Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades. The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’). The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys. An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results. In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey.

The rationalisation of drug potency using three-dimensional structures of protein-ligand complexes is a central paradigm in medicinal research. For over two decades, a major goal has been to find the rules that accurately relate the structure of any protein-ligand complex to its affinity. Addressing this problem is of great concern to the pharmaceutical industry, which uses virtual screens to computationally assay up to many millions of compounds against a protein target. A fast and trustworthy affinity estimator could potentially streamline the drug discovery process, reducing reliance on expensive wet lab experiments, speeding up the discovery of new hits and aiding lead optimization. Water plays a critical role in drug-protein interactions. To address the often ambiguous nature of water in binding sites, a water placement method was developed and found to be in good agreement with X-ray crystallography, neutron diffraction data and molecular dynamics simulations. The method is fast and has facilitated a large scale study of the statistics of water in ligand binding sites, as well as the creation of models pertaining to water binding free energies and displacement propensities, which are of particular interest to medicinal chemistry. Structure-based scoring functions employing the explicit water models were developed. Surprisingly, these attempts were no more accurate than the current state of the art, and the models suffered from the same inadequacies which have plagued all previous scoring functions. This suggests a unifying cause behind scoring function inaccuracy. Accordingly, mathematical analyses on the fundamental uncertainties in structure-based modelling were conducted. Using statistical learning theory and information theory, the existence of inherent errors in empirical scoring functions was proven. Among other results, it was found that even the very best generalised structure-based model is significantly limited in its accuracy, and protein-specific models are always likely to be better. The theoretical framework developed herein hints at modelling strategies that operate at the leading edge of achievable accuracy.

The main problem with air freight handling at Arlanda is the transportation of freight on airside, that is from the freight terminal to loading process at the aircraft. To approach this problem, a mapping of the physical flow as well as information flow has been made to identify underlying reasons to this problem. This has been the purpose of the study.The mapping has also facilitated the possibilities to identify improvements in the air freight handling process. To give a recommendation of what these improvements could be was the objective of the study.The underlying reasons for the main problem were identified. These causes were space restrictions on the apron, traffic congestion, and lack of freight storage areas by the gates. This aggravates the possibility to prepare freight for each flight departure. The recommendations to Swedavia are long-term measures that should be further explored. These recommendations regard total cost analysis of using fridge containers, co-owned ground handling equipment, IT possibilities,and comparison to other airports.

Esta tese alia dois enfoques principais dentro da Química Farmacêutica. Por um lado, busca explorar uma nova fonte de insumos naturais, cascas de Malus  domestica, com vistas a obtenção dos triterpenos ácidos ursólico (AU) e betulínico (AB); e por outro lado, estuda a relação dos derivados triterpênicos semissintéticos obtidos com a proteína-alvo (PfATP6) destacada atualmente na literatura da terapia da malária com vistas ao planejamento de novos antimaláricos. O primeiro Capítulo inclui o desenvolvimento de um método eficiente, fácil e extremamente rápido onde são combinadas as técnicas de extração por ultrassom (UAE) e análise por Cromatografia Líquida de Alta Eficiência Acoplada a Detector de Espectroscopia de Massas (LC-MS), para identificação e doseamento dos ácidos ursólico (AU) e betulínico (BA) em extratos de cascas frescas de maçã de cinco clones das cultivares Gala e Fuji (“Baigent”, “Fuji Mishima”, “Fuji Suprema”, “Fuji Select” and “Maxi Gala”) oriundas da Região Sul do Brasil. Os parâmetros cromatográficos do método analítico incluem: ionização por eletro spray em modo positivo (ESI+), fluxo de 1,0 mL/min, em modo de eluição isocrático, consistindo de 80% acetonitrila e 20% acetato de amônio 10 mM em pH 6,0 e temperatura ambiente. O método desenvolvido foi validado e mostrou ser seletivo, sensível (LOD e LOQ de 0,087 e 0,266 μg/mL para BA, e 0,398 e 2,117 μg/ mL para UA), coeficiente de regressão linear (r >0.99), preciso, exato e robusto para os analitos de interesse. A otimização do método combinado de UAE com LC-MS permitiu concluir os procedimentos de extração e análise em tempo inferior a 4 h, uma vez que o método não requer a secagem da amostra, etapa que demanda longos tempos de processamento. Este método foi aplicado e forneceu a primeira caracterização fitoquímica dos cinco clones de maçã estudados. Os resultados demonstraram que o método combinado de UAE-LC-MS é adequado às práticas do controle de qualidade. O segundo Capítulo apresenta o estudo da interação dos ligantes semissintéticos derivados dos AU e AB, sintetizados pelo nosso grupo de pesquisa, com a proteína Ca2+-ATPase do Plasmodium falciparum (PfATP6), através do emprego da técnica de Docking Molecular. A PfATP6 é descrita como um importante alvo para novos antimaláricos como Artemisinina (ART), cujo mecanismo de ação inclui, dentre outros, a modulação da homeostasia do cálcio intracelular. Investigações conduziram à hipótese do extravasamento do cálcio, do interior do retículo sarco-endoplasmático como mecanismo plausível para ação dos derivados triterpênicos do AU e AB. Os escores de energia determinados no Docking, de cada um dos nove ligantes (derivados triterpênicos) e quatro compostos de controle (ácidos ursólico e betulínico, artemisinina (ART) e tapsigargina (TPG) foram determinados (análises realizadas em triplicata) e correlacionados com os valores de IC50, para a atividade antimalárica. Os resultados mostraram excelente correlação entre os escores de energia (com a PfATP6) e os valores de IC50, superior a 80% (r > 0,83360). O estudo fornece fortes evidências de que a PfATP6 pode constituir um alvo para os derivados pentacíclicos do estudo, bem como permitiu identificar o perfil conformacional dos ligantes e os principais resíduos do sítio de ligação (SL) da PfATP6 envolvidos nas interações; bem como, contribuiu para a melhor compreensão das propriedades envolvidas na interação do ligante com o receptor e mecanismo de ação. O terceiro Capítulo faz uso de Métodos Clássicos e Quânticos para descrever as mudanças conformacionais da proteína PfATP6. As simulações de Dinâmica Molecular do receptor na forma isolada e complexada com os ligantes foram realizadas durante 10 ns. As conformações finais obtidas para os receptores foram avaliadas em termos RMSD, efeito da presença dos ligantes no sítio de ligação e tipos de interações estabelecidas entre o ligante e o receptor. Os resultados mostraram que as proteínas PfATP6 e SERCA tendem a manter sua conformação nativa e que o modelo utilizado é adequado aos propósitos do estudo. O monitoramento dos resíduos da região citoplasmática das proteínas permitiu evidenciar o efeito alostérico da presença dos ligantes AU e ART no SL, sobre os domínios A e N, da PfATP6. Esse efeito reproduz as conformações E1 e E2, bem estabelecidas para PfATP6, na presença e ausência de Ca2+. As análises de Dinâmica Molecular corroboram os achados do Capítulo II ao evidenciarem o estabelecimento de interações de hidrogênio com os resíduos importantes do SL da PfATP6. Esses resultados fundamentam os indícios de que as bombas de Ca2+-ATPase (SERCA), possam ser de fato, um alvo para os derivados triterpênicos dos AU e AB. / This thesis combines two main focuses within Pharmaceutical Chemistry. On the one hand, it seeks to explore a new source of natural inputs, bark of Malus domestica, in order to obtain ursolic (UA) and betulinic acid (BA) triterpenes. On the other hand, it studies the relation of the semi-synthetic triterpenic derivatives obtained with the target proteins (PfATP6), currently highlighted in the literature on malaria therapy with a view to planning new antimalarial drugs. The first chapter includes the development of an efficient, easy and extremely fast method where ultrasonic extraction techniques (UAE) and high-performance liquid chromatography coupled to mass spectroscopy (LC-MS) are combined for identification and assay of ursolic acid (UA) and betulinic acid (BA) in fresh apple peel extracts from five clones of the Gala and Fuji cultivars (Baigent, Fuji Mishima, Fuji Suprema, Fuji Select and Maxi Gala ") in the Southern Region of Brazil. Chromatographic parameters of the analytical method include: electrospray ionization (ESI +), flow rate of 1.0 mL/min in isocratic elution mode, consisting of 80% acetonitrile and 20% 10 mM ammonium acetate at pH 6.0 and room temperature. The method was validated and proved to be selective, sensitive (LOD and LOQ of 0.087 and 0.266 μg/mL for BA, and 0.398 and 2.117 μg/mL for UA), linear regression coefficient (r> 0.99), accurate, robust for analytes of interest. The optimization of the combined method of UAE with LC-MS allowed to complete the procedures of extraction and analysis in less than 4 h, since the method does not require drying the sample, a stage that demands long processing times. This method was applied and provided the first phytochemical characterization of the five apple clones studied. The results demonstrated that the combined UAE-LC-MS method is suitable for quality control practices. The second chapter presents the study of the interaction of the semi-synthetic ligands derived from the UA and BA, synthesized by our research group, with the Plasmodium falciparum Ca2+-ATPase protein (PfATP6), using the Molecular Docking technique. PfATP6 is described as an important target for new antimalarials such as Artemisinin (ART), whose action mechanism includes, among others, the modulation of intracellular calcium homeostasis. Investigations led to the hypothesis of extravasation of calcium from the interior of the sarco-endoplasmic reticulum as a plausible mechanism for the action of the triterpenic derivatives of UA and BA. The Docking energy scores (binding energy) of each of the nine ligands (triterpenic derivatives) and four control compounds (ursolic and betulinic acids, artemisinin (ART) and tapsigargine (TPG)) with PfATP6, were calculated (analyses performed in triplicate) and correlated with its antimalarial IC50 value. The results showed an excellent correlation between energy scores (with PfATP6) and IC50 values, higher than 80% (r > 0.83360). The study supplies strong evidence that PfATP6 may be a target for the pentacyclic derivatives of the study, and also allowed identifying the conformational profile of the ligands and the main residues of the PfATP6 binding site (BS) involved in the interactions. It further contributed to a better understanding of the properties involved in the interaction of the ligand with the receptor and its action mechanism. The third chapter uses Classical and Quantum Methods to describe the conformational changes of the PfATP6 protein. The Molecular Dynamics simulations of the receptor in the isolated and complexed form with the ligands were performed for 10 ns. The final conformations obtained for the receptors were evaluated in RMSD terms, effect of the presence of ligands at the binding site and types of interactions established between the ligand and the receptor. The results showed that the PfATP6 and SERCA proteins tend to maintain their native conformations and that the model used is adequate for the purposes of the study. The monitoring of the residues of the cytoplasmic region of the proteins allowed evidencing the allosteric effect of the presence of UA and ART ligands in BS, on the A- and N-domains of PfATP6. This effect reproduces the well-established E1 and E2 conformations for PfATP6, in the presence and absence of Ca2+, respectively. Molecular Dynamics analyses corroborate the findings of Chapter II, by showing the possibility of establishing hydrogen interactions with the important residues of PfATP6 BS. These results support the evidence that Ca2+-ATPase (SERCA) pumps may be a target for the triterpenic derivatives of UA and BA.

Introduction: Over recent decades, there has been an increase in the availability and use of Novel Psychoactive Substances (NPS) all over the world. They include several classes of chemicals that mimic the effects of illicit drugs and have been purposefully introduced into the market to circumvent or undermine the purpose of legal regulation. Currently, there is information lacking on the pharmacology of these substances; however, the increasing number of cases and outbreaks of intoxications/deaths is becoming a cause for deepening concern. Multi-disciplinary research in the fields of biology, chemistry, clinical medicine and web analysis is needed to develop responses against this tidal wave. Aim: The overall aim of this project is to gain insights into pharmacological, neurochemical and molecular properties of selected NPS to provide a reliable background needed for detection, assessment, and management of NPS-related harms. A range of approaches and methodologies was employed and a spectrum of different fields of knowledge has been engaged to gain some understanding into the complex multi-faceted phenomenon of NPS. Methods: Different substances have been selected as targets for the present project according to the clinical pattern of toxicity raised by their worldwide use and the lack of scientific knowledge available about them. The methods employed were: in vitro quantitative autoradiography (to evaluate the binding properties of the novel SCs BB-22, 5F-PB-22, 5F-AKB-48 and STS-135 at the cannabinoid receptor type 1 and N-methyl-D-aspartate receptor; and the binding properties of the synthetic stimulants 5-IT and 2-DPMP at the dopamine transporter in rat brain slices); in vitro Fast Scan Cyclic Voltammetry (to assess the effects of BB-22 on evoked dopamine efflux and dopamine re-uptake half-life in nucleus accumbens brain slices); in vivo microdialysis (to monitor dopamine release in terminal areas of the reward system after acute administration of the synthetic cannabinoids BB-22, 5F-PB-22, 5F-AKB-48 and STS-135; the dieting aid compound 2,4-DNP; the synthetic stimulants 2-DPMP and D2PM in freely moving animals); in silico molecular docking (to investigate the intermolecular interactions of the SCs BB-22, 5F-PB-22, 5F-AKB-48 and STS-135, and other referent compounds, with a homology model of the rodent cannabinoid receptor type 1 (CB1R) and the crystal structure of the human CB1R); and a web-based analysis approach (to analyse the information provided by a range of fora communities on 4,4'-DMAR use, additionally critical reviewing the available evidence-based literature on this topic). Results: Our in vitro quantitative autoradiography studies, confirmed that the index compounds BB-22, 5F-PB-22, 5F-AKB-48 and STS-135, behave as highly potent CB1R ligands able to compete with the radioligand [3H]CP-55,940 in cortical and striatal brain slices. On the other hand, all synthetic cannabinoids tested were unable to compete with the radioligand [3H]MK-801 in the same cerebral areas, rejecting the hypothesis of their potential binding to the N-methyl-D-aspartate receptor (NMDAR) at all concentrations investigated. Consistent with previous in vitro studies, 5-IT and 2-DPMP behaved as highly potent dopamine transporter (DAT) ligands able to compete with the radioligand [125 I]RTI-121 in a concentration-dependent way in the Caudate Putamen (CPu) and Nucleus Accumbens (NAc) brain slices. Notably, 2-DPMP was able to displace the radioligand in both cerebral regions, starting from lower concentrations compared to 5-IT. In vitro Fast Scan Cyclic Voltammetry findings demonstrated that local application of the synthetic cannabinoid BB-22 in brain slices, was unable to change evoked dopamine efflux and dopamine reuptake time-constant in the NAc shell at any doses tested. The results obtained would suggest the relative contributions of complex neuronal circuits, either within or outside the NAc, whose modulation would interfere with the interactions between BB-22 and dopaminergic neurons and represent critical pathways accounting for some of the rewarding properties of BB-22 exposure. In vivo microdialysis outcomes suggested that all SCs tested could increase dopamine release in the NAc shell at specific doses, while no changes in dopamine output were observed in other areas of the reward system, namely NAc core and medial prefrontal cortex (mPFCx) after BB-22 administration. These outcomes provided a circumstantial pre-clinical evidence for a greater putative abuse liability of SCs compared to the natural compound found in cannabis (Δ9‐THC). Furthermore, the acute treatment with 2,4-DNP did not cause any change in dopamine release in the NAc shell and CPu rejecting the hypothesis of psychoactivity of this substance at the dose tested. On the other hand, the synthetic stimulant 2-DPMP elicited a comparable increase of dopamine (DA) release in the NAc shell and CPu at the higher doses tested, while D2PM caused a selective increase of DA release in the NAc shell, providing a circumstantial preclinical evidence for a putative abuse liability of this compound at the highest dose assessed. The in silico molecular docking studies demonstrated that the SCs BB-22, 5F-PB-22, 5F-AKB-48 and STS-135 interact with CB1 receptor residues that, according to previous mutation and computational studies, are considered crucial for synthetic cannabinoid binding recognition. Additionally, they share some interacting residues with other aminoalkylindole derivatives (e.g. WIN-55,212-2). The web-based analysis focused on 4,4'-DMAR, suggested that fora members co-operate in exchanging an extensive body of knowledge about this drug, and the recurring topics of discussion include: routes of administration and dosages; desired and undesired effects; comparison and association with other drugs and medications; overall impression; provision of harm reduction advice. This approach has been useful to better understand some of the clinical and psychopharmacological issues pertaining to 4,4'-DMAR. Conclusions: Overall, these studies provided new pharmacological, neurochemical and molecular knowledge on a range of Novel Psychoactive Substances essential for identifying potential therapeutical approaches against their use/abuse. The novelty of this project lies in the adoption of a multi-disciplinary approach involving a range of methodologies from different areas of expertise (neurobiology, pharmacology, chemistry, netnography) all integrated to clarify some aspects of the index NPS, which were not yet available in the current literature. Additional studies are needed to better explain short and long-term effects of the index NPS, their abuse potential, and their interactions with other drugs of abuse.

L’inhibition de l’arginase a été montrée pour le traitement de la dysfonction endothéliale dans plusieurs pathologies. Des inhibiteurs sont actuellement commercialisés (nor-NOHA, ABH et BEC) mais en dépit de leur potentiel, ils sont incompatibles avec un usage médical per os. L’obtention de nouveaux inhibiteurs reste donc un challenge pour le développement de candidats médicaments. La source naturelle et la voie hémisynthétique notamment, restent encore des axes peu explorés. Visant d’abord le développement d’un test fiable et reproductible pour l’évaluation de la capacité inhibitrice de molécules, nous avons optimisé un test existant et mis en place un essai colorimétrique miniaturisé et partiellement automatisé, utilisant une arginase mammifère commerciale, purifiée de foie de bœuf. Ce test a été validé via l’utilisation d’inhibiteurs de référence (CI50 : nor-NOHA 1,7 μM / BEC 3,3 μM), avant d’être utilisé pour l’évaluation biologique d’une série de polyphénols naturels, mettant en évidence les potentialités inhibitrices de l’acide chlorogénique (acide caféoylquinique / CI50 10,6 μM) et du picéatannol (stilbène / CI50 12,1 µM). Des études de cinétique enzymatique ont montré que l’inhibition était réversible et compétitive tandis que des études de docking moléculaire ont montré l’intérêt de la partie caféique pour l’activité inhibitrice. Nous nous sommes alors focalisés sur l’obtention de dérivés d’hémisynthèse. Dix-neuf dérivés dérivés cinnamides ont été préparés ainsi qu’une série de cinq composés esters. Les études de relation structure-activité ont montré le rôle important du groupement catéchol pour l’activité de ces molécules. Le composé (E)-N-(2-phényléthyl)-3,4-dihydroxycinnamide ou « caffeic acid phenyl amide » (CAPA) a présenté la meilleure activité (CI50 6,9 μM). C’est un inhibiteur réversible et compétitif de l’arginase étudiée et ses études de docking avec le site catalytique de l’enzyme ont confirmé les interactions du catéchol avec des résidus conservés du site actif et les ions manganèse. La préparation des dérivés de stilbènes cibles n’a pas été couronnée de succès mais grâce à des collaborations, deux stilbènes naturels, l’astringine et le picéide, ainsi qu’une série de stilbénoïdes synthétiques ont pu être évalués. Cependant, aucun de ces composés n’a révélé d’activité intéressante.Finalement, notre projet de thèse a mis en évidence les activités prometteuses de deux composés naturels, l’acide chlorogénique et le picéatannol, ainsi que celle d’un composé hémisynthétique dérivés cinnamide de l’acide caféique (CAPA). Ces molécules ont en commun, au niveau structural, la présence d’une partie 3,4-dhydroxycinnamique (caféoyle), révélant l’intérêt de ce motif pour la conception d’autres molécules à capacité inhibitrice d’arginase. Ces résultats obtenus in silico et in vitro sur l’arginase bovine b-ARG I devront être confirmés sur l’arginase humaine h-ARG avant d’envisager d’éventuelles études in vivo pour ces candidats-médicaments potentiels. / Inhibition of the enzyme arginase has been shown its evidences for the treatment of endothelial dysfunction in several pathologies. Some arginase inhibitors are currently being marketed (nor-NOHA, ABH and BEC) but despite their potency, they are incompatible with an oral administration. Research of new arginase inhibitors remains a challenge for the development of drug candidates. Natural source and semisynthetic compounds, in particular, still remain widely unexplored avenues.Firstly focusing on development of a reliable and reproducible in vitro assay for evaluation of arginase inhibitory capacity of molecules, we optimized a previously published protocol, which resulted in a colorimetric, miniaturized and partially automated assay by using a commercial mammalian arginase, purified bovine liver arginase (b-ARG I). This test was validated by evaluating the reference inhibitors (IC50: nor-NOHA 1.7 µM / BEC 3.3 µM). Then we used it for the biological evaluation of a series of natural polyphenols. The most active compounds were chlorogenic acid (caffeoylquinic acid / IC50 10.6 µM) and piceatannol (stilbene / IC50 12.1 µM). Enzyme kinetic studies showed that the inhibition mechanism of these two polyphenols was reversible and competitive, whereas molecular docking studies demonstrated the importance of caffeic moiety for the inhibitory activity. We then continued on synthesis and biological evaluation of semisynthetic derivatives, which were inspired by natural arginase inhibitors. Nineteen cinnamide derivatives and a series of five ester compounds were prepared. Structure-activity relationships (SARs) have shown the important role of catechol group for arginase inhibitory activity of these molecules. The compound (E)-N-(2-phenylethyl)-3,4-dihydroxycinnamide or "caffeic acid phenyl amide" (CAPA) showed the best activity (IC50 6.9 µM). This compound was characterisized as a reversible and competitive inhibitor of arginase by enzyme kinetics. Docking studies suggested several interactions between catechol function of CAPA with crucial residues of the arginase active site and manganese ions. The preparation of stilbene derivatives was not successful during this work. However thanks to collaborations, two natural stilbenoid glucosides (astringin and piceid), as well as a series of synthetic stilbenoid derivatives were evaluated for their arginase inhibition. Nevertheless, none of these stilbenoids has revealed an interesting activity.Finally, our thesis project showed potential arginase inhibitory activity of two natural compounds, chlorogenic acid and piceatannol, as well as a semisynthetic cinnamide derivative (CAPA). Considering their structures, these molecules have the presence of 3,4-dihydroxycinnamoyl (caffeoyl) moiety in common, revealing the importance of this moiety for the design of new arginase inhibitors. The results obtained from in silico and in vitro studies on bovine arginase (b-ARG I) should be confirmed on human arginase assay, before being evaluated in in vivo models for the druggable candidates.

Au cours de leur métabolisme, les céramides, produits de novo au niveau du réticulum endoplasmique, sont transportés vers l'appareil de Golgi pour être convertis en sphingomyéline. Le mode principal de ce transport implique la protéine cytosolique CERT (CERamide Transfer). La surexpression de CERT, responsable d'un abaissement du taux intracellulaire en céramide pro-apoptotique, a été associée au phénomène de résistance aux agents chimiothérapeutiques de plusieurs lignées de cellules tumorales. L'inhibition de CERT permet de resensibiliser ces lignées cellulaires aux agents anti-cancéreux. Cependant, une seule famille d'inhibiteurs de CERT est connue à ce jour : les HPAs. A l'extrémité C-terminale de la protéine, le domaine START contient le site de liaison du céramide nécessaire à l'activité de transport de CERT. A partir de structures cristallographiques, une méthode d'identification de nouveaux ligands, combinant des outils in silico et in vitro, a été développée. La jaspine B, des analogues HPAs et des iminosucres ont été mis à jour en tant qu'antagonistes potentiels de CERT par cette méthode. Certains des composés identifiés ont été synthétisés et évalués in vitro. Des sondes fluorescentes de la jaspine B ont été conçues afin d'approfondir la compréhension de son mécanisme d'inhibition. En parallèle, un test de liaison in vitro HTR-FRET a été développé, permettant le criblage haut-débit de la Chimiothèque Nationale Essentielle. / During its metabolism, ceramides, produced de novo in the endoplasmic reticulum, are transported to the Golgi complex to be converted into sphingomyelin. The main way of this transport involves the cytosolic CERT protein (Ceramide Transfer). Overexpression of CERT, responsible for a diminution of intracellular level of proapoptotic ceramide, is associated with the phenomenon of resistance to chemotherapeutic agents in several tumor cell lines. The CERT inhibition allows to resensitize these cell lines to anticancer drugs. Yet, only a single family of inhibitors is known to date: HPAs. Located at the C-terminal region of the protein, the START domain contains the binding site of ceramide necessary for the transport activity of CERT. Based on crystallographic structures, a method for the identification of new CERT ligands, combining in silico and in vitro tools, was developed. Jaspine B, HPAs analogs and iminosugars were identified as potential antagonists using this method. Some of these compounds were synthesized and evaluated in vitro. Fluorescent probes of jaspine B were designed for a better understanding of it mechanism of action. In parallel, an in vitro HTR-FRET binding assay was developed, allowing the high-throughput screening of the National Essential Compound Library.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-01-12T11:50:46Z No. of bitstreams: 1 2016 - Otavio Augusto Chaves.pdf: 6300833 bytes, checksum: 156947ce06fa4e3b0674f5eaeaa4ef06 (MD5) / Made available in DSpace on 2017-01-12T11:50:46Z (GMT). No. of bitstreams: 1 2016 - Otavio Augusto Chaves.pdf: 6300833 bytes, checksum: 156947ce06fa4e3b0674f5eaeaa4ef06 (MD5) Previous issue date: 2016-07-19 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico - CNPq / The interactions between human serum albumin (HSA) with 18-PF, BZL, MTZ and MZ and between bovine serum albumin (BSA) with t-DCTN, PF, LF-B, PIA and ?-lap were studied by spectroscopic techniques (molecular absorption in the UV-Vis region, circular dichroism, emission fluorescence in the steady state and temporal resolution) under physiological conditions. Theoretical calculations by molecular docking were performed to complement the experimental data and thus offer accurate to the results. The results obtained for the fluorescence quenching rate constant (kq) is greater than the diffusion rate constant in water (kdiff ? 5,00x109 L/mol), indicating that there is formation of complex between albumin and biologically active molecules in the ground state (for the sample PIA we confirmed this data with time resolved fluorescence experiments). For t-DCTN and LF-B beyond the static mechanism it was observed the presence of dynamic fluorescence quenching mechanism. Finally, for PF and PIA F?rster theory shows that the energy transfer between the fluorophore and the quenchers can occurs with high probability. The thermodynamic values for Gibbs? free energy are in accordance with the spontaneity of the association, for all the samples. Thermodynamic parameters ?H? and ?S? provided evidence of the main intermolecular interactions in the association. The samples 18-FP, t-DCTN, LF-B, PIA, ?-lap, BZL and MTZ interact with albumin by hydrogen bonding and hydrophobic interactions. On the other hand, PF and MZ interact by hydrogen bonding and electrostatic forces. The number of binding sites shows that there is only one main cavity of the protein to the interaction. For 18-PF, PF and LF-B the binding is weak, for t-DCTN the binding is moderate and for PIA, ?-lap, BZL, MTZ and MZ the binding is strong. Circular dichroism results show that upon binding of samples with the albumin there are no significant perturbations on the secondary structure of the protein. Theoretical calculations by molecular docking are in full agreement with the spectroscopic results / As intera??es entre albumina s?rica humana (ASH) com 18-FP, BZL, MTZ e MZ e entre albumina s?rica bovina (ASB) com t-DCTN, PF, LF-B, PIA e ?-lap foram estudadas por t?cnicas espectrosc?picas (absor??o molecular no UV-Vis, dicro?smo circular, emiss?o de fluoresc?ncia no estado estacion?rio e com resolu??o temporal) sobre condi??es fisiol?gicas. C?lculos te?ricos por ancoramento molecular (do ingl?s molecular docking) foram executados para complementa??o dos dados experimentais e dessa forma obter resultados mais precisos. Os resultados obtidos para as constantes de velocidade de supress?o de fluoresc?ncia das albuminas (kq) s?o maiores do que a velocidade de difus?o em ?gua (kdiff ? 5,00x109 L/mols), indicando que h? forma??o de um complexo no estado fundamental entre as albuminas com as mol?culas biologicamente ativas (para amostra PIA tal dado foi confirmado com a fluoresc?ncia resolvida no tempo). Para as amostras t-DCTN e LF-B al?m do mecanismo est?tico foi observado ? presen?a do mecanismo din?mico e j? para as amostras PF e PIA o c?lculo de F?rster mostra alta probabilidade de ocorr?ncia de transfer?ncia de energia entre o fluor?foro e os supressores. Os valores termodin?micos de energia livre de Gibbs, calculados para todas as amostras est?o de acordo com a espontaneidade da associa??o. Par?metros termodin?micos de ?H? e ?S? forneceram ind?cios das principais intera??es intermoleculares na associa??o. As amostras 18-FP, t-DCTN, LF-B, PIA, ?-lap, BZL e MTZ associam com a albumina via liga??o de hidrog?nio e intera??es hidrof?bicas e j? PF e MZ por liga??o de hidrog?nio e intera??es eletrost?ticas. O n?mero de s?tios de liga??o para todas as amostras indicam que h? apenas uma principal cavidade da prote?na para a associa??o das mol?culas estudadas, sendo que essa associa??o ? moderada para 18-FP, PF e LF-B, fraca para t-DCTN e forte para PIA, ?-lap, BZL, MTZ e MZ. Estudos de dicro?smo circular demonstram que n?o h? perturba??es significativas na estrutura secund?ria da albumina com a associa??o. C?lculos te?ricos via ancoramento molecular est?o em total acordo com os resultados espectrosc?picos

Our research aim was to design, synthesize, and study the competitive enzyme inhibition kinetics of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) derivatives as potential non-²-lactam ²-lactamase inhibitors. All compounds (1-13) passed the Lipinski’s rule of 5 test and were docked into the active site of TEM-1 ²-lactamase. PBD derivatives 1-7 were synthesized in high yields and tested for their potency against TEM-1 and P99 ²-lactamases. Kinetic data showed that compounds 1, 4, 5, and 7 possessed inhibitory activity against TEM-1 ranging from 4-34 %. Docking results revealed significant interactive spanning of the active site of TEM-1 by PBDs. The limited inhibitory activity of the compounds, 1-7 could be attributed to the lack of solubility and bulky nature of the molecules, thus limiting the optimal ligand-enzyme interactions. 1,2,4- Oxadiazolinones (8-13) were further synthesized to reduce the steric hindrance of the PBD scaffolds while promoting the electrophilicity of the potentially active lactam and also evaluated for potency.

Docking is a computer simulation method used to predict the preferred orientation of two interacting chemical species that has been successfully applied to numerous macromolecules over the years. However, non-traditional targets have inherent difficulties associated with their screening. Large interfaces, lack of obvious binding sites, and transient pockets are some examples. Additionally, most natural ligands of challenging targets are inadequate models for identifying or designing new ligands. Therefore, it is not surprising that customary techniques of structure-based virtual screening are incompatible with these non-traditional targets. We hypothesized that an integrative virtual screening campaign comprised of docking followed by refinement of best receptor–ligand complexes would effectively identify small-molecule ligands of challenging receptors. We targeted the single-stranded DNA (ssDNA) binding groove of the human RAD52, and a cryptic allosteric pocket of the Helicobacter pylori Glutamate Racemase (GR). In this project, we first determined which docking method was more appropriate for each studied non-traditional target, and then examined how good our two-step docking workflow was in finding novel active ligand scaffolds. This research developed a powerful layered virtual screening workflow for the discovery of lead compounds against challenging protein targets. Furthermore, we successfully applied a statistical analysis method, which used receiver operating characteristic (ROC) curves, to validate the selected docking protocol that would be used in the screening campaigns. Using the validated workflow, we identified a natural compound that competes with ssDNA to bind to RAD52. The performed screening campaigns also provided new insights into the studied binding pockets, as well as structure-activity relationships (SAR) and binding determinants of the ligands. Our achievements reinforce the power of the ROC curve analysis approach in directing the search for the most appropriate docking protocol and helping to speed up drug discovery in pharmaceutical research.