Mycobacterium tuberculosis (Mtb), a deadly pathogen, has scourged mankind for many centuries and has remained a major threat to global world health. Tuberculosis, the disease caused by this bacterium, is a major cause of death in developing nations and there is potential for its re-emergence in developed countries. An alarming rise in cases of multidrug-resistant and extremely-drug resistant tuberculosis (MDR-TB and XDR-TB) that do not respond to the customary first-line antibiotics necessitates the urgent need for development of new anti-TB drugs. Mtb becomes engulfed in human macrophages post infection of the host, but persists in the harsh environment of the human lungs by utilization of host cholesterol as a carbon source. The P450s CYP125A1, CYP142A1 and CYP124A1 are responsible for catalysing the side-chain degradation of cholesterol, which is critical for cholesterol to be used in the Mtb β-oxidation pathway for energy production. This PhD thesis focuses on understanding the structure/mechanism of the Mtb cholesterol 27-oxidases with the aim of facilitating the development of novel inhibitors of these P450s, which are crucial for Mtb to infect the host and to sustain infection. CYP142A1 and CYP124A1 were purified through three chromatographic steps with contaminating proteins successfully removed to give highly pure forms of these enzymes following the final purification step. Spectrophotometric titrations indicate that CYP142A1 and CYP124A1 bind tightly to cholesterol and cholestenone (and also to branched-chain methyl lipids for CYP124A1), highlighting their physiological roles in sterol and fatty acid metabolism, respectively. Binding analyses with a range of azole antibiotics revealed tight binding to bifonazole, clotrimazole, miconazole and econazole, and weak binding to fluconazole. Studies with compounds from a fragment screening library revealed weak binding to fragment hits for the cholesterol oxidases, but much tighter binding to these enzymes was found for ‘elaborated’ hits from a previous fragment screen on the Mtb cyclodipeptide oxidase CYP121A1, indicative of improved ligand potency achieved via ‘fragment merging’ strategies, and of structural similarities between these diverse Mtb P450s. Light scattering data indicate that CYP142A1 exists in dimeric form in solution, but becomes monomeric when treated with DTT; while CYP124A1 is completely monomeric. Crystal structures of CYP142A1 and CYP124A1 in complex with cholestenone, econazole and fragment library hits were determined. CYP142A1 crystal structures with econazole and fragment hits revealed heme coordination via the heterocyclic nitrogen in an azole group, and provide important data towards design of superior inhibitor drugs. The binding of cholestenone within the active site channels of CYP124A1 and CYP142A1 revealed an alignment favourable for C27 hydroxylation of the cholestenone side chain, which supports the physiological roles of CYP142A1 and CYP124A1 (as well as CYP125A1) in host cholesterol catabolism.

The Electrospray (ES) technique is a promising particle generation method for drug delivery due to its capabilities of producing monodisperse PLGA composite particles with unique configurations and high drug encapsulation efficiency. In the dissertation work, the coaxial dual capillary ES was used to generate drug-loaded core-shell PLGA particles to study the effects of particle filling materials, drug loading locations and particle shell thicknesses on the resultant in vitro release behaviors of the hydrophilic and/ or hydrophobic model drugs. Through release profile characterization of drug-loaded PLGA particles (particle size: 400 nm and 1 μm), it was confirmed that the co-encapsulation of Budesonide (BUD, the hydrophobic small-molecule model drug) and Theophylline (THY, the hydrophilic small-molecule model drug) in the particle cores is the most effective drug loading strategy for extended release of the fixed combined BUD and THY. Particles composed of PLGA fillers with lower molecular weights and with greater shell layer thicknesses could release THY in a well controlled fashion. On the other hand, a slower release rate of Bovine Serum Albumin (BSA, the protein model drug) from PLGA particles with greater shell thickness was also observed. Sequential release of BSA and Paclitaxel (PTX, the hydrophobic small-molecule anti-cancer model drug) was achieved by the 400-nm PLGA (Mw: 7,000-17,000 g/mol, LA/GA: 50/50) particles with potential biopharmaceutical applications in cancer therapy.

Theranostics is an emerging treatment approach that combines diagnostics with therapy in order to personalize treatment regimens for individual patients and decrease cancer mortality. Previously, nanoparticles entrapping conventional fluorescent dyes were developed for cancer theranostics, but fluorescent nanoparticles did not allow clinicians to significantly improve cancer treatments. The use of fluorescent dyes that are sensitive to solvent acidity (halo-fluorochromism) and polarity (solvato-fluorochromism) may overcome the limitations of fluorescent nanoparticles and improve cancer therapy by enabling researchers to detect chemical properties within the nanoparticle core environment. The model halo- and solvato-fluorochromic dye Nile blue was attached to the core of nanoscale drug delivery systems called polymer nanoassemblies (PNAs), which were created by tethering hydrophilic polymers and hydrophobic groups to a cationic polymer scaffold. The fluorescence of empty PNAs increased by 100% at pH 5.0 compared to pH 7.4, and the fluorescence of drug-loaded PNAs increased up to 300% compared to empty PNAs. A comparison of the fluorochromic properties between PNAs with various core properties indicated that both hydrophobic pendant groups and scaffold amines contributed to the fluorochromism of PNAs. The halo-fluorochromism of PNAs allowed investigators to minimize the detection of fluorescence signals in healthy organs such as the liver. Fluorescence imaging of halo-fluorochromic PNAs diffused into tissue mimics indicated that fluorescence of PNAs in tissues increased by 100% at pH 7.0 compared to pH 7.4. In addition, halo-fluorochromic PNAs identified the acidic perimeter surrounding metastatic tumors in orthotopic metastatic tumor models. Computational simulations of metastatic lesions verified that some halo-fluorochromic PNAs accumulate in the hypoxic/acidic regions of metastatic tumors following intravenous administration. These simulations also indicated that the accumulation of PNAs in the hypoxic regions of tumors doubles at 12 hours post-treatment compared to 1.8 hours post-treatment. The solvato-fluorochromism of PNAs enabled the fluorescence-based measurement of drug release from the nanoassembly core during dialysis-based drug release measurements. Solvato-fluorochromic methods indicated faster drug release rates than HPLC-based methods. Mechanistic modeling of drug release indicated that solvato-fluorochromic methods were unaffected by released drugs that interfered with HPLC-based methods. However, mechanistic modeling also indicated that drug rebinding and diffusion did not account for all of the differences between drug release rates determined by solvato-fluorochromic- and HPLC-based methods. Based on this evidence, it was hypothesized that solvato-fluorochromic drug release methods measure drug diffusion from near the scaffold of PNAs in a small region of the nanoassembly core, and that this process contributes to overall drug release but does not indicate apparent drug release rates for PNAs. In order to develop PNAs for potential clinical applications, ionizable amines were removed from the polymer scaffold to increase drug loading and sustain the release of model drugs carfilzomib and docetaxel. The removal of primary amines decreased drug diffusivity in the core of PNAs (D from 3.9*10-18 cm2/s to 0.1*10-19 cm2/s) and increased the drug release half-life (t1/2 from 4 to 26 hours). The controlled release of carfilzomib from PNAs reduced drug metabolism by 60% for up to one hour and sustained proteasome inhibition in cancer cells at 72 h post-treatment compared to free drug. Overall, this work provides insight into the design of theranostic nanoparticles with beneficial properties for improving cancer treatment.

Biorelevant in vitro release/dissolution tests are designed to predict the in vivo behavior of a drug and are crucial in understanding its in vivo performance. Currently, there is no standardized compendial in vitro release testing methods or regulatory guidance’s for release/dissolution testing of implants due to their complex physiological locations.Furthermore, existing compendial methods do not capture the local release profile of ‘novel’ parenterals in physiological low fluid volume surrounding areas. Long acting and in situ forming implants with orthobiologic proteins and peptides have increased over the past few decades due to a better understanding of genetic engineering. One of these products, INFUSE® Bone Graft (Medtronics, MN, USA), is an implant which helps in bone regeneration at the trauma site and is comprised of a) an absorbable collagen sponge (ACS) and b) recombinant human bone morphogenetic protein-2 (rhBMP-2). INFUSE® Bone Graft is an FDA approved product for acute, open shaft tibial fractures, lumbar spinal fusions and sinus or ridge augmentations in the jaws. The evaluation of implant products such as INFUSE® Bone Graft requires a good understanding of local and systemic release in vivo in order to ensure safe, effective, and predictable product performance. The primary goal of this study is to develop a predictive ‘biorelevant’ release model, which factors in clinically relevant physiological parameters suitable for studying and effectively predicting extended release of implants, using INFUSE Bone Graft® as our model implant. A novel biorelevant in vitro model was designed and tested. The model was observed to be discriminatory between two different carrier formulations of rhBMP-2 using a model independent approach - similarity factor (f2). Additionally, a high throughput assay to quantify rhBMP-2 release using high performance liquid chromatography with UV/VIS detection was also developed and validated. Successful completion of this study facilitated an in vitro release study design that incorporated the complex biorelevant parameters of implant dosage forms, the model will offer crucial insights into biological performance, and aid in developing methods to characterize release of other similar dosage forms.

Computational methods have been extensively developed at various levels of approximation in recent years to model biomolecular interactions and for rational drug design. This research work aims to explore the feasibility of using quantum mechanical (QM) methods within the two broad categories of in silico ligand-based and structure-based drug design. First, density functional theory at the M06L level of theory was employed to examine structure-activity relationships of boron-based heterocyclic compounds, anti-inflammatory inhibitors targetting the interleukin-1β (IL-1β) cytokine. Our findings from computed energies and shapes of the molecular orbitals provide understanding of electronic effects associated with the inhibitory activity. We also found that the boron atom, specifically its electrostatic polarity, appears to be essential for the anti-IL-1β activity as evidenced by the biological assay of non-boron analogues selected from the ligand-based virtual screening results. Secondly, we aimed to dock ligands at the active sites of zinc-containing metalloproteins with reasonable computational cost and with accuracy. Therefore, an in-house docking scheme based on a Monte Carlo sampling algorithm using the semiempirical PM6/AMBER force field scoring function was compiled for the first time within the Gaussian 09 program. It was applied to four test cases, docking to cytidine deaminase and human carbonic anhydrase II proteins. The docking results show the method’s promise in resolving false-positive docking poses and improving the predicted binding modes over a conventional docking scheme. Finally, semiempirical QM methods which include dispersion and hydrogen-bond corrections were assessed for modelling conformations of β-cyclodextrin (βCD) and their adsorption on graphene. The closed in vacuo βCD cccw conformer was found to be in the lowest energy, in good agreement with previous ab initio QM studies. DFTB3, PM6-DH2 and PM7 methods were applied to model the intermolecular interactions of large βCD/graphene complexes, over a thousand atoms in size. We found that the binding preference of βCD on graphene is in a closed conformation via its C2C3 rim, agreeing with reported experimental and computational findings.

Many proteins are unstable in solution and must be formulated in the solid state. This has led to an increase in the use of lyophilized dosage forms. Lyophilization is a complicated processing method consisting of three major steps: freezing, primary drying, and secondary drying. This can lead to several formulation stability challenges including changes in ionization within the matrix, phase separation of the protein drug from added stabilizers, sufficient mobility within the system for movement of reactive species and protein side chains, and crystallization of excipients upon storage. Solid-State Nuclear Magnetic Resonance Spectroscopy (SSNMR) is used to characterize many important properties of lyophilized formulations including crystalline vs. amorphous content, polymorphic form, ionization profile, interaction between formulation components with domain sizes, and mobility within the cake matrix. In order to study ionization changes in lyophilized solids, SSNMR and UV/Vis Diffuse Reflectance spectroscopy were used. 13C-labeled fumaric, succinic, and butyric acids were added to formulations at various pH levels, and were used to quantify change in the ionization of the matrix by monitoring the ionization ratios of the carboxylic acid peaks using SSNMR. pH indicators were also added to the formulations and their ionization ratio was determined using UV/Visible Diffuse Reflectance Spectroscopy. The ionization profile in the solid state was compared with that in solution before lyophilization. A rank ordering of ionization shift was made in pharmaceutically relevant buffers. SSNMR proton relaxation times (1H T1 and 1H T1rho) for each formulation component can be compared to determine homogeneity within the lyophilized matrix. The concept of spin diffusion is used in order to determine the length scale on which the components are either homogeneous or phase separated. The domain size is typically 20-50 nm or 2-10 nm for 1H T1 and 1H T1rho, respectively. PVP and dextran polymers were phase separated on both domains for physical mixtures and lyophilized mixtures. BSA and lysozyme were both lyophilized with formulations containing sucrose, trehalose, or mannitol as the stabilizer. Mannitol crystallized, and the relaxation times showed phase separation. Sucrose and trehalose both formed homogeneous systems at both length scales when formulated in a 1:1 ratio with BSA or lysozyme. Aspartame was shown to be phase separated from trehalose. The SSNMR proton relaxation times were also used to measure the local mobility in the lyophilized matrix, as a timescale of picoseconds to nanoseconds is associated with the 1H T1 relaxation time. Mobility was monitored in formulations containing a fixed amount of sucrose and mannitol, but with a variable amount of an IgG2 protein. The 1H T1 relaxation times decreased as protein content increased. The formulations with the highest relaxation time (lowest mobility), was the most stable in accelerated temperature conditions as monitored by size exclusion chromatography and capillary isoelectric focusing. This method can be used to rank order the most stable formulations at time-zero. Anti-plasticization was also studied by formulating sorbitol in various ratios with trehalose. The 1H T1 relaxation times increased with increasing sorbitol content, while the glass transition temperature decreased. Sorbitol and trehalose glasses were also exposed to different temperature storage conditions. Sorbitol appears to promote aging, as the formulations with higher sorbitol content showed larger increases in proton relaxation time.

Schistosomiasis is a serious infectious disease that afflicts over 200 million people in tropical and subtropical regions. It is caused by Schistosoma blood flukes that live in human blood vessels and obtain nutrients from host hemoglobin, which is degraded by digestive proteases. Current therapy relies on a single drug and concern over resistance necessitates new drug development. In Schistosoma mansoni, cathepsin B1 (SmCB1) is a critical digestive protease that is a target molecule for therapeutic interventions. This thesis provides a comprehensive characterization of SmCB1 focused on structure-activity relationships and inhibitory regulation based on six crystal structures solved for SmCB1 molecular forms and complexes. SmCB1 is biosynthesized as an inactive zymogen in which the N-terminal propeptide operates as a natural intra-molecular inhibitor by blocking the active site. Detailed biochemical and structural analyses have identified a new and, so far, unique mechanism of SmCB1 zymogen activation through which the propeptide is proteolytically removed and the regulatory role of glycosaminoglycans in this process has been described. A study of SmCB1 proteolytic activity has revealed that the enzyme acts in two modes, as endopeptidase and exopeptidase, which makes it an efficient tool for host...

Malaria is prevalent in over 100 countries which is populated by half of the world’s population and culminates in approximately one million deaths per annum, 85% of which occurs in sub-Saharan Africa. The combined resistance of the mosquitoes and parasites to the currently available pesticides and antimalarial chemotherapeutic agents requires the concerted effort of scientists in the malaria field to identify and develop novel mechanisms to curb this deadly disease. In this study, a thorough understanding of the role players in the polyamine pathway of the parasite was obtained, which could aid future studies in the development of novel inhibitory compounds against these validated drug targets. The uniquely bifunctional S-adenosylmethionine decarboxylase/ornithine decarboxylase (AdoMetDC/ODC) of Plasmodium falciparum forms an important controlling node between the polyamine and methionine metabolic pathways. It has been speculated that the unique bifunctional association of the rate-limiting enzymes allows for the concerted regulation of the respective enzyme activities resulting in polyamine synthesis as per requirement for the rapidly proliferating parasite while the methionine levels are strictly controlled for their role in the methylation status. The results of this study showed that the enzyme activities of the bifunctional complex are indeed coordinated and subtle conformational changes induced by complex formation is suggested to result in these altered kinetics of the individual AdoMetDC and ODC domains. Studies also showed that the identification of the interaction sites between the domains, which allows for communication across the complex, may be targeted for specific interference with the enzyme activities. Furthermore, these studies showed that the current knowledge on the different subclasses of the AdoMetDC family should be re-evaluated since P. falciparum AdoMetDC shows diverse properties from orthologues and therefore points towards a novel grouping of the plasmodial protein. The extensive biochemical and biophysical studies on AdoMetDC has also provided important avenues for the crystallisation and solving of this protein’s 3D structure for subsequent structure-based identification of drug-like lead compounds against AdoMetDC activity. The application of structure-based drug design on malarial proteins was additionally investigated and consequently proved that the rational design of lead inhibitory compounds can provide important scaffold structures for the identification of the key aspects that are required for the successful inhibition of a specific drug target. Spermidine synthase, with its intricate catalytic mechanism involving two substrate binding sites for the products of the reactions catalysed by AdoMetDC/ODC, was used to computationally identify compounds that could bind within its active site. Subsequent testing of the compounds identified with a dynamic receptor-based pharmacophore model showed promising inhibitory results on both recombinant protein and in vitro parasite levels. The confirmation of the predicted interaction sites and identification of aspects to improve inhibitor interaction was subsequently investigated at atomic resolution with X-ray protein crystallography. The outcome of this doctoral study shows the benefit in applying a multidisciplinary and multinational approach for studying drug targets within the malaria parasite, which has led to a thorough understanding of the targets on both biochemical and structural levels for future drug design studies. / Thesis (PhD)--University of Pretoria, 2011. / Biochemistry / unrestricted

More than 20 years after its discovery HIV protease still remains one of the primary targets in HIV treatment. Currently there are 9 approved protease inhibitors on the market. However, due to immense replication rate and the high error prone nature of reverse transcriptase, resistance to each of them has already been described. Therefore, the search for new protease inhibitors with different binding mode is still active. A novel type of protease inhibitors (1, 4-benzodiazepine analogs) was recently discovered in our laboratory. Even though this new class of inhibitors is highly potent (Ki' in range of 10-9 ), it also has several undesirable qualities, such as low solubility and a high number of stereogenic centers. Primary objective of this study was to try to prepare more soluble compounds with lower number of possible stereoisomers, enzymologically characterize its binding to the wild-type and mutated HIV protease and to determine its structure in the complex with the enzyme. A small library of 1, 4-benzodiazepine inhibitors of HIV protease was synthesized and fully characterized using NMR spectroscopy and mass spectroscopy. The number of stereogenic centers was successfully reduced from 4 to 2 without loosing activity of the inhibitor. The improvement in solubility was always associated with a...

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