) et de microcalorimérie. Ces deux technologies mises ensemble vont permettre d’effectuer des mesures de la cinétique des interactions ainsi que des caractéristiques thermodynamiques. En premier lieu, les caractéristiques d’une interaction intermoléculaire à l’interface d’une réaction d’hybridation d’ADN furent définies afin d’en déduire un cahier des charges pour les transducteurs. Suite à cela, la conception des transducteurs microcalorimétrique et SPR furent réalisés en tenant compte des contraintes de chacun des transducteurs. Suite à la conception théorique des différentes parties du capteur, un procédé de fabrication compatible avec les méthodes de fabrication standard de la microélectronique fut défini et testé. Afin de s’assurer de la fonctionnalité des dispositifs ainsi fabriqués, des tests de fonctionnalisation de surface furent appliqués sur les échantillons afin de tester la compatibilité du procédé de fonctionnalisation avec les méthodes de fabrication et avec une chimie de surface type. Pour terminer, un système de mélange actif fut testé et caractérisé avec le dispositif de microcalorimétrie afin de s’assurer qu’il était possible de mélanger les fluides avec les produits biologiques pour s’assurer de la qualité de la réaction de surface. Le système développé pourra être utilisé pour effectuer la mesure d’hybridation d’ADN à l’interface. Le système intègre deux modalités permettant la caractérisation en temps réel des interactions intermoléculaires à l’interface liquide/solide. Ce type de système permet la mesure de la cinétique de différents modèles biologiques tels que les puces à sucre encore certains récepteurs cellulaires ou la mesure de conformation moléculaire à l’interface. Des mesures d’oxydation du glucose catalysée par la glucose oxydase sont montrées. / To begin with, the characteristics of a DNA hybridization intermolecular interaction at the interface were defined in order to deduce the specifications for our transducers. Following this, the SPR and microcalorimetric transducer will be design by taking into account the constraints of each one. Following the theoretical design of the sensor, a manufacturing process compatible with standard methods of microelectronics manufacturing was tested and identified. To ensure the functionality of the devices, a test of surface functionalization on the sensor was applied to test the compatibility of the manufacturing process with the surface functionalization methods. Finally, a system of active mixing was tested and characterized with a microcalorimetric device to ensure it was possible to mix fluids with organic products to be sure of the quality of the surface reaction. The system developed can be used to mesure DNA hybridization at the interface. This system incorporates two modalities for real-time characterization of intermolecular interactions near the solid/liquid interface. This type of system allows the kinetic measurement of different biological models such as cellular receptors or it is possible to have some molecular measure conformation near the interface. Oxidation of glucose with the enzyme glucose oxidase was shown to present the possibility to measure a biological interaction.

In der medizinischen Diagnostik, Bioverfahrenstechnik und Umwelttechnik besteht ein steigender Bedarf an kompakten Analysegeräten für die schnelle Vor-Ort-Detektion spezifischer biochemischer Substanzen. Im Rahmen der Arbeit wurde daher ein neuartiger faseroptischer Sensor entwickelt, der in der Lage ist kleinste Brechzahländerungen, z.B. durch molekulare Bindungsprozesse, zu detektieren. Die hohe Empfindlichkeit an der vergoldeten Spitze der Sensorfaser beruht auf der Oberflächenplasmonenresonanz (SPR) einer einzelnen Mantelmode, die durch ein langperiodisches Fasergitter (LPG) ermöglicht wird. Die Übertragungsfunktion des Sensors wurde unter Verwendung eines Schichtwellenleitermodells schnell und präzise modelliert. Es konnte gezeigt werden, dass in einem wässrigen Umgebungsmedium die höchste Empfindlichkeit im Spektralbereich um 660 nm unter Annahme einer rund 35~nm dicken und 2~mm langen Goldbeschichtung erreicht wird. Weiterhin wurde nachgewiesen, dass mit einer intermediale Schicht aus Cadmiumsulfid die SPR der Mantelmode in einen höheren Spektralbereich verschoben und damit die Empfindlichkeit deutlich verbessert werden kann. Um eine geringe Polarisationsabhängigkeit des Sensors sicherzustellen, wurde ein nasschemisches Abscheidungsverfahren für die allseitige Goldbeschichtung der Sensorfaser entwickelt. Die spezifischen optischen Eigenschaften dieser Abscheidungen wurden mit Hilfe von LPGs untersucht, die durch eine spezielle UV-Belichtung hergestellt wurden. Die Experimente ergaben, dass die komplexe Permittivität nasschemischer Abscheidungen mit Schichtdicken oberhalb von 50~nm mit aufgedampften Goldschichten vergleichbar ist. Die Verluste der adressierten Mantelmoden wurden mit einer äquivalenten Sensoranordnung aus zwei identischen LPG untersucht. Dabei konnte ein Skalierfaktor abgeleitet werden, der die effiziente Berechnung der Mantelmodendämpfung erlaubt. Es wurde nachgewiesen, dass die Brechzahlauflösung etablierter volumenoptischer SPR-Sensoren mit einer einfachen Transmissionsmessung an einer geeigneten Wellenlänge erreicht werden kann. Die äußerst kompakte Sensorfläche des faseroptischen Sensors ermöglicht darüber hinaus die Untersuchung deutlich kleinerer Probenvolumina ohne ein zusätzliches mikrofluidisches System zu benötigen. Es wurde gezeigt, dass sekundäre Brechzahländerungen aufgrund von Temperaturschwankungen oder unspezifische Ablagerungen durch eine differentielle Auswertung zweier identischer Sensoren kompensiert werden können. Die verbleibende Querempfindlichkeit wird durch die Polarisationsabhängigkeit der Sensoren bestimmt. Die geringste Querempfindlichkeit konnte daher mit einer homogenen nasschemischen abgeschiedenen Sensorfläche nachgewiesen werden. / Compact analysis devices which facilitate the rapid detection of specific biochemical substances are in increasing demand in the fields of point-of-care medical diagnostics, bioprocess engineering and environmental engineering. The aim of this work was therefore to design a novel fiber-optic sensor able to detect small refractive index changes such as those caused by molecular binding processes. The high level of sensitivity at the gold-plated tip of the sensor fiber stems from the surface plasmon resonance (SPR) of a single cladding mode, which is the result of a long-period fiber grating (LPG). The transfer function of the sensor was calculated quickly and accurately using a slab waveguide model. It was observed that the highest level of sensitivity in an aqueous ambient medium is achieved at a wavelength of 660 nm assuming a gold coating of 35 nm in thickness and 2 mm in length. Furthermore, it was demonstrated that an intermedial cadmium sulfide layer shifts the SPR of the cladding mode towards higher wavelengths, thus leading to significantly enhanced sensitivity. An electroless plating process for the omnidirectional deposition of gold on the sensor fiber was developed in order to minimize the sensor\'s dependency on polarization. The specific optical properties of the gold layer deposited were investigated with the aid of LPGs fabricated using a special UV exposure method. The experiments showed the complex permittivity of electroless platings with a thickness of over 50 nm to be comparable with that of evaporated gold layers. The losses of the addressed cladding modes were investigated using an equivalent sensor setup consisting of two identical LPGs. This facilitated the determination of a scaling factor enabling the effcient calculation of cladding mode attenuation. It was demonstrated that it is possible to obtain the refractive index resolution of established volume optical SPR sensors with the aid of simple transmission measurements at a specific wavelength. Moreover, the extremely compact sensing area of the fiber-optic sensor enables the investigation of smaller sample volumes without the need for an additional microfluidic system. Secondary refractive index changes caused by temperature fluctuations or unspecific binding events can be compensated for by means of the differential interrogation of two identical fiber-optic sensors. The residual cross sensitivity is determined by the polarisation dependency of the sensor. The lowest cross sensitivity was therefore demonstrated in combination with a homogeneous electroless plated sensor surface.

A mixed self assembling monolayer (mSAM) chip with attached heparin was developed to analyze heparin-protein interactions using a Reichert Inc, SR7000, surface plasmon resonance (SPR) instrument. The heparin was attached via streptavidin-biotin linkage where the streptavidin was covalently coupled to the mSAM and biotinylated heparin bound to it. These chips were then used to quantify the interactions of fibroblast growth factor-2 (FGF-2) with the surface bound heparin. Kinetic rate constants of association and disassociation were calculated. The association data of FGF-2 with heparin was fit to a single compartment, well-mixed model as the data did not exhibit mass transfer limitations. The results suggested that rebinding was prevalent and observed disassociation rates differed significantly in the presence of competing soluble heparin during disassociation. Our results indicate that the Reichert instrument and mSAM chips can be used to analyze heparin-protein interactions but that a careful protocol, outlined in this thesis, should be followed to obtain optimal data. / Master of Science

Tuberculosis affects millions of people worldwide every year. The current treatment for TB is divided into a regimen of both first- and second-line drugs, where first-line treatments are more tolerated and require shorter treatment lengths. With rising levels of resistance, alternative treatment regimes are urgently needed to fight this disease. Ethionamide, a second-line drug is administered as a prodrug which is activated in vivo by the enzyme EthA, which is in turn regulated by EthR. The disruption of the action of EthR could lead to novel therapeutics which could enhance the efficacy of ethionamide, and raise it to a first-line treatment. The work reported in this thesis examines the elaboration of three chemical scaffolds using fragment-based approaches to develop novel inhibitors capable of disrupting the EthR-DNA interaction. The first scaffold, 5-(furan-2-yl)isoxazole was investigated by fragment-merging approaches and produced compounds with the best of these having a KD of 7.4 uM. The second scaffold, an aryl sulfone was elaborated using fragment-merging strategies. This led to several modifications of the fragment, leading to several variants with KDs around 20 uM. With both of these series the affinity could not be improved below 10 uM and due to the synthetic complexity a further scaffold was prioritised. The third scaffold was explored was a 4-(4-(trifluoromethyl)phenyl)piperazine using fragmentgrowing from the NH of the piperazine to probe deeper into the EthR binding pocket. In addition to this, SAR around the 4-(trifluoromethyl)phenyl group was assessed to explore the interactions with EthR. These modifications led to compounds with nanomolar IC50s. A range of compounds were then screened by REMAssay to determine the boosting effect on ethionamide, and this identified compounds with up to 30 times boosting in the ethionamide MIC. The final chapter examines a concept where compounds were designed to exploit the dimeric nature of EthR by linking two chemical warheads with a flexible linker. These compounds are examined using mass spectrometry to investigate the stoichiometry of the interaction to provide insight into the binding of these extended compounds and exploring an alternative strategy to inhibit EthR. The work in this thesis demonstrated the successful use of fragment-based approaches for development of novel EthR inhibitors which showed significant ethionamide boosting effects.

Endotoxin or Lipopolysaccharide (LPS) is the invariant structural component of gram negative bacterial outer membranes and is the chief causative factor of Sepsis or endotoxic shock. Sepsis is a syndrome that has very high mortality rates even in this age of excellent therapeutics and critical patient care. The treatment for sepsis till date remains nonspecific and supportive due to lack of effective anti-endotoxic drugs. Sepsis is initiated when the circulating bacteria shed LPS from their cell envelopes. Shed LPS aggregates are recognized by LPS binding proteins and receptors, which activate the host's immune system. Uncontrolled and excessive stimulation of the host's immune system precipitates endotoxic shock which in advanced cases involving multiple system organ failure inevitably lead to patient's death. Many strategies have been tested out to combat this deadly affliction. One of the attractive clinical modalities in sepsis treatment is the use of peptides as LPS sequestering anti-endotoxic drugs. A classical peptide antibiotic of this class is Polymyxin B (PMB) a cyclic cationic acylated molecule, that recognizes LPS with a very high affinity. This thesis describes kinetics and thermodynamics of PMB-LPS interactions and applies these parameters over a framework of different models so as to gain insights into the structure-function relationships that govern the interactions of this peptide with endotoxin(s). Classical biophysical techniques like fluorescence, circular dichroism spectroscopy, stopped flow kinetics, titration calorirnetry (ITC) and the relatively new technique of Surface Plasmon Resonance (SPR) have been employed to dissect out the mechanism of the range of non-covalent forces that are involved in peptide-endotoxin recognition. Certain proteins that exhibit LPS binding activity have also been studied to gains insight about their mode of action. Implications of these studies for designing peptides that have better anti-endotoxic properties are also highlighted. The first chapter introduces and highlights the clinical features of sepsis. It also attempts to shed light on the LPS mediated signal transduction pathway that leads to endotoxic shock. This chapter also briefly explains the roles of many LPS receptors that are present in the human system and their specific roles in the signal transduction pathways. The second part of this chapter deals with the role of cationic peptides as anti-endotoxic drugs. Certain key functional aspects of these peptides, which impart in them, the desirable property of LPS recognition have also been discussed The second chapter describes the kinetic studies undertaken to unravel the exact mechanism of LPS-PMB interaction. The studies reveal that PMB recognizes LPS in a biphasic manner, with the second, unimolecular isomerization step of the reaction being the rate-limiting step. The initial reaction is shown to be influenced by the presence of salt in the reaction medium. The dissociation phase of this interaction also shows a biphasic pattern. These data allow us to speculate upon the exact mechanism by which PMB is able to recognize LPS. The studies also shed light on some structural aspects that govern and confer such high LPS binding activity to PMB. Based on these a model has been proposed to explain this recognition (C.J. Thomas et al, 1998). The second chapter discuses the mode of action of various PMB analogs. These analogs have been chosen in terms of their mode of action as well as their structural similarly to PMB. The affinities of these analogs to LPS and lipid A were quantified using the Surface plasmon resonance (SPR) method. SPR, a technique that relies on the quantification of change in mass during a binary binding process occurring between an immobilized entity and a flowing ligand, is a rapid and sensitive method to measure biologically relevant interactions. SPR studies provide us with the binding constants and thermodynamic parameters that allow evaluation of the affinities of these peptides towards LPS (C.J.Thomas and A.Surolia, 1999). The third chapter discusses a hitherto unknown mode by which PMB acts on a LPS lamellae. The results of this study wherein the binding affinities of PMB and its analogs were performed on monolayers and tethered liposomes, show that PMB is able to remove specifically LPS or lipid A from monolayers or bilayer assemblies such as tethered liposomes. The exact mode of action of PMB is deciphered in the light of these new studies, which allow us to posit on the observed efficacy of PMB in neutralizing the endotoxin as compared to peptides with nearly similar affinities for LPS (C.J Thomas et al 1999). In the fourth chapter a series of 23 residue peptides, based on the sequence corresponding to the anti-sense strand of magainin gene have been synthesized. Magainin an amphiphilic helical peptide obtained from frog skins plays a vital role in the innate immune defense mechanisms of these organisms. It also exhibits LPS binding activity that makes it an attractive target as an anti-endotoxic drug. Biochemical and biophysical characterization of these peptides reveal that they have the tendency to perturb both the inner and the outer membranes of E.coli. The peptides are amphiphilic and have helical structure in a membrane bound environment. Three of the peptides tested have high affinities for lipid A that approach the values shown by PMB. The kinetic parameters obtained by stopped flow and SPR studies in conjunction with the therrnodynamic parameters obtained using ITC studies allow us to highlight the key structural features that need to be exhibited by peptides that are designed to be LPS recognizers. The studies also project the fact that ionic forces play an important role in the initial recognition of LPS by these peptides. Fortification of the might of these ionic charges increases affinity for LPS where as the hydrophobic residues that interact at the next phase of binding are more amenable to disruptions in contiguity. These factors are discussed using the helical wheel diagram that shows the clear amphiphilicity displayed by these peptides. (C.J Thomas et al Manuscript under preparation, 2000) Chapter six discusses the mode of action of certain LPS binding proteins. Limulus anti endotoxic factor (LALF) plays a vital role in the innate immune based defense systems of the horseshoe crab. Galectin-3 is a metal ion independent, galactosc binding Icctin of human origin with unknown functions. Both these phylogcntically-unrclatcd proteins exhibit LPS/lipid A recognizing properties. ITC and SPR studies have been used to determine the binding constants displayed by these proteins for lipid A. LALF bind to lipid A with very high affinity than compared to Galectin-3 and is also able to take away selectively lipid A from both monolayers and tethered liposomes. Galectin-3 does not show this property of LALF, which might account for its lowered affinities. Also structurally LALF has amphiphilic nature that confers high lipid A binding activity, which is clearly lacking in Galectin-3. These studies in conjunction with the knowledge gained from the study of LPS-PMB interaction stress on the importance of amphiphilicity in LPS recognition. (C.J Thomas et al Manuscript under preparation, 2000). The final chapter is a general discussion that attempts to collate all these kinetic and thermodynamic observations in the pursuit of designing small easily manipulatable peptides that exhibit high LPS binding activity. These studies are aimed to act as rough guidelines to the design of LPS sequestering peptides that might have better therapeutic and pharmacokinetic properties. The appendix to the main body of work presented in thesis are two pieces of work pertaining to the elucidation the kinetics and mechanism of sugar lectin interactions, when sugars are presented as glycolipids in monolayers or bilaycrs liposomes. Mode of the presentation of sugars at cell-surfaces in the form of glycolipids as ligands influence their recognition by macromolecular receptors like lectins. Appendix 1 is a study of the mode of action of Ulex europeus I lectin binding to H-fucolipid containing tethered liposomes, by SPR. Fucosylated sugars are often used as key markers in histochemical analysis of malignant cancerous tissues. Ulex lectin plays a vital role as a marker for identification of these tissues. The kinetics and thermodynamic parameters that are obtained in this study throw some light on the mode of recognition of glycolipid receptor by Ulex europeus I lectin (C.J Thomas and A. Surolia 2000). Appendix 2 is a study, that attempts to quantify the initial kinetic parameters that correlate the recognition of glycolipid receptors with their inclination at the membrane surface and the influence of charge on them by soyabean agglutinin (SBA), Abrus agglutinin I and II. Studies on the soyabean agglutinin-globoside interaction highlights the divalent cation mediated reorientation of these receptors on their accessibility and recognition to the agglutinin. The divalent cations are speculated to orient the oligosaccharide head groups in a spatial geometry that allows a heightened kinetics of their interaction by SBA. These studies reveal that the reorganization of the binding pocket of a lectin can also have a profound influence on ihc rates of recognition of a glycospingolipid ligand by a lectin as exemplified by Abrus agglutinin II- GM1 interactions (C.J Thomas ct al, Manuscript under preparation).

It is widely known that early estimates about the binding properties of drug candidates are important in the drug discovery process. Surface plasmon resonance (SPR) biosensors have become a standard tool for characterizing interactions between a great variety of biomolecules and it offers a unique opportunity to study binding activity. The aim of this project was to develop a SPR based assay for pre-screening of low molecular weight (LMW) drug compounds, to enable filtering away disturbing compounds when interacting with drugs. The interaction between 47 LMW compounds and biological ligands were investigated using the instrument BiacoreTM, which is based on SPR-technology.