The work embodied in this thesis pertains to an attempt to understand better, the molecular basis of protein-carbohydrate recognition. For this purpose a systematic study was undertaken, not only of the energetics of lectin-sugar interactions, which serve as molecular recognition prototype of protein-carbohydrate interactions, but also of the complex effects of solvent water molecules surrounding both the species in solution state. The systems chosen for investigation include the specific recognition of sugars by lectins from diverse families, leguminosae and moraceae. The following salient aspects of the molecular recognition process constitute the focus of this thesis: • Effect of site specifically modified, deoxy-, fluorodeoxy-, or methoxy- substituted D-galactopyranoside binding to lectins. Isothermal titration calorimetric (ITC) investigations of the binding of these sugars to a model lectin permitted the correct prediction of the architecture of the primary binding site in the absence of x-ray crystal or NMR structure of the combining site (Ref. 7). The study provided the only unambiguous means of a site specific mapping of the hydrogen-bond donor- acceptor relationship of the monosaccharide within the primary combining site of the lectin. • Novel features of lectin-sugar recognition. Molecular interactions and forces contributing to the stabilization of the saccharides in the primary combining site of lectins. Binding of site specifically modified fluoro- substituted D- galactopyranosides to WBA I led to the demonstration of the involvement of C- F««»H-0 hydrogen bonds in stabilizing the saccharide within the combining site of lectin (Ref. 7). Implication of the novel C-H«**O hydrogen bonds at the specificity determining C-4 position in enabling the methoxy- substituted D- galactopyranoside to be stabilized within the primary binding site of galactose specific lectins WBA I and jacalin. • Development of a novel coupled osmotic-thermodynamic approach for investigating the role of water molecules in determining the specificity of lectin- sugar interactions. The results obtained led to the first direct demonstration of a differential uptake of water molecules accompanying the specific process of recognition of sugars by lectins (Ref 2) • On the origin of enthalpy-entropy compensation, a ubiquitous phenomenon accompanying the thermodynamics of several ligand binding reactions in aqueous solutions in general and the molecular recognition involving all known lectin-sugar interactions, in particular. The results provide the first unequivocal solution state proof of water reorganization as the source of enthalpy-entropy compensation (Ref 3). A new diagnostic test of a true osmotic effect in molecular recognition phenomena was proposed (Ref. 2) and validated (Ref. 3). As an introduction, Chapter 1 is a comprehensive review of literature that touches upon the diverse properties of lectins and our present understanding of their multifarious roles and applications, which has led to their christening, perhaps appropriately, as molecules that mediate the 'social' functions of cells and tissues. Although a challenge it is still, to decipher the "glycocode", it is apparent that the fundamental basis of the recognition function of lectin-sugar interactions is the initial specific binding of the saccharide molecule by the globular proteinaceous lectin molecule. It is imperative, therefore, that an incisive investigation of the origin of specificity of the binding reaction as well as the solvent effects influencing both the interacting species be undertaken for a better understanding of the complete molecular recognition process. Towards this end is introduced in Chapter 1 our present understanding of the results on lectin-sugar interactions from two complementary approaches viz structural, including X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, as well as thermodvnamic ones, which have provided important information on the architecture of the combining sites, the dynamic modes of saccharide recognition and forces involved therein. Despite a detailed knowledge available from such methods, a structure-energetics correlation has persisted as a current challenge of the field. Towards achieving this goal, studies on the energetics of the recognition of sugars by lectins were undertaken, with an aim to better understand the origin of specificity of lectin-sugar interactions. This thesis attempts to provide new insights on some of the possible lacunae precluding structure-energetics correlation and suggests ways to overcome them. Chapter 2 deals with ITC investigation of the effect of deoxy-, fluorodeoxy-, and methoxy- substitutions on the binding of monosaccharides to the primary combining site of the lectin WBA I isolated from the mature seeds of the leguminosae family member Psophocarpus tetragonolobus as well as the moraceae lectin jacalin. These studies provide valuable information on the hydrogen-bond donor-acceptor relationships within the combining site of the lectins wherein the sugar molecule is liganded with the amino-acid residues of the lectin. This study is relevant for understanding the origin of specificity of monosaccharide binding within the primary combining site of the lectins. It has recently become apparent that there is a predisposition in three-dimensional space, of the donor-acceptor pairs within the sugar binding site of the lectins. Hence there appears to be a stereochemical basis of distinguishing the recognition of the donor group vis-a-vis that of the acceptor group and that their spatial disposition determines the specificity of the saccharide recognition. Unambiguous assignment of which of the groups within the hydrogen bonded pairs is a donor and which one is the acceptor assumes greater importance. The ITC measurements of the binding of deoxy-, flurodeoxy-and methoxy-derivatives of D-galactopyranoside (oc-D-Gal) to the basic lectin from winged bean Psophocarpus tetragonolobus, WBA I revealed that each of the ligands bind to WBA I with the same stoichiometry of one per subunit (29 kDa) of WBA I. The binding enthalpies for various derivatives were essentially independent of temperature and showed complementary changes with respect to binding entropies. Replacement of the hydroxyl group by fluorine or hydrogen on C3 and C4 of the galactopyranoside eliminated their binding to the lectin, consistent with C3-OH and C4-OH acting as hydrogen bond donors. The affinity for C2 derivatives of galactose decreased in the order: GalNAc>2MeOGal>2FGal=Gal>2HGal which suggests that both polar and non-polar residues surround the C2 locus of galactose, consistent with the observed high affinity of WBA I towards GalNAc, where the acetamido group at C2 position is probably stabilized by both non-polar interactions with the methyl-group and polar interactions with the carbonyl group. The binding of C6 derivatives followed the order: Gal>6FGal>D-Fuc»6MeOGal=L-Ara indicating the presence of favourable polar interactions with a hydrogen bond donor in the vicinity. Based on these results the hydrogen bond donor-acceptor relationship of the complexation of methyl-a-D-galactopyranoside with the primary combining site of WBA I was proposed (Ref. /), which was subsequently validated by the crystal structure of methyl-a-D-galactopyranoside complexed with WBA I. This chapter also describes the results from ITC studies on the binding of monosaccharides and disaccharides to the lectin jacalin isolated from the mature seeds of the moraceae family member Artocarpus integrifolia. The novel observation about the existence of C-F*«*H-0 and C-H**»O hydrogen bonds in lectin-sugar interactions is also discussed in this chapter. Chapter 3 is a description of the detailed investigation on the role of water molecules in influencing the energetics of lectin-sugar recognition. A novel coupled osmotic-thermodynamic approach was developed to dissect the role of water molecules in determining the recognition of the sugars by lectins. For this purpose, the model system of mannotriose-concanavalin A was used because atomic level structural information on these complexes were available. The work described in this chapter, is the first solution state evidence for the role of water molecules in the specific interaction of carbohydrates with a legume lectin, concanavalin A (Con A) (Ref. 2). Sugar binding to Con A was accompanied by linear changes in the logarithm of binding constants as a function of neutral osmolyte strength, and were described by well defined negative slopes characteristic for each sugar. As these changes were independent of the chemical nature of the osmolyte used, the results were rationalized in terms of a true osmotic effect. It was demonstrated that the specific recognition of the branched trimannoside (3,6-di-0-(a-D-mannopyranosyl)~a-D-mannopyranoside), the individual dimannosidic arms (3-<9-(a-D-mannopyranosyl)-a-D-mannopyranoside, and 6-0-(a-D-marmopyranosyl)-a-D-mannopyranoside) and the monomeric unit D-mannopyranoside by Con A was accompanied by differential uptake of water molecules; 1,3 and 5 respectively. We also observed a conservation of the compensatory behaviour of binding enthalpies and entropies in the presence as well as absence of osmolytes. This provided the first definitive evidence that water-reorganization plays a direct role in effecting the phenomenon of enthalpy-entropy compensation in protein-ligand interactions in general and lectin-sugar interactions in particular, and that the specificity of lectin-sugar recognition is characterized by a differential uptake of water molecules. Chapter 3 also describes the first experimental identification of the origin of enthalpy-entropy compensation (EEC), a ubiquitous phenomenon accompanying the thermodynamics of multifarious biomolecular recognition processes. By coupling direct microcalorimetry with osmotic stress technique, an experimental handle was devised to test the hypothesis that solvent reorganization could be the source of EEC. The results provided an unequivocal demonstration that an osmotic change in water activity alone, at the same temperature and pH, is sufficient to result in the conservation of EEC during the molecular recognition of specific ligands by macromolecules belonging to thermodynamically diverse and unrelated systems, a compelling evidence that the primary source of EEC in aqueous solutions is attributable to reorganization of solvent water molecules, thus validating the test for the role of water reorganization as a source of EEC (Ref. 3). This provides the first definitive evidence for the notion that there is a direct involvement of water molecules in originating the EEC effect. Despite the generality of the results it is urged that several systems be subjected to a vigorous application of the coupled osmotic-thermodynamic approach proposed herein before constituting it as a proof. Suffice to say, it is perhaps heartening that at last one has a handle to test the role of water molecules in effecting EEC in the solution state and appreciate the diverse roles played by water molecules in mediating molecular recognition reactions. The proposal presented in Ref 2, that the strong isoequilibrium relationship of enthalpy with entropy during the recognition of saccharides by Con A studied under osmotic stress, be considered as diagnostic of a true osmotic effect was subsequently validated in a thermodynamically diverse and unrelated system of peptide recognition by monoclonal antibody, the results from which are discussed in an Appendix (A) to this thesis (Ref 4). That the stabilities of these lectins are not hampered in the presence of osmolytes was demonstrated using differential scanning calorimetry (DSC) (Ref 2). During the course of these DSC studies, we discovered an unusual feature in an animal galectin. Despite possessing the legume lectin fold, the 14-kDa S- type lectin exhibits multiple oligomeric states that are influenced profoundly by complementary ligands and surprisingly do not dissociate at the denaturation temperature. These results are discussed in an Appendix (B) to this thesis (Ref. 5). The general discussion and conclusions drawn from this work are summarized in chapter 4. Briefly, the following salient conclusions can be drawn from the work presented in this thesis: 1. Unambiguous assignment of hydrogen-bond donor-acceptor relationship at each of the hydroxyl group of the monosaccharide bound to the lectin belonging to different families has been demonstrated (Refs. 1,6). 2. First report of novel hydrogen bonds in lectin-sugar interactions such as C- F«MH-0 (Ref 1) and C-H^*O hydrogen bonds (Ref 6). 3. Unusual structural stabilities in a galectin with a fold similar to that in legume lectins but with starkly different thermodynamic stabilities (Ref 5). 4. We have demonstrated for the first time in solution state, that water molecules are involved in the specific recognition of sugars by concanavalin A (Ref 2). It appears that lectin-sugar recognition reactions are, in general, mediated by a net uptake of water molecules during the binding process (Ref 7). 5. We have provided the first experimental demonstration that reorganization of water molecules is the source of enthalpy-entropy compensation in molecular recognition processes (Ref 3). 6. We provide evidence for another facet in the recognition of antigens by antibodies, viz water release accompanying the binding reaction (Ref 4). The studies reported in this thesis provide the foundation for embarking on a systematic study not only of the origin of specificity of lectin-sugar recognition but also of the complex roles that water molecules play in mediating these molecular recognition processes. These specific binding reactions wherein non-linear thermodynamics predominates and precludes a direct structure-energetics correlation emphasize the need to account for the effect of solvent water molecules in lectin-sugar interactions in particular and, without any overemphasis, in molecular recognition processes in general.

L’accumulation excessive de leucocytes conduisant à un dysfonctionnement de la réponse immunitaire est caractéristique de plusieurs maladies inflammatoires. La première étape du recrutement des leucocytes aux sites d’inflammation est tributaire de l’interaction entre le tétrasaccharide sialyl LewisX (sLeX) et les protéines d’adhésion sélectines P et E, qui sont exprimés sur les cellules endothéliales des parois vasculaires. Par conséquent, les sélectines sont des cibles thérapeutiques importantes. Ainsi, la conception d’antagonistes des sélectines est une stratégie prometteuse pour traiter l'inflammation aiguë. Par exemple, l’administration d’analogues du sLeX chez les patients hospitalisés souffrant de crises vaso-occlusives ou de syndrome de détresse respiratoire aiguë (SDRA) peut atténuer les enjeux d'accumulation de cellules immunitaires. Tout en se basant sur la première génération d'antagonistes des sélectines développées par notre laboratoire, l’objectif de ce travail était de synthétiser et d'évaluer l’activité biologique d’une nouvelle série d’analogues du sLeX ciblant l'inflammation aiguë. Ce travail établit deux nouvelles stratégies qui permettent d'accéder à des analogues du sLeX incorporant un motif galactopyranoside bicyclique avec une fonctionnalité carboxylate ayant une conformation restreinte. Dans la première approche, l’intermédiaire bicyclique clé est formé en 13 étapes à partir du D-galactose pentaacétate avec un rendement global de 19 %. Indépendamment de la stéréochimie des précurseurs, une réaction de cyclisation intramoléculaire a permis de générer l’intermédiaire clé avec le carboxylate en position axiale. Un contrôle cinétique Curtin-Hammett serait à l'origine de la stéréosélectivité, une hypothèse supportée par une étude expérimentale et par calculs théoriques DFT. La série des carboxylates équatoriales a également été préparée par une stratégie de désilylation basée sur la migration d'un ester β,γ-insaturé. La deuxième approche implique une stratégie de double glycosidation orthogonale qui est influencée par la conformation restreinte du bicycle. L'intermédiaire bicyclique, portant un groupement nitrile en C9 (alpha), a été préparé en 12 étapes avec un rendement global de 53 %. Cette approche a mené à une série d'antagonistes des sélectines incorporant des modifications d'amide, d'amine et de tétrazole, ainsi qu'un analogue incorporant un C6-benzamide. Cette approche modulaire peut être exploitée pour préparer d’autres isostères d'acide carboxylique. Un analogue hybride a été préparé en combinant le galactopyranoside bicyclique avec la fonctionnalisation de la chaîne latérale qui se retrouve sur l’espaceur à base de tartrate. Cette voie de synthèse a également été conçue afin d'accéder aux analogues du sLeX portant une sonde de photoaffinité. Cet analogue servira comme outil dans le marquage par photoaffinité des sélectines pour élucider les résidus clés du site actif. Les analogues de la deuxième génération ont été évalués pour leur capacité à se lier aux sélectines et d’empêcher les cellules immunitaires d’adhérer. Une méthode qualitative permettant de classer l’affinité de nos composés aux sélectines à l'aide de la spectroscopie SPR ainsi qu'une expérience préliminaire d'inhibition compétitive en solution ont été développées. Les principaux composés ont également été évalués à l'aide de tests in vitro d'adhésion de cellules HL-60 et de roulement par imagerie des cellules vivantes. Un essai de migration cellulaire par lavage péritonéal in vivo a été utilisé pour valider l’activité de nos composés principaux et leur capacité à inhiber le recrutement des neutrophiles dans un modèle d'inflammation aiguë. Nos résultats démontrent l’augmentation de la puissance et de l’activité de nos analogues de deuxième génération comparativement à la première. La série de galactopyranosides a démontré une spécificité pour l'inhibition de la P-sélectine, alors que la série des arabinopyranosides, incorporant un motif tétrazole, a démontré une activité remarquable vers la E-sélectine. La combinaison des deux modifications ont produit une activité pan-sélectines exceptionnelle qui justifie une enquête plus approfondie. / The first step for leukocyte adhesion and rolling along the vascular endothelium during the immune system inflammatory response involves the recognition of the tetrasaccharide sialyl LewisX (sLeX) by selectin glycoproteins. Dysfunction of the immune response, a consequence of several pathologies of inflammatory disease, leads to an excessive influx of leukocytes that necessitates therapeutic intervention. The development of glycomimetics, small molecule therapeutics that imitate complex glycans, is a promising strategy for treating inflammation. Specifically, a targeted approach amenable to severe acute inflammation, such as in hospitalized patients suffering from vaso-occlusive crises (VOC) or acute respiratory distress syndrome (ARDS). Building off the first generation of selectin antagonists developed by our laboratory, the aim of this work was to synthesize and evaluate the potency of a new class of sLeX glycomimetics for use as selectin antagonists targeting acute inflammation. This work describes the development of two novel strategies for sLeX glycomimetics incorporating a challenging trans-bicyclo[4.4.0] 3-O,4-C-fused galactopyranoside scaffold with a conformationally restricted carboxylate moiety. In the first approach, the key bicyclic galactopyranoside intermediate was accessed through a 13-step sequence with 19% overall yield from D-galactose pentaacetate. An unprecedented intramolecular cyclization reaction provided the desired axially configured bicyclic intermediate independent of the precursor stereochemistry. The origin of stereoselectivity was proposed to be under Curtin-Hammett kinetic control; a hypothesis supported by an experimental study and theoretical DFT calculations. The equatorial carboxylate series was also prepared using a desilylation strategy capitalizing on the migration of an β,γ-unsaturated ester. The second approach is highlighted by an orthogonal dual-glycosidation strategy that takes advantage of the conformationally restricted scaffold. The key bicyclic intermediate, bearing an α-configured C9 nitrile moiety, was prepared in 12 steps with a 53% overall yield. This approach led to a series of selectin antagonists incorporating axially-locked amide, amine, and tetrazole modifications at the C9 position, as well as an analogue incorporating a C6-benzamide. The modular galactopyranoside framework achieved using this approach can be exploited to prepare additional carboxylic acid bioisosteres for future SAR studies. A hybrid analogue was prepared, that combines the bicyclic galactopyranoside scaffold and a synthetic approach to selectin antagonists incorporating sidechain modifications to the first-generation tartrate diester. This synthetic route was also elaborated to access sLeX glycomimetics bearing a benzophenone-based photoaffinity probe. This analogue will serve as a valuable tool in the photoaffinity labeling of selectin proteins to elucidate key active site residues. The second-generation analogues were evaluated for their ability to inhibit selectin adhesion. A qualitative method to rank the binding strength towards recombinant P- and E-selectin proteins using SPR biosensor technology was developed, as well as a preliminary competitive inhibition in solution experiment with immobilized PSGL-1. Several compounds were also evaluated using an in vitro HL-60 cell adhesion assay, and a live-cell imaging experiment. An in vivo peritoneal lavage cellular migration assay was used to validate the potency of our lead compounds at inhibiting neutrophil recruitment in an acute inflammation model. Key results from the biological evaluations include an improvement in activity by restricting the conformation of the carboxylate moiety to the axial configuration, as well as an enhancement in potency over the lead compound from the first-generation series. Remarkably, specificity for P-selectin inhibition was observed with the galactopyranoside series, while the arabinopyranoside series, incorporating a tetrazole bioisostere, displayed significant activity towards E-selectin. The combination of the two modifications yielded remarkable pan-selectin activity that warrants further investigation.