OpenUCT :: Browsing by Subject "Chemistry"

Browsing by Subject "Chemistry"

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Open Access
[1,2-Bis(diphenylphosphino)ethane]-diiodidoplatinum(II) dichloromethane disolvate
(2007) Sivaramakrishna, Akella; Su, Hong; Moss, John R
In the title compound, [PtI2(C26H24P2)]·2CH2Cl2, the PtI2(dppe) [dppe = 1,2-bis(diphenylphosphino)ethane] molecules possess twofold rotation symmetry. The Pt coordination displays a square-planar arrangement, with the sum of the angles around the Pt atom being 360.01 (2)°. The Pt-I distance is 2.6484 (5) Å. In the crystal structure, intermolecular C-H...I contacts link the PtI2(dppe) molecules into rows along the c axis, with a C...I distance of 3.873 (5) Å.
Open Access
A comparative study between the cubic spline and b-spline interpolation methods in free energy calculations
(2020) Kaya, Hikmet Emre; Naidoo, Kevin J
Numerical methods are essential in computational science, as analytic calculations for large datasets are impractical. Using numerical methods, one can approximate the problem to solve it with basic arithmetic operations. Interpolation is a commonly-used method, inter alia, constructing the value of new data points within an interval of known data points. Furthermore, polynomial interpolation with a sufficiently high degree can make the data set differentiable. One consequence of using high-degree polynomials is the oscillatory behaviour towards the endpoints, also known as Runge's Phenomenon. Spline interpolation overcomes this obstacle by connecting the data points in a piecewise fashion. However, its complex formulation requires nested iterations in higher dimensions, which is time-consuming. In addition, the calculations have to be repeated for computing each partial derivative at the data point, leading to further slowdown. The B-spline interpolation is an alternative representation of the cubic spline method, where a spline interpolation at a point could be expressed as the linear combination of piecewise basis functions. It was proposed that implementing this new formulation can accelerate many scientific computing operations involving interpolation. Nevertheless, there is a lack of detailed comparison to back up this hypothesis, especially when it comes to computing the partial derivatives. Among many scientific research fields, free energy calculations particularly stand out for their use of interpolation methods. Numerical interpolation was implemented in free energy methods for many purposes, from calculating intermediate energy states to deriving forces from free energy surfaces. The results of these calculations can provide insight into reaction mechanisms and their thermodynamic properties. The free energy methods include biased flat histogram methods, which are especially promising due to their ability to accurately construct free energy profiles at the rarely-visited regions of reaction spaces. Free Energies from Adaptive Reaction Coordinates (FEARCF) that was developed by Professor Kevin J. Naidoo has many advantages over the other flat histogram methods. iii Because of its treatment of the atoms in reactions, FEARCF makes it easier to apply interpolation methods. It implements cubic spline interpolation to derive biasing forces from the free energy surface, driving the reaction towards regions with higher energy. A major drawback of the method is the slowdown experienced in higher dimensions due to the complicated nature of the cubic spline routine. If the routine is replaced by a more straightforward B-spline interpolation, sampling and generating free energy surfaces can be accelerated. The dissertation aims to perform a comparative study between the cubic spline interpolation and B-spline interpolation methods. At first, data sets of analytic functions were used instead of numerical data to compare the accuracy and compute the percentage errors of both methods by taking the functions themselves as reference. These functions were used to evaluate the performances of the two methods at the endpoints, inflections points and regions with a steep gradient. Both interpolation methods generated identically approximated values with a percentage error below the threshold of 1%, although they both performed poorly at the endpoints and the points of inflection. Increasing the number of interpolation knots reduced the errors, however, it caused overfitting in the other regions. Although significant speed-up was not observed in the univariate interpolation, cubic spline suffered from a drastic slowdown in higher dimensions with up to 103 in 3D and 105 in 4D interpolations. The same results applied to the classical molecular dynamics simulations with FEARCF with a speed-up of up to 103 when B-spline interpolation was implemented. To conclude, the B-spline interpolation method can enhance the efficiency of the free energy calculations where cubic spline interpolation has been the currently-used method.
Open Access
A contribution to the vibrational analysis of metal complexes with pyridine and related ligands
(1984) Verhoeven, Paul Felix Maria
Open Access
A metallomic, proteomic and lipidomic investigation of the malaria parasites digestive vacuole and insights into the mediators of haemozoin formation
(2019) Mohunlal, Roxanne; Egan, Timothy John
Novel and unambiguous mechanistic details of the biochemical processes that enable the most virulent form of the malaria pathogen, Plasmodium falciparum, to thrive within the human host are desperately required in order to find innovative strategies to counteract emerging parasite resistance that will inevitably render current malarial therapies obsolete. This study focused on exploring the Plasmodium falciparum metallome and investigated the mediators of haemozoin formation, an ingenious parasite-specific process critical to host immune evasion as well as parasite survival and one that is surprisingly rather contentious. In order to obtain a comprehensive view of metal distribution, the trace metal content in parasites isolated at varying time-points over the 48 h intraerythrocytic cycle were measured by ICP-MS. The trace metals detected; namely, iron, magnesium, zinc, manganese and copper, were compared to control uninfected erythrocytes. With the malaria parasite being a haematophagous organism, iron was detected as the most abundant trace metal and found to exhibit a significant increase up to 32 h into the life cycle after which the measured iron content remained relatively constant and lower than the control. This was attributed to the maximum amount of haemoglobin having been ingested at this mature trophozoite stage and the active conversion of free haem (Fe(III)PPIX) into biocrystalline haemozoin. All other trace metals exhibited 2 to 4-fold increases in metal ion content as the parasite matured and were detected in amounts higher than those found in the erythrocyte control, demonstrating uptake of these ions from the external medium. These increases coincided with specific cellular events such as cell division and enhanced parasite metabolism. Qualitative proteomic analysis of parasite material identified several metalloproteins but most significant, was the discovery of magnesium and copper transporters. Together, these findings suggest that transition metal import is essential to promote important cellular events and parasite growth and are indicative of unique parasite-specific metal transport pathways. The mediators of crystal formation were investigated by interrogating the haemozoin proteome and lipidome. Haemozoin was obtained from parasitised erythrocytes following a fractionation approach which culminated in their release from purified digestive vacuoles (DVs) following multiple freeze-thaw cycles. Isolated crystals were extensively washed with aqueous sodium acetate buffer (0.5 M, pH 5.2), detergent(4% SDS) and organic solvents (acetone/methanol) prior to base dissolution (0.1 M NaOH). Mass spectrometry was used to investigate the biomolecules occluded by haemozoin by analysing extensively washed and dissolved crystals. Haem detoxification protein (HDP), a protein currently postulated to be potent in mediating haemozoin formation in vivo, was detected in high relative abundance in the dissolved haemozoin fraction by semi-quantitative label-free proteomics. Expression and purification of recombinant soluble HDP was optimised and both soluble and refolded protein were further investigated. Characterisation by circular dichroism and fluorescence spectroscopy revealed that soluble HDP differed in conformation to its refolded counterpart. In aqueous solution (pH 7.4), UV-vis spectrophotometric titrations showed soluble and refolded HDP to bind Fe(III)PPIX in a 1:1 ratio with a Kd of 1.2 ± 0.5 µM and 0.35 ± 0.04 µM respectively. Crucially, activity studies under biomimetic conditions (pH 5.2, 37°C) demonstrated that this protein was not competent to promote β-haematin (synthetic haemozoin) formation without the incorporation of detergent. Mass spectrometry-based lipidomics identified and quantified over 400 lipids in dissolved haemozoin. Neutral lipids were found to be the dominant class comprising 90% cholesterol, 2% cholesterol esters and 0.6% acylglycerols. The detected lipids were used to prepare a model lipid blend which was found to efficiently promote β-haematin formation in yields greater than 90% in under 10 minutes and at concentrations as low as 18 µM. Crystals synthesised using the model lipid blend were found to exhibit similar morphological traits to haemozoin naturally produced by the parasite. Live-cell imaging by spinning disk confocal microscopy revealed that neutral lipid bodies localised externally from the DV or in close contact with the DV membrane but were not found in the immediate vicinity of haemozoin. β-Haematin was found to occlude labelled protein and lipid when synthesised in their presence. Furthermore, occluded biomolecules were not readily displaced from the crystal surface through simple washing with aqueous buffer (pH 5.2) but were only released upon base dissolution of crystals. Pre-formed β-haematin and haemozoin incubated with labelled biomolecules resulted in no further occlusion which demonstrated that these crystals occlude material in a manner non-exchangeable with the DV lumen, thus providing a window into the molecules present at the time and site of crystal formation. Overall, this multidisciplinary omics approach has revealed that the malaria parasite has a unique metallome which may provide promising new drug targets. Significantly, this study has unequivocally demonstrated that haemozoin occludes proteins and lipids in detectable amounts in a non-exchangeable manner with the external milieu but, crucially, lipids occluded by haemozoin are present at the time and site of formation within the DV and are potent mediators of haemozoin formation in the malaria parasite.
Open Access
A theoretical study of metal-organic frameworks
(2018) Zwane, Reabetswe Robin; Venter, Gerhard; Oliver, Clive; Wilkinson, Karl
Among the options for carbon sequestration, the development of CO2 capture materials has gained momentum over the past two decades. The design and construction of chemical and physical absorbents for the capture of CO2 and clean energy storage are a crucial technology for a sustainable low-carbon future. Metal-organic frameworks (MOFs) provide a new vision for the adsorption of molecules on solid surfaces. The interest in MOFs is owed to their ultrahigh porosity, high surface areas and tuneable pore sizes and shapes. The main objective of this thesis was to adopt a rational predictive capacity used in MOF design to control properties such as framework porosity and flexibility on a molecular scale. The in-silico studies were carried out by using ab initio quantum mechanical approaches such as density functional theory and perturbation theory. In addition, semi-classical methods like the Grand Canonical Monte Carlo (GCMC) approach was also used. A structural motif called vicinal fluorination was adopted to study MOF linkers in isolation and in a framework. An extensive conformational study, in various solvents, was carried out to investigate the effect of vicinal fluorination on the isolated MOF linkers and therefore elucidate their conformational stability. The effect of fluorination on adsorption isotherms was also investigated. Moreover, various fluorination patterns were explored. Adsorption isotherms of a non-fluorinated copperbased MOF based on experimental work, and its various fluorinated analogues were predicted using the GCMC method. It was found that vicinal fluorination is not dominant in controlling conformations of some MOF linkers. Rather, an interplay of interactions, including solute and steric interactions, influence the conformational stability on rotational profiles. However, vicinal fluorination was shown to control the flexibility of the linkers used in MOFs as it controls the force constants around the minima of rotational profiles of isolated MOF linkers. The study also highlighted the importance of the solvent on the relative energies of the linker conformations – this has a potential impact on the synthesis of MOFs. With the help of computational methods and validation from experimental data, the structural and sorption properties of the framework, upon fluorination, were shown to have consequences on the adsorption properties of the MOF. Vicinally fluorinated frameworks were shown to have higher uptakes at a low temperature and low pressures.
Open Access
The adsorption of Ni, Cu, Zn, Cd and Pb by δ-MnO₂ and its inclusion in an equilibrium model of metal partitioning in soils
(1997) Pretorius, Patrius Julius; Linder, Peter W
Chemical equilibrium modelling provides a mechanistic tool for the prediction of metal partitioning in soils, which is important in predicting the fate and effects of metals in soil systems. In order to set up an equilibrium model of metal partitioning in soil systems, thermodynamic data for all processes influencing metal fate in soil systems are needed. In this work, the adsorption of the metals nickel, copper, zinc, cadmium and lead by δ-MnO₂ is investigated. This was done in order to provide thermodynamic data for an important adsorption phase in soils systems. Before this work, consistent adsorption data for only one adsorption phase, hydrous ferric oxide, were available. This precluded the inclusion of manganese dioxide in equilibrium models of metal fate in soil systems. Surface complexation properties of a synthetic manganese dioxide were investigated using glass electrode potentiometry. Experimental data were interpreted according to the surface complexation model in conjunction with the diffuse double layer model of the solid/solution interface. Adsorption constants were derived using the non-linear optimization program FITEQL. The surface complexation parameters determined in this fashion were validated against results obtained from the open literature. Following this, the surface complexation parameters were included in a chemical equilibrium model of soil systems. This model was used to predict the partitioning of nickel, copper, zinc, lead and cadmium in a number of soil samples collected in The Netherlands. Contrary to results presented by other workers, it was found that a non-homogeneous surface site model was needed to explain the potentiometric data obtained for proton and metal adsorption by manganese dioxide. Best fits of alkalimetric titration data were obtained with a two-site, three surface-species model of the δ-MnO₂ surface. Site concentrations of 2.231x10⁻³ mol.g⁻¹ and 7.656x10⁻⁴ mol.g⁻¹ were obtained. Corresponding equilibrium constants for the formation of the postulated surface species are -1.27 (=XO⁻), -5.99 (=YO⁻) and 3.52 (= YOH2₂⁺). This model was successful in a qualitative manner in describing adsorption results obtained from the open literature. The prediction of metal partitioning in soil systems showed that although the inclusion of manganese dioxide in the modelled to some improvement in the agreement between observed and predicted results, other factors are present which influence metal partitioning in soils. The discrepancy between observed and predicted results furthermore showed that the processes accounted for in the equilibrium model are incomplete.
Open Access
The adsorption of nitrogen and argon by evaporated films of sodium chloride
(1969) Rodgers, Allen L; Linder, Peter W
An ultra-high vacuum apparatus has been designed and constructed. Pressures of the order of 1 x 10⁻⁸ torr have been attained routinely. The adsorption of nitrogen by Pyrex has been investigated and the results obtained have shown good agreement with those in the literature. Rigorously cleaned evaporated films of sodium chloride have been prepared and the adsorption of nitrogen and argon by them has been investigated. Isosteric heats and entropies of adsorption have been determined and theoretical entropies calculated. The appearance of a group of sites of uniform activity, hitherto unavailable owing to contamination of the surface, is postulated. The adsorption of nitrogen and argon has been found to be reasonably well represented by the immobile, localized model with indications of the adsorbed argon molecules occupying a different set of sites from the adsorbed nitrogen. Two novel methods for the preparation of evaporated films of alkali halides are suggested.
Open Access
The adsorption of vinyl chloride and vinylidene chloride monomers on their polymers
(1970) Torrington, Ralph George; Linder, Peter W
Following semi-quantitative investigations of the kinetics and equilibria of:- (a) Vinyl chloride monomer vapour adsorbed on polyvinyl chloride; (b) Vinylidene chloride monomer vapour adsorbed on polyvinyl chloride; (c) Vinylidene chloride monomer vapour adsorbed on polyvinylidene chloride; it became evident that, for a number of reasons detailed in the text, it would be worthwhile to study system (a) in detail. Thorough investigations were therefore made at the two temperatures, 25⁰ C and 42.6⁰ C, and in the pressure range 20 torr to 600 torr, with the following results: (i) Attainment of equilibrium, especially at the higher pressures, was very slow and as a result only approximate isotherms could be obtained. These isotherms were shown to exhibit hysteresis. Comparison of the amount of monomer adsorbed at the higher pressures within the above limits, with the amount of krypton required to cover the surface with a monolayer, indicated that multimolecular adsorption occurred. The ascending branches of the isotherms appeared to obey the Freundlich isotherm and the approximate isosteric heats of adsorption calculated from the equilibrium data fell off linearly as the logarithm of the amount of monomer adsorbed increased; as would be expected if the Freundlich isotherm were obeyed. The values of the heats of adsorption found were such that comparison between them and the latent heat of vapourisation of the monomer made it difficult to decide whether the first layer on the surface was chemisorbed or physically adsorbed. (ii) The kinetic data showed that there was always an initial instantaneous adsorption which was reversible towards pressure, followed by a very much slower uptake of monomer. The kinetics of the slow uptake of monomer was studied, at the two temperatures, under both constant pressure and constant volume conditions and was shown to consist of two processes.
Open Access
Alkylated PTA platforms for mono- and polynuclear pre-catalysts for the aqueous biphasic hydroformylation of 1-octene
(2018) Ramarou, Diteboho Selina; Smith, Gregory S; Makhubela, Banothile C E
A series of mono-, di- and trimeric alkylated PTA ligands were synthesised. These ligands were reacted with the dimeric rhodium precursor, [RhCl(COD)]2, to produce the corresponding mono-, di- and trinuclear Rh(I)-PTA complexes. These complexes were then reacted with carbon monoxide to substitute the COD ligands with CO ligands, yielding the carbonyl analogues of the complexes. The ligands and complexes were fully characterised using various spectroscopic and analytical techniques, which include 1H, 13C and 31P NMR spectroscopy, FTIR spectroscopy, mass spectrometry, and elemental analysis. The ligands were found to have good solubility in water at room temperature, while the complexes showed water solubility at elevated temperatures. All the complexes were evaluated as catalyst precursors in the aqueous biphasic hydroformylation of 1-octene. The hydroformylation reactions showed that the complexes (6 – 18) were all active when used as catalyst precursors in the aqueous biphasic hydroformylation of 1-octene to yield aldehydes (linear and branched) and iso-octenes as side products. All complexes exhibited good chemoselectivity for aldehydes with the COD complexes displaying better chemoselectivity towards aldehydes than the CO complexes. However, the CO complexes exhibited better regioselectivity for linear aldehydes than the COD complexes. The trinuclear complex displayed accelerated catalytic rates than the dinuclear complexes which, in turn, displayed faster rates than the mononuclear complexes. The complexes could be recycled three times with a marked decrease in the conversion of 1-octene after each run for each catalyst precursor. Leaching studies showed a significant loss of the metal catalysts into the organic layer after each catalytic run. Mercury poisoning studies were conducted and confirmed that, under the catalytic conditions, all complexes behaved entirely as homogeneous catalysts when evaluated as catalyst precursors for the aqueous biphasic hydroformylation of 1-octene.
Open Access
Alpha emission from the interactions of 14-200 MeV neutrons on carbon-12
(1994) Nchodu, M R; Brooks, F D
Cross-sections for the production of alpha particles from the ¹²C(n,α)⁹Begs and ¹²C(n,n')3α reactions were measured for incident neutrons in the energy range 25 to 52 MeV. The measurements were reduced to absolute cross-sections by simultaneously observing deuteron recoils from n-d elastic scattering in the scintillator using D(n,n)D elastic scattering cross-section as a reference standard. Neutron energy was determined by time-of-flight and pulse shape discrimination (PSD) was used to identify and separate alphas and deuterons from other reaction products. The feasibility of distinguishing different mechanisms for the ¹²C(n,n')3α reaction by means of PSD was also investigated.
Open Access
An Activity-Based Proteomics Approach for Identifying Ajoene's S-thiolation Protein Targets in Blood and Cancer Cells
(2021) Kusza, Daniel Andreas; Hunter, Roger; Kaschula, Catherine
Garlic has been used as a medicinal plant since ancient times and is well-documented to produce several organosulfur compounds (OSCs) that show promising chemopreventative and therapeutic properties. The vinyl disulfide sulfoxide garlic rearrangement product, ajoene, is one of the phytochemicals in garlic that possesses a broad spectrum of biological activities against a variety of cancers both in vitro and in vivo. Our group's previous investigations into ajoene's cytotoxicity have shown that it modifies proteins by S-thioallylating redox-sensitive cysteine residues through a thioldisulfide exchange reaction. Further investigations into this exchange have been the primary aim of this PhD thesis using a biotinylation protocol for trapping out the said protein targets of ajoene to link them to anticancer signalling pathways. The thesis begins in Chapter One with an overview of the chemopreventative and antitumour activity of OSCs from garlic in which a particular emphasis is placed on OSC structure and mechanistic aspects of their cancer biology. Chapter Two discusses the various aspects of ajoene as the target natural product of the thesis. These include its biosynthesis and synthesis, in both native form and as derivatives, for SAR studies, for which a UCT synthesis is described. Mechanistic aspects of ajoene's cytotoxicity towards cancer cells in terms of S-thioallylation via disulfide exchange are then discussed at length. Of crucial importance for the chemical biology studies to follow was the conclusion that S-thioallylation by ajoene is regioselective at the vinyl sulfur, as well as effectively irreversible with suitably reactive cysteine thiol groups. Chapter Three presents an in-depth Chapter on the metabolism and pharmacokinetic properties of ajoene and selected derivatives in a murine xenograft model for human oesophageal cancer (WHCO1). This concluded, disappointingly, that no significant differences in terms of tumour volume, mass and growth rate were observed compared to an untreated control. A follow-up study using a small library of eight ajoene derivatives varying ajoene's different functional groups in a blood stability study, revealed a proportional relationship between the in vitro half-life in blood and the IC50 value for WHCO1 cancer cells. This led to mass spectrometry studies showing that ajoene Sthioallylates the βCys-93 residues in haemoglobin, a chemical modification that most likely explains both ajoene's blood instability and its lack of antitumour activity in vivo. Chapter Four describes the organic synthesis and characterisation of four biotin-ajoene chemical biology probes for chemical biology investigation of S-thiolation in which the background theory of activity-based protein profiling and biotin affinity purification is presented. In the synthesis of these probes, chemical stability emerged as a major stumbling block. Gratifyingly, after several trials, the fourth probe designed and constructed, using a simplified tether involving a convergent “Click”-strategy, turned out to be chemically stable. Subsequent biological validation studies confirmed that the probe retained cytotoxicity against cancer cell lines in vitro (human epithelial mammary gland adenocarcinoma cancer cells (MDA-MB-231) and WHCO1) and shared the same compound–target interaction as its parent ajoene; namely, the regioselective S-thiolation of cellular proteins. Chapter Five constitutes a proteomics study into ajoene's primary protein targets in the MDA-MB-231 cell line using our biotin-ajoene probe. Streptavidin-coated magnetic beads in conjunction with an affinity purification mass spectrometry protocol allowed the isolation and identification of 633 protein targets for ajoene in the MDA-MB-231 proteome. Pathway analyses revealed that ajoene interacts with several targets involved in the control of cell cycles (G2/M cell cycle checkpoint), energy metabolism (glycolysis and pentose phosphate pathway) and the regulation of protein metabolism (translation, folding, quality control and degradation), which supports previously reported cytotoxic modes of action for ajoene against MDA-MB-231 cancer cells. Importantly, we have validated that ajoene S-thioallylates glutathione S-transferase (GSTP1), which is a known cancer-therapy target in breast cancer. Overall, this study complements findings on the cancer-cell protein targets of allicin from crushed garlic, by identifying proteins regulating apoptotic and antiproliferative signalling pathways. These findings support the hypothesis that the anticancer activity of ajoene is due to its S-thioallylation of proteins essential to cellular functions. The thesis concludes with comprehensive experimental and reference sections.
Open Access
An excursion into the synthesis of novel flavanones
(2022) Mansoor, Rukaya; Hunter, Roger
The aim of this project was to develop new methodology for synthesizing flavanones asymmetrically in a manner that could be extended to the synthesis of novel indoloflavanone analogues. The designated approach was via an asymmetric aldol reaction catalysed by a chiral organocatalyst followed by an intramolecular Mitsunobu reaction. Following a review of the existing methodologies for the synthesis of racemic and asymmetric flavanones and various flavan analogues, an initial model reaction between acetophenone and para-nitrobenzaldehyde returned the aldol product using (S)- proline tetrazole as organocatalyst. Several experiments on optimization were conducted to identify the best stoichiometry/conditions as ketone (4): aldehyde (1): catalyst (10%): DMSO (2): H2O (2) at room temperature for three days, which returned the desired aldol product in 64% yield and a pleasing ee of 93%. Interestingly, it was found that the amount of water in the reaction played a role in dictating the stereogenicity of the product. Unfortunately, changing the ketone to the required 2- hydroxyacetophenone for a flavanone synthesis resulted in a very sluggish reaction, delivering the product in a very low conversion (~ 10%) after 3 days. This was attributed to the poor electrophilicity of the ketone carbonyl group in the enamine formation step because of the ortho electron-releasing phenolic hydroxyl group. For increasing the electrophilicity, the approach was changed to using a Knoevenagel condensation reaction between an activated β-ketoester derivative of 2- hydroxyacetphenone and para-nitrobenzaldehyde according to the optimised aldol reaction conditions. Although this successfully delivered chemically the required flavanone precursor with a satisfactory yield (77%), there was no enantioselectivity, which was attributed to either the chiral entity being too far away from the prochiral site or because of an increased rate of iminium ion hydrolysis prior to the oxa-Michael cyclisation step due to the electron-withdrawing ester group. Gratifyingly, however, this methodology could be applied to synthesis of a 2-indolylflavanone (in racemic form) as a B-ring indolylflavanone, setting up a prototype for a future, more detailed study. With regards to A-ring modification, 3-acetyl-2-hydroxyindole and various protected variants were tried out as the acetophenone partner in the methodology only to meet the same problems as described above due to strong electron donation into the carbonyl group. Similarly, we weren't able to extend this to a -ketoester variant via acetyl group C-carboxylation as before. Eventually, the problem was resolved by a C-3 acylation of N-Boc-2-indolone with cinnamoyl chloride, rendering a precursor for indoloflavanone synthesis via oxa-Michael cyclisation. Although the latter was not achieved because of time constraints, this acylation study opens up a novel entry for further study into the synthesis of A-ring indoloflavanones for biological evaluation.
Open Access
Analysis of platinum, palladium and rhodium at trace concentrations in lead using the time resolved spark emission technique called SAFT
(2000) Sundquist, L. P; Koch, Klaus R
The fire assay technique may be used to extract noble metals from platinum bearing ores. It allows for the use of relatively large quantities of ore sample from which trace quantities of noble metals are concentrated. The fire assay with lead as the collector is one such procedure, where preconcentration of the noble metals allows for direct analysis of the noble metals in lead The samples may be prepared by pyrochemically treating the ore sample with a litharge-based flux. These lead buttons require an homogenising remelt and rapid cast before direct determination of the noble metals can be made using a time resolved form of spectroscopy called SAFf, or Spark Analysis for Traces. The unique characteristics of this technique is that inunediately after the electrical spark discharge has taken place radiation from atomic species continues and is termed after-glow. Special electronic techniques are required to observe this phenomenon as it takes place in microseconds. By studying the emission characteristics of various spectral wavelengths it is possible to determine the time at which the photomultiplier measures the atomic radiation. and not the background radiation. The atomic emission line to background ratio is thus improved and hence precision and limits of detection. Initial investigations into the SAFf analysis of platinum. palladium and rhodium using synthetic standards prepared from pure noble metals and lead revealed an analytical method of great promise. However the method failed when applied to real ore samples for several reasons. The SAFf analysis is particularly sensitive to the effects due to changes of the matrix of the lead depending on the type of sample used to prepare the lead buttons. Corrections for these effects could not be applied as preparation of matrix matched standards also failedAnother serious problem experienced with the SAFf technique was the inherent insensitivity of the selected platinum wavelengths together with high background emissions. The platinum atomic emission to background ratio was thus poor, and hence scientifically inappropriate practice to measure platinum in lead under these circumstances. The most sensitive platinum emission wavelength could not be used because corrections for a spectral interference from nickel could not be applied. A certain portion of base metals are collected in the lead buttons along with the noble metals during the fusion process, and since nickel is present in all ore samples associated with platinum group metals the presence of nickel and platinum together in lead after collection is inevitable. Because of the nature of the ore samples used in the investigations, the concentration range of platinum, palladium and rhodium in lead even after preconcentration using fire assay, was very limited, and attempts to create calibrations using only these samples proved unsuccessful. Additional standards prepared from different ore samples were used to extend the concentration ranges of the calibrations, however this also proved to be of no use as the different matrices of these samples detracted from any possibility of defining an accurate calibration curve.
Open Access
Anti-cancer and anti-malarial 4-aminoquinoline derivatives : synthesis and solid-state investigations
(2006) Melo, Candice Soares de; Chibale, Kelly; Caira, Mino R
The work presented in this thesis is two-fold: (i) development of single agents that provide inhibition of both the growth of malaria parasites and of tumour cells in vitro, and (ii) inclusion of these potential novel inhibitors in cyclodextrin host molecules in an attempt to render these dual drugs water-soluble. Of all the current clinically established antimalarials, the 4-aminoquinolines haveproven to be the most significant and efficacious for the treatment and prophylaxis of malaria. However, their efficacy has decreased by the spread of drug resistant strains of the causative agent Plasmodium Jalciparum. Future research into 4-aminoquinoline derivatives as antimalarial agents is still warranted and justified on the basis of several considerations. The quinoline moiety has also been shown to be a substructure in multi-drug resistance reversal agents against certain cancer cell lines and antitumour agents which have demonstrated the ability to act as differentiation-inducing agents. The strategy employed for this project was to hybridize chalcone moieties and their Mannich base derivatives with the 4-aminoquinoline moiety. This dual drug concept uses the basic structure of the chalcone scaffold, which has a wide range of known antimalarial and anticancer activities, and is hybridised with the 4-aminoquinoline moiety, in order to exert maximal biological activity and overcome or prevent drug resistance. Structural variation on the aromatic rings of the chalcone scaffold allowed preliminary structure-activity relationship studies to be undertaken.
Open Access
Antimalarial and cysteine protease inhibitor pharmacophores as scaffolds for new antimalarial agents
(2005) Musonda, Chitalu Christopher; Chibale, Kelly
The work in this thesis is threefold: (i) A new series of antiplasmodial agents were initially designed based on the β-amino alcohol bioactiphore, a subunit that is found in a number of antimalarial agents. (ii) Various thiosemicarbozones and semicarbozones were designed and synthesized as potential mechanism-based inhibiotrs of parasitic cysteine proteases. (iii) Multicomponenet reactions offer the advantage of introducing chemical diversity in fewer steps than conventional multi step organic synthesis. New chloroquine-type compounds were designed and synthesized using the Ugi 4 component condensation reaction and its variants. The synthesized compounds ranged from simple peptidic molecules to rigid heterocycles.
Open Access
Antimalarial benzimidazoles and related structures incorporating an intramolecular hydrogen bonding motif: medicinal chemistry and mechanistic studies
(2021) Attram, Henrietta Dede; Chibale, Kelly
Malaria, an infectious disease caused by Plasmodium parasites, continues to take an enormous toll on human health, particularly in tropical regions. According to the World Health Organization (WHO), progress against malaria eradication has stalled, specifically in the African region. Global efforts to curb the disease are being undermined by the gaps in access to vital tools. In 2019, about 229 million cases were recorded compared to the 228 million cases recorded in 2018. This is an annual estimate that has not changed significantly over the last four (4) years. Also, children under the age of five (5) years account for most malaria deaths worldwide. Chemotherapy represents one of the most effective control measures to mitigate the malaria burden, with the WHO presently recommending the use of artemisinin combination therapies (ACTs) to treat uncomplicated malaria. However, there is compelling evidence from Southeast Asia and recently in Rwanda (Africa) describing the emergence and spread of ACT resistance, characterized by reduced clearance rates of P. falciparum parasites. In some countries, resistance to partner drugs such as amodiaquine has been observed. These developments highlight the need to expand the antimalarial drug arsenal by exploring and developing new compound classes, preferably with a combination of novel modes of action, multistage activity, good safety profile, efficacy at low doses and reduced tendency to the development of resistance. In this study, two classes of compounds, benzimidazoles and imidazopyridines, incorporating an intramolecular hydrogen bonding (IMHB) motif, were explored for their antimalarial potential. These two chemotypes were selected on account of their privileged nature due to their capacity to interact with various biological systems, leading to a wide variety of biological activities, including antimalarial activity. Structural modifications around the benzimidazole scaffold resulted in the classification of these analogues into 1H-benzimidazoles and N-benzyl benzimidazoles (astemizole-based). In this regard, 33 benzimidazole analogues were synthesized, fully characterized and evaluated in vitro for their antiplasmodium activity against both the drug-sensitive NF54 and the multidrug-resistant K1 strains of the Plasmodium parasite. As a result, the 1H-benzimidazole analogues manifested sub-micromolar potencies against the chloroquine-sensitive NF54 strain of P. falciparum, with IC50 values between 0.079 µM and 0.968 µM. The most potent analogue within this series was compound 1.3 (Figure 1) with an IC50 of 0.079 µM against the chloroquine-sensitive strain and 0.335 µM against the multidrug-resistant (K1) strain. The resistance index of compound 1.3 (RI = 4) suggests the possibility of cross-resistance with drugs like chloroquine. The N-benzyl benzimidazole (astemizole-based) also displayed sub-micromolar activity against the chloroquine-sensitive strain of the parasite, with compound 2.3 (Figure 1) displaying the highest potency (IC50 PfNF54 = 0.029 µM and IC50 PfK1 = 0.117 µM) within the series. Generally, the benzimidazole analogues exhibited poor activity against the sexual gametocyte stage of the Plasmodium parasite in comparison to the asexual blood stage. However, compound 1.3 displayed sub-micromolar potency (IC50 = 0.382 µM) against earlystage gametocytes. Furthermore, selected potent analogues showed low cytotoxicity (SI = 39- 1500) when tested in vitro against the Chinese Hamster Ovary cells. The N-benzyl benzimidazole analogues, designed based on the known antihistamine drug astemizole, were tested against the hERG (human ether-a-go-go-related)-encoded potassium ion channel. These analogues expressed >40% inhibition against the hERG ion channel at the highest test concentration with potencies between 0.96 and 13.24 µM. Regardless, these compounds showed an improved cardiotoxicity risk relative to verapamil, a potent hERG channel inhibitor (IC50 = 0.58 µM), and the control drug used in the experiment. In addition, the five (5) selected potent analogues displayed low microsomal metabolic stability in mouse, rat and human liver microsomes. This impeded the advancement of these potent analogues to in vivo efficacy studies. Meanwhile, metabolite identification studies provided insight into the metabolic hotspots, which can be addressed in future optimization campaigns to address this liability. On the other hand, the imidazopyridine analogues were designed using the 1H-benzimidazole frontrunner analogue 1.3 as a guide. A structure-activity relationship (SAR) plan was pursued to produce diverse analogues due to modifications around the core scaffold. The SAR was explored with aromatic and aliphatic groups. As a result, 19 structural variants were synthesized and evaluated in vitro for their antiplasmodium activity against both the drug sensitive NF54 and the multidrug-resistant K1 strains of the Plasmodium parasite. 13 of these analogues showed potencies of <1 µM with compound 3.14 (IC50 = 0.08 µM) displaying the highest potency within the series. Subsequently, most of the active analogues showed a favourable cytotoxicity profile against CHO cells, with compound 3.14 being the least cytotoxic (SI = 466). Like the benzimidazoles, selected potent imidazopyridine analogues exhibited low microsomal metabolic stability in mouse, rat and human liver microsomes, posing a hurdle to the progression of these compounds to in vivo proof of concept studies. Aqueous solubility studies and physicochemical profiling of all the target compounds were carried out. The solubility results obtained were correlated with physicochemical parameters such as cLogP, melting points, TLC retardation factors and HPLC retention times to establish a solubility-property relationship across both classes of compounds. The correlation assessment revealed that different factors simultaneously affect the solubility of compounds across a series; hence, it may be crucial to assess these factors based on individual cases rather than an entire class of compounds. Also, the physicochemical assessment showed that both the benzimidazoles and the imidazopyridines complied with Lipinski's RO5 and Veber's rule. Single crystal X-ray structure analysis, IR spectroscopy, and DFT calculations were used to ascertain the presence of IMHB in the target compounds. Representative analogues 1.2 and 2.2 were used for these studies. In an effort to elucidate the mechanism of action, novel fluorescent analogues [1.3-NBD (IC50 PfNF54 = 0.044 µM) and 3.14-NBD (IC50 PfNF54 = 0.049 µM)] of the frontrunner compounds 1.3 and 3.14 were synthesized and pharmacologically validated as suitable probes for fluorescence live-cell imaging. The extrinsic fluorophore 7-nitrobenz-2-oxa-1,3-diazole (NBD) was employed due to the absence of intrinsic fluorescence properties in both compounds. Live-cell microscopy showed localization of both fluorescent analogues in all the studied organelles except the nucleus. While this suggests that the nucleus may not be a site of action for antiplasmodium activity, incorrect localization due to the NBD tag cannot be excluded. Based on the results from the live-cell imaging where both fluorescent probes accumulated in acidic organelles like the digestive vacuole and the neutral lipid bodies that have been implicated in hemozoin formation, it was hypothesized that the parent compounds 1.3 and 3.14 could be inhibiting the formation of hemozoin. Docking studies employed to investigate this hypothesis predicted intermolecular interactions between the parent compounds and the heme/hemozoin surfaces to inhibit hemozoin formation. The heme fractionation studies of compound 1.3 showed a dose-dependent increase in heme levels with a subsequent decrease in hemozoin levels at increasing compound concentrations. In essence, these observations support hemozoin inhibition as a mechanism of action of compound 1.3 while pointing to other targets within the parasite based on widespread association with other organelles. However, compound 3.14 showed no significant change in heme levels, but a decrease in hemozoin levels with increasing compound concentration was observed. This indicates that compound 3.14 is not a hemozoin inhibitor but could be targeting different digestive vacuole processes.
Open Access
Antimalarial Evaluation of Quinoline-triazoleMn(I) and Re(I) PhotoCORMs
(2019) Ishmail, Fatima-Zahra; Smith, Gregory
Malaria remains a disease of global health concern, as thousands of people fall victim to it annually. Despite the continuous development of new malaria chemotherapies, the parasite has adapted and mutated, conferring multi-drug resistant strains. The constant emergence of drug-resistant strains of malaria and the decrease in efficacy of most front-line treatments calls for the urgent development of new antimalarial chemotherapeutic drugs. It is of great importance to develop compounds that target resistant strains of malaria. Chloroquine is one of the most significantly studied antimalarials to date and its derivatives have been mainstays in malaria treatment. It has also been established that carbon monoxide (CO) is able to prevent Experimental Cerebral Malaria (ECM) (a severe form of malaria) through the prevention of haemoglobin oxidation.This study investigated the synthesis, characterization and biological evaluation as antiplasmodial agents of two new quinoline-1,2,4-triazole ligands and their respective Mn(I) and Re(I) tricarbonyl complexes. The two ligands differ in the presence of an extended amino-propyl chain conjugated to the quinoline scaffold, which has proven to confer greater antimalarial activity. Furthermore, the complexes were evaluated for their potential as photoCORMs (photo-induced Carbon Monoxide Releasing Molecules) and the CO-releasing effects on the antiplasmodial activity were evaluated. Two manganese tricarbonyl complexes (Mn-1 and Mn-2: contains amino-propyl chain) were evaluated for their CO-releasing properties upon photoexcitation with UV light at 365 nm. Both complexes release CO upon photoexcitation in DCM, DMSO/PBS and DMSO/growth medium solutions. The rate of CO-release is medium-dependent and the Mn-1 complex releases CO faster than the Mn-2 complex. The ligands and metal complexes were evaluated for their in vitro antiplasmodial activity against the NF54-chloroquine-sensitive and the K1-chloroquine-resistant strains of Plasmodium falciparum (P. falciparum). All tested compounds show good antiplasmodial activity with IC50 values in the low micromolar range. The manganese and rhenium analogues exhibit similar antiplasmodial activities, with IC50 values of 3.81 μM and 4.61 μM in the CQ sensitive strain respectively. Both complexes retain their activity in the CQ-resistant strain with resistance indices of 1. The ligand containing the amino-propyl chain (L2) exhibits the greatest antiplasmodial activity with IC50 values of 0.33 μM and 0.69 μM in the CQ-sensitive and -resistant strains respectively. The manganese complex thereof (Mn-2) has IC50 values of 0.54 μM and 1.16 μM in the CQ-sensitive and -resistant strains respectively. The antiplasmodial activity of the manganese complexes Mn-1 and Mn-2 increases 7- and 3- fold respectively upon photoexcitation at 365 nm in the K1-CQ-resistant strain. The increase in antimalarial activity exhibited upon light-induced CO-release presents a promising mechanism of combating drug-resistant P. falciparum. Mechanistic studies of these compounds indicate that they potentially work via β-hematin inhibition, with the metal complexes being greater inhibitors than CQ. Upon photo-induced CO-release, the β-hematin inhibition of complex Mn-1 increases drastically.
Open Access
Antimalarials based on the arylpiperazine privileged substructure
(2005) Molyneaux, Carrie-Anne; Chibale, Kelly
Based on a previous study, arylpiperazines (2-chlorophenylpiperazine, 2-ethoxyphenylpiperazine and phenylpiperazine) were found to be significantly more potent against the chloroquine-resistant (K1) strain than against the chloroquine-sensitive(DIO) strain. In other studies, 8-hydroxy-2-(di-n-propylamino)tetralin (8-0H-DPAT) has been identified as a potential antimalarial agent for the inhibition of the 5-hydroxytryptamine type 1A receptor in Plasmodium falciparum. A number of arylpiperazines are also known to target this receptor in other systems. Coupled with the potential role of arylpiperazines as replacements for the antimalarial 8-OH-OPA T, these results prompted a further investigation into the antiplasmodial properties of a broader range of simple un substituted and substituted arylpiperazines against a broader range of chloroquine-sensitive and chloroquine-resistant strains of PlasmodiumJalciparum.
Open Access
Antimycobacterial 2-aminoquinazolinones and benzoxazole-based oximes: synthesis, biological evaluation, physicochemical profiling and supramolecular derivatization
(2017) Njaria, Paul Magutu; Chibale, Kelly; Caira, Mino R
Tuberculosis (TB) is a life-threatening infectious disease caused by Mycobacterium tuberculosis (Mtb). Globally, TB is a major public health burden with an estimated 10.4 million new cases and 1.8 million deaths reported in 2015. Although TB is curable, the treatment options currently available are beset by numerous shortcomings such as lengthy and complex treatment regimens, drug-drug interactions, drug toxicities, as well as emergence of widespread multi-drug resistance. Therefore, there is an urgent and compelling need to develop new, more effective, safer drugs with novel mechanisms of action, and which are capable of shortening treatment duration. This study focused on hit-to-lead optimization of two new classes of compounds with potential anti-TB properties: 2-aminoquinazolinones (AQZs) and benzoxazole-based oximes (BZOs). A hit compound for each of these classes with low micromolar antimycobacterial activity had previously been identified through phenotypic whole-cell in vitro screening.
Open Access
Antiplasmodial neolignans from Trema orientalis : identification, synthesis and analogue generation.
(2011) Pillay, Pamisha; Chibale, Kelly; Maharaj, Vinesh
Trema orientalis, a widely distributed evergreen tree with various medicinal properties including the treatment of malaria, was investigated as a potential source of new antimalarial lead compounds. Organic extracts of the young growing twigs of T. orientalis were reproducibly shown to be active against the chloroquine-sensitive (D10) and chloroquine resistant (K1) strains of Plasmodium falciparum. The 8-O-4' oxyneolignans, dadahols A and B, were identified as the major active compounds using two bioassay-guided fractionation approaches. The new accelerated “HPLC biogram” methodology allowed for early recognition of the active compounds in the complex plant extract, requiring considerably less time and material compared to the classical reiterative approach.