Thesis (M.Sc.)--University of Wollongong, 2004. / Typescript. Includes bibliographical references: leaf 121-148.

Thesis (Ph. D.)--University of Wisconsin, 1950. / Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves [71-73]).

Made available in DSpace on 2014-06-11T19:23:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-05-11Bitstream added on 2014-06-13T20:10:54Z : No. of bitstreams: 1 nicoleti_nh_me_bauru.pdf: 1244120 bytes, checksum: 82b0fc15919f6c3214248fe48efec3e6 (MD5) / Neste trabalho estudamos dois grupos de moléculas: as anilinoquinolinas e as sulfonamidas, inibidores do Plasmodium causador da malária, com o objetivo de correlacionar a estrutura eletrônica com a atividade antimalarial. Em nossas buscas utilizamos métodos empíricos e semi-empíricos para o estudo conformacional e obtenção dos descritores eletrônicos. Também aplicamos vários métodos estatísticos como: Regressão Linear Simples e Múltipla, Análise de Componentes Principais (PCA) e Análise Discriminante Linear (LDA), para verificar uma possível correlação estrutura-atividade dessas moléculas. Os resultados apontaram os descritores eletrônicos mais relevantes na classificação das moléculas antimalariais. / In this work we study two groups of antimalarial compounds: the anilinoquinolines and sulfonamides, aiming the correlation of the electronic structure with the antimalarial activity. In our studies we employ empirical and semi empirical quantum chemistry methods for the geometry optimization and calculation of the electronic descriptors. Also we employed the statistical methods Simple and Multiple Linear Regression, Principal Component Analysis (PCA) and Linear Discriminating Analysis (LDA), to verify the existence of a possible structure-activity correlation for these compounds. The results of this work have pointed out the best electronic descriptors in the classification of the active compounds.

Malaria continues to be an enormous health-threat in the developing world and the emergence of drug resistance has further compounded the problem. The parasite-specific enzyme, 1-deoxY-D-xylulose-S-phosphate reductoisomerase (DXR), has recently been validated as a promising antimalarial drug target. The present study comprises a combination of synthetic, physical organic, computer modelling and bioassay techniques directed towards the development of novel DXR inhibitors. A range of 2-heteroarylamino-2-oxoethyl- and 2- heteroarylamino-2-oxopropyl phosphonate esters and their corresponding phosphonic acid salts have been synthesised as analogues of the highly active DXR inhibitor, fosmidomycin. Treatment of the heteroarylamino precursors with chloroacetyl chloride or chloropropionyl chloride afforded chloroamide intermediates, Arbuzov reactions of which led to the corresponding diethyl phosphonate esters. Hydrolysis of the esters has been effected using bromotrimethylsilane. Twenty-four new compounds have been prepared and fully characterised using elemental (HRMS or combustion) and spectroscopic (1- and 2-D NMR and IR) analysis. A 31p NMR kinetic study has been carried out on the two-step silylation reaction involved in the hydrolysis of the phosphonate esters and has provided activation parameters for the reaction. The kinetic analysis was refined using a computational method to give an improved fit with the experimental data. Saturation transfer difference (STD) NMR analysis, computer-simulated docking and enzyme inhibition assays have been used to evaluate the enzyme-binding and -inhibition potential of the synthesised ligands. Minimal to moderate inhibitory activity has been observed and several structure-activity relationships have been identified. In silica exploration of the DXR active site has revealed an additional binding pocket and information on the topology of the active site has led to the de novo design of a new series of potential ligands. / KMBT_363 / Adobe Acrobat 9.54 Paper Capture Plug-in

Philosophiae Doctor - PhD / Introduction: There is an exigent need to develop novel antimalarial drugs in view of the mounting disease burden and emergent resistance to the presently used drugs against the malarial parasites. A large amount of natural products, especially those used in ethnomedicine for malaria, have shown varying in-vitro antiplasmodial activities. Facilitating antimalarial drug development from this wealth of natural products is an imperative and laudable mission to pursue. However, the limited resources, high cost, low prospect and the high cost of failure during preclinical and clinical studies might militate against pursue of this mission. Chemoinformatics techniques can simulate and predict essential molecular properties required to characterize compounds thus eliminating the cost of equipment and reagents to conduct essential preclinical studies, especially on compounds that may fail during drug development. Therefore, applying chemoinformatics techniques on natural products with in-vitro antiplasmodial activities may facilitate identification and prioritization of these natural products with potential for novel mechanism of action, desirable pharmacokinetics and high likelihood for development into antimalarial drugs. In addition, unique structural features mined from these natural products may be templates to design new potential antimalarial compounds. Method: Four chemoinformatics techniques were applied on a collection of selected natural products with in-vitro antiplasmodial activity (NAA) and currently registered antimalarial drugs (CRAD): molecular property profiling, molecular scaffold analysis, machine learning and design of a virtual compound library. Molecular property profiling included computation of key molecular descriptors, physicochemical properties, molecular similarity analysis, estimation of drug-likeness, in-silico pharmacokinetic profiling and exploration of structure-activity landscape. Analysis of variance was used to assess statistical significant differences in these parameters between NAA and CRAD. Next, molecular scaffold exploration and diversity analyses were performed on three datasets (NAA, CRAD and malarial data from Medicines for Malarial Ventures (MMV)) using scaffold counts and cumulative scaffold frequency plots. Scaffolds from the NAA were compared to those from CRAD and MMV. A Scaffold Tree was also generated for all the datasets. Thirdly, machine learning approaches were used to build four regression and four classifier models from bioactivity data of NAA using molecular descriptors and molecular fingerprints. Models were built and refined by leave-one-out cross-validation and evaluated with an independent test dataset. Applicability domain (AD), which defines the limit of reliable predictability by the models, was estimated from the training dataset and validated with the test dataset. Possible chemical features associated with reported antimalarial activities of the compounds were also extracted. Lastly, virtual compound libraries were generated with the unique molecular scaffolds identified from the NAA. The virtual compounds generated were characterized by evaluating selected molecular descriptors, toxicity profile, structural diversity from CRAD and prediction of antiplasmodial activity. Results: From the molecular property profiling, a total of 1040 natural products were selected and a total of 13 molecular descriptors were analyzed. Significant differences were observed between the natural products with in-vitro antiplasmodial activities (NAA) and currently registered antimalarial drugs (CRAD) for at least 11 of the molecular descriptors. Molecular similarity and chemical space analysis identified NAA that were structurally diverse from CRAD. Over 50% of NAA with desirable drug-like properties were identified. However, nearly 70% of NAA were identified as potentially "promiscuous" compounds. Structure-activity landscape analysis highlighted compound pairs that formed "activity cliffs". In all, prioritization strategies for the natural products with in-vitro antiplasmodial activities were proposed. The scaffold exploration and analysis results revealed that CRAD exhibited greater scaffold diversity, followed by NAA and MMV respectively. Unique scaffolds that were not contained in any other compounds in the CRAD datasets were identified in NAA. The Scaffold Tree showed the preponderance of ring systems in NAA and identified virtual scaffolds, which maybe potential bioactive compounds or elucidate the NAA possible synthetic routes. From the machine learning study, the regression and classifier models that were most suitable for NAA were identified as model tree M5P (correlation coefficient = 0.84) and Sequential Minimization Optimization (accuracy = 73.46%) respectively. The test dataset fitted into the applicability domain (AD) defined by the training dataset. The “amine” group was observed to be essential for antimalarial activity in both NAA and MMV dataset but hydroxyl and carbonyl groups may also be relevant in the NAA dataset. The results of the characterization of the virtual compound library showed significant difference (p value < 0.05) between the virtual compound library and currently registered antimalarial drugs in some molecular descriptors (molecular weight, log partition coefficient, hydrogen bond donors and acceptors, polar surface area, shape index, chiral centres, and synthetic feasibility). Tumorigenic and mutagenic substructures were not observed in a large proportion (> 90%) of the virtual compound library. The virtual compound libraries showed sufficient diversity in structures and majority were structurally diverse from currently registered antimalarial drugs. Finally, up to 70% of the virtual compounds were predicted as active antiplasmodial agents. Conclusions:Molecular property profiling of natural products with in-vitro antiplasmodial activities (NAA) and currently registered antimalarial drugs (CRAD) produced a wealth of information that may guide decisions and facilitate antimalarial drug development from natural products and led to a prioritized list of natural products with in-vitro antiplasmodial activities. Molecular scaffold analysis identified unique scaffolds and virtual scaffolds from NAA that possess desirable drug-like properties, which make them ideal starting points for molecular antimalarial drug design. The machine learning study built, evaluated and identified amply accurate regression and classifier accurate models that were used for virtual screening of natural compound libraries to mine possible antimalarial compounds without the expense of bioactivity assays. Finally, a good amount of the virtual compounds generated were structurally diverse from currently registered antimalarial drugs and potentially active antiplasmodial agents. Filtering and optimization may lead to a collection of virtual compounds with unique chemotypes that may be synthesized and added to screening deck against Plasmodium.

Antimalarial drug discovery remains a challenging endeavour as malaria parasites continue to develop resistance to drugs, including those which are currently the last line of defence against the disease. Plasmodium falciparum is the most virulent of the malaria parasites and it delivers its deadliest impact during the erythrocytic stages of the parasite’s life cycle; a stage characterised by elevated catabolism of haemoglobin and anabolism of parasite proteins. The present study investigates the use of nanotechnology in the form of metallic silver nanoparticles (AgNPs) against P. falciparum leucine aminopeptidase (PfLAP), a validated biomedical target involved in haemoglobin metabolism. AgNPs were also tested against the human homolog cytosolic Homo sapiens leucine aminopeptidase (HsLAP) to ascertain their selective abilities. PfLAP and HsLAP were successfully expressed in Escherichia coli BL21(DE3) cells. PfLAP showed optimal thermal stability at 25 °C and optimal pH stability at pH 8.0 with a Km of 42.7 mM towards leucine-p-nitroanilide (LpNA) and a Vmax of 59.9 μmol.ml⁻¹.min⁻¹. HsLAP was optimally stable at 37 °C and at pH 7.0 with a Km of 16.7 mM and a Vmax of 17.2 μmol.ml⁻¹.min⁻¹. Both enzymes exhibited optimal activity in the presence of 2 mM Mn²⁺. On interaction with polyvinylpyrrolidone (PVP) stabilised AgNPs, both enzymes were inhibited to differing extents with PfLAP losing three fold of its catalytic efficiency relative to HsLAP. These results show the ability of AgNPs to selectively inhibit PfLAP whilst having much lesser effects on its human homolog. With the use of available targeting techniques, the present study shows the potential use of nanotechnology based approaches as “silver bullets” that can target PfLAP without adversely affecting the host. However further research needs to be conducted to better understand the mechanisms of AgNP action, drug targeting and the health and safety issues associated with nanotechnology use.

The advent of advanced modern nanotechnology techniques offers new and exciting opportunities to develop novel nanotech-derived antimalarial nanodrugs with enhanced selective and targeting abilities that allow for lower effective drug dosages, longer drug persistence and reduced drug degradation within the body. Using a nanodrug approach also has the advantage of avoiding drug resistance problems that plague reconfigured versions of already-existing antimalarial drugs. In this study recombinant triosephosphate isomerase enzymes from Plasmodium falciparum (PfTIM) and Humans (hTIM) were recombinantly expressed, purified and characterised. PfTIM was shown to have optimal pH stability at pH 5.0-5.5 and thermal stability at 25°C with Km 4.34 mM and Vmax 0.876 μmol.ml⁻ₑmin⁻ₑ. For hTIM, these parameters were as follows: pH optima of 6.5-7.0; temperature optima of 30°C, with Km 2.27 mM and Vmax 0.714 μmol.ml⁻ₑmin⁻ₑ. Recombinant TIM enzymes were subjected to inhibition studies using polyvinylpyrrolidone (PVP) stabilised silver nanoparticles (AgNPs) of 4-12 nm in diameter. These studies showed that the AgNPs were able to selectively inhibit PfTIM over hTIM with an 8-fold greater decrease in enzymatic efficiency (Kcat/Km) observed for PfTIM, as compared to hTIM, for kinetics tests done using 0.06 μM of AgNPs. Complete inhibition of PfTIM under optimal conditions was achieved using 0.25 μM AgNPs after 45 minutes while hTIM maintained approximately 31% of its activity at this AgNP concentration. The above results indicate that selective enzymatic targeting of the important, key metabolic enzyme TIM, can be achieved using nanotechnology-derived nanodrugs. It was demonstrated that the key structural differences, between the two enzyme variants, were significant enough to create unique characteristics for each TIM variant, thereby allowing for selective enzyme targeting using AgNPs. If these AgNPs could be coupled with a nanotechnology-derived, targeted localization mechanism – possibly using apoferritin to deliver the AgNPs to infected erythrocytes (Burns and Pollock, 2008) – then such an approach could offer new opportunities for the development of viable antimalarial nanodrugs. For this to be achieved further research into several key areas will be required, including nanoparticle toxicity, drug localization and testing the lethality of the system on live parasite cultures.

Plasmodium is a genus of parasites causing malaria, a virulent protozoan infection in humans resulting in over a million deaths annually. Treatment of malaria is increasingly limited by parasite resistance to available drugs. Hence, there is a need to identify new drug targets and authenticate antimalarial compounds that act on these targets. A relatively new therapeutic approach targets proteolytic enzymes responsible for parasite‟s invasion, rupture and hemoglobin degradation at the erythrocytic stage of infection. Cysteine proteases (CPs) are essential for these crucial roles in the intraerythrocytic parasite. CPs are a diverse group of enzymes subdivided into clans and further subdivided into families. Our interest is in Clan CA, papain family C1 proteases, whose members play numerous roles in human and parasitic metabolism. These proteases are produced as zymogens having an N-terminal extension known as the prodomain which regulates the protease activity by selectively inhibiting its active site, preventing substrate access. A Clan CA protease Falcipain-2 (FP-2) of Plasmodium falciparum is a validated drug target but little is known of its orthologs in other malarial Plasmodium species. This study uses various structural bioinformatics approaches to characterise the prodomain‟s regulatory effect in FP-2 and its orthologs in Plasmodium species (P. vivax, P. berghei, P. knowlesi, P. ovale, P. chabaudi and P. yoelii). This was in an effort to discover short peptides with essential residues to mimic the prodomain‟s inhibition of these proteases, as potential peptidomimetic therapeutic agents. Residues in the prodomain region that spans over the active site are most likely to interact with the subsite residues inhibiting the protease. Sequence analysis revealed conservation of residues in this region of Plasmodium proteases that differed significantly in human proteases. Further prediction of the 3D structure of these proteases by homology modelling allowed visualisation of these interactions revealing differences between parasite and human proteases which will lead to significant contribution in structure based malarial inhibitor design.

Malaria, a mosquito-borne infectious disease, caused by the protozoan Plasmodium genus, is the greatest health challenges worldwide. The plasmodial vitamin B1 biosynthetic enzyme PfThzK diverges significantly, both structurally and functionally from its counterpart in higher eukaryotes, thereby making it particularly attractive as a biomedical target. In the present study, PfThzK was recombinantly produced as 6×His fusion protein in E. coli BL21, purified using nickel affinity chromatography and size exclusion chromatography resulting in 1.03% yield and specific activity 0.28 U/mg. The enzyme was found to be a monomer with a molecular mass of 34 kDa. Characterization of the PfThzK showed an optimum temperature and pH of 37°C and 7.5 respectively, and it is relatively stable (t₁/₂=2.66 h). Ag nanoparticles were synthesized by NaBH₄/tannic acid, and characterized by UV-vis spectroscopy and transmission electron microscopy. The morphologies of these Ag nanoparticles (in terms of size) synthesized by tannic acid appeared to be more controlled with the size of 7.06±2.41 nm, compared with those synthesized by NaBH₄, with the sized of 12.9±4.21 nm. The purified PfThzK was challenged with Ag NPs synthesized by tannic acid, and the results suggested that they competitively inhibited PfThzK (89 %) at low concentrations (5-10 μM) with a Ki = 6.45 μM.

Mefloquine hydrochloride is an antimalarial agent that has been used for the past 40 years. Numerous reports of neurological side effects have recently led the FDA to issue a strong warning regarding long-term neurological effects. This warning lead to the U.S. Army’s Special Forces and other components to discontinue its use in July of 2013. Despite reported adverse side effects, mefloquine remains in circulation and is recommended to travelers going to specific Asian countries. Mefloquine has been used as a treatment for those already infected with the malaria parasite (blood concentrations ranging from 2.1 to 23 µM), and as prophylaxis (blood concentrations averaging 3.8 µM) (Dow 2003). The purpose of this study was to quantify Mefloquine’s toxicity using spontaneously active nerve cell networks growing on microelectrode arrays in vitro and to identify compounds that alleviate or reduce toxic effects. The current literature on mefloquine toxicity is lacking electrophysiological data. These data will contribute to research on the mechanism of adverse side effects associated with mefloquine use. Sequential titration experiments were performed by adding increasing concentrations of mefloquine solution to cultured neurons. Network responses were quantified and reversibility was examined. In each network, activity decreases were normalized as a percent of reference activity yielding a mean IC50 value of 5.97 ± 0.44 (SD) µM (n=6). After total activity loss, no activity was recovered with two successive medium changes. To test for network response desensitization resulting from sequential applications over 5-6 hr periods, one-point titrations at varying concentrations were conducted with fresh networks. These experiments yielded a single concentration response curve with an IC50 value of 2.97 µM. This represents a statistically significant shift (p < 0.0001) to lower concentrations of mefloquine, demonstrating that sequential applications result in network desensitization. After mefloquine exposures, cells were evaluated for irreversible cytotoxic damage. Over a 12-hour period under 6 µM mefloquine, process beading and granulation of somal cytoplasm were observed. At 8 µM mefloquine cell stress was apparent after only 10 minutes with major glial damage and process beading at 120 minutes. In this study, quinolinic acid served as a neuroprotectant at 20 µM. There have been multiple studies on the endogenous concentrations of quinolinic acid and current literature is quite variable. Immunocompromised individuals have some of the highest blood levels of quinolinic acid (up to 20 µM). With 30 min pre-applications of quinolinic acid, the mefloquine IC50 value shifted from 5.97 ± 0.44 µM (n=6), to 9.28 ± 0.55 µM (n=3). This represents a statistically significant change to higher mefloquine concentrations and demonstrates neuroprotection.