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The development of Plasmodium falciparum malarial resistance to the current armoury of anti-malarial drugs requires the development of new treatments to help combat this disease. The marine environment is a well established source of potential pharmaceuticals. Of interest to us are isonitrile, isocyanate and isothiocyanate compounds isolated from marine sponges and molluscs which have exhibited nano-molar anti-plasmodial activities. Through quantitative structure-activity relation studies (QSAR), a literature precedent exists for a pseudoreceptor model from which a pharmacophore for the design of novel anti-malarial agents was proposed. The current theory suggests that these marine compounds exert their inhibitory action through interfering with the heme detoxification pathway in P. falciparum. We propose that the computational methods used to draw detailed conclusions about the mode of action of these marine compounds were inadequate. This thesis addresses this problem using contemporary computational methodologies and seeks to propose a more robust method for the rational design of new anti-malarial drug compounds that inhibit heme polymerization to hemozoin. In order to investigate the interactions of the marine compounds with their heme targets, a series of modern computational procedures were formulated, validated and then applied to theoretical systems. The validations of these algorithms, before their application to the marine compound-heme systems, were achieved through two case studies. The first was used to investigate the applicability of the statistical docking algorithm AutoDock to be used for the exploration of conformational space around the heme target. A theoretical P. falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR) enzyme model, constructed by the Biochemistry Department at Rhodes University, provided the ideal model to validate the AutoDock program. The protein model was accordingly subjected to rigorous docking simulations with over 30 different ligand molecules using the AutoDock algorithm which allowed for the docking algorithm’s limitations to be ascertained and improved upon. This investigation facilitated the successful validation of the protein model, which can now be used for the rational design of new PfDXR-inhibiting anti-plasmodial compounds, as well as enabling us to propose an improvement of the docking algorithm for application to the heme systems. The second case study was used to investigate the applicability of an ab initio molecular dynamics algorithm for simulation of bond breaking/forming events between the marine compounds and their heme target. This validation involved the exploration of intermolecular interactions in a naturally occurring nonoligomeric zipper using the Car-Parrinello Molecular Dynamics (CPMD) method. This study allowed us to propose a model for the intermolecular forces responsible for zipper self-assembly and showcased the CPMD method’s abilities to simulate and predict bond forming/breaking events. Data from the computational analyses suggested that the interactions between marine isonitriles, isocyanates and isothiocyanates occur through bond-less electrostatic attractions rather than through formal intermolecular bonds as had been previously suggested. Accordingly, a simple bicyclic tertiary isonitrile (5.14) was synthesized using Kitano et al’s relatively underutilized isonitrile synthetic method for the conversion of tertiary alcohols to their corresponding isonitriles. This compound’s potential for heme detoxification inhibition was then explored in vitro via the pyridine-hemochrome assay. The assay data suggested that the synthesized isonitrile was capable of inhibiting heme polymerization in a similar fashion to the known inhibitor chloroquine. Attempts to synthesize tricyclic analogues of 5.14 were unsuccessful and highlighted the limitation of Kitano et al’s isonitrile synthetic methodology.

Given the recent concern from multiple healthcare stakeholders that the pipeline of medical innovation is slowing, this thesis provides insights on how to spur breakthrough medical innovation in present day. The findings and recommendations are derived from one of the largest collections of interview transcripts from biomedical innovators (n=143) responsible for developing critical devices, drugs and diagnostics used in medicine today. An exemplary case (coronary artery stent) was selected for an in-depth analysis, which included a detailed recounting of stent development and an exhaustive analysis of the patent literature. External factors either catalyzed (e.g., supportive institutions, strong underlying science and collaboration) or hindered (e.g., technology transfer challenges, lack of funding and onerous conflict of interest rules) the development process. Strategies aimed towards promoting transformative medical innovation should focus on institutional-level policies targeting early stages of innovation. This includes providing individuals with unique expertise with the capacity to pursue innovative work. Technology transfer processes should be simplified to enable collaboration for individuals between institutions with disparate expertise. Policymakers should continue to support basic science research, which underlies future innovations. In contrast, policies that increase reimbursement or reduce taxes for industry or extend patent terms are less likely to impact transformative innovation.

Background: Postmenopausal osteoporosis which results in a reduction of bone quality and bone density is one of the most prevalent diseases affecting people around the world. Cathepsin K (CatK) is one of the most potent proteases in lysosomal cysteine proteases family, of which main function is to mediate bone resorption. Currently, the Odanacatib (ODN) developed by Merck & Co. is the only Phase III CatK inhibitor candidate with high efficacy in treating postmenopausal osteoporosis. Unfortunately, the development of ODN was finally terminated due to the cardio-cerebrovascular adverse effects. In order to enhance the specificity of ODN to osteoclasts for suppression of bone resorption in postmenopausal osteoporosis, we have previously designed and synthesized (D-Asp8)-ODN conjugate by linking ODN with a promising osteoclast-targeted moiety D-Asp8. The data showed that D-Asp8 could facilitate the conjugated ODN specifically approaching osteoclasts, with reduced distribution in non-bone tissues, to inhibit the functional CatK activity within bone tissues in healthy rats. In this thesis, we hypothesized that the in vitro antiresorptive effects of (D-Asp8)-ODN conjugate were comparable with that of ODN. On the other hand, we also developed a QQQ-LC/MS method for quantitation of (D-Asp8)-ODN conjugate in plasma, which will be a valuable tool to support further pre-clinical studies. Aim: (1) To compare the antiresorptive effect between (D-Asp8)-ODN conjugate and ODN in vitro. (2) To develop and validate a practicable method for pharmacokinetic profile of (D-Asp8)-ODN conjugate in rats. Materials and Methods: The cytotoxic effect of (D-Asp8)-ODN conjugate and ODN were evaluated and compared by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The effect of (D-Asp8)-ODN conjugate and ODN on Receptor activator of nuclear factor κB ligand (RANKL)-induced osteoclasts formation and osteoclast function-related genes were evaluated and compared by Tartrate-resistant acid phosphatase (TRAP) staining and quantitative real time polymerase chain reaction (qRT-PCR). The effect of (D-Asp8)-ODN conjugate and ODN on osteoclast bone resorption activities were evaluated and compared by bone resorption pit assay. Moreover, the pharmacokinetic profile of (D-Asp8)-ODN conjugate in rat plasma was determined by using triple quadrupole liquid chromatography-mass spectrometry (QQQ-LC/MS) system. Result: The cytotoxicity of (D-Asp8)-ODN conjugate was significantly lower than that of ODN on the murine macrophage RAW 264.7 cell line. (D-Asp8)-ODN conjugate had no effect on RANKL-induced osteoclast formation, which was comparable with that of ODN. (D-Asp8)-ODN conjugate had no effect on the mRNA level of CTSK, but it could upregulate the mRNA levels of ACP5 and OSCAR, which was comparable with that of ODN. (D-Asp8)-ODN conjugate inhibited osteoclast bone resorption activity, which was comparable with that of ODN. The newly established QQQ-LC/MS protocol had good precision and accuracy for detecting (D-Asp8)-ODN conjugate in rat plasma. Finally, the pharmacokinetic profile of (D-Asp8)-ODN conjugate in rat plasma was determined. Following subcutaneous administration, the time to reach maximum concentration (Tmax) was 1.0 h, the antibiotics area under the concentration time-curves from time zero to infinity (AUC0-∞) was found to be 27.78 ug·mL-1·h and the terminal half-life (t½) was 1.4 h. Conclusion: (D-Asp8)-ODN conjugate had no effect on RANKL-induced osteoclast formation, which was comparable with ODN. The antiresorptive effect of (D-Asp8)-ODN conjugate was comparable with that of ODN. On the other hand, a new QQQ-LC/MS protocol has been established for the pharmacokinetic profile of (D-Asp8)-ODN conjugate in rat.

Viruses are unique organisms that lack the protein machinery necessary for its propagation (like polymerase) yet possess other proteins that facilitate its propagation (like host cell anchoring proteins). This study explores seven different frameworks to assist rapid visualization of proteins that are common to viruses residing in a given host. The proposed frameworks rely only on protein sequence information. It was found that the sequence similarity-based framework with an associated profile hidden Markov model was a better tool to assist visualization of proteins common to a given host than other proposed frameworks based only on amino acid composition or other amino acid properties. The lack of knowledge of profile hidden Markov models for many protein structures limit the utility of the proposed protein sequence similarity-based framework. The study concludes with an attempt to extrapolate the utility of the proposed framework to predict viruses that may pose potential human health risks.

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology and Toxicology Student: Martina Klaučová Supervisor: prof. PharmDr. Petr Pávek, Ph.D. Consultant: PharmDr. Ivona Pávková, Ph.D. Diploma thesis title: Ames test in the drug development Background: Thesis objective is the determination of potential genotoxicity of newly developed drugs within primary testing and the introduction of the Ames microfluctuation test which can be used in common laboratory conditions. Methods: I used commercially supplied kit based on the principles of Ames test which detects reverse mutation through colour changes of the samples using bacterial strains S. typhimurium. At first I had to study literary sources and then I could design the procedures of the Ames microfluctuation test, preparation of the chemicals and storage of the strains which are optimal for all laboratories. Results: The drug samples T6445 and T6447 with 30 µM concentration tested by metabolic activation S9 on bacterial strain ST TA 98 show genotoxicity. The sample UOCHB1 with 30 µM concentration tested without activation shows possible genotoxicity on both strains ST TA 98 and ST TA 100. Other samples do not show any toxicity. I used 3 different procedures during the designation of assay. The most suitable version of the...

Submitted to the faculty of the Informatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in Bioinformatics in the School of Informatics Indiana University May 2006 / A plethora of genomic and proteomic information was uncovered by the U.S Human Genome Project (HGP) – mostly by means of bioinformatics tools and techniques. Despite the impact that bioinformatics and pharmacogenomics were projected to have in the drug discovery and development process, the challenges facing the pharmaceutical industry, such as the high cost and the slow pace of drug development, appear to persist. Socio-economic barriers exist that mitigate the full integration of bioinformatics and pharmacogenomics into the drug discovery and development process, hence limiting the desired and expected effects.

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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