yes / Type II congenitalLong QT syndrome (LQT2) is due to genetic mutations in hERG channel. Genetic or pharmacological factors could potentially affect hERG channel biogenesis and contributes to LQTS, for example, disease mutations G601S and T473P result in hERG trafficking deficiency [1,2]. Various rescue strategies for hERG dysfuction are being developed. Some correctors for CFTR channel have been reported to act indirectly on proteostasis pathways to promote folding and correction on hERG trafficking deficiency [3]. In this study, we tested the hypothesis that the CFTR corrector KM-11060 and the potentiator PG-01 may correct hERG mutation trafficking diseases. We use HEK293 cell line expressing a well-studied trafficking disease mutation G601S-hERG channel [4]. We treated cells with CFTR potentiator PG-01and corrector KM-11060, which function through different cellular mechanisms, and assessed whether correction occurred via immunoblotting. Whole cell proteins from HEK 293 cells expressing hERG channels were used for analysis [5]. Proteins were separated on 8% SDS-polyacrylamide electrophoresis gels for 1 hour, transferred onto PVDF membrane, and blocked for 1 h with 5% nonfat milk. The blots were incubated with the primary antibody (Santa Cruz Biotechnology) for 12-16 h at 4C temperature and then incubated with a donkey antigoat horseradish peroxidase-conjugated secondary antibody( Santa Cruz Biotechnology). Actin expression was used for loading controls. The blots were visualized using the ECL detection kit (Genshare).Results were deemed significantly different from controls by a one-way ANOVA (p < 0.05). Our results show that both KM-11060 (5, 10, 20uM) and PG-01(5, 15 uM) can correct G601S mutant alleles of hERG protein trafficking (Fig 1, 2). KM-11060 (20uM) but not PG-01(15 uM) enhance protein expression of wild type hERG channel (Fig 2). Further treatment on cells at low temperature with different drug concentration will be tested. Functional studies are also needed to test whether the drugs can correct the function of hERG mutation channel. These results could potentially provide novel insight into the correction mechanism of CFTR potentiator and also help to develop new treatment for LQT2.

Le patch-clamp planaire, technique utilisant des microtrous structurés sur un substrat plan, permet d'envisager la parallélisation des mesures de courants ioniques sur cellules individualisées, répondant ainsi à une demande des industries pharmaceutiques. Dans un premier temps, nous avons élaboré un démonstrateur de laboratoire permettant de tester des puces en silicium et démontrer leur potentiel pour l'enregistrement des courants ioniques. Nous avons ensuite procédé à l'amélioration de la sensibilité et des performances de la puce en optimisant l'interaction de la cellule avec les paramètres géométriques et physico-chimiques de la puce et en réduisant la capacité de la puce. Cette démarche a permis de concevoir une puce offrant 80 % de scellements exploitables et les validations électrophysiologiques présentées témoignent de la robustesse, de la fiabilité et de la sensibilité du système.

<p dir="ltr"><b>Background</b></p><p dir="ltr">Heart failure (HF) is a chronic clinical syndrome characterized by symptoms including breathlessness, fatigue, swelling of the ankles, and signs such as edema pulmonary crackles etc. During HF, pathogenic mechanisms including hemodynamic overload, ventricular remodeling, aberrant calcium handling, excessive neurohormonal stimulation contribute to the worsening and progression of the condition. Ventricular arrhythmias are the common cause of sudden cardiac death (SCD) in HF patients.</p><p dir="ltr">Hyperactivation of the sympathetic nervous system (SNS), a characteristic of HF, causes an increase in circulating catecholamines which becomes detrimental to-adrenergic receptors (-AR) leading to signaling dysfunction, and decrease in contractility and the ionotropic reserve. Expression of calcium/calmodulin-dependent protein kinase II (CaMKII), a downstream effector of-AR and a key regulator of calcium homeostasis, has been shown to be enhanced in HF. CaMKII-mediated mechanisms have been demonstrated to contribute to cardiac remodeling, arrhythmias by pathological regulation of ion channels, and contractile dysfunction.</p><p dir="ltr">The human ether-a-go-go related gene (hERG) encodes the pore-forming subunit of the voltage-gated potassium channel that conduct the rapid component of the delayed rectifier potassium current, <i>I</i>_Kr. The gating kinetics of <i>I</i>_Krmakes it a crucial determinant of the duration of the plateau phase of atrial and ventricular action potential (AP). Reduced <i>I</i>_Kr density due to loss-of-function mutations or pharmacological blockage of hERG channels precipitate arrhythmias. Downregulation of <i>I</i>_Kr density and protein have been reported in HF. Recent studies suggest that microRNAs (miRNAs) are involved in pathological downregulation of hERG.</p><p dir="ltr">miRNA are small non-coding RNAs of approximately 22 nucleotides in length that function as gene expression regulatory elements by repression translation. Aberrant miRNA expression has associated with cancer, cardiovascular, autoimmune, and inflammatory disorders.</p><p dir="ltr"><b>Objective</b></p><p dir="ltr">The overarching objective of this study is to investigate the mechanisms of CaMKII-mediated regulation of hERG function, including assessment of an interplay with miR-362-3p during sustained β-AR stimulation. In Specific Aim 1, the effect of CaMKII activation through sustained β-AR stimulation on hERG function and miR-362-3p expression will be assessed. The mechanism of miR-362-3p upregulation will be evaluated in Specific Aim 2, and in Specific Aim 3, the interactome of miR-362-3p and binding sites will be characterized and predicted, respectively.</p><p dir="ltr"><b>Methods</b></p><p dir="ltr">Whole-cell, voltage clamp electrophysiology experiments were performed in HEK 293 cells stably expressing hERG (hERG-HEK) and both hERG and wild-type CaMKIIδ<br>(hERG/CaMKII-HEK) following treatment with isoproterenol for 48 hours, and after transfection with miR-362-3p. The effect of CaMKII activation on miR-362-3p was assessed using real-time quantitative polymerase chain reaction (RT-qPCR). Total RNA was isolated 48 hours after isoproterenol treatment and the TaqMan assay was used to reverse transcribe and analyze miR-362-3p expression. Cells were transfected with cJun siRNA and precursor miR-362-3p to assess the role of cJun miR-362-3p upregulation during sustained β-AR stimulation with isoproterenol. The interactome of miR-362-3p was assessed in both cell lines using enhanced crosslinking immunoprecipitation (eCLIP) assay. miR-362-3p binding sites were predicted using RNAStructure Duplexfold after identification of miR-362-3p chimeric molecules from eCLIP experiment. Interaction analysis was performed using GeneMania in Cytoscape to identify genes that were potentially downregulated by miR-362-3p and been reported to interact with hERG.</p><p dir="ltr"><b>Results</b></p><p dir="ltr">In Specific Aim 1, the effect of sustained β-AR stimulation on hERG currents and endogenous miR-362-3p was assessed in hERG-HEK and hERG/CaMKII-HEK cells. Using whole-cell voltage clamp electrophysiology, we demonstrated that 48 hours treatment with 100 nM isoproterenol reduced hERG currents in hERG/CaMKII-HEK cells (p = 0.032) but had no effect on the voltage dependence of activation (p = 0.61) relative to control vehicle. Isoproterenol treatment for 48 hours, however, had no effect on hERG currents (p = 0.58) and the voltage dependence of activation (p = 0.99) in hERG-HEK cells. The effect of sustained isoproterenol treatment on miR-362-3p was also assessed using RT-qPCR. In hERG/CaMKII cells, 48 hours isoproterenol treatment increased miR-362-3p expression (2.3 folds; p = 0.038) relative to control vehicle. hERG/CaMKII-HEK cells were also treated with 500 nM KN-93 or its inactive analogue, KN-92, in an attempt to reverse CaMKII effect on miR-362-3p expression. Treatment with KN-93 decreased miR-362-3p expression (0.5-fold; p = 0.002) relative KN-92 treatment. Isoproterenol treatment had no effect on miR-362-3p expression in hERG-HEK cells (p = 0.38).</p><p dir="ltr">The regulatory mechanism of miR-362-3p expression was evaluated in Specific Aim 2. The role of an activator protein-1 (AP-1)-like sequence located at 98 base pairs upstream of miR-362-3p transcription start site was probed using siRNA inhibition of cJun, a central protein of the AP-1 complex, and deletion of the site sequence. The effect of exogenous miR-362-3p on hERG currents were first assessed. Precursor miR-362-3p decreased hERG currents (p = 0.003) compared to control plasmid. The effect of CaMKII overexpression was also assessed on exogenous miR-363-3p expression. Isoproterenol treatment in hERG/CaMKII-HEK cells transfected with precursor miR-362-3p increased mature miR-362-3p expression (0.029) compared to control vehicle treatment. Inhibition of cJun inhibition with cJun-specific siRNA decreased mature miR-362-3p expression (0.5-fold; p = 0.027) compared to scramble siRNA in hERG-HEK cells. In hERG-HEK cells transfected with mutated precursor miR-362-3p (AP-1-like site deleted), cJun inhibition with siRNA had no effect on miR-362-3p expression (p = 0.40).</p><p dir="ltr">The focus of Specific Aim 3 was to characterize the interactome of miR-362-3p as well as predict the miRNA response element (MRE) of its target mRNAs using enhanced crosslinking immunoprecipitation. A network analysis was also performed to identify miR-362-3p targets that have been reported to interact with hERG. Approximately 23% of miR-362-3p mRNA targets from the eCLIP assay have also been catalogued in miRNA database, TargetScanHuman, as miR-362-3p targets. miR-362-3p chimeric molecules with 853 unique targets, of which 75 were identified to interact with hERG through the network analysis. Four unique chimeric molecules between miR-362-3p and hERG mRNA were identified, but the interactions were non-canonical (located in the coding sequence of hERG and outside the seed region of miR-362-3p). Thirty five of the 75 miR-362-3p targets that were identified to interact had a chimeric read ≥ 3, a cutoff number indicating non-random chimeric formation. Using RNAStructure DuplexFold, miR-362-3p was predicted to form canonical binding with 12 of 35 mRNA targets. HSPA4, a heat shock protein involved in the maturation and trafficking of hERG, was identified in a canonical interaction (8-mer) with miR-362-3p.</p><p dir="ltr"><b>Conclusion</b>:</p><p dir="ltr">Sustained β-AR stimulation increases miR-362-3p expression and decreases hERG currents in CaMKII overexpressing cells. cJun mediates miR-362-3p upregulation by interacting with an AP-1-like sequence upstream of miR-362-3p transcription start site. Pathological regulation of <i>I</i>_Kr by CaMKII mediated by miR-362-3p during sustained-AR may contribute to increased risk of arrhythmias in states of increase catecholaminergic activity, such as HF.</p>

No description available.

Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target.  In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.

Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets. We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies. A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate. Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies. The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed.  Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.

Le canal Kv11.1, dont l’inhibition occasionne une prolongation de l’intervalle QT, est directement impliqué dans des cas d’effets secondaires cardiotoxiques. Depuis 2006, Santé Canada exige que les nouvelles molécules et leurs métabolites soient évalués en phase préclinique pour le risque d’allongement de l’intervalle QT. La méthode de référence évalue l’électrophysiologie des cardiomyocytes en culture lors d’une courte exposition au médicament (<30min). Bien que cette méthode soit la plus fiable actuellement, elle permet seulement d’identifier les molécules qui bloquent directement le passage des ions dans le pore du canal (effet aigu). La méthode HERG-BRET vise à identifier les molécules susceptibles d’interagir avec le canal Kv11.1 par le moyen d’une altération du trafic vésiculaire (effet chronique). Ce type d’interaction est considéré comme un biomarqueur de la capacité à bloquer l’activité de ce canal. L’étude présentée tente de déterminer si un test de localisation cellulaire de hERG basé sur le BRET permettra un criblage à haut débit et une meilleure évaluation de l’affinité d’interaction avec hERG, comparativement aux méthodes alternatives actuelles. Dans le modèle HERG-BRET, la protéine hERG fusionnée à la luciférase de renilla (donneur d’énergie) est exprimée dans une lignée cellulaire HEK293. Cette même lignée exprime également une protéine verte fluorescente modifiée (accepteur d’énergie) qui est ancrée à la membrane plasmique. L’échange d’énergie entre le donneur et l’accepteur est un indice de la localisation de hERG à la membrane plasmique. Les fluctuations de ratio BRET suite à une exposition de 16h à un composé pharmaceutique reflètent donc l’effet du composé sur la translocation de Kv11.1. Vingt-cinq composés pharmaceutiques déjà caractérisés dans la littérature scientifique ont été testés : 12 ont été classés comme chaperons pharmacologiques, 4 comme inhibiteurs du trafic, 1 comme inhibiteur ayant les deux effets mentionnés et 8 n’ont pas pu être classés. Le comportement du biosenseur à l’égard des composés testés suggère que la méthode HERG-BRET ne peut pas être utilisée seule pour évaluer le risque cardiotoxique des médicaments. Toutefois, elle peut fournir des informations complémentaires pertinentes quand à la nature de l’interaction entre un composé pharmaceutique et la sous unité hERG du canal Kv11.1. / The Kv11.1 channel is directly involved in cardiotoxic adverse effects since its inhibition is responsible for a prolongation of the QT interval. In 2006, Health Canada established a guideline that constrains drug developers to a preclinical evaluation of QT prolongation risks for new molecules and their metabolites. The gold standard method (patch-clamp) consists in electrophysiology measurements on cultured cardiomyocytes for a brief exposition to the tested compound (<30min). Even though this method is the most reliable, it only allows the identification of molecules that inhibit the channel by preventing ions from traveling through the pore (acute effect). The HERG-BRET method aims to identify molecules that can interact with Kv11.1 and alter its vesicular transport as a proxy for inhibiting the activity of the channel (chronic effects). This study attemps to determine if a BRET-based cellular localization assay will allow a high throughput screening and a better evaluation of the affinity of pharmaceuticals compounds with hERG, in comparison to alternative methods. In the HERG-BRET model, a fusion protein generated with the gene sequence for hERG and the one for the renilla luciferase (energy donor) is stably expressed in a HEK 293 cell line. The same cell line also stably expresses a green fluorescent protein (energy acceptor) that is anchored at the plasma membrane. The energy transfer that occurs between the donor and the acceptor suggests that hERG is located at the membrane. Variations of BRET ratios following a 16 hours inucabtion with a compound reflects the compound’s effects on Kv11.1’s translocation. Twenty-five compounds that have been previously characterized in the literature were tested: 12 were categorized as pharmacological chaperones, 4 as traffic inhibitors, 1 as an inhibitor that undergoes both effects and 8 remain uncategorized. The biosensor’s behavior towards the tested compounds suggests that the HERG-BRET method cannot be used alone to assess cardiotoxic liability, but it can bring interesting facts to our attention regarding the nature of the interaction between the hERG subunits of Kv11.1 and a tested compound.

Les azacycles tels que les morpholines ou les pyrrolidines, sont très répandus dans le domaine de l’organocatalyse et de la chimie médicinale. Cette thèse traitera d’analogues contraints de ces azacycles, qui peuvent moduler de par leurs structures, les propriétés de certains médicaments ou la sélectivité de certaines réactions. Le cas de l’halopéridol, qui est connu pour son activité sur les récepteurs dopaminergiques D2 et D4, est au centre de la première partie de cette thèse, dans laquelle de nouveaux analogues contraints de type 2-oxa-5-azabicyclo[2.2.2]octane ont été développés pour pallier ses problèmes de stabilité métabolique. Dans une seconde partie, la synthèse de deux nouvelles chimères morpholine-proline pontées est rapportée. Leurs structures rigides et conformationnellement verrouillées permettent aux doublets d’électrons non liants sur les atomes d'azote et d'oxygène d’être respectivement orientés dans des directions « Est-Ouest » et « Nord-Est » spatialement différentes. En combinaison avec la présence d'un acide carboxylique, les propriétés électroniques de ces composés peuvent être utiles dans le contexte de la conception peptidomimétique de composés biologiquement pertinents. Des estimations quantitatives de la basicité des atomes d'azote ont été obtenues en utilisant une analyse DFT conceptuelle. Dans la troisième partie de cette thèse, la synthèse de nouvelles pyrrolidines oxabicycliques sera développée. Les cyclopentan[c]pyrroles sont très répandus dans la littérature, et connus pour leurs propriétés analgésiques. Des dérivés fonctionnalisés en positions 4 et 5, synthétisés par Servier, ont notamment présenté de bonnes activités en tant que ligands nicotiniques 7, mais aussi des problèmes d’inhibition de hERG. Afin d’obtenir des composés moins lipophiles et donc de pallier les problèmes d’inhibition hERG, de nouveaux analogues oxygénés de type furo[2,3-c]pyrroles ont été développés par différentes voies de synthèse. Ces nouveaux composés pourront notamment être obtenus sous formes énantiomériquement enrichies, grâce à une étape clé de résolution enzymatique. La proline a été largement utilisée ces dernières années comme organocatalyseur au sein d’importantes transformations asymétriques comme les aldolisations ou les additions de Michael. Cependant, malgré le succès de ce motif, plusieurs de ses dérivés ont été rapportés dans la littérature. C’est notamment le cas des 4,5-méthanoprolines qui furent rapportées pour la première fois par Hanessian en 1997, dont l’efficacité en tant qu’organocatalyseur pour la réaction de Hajos-Parrish ainsi que plusieurs autres types de réaction fut par la suite établie. Les dernières parties de cette thèse viennent compléter ces études. La synthèse de nouvelles 4,5-ethanoprolines a été développée, ainsi que leurs utilisations comme catalyseur lors de réactions de Hajos-Parrish et d’addition catalytique asymétrique de nitroalcanes sur des énones cycliques. Une étude DFT a été effectuée afin d’expliquer l’inversion de sélectivité observée pour ces nouveaux catalyseurs lors des réactions de Hajos-Parrish, le mécanisme de formation des énamines réactives a aussi été investigué. / Azacycles such as morpholines and pyrrolidines, are very widespread in chemistry, especially in the fields of organocatalysis and medicinal chemistry. This thesis will deal with constrained analogues of those azacycles, which, depending on their structures, can modulate the properties of certain drugs or the selectivity of certain reactions. The case of haloperidol, which is known for its activity on the dopamine D2 and D4 receptors, is at the center of the first part of this thesis, in which new constrained analogs of the 2-oxa-5-azabicyclo type [2.2.2] octane have been developed to overcome its metabolic stability problems. In a second part, the synthesis of two new bridged morpholine-proline chimeras are reported. Their rigid structures allow the lone pairs on the nitrogen and oxygen atoms to be oriented in spatially different "East-West" and "North-East" directions, respectively. In combination with the presence of a carboxylic acid, the electronic properties of these compounds could be useful in the context of the design of biologically relevant peptidomimetics. Quantitative estimations of the basicity of the nitrogen atoms were obtained using DFT analysis. In the third part of this thesis, the synthesis of new oxabicyclic pyrrolidines is described. Cyclopentan[c]pyrroles are widely encountered and known for their analgesic properties. The Servier laboratories have synthesized derivatives with substituents at positions 4 and 5, exhibiting good activities as 7 nicotinic ligands, but problems of hERG inhibition. In order to obtain less lipophilic compounds and therefore overcome the problems of hERG inhibition, new oxygenated analogs of the furo[2,3-c]pyrrole type have been developed by different synthetic routes. These new compounds were obtained in enantiomerically enriched forms, using enzymatic resolution. Proline has been widely used in recent years as an organocatalyst in asymmetric transformations such as aldolizations or Michael additions The success of this motif, has inspired synthesis of derivatives, such as 4,5-methanoprolines, which were first reported by Hanessian in 1997, and shown to be effective as organocatalysts in the Hajos-Parrish and other reactions. The last parts of this thesis develop further these studies by the synthesis of new 4,5-ethanoprolines which act as a catalysts in the Hajos-Parrish reaction and the asymmetric catalytic addition of nitroalkanes to cyclic enones. A DFT study was carried out to explain the reversal of selectivity observed for the new catalysts in Hajos-Parrish reaction and to investigate formation of a reactive enamine in the mechanism.