Molecular docking is a computational tool commonly applied in drug discovery projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, (ii) screen a collection of small-molecules against a receptor and rank ligands by their likelihood of being active, and (iii) given a ligand molecule and a target receptor, predict the binding affinity of the two. Here, we focus on the first two questions, namely ranking and pose prediction. Currently, state-of-the-art docking algorithms predict poses within 2A of the native pose in a rate lower than ∼60% and in many cases, below 40%. In ranking, their ability to identify active ligands is inconsistent and generally suffers from high false-positive rate. In this thesis we present novel algorithms to enhance the ability of molecular docking to address these two questions. These algorithms do not substitute traditional docking but rather being applied on top of them to provide synergistic effect. Our algorithms improve pose predictions by 0.5-1.0A and ranking order for 23% of the targets in gold-standard benchmarks. As importantly, the algorithms improve the consistence of the posing and ranking predictions over diverse sets of targets and screening libraries. In addition to the posing and ranking, we present the pharmacophore concept. A pharmacophore is an ensemble of physiochemical descriptors associated with a biological target that elucidates common interaction patterns of ligands with that target. We introduce a novel pharmacophore inference algorithm and demonstrate its utilization in molecular docking. This thesis is outlined as follow. First we introduce the molecular docking approach for pose prediction and ranking. Second, we discuss the pharmacophore concept and present algorithms for pharmacophore inference. Third, we demonstrate the utilization of pharmacophores for pose prediction by re-scoring candidate poses generated by docking algorithms. Finally, we present algorithms to improve ranking by reducing bias in scoring functions employed by docking algorithms.

Molecular docking is a computational tool commonly applied in drug discovery projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, (ii) screen a collection of small-molecules against a receptor and rank ligands by their likelihood of being active, and (iii) given a ligand molecule and a target receptor, predict the binding affinity of the two. Here, we focus on the first two questions, namely ranking and pose prediction. Currently, state-of-the-art docking algorithms predict poses within 2A of the native pose in a rate lower than ∼60% and in many cases, below 40%. In ranking, their ability to identify active ligands is inconsistent and generally suffers from high false-positive rate. In this thesis we present novel algorithms to enhance the ability of molecular docking to address these two questions. These algorithms do not substitute traditional docking but rather being applied on top of them to provide synergistic effect. Our algorithms improve pose predictions by 0.5-1.0A and ranking order for 23% of the targets in gold-standard benchmarks. As importantly, the algorithms improve the consistence of the posing and ranking predictions over diverse sets of targets and screening libraries. In addition to the posing and ranking, we present the pharmacophore concept. A pharmacophore is an ensemble of physiochemical descriptors associated with a biological target that elucidates common interaction patterns of ligands with that target. We introduce a novel pharmacophore inference algorithm and demonstrate its utilization in molecular docking. This thesis is outlined as follow. First we introduce the molecular docking approach for pose prediction and ranking. Second, we discuss the pharmacophore concept and present algorithms for pharmacophore inference. Third, we demonstrate the utilization of pharmacophores for pose prediction by re-scoring candidate poses generated by docking algorithms. Finally, we present algorithms to improve ranking by reducing bias in scoring functions employed by docking algorithms.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès En aquesta tesis es pretén aplicar metodologies computacionals (generació de farmacòfors i docking proteïna lligand) en l'àmbit de la nutigenòmica (ciència que pretén entendre, a nivell molecular, com els nutrients afecten la salut). S'aplicaran metodologies in silico per entendre a nivell molecular com productes naturals com els compostos fenòlics presents en la nostra dieta, poden modular la funció d'una diana comportant un efect en la salut. Aquest efecte es creu que podria ser degut a la seva interacció directa amb proteïnes de vies de senyalització molecular o bé a la modificació indirecta de l'expressió gènica. Donat que el coneixement de l'estructura del complex lligand-receptor és bàsic per entendre el mecanisme d'acció d'aquests lligands s'aplica la metodologia docking per predir l'estructura tridimensional del complex. En aquest sentit, un dels programes de docking és AutoGrid/AutoDock (un dels més citats). No obstant, l'automatització d'AutoGrid/AutoDock no és trivial tan per (a) la cerca virtual en una llibreria de lligands contra un grup de possibles receptors, (b) l'ús de flexibilitat, i (c) realitzar un docking a cegues utilitzant tota la superfície del receptor. Per aquest motiu, es dissenya una interfície gràfica de fàcil ús per utilitzar AutoGrid/AutoDock. Blind Docking Tester (BDT) és una aplicació gràfica que s'executa sobre quatre programes escrits en Fortran i que controla les condicions de les execucions d'AutoGrid i AutoDock. BDT pot ser utilitzat per equips d'investigadors en el camp de la química i de ciències de la vida interessats en dur a terme aquest tipus d'experiments però que no tenen suficient habilitats en programació. En la modulació del metabolisme de la glucosa, treballs in vivio i in vitro en el nostre grup de recerca s'han atribuït els efectes beneficiosos de l'extracte de pinyol de raïm en induir captació de glucosa (punt crític pel manteniment de l'homeostasis de la glucosa). No obstant alguns compostos fenòlics no tenen efecte en la captació de la glucosa, d'altres l'inhibeixen reversiblement. En alguns casos aquesta inhibició és el resultat de la competició dels compostos fenòlics amb ATP pel lloc d'unió de l'ATP de la subunitat catalítica de la fosfatidil inositol 3-kinasa (PI3K). Estudis recents amb inhibidors específics d'isoforma han identificat la p110α (la subunitat catalítica de PI3Kα) com la isoforma crucial per la captació de glucosa estimulada per insulina en algunes línies cel·lulars. Els programes computacionals han estat aplicats per tal de correlacionar l'activitat biològica dels compostos fenòlics amb informació estructural per obtenir una relació quantitativa estructura-activitat (3D-QSAR) i obtenir informació dels requeriments estructura-lligand per augmentar l'afinitat i/o selectivitat amb la diana (proteïna). Tot hi haver-se demostrat que l'adició d'extractes de compostos fenòlics en l'aliment pot tenir en general un benefici per la salut, s'ha de tenir en compte que l'estudi 3D-QSAR (construït a partir d'inhibidors sintètics de p110α) prediu que algunes d'aquestes molècules poden agreujar la resistència a la insulina en individus susceptibles dificultant la capatació de glucosa en múscul i teixit adipós i, per tant, produir un efecte secundari indesitjat. Resultats en el nostre grup de recerca han demostrat que compostos fenòlics presents en extractes de llavor de raïm incrementen l'activitat del receptor "farnesoid x receptor" (FXR) de manera dosi depenent quan el lligand natural de FXR (CDCA) és present. Les metodologies in silico, docking i 3D-QSAR, han estat aplicades juntament amb dades biològiques d'agonistes no esteroidals de FXR que s'uneixen a un lloc d'unió proper però diferent al lligand esteroidal 6CDCA. Els resultats han mostrat que els compostos fenòlics no són capaços d'activar FXR per ells mateixos però poden afegir noves interaccions que estabilitzarien la conformació activa de FXR en presència del lligand natural CDCA. Els compostos fenòlics podrien induir canvis conformacionals específics que augmentarien l'activitat de FXR. In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès This thesis was written with the aim of applying computational methods that have already been developed for molecular design and simulation (i.e. pharmacophore generation and protein-ligand docking) to nutrigenomics. So, in silico tools that are routinely used by the pharmaceutical industry to develop drugs have been used to understand, at the molecular level, how natural products such as phenolic compounds (i.e. molecules that are commonly found in fruits and vegetables) can improve health and prevent diseases. Therefore, we first focused on predicting the structure of protein-ligand complexes. The docking algorithms can use the individual structures from receptor and ligand to predict (1) whether they can form a complex and (2) if so, the structure of the resulting complex. This prediction can be made, for instance, with AutoGrid/AutoDock, the most cited docking software in the literature. The automation of AutoGrid/AutoDock is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. Therefore, in order to circumvent these limitations, we have designed BDT (i.e. blind-docking tester; http://www.quimica.urv.cat/~pujadas/BDT), an easy-to-use graphic interface for using AutoGrid/AutoDock. BDT is a Tcl/Tk graphic front-end application that runs on top of four Fortran programs and which controls the conditions of the AutoGrid and AutoDock runs. As far as the modulation of the glucose metabolism is concerned, several in vivo and in vitro results obtained by our group have shown that grape seed procyanidin extracts (GSPE) stimulate glucose uptake in 3T3-L1 adipocytes and thus help to maintain their glucose homeostasis. In contrast, it is also well known that although some phenolic compounds do not affect glucose uptake, others reversibly inhibit it in several cell lines. Moreover, for at least some of these phenolic compounds, this inhibition is the result of their competition with ATP for the ATP-binding site in p110α (i.e. the α isoform of the catalytic subunit of phosphoinositide 3-kinase or PI3Kα). Furthermore, recent studies with isoform-specific inhibitors have identified p110α as the crucial isoform for insulin-stimulated glucose-uptake in some cell lines. Therefore, although it has been proved that the addition of phenolic compound extracts to food can have an overall benefit on health, it should be taken into account that some of these molecules may exacerbate insulin resistance in susceptible individuals via impaired glucose uptake in muscle and adipose tissues and, therefore, produce an undesirable side effect. In this context, we have applied computational approaches (i.e. protein-ligand docking and 3D-QSAR) to predict the IC50 (i.e. the concentration that reduces the p110α activity to 50%). Our results agree with previous experimental results and predict that some compounds are potential inhibitors of this enzyme. Recent results in our research group have demonstrated that the phenolic compounds in GSPE increase the activity of the farnesoid X receptor (i.e. FXR) in a dose-dependent way when the natural ligand of FXR (i.e. CDCA) is also present. The phenolic compounds might induce specific conformational changes that increase FXR activity and then contribute to cardioprotection through mechanisms that are independent of their intrinsic antioxidant capacities but that involve direct interaction with FXR to modulate gene expression. Taking into account this hypothesis a 3D-QSAR analysis was made in an attempt to understand how phenolic compounds activate FXR. So, our results explain why phenolic compounds cannot activate FXR by themselves and how they can add new interactions to stabilize the active conformation of FXR when its natural ligand (i.e. CDCA) is present. Therefore, we proposed a mechanism of FXR activation by dietary phenolic compounds in which they may enhance bile acid-bound FXR activity.

Résumé Le virus de l’immunodéficience humaine (VIH) est l’agent pathogène responsable du Syndrome del’Immunodéficience Acquise (SIDA). A l’heure actuelle, le traitement des patients infectés par le VIH estbasé sur l’emploi de substances chimiques destinées à perturber les différentes étapes du cycle deréplication du virus (chimiothérapie). Même si elles permettent d’améliorer l’état de santé des patientset d’augmenter leur espérance de vie, ces thérapies restent coûteuses, contraignantes et imparfaites.La recherche de nouveaux composés plus efficaces reste donc d’actualité. Ce travail de thèse est dédié à la conception rationnelle et à l’étude d’inhibiteurs non nucléosidiques dela transcriptase inverse du VIH-1 (INNTI) une enzyme essentielle au cycle de réplication de ce virus.Les molécules étudiées dérivent du cycle 2-pyridinone dont sont déjà issues plusieurs familles d’INNTIdécrites dans la littérature. La conception rationnelle de molécules d’intérêt pharmaceutique nécessite une bonne compréhensiondes interactions mises en jeu entre la macromolécule cible et ses ligands. Etant donné qu’aucunestructure cristallographique d’un complexe TI-pyridinone n’est disponible dans la littérature, la premièrepartie de ce travail est consacrée à la proposition d’un mode d’interaction TI-pyridnone et à larationalisation des relations structure-activité liées à cette famille de molécules. Les informationsrecueillies lors de cette étude théorique sont ensuite exploitées dans le but d’aider au développementd’une nouvelle série d’inhibiteurs. Abstract Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immune DeficiencySyndrome (AIDS). Treatment of HIV-infected patients is currently based on the use of chemicalcompounds that interfere with various steps of the viral replication cycle (chemotherapy).Although these therapies allow for a significant improvement of a patient’s health, theynonetheless remain imperfect and expensive. Research for new and improved anti-HIVcompounds is therefore necessary. This Ph. D. thesis is dedicated to the rational design and analysis of new non nucleosideinhibirors of HIV-1 reverse transcriptase (NNRTI), a key enzyme in HIV lifecycle. Most of thestudied compounds are derived from the 2-pyridinone ring, that is part of several NNRTIfamilies. Rational drug design usually requires a good understanding of the main interactions betweenthe macromolecular target (RT) and its ligands. However, no crystal structure of a RT-pyridinone complex has been reported yet. Our first objective was therefore to build atheoretical model describing RT-pyridinone interactions and providing a better understanding ofstructure-activity relationships among pyridinones. The information obtained in this theoreticalmodel was then used in order to develop new and potent inhibitors.

The current project examined the ability of a novel series of guandine and amidine-containing nicotine analogs to interact with several native and recombinantlyexpressed mammalian neuronal nicotinic-acetylcholine receptor (nAChR) subtypes. Rational drug design methods and parallel organic synthesis was used to generate a library of guanidine-containing nicotine (NIC) analogs (AH compounds). A smaller series of amidine-containing nicotine analogs (JC compounds) were also synthesized. In total, >150 compounds were examined. Compounds were first assayed for affinity in a high-throughput [3H]epibatidine radioligand-binding screen. Lead compounds were evaluated in subtype-selective binding experiments to probe for affinity at the α4β2* and α7* neuronal nAChRs. Several compounds were identified which possess affinity and selectivity for the α4β2* subtype [AH-132 (Ki=27nm) and JC-3-9 (Ki=11nM)]. Schild analysis of binding suggests a complex one-site binding interaction at the desensitized high-affinity nAChR. Whole-cell functional fluorescence (FLIPR) assays revealed mixed subtype pharmacology. AH-compounds were identified which act as activators and inhibitors at nAChR subtypes, while lead JC-compounds were found which possess full agonist activity at α4β2* and α3β4* subtypes. Compounds were identified as partial agonists, full agonists and inhibitors of multiple nAChR subtypes. Several SAR-based, ligand-receptor pharmacophore models were developed to guide future ligand design. Second-generation lead compounds were identified.

Organic cations (OCs) make up ~40% of all prescribed drugs and renal secretion plays a major role in clearing these (and other OCs), from the plasma. The active and rate-limiting step of renal OC secretion is mediated by luminal OC/H+ exchange, the molecular basis of which is suspected to involve two homologous transport proteins, Multidrug And Toxin Extruders 1&2-K (MATE1 and MATE2-K). This study has two aims to resolve outstanding issues dealing with the mechanism of MATE-mediated OC transport: (Aim 1) develop predictive models of ligand interaction with hMATE1; (Aim 2) establish the kinetic mechanism(s) of ligand interaction with MATE transporters and the extent to which inhibitory ligands serve as transported substrates of MATE transporters. Transport was measured using human MATE1 and MATE2-K stably expressed in Chinese Hamster Ovary cells. Both MATEs had similar affinities for the prototypic OC substrate, 1-methyl-4-phenylpyridinium (MPP), and had overlapping selectivity for most of the test inhibitors. The IC50 values for 59 structurally diverse inhibitory ligands were used to generate a common features (HIPHOP) pharmacophore and three quantitative pharmacophores for hMATE1 (each displaying a significant correlation between predicted and measured IC50 values). The models identified (i) structural features that influence ligand interaction with hMATE1, including hydrophobic regions, H-bond donor and acceptor sites and an ionizable feature; and (ii) novel high affinity inhibitors of MATE-mediated transport from 13 new drug classes. Whereas metformin and creatinine were shown to be competitive inhibitors of MPP, the inhibition of MATE1-mediated MPP transport produced by pyrimethamine (PYR) and related analogs was not competitive but, instead, had a "linear, mixed-type" inhibitory profile suggestive of a MATE binding surface rather than a singular binding site. "Competitive exchange diffusion" showed that selected inhibitory ligands (including quinidine, caffeine, and the organic anion, PAH) also serve as transported substrates for MATE1. In conclusion, these data are consistent with the presence of a MATE binding surface with multiple, non-overlapping binding sites that can display different kinetic interactions with structurally distinct substrates. The creation of hMATE1 pharmacophores offers insight into development and interpretation of predictive models of drug-drug interaction in the kidney.

Depression is a major psychological disorder that affects a person's mental and physical abilities. The National Institute of Mental Health (NIMH) classified it as a serious medical illness. It causes huge economic, as well as financial impact on the people, and it is also becoming a major public health issue. Antidepressant drugs are prescribed to mitigate the suffering caused by this disorder. Different generations of antidepressants have been developed with dissimilar mechanisms of action. According to the Center for Disease Control, the usage of antidepressants has skyrocketed by 400 percent increase over 2005- 2008 survey period. This dramatic rise in usage indicates that these are the most prescribed drugs in the US. Even with the FDA mandated "black box" warning of increased suicidal thoughts upon use of selected antidepressants, these drugs are still being used at a higher rate. <br>All classes of antidepressants are plagued by side effects with mainly sexual dysfunction common among them. To avoid the adverse effects, an emphasis is to discover novel structural drug scaffolds that can be further developed as a new generation of antidepressants. The importance of this research is to discover structurally novel antidepressants by performing in silico virtual screening (VS) of chemical databases using the serotonin transporter (SERT). In the absence of a SERT crystal structure, a homology model was developed. The homology model was utilized to develop the first structure-based pharmacophore for the extracellular facing secondary ligand binding pocket. The pharmacophore captured the necessary drug-SERT interaction pattern for SERT inhibitory action. This pharmacophore was employed as one of the filters for VS of candidate ligands. The ten compounds identified were purchased and tested pharmacologically. Out of the ten hits, three structurally novel ligands were identified as lead compounds. Two of these compounds exhibited selectivity towards SERT; the remaining lead compound was selective towards the dopamine transporter and displayed cocaine inhibition. The two SERT selective compounds will provide new opportunities in the development of novel therapeutics to treat depression. <br>For dopamine transporter (DAT), the study was based on recently developed structurally diverse photo probes. In an effort to better understand the binding profile similarities among these different scaffolds, the photo probes were docked into DAT. The finger print analysis of the interaction pattern of docked poses was performed to identify the inhibitor-binding sites. <br>For mitogen activated protein kinase 5 (MEK5), given the lack of structural information, a homology model of MEK5 was developed to guide the rational design of inhibitors. Docking of known MEK5 inhibitors into the homology model was performed to understand the inhibitory interaction profile. Several series of analogues were designed utilizing the generated interaction profile. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / PhD / Dissertation