In the 1980's, Nicholas Farrell developed a range of structurally distinct multinuclear Pt complexes that form long-range interstrand crosslinks (IXLs) in DNA. The dinuclear complex [{trans-PtCl2(NH3)}2-µ-(H2N(CH2)6NH2)]2+ (1,1/t,t) was the first of this series to show promising results, however, it was the trinuclear complex [{trans-PtCl2(NH3)}2-µ-trans-Pt(NH3)2(H2N(CH2)6NH2)2]4+ (1,0,1/t,t,t or BBR3464) that was chosen for clinical trials based on significantly increased cytotoxicity compared to 1,1/t,t and cisplatin. Molecular biology experiments have shown that 1,1/t,t exclusively forms IXLs in DNA in the 5'¿ 5' direction, whilst 1,0,1/t,t,t can form IXLs in both the 5'¿5' and 3'¿3' directions. Previously, 2D [1H,15N] HSQC NMR has been used to study the formation of 5'–5' 1,4–GG IXLs. The formation of 3'–3' 1,4–GG IXLs have been studied as part of this thesis. More recently, Pt complexes such as [{trans–PtCl2(NH3)}2{H2N(CH2)6(NH2(CH2)2NH2)(CH2)6NH2}]4+ (1,1/t,t–6,2,6) and [{trans–PtCl2(NH3)}2{H2N(CH2)6(NH2)(CH2)6NH2}]3+ (1,1/t,t–6,6), where the charged central Pt moiety of 1,0,1/t,t,t is replaced by a polyamine linker, have been developed in the Farrell group and show increased potency compared to 1,0,1/t,t,t. The complex 1,1/t,t 6,2,6 is a lead candidate currently undergoing Phase I clinical trials. Prior to the work presented in this thesis, little was known about the aquation chemistry or kinetics of DNA binding of these novel complexes. Reported in Chapter 3 is the study of the formation of 3'–3' 1,4–GG IXLs by both 1,0,1/t,t,t and 1,1/t,t in the duplex 5' {d(TATACATGTATA)2} (33–14XL) (pH 5.4, 298K). A combination of 1D 1H and 2D [1H, 15N] HSQC NMR experiments was used to directly compare the results with the stepwise formation of the 5'–5' 1,4–GG IXL with the previously studied duplex, 5' {d(ATATGTACATAT)2} (55–14XL), under the same conditions. Preassociation as well as aquation were similar, however, differences were observed at the monofunctional binding step with evidence for numerous monofunctional adducts. Both reactions did not yield a single 3'–3' 1,4–GG IXL, rather several adducts that could not be characterised. Molecular dynamics simulations of the 3'–3' 1,4–GG IXLs showed highly distorted lesions that may have implication in cellular repair processes.

Les biosenseurs sont des dispositifs analytiques utilisés pour la détection de reconnaissance moléculaire. Ils consistent en un élément biologique immobilisé en contact intime avec un transducteur approprié qui convertit un signal biochimique en un signal électrique quantifiable. Leur principe est basé sur la reconnaissance d'une ou plusieurs molécules d'intérêt en solution (le ligand), par un composant biologique (le récepteur) étroitement lié au substrat transducteur. Le senseur réagit aux interactions récepteur-ligand et produit un signal mesurable, généralement proportionnel à la concentration du ligand fixé. Les biosenseurs sont déjà utilisés dans beaucoup de domaines différents, notamment dans le domaine médical (diagnostique et thérapeutique), le contrôle de l’environnement, et l’analyse et le monitoring de processus biotechnologiques. <p><p>La recherche concerne la mise au point d’un nouveau type de biosenseurs polyvalents à haute performance. Ces senseurs utilisent un élément de transduction optique dont la surface a été fonctionnalisée en vue de permettre la détection sélective d'interactions récepteur-ligand ainsi que le dosage des molécules fixées aux récepteurs. La technique utilisée pour la détection et le dosage est celle de la Spectroscopie ATR-FTIR (Spectroscopie Infra Rouge à Transformée de Fourrier en Réflexion Total Atténuée). Le système permet la détection directe, en temps réel, et sans marquage des molécules ciblées. La spectroscopie ATR-FTIR fournit une analyse des molécules sur base de leur empreinte spectrale infra rouge (IR) caractéristique, ce qui offre une mine d'informations pour identifier les ligands. Ce nouveau système de biosenseur, appelé BIA-ATR (Biospecific Interaction Analysis – Attenuated Total Reflection) est original et offre des avantages majeurs par rapport à la plus part des biosenseurs commercialement disponibles. Il fournit à l’utilisateur le spectre IR entier du ligand étudié, permettant non seulement le dosage quantitatif de ce dernier, mais aussi d’identifier sa nature intrinsèque. Un autre avantage est sa grande sensibilité ;le senseur BIA-ATR peut détecter la fixation de petites molécules et dans certains cas, aussi les réactions chimiques associées. <p><p>Le potentiel de cette nouvelle technologie de senseur est évalué dans ce travail par son application à plusieurs systèmes d’intérêt biologique et médical :la détection de protéines en milieux complexes, appliquée à la détection du Facteur VIII de coagulation du sang impliqué dans l’hémophilie de type A ;la fixation d’une petite molécule, le phosphate (phosphorylation), sur l’ATPase gastrique, un récepteur protéique de grande taille responsable de la sécrétion d’acide dans l’estomac et la détection et dosage d’un antibiotique, la vancomycine, utilisé en soins intensifs hospitaliers dans les cas d’infections bactériennes sévères à Staphylocoques dorés.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Cancer is a leading cause of death worldwide. Development of new cancer drugs is increasingly costly and time-consuming. By exploiting massive amounts of biological data, computational repositioning proposes new uses for old drugs to reduce these development hurdles. A promising approach is the systematic analysis of structural data for identification of shared binding pockets and modes of action. In this thesis, I developed the Protein-Ligand Interaction Profiler (PLIP), which characterizes and indexes protein-ligand interactions to enable comparative analyses and searching in all available structures. Following, I applied PLIP to identify new treatment options in cancer: the heat shock protein Hsp27 confers resistance to drugs in cancer cells and is therefore an attractive target with a postulated drug binding site. Starting from Hsp27, I used PLIP to define an interaction profile to screen all structures from the Protein Data Bank (PDB). The top prediction was experimentally validated in vitro. It inhibits Hsp27 and significantly reduces resistance of multiple myeloma cells against the chemotherapeutic agent bortezomib. Besides computational repositioning, PLIP is used in docking, binding mode analysis, quantification of interactions and many other applications as evidenced by over 12,000 users so far. PLIP is provided to the community online and as open source.

Orientador: Ljubica Tasic / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-20T16:55:17Z (GMT). No. of bitstreams: 1 Prando_Alessandra_D.pdf: 9977861 bytes, checksum: 15d25bce7d95433f95b938e68fdeaac8 (MD5) Previous issue date: 2012 / Resumo: Até o momento, pouco se sabe sobre os mecanismos de virulência da bactéria Xanthomonas axonopodis pv. citri (XAC), agente causador do cancro cítrico. Acredita-se que chaperonas de secreção (CS) estão envolvidas no processo de patogenicidade de XAC primeiramente formando complexos com fatores de virulência e auxiliando no encaminhamento desses para os sistemas de secreção utilizando o ATP como fonte de energia. Neste trabalho foram adquiridos dados de fluorescência de emissão, dicroísmo circular, desenovelamento térmico e de ressonância magnética nuclear de H NMR e de 2D {N,H} HSQC de duas proteínas da XAC, a XAC1990 (FlgN) e XACb0033. Para ambas proteínas foram propostas estruturas 3D usando a análise de footprinting com restrições SASA e rmsd. Para as estruturas propostas foi verificado que os dados de fluorescência corroboram com a estrutura 3D não ocorrendo o mesmo para os dados de CD e NMR que revelaram baixo conteúdo helicoidal além de ausência de estrutura 3 D. A interação da proteína FlgN com a sua proteína parceira FlgK também foi sugerida através das análises de CD e fluorescência. Na segunda parte do trabalho foram estudadas as interações entre a proteína Hsp90 da laranja com diferentes ligantes aplicando a técnica de Saturation Transfer Difference (STD-NMR) e espectroscopia de fluorescência. Estas análises revelaram dados que corroboraram com o modelo proposto e, além disso, indicaram que os hidrogênios H-8 e H-2 da adenina e H-1'da ribose estão localizados no sítio ligante da proteína com os fosfatos orientados para fora. Através da fluorescência foram calculados os valores de Kd e foi verificado que a geldanamicina é um potente inibidor de Hsp90 da laranja / Abstract: So far, the Xanthomonas axonopodis pv. citri (XAC) mechanisms of bacterial virulence is unknown. It is believed that secretion chaperones (CS) are involved in the XAC's virulence process by first forming complexes with virulence factors, and assisting in their presentation to corresponding secretion systems using ATP as a source of energy. Fluorescence emission, circular dichroism, thermal unfolding and nuclear magnetic resonance NMR H and 2D {N,H} HSQC data from two proteins of XAC, XAC1990 (FlgN) and XACb0033 were collected. For both proteins, 3D structures were proposed using the footprinting analysis with RMSD and SASA restrictions. For the proposed structures were verified which the fluorescence data were consistent with the 3D structure. The CD and NMR data revealed low-helical content and absence of 3D structure. The interaction of the protein FlgN with its partner, FlgK, was suggested by CD and fluorescence analysis. In the second part, the interactions between the orange's Hsp90 protein with different ligants using Saturation Transfer Difference (STD-NMR) and fluorescence spectroscopy techniques were studied. These analyzes revealed which the data were consistent with the proposed model and moreover showed that the adenine's hydrogens H-8 and H-2 and ribose's hydrogen H-1'are located in the protein binding site with the phosphate driven out. By fluorescence values were calculed Kd and it was verified that geldanamycin is a potent inhibitor of orange's Hsp90 / Doutorado / Quimica Organica / Doutor em Ciências

No description available.

Allostery is a regulatory process whereby a perturbation by an effector at one discrete locus creates a conformational change that stimulates a functional change at another. The two sites communicate through networks of interacting residues that respond in a concerted manner to the allosteric perturbation. These allosteric networks are traditionally mapped with high resolution structure determination techniques to understand the conformational changes that regulate protein function as well as its modulation by allosteric ligands and its dysfunction caused by disease-related mutations (DRMs). However, high resolution structural determination techniques, such as X-ray crystallography, cryo-electron microscopy and nuclear Overhauser effect NMR spectroscopy are not always amenable for systems plagued by poor solubility and line broadening caused by μs-ms dynamics or systems where allostery relies primarily on dynamical rather than structural changes. This dissertation discusses methodologies to map the allosteric sites and pathways for such challenging systems. The foundation of this approach is to model allosteric pathways in the context of their respective thermodynamic cycles. In chapter 2, the thermodynamic cycle of a DRM in the hyperpolarization-activated cyclic nucleotide-gated ion channel 4 (HCN4) is analyzed with respect to structure, dynamics and kinetics, revealing how the DRM remodels the free energy landscape of HCN4 and results in a loss-of-function disease phenotype. In chapter 3, the mechanism of action of an uncompetitive inhibitor for the exchange protein activated by cAMP is elucidated by characterizing its selectivity for distinct conformations within the thermodynamic cycle that are trapped using a combination of mutations and ligand analogs. In chapter 4, we discuss two new protocols for the chemical shift covariance analysis (CHESCA). The CHESCA is an approach that identifies allosteric signaling pathways by measuring concerted residue responses to a library of chemical perturbations that stabilize conformational equilibria at different positions. Overall, the approaches discussed in this dissertation are widely applicable for mapping the mechanisms of allosteric perturbations that arise from ligand binding, post-translational modifications and mutations, even in systems where traditional structure determination techniques remain challenging to implement. / Thesis / Doctor of Philosophy (PhD) / Allostery is a regulatory mechanism for proteins, which controls functional properties of one distinct site through the perturbation of another distinct, and often distant, site. The two sites are connected via a series of residues that undergo conformational changes once perturbed by the allosteric effector. Mapping these communication pathways reveals mechanisms of protein regulation, which are invaluable for developing pharmacological modulators to target these pathways or for understanding the mechanisms of disease mutations that disrupt these pathways. Allosteric pathways have been traditionally determined using structure determination approaches that provide a static snapshot of the protein’s structure. However, these approaches are typically not effective when allostery relies extensive changes in dynamics. The goal of this thesis was to develop methods to characterize systems that are dynamic or otherwise unsuitable for traditional structure determination. Herein, we utilize NMR spectroscopy to analyze the allosteric mechanisms of three cAMP-binding proteins involved in cardiovascular health.

ABCG2 est un transporteur de la famille ABC impliqué dans le phénotype de résistance aux drogues développé par certaines cellules, par exemple les cellules cancéreuses. Ce transporteur a aussi un rôle physiologique de détoxication de composés endogènes, notamment les porphyrines, molécules indispensables mais qui présentent une toxicité potentielle. Cette toxicité nécessite une prise en charge particulière, évitant à ces composés d’être libres en solution. Dans ce contexte, nous avons fait l’hypothèse qu’ABCG2 pourrait participer à cette détoxication en limitant l’accumulation des porphyrines dans les cellules en les présentant à un partenaire extracellulaire. Nous montrons qu’ABCG2 transporte de l’hème ainsi que certains de ses dérivés et précurseurs et que ces porphyrines, contrairement aux autres substrats d’ABCG2, se fixent sur un domaine extracellulaire spécifique d’ABCG2, ECL3, composé d’environ 70 acides aminés. L’affinité d’ECL3 pour les porphyrines est de 0,5 à 3,5 μM, suffisamment affine pour permettre leur fixation après transport.Nous montrons aussi que l’albumine sérique humaine, impliquée dans la détoxication de l’hème, récupère les porphyrines fixées sur ECL3 par une interaction directe avec ABCG2. L’ensemble de ce travail a donc permis d’une part de mieux comprendre le rôle d’ABCG2 dans la régulation de l’homéostasie des porphyrines, notamment l’hème, et d’autre part, de façon originale, d’identifier le mécanisme moléculaire par lequel cette détoxication s’effectue. / ABCG2 belongs to the ABC-transporter family, involved in drug resistance developed by cells, notably cancer cells. This transporter has also a physiological role of endobiotic detoxification, in particular porphyrins that are essential but potentially toxic molecules. This toxicity implies a specific handle, to avoid them to remain free in solution. In that context, we hypothesized that ABCG2 participate to this detoxification, limiting the intracellular porphyrin accumulation by presenting them to an extracellular partner. We show that ABCG2 transports heme and some of its derivatives and precursors. Interestingly, these porphyrins, unlike other ABCG2 (non-porphyric) substrates, can bind to an extracellular domain, specific of ABCG2, ECL3, 70 residues-long. ECL3 displays affinities for porphyrins in the range of 0.5 to 3.5 μM, high enough to allow their binding after transport. We also show that human serum albumin, implicated in heme detoxification, releases porphyrins bound to ECL3 by a direct interaction with ABCG2. This work established a better comprehension of ABCG2 role in porphyrin and in particular heme homeostasis regulation. In addition, our results contribute to elucidate part of the molecular mechanism by which such regulation is carried out.

Les enzymes et leur diversité d’actions sont appréciées dans des domaines d’applications variés allant del’agroalimentaire à la thérapeutique. Ainsi, une attention toute particulière est portée à leur étude afin d’améliorer uneaction (contre le vieillissement de la peau, antivirale, anticancéreuse…) ou un procédé de synthèse. Ce projet derecherche s’inscrit dans une démarche de développement d’outils analytiques basés sur la spectrométrie de masse,permettant le suivi rapide et sensible d’interactions enzyme-ligand.Dans une première étude, l’approche TLC couplée à une détection par UV a été évaluée pour la déterminationde constantes enzymatiques de l’enzyme invertase. Cette approche couplée à un MALDI/TOF MS a permis d’identifierdes substrats spécifiques de l’invertase au sein d’extraits de plantes. Pour preuve de concept, l’interactioncellobiohydrolase II–ligand est présentée dans le cadre de l’identification d’inhibiteur par TLC-MALDI/TOF et TLCENALDIMS.En seconde étude, nos travaux ont porté sur la caractérisation directe de différentes enzymes kinases, puis auxsuivis des réactions de phosphorylation de nucléosides /tides endogènes. Ces études, basées sur des approches « offline» (Flow Injection Analysis, FIA) et « on-line » (Frontal Affinity Chromatography, FAC) couplées à unspectromètre de masse haute résolution, ont été réalisées au moyen de ces kinases libres et immobilisées. Dans le cadrede la recherche de nouveaux candidats médicamenteux antiviraux, le suivi d’une phosphorylation spécifique desmolécules de synthèse, au regard de souches humaine ou virale de kinase, a également été évalué par ces deuxméthodologies. / Enzymes are very appreciated and useful in various application fields from agri-business to therapeutic due to theirdiversity of actions. Therefore, their action mechanisms are widely studied in order to enhance an action (anti-aging ofskin, antiviral, antitumorous) or a synthesis process. This research project is part of the approach to propose analyticaltools based on mass spectrometry, allowing rapid and sensitive follow-up of enzyme-ligand interactions.In a first study, the Thin-Layer Chromatography (TLC) approach coupled with UV detection was evaluated forthe determination of invertase kinetic constants. This approach coupled with a MALDI / TOF-MS led to theidentification of invertase substrates in plant extracts. As a proof of concept, the cellobiohydrolase II - ligand interactionwas presented in the framework of the identification of inhibitor by TLC-MALDI / TOF and TLC-ENALDI MS.In the second study, our work aimed at developing a direct method for the determination of kinetic parametersof kinases and following-up the phosphorylation reactions of endogenous nucleosides / tides. These studies, based on“off-line” (Flow Injection Analysis, FIA) and “on-line” (Frontal Affinity Chromatography, FAC) approaches coupledwith a high-resolution mass spectrometer, were carried out using free and immobilized kinases. In the context of thesearch for new antiviral drug candidates, a specific phosphorylation of synthetic molecules regards to human or viralkinase was also evaluated by these both approaches.

Ce projet de recherche se focalise sur les infections par mycobacterium ulcerans (maladie de l’ulcère de Buruli), une maladie de la peau dévastatrice caractérisée par la formation de lésions nécrotiques progressives et l’absence d’une réponse inflammatoire. Bien que négligée, cette infection est la troisième maladie mycobactérienne la plus répandue après la tuberculose et la lèpre et des cas sont rapportés dans plus de 30 pays à travers le monde. Mycobacterium ulcerans sécrète une toxine polycétidique complexe, appelée mycolactone A/B, qui est directement responsable des effets pathogènes de la maladie. Depuis sa découverte, les propriétés biologiques inhabituelles de la mycolactone A/B ont suscité de nombreux efforts de recherche dans différents domaines. Dans ce contexte, ce projet s’intéresse à l’élucidation du mécanisme d’action des mycolactones en utilisant la synthèse totale comme outil principal. Dans cette optique, notre équipe a mis en place une voie de synthèse permettant un accès facile et robuste à différents mimes de mycolactone. L’utilisation de cette méthode a conduit à la préparation de 13 mimes de la toxine au cours de cette thèse. D’autre part notre équipe s’intéresse également à la préparation de mimes possédant un ou plusieurs atomes de fluor. Ces derniers présentent un intérêt particulier pour améliorer la compréhension des interactions ayant lieu entre la toxine et sa cible cellulaire. Les travaux réalisés autours de la synthèse de mycolactones fluorés ont conduit à la mise au point d’une méthode générale et simple pour introduire un groupe trifluorométhyle sur un alcyne terminal, permettant ainsi des modulations inédites de la structure de la toxine. / This research project focuses on mycobacterium ulcerans infection (Buruli ulcer disease), a severe skin disease characterized by the formation of progressive necrotic lesions and the lack of an acute inflammatory response. Although neglected, this infection is the third most common mycobacteriosis after Mycobacterium tuberculosis and Mycobacterium leprae, and cases are reported in more than 30 countries worldwide. Mycobacterium ulcerans secretes a complex polyketidic macrolide, called mycolactone A/B, which is directly involved in the biological effects of the disease. Since its discovery, the unusual biology triggered by this toxin has spurred research efforts. In this context, this research project aims at a better understanding of mycolactone A/B molecular interactions by using total synthesis as main tool. To this end, our research team has developed an efficient synthetic pathway allowing the preparation of different mimetics of the toxin. This synthesis has been used to prepare thirteen new mycolactone mimetics during this thesis. Moreover our team has also been interested in the synthesis of fluorinated mycolactone analogs. Such fluorinated mycolactones are of great interest to improve the interactions that occur between the toxin and its biological binding site. Work in this field led to the development of a simple and general method to introduce a trifluoromethyl group onto a terminal alkyne, allowing novel modulation of the structure of the toxin.

BIOLOGICAL processes are governed through specific interactions of macromolecules. The three-dimensional structural information of the macromolecules is necessary to understand the basis of molecular recognition. A large number of protein structures have been determined at a high resolution using various experimental techniques such as X-ray crystallography, NMR, electron microscopy and made publicly available through the Protein Data Bank. In the recent years, comprehending function by studying a large number of related proteins is proving to be very fruitful for understanding their biological role and gaining mechanistic insights into molecular recognition. Availability of large-scale structural data has indeed made this task of predicting the protein function from three-dimensional structure, feasible. Structural bioinformatics, a branch of bioinformatics, has evolved into a separate discipline to rationalize and classify the information present in three-dimensional structures and derive meaningful biological insights. This has provided a better understanding of biological processes at a higher resolution in several cases. Most of the structural bioinformatics approaches so far, have focused on fold-level analysis of proteins and their relationship to sequences. It has long been recognized that sequence-fold or fold-function relationships are highly complex. Information on one aspect cannot be readily extrapolated to the other. To a significant extent, this can be overcome by understanding similarities in proteins by comparing their binding site structures. In this thesis, the primary focus is on analyzing the small-molecule ligand binding sites in protein structures, as most of the biological processes ranging from enzyme catalysis to complex signaling cascades are mediated through protein-ligand interactions. Moreover, given that the precise geometry and the chemical properties of the residues at the ligand binding sites dictate the molecular recognition capabilities, focusing on these sites at the structural level, is likely to yield more direct insights on protein function. The study of binding sites at the structural level poses several problems mainly because the residues at the site may be sequentially discontinuous but spatially proximal. Further, the order of the binding site residues in primary sequence, in most of cases has no significance for ligand binding. Compounding these difficulties are additional factors such as, non-uniform contribution to binding from different residues, and size-variations in binding sites even across closely related proteins. As a result, methods available to study ligand-binding sites in proteins, especially on a large-scale are limited, warranting exploration of new approaches. In the present work, new methods and tools have been developed to address some of these challenges in binding site analysis. First, a novel tool for site-based function annotation of protein structures, called PocketAnnotate was developed ( http://proline.biochem.iisc.ernet. in/pocketannotate/). PocketAnnotate, detects the putative binding sites from a given protein structure and compares them to known binding sites in PDB to derive functional annotation in terms of ligand association. Since the tool derives functional annotation at the level of binding sites, it has an advantage over other methods that solely utilize fold or sequence information. This becomes even more important for cases where there is no detectable homology with entries in existing databases, as Pocket Annotate does not depend on evolutionary based information for annotation. Second, a web-accessible tool for in silico almandine scanning mutations of binding site residues called ABS-Scan has been developed ( http://proline.biochem.iisc.ernet.in/abscan/). This tool helps in assessing the contribution of the individual residues of binding sites in the protein towards ligand recognition. All residues, one at a time, in a binding site are mutated systematically to an alanine and the ability of the corresponding mutant to bind a given ligand is analyzed. The contribution of each residue towards ligand binding is calculated through a G value derived by comparing the binding affinity to the wild-type protein-ligand complex. Third, a database called Protein-Ligand Interaction Clusters (PLIC) has been developed to identify and analyze the information of similarity across binding sites in PDB, which has been provided in the form of a web-accessible database ( http://proline.biochem.iisc.ernet/ PLIC). Protein-ligand interactions are primarily explored using three different computational approaches - (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of chemical probes, (ii) atomic contacts between protein and ligands (iii) binding energetics involved in interactions derived from scoring functions developed for docking. The information on variations in these features derived from different computational tools is also included in the database for enabling the characterization of the binding sites. As a case study to demonstrate the usefulness of these tools, they have been applied to decipher the complexity of S-adenosyl methionine interactions with the protein. Around 1,213 binding sites of SAM or SAM-like compounds could be extracted from the PLIC database. The SAM or SAM-like compounds were observed to interact with ∼18 different protein-fold types. The variations in different protein-ligand contacts across fold types were analyzed. The fold-specific interaction properties and contribution of individual residues towards SAM binding are identified. The tools developed and example analyses using them are described in Chapter 2. Chapter 3 describes a large-scale pocketome analysis from structural complexes in PDB, in an effort to characterize the known pocket space of protein-ligand interactions. Tools devel-opted as described in Chapter 2 are used for this. A set of 84,846 binding sites compiled from PDB, have been comprehensively analyzed with an objective of obtaining (a) classification of binding sites, (b) sequence-fold-site relationships among proteins, (c) a minimal set of physicochemical attributes sufficient to explain ligand recognition specificity and (d) site-type specific signatures in terms of physicochemical features. A new method to describe binding sites was developed in the form of BScIds such that the structural fold information is well captured. Binding sites and similarities among them were abstracted in the form of networks where each node represents a binding site and an edge between two nodes represents significant similarity between the sites at the structural level. Pocketome networks were constructed from the large-scale information on protein-ligand interactions in the PLIC database. The large pocketome network was then studied to derive relationships between protein folds and chemical entities they interact with. A classification of the binding pockets was achieved by analyzing the pocketome network using graph theoretical approaches combined with clustering methods. 10,858 clusters were identified from the network, each indicating a site-type. Thus, it can be said that there are about 10,858 site-types. Classification of ligand associations into specific site-types helps greatly in resolving the complex relationships by yielding specific site-type ligand associations. The observed classification was further probed to understand the basis of ligand recognition by representing the pockets through feature vectors. These features capture a wide range of physicochemical properties that can be used to derive site-type specific signatures and explore the pocket-space of protein-ligand interactions. A principal component analysis of these features reveals that binding site feature space is continuous in the entire PDB and minor changes in specific features can give rise to significant differences in ligand specificity, consequently defining their distinct functional roles. The weights were also derived for these features through the use of different information theoretic approaches to explain the multiple-specificity of protein-ligand interactions. Analysis of binding sites arising from contribution of residues from different protein fold-types revealed increasing diversity of physicochemical properties at the site, supporting the hypothesis that combination of folds could give rise to new binding sites. Given that a finer appreciation of the molecular mechanisms within the cell is possible only with the structural information, the next objective was to explore if a structural view of an entire proteome can be obtained and if a pocketome could be constructed and analyzed. With this in mind, the causative agent of tuberculosis - Mycobacterium tuberculosis (Mtb) was chosen. Mtb is also being studied in the laboratory from a systems biology perspective, which enabled exploration of how systems and the structural perspectives could be combined and applied for drug discovery. Chapters 4 to 6 describe this effort. The genome sequence of Mycobacterium tuberculosis (Mtb) H37Rv, indicates the presence of ∼4,000 protein coding genes, of which experimentally determined structures are available for ∼300 proteins. Further, advances in homology modeling methods have made it feasible to obtain structural models for many more proteins in the proteome. Chapter 4 describes the efforts for obtaining the Mtb structural proteome, through which the three-dimensional struc-tures were derived for ∼70% of the proteins in the genome. Functional annotation of each protein was derived based on fold-based functional assignments, binding-site comparisons and consequent ligand associations. PocketAnnotate, a site-based function annotation pipeline was utilized for this purpose and is described in Chapter 2. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides a unique opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 unique folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1,728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses, yielding a list of ligands that can participate in various biochemical events in the mycobacterial cell. A web-accessible database MtbStructuralproteome has been developed to make the data and the analyses available to the community, ( http://proline.physics.iisc.ernet.in/Tbstructuralannotation). The resource, being one of the first to be based on structure-based functional annotations at a genome scale, is expected to be useful for better understanding of tuberculosis and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well. Chapter 5 describes the characterization of the Mtb pocketome. For the structural models of the Mtb proteome described in chapter 4, a genome-scale binding site prediction exercise was carried out using three different computational methods and subsequently obtaining consensus predictions. The three methods were independent and were based on considering geometry, inter-molecular energies with probes and sequence conservations in evolutionarily related proteins respectively. In all, 13,858 consensus binding pockets were predicted in 2,877 proteins. The pocket space within Mtb was then explored through systematic all-pair comparisons of binding sites. The number of site-types within Mtb was found to be 6,584, as compared to the ∼400 structural folds and 1,831 unique sequence families. This reveals that the pocket space is larger than the sequence or fold-space, suggesting that variations at the site-level contribute significantly to functional repertoire of the organism. By comparing the pockets with the PDB sites enclosing known ligands, around 6906 binding sites were observed to exhibit significant similarity in the entire pockets to some or the other known binding site in PDB. 1,213 metabolites could be mapped onto 665 enzymes covering most of the metabolic pathways. The identified ligands serve as a predicted metabolome for unit abundances of the proteins. A list of proteins containing unique pockets is also identified. The binding pockets, similarities they share within Mtb and the ligands mapped onto them are all made available in a web-accessible database at http://proline.biochem.iisc.ernet.in/mtbpocketome/. The availability of structural information of the pocketome at a genome-scale opens up several opportunities in drug discovery. They can be directly applied for understanding mechanism of drug action, predicting adverse effects and pharmacodynamics of a drug. Moreover, it enables exploration of new ideas in drug discovery. Polypharmacology is a new concept that aims at modulating multiple drug targets through a single chemical entity. Currently, there are no established approaches to either select appropriate target sets or design polypharmacological drugs. In this study, a structural-proteomics approach is explored to first characterize the pocketome and then utilize it to identify similar binding sites. The knowledge of similarity relationships between the binding sites within the genome can be used in identifying possible polypharmacological drug targets. A pocket similarity based clustering of binding site residues resulted in identification of binding site sets, each having a theoretical potential to interact with a common ligand. A polypharmacological index was formulated to rank targets by incorporating a measure of drug ability and similarity to other pockets within the proteome. By comparing with known drug binding sites from databases such as the Drug Bank, the study has yielded a ready shortlist that includes sets of promising drug targets with polypharmacological possibilities and at the same time has identified possible drug candidates either directly for repurposing or at the least as significant lead clues that can be used to design new drug molecules against the entire group of proteins in each set. This analysis presents a rational approach to identify targets with polypharmacological potential, clues about lead compounds and a list of candidates for drug repurposing. This thesis demonstrates the feasibility of utilizing the structural bioinformatics approaches at a genome-scale. The tools developed for analyzing large-scale data on protein-ligand inter-actions could be applied to characterize the pocket-space of protein-ligand interactions. The network theory approaches applied in this work, make large-scale data tractable and enable binding-site typing. The binding site analysis at a genome-scale for Mtb is first of its kind and has provided novel insights into the pocket space. The binding site analysis performed on a genome-scale for Mtb provided an opportunity to rationalize the polypharmacological target selection and explore drugs for repurposing in TB. In the larger context, structural modelling of a proteome, mapping the small-molecule binding space in it and understanding the determinants of small-molecule recognition forms a major step in defining a proteome at higher resolution. This in turn will serve as a valuable input towards the emerging field of structural-systems biology, which seeks to understand the biological models at a systems level without compromising on the resolution of the study.