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1
Wuitschik, Georg. "Oxetanes in drug discovery /." Zürich : ETH, 2008. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=17929.
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Herzberg, Benjamin. "Fluorous Drug-Affinity Proteomics for Cancer Drug Discovery." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:15821582.
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Identifying the intracellular targets of small molecules – target ID – is a major problem in chemical biology with broad application to the discovery and development of novel therapies. Traditional target ID studies have relied on drug-affinity chromatography to separate biological mixtures combined with mass spectrometry shotgun sequencing for peptide identification. This workflow is limited, however, by low specificity for unique peptides, high demand for cellular material, unknown depth of profiling, and other problems. To address these problems, we explore and describe here a novel strategy for cell lysis and drug-affinity that we call “fluorous proteomics.” By conjugating a small molecule to a perfluorinated alkane, we hypothesized that we could achieve superior recovery, specificity, and identification, allowing us to identify previously unknown drug targets with drug-affinity methods. We establish the conditions for fluorous proteomics and synthesize fluorinated probes for two drugs as a proof-of-concept. Lenalidomide, a derivative of thalidomide with unknown intracellular targets but widespread clinical use, is investigated and novel binders are identified. A particular derivative, 5HPP33, is singled out for potential future drug development. JQ1, an inhibitor of BET bromodomains in development as a treatment for hematological malignancies, is used to compare biotinylated versus fluorous tags and to identify new binders of possible therapeutic relevance. We conclude that fluorous proteomics retains high potential as an alternative to traditional drug-affinity chromatography strategies and may aid in target ID going forward, but is not without complications.
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Williams, Kevin. "Active Learning for drug discovery." Thesis, Aberystwyth University, 2014. http://hdl.handle.net/2160/eaf6e66e-17fe-41a9-ac1d-9939abbb8331.
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This thesis describes work conducted to enable Robot Scientist Eve to autonomously evaluate drug-like chemicals during high throughput experiments. Eve tests libraries of chemical compounds against yeast-based targets expressing parasite and host (human) proteins (i.e. DHFR, NMT & PGK); the parasites included in this study are responsible for an array of neglected tropical diseases. The raw data for yeast growth curves from an initial screen were evaluated, and decision tree rules were constructed to describe the relative activity and toxicity of compounds. These rules were verified, and versions were subsequently developed for application to routine mass and confirmation screens. Consequently, many potential lead drug-like candidates have been identified in the Maybridge Hitfinder library; several compounds from an approved drug library (the Johns Hopkins Clinical Compound Library) have also been confirmed as exhibiting activity against these yeast-based targets. Further in vivo study of some JHCCL compounds is in progress using extracted parasite proteins; preliminary results indicate the potential for repositioning Triclosan and Tnp-470 as having anti-malarial behaviour based on their interaction with Plasmodium sp. DHFR proteins. In the second phase of the programme, a prototype Active Learning strategy was applied (active k-optimisation) to partial mass screen data as a seed; this allowed Eve to select compounds by assessing and predicting quantitative structure activity relationships (QSAR) between seed and unknown compounds. Simulations of learning and testing QSAR cycles showed that Eve would be able to select active compounds more efficiently under such a regime. Other strategies have been developed that further improve selection efficiency for active compounds, and also promote the ability to find rare category compounds. An econometric model has been developed to demonstrate the potential beneficial impact of Active Learning strategies on the execution costs for such screens.
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Bhalla, Nikhil. "Biosensors for drug discovery applications." Thesis, University of Bath, 2016. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.683538.
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This research developed a biosensor for kinase drug discovery applications. In particular it combined electronic techniques with optical techniques to understand the phosphorylation of proteins. There are two major electronic characteristics of phosphorylation that aid in its detection and subsequently biosensor development: first is the release of a proton upon phosphorylation of a protein (change in pH) and second is the addition of negative charge to the protein upon its phosphorylation. The work in this thesis reports an electrolyte–insulator–semiconductor sensing structures to detect the pH changes associated with phosphorylation and metal–insulator–semiconductor structures to detect the charge change upon phosphorylation of proteins. Major application of the developed devices would be to screen inhibitors of kinase that mediate phosphorylation of proteins. Inhibitors of kinase act as drugs to prevent or cure diseases due to the phosphorylation of proteins. With the advancements in VLSI and microfluidics technology this method can be extended into arrays for high throughput screening for discovering drugs.
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Sriram, Ranganath. "Inventory management for drug discovery." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43863.
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Thesis (S.M.)--Massachusetts Institute of Technology, Engineering Systems Division; and, (M.B.A.) -- Massachusetts Institute of Technology, Sloan School of Management; in conjunction with the Leaders for Manufacturing Program at MIT, 2008.Includes bibliographical references (p. 67-69).
This thesis documents a study carried out at the Novartis Institutes for BioMedical Research (NIBR) in Cambridge, MA. The study focused on the development of inventory management processes for laboratory consumables. The pharmaceutical R&D process is characterized by a dynamic project portfolio, which results in a great diversity of stock-keeping-units, low repeat order rates and high variability in consumption rates. These factors create significant challenges for the design of inventory management processes. We first present an assessment and diagnosis of the current state of inventory management at NIBR, using data gathered from various NIBR sites as well as other companies. We discuss underlying drivers that influence current behavior, and identify opportunities for improvement. We then develop alternative models for inventory management and compare these models along several dimensions such as stock room location & control, inventory ownership and replenishment options. We recommend the use of consolidated department level stock rooms as the most suitable option for NIBR. Detailed implementation plans are then developed and validated through a case study. We present key findings and recommendations for implementation, and discuss opportunities for future projects.
by Ranganath Sriram.
M.B.A.
S.M.
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Roberts, Rebecca Anne M. B. A. Massachusetts Institute of Technology. "Process optimization in drug discovery." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/39693.
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Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 2007.Includes bibliographical references (p. 69-70).
Novartis is one of the largest pharmaceutical companies in the world, with their research headquarters (Novartis Institutes for BioMedical Research) located in Cambridge MA. In this thesis, I explore Novartis's process for developing drugs, specifically the earlier stages of research leading to high throughput screening. During the course of a 6.5 month, on-site project, Novartis's processes were identified, data were collected and relevant literature in product development and organizational structure were surveyed. Based on the accumulation of this information, several opportunities for improvement were identified and from these, recommendations were developed and implemented. This thesis considers the improvements Novartis could see in their drug discovery process by improving communication between organizations. In particular, I suggest that the company could benefit in cycle time and quality by designing and following more robust lateral processes and by moving their communication mode closer to integrative problem solving.
(cont.) Following these recommendations, I investigated why Novartis did not already have these processes in place. I hypothesize that the main reason for this is because the research organization at Novartis is focused primarily on exploration, therefore their ability and need to coordinate has not been an area of focus. Novartis has made a very deliberate effort to design an organization that promotes novel drug discovery; perhaps sacrificing cycle time and process efficiency. Because of this strong focus on drug discovery, Novartis has not had opportunity to design and implement efficient processes. By bring in interns from MIT's Leaders for Manufacturing Program, the company is beginning to explore ways to improve their processes without sacrificing their ability to develop novel drugs.
by Rebecca Anne Roberts.
S.M.
M.B.A.
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Tan, Eu Vian. "Holographic sensors for drug discovery." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611525.
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Wilson, Ian. "Halogenated heterocycles for drug discovery." Thesis, Durham University, 2011. http://etheses.dur.ac.uk/863/.
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Within a number of industries, and particularly within the pharmaceutical industry, there is a desire for reliable, high yielding routes towards large numbers of valuable small molecules that allow a wide range of products to be synthesised. Heterocyclic compounds are particularly sought after as useful compounds, with an estimated 70% of pharmaceutical products being based on heterocyclic structures. A drawback of many traditional routes towards heterocyclic compounds is that the range of substituents that may be placed around the ring is limited. This is especially limiting if ring substituents have to be placed early in a synthesis, reducing the opportunities for elaboration at a late stage. Our approach is to take highly halogenated heterocyclic systems and use them as scaffolds for the synthesis of novel compounds by the sequential replacement of halogen atoms with other functionalities. This approach has led to the generation of a number of novel highly substituted heterocyclic species.
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Gage, Zoe O. "Interferon, viruses and drug discovery." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/10127.
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The interferon (IFN) response is a crucial component of cellular innate immunity, vital for controlling virus infections. Dysregulation of the IFN response however can lead to serious medical conditions including autoimmune disorders. Modulators of IFN induction and signalling could be used to treat these diseases and as tools to further understand the IFN response and viral infections. We have developed cell-based assays to identify modulators of IFN induction and signalling, based on A549 cell lines where a GFP gene is under the control of the IFN-β promoter (A549/pr(IFN-β).GFP) and the ISRE containing MxA promoter (A549/pr(ISRE).GFP) respectively. The assays were optimized, miniaturized and validated as suitable for HTS by achieving Z' Factor scores >0.6. A diversity screen of 15,667 compounds using the IFN induction reporter assay identified 2 hit compounds (StA-IFN-1 and StA-IFN-4) that were validated as specifically inhibiting IFNβ induction. Characterisation of these molecules demonstrated that StA-IFN-4 potently acts at, or upstream, of IRF3 phosphorylation. We successfully expanded this HTS platform to target viral interferon antagonists acting upon IFN-signalling. An additional assay was developed where the A549/pr(ISRE).GFP.RBV-P reporter cell line constitutively expresses the Rabies virus phosphoprotein. A compound inhibiting viral protein function will restore GFP expression. The assay was successfully optimized for HTS and used in an in-house screen. We further expanded this assay by placing the expression of RBV-P under the control of an inducible promoter. This demonstrates a convenient approach for assay development and potentiates the targeting of a variety of viral IFN antagonists for the identification of compounds with the potential to develop a novel class of antiviral drugs.
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Maniyar, Dharmesh M. "Probabilistic methods for drug discovery." Thesis, Aston University, 2006. http://publications.aston.ac.uk/10615/.
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This thesis introduces a flexible visual data exploration framework which combines advanced projection algorithms from the machine learning domain with visual representation techniques developed in the information visualisation domain to help a user to explore and understand effectively large multi-dimensional datasets. The advantage of such a framework to other techniques currently available to the domain experts is that the user is directly involved in the data mining process and advanced machine learning algorithms are employed for better projection. A hierarchical visualisation model guided by a domain expert allows them to obtain an informed segmentation of the input space. Two other components of this thesis exploit properties of these principled probabilistic projection algorithms to develop a guided mixture of local experts algorithm which provides robust prediction and a model to estimate feature saliency simultaneously with the training of a projection algorithm. Local models are useful since a single global model cannot capture the full variability of a heterogeneous data space such as the chemical space. Probabilistic hierarchical visualisation techniques provide an effective soft segmentation of an input space by a visualisation hierarchy whose leaf nodes represent different regions of the input space. We use this soft segmentation to develop a guided mixture of local experts (GME) algorithm which is appropriate for the heterogeneous datasets found in chemoinformatics problems. Moreover, in this approach the domain experts are more involved in the model development process which is suitable for an intuition and domain knowledge driven task such as drug discovery. We also derive a generative topographic mapping (GTM) based data visualisation approach which estimates feature saliency simultaneously with the training of a visualisation model.
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Ebejer, Jean-Paul. "Data driven approaches to improve the drug discovery process : a virtual screening quest in drug discovery." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:96d73300-f767-4ed6-8dda-a13a4aeb40e0.
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Drug discovery has witnessed an increase in the application of in silico methods to complement existing in vitro and in vivo experiments, in an attempt to 'fail fast' and reduce the high attrition rates of clinical phases. Computer algorithms have been successfully employed for many tasks including biological target selection, hit identification, lead optimization, binding affinity determination, ADME and toxicity prediction, side-effect prediction, drug repurposing, and, in general, to direct experimental work. This thesis describes a multifaceted approach to virtual screening, to computationally identify small-molecule inhibitors against a biological target of interest. Conformer generation is a critical step in all virtual screening methods that make use of atomic 3D data. We therefore analysed the ability of computational tools to reproduce high quality, experimentally resolved conformations of organic small-molecules. We selected the best performing method (RDKit), and developed a protocol that generates a non-redundant conformer ensemble which tends to contain low-energy structures close to those experimentally observed. We then outline the steps we took to build a multi-million, small-molecule database (including molecule standardization and efficient exact, substructure and similarity searching capabilities), for use in our virtual screening experiments. We generated conformers and descriptors for the molecules in the database. We tagged a subset of the database as `drug-like' and clustered this to provide a reduced, diverse set of molecules for use in more computationally-intensive virtual screening protocols. We next describe a novel virtual screening method we developed, called Ligity, that makes use of known protein-ligand holo structures as queries to search the small-molecule database for putative actives. Ligity has been validated against targets from the DUD-E dataset, and has shown, on average, better performance than other 3D methods. We also show that performance improved when we fused the results from multiple input structures. This bodes well for Ligity's future use, especially when considering that protein structure databases such as the Protein Data Bank are growing exponentially every year. Lastly, we describe the fruitful application of structure-based and ligand-based virtual screening methods to Plasmodium falciparum Subtilisin-like Protease 1 (PfSUB1), an important drug target in the human stages of the life-cycle of the malaria parasite. Our ligand-based virtual screening study resulted in the discovery of novel PfSUB1 inhibitors. Further lead optimization of these compounds, to improve binding affinity in the nanomolar range, may promote them as drug candidates. In this thesis we postulate that the accuracy of computational tools in drug discovery may be enhanced to take advantage of the exponential increase of experimental data and the availability of cheaper computational power such as cloud computing.
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Beau, Jeremy. "Drug Discovery from Floridian Mangrove Endophytes." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4287.
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A significant challenge of the 21st century is the growing health threat stemming from drug-resistant infectious diseases. There is an undeniable need to discover new, safe and effective drugs with novel mechanisms of action to combat this threat. A study of drugs currently on the market showed that natural products account for approximately 75% of new anti-infective drugs, either as new agents or analogs based upon their structure. Unfortunately, major pharmaceutical companies have cut back tremendously in natural products research in part due to the frustrating obstacle of frequent rediscovery of compounds. Fungi in particular are difficult to work with in that they do not always produce the same variety and quantities of secondary metabolites under laboratory conditions. One of the groundbreaking discoveries evolving from genomics research is the observation that many fungi possess more gene clusters encoding for the production of secondary metabolites than the reported number of natural products isolated from those organisms. Simple epigenetic modifications such as DNA methlytransferase or histone deacetylase inhibition can activate silenced genes leading to the genesis of novel chemistry from the fungus. The work presented herein is a study of the isolation and characterization of anti-infective compounds from Floridian mangrove endophytes. In addition, epigenetic modifications were explored in order to increase the production of secondary metabolites as well as for the purpose of generating new analogs not found in the controls. Finally, structure activity relationship studies were performed in order to maximize the anti-malarial and antibiotic activity of cytosporone E.
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Tsinopoulos, Christos Dimitris. "The evolution of drug discovery strategies." Thesis, University of Warwick, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399447.
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Guimaraes, A. "Screening molecular interactions for drug discovery." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1389941/.
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In biological systems, many proteins have specific binding sites for small-molecules or other proteins critical for their activity and function. Discovery of small-molecules that inhibit such protein interactions is useful in understanding and controlling protein function in disease. Hypoxia inducible factor (HIF1) is a heterodimeric transcription factor and its C-terminal activation domain (CTAD) interacts with the CH1 domain of p300 forming a complex known to regulate many genes. Spectral variants of green fluorescent protein were fused to the CTAD and CH1 to monitor the interaction between these proteins. Fluorescence resonance energy transfer (FRET) between these two chromophores occurred when the complex formed. A homogeneous screening assay was then developed for small-molecules with potential to inhibit the formation of the CTAD-CH1 complex. As part of the assay validation, some new small-molecule inhibitors previously tested by an alternative heterogeneous assay were found to inhibit within the same 100-500 μM concentration range. The new homogenous assay has promising potential for high-throughput screening of large chemical libraries. Novobiocin, a member of the aminocoumarin family can act as an antibacterial or anticancer agent. The clinical use of this class of antibiotics has been limited due to their low water solubility, low activity against gram-negative bacteria, and toxicity against cancer. Glycosyltransferases have been established as important tools in new drug development and are used here to improve water solubility and cell uptake. Glycosylation can be achieved enzymatically or chemically. A mass spectrometry based high-throughput screening (HTS) method was developed and used to find novel glycosylated aminocoumarins generated using a panel of glycosyltransferases and native/non-native sugar donors. The novobiocin derivatives were also re-synthesized chemically. The MIC for novobiocin in a DNA gyrase assay was 1 μM, and the derivatives showed similar MICs. However against a panel of human cancer cell lines these derivatives showed more than twice the activity.
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Matthews, H. "Accelerating antimalarial drug discovery through repositioning." Thesis, University of Salford, 2013. http://usir.salford.ac.uk/36885/.
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Of the plethora of parasitic diseases that afflict mankind, malaria remains the most significant with 100-300 million cases reported annually and 600,000 fatalities. Treatment and control measures have been hampered by the emergence of drug resistance to most antimalarial therapies. Early signs of drug resistance to the current frontline option, the artemisinins, make it imperative that novel drug candidates are discovered. One possible short-term solution is drug repositioning, via screening existing FDA-approved (Food and Drug Administration agency) drug libraries for antimalarial activity. Towards this goal, two, fast, simple, and reliable in vitro SYBR Green-based drug susceptibility assays were optimised. The first, the SYBR Green microplate method offered a medium throughput option that was used to screen two FDA-approved libraries (Z score = 0.68 +0.06), LOPAC and ENZO (~700 compounds). Approximately 60 hits, defined as > 50 % inhibition at 2.5 µM, were identified by the preliminary screen. The SYBR Green flow cytometer method, capable of providing direct parasitaemia estimates and stage-specific information, was used for second-phase characterisation of the hits. From these, antiamoebic compound emetine dihydrochloride hydrate was identified as a potent inhibitor of the multidrug resistant Plasmodium falciparum, strain K1, with an IC50 of 47 nM (95 % confidence interval 44.92-49.17). Further characterisation of the compound involved analysis of the parasite killing profile, to determine the parasite reduction ratio (PRR) and parasite clearance time (PCT) as well drug interaction analysis with existing antimalarials. Emetine was shown to have a similar killing profile to atovaquone inferring a similar mitochondrial mode of action, corroborated by fluorescence staining with the JC-1 mitochondrial probe. Taken together, emetine’s pharmacokinetic matching and synergy with atovaquone provide an exciting drug combination for further investigation. The relatively high hit rate presented in the study, and in vitro workflow outlined for emetine, also showed drug repositioning to be a promising option for antimalarial drug discovery.
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Zhang, Qian. "Natural Product Drug Discovery Targeting Cancer." Thesis, Griffith University, 2017. http://hdl.handle.net/10072/370435.
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Chemotherapy is one of the most effective approaches for cancer treatment. However, to improve efficacy, the therapeutic targets should be identified and characterised. Moreover, new drugs need to be discovered and developed to target different cancer pathways. Current therapeutics can eliminate most of the cancer cells. However, recurrence and metastasis still remain a major failure of cancer therapy. Emerging evidence demonstrates that multidrug resistance (MDR) and the existence of cancer stem cells (CSCs) are two major contributors for the failure of chemotherapy. MDR is a phenomenon in which cancer cells become resistant to structurally and functionally unrelated anticancer agents. CSCs are a small population of cells within cancer cells with capacity for self-renewal, tumor metastasis and differentiation. CSCs are also believed to be associated with chemoresistance. Thus, MDR and CSCs are the greatest challenges for cancer chemotherapy. Significant effort has been made to search for agents that specifically target MDR cells and CSCs. Consequently, some agents derived from nature have been developed to overcome MDR and CSCs. However, the developed chemotherapeutics cannot be used for all the cancers and some of them display severe cytotoxicity. Hence, there is an urgency to investigate the mechanism of drug resistance and to characterise cancer stem cells to identify potential new therapeutic targets. Natural products lie in the heart of the drug discovery. The developed chemotherapeutic compounds mainly originates from the secondary metabolites of microbes, terrestrial plants and marine organisms. In this study, MDR cancer cells were derived from tissue cultured cancer cells by the treatment the cells with fluorouracil (5-FU) and cisplatin (CDDP). CSCs were developed by treatment in serum-free medium with different factors. Fractions and compounds from Nature Bank (Griffith Institute for Drug Discovery, Griffith University), Compounds Australia (Griffith Institute for Drug Discovery, Griffith University) and Traditional Chinese Medicine (TCM) were screening by high through-put screening (HTS). As a result, one potential anticancer flavonoid was isolated from the Australian plant Cryptocarya (QID025519) which was identified by NMR spectroscopic data, in combination with LC-MS. Extracts, fractions and isolated pure compounds from Bruguiera gymnorrhiza andSchisandraviridis were identified as potential agents for the treatment of tongue cancer and breast cancer. The DCM and MeOH extracts and HPLC fractions of B. gymnorrhiza showed antiproliferation activity against cancer cells in a concentration-dependent manner. Further purification of the active fractions led to the isolation of five flavonoids namely rutin, myricetin 3-rutinoside, methoxyflavone, 5-Methoxyluteolin, and 7,3',4',5'-tetrahydroxy-5- gramrione. All five compounds showed antiproliferation activity against CAL27 and MCF7 and MDR cells in a concentration-dependent manner. Methoxyflavone demonstrated the strongest anticancer potential against CAL27 cells, MCF7 cells, CAL27 MDR cells while 7,3',4',5'-tetrahydroxy-5- gramrione illustrated the highest inhibitory effect on MCF7 MDR cells. Both aqueous and ethanol extracts showed activities against MCF7 and CAL27 cancer cells. Bioassay-guided fractionation and purification of the extracts from S.viridis resulted in six active principles, including five dibenzocyclooctene lignans namely gomisin H (1), schisandrin (2), angeloylgomisin H (3), (+)-gomisin M2 (4) and rubschisandrin (5), and one terpenoid, schisanol (6). Compounds 1-3 showed moderate anticancer activities with an IC50 value ranging from 100-200 μg/mL against MCF7 and CAL27 cell lines. Dioxane containing lignans 4-5 and triterpenoid 6 were 10 times more active with IC50 values of14.5, 13.4, 10.6 μg/mL against MCF7, and 21.2, 17.9, 11.7 μg/mL against CAL27, respectively. In addition, two compounds from Compounds Australia exhibited a potential application prospects for tongue cancer and breast cancer therapy. One compound SN00802961 exhibited significant inhibition on MCF7 cells, but low inhibitory effects on fibroblast cells. Meanwhile, it exhibited moderate inhibition on CAL27 MDR cells, CAL27 cells and CSCs. Compound SN00802961 has potently targeted the MAPK/ERK1/2 signaling pathway to induce cytotoxicity in MCF7 cells. Another agent SN00771077 for breast cancer cells in vitro was investigated. The effects of compound SN00771077 on cell viability in vitro were evaluated by treatment of MCF-7 and T47D cells. An in vitro viability assay demonstrated that compound SN00771077 inhibited the cell growth in a dose-dependent manner. The antiproliferative activity of compound SN00771077 is related to its activity on monomeric actin and the subsequent inhibition of polymerization of G-actin monomers. Exposure to compound SN00771077 induced the inhibition of Raf/MEK/ERK pathway in T47D cells. All the results indicated that compound SN00771077 had a strong cytotoxic effects on cancer cells, and shows potential in the treatment of breast cancer by causing the depolymerizing actin cytoskeleton.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
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Sarnpitak, Pakornwit. "Scaffold-oriented Synthesis for Drug Discovery." Thesis, Griffith University, 2017. http://hdl.handle.net/10072/366103.
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The design and synthesis of three different scaffolds of nitrogen heterocycles have been achieved by using either methods described in the literature or newly developed synthetic methodologies/routes. The three synthesised libraries in this thesis were based on Pd-catalysed N-arylations, Castagnoli-Cushman multicomponent reaction, and Rh(II)-catalysed intramolecular C-H insertions. The compounds were successfully synthesised in moderate to excellent yields. Firstly, one of the synthesised diaryl imidazolines was found to be a selective COX-2 inhibitor due to its comparable activity to the approved drugs, celecoxib, and the binding mode was identical to the native ligand and other similar compounds. These observations are good starting points for the further development of selective COX-2 inhibitors based on imidazoline and related scaffolds. Secondly, the synthesis of novel scaffolds, pyrazino- and diazepino-fused isoquinolones, has been explored by using aryl glyoxals and diamines in the Castagnoli-Cushman multicomponent reaction, followed by post-MCR modifications. Unfortunately, all compounds in the library and their intermediates were inactive for antimicrobial activity. Moreover, the Rh(II)-catalysed intramolecular C-H insertion reactions of diazoesters to the C-H bond adjacent to the nitrogen atom yielded 2,3-disubstituted pyrrolidines. The selectivity of this reaction was influenced by the electron density of the C-H bonds undergoing insertion and steric hindrance around the reaction sites.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
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Trotter, M. W. B. "Support vector machines for drug discovery." Thesis, University College London (University of London), 2007. http://discovery.ucl.ac.uk/1445885/.
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Support vector machines (SVMs) have displayed good predictive accuracy on a wide range of classification tasks and are inherently adaptable to complex problem domains. Structure-property correlation (SPC) analysis is a vital part of the contemporary drug discovery process, in which several components of the search for novel molecular compounds with therapeutic potential may be performed by computer (in silicd). Inferred relationships between molecular structure and biological properties of interest are used to eliminate compounds unsuitable for further development. In order to improve process efficiency without rejecting useful compounds, predictive accuracy of such relationships must remain high despite a paucity of data from which to infer them. This thesis describes the application of SVMs to SPC analysis and investigates methods with which to enhance performance and facilitate integration of the technique into present practice. Overviews of contemporary drug discovery and the role of machine learning place the investigation into context. Computational discrimination between compounds according to their structures and properties of interest is described in detail, as is the SVM algorithm. A framework for the assessment of supervised machine learning performance on SPC data is proposed and employed to assess SVM performance alongside state-of-the-art techniques for in silico SPC analysis on data provided by GlaxoSmithKline. SVM performance is competitive and the comparison prompts adaptations of both data treatment and algorithmic application to explore the effects of data paucity, class imbalance and outlying data. Subsequent work weights the SVM kernel matrix to recognise heavily populated regions of training data and suggests the incorporation of domain-specific clustering methods to assist the standard SVM algorithm. The notion that SVM kernel functions may incorporate existing domain-specific methods leads to kernel functions that employ existing pharmaceutical similarity measures to treat an abstract, binary representation of molecular structure that is not used widely for SPC analysis.
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Uusitalo, J. (Jouko). "The role of drug metabolism in drug discovery and development:case ospemifene." Doctoral thesis, Oulun yliopisto, 2015. http://urn.fi/urn:isbn:9789526210223.
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Abstract Drug metabolism is one of the most important events a drug faces after administration. Traditionally, drug metabolism has only been considered as a major clearance and elimination step in the pharmacokinetics of a drug. However, drug metabolism is also one of the important factors behind safety and toxicity issues in drug discovery and development. Some of the mechanisms behind metabolism-related toxicity we do understand well while others, especially the role of reactive metabolites, need further research. The thesis reviews the role of drug metabolism in the drug discovery and development process from the point of view of metabolism and metabolites. Special emphasis is put on reviewing the metabolism behind human toxicity and safety, and the roles of circulating and reactive metabolites in particular. Ospemifene is a nonsteroidal selective estrogen receptor modulator recently approved for the treatment of vulvar and vaginal atrophy in postmenopausal women with moderate to severe dyspareunia. The present study characterized the in vitro and in vivo metabolism and potential drug interactions of ospemifene. The principal human metabolites were identified and the adequacy nonclinical animal exposure was evaluated. The major human cytochrome P450 enzymes involved in the formation of principal metabolites were also identified and the clinical consequences assessed. Finally, the interaction potential of ospemifene as a cytochrome P450 enzyme inducer or inhibitor was investigated. As a result, ospemifene was considered to be safe drug from a metabolic interaction point of view. This study was part of the drug development program of ospemifene and practically all of the in vitro study data were included in the marketing authorization application of ospemifene. Ospemifene was also a case molecule in the development of new methodologies to study drug metabolism and drug-drug interactionsTiivistelmä Lääkeainemetabolia on lääkeaineen farmakokinetiikassa tärkeä puhdistuma- ja eliminaatioaskel, jonka rooli on ymmärretty varsin hyvin. Lääkeainemetabolialla on myös merkittävä vaikutus lääkeaineen toksisuuteen ja lääkkeen käytön turvallisuuteen. Osa lääkeainemetaboliaan liittyvistä toksisuusmekanismeista selvitetty hyvin, mutta erityisesti reaktiivisiin metaboliitteihin liittyvä osa vaatii vielä tutkimusta. Tämän työn kirjallisuusosassa katselmoidaan lääkeainemetabolian merkitystä lääkekehitysprosessissa painottaen erityisesti lääkeainemetabolian sekä reaktiivisten ja verenkierrossa kiertävien metaboliatuoteiden vaikutusta toksisuuteen ihmisellä ja merkitystä turvalliseen lääkkeiden käyttöön. Ospemifeeni on uusi ei-steroidinen selektiivinen estrogeenireseptorimodulaattori, joka on hyväksytty yhdynnänaikaisesta kivusta kärsivien postmenopausaalisten naisten vulvan ja vaginan limakalvojen kuivumisen hoitoon. Tässä tutkimuksessa selvitettiin ospemifeenin lääkeainemetaboliaa ihmisellä ja koe-eläimillä sekä mahdollisia lääkeinteraktioita. Tutkimuksessa tunnistettiin tärkeimmät metaboliitit ihmisellä ja arvioitiin eläinkokeissa käytettyjen koe-eläinten altistumisen kattavuus niille. Työssä selvitettiin myös tärkeimmät päämetaboliitteja katalysoivat sytokromi P450 -entsyymit ja arvioitiin löydösten kliinistä merkitystä. Lisäksi tutkittiin aiheuttaako ospemifeeni lääkeinteraktioita muille lääkeaineille indusoimalla tai inhiboimalla sytokromi P450 -entsyymejä. Tutkimustulosten perusteella ospemifeenia voidaan pitää lääkeainemetabolian suhteen turvallisena lääkkeenä. Tämä tutkimus oli osa ospemifeenin lääkekehitysohjelmaa ja käytännössä kaikki tutkimustyön in vitro -tietoaineisto oli mukana ospemifeenin myyntilupa-hakemuksissa lääketurvallisuusviranomaisille. Ospemifeenia käytettiin tutkimustyön aikana myös yhtenä esimerkkimolekyylinä kehitettäessä uusia menetelmiä lääkeainemetabolian ja lääkeinteraktioiden tutkimiseen
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Rynn, Caroline. "Investigations into rat hepatobiliary drug clearance pathways in early drug discovery." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/investigations-into-rat-hepatobiliary-drug-clearance-pathways-in-early-drug-discovery(cea9825c-5b49-4212-a85a-803139dc1ebf).html.
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Conventional ‘well-stirred’ extrapolation methodology using intrinsic metabolic clearance data from rat liver microsomes poorly predicts in vivo clearance for approximately half of drug discovery compounds. The aim of this present study was to gain a more detailed understanding of the hepatobiliary disposition pathways which influence drug clearance. A set of 77 new chemical entities (NCEs), demonstrating a range of physicochemical properties and in vitro-in vivo clearance correlations (IVIVC), were employed to explore relationships between hepatobiliary disposition pathways in rat and physicochemical, structural and molecular properties of the NCEs. Primary rat hepatocytes with >80% cell viability were successfully isolated from male Han Wistar rats and used to establish in vitro models of drug uptake and biliary efflux. Preliminary studies with cultured primary rat hepatocytes indicated that uptake of d8-taurocholic acid and pitavastatin was time, concentration and temperature dependent. Initial studies with sandwich cultured primary rat hepatocytes demonstrated that cellular accumulation and biliary efflux of [3H]-Taurocholic acid was time and concentration dependent. These in vitro rat hepatocyte models were then used to investigate drug uptake and biliary efflux for all NCEs. In general, NCEs with high (passive) permeability showed better IVIVC and a lower incidence of active uptake and biliary efflux compared to NCEs with lower permeability, suggesting permeability is a key property influencing hepatobiliary drug disposition in rat. Preliminary in silico models analysing structural and molecular descriptors of substrates of active transport in rat hepatocytes were developed and indicated modest potential to highlight clearance pathways beyond hepatic metabolism but further follow up work with larger, more diverse compound sets is warranted to gain confidence in these models. Extended clearance models were investigated to estimate the effect of hepatic transporters on clearance and to predict the overall hepatic clearance of the NCEs. None of these models resulted in a 1 to 1 correlation but in general, improvements in clearance predictions were made when drug transport processes were accounted for. In vivo excretion studies using bile duct cannulated rats demonstrated that NCEs with high permeability and good IVIVC were not directly eliminated in bile or urine as unchanged drug, whereas NCEs with lower permeability and poor IVIVC (> 3-fold under predicted) were all directly eliminated unchanged indicating key drivers of clearance beyond metabolism. In conclusion these investigations confirmed a role for hepatic transporters in clearance but the complex nature of active transport mechanisms and a lack of robust in vitro tools create challenges in the quantitative prediction of hepatobiliary clearance. However, one of the key findings from this research, which is highly applicable in early drug discovery, was to identify the existence of disposition permeability relationships. These can be anticipated by observing physicochemical parameters of NCEs in conjunction with conventional IVIVC, since NCEs that are not highly permeable, possess some hydrophobic characteristics, and which are poor substrates of cytochrome P450 enzymes are more likely to be good substrates of transporters and be directly eliminated in bile and/or urine. The present study focused on exploring hepatobiliary disposition pathways using rat as the investigative species. Whilst there is no guarantee that pathways relevant to rat will be similar to other preclinical species or even humans, an early diagnosis of dominant clearance pathways can guide a more efficient use of the ADME-PK toolbox.
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Galli, C. "NONCOVALENT FLUOROUS INTERACTIONS: NEW APPROACHES FOR DRUG DISCOVERY AND DRUG DELIVERY." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/540156.
Full textAbstract:
The unique chemical properties of fluorine atom (high electronegativity, high ionization potential, low polarizability and low van der Waals interactions) modify the chemical properties of organic compounds as well as their reactivity when hydrogen atoms are replaced by fluorines. Actually, fluorocarbons show low polarity, which is responsible for the high hydrophobicity of these molecules. Additionally, the low polarizability of fluorines leads to weaker van der Waals interactions, which makes fluorocarbons lipophobic. Therefore, fluorinated compounds show an amphiphilic character that leads to the formation of the fluorous phase, which is separated to both aqueous and organic layers.
The aim of my project was applying the strong and noncovalent fluorous interactions to drug discovery and drug delivery.
The first part of my thesis is focused on the development of a new strategy for target identification able to overcome the several limitations associated to classic chemical proteomics techniques. Indeed, traditional chemical proteomics methodology uses agarose beads covalently bound to streptavidin as stationary phase for affinity purification. This resin is able to retain biotin-tagged proteins as well as sticky components abundant in the lysate. These contaminants might be aspecifically eluted with the biological targets, complicating the mass analysis and therefore the target identification. In order to increase the selectivity of the proteomics approach, we designed an innovative fluorous proteomics methodology using the strong fluorous-fluorous interactions as recognition system for affinity purification. Indeed, perfluorinated stationary phase can anchor only fluorinated species, avoiding aspecific binding. To test the fluorous proteomics approach, papain was considered as biological target. Fluorinated inhibitors of papain with different fluorinated-chain length were synthesized. The number of fluorine atom of the inhibitor is crucial for the interaction with the fluorinated stationary phase in the purification step. Actually, only papain inhibitors with a long fluorous alkyl chain are able to bind the fluorinated resin and therefore immobilize papain. In contrast, inhibitors with a short fluorous alkyl chain cannot bind the fluorinated stationary phase by means of fluorous-fluorous interactions. Consequently, papain cannot be anchored to the resin.
The second part of my thesis is focused on the application of fluorous interactions for drug delivery. This project was carried out in the School of Pharmacy, University of Wisconsin-Madison (Madison, WI, U.S.A.) under the supervision of Professor Sandro Mecozzi. The aim was designing and synthesizing semifluorinated dibranched polymers. The synthesis of fluorinated molecules is a challenge, due to their poor reactivity and low solubility in commonly-used organic solvents. To increase the final yield, each step of the synthesis of the semifluorinated dibranched polymers was optimized. The dibranched fluorinated polymers will be used to prepare oil-in-water nanoemulsions for controlled drug release of paclitaxel. We reasoned that semifluorinated polymers with different chemical structures might lead to nanoemulsions with different stability and drug release profile. Small diameter of the nanoemulsion droplets and long half-lives are desired to maximize the tumoritropic accumulation of these nanosystems by EPR effect before drug release. This allows the release of the drug within the tumor instead of in the bloodstream, avoiding side effects due to the interaction of the drug with off targets and consequently reducing the systemic toxicity.
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Blasi, Pérez Daniel. "Drug Discovery Targeted to Transthyretin Related Amyloidosis." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/108283.
Full textAbstract:
Several drug discovery approaches has been performed to find new compounds able to interact with high affinity with the hormone binding site of the homotetrameric protein transthyretin (TTR), and stabilize this tetramer, becoming drug candidates to treat several rare amyloid diseases associated with TTR.
With this aim, several computational workflows and chemico-biological databases have been developed, and in collaboration with two experimental research laboratories of our TTR Consortium (one contributing with the chemical synthesis or acquisition of the designed compounds, and the other contributing with the biological activity assay results for the synthesized or acquired compounds).
The specific objectives of this thesis are:
a) The generation of a chemico-biological database containing the historical and newly generated results of the TTR Consortium, containing the chemical structures and biological activities of the TTR ligands.
b) Explore the possibility of using repurposing techniques applied to the discovery of new TTR inhibitors among the existing drugs, with particular focus on anti-inflammatory drugs, which are known to be good TTR ligands.
c) Design of new flavonoid compounds as TTR ligands by means of structure-based drug design.
d) Incorporate the Ligand Efficiency Indices analysis (both retrospective and prospective) as a new tool for designing new compounds with increased efficiency as TTR ligands.
e) The computational development of a combined predictive/experimental workflow for the analysis of the metabolic stability of TTR ligands, as a tool for improving the prioritized compounds in our in-house database to obtain new compounds with better metabolic and pharmacokinetic properties.
Among this thesis those workflows have been developed in order to obtain possible new amyloidogenic inhibitors:
a) A computational workflow to obtain TTR ligand fingerprints has been developed, and the application of this workflow to the repurposing of marketed antiinflammatory drugs has delivered 3 compounds as new TTR stabilizers.
b) A computational workflow to obtain a TTR-protein structure based pharmacophore has been developed, and the application of this workflow to a database of flavonoid compounds has delivered one compound as a new TTR stabilizer.
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Ullman, Carl Fredrik Michael. "Measuring and increasing productivity in drug discovery /." Zürich : ETH, 2008. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=17877.
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Álvarez, García Daniel. "Protein solvation preferences: applications to drug discovery." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/285451.
Full textAbstract:
Computer-aided drug design is a key player in current drug discovery projects. Structure-based computational approaches use the target structural information to suggest potentially active and safe drugs. However, the process is far from trivial and novel methodologies are continuously sought to address two main factors usually simplified and overlooked: Target flexibility and the effect and structure of water molecules at the binding site.
As demonstrated by different NMR and crystallography experiments, small organic solvents (e.g. ethanol, isopropanol, acetonitrile) are able to identify binding sites and provide clues for rational drug design. MDmix is a simulation-based method that exploits this natural behavior in silico. By using small organic molecules and water mixtures, each one with a distinct chemical nature, key interaction spots are identified on the protein surface allowing the identification and characterization of binding sites for hit discovery and lead optimization.
The work presented in this thesis is divided in two main publications: In the first one, the effect of target flexibility was investigated to establish some guidelines on how to treat this important factor during the simulations. We found that flexibility is essential for correctly identifying induced binding sites but might lead to uninterpretable results when large conformational changes occur. Soft restraints applied during the simulation are suggested as a way to obtain reproducible results and still characterize high affinity interaction sites (hot spots) with mild errors on the energy estimates.
In the second publication, the use of solvent mixtures for the identification of experimentally known pharmacophores was evaluated in two test systems for which many inhibitors are known (e.g. heat shock protein 90 and HIV protease 1). The explicit treatment of water molecules provides interaction maps which identify the most favorable interactions in the binding site with unprecedented accuracy when compared to classical molecular interaction potentials. Moreover, we demonstrate how the interaction maps obtained for the water molecules accompanying the small organic solvents are useful to identify non-displaceable waters. Both the solvent interaction maps and the water interaction maps are extremely useful information for the identification of novel active molecules and for the optimization of potency for already active ones.
Finally, a software package is presented that aims at facilitating the use of the methodology and at helping in adopting it to everyday drug design projects. A final chapter treats ongoing and future research where method improvements and practical uses in real examples are discussed.
MDmix being a simulation-based method, the target flexibility and the explicit treatment of the solvent provide significant advantages over traditional approaches for binding site finding and characterization. This novel approach, which is applicable to previously unmet targets and binding sites, offers a new alternative in the challenging process of drug design.El diseño de fármacos asistido por ordenador es actualmente un actor fundamental en el proceso de descubrimiento de nuevos fármacos. Las aproximaciones basadas en estructura usan la información estructural de la Diana terapéutica para proponer moléculas activas y seguras. Sin embargo, el proceso dista de ser sencillo y nuevas metodologías están continuamente siendo investigadas para solventar las limitaciones actuales, siendo la flexibilidad de la diana y el tratamiento y la estructura del agua en la cavidad, dos factores usualmente obviados o simplificados. Como ha sido demostrado por varios experimentos de NMR y cristalografía, moléculas pequeñas de solventes orgánicos (p.e. etanol, acetamida o acetonitrilo), son capaces de identificar sitios de unión y proporcionan pistas para el diseño racional de nuevas moléculas bioactivas. MDmix es un método basado en simulación molecular que explota dicho fenómeno in silico. Usando mezclas de moléculas orgánicas pequeñas y agua, cada una con propiedades químicas diferentes, se identifican mapas energéticos de interacción sobre la superficie de la diana. Esta información nos permite identificar sitios de unión para ligandos y caracterizar dicha interacción para guiar el proceso de identificación de hits y la optimización de cabezas de serie. El trabajo presentado en esta tesis se puede dividir en dos publicaciones principales: En la primera, el efecto de la flexibilidad de la diana es estudiado para establecer unas guías de actuación a la hora de simular el sistema. Encontramos que la flexibilidad es fundamental a la hora de identificar cavidades inducidas o con alto grado de flexibilidad pero, a la vez, la interpretación de los resultados es mucho más compleja cuando hay cambios conformacionales. Por otra banda, aplicando restricciones suaves a la movilidad de los átomos, se gana reproducibilidad en los resultados y los errores en la estimación energética son mínimos. En la segunda publicación, se estudió el uso de diferentes mezclas de solventes para la identificación de farmacóforos experimentales en dos sistemas test (heat shock protein 90 y HIV proteasa 1). El tratamiento explícito del agua proporciona mapas energéticos capaces de identificar correctamente los puntos de interacción más favorables con una precisión sin precedentes cuando se compara con otros métodos. Además, demostramos como los mapas energéticos obtenidos para las moléculas de agua son capaces de discernir entre aguas desplazables y no desplazables por un potencial ligando. La información extraída de dichos mapas puede ser de alta utilidad para guiar la identificación de nuevas moléculas activas y para la optimización de la potencia de ligandos ya identificados. Finalmente, se presenta un programa de código abierto escrito en python cuyo objetivo es facilitar el uso de la metodología así como su adopción en cualquier proyecto de diseño de fármacos. En el capítulo final se discuten posibles mejoras y aplicaciones prácticas del método en proyectos actualmente en investigación y direcciones futuras a seguir. MDmix, siendo un método basado en simulación molecular, permite incorporar la flexibilidad de la diana y tratar explícitamente el efecto del solvente. Por ello, ofrece ventajas significativas sobre aproximaciones tradicionales en la identificación de sitios de unión y su caracterización. Siendo aplicable sobre cualquier diana, aún sin conocimiento previo, ofrece una nueva alternativa en el siempre desafiante proceso del diseño de fármacos.
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Inman, Martyn William. "Catalytic processes in anti-cancer drug discovery." Thesis, University of Leeds, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.493304.
Full textAbstract:
The introduction (Chapter 1) reviews progress made in the last eight years in the field of multicomponent palladium-catalysed reactions, with particular attention paid to those processes which may be easily applied to the synthesis of compound libraries. The Results and Discussion (Chapters 2 to 7) provides an account of the author's work in the development of palladium-catalysed reactions of allene, and the application of such reactions to the synthesis of novel histone deacetylase inhibitors for the treatment of cancer.
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Ma, Wai Sheung. "Natural Product Drug Discovery against Tropical Diseases." Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3224.
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This dissertation describes the isolation of secondary metabolites from natural origins through a series of chromatographic techniques and spectrometric characterization in the effort of drug discovery. The isolated compounds obtained were used as drug leads against tropical diseases, namely malaria and leishmaniasis. While first chapter offers an introduction on the use of a natural product by itself as an effective therapeutic and its role on inspiring the discovery of new drugs, the later chapters will concentrate on isolation and characterization of bioactive natural products from an Antarctic sponge and mangrove endophytic fungi during the dissertation work.
The second chapter describes the attempt to develop a new method of solving the absolute configuration of tertiary alcohol using lanthanide chiral shift reagent and 13C NMR spectroscopy. The third chapter describes the isolation of five new steroids, norselic acids A-E, from Crella sp. collected in Antarctica. The structures of the norselic acids were established by NMR and MS techniques. The absolute stereochemistry of norselic acid A was elucidated by SXRD. The antimicrobial and anti-leishmania activities of norselic acid A have been studied. Norselic acid A displays antimicrobial activities against methicillin-resistant S. aureus (MRSA), S. aureus, E. faecium, and C. albicans. Norselic acids B-E exhibit mild antimicrobial activities. All norselic acids exhibit strong cytotoxicity against leishmania.
The fourth and fifth chapters describe a Medicine for Malaria Venture (MMV) funded malaria bioassay-guided screening program. The chemical investigation of the crude endophytic fungal extracts has led to the isolations of a series of known cytochalasins along with the discovery of a few new compounds, including a new simple carboxylic acid, and several known and novel compounds belonging to the dimeric xanthone family. Majority of the cytochalasins display mild cytotoxicity and outstanding inhibition to chloroquine-resistant reference strain Plasmodium falciparum (W2) with IC50 ranging from 25.8 nM to 2900nM. However, their cytostatic properties hinder them from being a good drug candidate. The dicerandrols display good activity with the lowest IC50=0.63 μM against malaria with low cytotoxicity. The structures of the compounds isolated and the associated anti-malarial activities are reported herein.
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Price, K. E. "Antimalarial drug discovery : exploring the MEP pathway." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3005814/.
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Cai, Xiaoshu. "DEVELOPMENT OF COMPUTATIONAL APPROACH FOR DRUG DISCOVERY." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1465403528.
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Robertson, Luke. "Anti-malarial Drug Discovery from Australian Flora." Thesis, Griffith University, 2018. http://hdl.handle.net/10072/381516.
Full textAbstract:
Malaria is a mosquito-borne disease caused by the parasitic protozoan Plasmodium that is
responsible for approximately half a million deaths every year. The vast majority of these
deaths are caused by P. falciparum in Sub-Saharan Africa (SSA). Although most cases of P.
falciparum malaria can currently be treated effectively using artemisinin-based combination
therapies (ACTs), resistance to ACTs is beginning to emerge in South-East Asia. This resistance
is likely to proliferate and spread into SSA, after which a public health catastrophe is likely to
follow. There is currently no drug poised to replace ACTs as the front-line treatment for
malaria and there is a need for the discovery of new drugs. Historically, natural products from
plants have been our best source of anti-malarial drugs: the alkaloid quinine (from the bark of
the Cinchona tree) and the sesquiterpene lactone artemisinin (from the leaves of Artemisia
annua) have formed the backbone of anti-malarial chemotherapeutics for centuries.
The primary goal of this thesis was to respond to the need for new anti-plasmodial
compounds. This was achieved by collecting and screening a library of Australian Rutaceae
species against P. falciparum, selecting species that showed high bioactivity and performing
large-scale natural product purification. Isolated natural products were screened against
chloroquine-resistant and sensitive P. falciparum and human embryonic kidney (HEK-293) cells
to evaluate bioactivity and parasite selectivity. This forms the majority of the thesis (Chapters
2-6).
Chapter 2 reports the initial collection, screening and fingerprinting of a library of 30 Australian
Rutaceae species. Chemical fingerprinting using LC-MS was used to identify species that were
most likely to contain new natural products. From these results, four species were selected for
investigation: Clausena brevistyla (Chapter 2) Flindersia pimenteliana (Chapters 3-4),
Acronychia pubescens (Chapter 5) and Pitaviaster haplophyllus (Chapter 6). This chapter also
reports the isolation of two known pyranocoumarins from C. brevistyla. One of the
pyranocoumarins showed potent and selective activity against P. falciparum, with IC50 values
between 466 – 822 nM.
Chapter 3 reports the chemical investigation of F. pimenteliana leaf material. From this plant, a
new class of ascorbic-acid adduct indole alkaloids, pimentelamines A-C, were isolated along
with one new indole alkaloid, 2-isoprenyl-N,N-dimethyltryptamine. Five known compounds
were also isolated. Although the new natural products did not show strong bioactivity, three of
the isolated bis-indole alkaloids, borreverine, 4-methylborreverine and
dimethylisoborreverine, showed potent activity with IC50 values between 190 – 670 nM against
P. falciparum
Chapter 4 reports the isolation of three new isoborreverine-type alkaloids, 10,10’-
dimethoxydimethylisoborreverine, 10-methoxydimethylisoborreverine and 10’-
methoxydimethylisoborreverine from the bark of F. pimenteliana. Two known borreverinetype alkaloids were also isolated. The moderate anti-plasmodial activity of these alkaloids is
reported, with IC50 values ranging from 959 – 2407 ng/mL. Further insights into structureactivity relationships of borreverine-type alkaloids are also discussed.
Chapter 5 reports the chemical investigation of the roots of A. pubescens, from which a highly
unusual oxidized furo[2,3-c]xanthene, acrotrione, was isolated along with two known
acetophenones. Acrotrione is the first natural product of its class to be isolated. Moderate
anti-plasmodial activity for the natural products is reported, with IC50 values ranging from 1.7
to 4.7 µM.
Chapter 6 reports the isolation of one new quinoline alkaloid, leptanoine D, from P.
haplophyllus. Nine known alkaloids were also isolated. The chemotaxonomic relationships
between the monotypic Pitaviaster genus and the related Australian genera Euodia, Melicope
and Acronychia are discussed.
The secondary goal of this thesis was to investigate the factors that influence diversity of
natural products in Australian plants. In recent years, natural product-driven drug discovery
has seen a decrease in popularity in the pharmaceutical industry, part of which has been
caused by the repeated isolation of known natural products. In response to this, there is a
requirement for the development of new ideas that expedite the discovery of new natural
products. Some recent publications have noted that natural product diversity is positively
correlated with diversity of plant-herbivore communities. This may suggest that plants in
regions of high biotic stress (i.e. rainforests) should be the focal point of terrestrial plant
natural product drug discovery. We aimed to validate this hypothesis by using the Australian
Rutaceae genus Flindersia as a case study. Contrary to expectations, our results showed that
Flindersia species growing in arid regions of central Australia produced a significantly higher
number of structurally unique alkaloids than rainforest species. These unexpected results
highlight the potential of the Australian arid zone as a source of new natural products.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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Vance, Nicholas Robert. "Targeting dynamic enzymes for drug discovery efforts." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6517.
Full textAbstract:
Proteins are dynamic molecules capable of performing complex biological functions necessary for life. The impact of protein dynamics in the development of medicines is often understated. Science is only now beginning to unravel the numerous consequences of protein flexibility on structure and function. This thesis will encompass two case studies in developing small molecule inhibitors targeting flexible enzymes, and provide a thorough evaluation of their inhibitory mechanisms of action.
The first case study focuses on caspases, a family of cysteine proteases responsible for executing the final steps of apoptosis. Consequently, they have been the subject of intense research due to the critical role they play in the pathogenesis of various cardiovascular and neurodegenerative diseases. A fragment-based screening campaign against human caspase-7 resulted in the identification of a novel series of allosteric inhibitors, which were characterized by numerous biophysical methods, including an X-ray co-crystal structure of an inhibitory fragment with caspase-7. The fragments described herein appear to have a significant impact on the substrate binding loop dynamics and the orientation of the catalytic Cys-His dyad, which appears to be the origin of their inhibition. This screening effort serves the dual purpose of laying the foundation for future medicinal chemistry efforts targeting caspase proteins, and for probing the allosteric regulation of this interesting class of hydrolases.
The second case study focuses on glutamate racemase, another dynamic enzyme responsible for the stereoinversion of glutamate, providing the essential function of D-glutamate production for the crosslinking of peptidoglycan in all bacteria. Herein, I present a series of covalent inhibitors of an antimicrobial drug target, glutamate racemase. The application of covalent inhibitors has experienced a renaissance within drug discovery programs in the last decade. To leverage the superior potency and drug target residence time of covalent inhibitors, there have been extensive efforts to develop highly specific covalent modifications to reduce off-target liabilities. A combination of enzyme kinetics, mass spectrometry, and surface-plasmon resonance experiments details a highly specific 1,4-conjugate addition of a small molecule inhibitor with the catalytic Cys74 of glutamate racemase. Molecular dynamics simulations and quantum mechanics-molecular mechanics geometry optimizations reveal, with unprecedented detail, the chemistry of the conjugate addition. Two compounds from this series of inhibitors display antimicrobial potency comparable to β-lactam antibiotics, with significant activity against methicillin-resistant S. aureus strains. This study elucidates a detailed chemical rationale for covalent inhibition and provides a platform for the development of antimicrobials with a novel mechanism of action.
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Giglio, Valentina. "Biofunctionalized systems for drug discovery and delivery." Doctoral thesis, Università di Catania, 2016. http://hdl.handle.net/10761/3893.
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During this doctoral research work new potential drug delivery vehicles for targeted treatment of cancers were developed. For this purpose, both soft and hard materials were subject of study.
Firstly, the synthesis, the characterization and the biological evaluation of monomeric â-cyclodextrins functionalized with folic acid (FA) were the focus of this research. In particular, four new conjugates (CyD-FAs), both 3- and 6-functionalized â-CyDs (â-CyD3 and â-CyD6) linked to the á- or ã-carboxylic group of the FA were synthesized, isolated and fully characterized. Furthermore, the ability of these compounds to include the anticancer drug LA-12 and to deliver it selectively to FR (+) tumor cell lines was investigated.
Since the promising results obtained with these CyD-FA conjugates as carriers for LA-12, polymeric nanoparticles based on cross-linked cyclodextrins were designed for drug delivery purposes. These systems, offer the advantages of CyD-type complexation in a synergistic way, resulting more effective than the parent CyDs. In particular, CyD-based polymers and oligomers were synthesized, functionalized with FA and tested as delivery systems towards different hydrophobic anticancer or anti-inflammatory agents. Furthermore, for selected systems, the binding constants of the formed inclusion complexes were determined as well.
Concerning hard materials, mesoporous silica nanoparticles were investigated. A new disc-shaped mesoporous material, the nanodiscs (NDs), was synthesized, isolated and fully characterized. This material was firstly used for the preparation of self-assembled monolayers (SAM), to be employed in targeted cancer cell adhesion and in-situ drug delivery. For this purpose, the NDs-monolayers were functionalized with FA as targeting moiety. Thanks to their large surface area and the possibility of high density of superficial functionalization with bioactive molecules, these systems resulted effective in binding cancer cells even upon short contact times. Moreover, exploiting the porosity of the synthesized particles, the intracellular release of small hydrophobic molecules pre-loaded in the channels of the NDs were achieved.
Secondly, preliminary biological experiments carried out to test the cellular uptake of NDs, and the drug-carrier ability were performed. Finally, in the attempt to increase the biodegradability of these interesting structures, disulfide-doped mesoporous silica nanodiscs (ss-NDs) were also prepared. Full characterization and preliminary biological assays of these hybrid materials was also performed, and their degradation in redox conditions investigated. This novel material, taking advantage of bio-redox reactions, undergoes a controlled disintegration process in presence of reducing agents (i.e. glutathione), displaying an improved drug delivery action.
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Lianza, Mariacaterina <1990>. "New approaches to plant-based drug discovery." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amsdottorato.unibo.it/9715/1/Lianza_Mariacaterina_Tesi.pdf.
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Natural products have been used to treat or prevent diseases since time immemorial. Although their value is widely recognised, plant-based drug discovery presents several challenges. New methods are needed for the rapid analysis of plant extracts, with minimal consumption of starting plant material, resources and time. Moreover, techniques enabling the extrapolation of many types of information with a single analysis are required.
Considering these challenges, new approaches for the study of plant extracts and the identification of the active metabolites are presented in this thesis.
Among the recent techniques, metabolomics coupled with chemometrics is particularly outstanding. The metabolomic-chemometric approach was applied in a screening of thirty-six plant extracts for antibacterial activity. The PCA model enabled the identification of the most promising extracts and provided an insight allowing several considerations and inputs for future studies. The same technique was used to reap phytochemical variations of Arbutus unedo leaves samples, collected under different conditions. The most phytochemically diverse samples exhibited different antibacterial activities, demonstrating that the composition and biological activity of plant extracts are highly dependent on the conditions under which samples are collected. One of the compounds responsible for antibacterial activity, kaempferol-3-O-rhamnoside, was identified.
Another important issues of plant-based drug discovery is the rapid identification of known molecules, that is referred to dereplication approach. Amaryllidaceae alkaloids are secondary metabolites with a wide range of biological activities and structural variety. The most occurring alkaloids are widely known, hence, they were selected for the development of a dereplication protocol. The method allowed the characterization of the bulb extract of Urceolina peruviana working directly on the extract fractions without resorting to purification processes, saving time and resources. Only the fraction containing an alkaloid whose NMR profile was absent in the databases was purified. This alkaloid was named 6-dehydroxy-6-acetamido-nerinine.
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Schreiber, Kimberly C. M. "Assay development for use in drug discovery against Bovine Trichomoniasis." Scholarly Commons, 2007. https://scholarlycommons.pacific.edu/uop_etds/650.
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Bovine trichomoniasis is a venereal disease that affects cattle. The causative agent of this disease is Tritrichomonas foetus, a flagellated protozoan. There is no current FDA approved treatment for this disease. The purpose of this study was to develop new compound screening assays that will make the discovery of new compounds faster and more accurate. The CellTiter-Glo Luminescent Cell Viability Assay, a high throughput screening (HTS) assay from Promega, was found to be as affective at measuring cytotoxicity as traditional assaying techniques. For the first time. preen florescent protein. a reporter gene used in cell viability assavs was successfully transformed into T. foetus for use in HTS systems. This study also identified new compounds that can potentially be used as new treatments for this disease.
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Mohiddin, Syed Basha. "Development of novel unsupervised and supervised informatics methods for drug discovery applications." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1138385657.
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Mukherjee, Sreya. "Applications of Molecular Modelling and Structure Based Drug Design in Drug Discovery." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6331.
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Calcium ions have important roles in cellular processes including intracellular signaling, protein folding, enzyme activation and initiation of programmed cell death. Cells maintain low levels of calcium in their cytosol in order to regulate these processes. When activation of calcium-dependent processes is needed, cells can release calcium stored in the endoplasmic reticulum (ER) into the cytosol to initiate the processes. This can also initiate formation of plasma membrane channels that allow entry of additional calcium from the extracellular milieu. The change in calcium levels is referred to as calcium flux. A key protein involved in initiation of calcium flux is Stromal Interaction Molecule 1 (STIM1), which has recently been identified as a sensor of ER calcium levels. STIM1 is an ER transmembrane protein that is activated by a drop in ER calcium levels. Upon activation, STIM1 oligomerizes with a plasma membrane protein, ORA1, to form calcium-selective plasma membrane channels. Dysregulation of calcium flux has been reported in cancers, autoimmune diseases and other diseases. STIM1 is a promising target in drug discovery due to its key role early in calcium flux. Here we review the involvement and importance of STIM1 in diseases and we discuss STIM1 as a viable target for drug discovery using computational chemistry methods to rapidly identify new molecules to target STIM1. Herein, computational techniques were used to understand the mechanistic role of STIM1 and virtual screening is in process to discover potential inhibitors of STIM1 activity. Also mutational analysis on STIM1 was performed computationally to see the effect it had on the protein computationally.
It has been found that tumor cells and tissues, compared to normal cells, have higher levels of copper and possibly other metal ions. This presents a potential vulnerability of tumor cells that can serve as a physiological difference between cancer cells and normal cells and allows design of compounds that selectively target tumor cells while sparing normal cells. Recently we have identified compounds that have potential to inhibit the proteasome in tumor cells and induce cell death by mobilizing endogenous tumor copper resulting in in cellulo activation of the compound. These compounds hence act as pro-drugs, becoming active drugs in tumor cells with high copper content but remaining essentially inactive in normal cells, thereby greatly reducing adverse effects in patients. Such use would be of significant benefit in early detection and treatment of cancers, in particular, aggressive cancers such as pancreatic cancer which is usually not detected until it has reached an advanced stage. Six compounds were identified following virtual screening of the NCI Diversity Set with our proteasome computer model followed by confirmation with a biochemical assay that showed significant inhibition of the proteasome by the compounds in the presence of copper ions. In a dose response assay, NSC 37408 (6, 7-dihydroxy-1-benzofuran-3-one), our best compound, exhibited an IC50 of 3µM in the presence of 100 nM copper.
Chagas’ Disease, a parasitic disease caused by the parasite Trypanosma Cruzi, is endemic to Latin America. The disease manifests itself in a short acute phase and a long chronic phase. Current treatments are effective only in the acute phase and are not used in the chronic phase due to toxicity of the drugs. Hence a new drug discovery approach was chosen for this disease. Cruzain is the major etiologic enzyme involved in the disease and is only present in the parasite. It is also an enzyme expressed by the parasite in both phases. Herein, a novel peptoid library containing hydromethylketones was constructed and screened against a virtual structure of cruzain. The peptoids thus found through this drug discovery effort can be used as potential drug candidates against cruzain. Computational techniques will help achieve a high degree of specificity and aid in proposing assays for determining compounds with high activity
Alzheimer disease is the most common form of dementia. Its pathogenesis incorporates many potential targets for treatment. Among the targets identified, Apolipoprotein E4 (apoE4) is especially interesting due to its catalytic role in the degradation and clearance of amyloid beta (Aβ), a risk factor for Alzheimer disease. ApoE exists in 3 isoforms which directly impact its functionality in the body. There are characteristic structural differences between them. In ApoE4 ionic interactions exist between Arg-61 and Glu-255 residues, unlike the other isoforms. Hence interruption of this interaction by inhibitors may change the structure of apoE4 to a more linear structure as observed in the other isoforms. Virtual screening of the NCI diversity set on an energy minimized protein virtual structure was performed to identify potential small molecule inhibitors and to gain further understanding of interactions that can be targeted to inhibit this protein. From the top ligands in the NCI diversity set, a peptide library was designed to target the protein.
Previous research has indicated that liquid assisted grinding (LAG) is efficient and reliable for cocrystal formation when compared to solvent crystallization and dimethyl formamide is the best solvent for grinding. Herein, we report the comparison of four screening processes: Slurry, solvent crystallization, LAG and dry grinding. Thirty-eight crystal forms containing the Narom··· COOH, Narom···OH supramolecular heterosynthons were screened in the process, and it was observed that slurry methodology is as efficient and reliable in forming cocrystals as solution crystallization. Twenty-four new crystal forms were also isolated herein. LAG was found to be more efficient as compared to dry grinding and was successful in the formation of twenty-five crystal forms of the thirty-eight screened. Dimethyl formamide still remains the best solvent for LAG. All our slurry experiments were performed in water and it was found that water can be used reliably for this method for compounds within a wide range of solubility, thereby increasing the versatility and usability of this method for future screening procedures.
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Cereto, Massagué Adrià. "Development of tools for in silico drug discovery." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/454678.
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El cribratge virtual és un mètode quimioinformàtic que consisteix en cribrar molècules bioactives de grans bases de dades de molècules petites. Això permet als investigadors d’estalviar-se el cost de provar experimentalment cents o milers de compostos candidats, reduïnt-ne el nombre fins a quantitats manejables. Per a la validació dels mètodes de cribratge virtual calen biblioteques de molècules cimbell. El programari DecoyFinder fou desenvolupat com a aplicació gràfica de fàcil ús per a la construcció de biblioteques de molècules cimbell, i fou posteriorment ampliat amb les troballes de recerca posterior sobre la construcció i rendiment de biblioteques de molècules cimbell.
El Protein Data Bank (PDB) és molt útil perquè proporciona estructures tridimensionals per a complexos proteïna-lligand, i per tant, informació sobre com interactuen. Pels mètodes de cribratge virtual que en depenen, n’és extremadament important la seva fiabilitat. El VHELIBS fou desenvolupat com a eina per a inspeccionar i identificar, fàcilment i intuitiva, les estructures fiables del PDB, basant-se en com de bo n’és l’encaix amb els seus corresponents mapes de densitat electrònica.
Mentre que el cribratge virtual prova de trobar noves molècules bioactives per determinades dianes, l’enfoc invers també s’empra: arran d’una molècula, cercar-ne dianes amb activitat biològica no documentada. Aquest cribratge invers és conegut en anglès com a “in silico target fishing”, o pesca de dianes “in silico”, i és especialment útil a l’àmbit de la reutilització de fàrmacs En començar aquesta tesi, no hi havia cap plataforma de “target fishing” de lliure accés, i tot i que durant els anys se n’han desenvolupat algunes, en tots els casos la seva predicció de bioactivitat és qualitativa. Per això es desenvolupà una plataforma pròpia de “target fishing” de lliure accés, amb la implementació d’un nou mètode que proporciona la primera predicció quantitativa de bioactivitat per aquest tipus de plataforma.El cribado virtual es un método quimioinformático que consiste en la criba de moléculas bioactivas de grandes bases de datos de moléculas pequeñas. Esto permite a los investigadores ahorrarse el coste de probar experimentalmente cientos o miles de compuestos candidatos, reduciéndolos hasta cantidades manejables. Para la validación de los métodos de cribado virtual hacen falta bibliotecas de moléculas señuelo. El software DecoyFinder fue desarrollado como aplicación gráfica de fácil uso para la construcción de bibliotecas de moléculas señuelo, y fue posteriormente ampliado con los hallazgos de investigación posterior sobre la construcción i rendimiento de bibliotecas de moléculas señuelo. El Protein Data Bank (PDB) es muy útil porque proporciona estructuras tridimensionales para complejos proteina-ligando, y por tanto, información sobre como interactúan. Para los métodos de cribado virtual que dependen de ellas, es extremadamente importante su fiabilidad. VHELIBS fue desarrollado como herramienta para inspeccionar e identificar, fácil e intuitivamente, las estructuras fiables del PDB, basándose en como de bueno es su encaje con sus correspondientes mapas de densidad electrónica. Mientras que el cribado virtual intenta encontrar nuevas moléculas bioactivas para determinadas dianas, el enfoque inverso también se utiliza: a partir de una molécula, buscar dianas donde presente actividad biológica no documentada. Este cribado inverso es conocido en inglés como “in silico target fishing”, o pesca de dianas “in silico”, y es especialmente útil en el ámbito de la reutilización de fármacos. Al comenzar esta tesis, no había ninguna plataforma de “target fishing” de libre acceso, y aunque durante los años se han desarrollado algunas, en todos los casos su predicción de bioactividad es cualitativa. Por eso se desarrolló una plataforma propia de “target fishing” de libre acceso, con la implementación de un nuevo método que proporciona la primera predicción cuantitativa de bioactividad para este tipo de plataforma.
Virtual screening is a cheminformatics method that consists of screening large small-molecule databases for bioactive molecules. This enables the researcher to avoid the cost of experimentally testing hundreds or thousands of compounds by reducing the number of candidate molecules to be tested to manageable numbers. For their validation, virtual screening approaches need decoy molecule libraries. DecoyFinder was developed as an easy to use graphical application for decoy library building, and later updated after some research into decoy library building and their performance when used for 2D similarity approaches. The Protein Data Bank (PDB) is very useful because it provides 3D structures for protein-ligand complexes and, therefore, information on how certain ligands bind and interact with their targets. For virtual screening apporaches relying on these structures, it is of the utmost importance that the data available on the PDB for the ligand and its binding site are reliable. VHELIBS was developed as a tool to easily and intuitively inspect and identify reliable PDB structures based on the goodness of fitting between ligands and binding sites and their corresponding electron density map. While virtual screening aims to find new bioactive molecules for certain targets, the opposite approach is also used: starting from a given molecule, to search for a biological target for which it presents previously undocumented bioactivity. This reverse screening is known as in silico or computational target fishing or reverse pharmacognosy, and it is specially useful for drug repurposing or repositioning. When this thesis was started, there were no freely available target fishing platforms, but some have been developed during the years. However, they are qualitative in the nature of their activity prediction, and thus we set out to develop a freely accessible target fishing web service implementing a novel method which provides the first quantitative activity prediction: Anglerfish.
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Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.
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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.
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Blake, Lynn Dong. "Antimalarial Exoerythrocytic Stage Drug Discovery and Resistance Studies." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6182.
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Malaria is a devastating global health issue that affects approximately 200 million people yearly and over half a million deaths are caused by this parasitic protozoan disease. Most commercially available drugs only target the blood stage form of the parasite, but the only way to ensure proper elimination is to treat the exoerythrocytic stages of the parasite development cycle. There is a demand for the discovery of new liver stage antimalarial compounds as there are only two current FDA approved drugs for the treatment of liver stage parasites, one of which fails to eliminate dormant forms and the other inducing hemolytic anemia in patients with G6PD deficiency. In efforts to address the dire need for liver stage drugs, we developed a high-throughput liver stage drug-screening assay to identify liver stage active compounds from a wide variety of chemical libraries with known blood stage activity. The liver stage screen led us to further investigate an old, abandoned compound known as menoctone. Menoctone was developed as a liver stage active antimalarial, however, the development of more potent compounds led to the abandonment of further menoctone research. Our research demonstrated that resistant parasites can transmit mutations through mosquitoes, which was previously believed to not be possible. Furthermore, we studied a novel genetic marker that may indicate potential resistance against malaria parasite infection and the cytotoxic effects associated with the disease. Future experiments aim to identify and advance our methods for the elimination of Plasmodium exoerythrocytic parasites.
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Croset, Samuel. "Drug repositioning and indication discovery using description logics." Thesis, University of Cambridge, 2014. https://www.repository.cam.ac.uk/handle/1810/246260.
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Drug repositioning is the discovery of new indications for approved or failed drugs. This practice is commonly done within the drug discovery process in order to adjust or expand the application line of an active molecule. Nowadays, an increasing number of computational methodologies aim at predicting repositioning opportunities in an automated fashion. Some approaches rely on the direct physical interaction between molecules and protein targets (docking) and some methods consider more abstract descriptors, such as a gene expression signature, in order to characterise the potential pharmacological action of a drug (Chapter 1). On a fundamental level, repositioning opportunities exist because drugs perturb multiple biological entities, (on and off-targets) themselves involved in multiple biological processes. Therefore, a drug can play multiple roles or exhibit various mode of actions responsible for its pharmacology. The work done for my thesis aims at characterising these various modes and mechanisms of action for approved drugs, using a mathematical framework called description logics. In this regard, I first specify how living organisms can be compared to complex black box machines and how this analogy can help to capture biomedical knowledge using description logics (Chapter 2). Secondly, the theory is implemented in the Functional Therapeutic Chemical Classification System (FTC - https://www.ebi.ac.uk/chembl/ftc/), a resource defining over 20,000 new categories representing the modes and mechanisms of action of approved drugs. The FTC also indexes over 1,000 approved drugs, which have been classified into the mode of action categories using automated reasoning. The FTC is evaluated against a gold standard, the Anatomical Therapeutic Chemical Classification System (ATC), in order to characterise its quality and content (Chapter 3). Finally, from the information available in the FTC, a series of drug repositioning hypotheses were generated and made publicly available via a web application (https://www.ebi.ac.uk/chembl/research/ftc-hypotheses). A subset of the hypotheses related to the cardiovascular hypertension as well as for Alzheimer’s disease are further discussed in more details, as an example of an application (Chapter 4). The work performed illustrates how new valuable biomedical knowledge can be automatically generated by integrating and leveraging the content of publicly available resources using description logics and automated reasoning. The newly created classification (FTC) is a first attempt to formally and systematically characterise the function or role of approved drugs using the concept of mode of action. The open hypotheses derived from the resource are available to the community to analyse and design further experiments.
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Olsson, Ing-Marie. "Experimental Designs at the Crossroads of Drug Discovery." Doctoral thesis, Umeå : Department of Chemistry, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-693.
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Tjernberg, Agneta. "Protein mass spectrometry in the drug discovery process /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-251-9/.
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Acoca, Stephane. "In silico methods in drug discovery and development." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=110376.
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Computational drug design methods have become increasingly invaluable in the drug discovery and development process. Throughout this thesis will be described the development and application of methods that are used at every stage of the drug discovery and development pipeline. In Chapter 2 will take a look at the use computational methods towards the understanding and development of two novel Bcl-2 inhibitors, Obatoclax and ABT-737, being developed for the treatment of Cancer. The study proposes certain mechanisms through which ABT-737 displays selectivity towards certain targets within the Bcl-2 family. Additionally, we propose a binding mode for Obatoclax which is in accordance with experimental data. The following Chapter addresses the use of virtual screening for the identification of novel lead compounds. Trypanosoma brucei RNA Editing Ligase 1 was chosen as the target for the development of treatments against Trypanosoma infections and C35, a potent novel inhibitor of the enzyme, was identified. Furthermore, our research shows that the action of C35 extends to inhibition of several critical enzyme activities required for the RNA editing process as well as compromising the integrity of the multiprotein complex which carries it out. The following Chapter takes a look at the use of mass spectrometry data in order to expedite discovery of bioactive compounds in natural products. We developed an algorithm which analyses MS/MS data in order to derive the Molecular Formula of the compound. The novel algorithm obtained a 95% success rate on a test set of 91 compounds. The last Chapter of the thesis explores the use of molecular dynamics to generate a conformational ensemble of targets for virtual screening. Conformational ensembles were generated for a target test set taken from the Directory for Useful Decoys. The results showed that molecular dynamics-based conformational ensembles provided remarkable improvements on 2 of the targets tested due to the enhanced capacity to properly dock compounds in otherwise restricted structures. The last Chapter of the thesis is a general discussion on the work of the thesis and a proposal on how all can be integrated within the drug discovery and development pipeline.Les méthodes the modélisation sont devenues un outil inestimable dans le processus de découverte et de développement de nouveaux médicaments. Au cours de cette thèse va être décrit le développement et l'application de méthodes utilisés à chaque stage de la découverte et du développement de produits pharmaceutiques. Le Chapitre 2 est un aperçu sur l'utilisation de méthodes computationnelles vers le développement de deux nouveaux inhibiteurs des protéines Bcl-2, Obatoclax et ABT-737, en développement pour le traitement du Cancer. L'étude propose certains mécanismes d'ABT-737 qui expliquent ca sélectivité envers les membres de la famille Bcl-2. De plus, nous proposons un mécanisme d'attachement pour Obatoclax qui conforme aux données expérimentales. Le Chapitre suivant adresse l'utilisation du dépistage virtuel pour l'identification de nouvelles molécules mère. La Ligase de l'Edition d'ARN du Trypanosoma brucei a été choisie comme cible pour le développement de traitements contre des infections dû au Trypanosome et C35 a été identifié comme nouvel inhibiteur de l'enzyme. En outre, notre recherche démontre que l'action de C35 s'étends a l'inhibition de plusieurs enzymes nécessaires pour le mécanisme d'édition de l'ARN en plus de compromettre l'intégrité du complexe multi-protéinique qui l'effectue. Le Chapitre suivant prends regard a l'utilisation de donnes dérivant de la spectrométrie de masse pour but d'accélérer la découverte de molécules bioactives venant de sources naturelles. Nous avons développé un algorithme qui analyse les données MS/MS pour but de dériver la formule moléculaire du composé. Le nouvel algorithme a obtenu un taux de succès s'élevant à 95% sur un ensemble test de 91 molécules. Le dernier Chapitre de la thèse explore l'utilisation de simulations de dynamique moléculaire pour générer en ensemble conformationel de protéines cible pour son utilisation dans le dépistage virtuel. Les ensembles conformationel ont étés généré pour une série test obtenu d'un répertoire attitré 'Directory for Useful Decoys'. Les résultats démontrent que les ensembles conformationel dérivés de la dynamique moléculaire ont apporté des améliorations remarquables sur deux des cibles testées dû à une capacité accrue de placement approprié des molécules dans un site qui est autrement très restreint. Le dernier Chapitre de cette thèse est une discussion générale sur le travail accomplie et une proposition sur la manière dont tous les éléments sont intégrer dans un protocole de découverte et de développement de produits pharmaceutiques.
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Moshiri, Houtan. "Targeting the editosome - from drug discovery to function." Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=117029.
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Trypanosomatid pathogens cause devastating diseases in humans and animals and continue to pose a major challenge in the drug development. Mitochondrial gene expression in trypanosomatid pathogens requires extensive post transcriptional modification, known as RNA editing which generates translatable transcripts for essential components of parasite respiratory complex. RNA editing is catalyzed by a multiprotein complex called editosome. Most of the editosome proteins are essential for parasite survival, thereby making editosome a suitable target for drug discovery. However, how editosome proteins are assembled and perform RNA editing is not fully understood. We hypothesized that identification of novel compounds targeting and perturbing this unique process will not only help to determine the function and assembly of the editosome proteins but may also be used as compounds against all three major trypanosomatid pathogens. In the first part of the thesis, I present developing and testing of a fluorescence resonance energy transfer (FRET)-based high throughput screening assay for identification of compounds that inhibit editosome function. Furthermore, we use our assay to confirm inhibiting effect of known inhibitors of an essential editosome protein, T. brucei RNA editing ligase 1(TbREL1). Using our assay, we also show that these inhibitors are able to inhibit RNA editing in the context of partially purified editosome.The second part of thesis describes a pilot screen of a small set of compounds that were identified via virtual screening of a chemical library against TbREL1. Using secondary biochemical assays we confirmed the specificity of inhibition and showed that these compounds find other targets in addition to the intended TbREL1 target. We showed for the first time that the inhibitory compounds interfere with the interaction of editosome with substrate RNA and consequently lead to the loss of all activities associated with the functional editosome. Moreover, we show that this inhibition is able to interfere with the assembly of the editosome proteins and propose a model to describe possible mode of inhibition by these compounds. In the third part of thesis, I present a study that compares the mechanism of action of inhibitory compounds in the context of recombinant versus native TbREL1 in the editosome. We show that these compounds interfere with RNA substrate binding activities of the editosome accessory factors MRP1&MRP2 (mitochondrial RNA binding proteins 1&2) which result in perturbing other editing activities. We show that these compounds can only inhibit TbREL1 function when the accessory factors are not present. Furthermore, we performed alanine mutagenesis of the amino acid residues of TbREL1 that are predicted to bind inhibitors. We provide a detailed map of the structure of enzyme-inhibitor complex with an opportunity for future design of more potent inhibitors of TbREL1. These studies have led to identification and characterization of novel inhibitors that result in inactivation of editosome function. Moreover, elucidation of the mechanism of RNA editing inhibition provides a basis for future selection of more efficient and potent inhibitors against the editosome proteins. Therefore, this work contributes to both the functional studies of an essential gene expression mechanism and to an exciting possibility for future drug development against three related trypanosomatid pathogens.Pathogènes des trypanosomatides sont responsable de maladies dévastatrices chez les humains et les animaux et continuent de poser un défi majeur dans le développement de médicaments. L'expression du gène mitochondrial chez les agents pathogènes de la famille des trypanosomatides nécessite une modification post transcriptionnelle vaste, connue sous le nom d'édition de l'ARN, qui génère des transcrits traduisibles pour les composants essentiels du complexe respiratoire du parasite. L'édition de l'ARN est catalysée par un complexe multiprotéique appelé éditosome, dont la plupart des protéines sont essentiels pour la survie du parasite, ce qui fait de l'éditosome une cible appropriée pour la découverte de médicaments. Cependant, la façon dont les protéines de l'éditosome sont assemblés et effectue l'édition de l'ARN n'est pas entièrement comprise. Nous émettons l'hypothèse que l'identification de nouveaux composés ciblant et perturbant ce processus unique permettra non seulement de déterminer la fonction et l'assemblage des protéines de l'éditosome mais également d'être utilisé en tant que composés contre les trois principaux pathogènes de la famille des trypanosomatides. Dans la première partie de la thèse, je présente l'élaboration et l'essai basé sur la fluorescence avec un criblage à haut débit pour l'identification de composés qui inhibent la fonction de l'éditosome. En outre, nous avons utilisé notre test pour confirmer l'effet inhibiteur des inhibiteurs connus d'une protéine essentielle de l'éditosome, T. brucei RNA editing ligase 1(TbREL1). Grâce à notre test, nous avons montré également que ces inhibiteurs sont capables d'inhiber la fonction d'édition de l'ARN dans le contexte de l'éditosome partiellement purifié. La deuxième partie de la thèse décrit un essai pilote d'un petit ensemble de composés qui ont été identifiés par criblage virtuel contre TbREL1. En utilisant des tests secondaires, nous avons confirmé la spécificité de l'inhibition et montré que ces composés ont trouvé d'autres cibles en plus de celle de TbREL1. Nous avons montré pour la première fois que les composés inhibiteurs interférent avec l'interaction de l'éditosome à l'ARN substrat et par conséquent entraîne la perte de toutes les activités liées à la fonction de l'éditosome. De plus, nous avons montré que cette inhibition est capable d'interférer avec l'assemblage des protéines de l'éditosome et avons proposé un modèle pour décrire le mécanisme possible d'inhibition par ces composés. Dans la troisième partie de la thèse, je présente une étude qui compare le mécanisme d'action des composés inhibiteurs dans le contexte de TbREL1 recombinant ou natif dans l'éditosome. Nous avons montré que ces composés interfèrent avec les activités de liaison à l'ARN des facteurs accessoires de l'éditosome MRP1 et MRP2 (protéines liant les ARN mitochondriaux 1 & 2) qui aboutissent à la perturbation d'autres activités d'édition. Nous avons montré que ces composés peuvent seulement inhiber la fonction de TbREL1 en l'absence des facteurs accessoires. En outre, nous avons effectué une mutagenèse d'alanine des résidus d'acides aminés de TbREL1 qui sont prévus dans la liaison aux inhibiteurs. Nous fournissons une carte détaillée de la structure du complexe enzyme-inhibiteur avec une opportunité de conception future de plus puissants inhibiteurs de TbREL1. Ces études ont conduit à l'identification et la caractérisation de nouveaux inhibiteurs qui se traduisent par l'inactivation de la fonction de l'éditosome. En outre, l'élucidation du mécanisme d'inhibition de l'édition de l'ARN fournit une base pour la sélection future d'inhibiteurs plus efficaces et plus puissants contre les protéines de l'éditosome. Par conséquent, ce travail contribue à la fois aux études fonctionnelles d'un mécanisme d'expression d'un gène essentiel et à une possibilité passionnante pour le développement de futur médicament contre trois agents pathogènes liés de la famille des trypanosomatides.
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Khotavivattana, Tanatorn. "¹⁸F-labelling of new chemotypes for drug discovery." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:d4e8c8fd-f07d-44c3-b95b-5e7ad4127dde.
Full textAbstract:
In this thesis, the 18F-labelling of new "chemotypes" will be described with the aim of application in pharmaceutically interesting targets. In Chapter 1, a general introduction to the effect of fluorine substituents on molecular properties and reactivity is provided. This includes the application of organofluorine in both medicinal chemistry and positron emission tomography. Chapter 2 describes a novel silver-mediated 18F-labelling of Ar-SCF3, Ar OCF3 and Ar-OCF2H, including [18F]Riluzole, the 18F labelled version of a drug for treatment of amyotrophic lateral sclerosis (ALS). This work demonstrates that AgOTf can induce halogen exchange nucleophilic 18F-fluorination under mild reaction conditions with a wide range of substrates. In addition, the 18F-labelled Ar-SCF3 substrate is further transformed into the [18F]Umemoto reagent in a single step. The Umemoto reagent has been extensively used for electrophilic trifluoromethylation of various functional groups. Therefore the labelling of this reagent could potentially expand the radiochemical space available for PET applications. To augment the utility of this reagent, we developed a late-stage stereoselective trifluoromethylation-thiocyclisation of alkenes using electrophilic trifluoromethylating reagents such as Umemoto reagent or Togni reagent, which will be discussed in Chapter 3. In this process, thiourea acts as both S-nucleophile and CF3 radical initiator; therefore no metal or photoredox catalyst is required. The reaction affords novel trifluoromethylated 2-amino-thiazolines and 2-amino-thiazines, important scaffolds in the development of aspartate beta-secretase enzyme (BACE-1) inhibitors, a therapeutic target for Alzheimer's disease. Chapter 4 investigates the 18F-labelling of a,a-difluoro-a-aryloxyacetic acid, a class of substrate that can serve as a versatile intermediate which can undergo various decarboxylative functionalisation reactions to afford a wide range of novel 18F labelled a fluorinated aryl ethers. Finally, Chapter 5 gives full experimental procedures and characterisation data for all compounds.
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Paterson, Andrew. "Selective catalytic C-H functionalisation for drug discovery." Thesis, University of Bath, 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.720659.
Full textAbstract:
This thesis details the current methods for meta-selective C-H functionalisation and contains three chapters relating to the area of ruthenium catalysed meta selective functionalisation by σ-activation. The first of which contains a published manuscript entitled “Catalytic meta-selective C-H functionalization to construct quaternary carbon centres” and describes a meta selective tertiary alkylation procedure on 2-phenylpyridine substrates. Key findings from this work provide good evidence for a radical based mechanism and proposes a catalytic cycle involving two distinct roles for the ruthenium catalyst; both in the activation of the substrate molecule and in the formation of a tertiary radical coupling partner. The second chapter contains another published manuscript entitled “Mechanistic insight into ruthenium catalysed meta-sulfonation of 2-phenylpyridine” and provides mechanistic analysis for the meta selective sulfonation of 2-phenylpyridine. Key findings from this work show through stoichiometric experiments that sulfonation occurs at the position para to the C-Ru bond formed following cyclometalation with a radical addition being implied. The work also shows that the catalytic species involved do not require an arene ligand and deuterium labelling studies identified a likely rate limiting radical sulfonation step. The final chapter contains additional work relating to the use of α-halo carbonyl coupling reagents to enable meta selective primary, secondary and tertiary alkylations. The use of a triphenylphosphine ligand source was necessary for the coupling of primary α-halo carbonyl coupling partners at the meta position. Crucially, this transformation was not possible with simple, straight-chain alkyl halides, highlighting the privileged reactivity of α-halo carbonyl coupling reagents. This work also contains experimental and computational mechanistic analysis which reveals additional support for a dual activation pathway.
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Heiney, John P. (John Patrick). "Optimization of preclinical profiling operations in drug discovery." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/39595.
Full textAbstract:
Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 2007.Includes bibliographical references (p. 55-56).
In early-stage drug discovery, thousands of compounds must be tested using in vitro assays to determine their exposure and safety characteristics. This data is used to guide the selection of potential drug candidates and to help chemists in optimize the properties of those compounds. At Novartis, an internal service organization called Preclinical Compound Profiling (PCP) provides these services to the company as a whole. The purpose of this internship was to help PCP make significant improvements in cycle time and cost effectiveness without reducing the quality of information provided to their customers. The project utilized a series of deterministic and stochastic models to predict the impact of multiple operational changes on cost and cycle time. The data from each model was synthesized to create a unified view allowing combinations of changes to be analyzed together. This data was evaluated in the context of the customer needs and organizational strategy to present recommendations. Changes were implemented that will reduce materials spending by $500,000 per year while simultaneously increasing capacity, reducing cycle time, and improving customer value. Additional recommendations were developed that will enable further improvements.
by John P. Heiney.
S.M.
M.B.A.
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Davis, Katherine A. D. "Antibody drug discovery: From Idea to Biotherapeutic Molecule." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104261.
Full textAbstract:
Thesis: M.B.A., Massachusetts Institute of Technology, Sloan School of Management, 2016.Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 90-91).
Graybel (a fictitious name used for privacy reasons) is a large developer of pharmaceuticals. Graybel's Antibody Protein Engineering Group (APEG) is responsible for early stage drug development of biotherapeutic molecules. Part of this responsibility is delivering high quality molecules while meeting tight deadlines. Across the industry there is constant pressure to decrease timelines, while at the same time the complexity of molecules is increasing. In order to meet this challenge, APEG must be highly adaptable. Unfortunately, unanticipated biology, long project lead times, unpredictable workflows and inadequate workflow tracking systems make it difficult to precisely determine what causes delays. This uncertainty, combined with the inability to quickly pilot changes to process or methodology, makes each potential change both risky and costly. The goal of this project was to provide APEG with two things: the knowledge needed to build a robust workflow tracking system and simulations that would assist in finding root causes of issues and allow for low-cost piloting of potential solutions. Combined, a workflow tracking database and decision tool would greatly reduce the risk associated with implementing changes, allowing APEG to adapt to meet increasingly difficult industry standards. Multiple avenues were used to collect the data needed on APEG's workflow. The primary source of data is interviews, with both management and experienced bench workers. These interviews provided data on workflow paths and estimates for workflow stage durations that could not be found elsewhere. In addition, they provided a way for APEG members to be involved in the project. Additional data was gathered from rudimentary systems that are used to track workflow within some functional groups. This data was then used to create detailed process maps, and simulations. Once validated, simulation results were analyzed and experimented with to determine current bottlenecks, potential future issues and possible fixes for these problems. In addition, a new metric was introduced for quantitatively evaluating the difficulty of a project called the Technology Readiness Level (TRL). Essential project decisions were identified, and recommendations made to track those issues. Bottlenecks were identified through queue analysis. Potential changes to fix these and other issues were piloted to determine effect. Future states, both with and without these changes, were simulated to determine potential problems. From this, causes of current and potential future delay were identified and recommendations developed. Recommendations included staffing changes, cross training, real-life piloting and developing a deeper understanding of certain processes.
by Katherine A.D. Davis.
M.B.A.
S.M.
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Nigsch, Florian. "Computational prediction of molecular properties for drug discovery." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611123.
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Islam, R. S. "Novel engineering tools to aid drug discovery processes." Thesis, University College London (University of London), 2007. http://discovery.ucl.ac.uk/1444794/.
Full textAbstract:
A major bottleneck in drug discovery is the production of soluble human recombinant protein for functional, biochemical and structural analyses. The level of recombinant protein expression is controlled by a complex relationship between both biological and engineering variables. Due to the inter-play between these variables and standard experimental methods, the identification of the key variables which lead to improved protein expression can sometimes be missed. This thesis presents a framework which underpins the generation of large quantities of soluble recombinant protein in E. coli in a rapid and cost-effective manner. To achieve this goal, Design of Experiments (DoE) was first employed in combination with microwell plate (MWP) fermentations to investigate the wide array of protein expression variables. These tools are well suited to high-throughput expression requirements as they afford large savings in time, cost and resource requirements. The information generated from these MWP experiments was then exploited to devise a strategy for reproducing the process within stirred- tank reactors (STRs). The DoE methodology was first used to identify relevant protein expression variables including fermentation variables (media type and fermentation time), protein induction variables (inducer concentration and induction time) and environmental variables such as oxygen transfer rate, temperature and pH. Ten factors were screened overall at the microwell scale and three were investigated further through optimisation designs. The application of DoE led to a robust understanding of the process and resulted in protein yields five-fold greater than those obtained under standard shake-flask conditions. The most significant factors were post-induction period and shaking speed, the latter of which is strongly related to the mass transfer coefficient, faa. In order to translate this stable and optimised small-scale expression system to a production-scale stirred-tank reactor (STR), an understanding of the engineering parameters at both scales of operation was crucial. This need was complicated by significant differences between the MWPs and STRs such as geometry, mode of aeration and agitation, and the effects of surface tension. In this work, the MWP fermentation results led to the hypothesis that operation at a constant kia value would facilitate predictable scale translation. However, there currently exists very little published work on the characterisation of kia within MWPs. Miniature oxygen probes were, therefore, used to characterise MWP kia values directly via the static gassing-out method over a range of square-well MWP formats and shaking speeds. This information was then used to translate the performance of a 3ml MWP E. coli fermentation, on the basis of matched faa, to STR working volumes of 51 and 451. The efficacy of scale-up was confirmed by performing F tests on pairs of profiles for cell growth and expression levels of recombinant firefly luciferase. This rapid, accurate and direct method of kia characterisation within MWPs enabled a 15,000-fold direct scale-up of fermentation performance in terms of cell growth and protein expression from MWP to STR.
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Roberts, N. J. "Old and new targets in antimalarial drug discovery." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3007683/.
Full textAbstract:
The increasing emergence of resistance to commonly used therapies has placed a huge strain on the prevention and control of malaria; therefore, there is an urgent need to develop novel antimalarial agents. The aim of this research was to design and synthesise a library of potent antimalarial compounds, with desirable pharmacokinetic profiles, in order to identify a drug candidate suitable for preclinical development. This research was divided into two main sections: x The synthesis of compounds deigned to inhibit IspD, a novel target in antimalarial drug discovery x The late stage development of a series of endoperoxide-based antimalarials, which are derived from the structure of artemisinin A library of benzisothiazolinone compounds was generated to target the IspD enzyme. Many of these compounds displayed low micromolar inhibitory activity against both enzymatic and phenotypic assays in vitro and an investigation into structure-activity relationships around the core of these benzisothiazolinones was also conducted. The most potent compound to emerge, a CH2 linked benzisoselenazolone, had an IC50 of 0.17 μM against PfIspD and 5.54 μM against Pf3D7. These compounds represent a novel class of IspD inhibitor, which have the potential for further development as antimalarial agents. A number of 1,2,4,5-tetraoxane analogues were also prepared in order to develop an antimalarial agent suitable for a single-dose cure. The most potent analogue, N205, had an IC50 of 1.3 nM and an average mouse survival of 26.3 days (66% cure rate) following a single dose. A less than optimal stability profile for N205 led to the further development of another potent tetraoxane analogue, E209. Optimisation of the synthetic pathway led to the generation of E209 in a series of five high-yielding steps that are suitable for large-scale production. E209 represents the first 1,2,4,5-tetraoxane that is comparable, in terms of both efficacy and PK/PD profiles, to OZ439, and is a candidate for pre-clinical development.