Compartmentalisation and metabolism are two universal features observed among all living organisms. Their emergence and harmonious functioning are considered critical for the emergence of life. In an attempt to understand the chemical processes that may have resulted in the emergence of life, origin(s)-of-life researchers have investigated 1. possible mechanisms of prebiotic compartmentalisation and 2. plausible protometabolic reactions as precursors to metabolic chemistry. Historically, these two aspects of origin(s)-of-life research have been investigated in isolation. However, there is a growing consensus regarding the necessity of investigating prebiotic compartmentalisation and protometabolic reactions in tandem. Prebiotic compartmentalisation via formation of lipid vesicles have long been regarded as a general route for protocell formation. However, modern views on protocell formation suggest that such structures might be insufficient, in the absence of specialised transport proteins, to efficiently create suitable environments for sustaining out-of-equilibrium reactions, necessary for the emergence of life. This, coupled with the discovery of membrane-less organelles, formed through liquid-liquid phase separation (LLPS) in modern cells, and their ever increasingly identified roles in biology, has sparked renewed interest among origin(s)-of-life researchers in the synergy between prebiotic reactions and Oparin’s hypothesis of prebiotic compartmentalisation via coacervation. To date, most of the work, investigating the effect of coacervation on chemical reactions, have focused on biochemical reactions catalysed by complex biomolecules such as proteinaceous enzymes and ribozymes. Moreover, historically, the phenomenon of complex coacervation has primarily been associated with long-chain polymers. However, recent demonstrations of complex coacervation among several prebiotically relevant metabolites necessitates the need for developing experimental strategies that can comprehensively investigate complex coacervation, in terms of phase diagrams, involving such prebiotically relevant metabolites. Such understanding is essential to enhance the design of experiments that aim to combine protometabolic reactions and complex coacervation. To this end, the research presented in this thesis, at first, demonstrates a highthroughput screening methodology for complex coacervate formation, in chapter 2, using automated liquid handling strategies and random forest classifier machine learning algorithm based classification of bright-field microscopy images. This methodology has then been utilised to obtain the conditions in which oxidised and reduced nicotineamide adenine dinucleotide (NAD+ and NADH) form coacervate with 50-mer poly-lysine and poly-arginine. Further, the precipitation properties of 50-mer poly-arginine in sodium bicarbonate solution have been investigated. In chapter 3, incorporation of complex coacervation in three different protometabolic reactions in three different ways have been exhibited. In “Protometabolic NAD+ reduction using pyruvate”, NADH, which is the product of the reaction, participates in coacervation with 50-mer poly-arginine. In “Coenzyme A catalysed peptide ligation”, the catalyst of the reaction, coenzyme A contributes to coacervation with 10-mer polyarginine. In “Heme catalysed oxidation of Amplex Red”, the coacervate is formed form polymers, such as carboxymethyl dextran and poly-diallyldimethylammonium, that are not reactants, products or catalyst of the studied reaction. It has been further shown that the incorporation of coacervation, to “Protometabolic NAD+ reduction using pyruvate”, results in the enhancement of NADH formation by 2.5 times in comparison to the amount of NADH produced in the absence of any poly-cations. Preliminary results also suggest that the presence of coacervation resulted in the suppression of both “Coenzyme A catalysed peptide ligation” and “Heme catalysed oxidation of Amplex Red”. This study elucidates an unprecedented methodology for screening of coacervate formation as well as highlighting the various ways in which coacervation of prebiotically relevant metabolites can be embedded into protometabolic reactions. Further, this study also sheds light on the influence of coacervation on protometabolic reactions, revealing patterns that were previously primarily observed in biochemical reactions catalysed by enzymes (or ribozymes).

The drug development process is lengthy and expensive, with a 90% failure rate among drugs entering clinical trials due to the inadequacy of predictive models in the initial phases of drug development. To overcome these limitations, there is a paradigm shift towards developing micro physiological systems often referred as Organ-on-a-Chip that have be shown to recapitulate organ level functions in vitro. However, despite their promise, these systems often have limited throughput, restricting their widespread use in the drug development process. The work outlined in this thesis aims to bridge this gap by integrating the physiological relevance offered by micro physiological systems with the high throughput capabilities of traditional 2D multi-well plate cultures. The thesis outlines the development of two novel micro physiological systems, engineered in a high throughput multi-well format called the IFlowPlate and AngioPlate. Both the platforms have an open-top design and unlike tradition microphysiological platforms does not need complex pump systems and have built-in connections to achieve perfusion making it more scalable and user-friendly. The IFlowPlate leverages the self-assembly capability of endothelial cells to create a perfusable vascular network. This platform technology was utilized in this work to achieve intravascular perfusion of colon organoids for the first time and demonstrated immune cell circulation and recruitment in response to injury. AngioPlate, the other platform that was developed as a part of this work, utilizes a pre-patterned scaffold completely embedded in native hydrogel matrix to guide cells in forming organ-specific geometries and tubular structures using a novel subtractive manufacturing technique. This platform allowed for fabricating complex and intricate networks to model vascularized terminal lung alveoli and renal proximal tubules. This work demonstrated for the first time that highly complex perfusable tissues embedded in hydrogel can be integrated with multi-well plates to mimic tissue specific structures and interfaces without the use of synthetic membranes or plastic channels. The built-in perfusion channel and the flexible hydrogel matrix allowed for the terminal lung alveoli model to be mechanically actuated to mimic breathing motions. The renal proximal tubule model was used to mimic glucose reabsorption in kidney and model renal inflammation. The latter part of this work focusses on further improving this platform to increase platform robustness and to allow for incorporating supporting cells such as fibroblasts into the hydrogel matrix. This allowed us to model tubular injuries in kidney such as cisplatin induced -nephrotoxicity and TGF- β1 induced- tubulointerstitial fibrosis. Furthermore this work also describes the development of a high-throughput TEER meter that can be integrated with the AngioPlate platform allowing for rapid, non-invasive measurement of renal epithelial barrier integrity. Given that both platforms are designed in a 384-well plate format, they are high throughput and compatible with existing technologies like high-content imaging systems, robotic liquid handling systems, and microplate readers allowing for widespread adoption across diverse research settings. It is anticipated that the contributions described in this work will significantly advance our understanding of disease propagation and accelerate drug development process. / Thesis / Candidate in Philosophy / Drug development is a complex and expensive process, often hindered by a high failure rate in clinical trials. This failure is partly due to the inadequacy of current predictive models in the early stages of development. To address this, researchers are turning to innovative microphysiological systems known as Organ-on-a-Chip, which mimic organ structure and functions in the lab. However, these systems have been limited in their use due to low throughput. To overcome this limitation, microphysiological systems in multi-well formats called the IFlowPlate and AngioPlate were developed through the works outlined in this thesis. These platforms are designed to be high-throughput, scalable, user-friendly, and are compatible with existing technologies, such as microplate readers, high-content imaging systems and robotic liquid handlers, making them accessible to a wide range of researchers. By combining the physiological relevance of microphysiological systems with the high-throughput capabilities, these platforms aim to transform the way we study diseases and test drugs.

Acetylcholinesterase (AChE) is an essential enzyme with an evolutionary conserved function: to terminate nerve signaling by rapid hydrolysis of the neurotransmitter acetylcholine. AChE is an important target for insecticides. Vector control by the use of insecticide-based interventions is today the main strategy for controlling mosquito-borne diseases that affect millions of people each year. However, the efficiency of many insecticides is challenged by resistant mosquito populations, lack of selectivity and off-target toxicity of currently used compounds. New selective and resistance-breaking insecticides are needed for an efficient vector control also in the future. In the work presented in this thesis, we have combined structural biology, biochemistry and medicinal chemistry to characterize mosquito AChEs and to develop selective and resistance-breaking inhibitors of this essential enzyme from two disease-transmitting mosquitoes.We have identified small but important structural and functional differences between AChE from mosquitoes and AChE from vertebrates. The significance of these differences was emphasized by a high throughput screening campaign, which made it evident that the evolutionary distant AChEs display significant differences in their molecular recognition. These findings were exploited in the design of new inhibitors. Rationally designed and developed thiourea- and phenoxyacetamide-based non-covalent inhibitors displayed high potency on both wild type and insecticide insensitive AChE from mosquitoes. The best inhibitors showed over 100-fold stronger inhibition of mosquito than human AChE, and proved insecticide potential as they killed both adult and larvae mosquitoes.We show that mosquito and human AChE have different molecular recognition and that non-covalent selective inhibition of AChE from mosquitoes is possible. We also demonstrate that inhibitors can combine selectivity with sub-micromolar potency for insecticide resistant AChE.

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are defined by neurodegeneration and accumulations of misfolded proteins that spread through the brain in a well characterized manner. In AD these accumulations consist mainly of β-amyloid (Aβ) and tau, while in PD, α-synuclein (α-syn) make up the characteristic lewy pathology.     The general aim of this thesis was to investigate mechanisms associated with neurotoxic peptide activity by Aβ, tau and α-syn in relation to cellular degradation and transfer with a cell-to-cell transfer model system.    We found that intercellular transfer of oligomeric Aβ occurs independently of isoform. However, the amount of transfer correlates with each isoforms ability to resist degradation or cellular clearance. The Aβ1-42 isoform showed particular resistance to clearance, which resulted in higher levels of cell-to-cell transfer of the isoform and lysosomal stress caused by accumulation.    As Aβ accumulations can inhibit the proteasomal degradation we investigated how reduced proteasomal degradation affected neuron-like cells. We found increased levels of phosphorylated tau protein, disturbed microtubule stability and impaired neuritic transport after reduced proteasomal activity. These changes was partly linked to c-Jun and ERK 1/2 kinase activity.    We could also show that α-syn transferred from cell-to-cell in our model system, with a higher degree of transfer for the larger oligomer and fibrillar species. Similar to Aβ, α-syn mainly colocalized with lysosomes, before and after transfer.     Lastly, we have developed our cell-to-cell transfer system into a model suitable for high throughput screening (HTS). The type of cells have been upgraded from SH-SY5Y cells to induced pluripotent stem cells (iPSCs), with a differentiation profile more similar to mature neurons. The next step will be screening a small molecular library for substances with inhibitory effect on cell-to-cell transfer of Aβ peptides.     The importance of the degradative systems in maintaining protein homeostasis and prevent toxic accumulations in general is well known. Our findings shows the importance of these systems for neurodegenerative diseases and also highlight the link between degradation and cell-to-cell transfer. To restore or enhance the degradative systems would be an interesting avenue to treat neurodegenerative diseases. Another way would be to inhibit the transfer of misfolded protein aggregates. By using the HTS model we developed, a candidate substance with good inhibitory effect on transfer can hopefully be found.

Autophagy, senescence and apoptosis are tightly linked processes which together determine the fate of cells in response to various stresses. There is ample evidence supporting the notion that senescent cells are highly dependent on autophagy and this process is here much more intensive than in nonsenescent cells. Autophagy may to some extent compensate increased energetic and metabolic demands of senescent cells and also helps with removal of toxic products such as oxidized proteins, protein aggregates and damaged organelles resulting from an overloaded metabolism of some senescent cells. In addition, some studies reported the need of autophagy for the adoption of senescent phenotype. However, there are also studies with seemingly contradictory results claiming that increased autophagy prevents or delays cellular senescence. Relationship of autophagy to apoptosis is similarly ambivalent. Whereas intact autophagy is necessary for the cell, while slightly increased autophagy still has a rather positive impact, excessive autophagy may lead to degradation of critical components necessary for cell function and survival and can trigger one of the modes of programmed cell death. In the first part of this work, we focused on the analysis of autophagic response in senescent and proliferating pancreatic...

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Ce travail traite de l’exploration de la biodiversité des Baeyer-Villiger MonoOxygénases (BVMOs) : des enzymes utilisées en biocatalyse pour la production de lactones optiquement pures à partir de cétones. Pour mettre à bien cet objectif nous avons réalisé, en association avec le Génoscope d’Evry, une sélection de plusieurs centaines d’enzymes couvrant une forte diversité génétique. Après clonage et criblage à haut débit sur plus de vingt substrats différents nous avons obtenus plus de 90 nouvelles BVMOs. Avec ce résultat nous avons triplé le nombre de BVMOs connues dans la littérature. Dans un second temps nous avons étudié l’activité de certaines de ces nouvelles enzymes sur les cétones α,β-insaturées (ou enone), Ces substrats sont peu étudiés en biocatalyse et, lors de la réaction chimique, aboutissent à la formation de nombreux sous-produits. Deux enzymes d’O.batsensis et de P. lavamentivorans se sont révélées être actives aboutissant à la production d’ene-lactone et d’enol-lactone respectivement. La conversion de certaines enones chirales a abouti à des lactones présentant un fort excès énantiomérique.Nous avons ensuite étudié la régio-sélectivité de 35 enzymes issues du criblage sur une série de cétones aliphatiques acycliques. Alors que la formation de l’ester méthylique est très rare, nous avons obtenu des résultats très variés pour la formation de l’ester éthylique allant jusqu’à 80%. Le travail de thèse s’est terminé par le développement d’une cascade enzymatique sur la production d’ester à partir d’alcool secondaire. La cascade implique deux enzymes : une Alcool Déshydrogénase et une BVMO. La cascade est à la fois fonctionnelle et est très efficace. / -

<p>Many of the biological roles of proteins are modulated through protein-ligand interactions, making proteins important targets for drug therapies and diagnostic imaging probes. The discovery of novel ligands for a protein of interest often relies on the use of high throughput screening (HTS) technologies designed to detect protein-ligand binding. The basis of one such technology is a recently reported mass spectrometry-based assay termed SUPREX (stability of unpurified proteins from rates of H/D exchange). SUPREX is a technique that uses H/D exchange and MALDI-mass spectrometry for the measurement of protein stabilities and protein-ligand binding affinities. The single-point SUPREX assay is an abbreviated form of SUPREX that is capable of detecting protein-ligand interactions in a high throughput manner by exploiting the change in protein stability that occurs upon ligand binding.</p><p>This work is focused on the development and application of high throughput SUPREX protocols for the detection of protein-ligand binding. The first step in this process was to explore the scope of SUPREX for the analysis of non-two-state proteins to determine whether this large subset of proteins would be amenable to SUPREX analyses. Studies conducted on two model proteins, Bcl-xL and alanine:glyoxylate aminotransferase, indicate that SUPREX can be used to detect and quantify the strength of protein-ligand binding interactions in non-two-state proteins.</p><p>The throughput and efficiency of a high throughput SUPREX protocol (i.e., single-point SUPREX) was also evaluated in this work. As part of this evaluation, cyclophilin A, a protein target of diagnostic and therapeutic significance, was screened against the 880-member Prestwick Chemical Library to identify novel ligands that might be useful as therapeutics or imaging agents for lung cancer. This screening not only established the analytical parameters of the assay, but it revealed a limitation of the technique: the efficiency of the assay is highly dependent on the precision of each mass measurement, which generally decreases as protein size increases. </p><p>To overcome this limitation and improve the efficiency and generality of the assay, a new SUPREX protocol was developed that incorporated a protease digestion step into the single-point SUPREX protocol. This new protocol was tested on two model proteins, cyclophilin A and alanine:glyoxylate aminotransferase, and was found to result in a significant improvement in the efficiency of the SUPREX assay in HTS applications. This body of work resulted in advancements in the use of SUPREX for high throughput applications and laid the groundwork for future HTS campaigns on target proteins of medical significance.</p> / Dissertation

Type-1 diabetes is caused by the autoimmune destruction of insulin-producing beta cells in the pancreas. Beta-cell apoptosis involves a complex set of signaling cascades initiated by \(interleukin-1\beta (IL-1\beta)\), \(interferon-\gamma (IFN-\gamma)\), and \(tumor necrosis factor-\alpha (TNF-\alpha)\). \(IL-1\beta\) and \(TNF-\alpha\) induce \(NF\kappa B\) expression, while \(IFN-\gamma\) induces STAT1 activation. These cytokines lead to a decrease of beta-cell function. The goal of this thesis is to identify small-molecule suppressors of cytokine-induced beta-cell apoptosis using high-throughput screening approach. Using the rat INS-1E beta-cell line, I developed an assay to measure cellular viability after 48 hours of cytokine treatment. I screened 29,760 compounds for their ability to suppress the negative effects of the cytokines. I identified several compounds to be suppressors of beta-cell apoptosis. These efforts led to the discovery of \(GSK-3\beta\) and HDAC3 as novel targets for suppressing beta-cell apoptosis. I also followed up on BRD0608, a novel suppressor that increased ATP levels and decreased caspase activity in the presence of cytokines. To follow up this compound, 35 analogs related to BRD0476 were synthesized using solid-phase synthesis and tested for their protective effects in the presence of cytokines. A structurally related analog, BRD0476, was found to be more potent and active in human islets, decreasing caspase activation and increasing insulin secretion after a 6-day treatment. I performed gene-expression profiling of INS-1E cells treated with the cytokine cocktail in the absence or presence of \(10\mu M\) BRD0476. Gene-set enrichment analysis revealed that the gene sets most significantly changed by BRD0476 involved cellular responses to \(IFN-\gamma\). I therefore assessed the effects of BRD0476 on STAT1 transcriptional activity. Cytokine treatment increased the reporter-gene luciferase activity, while co-treatment with BRD0476 reduced this activity significantly. To identify the intracellular target(s) of BRD0476, I collaborated with the Proteomics Platform in Broad Institute using SILAC (stable isotope labeling by amino acids in cell culture). SILAC is a mass spectrometry-based method to identify proteins that bind a small molecule attached to a bead. Deubiquitinase USP9X was pulled down by BRD0476. Knock-down of USP9X by siRNA phenocopied the protective effects of BRD0476. Binding assays were performed to identify interactions between BRD0476 and USP9X. / Chemistry and Chemical Biology

Enantioselective indicator displacement assays (eIDAs), was transitioned to a high-throughput screening protocols, for the rapid determination of concentration and enantioselectivity (ee) of chiral diols and α-hydroxycarboxylic acid. To improve the design of our previously established receptor based on o-(N,N-dialkylaminomethyl)arylboronate scaffolds for eIDAs. The rigidity of the receptor, which pertinent from the formation of an intramolecular N-B dative bond was investigated. o-(Pyrrolidinylmethyl)phenylboronic acid its complexes with bifunctional substrates such as catechol, [alpha]-hydroxyisobutyric acid, and hydrobenzoin was studied in detail by x-ray crystallography and ¹¹B NMR. Our structural study predicts that the formation of an N-B dative bond, and/or solvolysis to afford a tetrahedral boronate anion, depends on the solvent and the complexing substrate present. To simplify the operation of eIDAs, we introduced an analytical method, which utilize a dual-chamber quartz cuvette, which reduces the number of spectroscopic measurements from two to one and introduced artificial neural networks (ANNs) which simplifies data analysis. In a second example a high-throughtput screening protocol for hydrobenzoin was developed. The method involves the sequential utilization of what we define herein as screening, training, and analysis plates. Several enantioselective boronic-acid based receptors were screened using 96-well plates, both for their ability to discriminate the enantiomers of hydrobenzoin and to find their optimal pairing with indicators resulting in the largest optical responses. The best receptor/indicator combination was then used to train an ANN to determine concentration and ee. To prove the practicality of the developed protocol, analysis plates were created containing true unknown samples of hydrobenzoin generated by established Sharpless asymmetric dihydroxylation reactions, and the best ligand was correctly identified. The system was extended to pattern recognition for the rapid determination of identity, concentration, and ee of chiral vicinal diols. A diverse enantioselective sensor array was generated with three chiral boronic acid receptors and pH indicators. The optical response produced by the sensor array, was analyzed by two pattern recognition algorithms: principal component analysis (PCA) and ANNs. The PCA plot demonstrated good chemoselective and enantioselective separation of the analytes, and ANNs was used to accurately determine the concentration and ee of five unknown samples. / text