Drug repositioning applies existing drugs to new disease indications. A prerequisite for drug repurposing is drug promiscuity - a drug's ability to bind to several targets, possibly leading to side effects on the other hand. One reason for drug promiscuity is binding site similarity between (otherwise unrelated) proteins. In this thesis, a new algorithm for remote binding site similarity assessment and its application to the whole of the Protein Data Bank (PDB) is presented, forming the base for off-target identification and drug repositioning. The present thesis contributes to a long-standing debate on the reasons for drug promiscuity, being one of the pioneer studies investigating these from a protein structural point of view. Except for a small influence of flexibility, the analysis of all promiscuous drugs in the PDB revealed that drug properties are of minor importance. However, a strong correlation between promiscuity and binding site similarity of protein targets is found (r = 0.81), suggesting binding site similarity as the main reason for drug promiscuity. For 71 % of the promiscuous drugs at least one pair of their targets' binding sites is similar and for 18 % all are similar. In order to overcome issues in detection of remotely similar binding sites, a score for binding site similarity is developed: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary binding site alignments and also works on distinct ligands on a structural proteome scale. To answer the question on which other targets might be hit when targeting a particular protein, an all-to-all binding site alignment of 32,202 protein structures is analyzed. Of the hundreds of million possible protein pairs, 0.27 % were found to have similar binding sites. Extrapolating to the human proteome, for one human protein are 54 proteins with a similar binding site expected on average. Clearly, this is in contrast to the one drug-one target paradigm in drug development. Based on these data, disadvantageous off-targets can be uncovered and drug-repositioning candidates inferred. The enormous potential is demonstrated with the example of Viagra, proposing it for repositioning to Alzheimer's disease and prostate cancer. The findings in this thesis question the established single-target dogma in drug discovery. Drugs are triggered to modulate multiple targets simultaneously by the widespread binding site similarity. With the presented pipeline, drug targets can be reliably predicted: Starting from a target protein, additional targets are predicted based on binding site similarity and prioritized according to the resulting ligand structural overlap. Identifying drug targets helps to understand severe side effects and opens the door for drug repositioning.

The chloride/proton antiporter ClC-5 is primarily expressed in the kidney where it aids in re-absorption of proteins from the glomerular filtrate. Functional disruption of ClC-5 causes Dent’s Disease – a renal condition characterized by proteinuria and kidney failure in a third of all cases. The majority of disease-causing mutations translate into premature truncations of the carboxy-terminal (Ct) region of ClC-5 and are predicted to disrupt the protein-protein interactions mediated by this domain. In this thesis, direct ATP binding to the two cystathionine β-synthase (CBS) domains of ClC-5 was demonstrated. ATP binding enhanced the global compactness of the ClC-5 Ct region likely through a clamping motion of the CBS domains around the nucleotide. Along with ATP, the sodium proton exchange regulatory factor 2 (NHERF2) also binds ClC-5; however, the molecular mechanism behind this interaction was unknown as ClC-5 lacked the PDZ binding motif traditionally localized at the Ct end of bait proteins. Here, we also identified a class I PDZ binding motif (657-660; TSII) within the internal sequence of ClC-5. Despite the buried position of this motif in the Ct peptide’s X-ray crystal structure (PDB: 2J9L), the high propensity of this region for dynamic flexibility prompted us to test whether it could mediate NHERF2 interactions. In support of this hypothesis, we demonstrated that the motif is transiently available to interact directly with NHERF2 in vivo and to enable an enhancement in receptor-mediated endocytosis in mammalian cells. Collectively, these results gave further evidence that the intracellular Ct region of ClC-5 serves as a hub to mediate interactions essential for its maturation, stability, and trafficking in renal epithelium, as well as providing further insights into the molecular basis of Dent’s Disease.

Magister Scientiae - MSc / OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled. / South Africa

Philosophiae Doctor - PhD / Tsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative magents of Human African Trypanosomiasis (HAT). HAT is a debilitating disease that continues to present a major public health problem and a key factor limiting rural development in vast regions of tropical Africa. To augment vector control efforts, the International Glossina Genome Initiative (IGGI) was established in 2004 with the ultimate goal of generating a fully annotated whole genome sequence for Glossina morsitans. A working draft genome of Glossina morsitans was availed in 2011. In this thesis, transcriptional regulatory features in Glossina morsitans were analysed using the draft genome. A method for TSS identification in the newly sequenced Glossina morsitans genome was developed using TSS-seq tags sampled from two developmental stages of Glossina morsitans. High throughput next generation sequencing reads obtained from Glossina morsitans larvae and pupae were used to locate transcription start sites (TSS) in the Glossina morsitans genome. TSS-seq tag clusters, defined as a minimum number of reads at the 5’ predicted UTR or first coding exon, were used to define transcription start sites. A total of 3134 tag clusters were identified on the Glossina genome. Approximately 45.4% (1424) of the tag clusters mapped to the first coding exons or their proximal predicted 5’UTR regions and include 31 tag clusters that mapped to transposons. A total of 1101 (35.1%) tag clusters mapped outside the genic region and/or scaffolds without gene predictions and may correspond to previously un-annotated transcripts or noncoding RNA TSS. The core promoter regions were classified as narrow or broad based on the number of TSS positions within a TSS-seq cluster. Majority (95%) of the core promoters analysed in this study were of the broad type while only 5% were of the narrow type. Comparison of canonical core promoter motif occurences between random and bona fide core promoters showed that, generally, the number of motifs in biologically functional genomic windows in the true dataset exceeded those in the random dataset (p <= 0.00164, 0.00135, 0.00185 for the narrow, broad with peak and broad without peak categories respectively). Frequency of motif co-occurrence in core promoter was found to be fundamentally different across various initiation patterns. Narrow core promoters recorded higher frequency of the TATA-box and INR motifs and two-way motif co-occurrence showed that the TATA-box-INR pair is over-represented in the narrow category. Broad core promoters showed higher frequency of the BREd and MTE motifs and two-way motif co-occurrence showed that the MTE-DPE pair is over-represented in broad core promoters. TATA-less promoters account for 77% of the core promoters in this analysis. TATA-less core promoters showed a higher frequency of the MTE and INR motifs in contrast to observations in Drosophila where the DPE motif has been reported to occur frequently in TATA-less promoters. These motif combinations suggest their equal importance to transcription in their corresponding promoter classes in Glossina morsitans.

Protein-peptide interactions play a major role in several biological processes, such as cellproliferation and cancer cell life-cycles. Accurate computational methods for predictingprotein-protein interactions exist, but few of these method can be extended to predictinginteractions between a protein and a particularly small or intrinsically disordered peptide. In this thesis, PePIP is presented. PePIP is a pipeline for predicting where on a given proteina given peptide will most probably bind. The pipeline utilizes structural aligning to perusethe Protein Data Bank for possible templates for the interaction to be predicted, using thelarger chain as the query. The possible templates are then evaluated as to whether they canrepresent the query protein and peptide using a Random Forest classifier machine learningalgorithm, and the best templates are found by using the evaluation from the Random Forest in combination with hierarchical clustering. These final templates are then combined to givea prediction of binding site. PePIP is proven to be highly accurate when testing on a set of 502 experimentally determinedprotein-peptide structures, suggesting a binding site on the correct part of the protein- surfaceroughly 4 out of 5 times.

Philosophiae Doctor - PhD / It was postulated that each gene has three main sets of transcriptional elements: one which is gene-specific, one which is family-specific, and a third which is tissue-specific.The starting hypothesis for this project had been: “Each family of genes has a distinct set of transcriptional elements that is unique onto this family”. The primary aim of this project was therefore the identification of the family-specific set of transcriptional elements within the AMPA receptor gene family. The question then is how does one measure or identify this uniqueness within the promoters of this family of genes. The answer seemed to lie in making an assessment of the promoters of this family of genes against a background of a comprehensive set of promoter sequences and in the process,to try to find the transcriptional elements that were present in the AMPA receptor gene promoters but were not so common in the general population of gene promoters.To achieve the primary aim of this project, it was essential that a comprehensive dataset of promoter sequences was available. There are ample data freely available through the web. However, it is often not available in a form that we might want it in. Another problem that one constantly encounters is the lack of general consensus among the research community in agreeing on a standard annotation. For example, a gene can sometimes be given 2 or 3 different names by different laboratories which have successfully cloned the same gene. This, in turn, hinders the data collection process. At the start of this project, there was an existing curated database of experimentally-verified eukaryotic promoter sequences called the Eukaryotic Promoter Database (EPD) and a software called Promoter Extraction from GenBank (PEG) which, as its name implies, extracts promoter sequences available through GenBank (Cavin Périer et al., 1998;Zhang & Zhang, 2001; Praz et al., 2002; Schmid et al., 2004). However, limitations existed in both these resources. For EPD, the number of curated promoter sequences available was low and also, the length of these promoter sequences was short. For PEG,the main limitation was that the extraction from GenBank would result in extraction of sequences of variable lengths.Therefore, the 5’-end Information Extraction (FIE)system was developed for the expressed purpose of collecting promoter sequences without the limitations of PEG. This software relies on the alignment of multiple mRNA/cDNA sequences that are representative of a gene on the human genomic sequence to determine the transcription start site (TSS) of the gene and thus, with this information, extract the promoter sequence for the gene from the available human genomic sequence. This was the first promoter extraction software to work on this principle (Chong et al., 2002). This method was later supported by experimental work carried out by Coleman and colleagues (2002). Using the FIE2 software (Chong et al.,2003), some 10,000-odd human promoter sequences was extracted, starting at 1500bp uptream and ending at 1000bp downstream of the 5’-most TSS.Following the collection of the human promoter sequences, the approach developed by Bajic et al. (2004) was applied to study the promoters of the AMPA receptor genes. This approach relies on both the MATCH program to map putative transcription factor binding sites (TFBSs) to the promoter sequences and a software developed by Bajic etal. (2004) that calculates to the density for each TFBS or composite element. Having calculated the densities for the TFBSs and composite elements for both the target promoters (in this case, the AMPA receptor gene promoters) and the background promoters (the 10,000-odd human promoters), the software then calculates the degree of over-representation of each TFBS and composite element in the target promoters(measured against the background promoters) and then ranks the “singles”, “pairs” and “triplets” in the order of their degree of over-representation. Using this method, I identified the top 3 ranked “single”, “pair” and “triplet” transcriptional elements found commonly within the AMPA receptor promoters. In addition, a conventional phylogenetic footprinting study was also carried out for the human, mouse and rat GRIA1 promoter to identify key transcriptional elements within this subunit’s promoter.While the approach developed by Bajic et al. (2004) identifies key family-specific transcriptional elements, the phylogenetic footprinting study helps identify key genespecific transcriptional elements. Thus, they complement one another.The approach developed by Bajic et al. (2004) yielded an interesting result. It was found that the combination of the top 3 ranked “single”, “pair” and “triplet” transcriptional elements found in the AMPA receptor promoters were also found in 47 other genes. It was postulated that these 47 genes might, in fact, be co-regulated / co-expressed with the GRIAs and thus, explaining the existence of a shared promoter profile with the GRIA promoters. In support of this hypothesis, supporting evidence was found in published literature that 7 of these 47 genes (VAMP4, Rab3B, FKBP8, 3-OST-3A, CLSTN3,SOCS1 and IκBβ) might indeed be involved in the expression and functioning of the AMPA receptors.

Malaria is a major public health problem that affects millions of lives globally. The increased burden of malaria requires new interventions that will address the eradication of the disease. Current interventions include vector control by using insecticide-treated bed nets and indoor residual spraying, and antimalarial drugs to control the parasite. Parasite resistance has been reported for the currently used effective antimalarial drugs. To pre-empt the impact of parasite resistance a continued development of new antimalarial drugs that have novel mechanisms of action should be pursued. Antimalarial drug discovery requires that potential antimalarial drugs should have different drug targets to those already targeted, to lower the chances of resistance. Potential antimalarial drugs should preferably provide a single radical cure to prevent reproduction at all life cycle stages. This study tested the effects of in silico designed compounds targeting plasmodial Ca2+- dependent protein kinases (CDPK) 1 & 4, FIKK kinases and bromodomain proteins on the Plasmodium parasite. These enzymes are involved in gene regulation and are important factors during gene transcription. In P. falciparum the gatekeeper kinases contain small hydrophobic pockets near the ATP-binding site. These hydrophobic pockets allow for selective inhibition of these proteins at the ATP-binding site. The compounds were tested in vitro to determine their antiplasmodial activity. These compounds are shown to be potential inhibitors of the intra-erythrocytic P. falciparum parasites as three of the compounds showed selective cytotoxic activity at less than 1 μM against the chloroquine sensitive laboratory strains (3D7 and NF54). Even though the proteins targeted by these compounds have been previously indicated to play a role at specific stages during the parasite’s life cycle, the compounds tested here were not able to target the sexual gametocyte stages of the Plasmodium parasite. Further optimisation of these compounds should be performed to improve activity against both the asexual and sexual stages of the parasites. / Dissertation (MSc)--University of Pretoria, 2017. / Pharmacology / MSc / Unrestricted

N-methyl-D-aspartate (NMDA) receptors are glutamatergic ionotropic receptors involved in excitatory synaptic transmission, synaptic plasticity and excitotoxicity. They are heteromeric complexes of GluN1 combined with GluN2A-D and/or GluN3A-B subunits that are activated by glutamate and glycine. Many allosteric modulators can influence the activity of these receptors including neurosteroids. Pregnanolone sulfáte (3α5βS) is an endogenous neurosteroid that inhibits NMDA receptors in a use-dependent manner and has neuroprotective effect. Binding site for 3α5βS on the NMDA receptor molecule is still not indentified. The aim of my work was to contribute to the identification of the biding site by kinetic analysis of rate of response return from 3α5βS inhibition. Using the point mutation we also attempted to identify the amino acids residues that could be involved in the neurosteroid binding. In order to study the effect of 3α5βS on NMDA receptors the electropfysiological recordings on human embryonic kidney 293T cells expressing recombinant GluN1/GluN2B receptors was performed. We confirm that the effect of 3α5βS on GluN1/GluN2B receptors is voltage-independent. The results of my work indicate that steroids can reach the binding site on the NMDA receptors through the membrane rather than directly from the aqueous...

The inhibition of HIV-1 protease plays an important role in combating HIV. Nine HIV-1 protease inhibitors have been succesfully marketed for the treatment since 1995. However, their efficiencies decrease due to the resistance development. More potent compounds with novel structural motifs and mechanisms of action are therefore still needed. Several inhibitory compounds have been reported to bind to the protease at the loci different from the active site. Interestingly, darunavir, which is the last approved inhibitor with supposedly competitive mode of action, was also suggested to bind to the flap region of the protease. Two studies discussed this alternative binding mode based on the X-ray structural and kinetic analysis, respectively. Nevertheless, it is questionable, if such a mechanism is relevant also in physiological conditions or if it is only an artifact of crystallization. Another study provided a strong evidence for the alternative binding of darunavir to highly mutated HIV-1 protease. Based on thermodynamic analysis, it was shown that two molecules of darunavir bind to the protease dimer. Surprisingly, this observation was not confirmed by the X-ray structure analysis since the inhibitor was bound only within the active site. However, this protease variant was employed in further...

Persistent organochlorines such as chlordecone (CD), DDT, and DDT degradation products bioaccumulate in fish and potentially impair reproduction or development via estrogenic actions. We evaluated the estrogenicity of CD, o,p'-DDT, o,p'-DDE, and p,p'-DDE injuvenile rainbow trout by assessing their potential to induce vitellogenesis; estrogen-regulated hepatic synthesis of the yolk-protein precursor, vitellogenin (Vg). In order to compare the sensitivities of various markers of estrogen stimulation, trout were injected with 17β-estradiol (0-10 mg kg-1) on days 0 and 3 and were sampled on days 3-12. Estradiol (5 mg kg-1) increased plasma Vg (2400%; 640 μg l-1), liver somatic index (200%) and hepatic cytosolic estrogen binding site levels (EBS, 300%) on day 6. These results suggested plasma Vg was the most sensitive marker of estrogen exposure. Chronic dietary exposure to CD (0.4 mg kg-1 day-1, 33 weeks) elevated plasma Vg (0.9 μg l-1), but not hepatic EBS concentrations, and resulted in relatively high hepatic CD concentrations (16 μg g-1). The in vivo estrogenicity of DDT was examined by injecting trout at 14 day intervals with single or triplicate doses of o,p'-DDT, o,p'-DDE or p,p'-DDE (0, 5, 15 or 30 mg kg-1) and monitoring vitellogenesis 14 days after the final injection. Plasma Vg and hepatic EBS concentrations were significantly elevated by o,p'-DDT and o,p'-DDE (total dose 45 and 90 mg kg-1; 23-24 μg Vg l-1) but not p,p'-DDE. Target organ doses were estimated by conducting a disposition study in which trout were injected with three doses of 14C]p,p'-DDE (30 mg kg-1), at 14 day intervals. Hepatic [14C]p,p'-DDE equivalent concentrations, 14 days after the final injection, averaged 14 μg g-1 Additionally, we evaluated the relative affinity of CD and DDT or DDE for trout hepatic EBS utilizing in vitro competitive binding assays. CD had relatively low affinity (1000-fold less than moxestrol, a synthetic estradiol) for trout hepatic EBS. o,p'-DDT and o,p'-DDE, but not p,p'-DEE also exhibited low EBS affinity (approximately 156000-fold less than moxestrol). Collectively, these results indicated that CD, o,p'-DDT and o,p'-DDE were weakly estrogenic in juvenile trout.