Invasion of host erythrocytes is an essential stage in the life cycle of Plasmodium parasites and in development of the pathology of malaria. The stages of erythrocyte invasion, including initial contact, apical reorientation, junction formation, and active invagination, are directed by the coordinated release of specialised apical organelles and their parasite protein contents. Among these proteins, and central to invasion by all species, are two parasite protein families, the reticulocyte-binding protein homologue (RH) and the erythrocyte-binding like (EBL) proteins, that mediate host-parasite interactions. RH5 from Plasmodium falciparum (PfRH5) is the only member of either family demonstrated to be necessary for erythrocyte invasion in all tested strains, through its interaction with the erythrocyte surface protein basigin. Indeed, antibodies targeting either PfRH5 or basigin can block parasite invasion with high efficiency in vitro, making PfRH5 an excellent candidate for a vaccine to protect against the most deadly form of malaria. Here I present crystal structures of PfRH5 in complex with basigin and with two distinct inhibitory antibodies. This is the first structure of any RH protein, revealing a novel fold in which two three-helical bundles come together to form a kite-like architecture. The two immunoglobulin domains of basigin and the inhibitory antibodies bind to one tip of the kite. These findings provide the first structural insights into erythrocyte binding by the Plasmodium RH protein family and identify novel inhibitory epitopes to guide the design of a new generation of vaccines against the blood-stage parasite.

MSc., Faculty of Science, University of the Witwatersrand, 2011 / This dissertation presents the results of a crystallographic investigation into nineteen novel n-aminopyridinium perhalometallates of the general formula (C5H7N2 +)2MX4 2- where n = 2, 3 or 4, M = Zn, Cd or Hg and X = Cl, Br or I. The aim was to identify positional effects of the cation hydrogen bonding donor groups on the structures and to possibly identify robust synthons. Overall structural trends were also studied. The hybrid crystals were synthesized using temperature controlled crystallization methods and were characterized using X- ray diffraction techniques. Eighteen of the nineteen hybrid crystals displayed isolated tetrahedral perhalometallate anions. The results were classified into six different classes of isostructural compounds. Eight of the nineteen hybrid structures (42%) contained water. The 42% include two 3-ammoniopyridinium structures and all cadmium and mercury containing 4-aminopyridinium structures. The effect of a change in metal and/ or halide on the structure was investigated, and the overall structural trends in each n-aminopyridinium family were identified. Four different synthons were observed in the 2-aminopyridinium series while one synthon was observed throughout the 4-aminopyridinium series. A common synthon was observed in both the 3-aminopyridinium and 3-ammoniopyridinium series.

Student Number : 0011001D - PhD thesis - School of Chemistry - Faculty of Science / The subject of this thesis is the development of a potentially simple, general and economical synthetic protocol for the potent antimalarial alkaloid febrifugine (1) and its analogues. In Chapter 1, the interesting history of 1, which includes a description of several reported total syntheses of 1, is discussed. Natural products derived from 1, as well as promising synthetic derivatives that display good antimalarial activity, are also discussed. The structure-activity relationships determined to date for 1 and its derivatives are presented in order to substantiate the need for the development of new synthetic strategies towards derivatives of 1 and its 3″-unsubstituted analogue, (±)- deoxyfebrifugine (14). A brief overview of the general strategies used in the Organic Chemistry Group at the University of the Witwatersrand for the synthesis of alkaloids is given in Chapter 2. The Eschenmoser sulfide contraction reaction between a thiolactam and an α- bromocarbonyl compound results in the formation of a vinylogous amide (or “enaminone”) product, which can be further manipulated to produce commonly encountered alkaloidal molecular skeletons. The chosen approach to 1 is based on reaction between the pivotal bromide 3-(3-bromo-2-oxopropyl)quinazolin-4(3H)-one (105) and suitable 3-substituted piperidine-2-thiones. A series of model studies, described in Chapter 3, was performed in order to test the feasibility of the synthetic strategy. These studies resulted in a new preparation of the key bromide 105 and a new and efficient synthesis of (±)-deoxyfebrifugine (14). Enaminone analogues derived from five-, seven-, eight-, nine- and thirteen-membered thiolactams were also prepared for comparison. An interesting difference in the sensitivity of the five- and six-membered model cyclic vinylogous amides towards reducing agents was observed. Whereas three piperidine analogues of 14 could be prepared in high yields by the chemoselective hydrogenation of six-membered cyclic vinylogous amide precursors, the five-membered analogues either reacted nonselectively under various standard hydrogenation conditions, or resisted reduction entirely. An extension of the approach towards the synthesis of a 3″-amino analogue of febrifugine (1) from L-ornithine is discussed in Chapter 4. Several 3-aminated piperidin-2-ones and thiones were prepared, but the subsequent enaminones were stable and characterizable only when the piperidinylidene ring nitrogen was alkylated. However, chemoselective reduction of the enaminone C=C bond in 3-{(E)-3-[(3S)-3- (tert-butoxycarbonylamino)-1-(4-methoxybenzyl)piperidin-2-ylidene]-2-oxopropyl}- quinazolin-4(3H)-one (221), an interesting 3-acylamino dehydro analogue of 1, did not give the desired azafebrifugine, but instead yielded a 5,6,7,8-tetrahydro-1Hpyrido[ 3,2-c][1,2]oxazine derivative. Several approaches to febrifugine (1) itself based on the successful model studies are discussed in Chapter 5. Initially, stereoselective α-bromination and subsequent substitution by oxygen of piperidin-2-ones derived from the chiral auxiliary (S)- phenylglycinol was explored. Unexpected racemization occurred at the α-position of the lactam during this route. A second approach to 3-hydroxypiperidin-2-one from Larginine was also problematic. Finally, the utility of α-hydroxylation methodology (including Davis methodology) on N-substituted piperidin-2-ones was explored. This route yielded a range of 3-oxygenated lactams and thiolactams, many of which displayed optical activity. The crystal structures of several 3-substituted thiolactams were determined and compared. However, attempts to apply the sulfide contraction procedure to these precursors were unsuccessful. Some investigations designed to explore the structural differences between vinylogous amides derived from the quinazoline-containing bromide 105 and thiolactams of different ring sizes are discussed in Chapter 6. Single crystal X-ray diffraction and NMR spectral data are compared for this series of compounds, the results revealing that the enaminone group in the five-membered ring derivative 3- [(3Z)-2-oxo-3-(pyrrolidin-2-ylidene)propyl]quinazolin-4(3H)-one 155 possesses a significantly different electronic distribution to the other analogues in the series.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2016. / In this PhD thesis, the synthesis, crystal chemistry and thermoresponsive behaviour of non-porous borophosphates [ABPO5 (A= Ca, Sr, Ba) and BPO4] and porous borophosphates [NH4Fe(III)[BP2O8(OH)] and MIxMIIz(H2O)2[BP2O8].zH2O (MI = Na, NH4 and MII = Mn, Co)] phases were investigated. Understanding the crystal structure dynamics as a function of temperature of the selected porous and non-porous borophosphates revealed the thermal stability of the studied compounds, while serving as a predictive measure of the effects of temperature on other materials properties and subsequent applications. The non-porous borophosphates were synthesized using the solid state method, whereas the porous borophosphates were synthesized using the hydrothermal method. The powder X-ray diffraction (PXRD) technique, along with the application of the Rietveld refinement method, was the principle characterisation technique employed for the non-destructive and non-invasive thermoresponsive characterisation of the studied borophosphate phases. This thesis consists of seven chapters, four of which are independent papers corresponding to four chapters. Chapter 1 reviews the relevant scientific literature, while chapter 2 describes the methods of characterisation used in this thesis. Concerning the highly thermally stable non-porous borophosphates, chapter 3 presents the thermal expansion behaviour of ABPO5 compounds, which have been determined from the sequential application of the Rietveld refinement method of variable temperature powder X-ray diffraction (VT-PXRD) data. For trigonal ABPO5 compounds, a near linear expansion of the unit cell axes was found for all structures as a function of temperature. The variation of the crystal structure with temperature of ABPO5 compounds was also established. With the general understanding that borophosphates display intriguing crystal structure architectures, chapter 4 describes the synthesis and characterisation of four metal borophosphate hydrates: NaMII(H2O)2[BP2O8](H2O); MII = Co (I), Mn (II) and (NH4)0.5MII1.25(H2O)2[BP2O8](H2O)0.5; MII = Co (III), Mn (IV). The structures refined at room temperature from PXRD data revealed that isostructural phases I and II have an ordered arrangement of water molecules in the voids, whereas isostructural phases III and IV have fractional and disordered distribution of water molecules in the voids. Scanning electron microscope (SEM), fourier transform infrared spectroscopy (FT-IR), variable temperature powder X-ray diffraction (VT-PXRD) and thermogravimetric analysis (TGA) for all compounds are also presented. Chapter 5 was an investigation into the synthesis, crystal structure and thermal properties of the porous iron borophosphate NH4Fe(III)[BP2O8(OH)]. Variable temperature PXRD and thermogravimetric analysis were used to investigate the compounds thermal stability and expansion behaviour. Thermal investigations indicated that the compound is stable up to 470 °C. Of great importance to the accurate and/or precise measurement of the crystal structures and lattice parameters of the phases investigated using powder diffraction was the correct application of the Rietveld refinement method to the measured diffraction data. Therefore, chapter 6 is an investigation into a number of different Rietveld refinement approaches, which were aimed at modelling the changes in the atomic coordinates of BPO4 as a function of temperature. Parametric Rietveld refinements and rigid body Rietveld refinements were among the refinement strategies employed. / LG2017

Thesis advisor: Evan R. Kantrowitz / For nearly 60 years the ATP activation and the CTP inhibition of Escherichia coli aspartate transcarbamoylase (ATCase) has been the textbook example of allosteric regulation. We present kinetic data and 5 X-ray structures determined in the absence and presence of a Mg2+ concentration within the physiological range. In the presence of 2 mM divalent cations (Mg2+, Ca2+, Zn2+) CTP does not significantly inhibit the enzyme while the allosteric activation by ATP is enhanced. The data suggest that the actual allosteric inhibitor in vivo of ATCase is the combination of CTP, UTP and a M2+ cation and the actual allosteric activator is ATP and M2+ or ATP, GTP and M2+. The structural data reveals that two NTPs can bind to each allosteric site with a Mg2+ ion acting as a bridge between the triphosphates. Thus the regulation of ATCase is far more complex than previously believed and calls many previous studies into question. The X-ray structures reveal the catalytic chains undergo essentially no alternations, however, several regions of the regulatory chains undergo significant structural changes. Most significant is that the N-terminal regions of the regulatory chains exist in different conformations in the allosterically activated and inhibited forms of the enzyme. Here, a new model of allosteric regulation is proposed. / Thesis (MS) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis (Ph.D.)--Montana State University--Bozeman, 2006. / Typescript. Chairperson, Graduate Committee: C. Martin Lawrence. Includes bibliographical references (leaves 146-159).

More than 90% of human genes undergo a processing step called splicing, whereby non-coding introns are removed from initial transcripts and coding exons are ligated together to yield mature messenger RNA. Roughly 50% of human genetic diseases correspond to aberrant splicing. Splicing is catalyzed by an RNA/protein machine called the spliceosome. RNA components of the spliceosome are at least partly responsible for splicing catalysis. In addition, in vitro analyses implicate an essential and very highly conserved protein, Prp8, in orchestrating key steps in spliceosome assembly and possibly catalysis. Interestingly, mutant alleles of Prp8 are the cause of retinitis pigmentosa, an inherited form of retinal degeneration. A key goal is elucidation of the precise role of Prp8 in the spliceosome by high resolution structural analysis. The large size of Prp8 and its insolubility hinder progress in this regard. Instead, structural understanding of Prp8 can be gained by investigating domains in isolation; however there is only limited information as to what domain boundaries are and few hints about the functional relevance of putative domains. Here we have further defined the previously proposed domain IV in Prp8, and identified the domain IV core. Structural determination of the domain IV core reveals an RNase H fold, which could not be predicted based on primary sequence alone. RNase H recognizes A-form nucleic acid duplexes, which strongly suggests the domain IV core interacts with double-stranded RNA in the context of the spliceosome. Characterizing the binding preferences of the domain IV revealed the highest affinity is for a 4-helix junction structure adopted by the very RNAs at the spliceosome active site. Our characterization of the protein/RNA binding interface by complementary footprinting techniques currently provides the best model of how RNA interacts with an essential protein component at the heart of the spliceosome.

Compound I of myeloperoxidase is capable of both one-electron oxidation and two-electron oxidation reactions. Halides and pseudohalides are the substrates for the two-electron oxidation and other compounds including a large variety of aromatic alcohols and amines can be oxidized via the single electron oxidation pathway. To investigate the catalytic mechanism of myeloperoxidase four structures of complexes of myeloperoxidase were solved. Two of them are complexes with hydroxamic acids and the other two are complexes with nitrite. Hydroxamic acids (salicylhydroxamic acid and benzylhydroxamic acid) can function as structural analogues for the aromatic alcohol and amine substrates of myeloperoxidase. The crystal structures of complexes of MPO with both hydroxamic acids have been solved at 1.85 Å resolution and their binding to myeloperoxidase is compared. The models show similar binding of their hydroxamic acid moieties but different orientations of their aromatic rings. The absence of the hydroxyl group covalently bound to the benzyl group in benzylhydroxamic acid creates an environment that does not permit the same favorable interactions with MPO when compared to salicylhydroxamic acid. These findings could explain the three orders of magnitude difference in the value of the dissociation constants of the two complexes. Nitrite has been shown to bind myeloperoxidase and also to reduce Compound I and Compound II. Crystal structures of the complex between myeloperoxidase and nitrite confirmed the binding of nitrite to the native enzyme both in the distal cavity and the chloride-binding site. The binding in the distal cavity occurred to the heme iron in the nitro mode. In the MPO-cyanide-nitrite ternary complex, nitrite had been shown to bind only at the chloride-binding site. No secondary site for nitrite binding had been seen in the distal cavity when cyanide was liganded to the iron. Overall, this study is the first to show from a crystallographic point of view a comparison in the mode of binding of the two hydroxamic acids to a mammalian peroxidase and also the binding of nitrite to a heme peroxidase.

Thesis (Ph. D.)--University of Delaware, 2006. / Principal faculty advisor: Tatyana Polenova, Dept. of Chemistry & Biochemistry. Includes bibliographical references.

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 152-164).