<strong>Chapter 1</strong> Provides an overview of drug discovery with particular emphasis on library selection and hit identification methods using virtual based approaches. <strong>Chapter 2</strong> Gives an outline of the bone morphogenetic protein (BMP) signalling pathway and literature BMP pathway modulators. The association between the regulation of BMP pathway and cardiomyogenesis is also described. <strong>Chapter 3</strong> Describes the use of ligand based virtual screening to discover small molecule activators of the BMP signalling pathway. A robust cell based BMP responsive gene activity reporter assay was developed to test the libraries of small molecules selected. Hit molecules from the screen were synthesised to validate activity. It was found that a group of known histone deacetylase (HDAC) inhibitors displayed most promising activity. These were evaluated in a secondary assay measuring the expression of two BMP pathway regulated genes, hepcidin and Id1, using reverse transcription polymerase chain reaction (RT-PCR). 188 was discovered to increase expression of both BMP-responsive genes. <strong>Chapter 4</strong> Provides an overview of existing cannabinoid receptor (CBR) modulating molecules and their connection to progression of atherosclerosis. <strong>Chapter 5</strong> Outlines the identification and optimisation of selective small molecule agonists acting at the cannabinoid 2 receptor (CB₂R). Ligand based virtual screen was undertaken and promising hits were synthesised to allow structure activity relationship (SAR) to be developed around the hit molecule providing further information of the functional groups tolerated at the active site. Subsequent studies led to the investigation and optimisation of physicochemical properties around 236 leading to the development of a suitable compound for in vivo testing. Finally, a CB₂R selective compound with favourable physicochemical properties was evaluated in vivo in a murine inflammation model and displayed reduced recruitment of monocytes to the site of inflammation.

In recent years, the potential benefits of high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking, since proteins are sophisticated structures with complicated interactions for which either molecule might reshape itself. Even the very limited flexibility model to be considered here, using ligand conformation ensembles, requires six dimensions of exploration - three translations and three rotations - per rigid conformation. The functions for evaluating pose suitability can also be complex to calculate. Consequently, the programs being written for these biochemical simulations are extremely resource-intensive. This work introduces a pure computer science approach to the field, developing techniques to improve the effectiveness of such tools. Their architecture is generalized to an abstract pattern of nested layers for discussion, covering scoring functions, search methods, and screening overall. Based on this, new stratagems for molecular docking software design are described, including lazy or partial evaluation, geometric analysis, and parallel processing implementation. In addition, a range of novel algorithms are presented for applications such as active site detection with linear complexity (PIES) and small molecule shape description (PASTRY) for pre-alignment of ligands. The various stratagems are assessed individually and in combination, using several modified versions of an existing docking program, to demonstrate their benefit to virtual screening in practical contexts. In particular, the importance of appropriate precision in calculations is highlighted.

Le virus de l’hépatite C (VHC) est un agent causateur de maladies du foie important responsable d’une pandémie affectant près de 180 millions d’individus mondialement. L’absence de symptômes dans les premières années d’infection entraîne des diagnostics tardifs qui empêchent la prise en charge rapide des patients avant l’apparition d’une fibrose et, dans près de 16 % des cas d’infection, d’une cirrhose. En exploitant les interactions protéine-protéine membranaires, des essais utilisant la technologie BRET, dans les cellules vivantes, ont été précédemment optimisés afin d’établir le réseau complet des interactions du VHC. En utilisant les fondements de cette étude, un essai à haut débit dans les cellules vivantes a été réalisé pour identifier de nouveaux composés anti-VHC ciblant une nouvelle interaction NS3/4A-NS3/4A. Approximativement 110,000 petites molécules ont été criblées pour leurs effets sur l’homodimérization de NS3/4A et ont été classées par rapport à leur spécificité et à leur puissance contre le VHC. Au terme de cette étude, UM42811 a été identifié comme un activateur potentiel de l’interaction NS3/4A-NS3/4A offrant une activité antivirale prometteuse dotant une excellente fenêtre thérapeutique. Par la suite, un séquençage exhaustif des virus, soumis à un traitement de UM42811, a permis d’établir le profil de résistance du VHC contre ce composé. Grâce à cette fine cartographie, il a été possible d’identifier un nouveau mécanisme d’inhibition de NS3/4A qui est indépendant de son activité protéase. En utilisant les données de notre groupe sur les interactions VHC-hôte, il a été possible de continuer la caractérisation fonctionnelle du composé UM42811 en étudiant son effet sur les interactions potentiellement bénéfiques à la persistance virale. Pour ce faire, les protéines associées au transport nucléaire et mitochondriale qui sont des interactants de choix de NS3/4A ont été priorisées. Parmi ces facteurs de l’hôte, l’étude de karyopherin subunit beta 1 (KPNB1) et de heat shock protein 60 (HSP60) a été priorisée. De façon intéressante, les expériences de co-immunoprécipitation ont démontré que UM42811 était capable de prévenir l’interaction KPNB1-NS3/4A ainsi que l’interaction HSP60-NS3/4A. De plus, les études ii fonctionnelles et les analyses d’immunobuvardage de type western ont démontré que l’interaction KPNB1-NS3/4A avait des effets délétères sur l’induction des gènes stimulés par l’interféron (ISG). Finalement, il a été démontré que KPNB1 est possiblement clivé par NS3/4A suggérant la présence potentielle d’un mécanisme de subversion ou d’échappement. En bref, cette étude démontre la puissance des stratégies impliquant les interactions protéine-protéine dans les cellules vivantes pour l’identification de nouveaux composés inhibiteurs, caractérise un nouveau mécanisme d’inhibition anti-VHC et révèle la possibilité d’un nouveau mécanisme d’évasion du système immunitaire. / Hepatitis C virus (HCV) is an important causative agent for liver diseases and is responsible for a worldwide pandemic affecting roughly 180 million individuals worldwide. Late diagnosis following the progression to fibrosis and to cirrhosis, in nearly 16% of chronic infections, is attributed to the absence of symptoms in the first years of infection. By exploiting membrane protein-protein interactions (PPI), live cell assays using bioluminescence resonance energy transfer (BRET) technology have previously been optimized to complete a comprehensive hepatitis C virus (HCV) protein interaction network. Using the groundwork laid by this network study, a high-throughput assay (HTS) cell-based assay was implemented to identify novel inhibitory compounds targeting an unreported NS3/4A-NS3/4A interaction. Approximately 110,000 compounds from a small-molecule collection were screened to monitor modulation of NS3/4A homodimerization and were discriminated based on specificity and potency. UM42811 was identified as a potential NS3/4A-NS3/4A interaction activator and found to have a promising antiviral activity boasting an excellent therapeutic window. Combined deep sequencing and mutation mapping have yielded a resistance profile based on statistical and functional probability pointing towards a novel inhibitory mechanism targeting the HCV NS3/4A independent from protease activity inhibition. Data from an HCV to host protein interaction network generated by our group was used to analyze alternative effects of UM42811 on interactions which potentially benefit viral persistence. NS3/4A-specific host interactors were heavily associated with nuclear and mitochondrial transport based on Gene Ontology (GO). Among these specific interactors, karyopherin subunit beta 1 (KPNB1) and heat shock protein 60 (HSP60) were selected for further study. Interestingly, co-immunoprecipitation experiments revealed that UM42811 was able to prevent both KPNB1-NS3/4A and HSP60-NS3/4A interactions. Moreover, functional and western analysis revealed the KPNB1-NS3/4A interaction to have deleterious effects on iv interferon stimulated gene (ISG) induction. Unexpectedly, analysis revealed a putative NS3/4A mediated cleavage of KPNB1. Overall, this study demonstrates the strength of cell-based PPI strategies in the identification of novel HCV antiviral compounds, characterizes a novel inhibitory mechanism for HCV and reveals a potentially novel viral immune evasion mechanism.

Confronted with the global demographic changes and the increasing pressure on modern healthcare system, there has been a surge of developing new technology platforms in the past decades. Droplet microfluidics is a prominent example of such technology platforms, which offers an efficient format for massively parallelized screening of a large number of samples and holds great promise to boost the throughput and reduce the costs of modern biomedical activities. Despite recent achievements, the realization of a compact and generic screening system which is suited for resource-limited settings and point-of-care applications remains elusive. To address the above challenges, the dissertation focuses on the development of a compact multifunctional droplet micro-magnetofluidic system by exploring the advantages of magnetic in-flow detection principles. The methodologies behind a novel technique for biomedical applications, namely, magnetic in-flow cytometry have been put forth, which encompass magnetic indexing schemes, quantitative multiparametric analytics and magnetically-activated sorting. A magnetic indexing scheme is introduced and intrinsic to the magnetofluidic system. Two parameters characteristic of the magnetic signal when detecting magnetically functionalized objects, i.e. signal amplitude and peak width, providing information which is necessary to perform quantitative analysis in the spirit of optical cytometry has been proposed and realized. Magnetically-activated sorting is demonstrated to actively select individual droplets or to purify a population of droplets of interest. Together with the magnetic indexing scheme and multiparametric analytic technique, this functionality synergistically enables controlled synthesis, quality administration and screening of encoded magnetic microcarriers, which is crucial for the practical realization of magnetic suspension arrays technologies. Furthermore, to satisfy the needs of cost-efficient fabrication and high-volume delivery, an approach to fabricate magnetofluidic devices on flexible foils is demonstrated. The resultant device retains high performance of its rigid counterpart and exhibits excellent mechanical properties, which promises long-term stability in practical applications.

Animal testing is still the common method to test the efficacy of new drugs, but tissue engineered in vitro models are becoming more acceptable for replacing and reducing animal testing in anti-cancer drug screening by developing in vitro three-dimensional (3D) tumour models for anti-cancer drug testing. In this study, three-dimensional (3D) culture methods were developed to mimic the tumour microenvironment. 3D culturing is to seed, maintain and expand cultured cells in three-dimensional space, in contrast to the traditional two-dimensional (2D) method in which the cells attach to the bottom of culture containers as monolayers. To mimic the intercellular interplay for tumour study, cell co-culture was applied. In this thesis, perfusion culture showed a better homeostasis for 3D tumour model growth over 17 days, with a more controllable working platform and a more reliable response-dose correlation for data interpretation. In the Matrigel sandwich system, the co-culture of breast cancer cells and endothelial cells demonstrated the morphology featuring a vascular network and tumour structures, with the thickness of the three-dimensional structure around 100µm and tubule length 200-400 µm, and maintained for 10 days. The comparisons studies between Matrigel sandwich and other methods suggest that though not fully characterised, Matrigel is still a valuable scaffold choice for developing co-culture 3D tumour model. Finally, the combination of perfusion and co-culture showed the potential of applying this model in angiogenesis assay, with a drug response profile combining cell viability and morphology to mimic in vivo tumour physiology.

A major therapeutic challenge in musculoskeletal regenerative medicine is how to effectively replenish bone tissue lost due to pathological conditions such as fracture, osteoporosis, or rheumatoid arthritis. Mesenchymal stem cells are currently investigated for applications in bone-tissue engineering and human bone marrow-derived mesenchymal stem cells (hMSCs) could be a promising source for generation of tissue-engineered bone. However, the therapeutic potential of MSCs has not been fully exploited due to a lack of knowledge regarding the identity, nature, and differentiation of hMSCs. Epigenetic mechanisms regulating the chromatin structure as well as specific gene transcription are crucial in determination of stem cell differentiation. With the aim to systematically identify epigenetic factors that modulate MSC differentiation, the work in this thesis encompasses an approach to identify epigenetic mechanisms underlying, initiating, and promoting osteoblast differentiation, and the investigation of individual epigenetic modulators. Various osteogenic inducers were validated for differentiation of MSCs and an assay allowing assessment of differentiation outcome was developed. This assay was subsequently employed in knockdown experiments with lentiviral short hairpin RNAs and inhibitor screens with small molecules targeting putative druggable epigenetic modulator classes. This approach identified around 100 epigenetic modulator candidates involved in osteoblast differentiation, of these candidates approximately 2/3 downregulated and 1/3 upregulated alkaline phosphatase (ALP) activity. Serving as a proof-of-concept, orthogonal validation experiments employing locked nucleic acid (LNA) knockdown were performed to validate a subset of candidates. Two identified target genes were selected for further investigation. Bromodomain-containing protein 4 (BRD4) was identified as one component of epigenetic regulation; its inhibition led to a decrease in ALP expression, downregulation of key osteoblast transcription factors Runx2 and Osterix, as well as impaired bone matrix formation. Knockdown of lysine (K)-specific demethylase 1A (KDM1A/LSD1) upregulated ALP activity and treatment with a small molecule inhibitor targeting KDM1A led to an increase in ALP, RUNX2, and bone sialoprotein expression. Intriguingly, in a transgenic mouse model overexpressing Kdm1a a decrease in bone volume and bone mineral density was observed, thus supporting the hypothesis that KDM1A is a central regulator of osteoblast differentiation.

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand. / Human dihydrofolate reductase (hDHFR) is an essential enzyme for cellular proliferation and it has long been the target of antifolate drugs for the treatment of various types of cancer. Despite the clinical effectiveness of current antifolate treatments, new drugs are required to reduce the side-effects associated with their use. An essential requirement for design of new antifolates is a better understanding of how these drugs interact with their targets. We applied directed evolution to identify mutant hDHFR variants with modified binding to some clinically relevant antifolates. A saturation mutagenesis approach was used to create genetic diversity at active-site residues of hDHFR and a new, efficient screening strategy was developed to identify the amino acids that preserved native activity and/or conferred antifolate resistance. The screening method consists in a high-throughput first-tier bacterial selection coupled with a second-tier in vitro assay that allows for rapid detection of the best variants among the leads, according to user-defined parameters. Many active, antifolate-resistant mutants of hDHFR were identified. Moreover, the approach has proven efficient in rapidly assessing kinetic (kcat) and inhibition parameters of the hDHFR variants (IC50). Structure-function relationship analysis based on kinetic investigation, available structural and functional data as well as modeling were performed. By monitoring which mutations have the greatest effect on binding, we have begun to build a molecular picture of the contacts involved in drug binding. By varying the drugs we test against, we gain a better understanding of the specific binding properties that determine ligand discrimination.

This thesis further delineates the molecular genetic basis of a relatively common craniofacial condition, coronal craniosynostosis. It used whole-exome sequencing to identify novel disease genes in patients with non-syndromic coronal synostosis and negative genetic testing. Initially, 2 patients were identified with damaging, frameshift mutations in a gene not previously linked with craniosynostosis – Transcription Factor 12 (TCF12). A further intronic mutation was identified in a third patient. This gene encodes a transcription factor that dimerises with TWIST1, mutations of which cause Saethre-Chotzen syndrome, also associated with coronal synostosis. Screening 344 undiagnosed patients identified 35 further mutations, all with coronal synostosis with 14 cases arising de novo. This work was published and testing for TCF12-related craniosynostosis was translated clinically. Significant non-penetrance (60%) was identified in mutation-positive relatives and the genetic background was investigated. Firstly, analysis of parental origins of de novo mutations identified 6 of paternal origin and helped refine haplotype assignment. Secondly, haplotype analysis of TCF12-mutation carriers revealed modest correlation with phenotypic status, but this was insufficient to be useful in clinical testing. Thirdly, TCF12 haplotypes were analysed for association with non-syndromic coronal synostosis, but no significant association was found. Further exome sequencing revealed a de novo frameshift mutation in Transcription Factor 20 (TCF20) in a patient with coronal synostosis and autism, although the mutation only correlated with the latter phenotype. Analysis of 5 trios revealed a novel variant in myosin heavy chain 4 (MYH4) in 1 family, although its role in suture development is uncertain. Reviewing pooled exome data from 19 mutation-negative patients revealed no further disease genes. In summary, this thesis describes novel gene discovery, defines a new clinical entity and investigates genetic background of penetrant and non-penetrant individuals. Further exome sequencing identified another disease gene, a de novo mutation and compiled lists of damaging variants to allow future work.

No description available.

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand. / Human dihydrofolate reductase (hDHFR) is an essential enzyme for cellular proliferation and it has long been the target of antifolate drugs for the treatment of various types of cancer. Despite the clinical effectiveness of current antifolate treatments, new drugs are required to reduce the side-effects associated with their use. An essential requirement for design of new antifolates is a better understanding of how these drugs interact with their targets. We applied directed evolution to identify mutant hDHFR variants with modified binding to some clinically relevant antifolates. A saturation mutagenesis approach was used to create genetic diversity at active-site residues of hDHFR and a new, efficient screening strategy was developed to identify the amino acids that preserved native activity and/or conferred antifolate resistance. The screening method consists in a high-throughput first-tier bacterial selection coupled with a second-tier in vitro assay that allows for rapid detection of the best variants among the leads, according to user-defined parameters. Many active, antifolate-resistant mutants of hDHFR were identified. Moreover, the approach has proven efficient in rapidly assessing kinetic (kcat) and inhibition parameters of the hDHFR variants (IC50). Structure-function relationship analysis based on kinetic investigation, available structural and functional data as well as modeling were performed. By monitoring which mutations have the greatest effect on binding, we have begun to build a molecular picture of the contacts involved in drug binding. By varying the drugs we test against, we gain a better understanding of the specific binding properties that determine ligand discrimination.