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Computational search for nature-derived dual-action inhibitors of HIV-1 reverse transcriptase and integrase: a potential strategy to mitigate drug resistance progression

  • Authors: Mwiinga, Luyando
  • Date: 2024-10-11
  • Subjects: HIV (Viruses) , Reverse transcriptase , Antiretroviral agents , RDKit , Drug resistance , Docking
  • Language: English
  • Type: Academic theses , Master's theses , text
  • Identifier: http://hdl.handle.net/10962/463930 , vital:76458
  • Description: Human immunodeficiency virus Type 1 (HIV-1) is a devastating viral infection affecting millions worldwide and presents significant challenges in treatment and management. In 2022, approximately 39 million people were living with HIV with Sub-Saharan Africa having two thirds of these infections. Devastatingly, there were approximately 300 000 HIV/AIDS related deaths in Sub-Saharan Africa alone in 2022 alone. Antiretroviral therapy (ART) which is fundamental for HIV treatment, comprises of a combination of drugs such as nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTs), protease inhibitors (PIs) and integrase strand transfer inhibitors (INSTIs). However, although 28.7 million people out of the estimated 38.4 million people living with HIV in 2021 were receiving ART, the emergence of drug-resistant strains further complicates treatment efforts, highlighting the need for novel therapeutic approaches. This study aimed to address the challenges raised by drug resistance and significant side effects by identifying potential dual inhibitors against HIV-1 Reverse Transcriptase (RT) and Integrase (IN) using in silico techniques. RT RNase H and IN were chosen as targets for their shared dependency on Mg2+ ions within their active sites, which are crucial for catalytic activity. The selection of dual inhibitors was motivated by the fact that the virus would need to replicate at two points simultaneously to develop resistance, making it less likely. The objectives of this study included the creation of a natural derivative compound library using RDKit with the aid of SciFinder, utilizing (-)-epigallocatechin-3-O-gallate (EGCG), because of its dual inhibitory effects against RT and IN, as indicated by a study conducted by Sanna et al. 2019. The natural derivatives were chosen to take advantage of their chemical diversity and to explore potential novel therapeutic options for combating HIV drug resistance. The compound library created comprised of 125 203 compounds. Then docking studies were conducted to assess proteinligand binding. After the correlation of the RT and IN docking studies, 288 compounds were filtered to have potential dual inhibitory activity. Then quantitative estimation of druggability (QED) analysis identified three compounds with superior properties compared to EGCG and FDAapproved drug raltegravir (RAL). Molecular docking simulations revealed interactions between the inhibitors and the key active site residues of RT and IN, along with the chelation of at least one 3 Mg2+, suggesting the potential for enzymatic disruption. Furthermore, molecular dynamic (MD) simulations were then conducted to assess protein-ligand system behavior, through RMSD and RMSF analysis. The RMSD analysis uncovered instability in the IN-Sci30703 complex, leading to its exclusion as a potential dual action inhibitor. RMSF analysis for IN showed that all the inhibitors had the ability to limit the flexibility of the catalytic loop which is essential for catalytic activity. Therefore, further in vitro studies are required to evaluate the effectiveness of the remaining two EGCG derivatives (Sci33211 and Sci48919) in inhibiting RT and IN through the chelation of at least one Mg2+ ion to determine if they have superior dual inhibitory effects compared to EGCG. This study adds to the ongoing efforts to develop effective strategies against HIV-1 drug resistance and emphasizes the importance of continued research in this field. , Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology & Bioinformatics, 2024
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  • Date Issued: 2024-10-11

Experiences of youths participating in combination social protection and HIV prevention programme in resource constrained settings of Gauteng Province in South Africa: a collective case study design

  • Authors: Zibengwa, Enock
  • Date: 2023-04
  • Subjects: HIV infections -- Prevention , HIV (Viruses) , HIV infections -- Africa
  • Language: English
  • Type: Doctoral theses , text
  • Identifier: http://hdl.handle.net/10353/27347 , vital:66944
  • Description: South Africa continues to experience unacceptably high Human Immunodeficiency Virus HIV incidence rates among youths aged 15 to 24 years. Remarkably, this is despite the numerous youth HIV prevention programmes that have been implemented in the country. Unfortunately, the programmes have not significantly curbed the spread of HIV due to the partial and fragmented nature of their implementation. The programmes are also observed to be weak in addressing complex economic factors recognised as important structural drivers for vulnerabilities that put youths at risk of HIV infection. To address this challenge, there is increased adoption and implementation of the Combination Social Protection introduced in this research as the CSP by Non-Governmental Organisations NGOs. The CSP is a youth empowerment programming strategy whose critical foundations are entrenched in combining economic strengthening interventions and HIV prevention education. CSP could provide youths with a set of indispensable life skills that enhance their competencies and agency to make informed and effective decisions regarding their health and economic lives. Despite its growing traction, little is known regarding links between the CSP and its abilities to improve HIV prevention outcomes for youths. Given the paucity of research, this study aimed to explore the experiences of youths participating in the CSP and HIV prevention programme, with a particular focus on the resource-constrained settings of Gauteng Province in South Africa. This study employed a collective case study design, within the qualitative approach, and was exploratory. In-depth individual interviews were conducted with 30 youths from six established NGOs in the City of Johannesburg (CoJ). Qualitative thematic analysis was employed as a data analysis strategy. Focus groups were separately with six practitioners from the same six NGOs, and five officials from the Department of Social Development (DSD). Both phases of data collection were guided by interview themes, which were aligned with the objectives of the study. The findings of the study point to the fact that the CSP’s innovative and holistic approach offered numerous transformative and empowering benefits to youths. It equipped them with basic informational resources, capabilities, and social assets to safeguard their health and aid their economic advancement. The programme’s mixedgender sessions provided space, freedom, and support for youths to engage on issues of gender, differential access to health and socio-economic opportunities. Another major finding of the study was that improvement of economic aptitude (brought about by financial literacy education), employability, and entrepreneurship training stirred a sense of agency and purposefulness among youths, which in turn, prompted them to be more focused on achieving long-term objectives instead of indulging in risky sexual practices. Conversely, findings revealed that the programme had limited opportunities and did not create an adequate supportive environment for youths to develop successful entrepreneurial or income-generating projects. There was also no structure to assist youths to access apprenticeship and employment markets. The study specifically recognised that the programme’s efforts to develop youths’ entrepreneurship and employability capabilities were curtailed by a lack of mentorshipnand access to financial capital for start-up costs. With these findings in mind, recommendations are made for the creation of an enabling environment by purposefully engaging youths, establishing collaborative relations with communities, and building networks with businesses and financial institutions that can help youths with capital, mentorship, and linkages to internship and wage employment. Such collaborations could be fundamental in unravelling the impact of the programme on building livelihoods and reducing HIV among youths. Hence, this study proposes a model with strategies to support the successful implementation of economic strengthening interventions for youths. , Thesis (PhD) -- Faculty of Social Sciences and Humanities, 2023
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  • Date Issued: 2023-04

A self-emulsifying delivery system loaded with efavirenz: The case for flax-seed oil

  • Authors: Mazonde, Priveledge
  • Date: 2021-10-29
  • Subjects: Drug delivery systems , Linseed oil , Antiretroviral agents , HIV (Viruses) , Drug carriers (Pharmacy) , Solubility , High performance liquid chromatography , Efavirenz
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10962/192944 , vital:45283
  • Description: The feasibility of incorporating efavirenz (EFV), an antiretroviral agent against HIV into a lipid-based self-emulsifying drug delivery system (SEDDS) containing vegetable oils was investigated. EFV has poor aqueous solubility and is classified under the Biopharmaceutical Classification System (BCS) as a class II compound with highly permeability, its aqueous solubility is less than 10 mg/ml and is defined as a practically insoluble compound with a consequent poor bioavailability of approximately 40%, and erratic dissolution behaviour. SEDDS formulations have been shown to improve the aqueous solubility and consequently the bioavailability of BCS II compounds such as EFV. EFV is a first line antiviral agent used in combination with other agents in antiretroviral therapy (ART). Among the number of NNRTIs approved for use in HIV treatment, EFV is one of the most commonly prescribed drug. Statistical methods and Design of Experiments (DoE) using Response Surface Methodology (RSM), specifically a Central Composite Design (CCD), were used to facilitate the development of a reversed-phase high performance liquid chromatographic (HPLC) method for the quantitation of EFV during formulation product and process development studies. A rapid, accurate, precise and sensitive HPLC method with ultraviolet (UV) detection was developed, optimised and validated for the in-vitro analysis of EFV in a total run time under 10 minutes for the elution of both EFV and loratidine which was used as the internal standard (IS). The method was then successfully applied to the determination of EFV in commercially available tablets. Excipient screening was undertaken using solubility studies and revealed that EFV had highest solubility in flaxseed oil in comparison to soybean, macadamia, grapeseed, sunflower and olive oils. The non-ionic Tween® 80 and Span® 20 were selected as surfactant and co-surfactant, respectively with ethanol co-solvent as they exhibited improved miscibility with co-solvent. Pre-formulation studies were undertaken to investigate the compatibility of the API with excipients and to identify a nano-emulsion region and other emulsion types using pseudoternary phase diagrams. The phase behaviour of crude cold pressed flaxseed oil with the selected non-ionic surfactants revealed an area within pseudo-ternary phase diagrams for different surfactant-mixtures formed gels/semisolid structures which can be exploited for other drug delivery strategies that require such properties. Fourier transform infrared spectroscopy (FT-IR), powder x-ray diffraction (XRD) and Raman spectroscopy were used to identify and assess the compatibility of EFV with chosen excipients. 2 A reduction in the peak intensity was observed for EFV when combined with each hydrophobic/lipid excipient evaluated revealing that there was a marked reduction in the crystallinity of the EFV. A decrease in crystallinity in comparison with the bulk API may indicate that EFV were amorphous or sequestered in a molecular dispersion and exhibited an increased solubility for the molecule. Flaxseed oil was used as the oil phase in studies for the optimization of surfactant mixtures undertaken using DoE, specifically a D-optimal mixtures design with the flaxseed oil content set at 10% m/m was performed. Solutions from the desired optimization function were produced based on desirability and five nanoemulsion formulations were produced and characterized in terms of in vitro release of efavirenz, drug loading capacity, Zeta Potential, droplet sizes and polydispersity index (PDI). Kinetically stable nanoemulsions containing 10% m/m flaxseed oil were successfully manufactured and assessed. Droplet sizes ranged between 156 and 225 nm, Zeta Potential between −24 and −41 mV and all formulations were found to be monodisperse with polydispersity indices ≤ 0.487. SEDDS formulations of EFV in nano-sized carriers were developed and optimised, in vitro drug release varied with varying amounts of ethanol in the formulation producing formulations that exhibited differently modulated drug in-vitro release profiles that may be further manipulated for better performance and therapeutic outcomes in terms of solubility and possibly bioavailability of EFV when delivered using SEDDS rather than using tablets which in turn may lead to better therapeutic outcomes for patients with HIV. , Thesis (MSc) -- Faculty of Pharmacy, Pharmacy, 2021
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  • Date Issued: 2021-10-29

Synthesis of novel heterocyclic systems as potential inhibitors of HIV-1 enzymes

  • Authors: Sekgota, Khethobole Cassius
  • Date: 2020
  • Subjects: Protease inhibitors , Heterocyclic compounds , HIV (Viruses) , Quinoline , Amides , Nuclear magnetic resonance , Antiretroviral agents , AIDS vaccines , Nitrobenzaldehyde , Propylphosphonic acid anhydride
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10962/146502 , vital:38531
  • Description: This study has focussed on the application of Baylis-Hillman methodology in the development of efficient synthetic pathways to libraries of novel 3-[(N-cycloalkylbenzamido)methyl]-2-quinolones and indolizine-2-carboxamides and on an exploration of their medicinal potential. The approach to 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones involved a six-step pathway comprising: Baylis-Hillman reaction of 2-nitrobenzaldehyde derivatives and methyl acrylate to afford nitro-Baylis-Hillman adducts; thermal cyclisation of the adducts to give a range of 3-(acetoxymethyl)-2(1H)-quinolones in good to excellent yields; hydrolysis of the acetates; conversion of the resulting alcohols to the 3-chloromethyl analogues; amination; and, finally, acylation to afford the target amides. Variable temperature NMR methods were used to facilitate analysis of the ¹H and ¹³C NMR spectra which were complicated by internal rotation and cycloalkyl ring-flipping effects. On the other hand, the indolizine-2-carboxamides were obtained in several steps commencing with the Baylis-Hillman reaction of pyridine-2-carboxaldehyde and methyl acrylate. Thermal cyclisation of the Baylis-Hillman adduct afforded indolizine esters, hydrolysis of which gave the corresponding acids which served as precursors to the target indolizine-2-carboxamides. The final amidation step, however, proved to be particularly challenging. Various coupling strategies were explored to access indolizine-2-carboxamides. These included the use of 2,2,2-trifluoroethyl borate which showed limited promise, but propylphosphonic acid anhydride (T3P) proved to be the most effective coupling agent, permitting the formation of 24 novel indolizine-2-carboxamides from hydrazines, aliphatic amines and a range of heterocyclic amines. A high-field NMR-based kinetic study of the mechanism of the Baylis-Hillman reaction of pyridine-4-carboxaldehyde and methyl acrylate in the presence of 3-hydroxyquinuclidine in deuterated chloroform was initiated, reaction progress being followed by the automated collection of ¹H and DEPT 135 NMR spectra over ca. 24 hours using a high-field (600 MHz) NMR instrument. The results have provided critical new insights into the mechanism. NMR analysis has also been used to elucidate the multiplicity of signals associated with rotameric equilibria observed at ambient probe temperature. Variable temperature 1D- and 2D-NMR spectra were used to facilitate the unambiguous characterisation of the 2-quinolone benzamides and some of the indolizine-2-carboxamides. The 3-[(N-cycloalkylbenzamido)methyl]-2(1H)-quinolones, together with selected precursors, and a number of the indolizine-2-carboxamides have been screened in vitro as potential HIV-1 enzyme inhibitors. A survey of the activity of the 2-quinolones against HIV-1 integrase, protease and reverse transcriptase revealed selective inhibition of HIV-1 integrase with the most active IN inhibitor, 3-[(cyclopentylamino)methyl-6-methoxy-2(1H)-quinolone 115e, producing residual enzyme activity of 40% at a concentration of 20 μM. Many of the 2-quinolones exhibited no significant cytotoxicity against HEK 293 cells at 20 μM concentrations. 3-[(N-Cyclohexylamino)methyl]-6-methoxy-2(1H)-quinolone 114e was the only compound to exhibit ant-plasmodial activity (55% pfLDH activity). The survey of indolizine-2-carboxamides also revealed encouraging inhibition against HIV-1 integrase. None of these compounds exhibited cytotoxicity at 20 μM against HEK 293 cells, while a number of them exhibited some activity against Plasmodium falciparum (3D7 strain) and Trypanosoma brucei. Selected indolizine-2-carboxamides exhibited significant anti-tubercular activity in the 7H9 CAS GLU Tx and 7H9 ADC GLU Tw media. In view of the inherent fluorescent character and biological potential of the synthesised indolizine-2-carboxamides, their photophysical properties were explored to establish their possible dual use as bio-imaging and therapeutic agents. The major absorption and corresponding emission bands, and the associated molar absorption coefficients (Ɛ) expressed in the form of log Ɛ were determined. Their high extinction coefficients, large Stokes shift and red-shifted emissions in the visible region indicate their potential for use as fluorophores.
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  • Date Issued: 2020

Synthesis of peptidomimetic compounds as HIV-1 protease inhibitors

  • Authors: Kayembe, Jean-Pierre
  • Date: 2020
  • Subjects: Protease inhibitors , HIV (Viruses) , HIV infections Treatment , Peptidomimetics‎
  • Language: English
  • Type: Doctoral theses , text
  • Identifier: http://hdl.handle.net/10962/124397 , vital:35604 , DOI https://dx.doi.org/10.21504/10962/124397
  • Description: This research project has involved the design, synthesis and evaluation of novel peptidomimetics compounds as HIV-1 protease inhibitors. Here is presented one-step, two-step and three-step syntheses and the in vitro bio-assay studies of a series of fully characterized peptidomimetics as HIV-1 protease inhibitors candidate using the shortest and most cost effective synthetic routes. The first series of compounds were accessed via a synthetic elaboration of Morita-Baylis-Hillman adducts by a Michael addition with benzylamine, proline or glycine esters to afford a series of β-amino-β’-hydroxycarboxylate esters in moderate to good yields. Base-catalyzed cyclization of non-benzylated aza-Michael adducts afforded a series of coumarin-3-hydroxy-2-methylenepropanoate esters in moderate yields. The uncatalyzed direct amidation of diethyl tartrate/tartaric acid and tartaric acid osazone with selected amines/amino acids afforded a series of C2-symmetrical and unsymmetrical 1,2-dihydroxycarboxylates in moderate to very high yields. All the synthesized compounds were fully characterized using spectroscopic techniques. These conjugates, designed as potential HIV-1 inhibitors, were tested against the HIV-1 protease enzyme. A number of these ligands have exhibited inhibition levels and IC50 values comparable to ritonavir, permitting, therefore, their identification as lead compounds for the development of novel inhibitors. , Thesis (PhD) -- Faculty of Science, Chemistry, 2020
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  • Date Issued: 2020

An in-silico investigation of Morita-Baylis-Hillman accessible heterocyclic analogues for applications as novel HIV-1 C protease inhibitors

  • Authors: Sigauke, Lester Takunda
  • Date: 2015
  • Subjects: Protease inhibitors , Heterocyclic compounds , HIV (Viruses) , HIV infections , Drug resistance , Cheminformatics
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4152 , http://hdl.handle.net/10962/d1017913
  • Description: Cheminformatic approaches have been employed to optimize the bis-coumarin scaffold identified by Onywera et al. (2012) as a potential hit against the protease HIV-1 protein. The Open Babel library of commands was used to access functions that were incorporated into a markov chain recursive program that generated 17750 analogues of the bis-coumarin scaffold. The Morita-Baylis-Hillman accessible heterocycles were used to introduce structural diversity within the virtual library. In silico high through-put virtual screening using AutoDock Vina was used to rapidly screen the virtual library ligand set against 61 protease models built by Onywera et al. (2012). CheS-Mapper computed a principle component analysis of the compounds based on 13 selected chemical descriptors. The compounds were plotted against the principle component analysis within a 3 dimensional chemical space in order to inspect the diversity of the virtual library. The physicochemical properties and binding affinities were used to identify the top 3 performing ligands. ACPYPE was used to inspect the constitutional properties and eliminated virtual compounds that possessed open valences. Chromene based ligand 805 and ligand 6610 were selected as the lead candidates from the high-throughput virtual screening procedure we employed. Molecular dynamic simulations of the lead candidates performed for 5 ns allowed the stability of the ligand protein complexes with protease model 305152. The free energy of binding of the leads with protease model 305152 was computed over the first 50 ps of simulation using the molecular mechanics Poisson-Boltzmann method. Analysis structural features and energy profiles from molecular dynamic simulations of the protein–ligand complexes indicated that although ligand 805 had a weaker binding affinity in terms of docking, it outperformed ligand 6610 in terms of complex stability and free energy of binding. Medicinal chemistry approaches will be used to optimize the lead candidates before their analogues will be synthesized and assayed for in vivo protease activity.
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  • Date Issued: 2015

Design, development and evaluation of novel lead compounds as HIV-1 enzyme inhibitors

  • Authors: Sekgota, Khethobole Cassius
  • Date: 2015
  • Subjects: Enzyme inhibitors , Viruses -- Reproduction , HIV (Viruses)
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4546 , http://hdl.handle.net/10962/d1017926
  • Description: This project has been concerned with the application of the Baylis-Hillman methodology to the synthesis of medicinally important diketo acid analogues (cinnamate ester-AZT conjugates and 3-hydroxy ester-AZT conjugates) as dual-action HIV-1 IN/RT inhibitors; and on exploratory studies in the preparation of 3-(amidomethyl)-(1H)-2-quinolones as PR inhibitors; and (1H)-2- quinolone-AZT conjugates as dual action IN/RT inhibitors. A series of Baylis-Hillman adducts has been prepared, typically in moderate to excellent yield, by reacting 2-nitrobenzaldehyde with methyl acrylate, ethyl acrylate and methyl vinyl ketone in the presence of 1,4- diazabicyclo[2.2.2]octane (DABCO). Subsequently, various transformations that include conjugate addition of primary and secondary amines to the α,ß-unsaturated moiety to obtain 2- (aminomethyl)-3-hydroxy-3-(2-nitrophenyl)propanoate derivatives, effective SN2´ substitution of the BH ß-hydroxy by a Vilsmeier-Haack in situ-generated chloride to afford Baylis-Hillman allyl chlorides, iron in acetic acid-catalyzed cyclisation to 3-acetoxymethyl-(1H)-2-quinolone derivatives were achieved. Thus, using the Baylis-Hillman methodology, two nuanced classes of diketo acid analogues were constructed. These involved conjugating appropriate propargylamine derivatives with AZT using the „click‟ reaction. In an exploratory study, the quinolone derivative, precisely 3-acetoxymethyl- (1H)-quinol-2-one, was transformed into 3-hydroxymethyl-(1H)-quinol-2-one using potassium carbonate in a mixture of methanol and water (1:1). Following successful hydrolysis, the resulting alcohol was transformed to the corresponding chloride, 3-chloromethyl-(1H)-quinol-2- one, using thionyl chloride. Subsequent nucleophilic substitution afforded 3-(aminomethyl)- (1H)-2-quinolone derivatives which were subsequently transformed to 3-(amidomethyl)-(1H)-2- quinolones; and 3-[(propargylamino)-methyl]-(1H)-quinol-2-one as precursors to quinolone- AZT derivatives. All compounds were characterized by NMR, IR, and where appropriate, high resolution MS
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  • Date Issued: 2015

Structural studies on yeast eIF5A using biomolecular NMR and molecular dynamics

  • Authors: Sigauke, Lester Takunda
  • Date: 2015
  • Subjects: Molecular dynamics , Reverse transcriptase , HIV (Viruses) , HIV infections , Eukaryotic cells , Yeast
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4547 , http://hdl.handle.net/10962/d1017927
  • Description: Eukaryotic initiation factor 5A, eIF5A, is a ubiquitous eukaryotic protein that has been shown to influence the translation initiation of a specific subset of mRNAs. It is the only protein known to undergo hypusination in a two-step post translational modification process involving deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) enzymes. Hypusination has been shown to influence translation of HIV-1 and HTLV-1 nuclear export signals, while the involvement of active hypusinated eIF5A in induction of IRES mediated processes that initiate pro-apoptotic process have inspired studies into the manipulation of eIF5A in anti-cancer and anti-diabetic therapies. eIF5A oligomerisation in eukaryotic systems has been shown to be influenced by hypusination and the mechanism of dimerisation is RNA dependent. Nuclear magnetic resonance spectroscopy approaches were proposed to solve the structure of the hypusinated eIF5A in solution in order to understand the influence of hypusination on the monomeric arrangement which enhances dimerisation and activates the protein. Cleavage of the 18 kDa protein monomer by introduction of thrombin cleavage site within the flexible domain was thought to give rise to 10 kDa fragments accessible to a 600 MHz NMR spectrometer. Heteronuclear single quantum correlation experiments of the mutated isotopically labelled protein expressed in E. coli showed that the eIF5A protein with a thrombin cleavage insert, eIF5AThr (eIF5A subscript Thr), was unfolded. In silico investigations of the behaviour of eIF5A and eIF5AThr (eIF5A subscript Thr) models in solution using molecular dynamics showed that the mutated model had different solution dynamics to the native model. Chemical shift predictors were used to extract atomic resolution data of solution dynamics and the introduction of rigidity in the flexible loop region of eIF5A affected solution behaviour consistent with lack of in vivo function of eIF5AThr (eIF5A subscript Thr) in yeast. Residual dipolar coupling and T₁ relaxation times were calculated in anticipation of the extraction of experimental data from RDC and relaxation dispersion experiments based on HSQC measurable restraints.
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  • Date Issued: 2015

Studies towards the development of novel HIV-1 integrase inhibitors

  • Authors: Lee, Yi-Chen
  • Date: 2010
  • Subjects: HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Nuclear magnetic resonance , Heterocyclic compounds -- Derivatives , Enzyme inhibitors , Chemical inhibitors , Quinoline
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4357 , http://hdl.handle.net/10962/d1005022 , HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Nuclear magnetic resonance , Heterocyclic compounds -- Derivatives , Enzyme inhibitors , Chemical inhibitors , Quinoline
  • Description: The project has focused on the preparation of several series of compounds designed as potential HIV-1 integrase inhibitors. Various 2-nitrobenzaldehydes have been reacted with two activated alkenes, methyl vinyl ketone (MVK) and methyl acrylate, under Baylis-Hillman conditions to afford α-methylene-β-hydroxylalkyl derivatives in moderate to excellent yields. The reactions were conducted using the tertiary amine catalysts, 1,4-diazabicyclo[2.2.2]octane(DABCO) or 3-hydroxyquinuclidine (3-HQ) with chloroform as solvent, and yields were optimised by varying the catalyst, reagent concentrations and the reaction time. Reductive cyclization of the Baylis-Hillman adducts via catalytic hydrogenation, using 10% palladiumon-carbon catalyst in ethanol, afforded quinoline and quinoline N-oxide derivatives. In some cases “acyclic” reduction products were also isolated. Reaction of the Baylis-Hillman MVK adducts with HCl, has resulted in effective nucleophilic (SN’) displacement of the hydroxyl group to afford allylic chloride derivatives. Direct substitution of these chloro derivatives by secondary or primary amines, followed by catalytic hydrogenation gave quinoline derivatives containing a 3-aminomethyl substituent. The Baylis-Hillman ester adducts obtained from reaction with methyl acrylate were treated directly with various amines to give diastereomeric conjugate addition products. Reactions with piperazine gave N,N’-disubstituted piperazine products. The piperidine derivatives have been dehydrated to give cinnamate esters in moderate yields. The products, which have all been satisfactorily characterised by elemental (HRMS) and spectroscopic (1- and 2-D NMR) analysis, constitute a “library” of compounds for in silico and in vitro studies as potential HIV integrase inhibitors.
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  • Date Issued: 2010

Studies directed towards the synthesis of chromone carbaldehyde-derived HIV-1 protease inhibitors

  • Authors: Molefe, Duduzile Mabel
  • Date: 2008
  • Subjects: Protease Inhibitors , HIV infections , HIV (Viruses) , AIDS (Disease) , Proteolytic enzymes , Heterocyclic compounds -- Derivatives , Chemical kinetics , Nuclear magnetic resonance spectroscopy
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:4526 , http://hdl.handle.net/10962/d1015542
  • Description: A series of chromone-3-carbaldehydes have been prepared using Vilsmeier-Haack methodology while a corresponding series of chromone-2-carbaldeydes have been synthesized via the Kostanecki-Robinson reaction. Baylis-Hillman reactions have been conducted on both series of chromone carbaldehydes using three different catalysts, viz., 1,4-diazabicyclo(2.2.2]octane (DABCO), 1,8-diazabicyclo[5.4.0]undec- 7-ene (DBU) and 3-hydroxyquinuclidine (3HQ), and acrylonitrile, methyl acrylate and methyl vinyl ketone as the activated alkenes. These reactions have typically (but not always!) afforded both normal Baylis-Hillman and dimeric products. Attention has also been given to the use of 1-methyl-2-pyrrolidine (1-NMP), an ionic liquid, to replace normal organic solvents, and it has been found that, in the presence of DABCO, chromone-3-carbaldehydes afford the dimeric products alone. Reactions of chromone-3-carbaldehydes with methyl vinyl ketone have yielded unexpected, novel adducts, which appear to arise from preferential attack at C(2) in the chromone nucleus. Research on chromone-2-carbaldeydes under Baylis-Hillman conditions has also resulted in the formation of some interesting products instead of the expected Baylis-Hillman adducts. The Baylis-Hillman products have been explored as substrates for aza-Michael reactions using various amino derivatives including protected amino acids in the presence of the tetrabutylammonium bromide (TBAB) and the ionic liquid, 3-butyl-1- methylimidazoleboranetetrafluoride (BmimBF₄), as catalysts. The aza-Michael products have been targeted as truncated ritonavir analogues for investigation as potential HIV -1 protease inhibitors, and representative compounds have been subjected to enzyme inhibition assays to explore the extent and type of inhibition. Lineweaver-Burk and Dixon plots have indicated competitive inhibition in one case as well as non-competitive inhibition in another, and the inhibition constants (Ki) have been compared with that of the ritonavir. Computer modelling studies have also been conducted on selected chromonecontaining derivatives, using the ACCELRYS Cerius² platform. Interactive docking of the chromone-containing ligands into the HIV -1 protease receptor site, using the Ligandfit module, has indicated the importance of hydrogen-bonding interactions mediated by bridging water molecules situated in the receptor cavity. NMR spectroscopy has been used to elucidate complex and competing mechanistic pathways involved in the Baylis-Hillman reactions of selected 2-nitrobenzaldehydes with MVK in the presence of DABCO - reactions which afford the normal BaylisHillman product, the MVK dimer and syn- and anti-Baylis-Hillman type diadducts. The kinetic data confirm the concomitant operation of two pathways and reveal that, in the initial stage of the reaction, the product distribution is kinetically controlled, whereas in the latter stage, thermodynamic control results in the consumption of the normal Baylis-Hillman product and predominance of the anti-diadduct.
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  • Date Issued: 2008

Studies towards the synthesis of novel, coumarin-based HIV-1 protease inhibitors

  • Authors: Rashamuse, Thompho Jason
  • Date: 2008
  • Subjects: Coumarins , Protease Inhibitors , HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Heterocyclic compounds -- Derivatives
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4359 , http://hdl.handle.net/10962/d1005024 , Coumarins , Protease Inhibitors , HIV infections -- Treatment , HIV (Viruses) , AIDS (Disease) -- Treatment , Heterocyclic compounds -- Derivatives
  • Description: A series of the Baylis-Hillman adducts have been obtained by reacting protected O-benzylated and unprotected substituted salicylaldehydes with methyl acrylate or tertbutyl acrylate, respectively, using DABCO as catalyst. Treatment of the Baylis-Hillman adducts with HCl in a mixture of acetic acid and acetic anhydride afforded the corresponding 3-(chloromethyl)coumarin derivatives with yields of up to 94%. Similar use of HI afforded the corresponding 3-(iodomethyl)coumarins but, depending on the reaction time, the reduced 3-methyl analogues could also be obtained. Arbuzov reactions of the 3-(halomethyl)coumarin derivatives have been undertaken to afford 4-phosphorylated and 1’-phosphorylated derivatives, regioselectivity being dependent on the halide-leaving group. The 3-(chloromethyl)coumarin derivatives have been subjected to nucleophilic (SN) attack by benzylamine to give the corresponding 3- [(benzylamino)methyl]coumarin derivatives in yields of up to 74%. Further treatment of the 3-[(benzylamino)methyl]coumarin derivatives with chloroacetyl chloride afforded the chloroacetamide derivatives, which exhibit hindered rotation about the amine C(O)-N bond. The acetamide derivatives have also been subjected to Arbuzov reaction conditions to afford the phosphorylated derivatives in yields of up to 86%. In a preliminary modelling study, hydrolysed analogues of the synthesized phosphorylated derivatives have been docked into the active site of the HIV-1 protease enzyme using the Cerius-2 Ligandfit software module to provide an insight into potential receptor-ligand hydrogen bonding interactions.
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  • Date Issued: 2008
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