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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

Data management and dispensary: missing link contributing to antiretroviral loss to follow-Up in Lejweleputswa District

  • Authors: Moatlhodi, Charlotte Motshele
  • Date: 2022-09
  • Subjects: Health services administration , Drug monitoring , Antiretroviral agents
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10353/26973 , vital:66207
  • Description: Background and aim: The widespread use and access to Anti-Retro Viral Treatment (ART) world-wide has contributed to full preventive and therapeutic benefits. An estimated amount of 68percent of HIV positive people received ART in South Africa (SA) as of 2018. However, reports from TIER.Net and DHIS (District Health Information System), indicate that the retention of patients on ART (specifically first line triple combination therapy Tenofovir Emtricitabine Efavirenz (TEE)) continues to decline. Meanwhile, data on TEE dispensed from the dispensary shows increasing quantities patients across the Free State province on a monthly basis. The aim of this study is to determine factors contributing to the discrepancy between Fixed Dose Combination (FDC) TEE dispensing data and patients on FDC TEE captured on TIER.Net and Health Patient Registration System (HPRS), as a means of improving identification and monitoring of patients that carry the potential risk of being lost to subsequent follow-ups (ART collection / clinical visits). Methods: A retrospective, quantitative, and descriptive record review of 382 medical records of HIV positive patients, along with TIER.Net and Health Patient Registration System (HPRS) reports, was conducted at five primary healthcare (PHC) facilities, each representing the five sub-districts found in Lejweleputswa district using a self-designed data collection tool. Descriptive statistics was used to summarise and present data. Results: Sixty five percent the TEE collected from the dispensary was captured on TIER. Net. It could not be determined on none of the medical records whether or not the administrative clerk captured dispensed TEE on the same date of collection from the dispensary on TIER.Net. Subsequently, the actual date of capturing the TEE dispenses on TIER.Net following collection of the treatment from the dispensary could also not be determined. The overall data on TEE dispensed/collected from the dispensary the same was not the same as the data captured on TIER.Net. Thirty five percent of patients were reported to have collected their ART according to dispensary data than that reported on TIER.Net. Eighty percent of the TEE collected from the dispensary was captured on HPRS. Eighty percent of facilities had an area and computer dedicated for HPRS and TIER.Net but none had a backup computer in cases of theft/breakage. None of the facilities had access to back up connectivity, a manual capturing process in the form of paper-based head count registers was instead utilised as back-up. Conclusion: The following factors were found to contribute to the discrepancy between the TEE dispensing data, TIER.net and HPRS: Poor records keeping, unauthorised dispensing of prescriptions, poor data management, delays and non-capturing of ART medical records and infrastructural and human resource challenges that exist in the data management of the patient medical records. There is a need to address these gaps in order to improve reliability of dispensary data, as well as reports from TIER.Net and HPRS, in order to streamline the identification and monitoring of patients at risk of becoming lost to follow-up. , Thesis (MPA) -- Faculty of Health Sciences
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  • Date Issued: 2022-09

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

Application of machine learning, molecular modelling and structural data mining against antiretroviral drug resistance in HIV-1

  • Authors: Sheik Amamuddy, Olivier Serge André
  • Date: 2020
  • Subjects: Machine learning , Molecules -- Models , Data mining , Neural networks (Computer science) , Antiretroviral agents , Protease inhibitors , Drug resistance , Multidrug resistance , Molecular dynamics , Renin-angiotensin system , HIV (Viruses) -- South Africa , HIV (Viruses) -- Social aspects -- South Africa , South African Natural Compounds Database
  • Language: English
  • Type: text , Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10962/115964 , vital:34282
  • Description: Millions are affected with the Human Immunodeficiency Virus (HIV) world wide, even though the death toll is on the decline. Antiretrovirals (ARVs), more specifically protease inhibitors have shown tremendous success since their introduction into therapy since the mid 1990’s by slowing down progression to the Acquired Immune Deficiency Syndrome (AIDS). However, Drug Resistance Mutations (DRMs) are constantly selected for due to viral adaptation, making drugs less effective over time. The current challenge is to manage the infection optimally with a limited set of drugs, with differing associated levels of toxicities in the face of a virus that (1) exists as a quasispecies, (2) may transmit acquired DRMs to drug-naive individuals and (3) that can manifest class-wide resistance due to similarities in design. The presence of latent reservoirs, unawareness of infection status, education and various socio-economic factors make the problem even more complex. Adequate timing and choice of drug prescription together with treatment adherence are very important as drug toxicities, drug failure and sub-optimal treatment regimens leave room for further development of drug resistance. While CD4 cell count and the determination of viral load from patients in resource-limited settings are very helpful to track how well a patient’s immune system is able to keep the virus in check, they can be lengthy in determining whether an ARV is effective. Phenosense assay kits answer this problem using viruses engineered to contain the patient sequences and evaluating their growth in the presence of different ARVs, but this can be expensive and too involved for routine checks. As a cheaper and faster alternative, genotypic assays provide similar information from HIV pol sequences obtained from blood samples, inferring ARV efficacy on the basis of drug resistance mutation patterns. However, these are inherently complex and the various methods of in silico prediction, such as Geno2pheno, REGA and Stanford HIVdb do not always agree in every case, even though this gap decreases as the list of resistance mutations is updated. A major gap in HIV treatment is that the information used for predicting drug resistance is mainly computed from data containing an overwhelming majority of B subtype HIV, when these only comprise about 12% of the worldwide HIV infections. In addition to growing evidence that drug resistance is subtype-related, it is intuitive to hypothesize that as subtyping is a phylogenetic classification, the more divergent a subtype is from the strains used in training prediction models, the less their resistance profiles would correlate. For the aforementioned reasons, we used a multi-faceted approach to attack the virus in multiple ways. This research aimed to (1) improve resistance prediction methods by focusing solely on the available subtype, (2) mine structural information pertaining to resistance in order to find any exploitable weak points and increase knowledge of the mechanistic processes of drug resistance in HIV protease. Finally, (3) we screen for protease inhibitors amongst a database of natural compounds [the South African natural compound database (SANCDB)] to find molecules or molecular properties usable to come up with improved inhibition against the drug target. In this work, structural information was mined using the Anisotropic Network Model, Dynamics Cross-Correlation, Perturbation Response Scanning, residue contact network analysis and the radius of gyration. These methods failed to give any resistance-associated patterns in terms of natural movement, internal correlated motions, residue perturbation response, relational behaviour and global compaction respectively. Applications of drug docking, homology-modelling and energy minimization for generating features suitable for machine-learning were not very promising, and rather suggest that the value of binding energies by themselves from Vina may not be very reliable quantitatively. All these failures lead to a refinement that resulted in a highly sensitive statistically-guided network construction and analysis, which leads to key findings in the early dynamics associated with resistance across all PI drugs. The latter experiment unravelled a conserved lateral expansion motion occurring at the flap elbows, and an associated contraction that drives the base of the dimerization domain towards the catalytic site’s floor in the case of drug resistance. Interestingly, we found that despite the conserved movement, bond angles were degenerate. Alongside, 16 Artificial Neural Network models were optimised for HIV proteases and reverse transcriptase inhibitors, with performances on par with Stanford HIVdb. Finally, we prioritised 9 compounds with potential protease inhibitory activity using virtual screening and molecular dynamics (MD) to additionally suggest a promising modification to one of the compounds. This yielded another molecule inhibiting equally well both opened and closed receptor target conformations, whereby each of the compounds had been selected against an array of multi-drug-resistant receptor variants. While a main hurdle was a lack of non-B subtype data, our findings, especially from the statistically-guided network analysis, may extrapolate to a certain extent to them as the level of conservation was very high within subtype B, despite all the present variations. This network construction method lays down a sensitive approach for analysing a pair of alternate phenotypes for which complex patterns prevail, given a sufficient number of experimental units. During the course of research a weighted contact mapping tool was developed to compare renin-angiotensinogen variants and packaged as part of the MD-TASK tool suite. Finally the functionality, compatibility and performance of the MODE-TASK tool were evaluated and confirmed for both Python2.7.x and Python3.x, for the analysis of normals modes from single protein structures and essential modes from MD trajectories. These techniques and tools collectively add onto the conventional means of MD analysis.
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  • Date Issued: 2020

Formulation and evaluation of liposomal films for buccal delivery of antiretroviral drug

  • Authors: Okafor, Nnamdi Ikemefuna
  • Date: 2020
  • Subjects: Liposomes , Highly active antiretroviral therapy , Antiretroviral agents , HIV infections -- Prevention
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/117161 , vital:34485
  • Description: The human immune deficiency virus (HIV) infection has been ranked as one of the most devastating microbial infections in the world. This status is a result of the HIV rapid genetic variation, which limits discovery of a vaccine. Use application of antiretroviral therapy (ARVT) in treatment of the disease caused by the HIV infection (known as acquired immunodeficiency syndrome, HIV-AIDS) is frequently compromised by several factors such as the low bioavailability and severe adverse effects associated with the existing antiretroviral drugs (ARVDs). This underlines the need for controlling the pharmacokinetics profiles of ARVD using effective vehicles that can modify drug biodistribution. The same is true for many other conditions, where delivery systems can determine the success or failure of treatment by controlling pharmacokinetic and dynamic properties. The mucosal linings of the oral cavities in addition offer adorable route of administration for systematic drug delivery, improving drug therapeutic performance and often preferred by clinicians and patients. Liposomes are tiny spherical sacs of phospholipid molecules enclosing water droplets, formed (artificially) to carry drugs or other substances into the tissues by crossing and targeting to specific organelles. This work therefore focused on preparation of liposomes and liposomal buccal films (BFs) for potential buccal delivery of efavirenz, an ARVD model endowed with poor solubility and several side effects. The liposomes were prepared by thin film hydration method using crude soybean lecithin (CL) and cholesterol. Efavirenz loaded liposomes were evaluated for particle size, Zeta potential (ZP), morphology, encapsulation efficiency (EE%) and release kinetics studies. The physiochemical properties of the liposomes were also evaluated using Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD), energy dispersity spectroscopy (EDS), and Fourier transform infrared (FTIR), while the formulation with the best encapsulation efficiency was used as the solvent medium for the buccal film formation. The buccal films were prepared using solvent casting method, where the liposomal suspension was used as the dispersing medium. The films were optimized for physical properties (thickness, weight variation and folding endurance) using digital Vernier calliper and digital weighing balance. The physiochemical properties of the selected BFs films made of Carbopol (CP) and its combination with Pluronic F127 (PF127) were further characterized using XRD, DSC, FTIR, Transmission Electron Microscopy (TEM), EDS and Scanning Electron Microscopy (SEM). The permeation study of the selected BFs was investigated using Franz diffusion cell. The BFs composed of CP alone or its combination with PF127 demonstrated much better bio-adhesive properties than the films made of other polymers (like Hydroxyl propyl methyl cellulose, HPMC) alone or in combination with PF127. The developed liposome formulation showed high encapsulation 98.8 ± 0.01 % in CL to cholesterol mass ratio of 1:1 and total lipid to drug mass ratio of 2:1. The average particle size 104.82 ± 2.29 nm and Zeta potential -50.33 ± 0.95 mV of these liposomes were found to be attractive for targeted delivery to the HIV infected cells. The CP based BFs (without and with PF127) exhibited good film thickness 0.88 ± 0.10 and 0.76 ± 0.14 mm, with weight uniformity 68.22 ± 1.04 and 86.28 ± 2. 16 mg, satisfactory flexibility values 258 and 321, and slightly acidic pH 6.43 ± 0.76 and 6.32 ± 0.01. The swelling percentage was found to be 50 % for CP film alone and 78 % for CP film with PF127. The cumulative amount of drug that permeated through the buccal epithelium over 24 hours was about 66 % from CP film alone and 75 % from CP film with PF127. Since no evidence of the liposomal encapsulation of EFV have been reported to our knowledge, we find the insights from the present study valuable as a set of preliminary data to encourage further investigations of the encapsulation and delivery of EFV like antiretrovirals for enhanced solubility, site targeting and prolonged release using crude soybean lecithin and mucoadhesive polymers, which holds some added economical values as naturally occurring lipid and polymeric mixtures as a promising delivery systems for buccal delivery of ARVDs.
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  • Date Issued: 2020

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

Genetic diversity, resistance profile of hiv and risk assessment of mother-to-child transmission in pregnant women on antiretroviral therapy in the Eastern Cape, South Africa

  • Authors: Adeniyi, Oladele Vincent
  • Date: 2019
  • Subjects: Antiretroviral agents , HIV infections -- Treatment -- South Africa
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10353/15120 , vital:40183
  • Description: Despite the initiation of life-long ART in HIV-infected pregnant women, the rate and determinants of infant HIV transmission are not known, especially in the poor resource settings of the Eastern Cape, South Africa. Maternal anti-retroviral therapy (ART) is crucial for elimination of mother-to-child transmission (MTCT) of HIV. However, the inevitable risks of emergence of HIV drug resistance poses significant threat to achieving this goal of HIV-free generation and keeping mothers alive. Also, it is unclear if women with high viral load at delivery have acquired clinically relevant mutations, which could confer resistance to the ART, thus, further increasing the risks of motherto-child transmission of HIV-drug resistance strains. In addition to the gaps identified in the prevention of mother-to-child transmission (PMTCT) context, the understanding of regional epidemics is crucial to the broader epidemiological profiling of HIV infections in the country. Despite the rapid influx of foreign nationals to South African and Eastern Cape Province, there has not been any molecular epidemiological studies profiling the HIV diversity in the Eastern Cape.
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  • Date Issued: 2019

Genetic diversity, resistance profile of HIV and risk assessment of mother-to-child transmission in pregnant women on anti-retroviral therapy in the Eastern Cape, South Africa

  • Authors: Adeniyi, Oladele Vincent
  • Date: 2018-12
  • Subjects: Antiretroviral agents , AIDS (Disease) in infants
  • Language: English
  • Type: Doctoral theses , text
  • Identifier: http://hdl.handle.net/10353/19817 , vital:43254
  • Description: Despite the initiation of life-long ART in HIV-infected pregnant women, the rate and determinants of infant HIV transmission are not known, especially in the poor resource settings of the Eastern Cape, South Africa. Maternal anti-retroviral therapy (ART) is crucial for elimination of mother-to-child transmission (MTCT) of HIV. However, the inevitable risks of emergence of HIV drug resistance poses significant threat to achieving this goal of HIV-free generation and keeping mothers alive. Also, it is unclear if women with high viral load at delivery have acquired clinically relevant mutations, which could confer resistance to the ART, thus, further increasing the risks of motherto- child transmission of HIV-drug resistance strains. In addition to the gaps identified in the prevention of mother-to-child transmission (PMTCT) context, the understanding of regional epidemics is crucial to the broader epidemiological profiling of HIV infections in the country. Despite the rapid influx of foreign nationals to South African and Eastern Cape Province, there has not been any molecular epidemiological studies profiling the HIV diversity in the Eastern Cape. , Thesis (PhD) (Microbiology) -- University of Fort Hare, 2018
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  • Date Issued: 2018-12

A narrative study of patients’ illness experiences on antiretroviral treatment

  • Authors: Tsope, Lindiwe
  • Date: 2018
  • Subjects: AIDS (Disease) Social aspects South Africa , HIV infections Social aspects South Africa , Stigma (Social psychology) , Antiretroviral agents , Disclosure of information , Social media in medicine South Africa , Discourse analysis, Narrative
  • Language: English
  • Type: text , Thesis , Masters , MSocSc
  • Identifier: http://hdl.handle.net/10962/63032 , vital:28356
  • Description: Eight female respondents, who have publicly disclosed their HIV-positive status on social media, were involved in a semi-structured in-depth interview process. Using the theoretical frameworks of symbolic interactionism and social constructionism, the study explores the effects of antiretroviral treatment on patients’ illness experiences, looking at the personal and social symbolisms and meanings attached to taking antiretrovirals. The study revealed a positive and inspirational aspect of living with HIV/AIDS and especially consuming antiretroviral therapy. It became evident that the knowledge participants had of antiretrovirals before consuming them was misguided and based more on false ‘general knowledge’ among laypersons than actual medical fact. Moreover, the study revealed that there is a social reconstruction of narratives that has taken place in each participant’s life due to consuming antiretrovirals. Publicly disclosing their statuses has also proved to have both negative and positive consequences for the individuals and for society at large. While there is a consensus that participants’ illness experiences are directly affected by antiretroviral treatment, each participant’s narrative is different, yet positive.
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  • Date Issued: 2018

A new synthetic approach for preparation of Efavirenz

  • Authors: Chada, Sravanthi
  • Date: 2017
  • Subjects: Antiretroviral agents , Asymmetric synthesis , Enzyme inhibitors , HIV (Viruses) -- Enzymes
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10948/15512 , vital:28265
  • Description: Efavirenz, a drug that is still inaccessible to millions of people worldwide, is potent non nucleoside reverse transcriptase inhibitor (NNRTI), is one of the preferred agents used in combination therapy for first-line treatment of the human immunodeficiency virus (HIV). NNRTIs attach to and block an HIV enzyme called reverse transcriptase, by blocking reverse transcriptase; NNRTIs prevent HIV from multiplying and can reduce the amount of HIV in the body. Efavirenz can't cure HIV/AIDS, but taken in combination with other HIV medicines (called an HIV regimen) every day helps people with HIV live longer healthier lives. Efavirenz also reduces the risk of HIV transmission and can be used by children who are suffering from HIV/AIDS. All the above therapeutic uses of efavirenz prompted us to identify the novel and hopefully cost efficient synthetic methodology for the preparation of efavirenz. In this thesis a new synthetic method for asymmetric synthesis of efavirenz is described. This route started from commercially available starting materials and it is first established in traditional batch chemistry and further the parameters transferred to a semi continuous flow protocol for optimization.
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  • Date Issued: 2017

The cognitive rehabilitation of a sample of children living with HIV : a specific focus on the cognitive rehabilitation of sustained attention

  • Authors: Basterfield, Candice
  • Date: 2015
  • Subjects: HIV-positive children -- Rehabilitation , Antiretroviral agents , HIV (Viruses) -- Side effects , Brain damage -- Patients -- Rehabilitation , Cognition disorders -- Patients -- Rehabilitation
  • Language: English
  • Type: Thesis , Masters , MSocSc
  • Identifier: vital:3258 , http://hdl.handle.net/10962/d1017881
  • Description: Pharmacological interventions to treat Human Immunodeficiency Virus (HIV) with antiretrovirals (ARVs), have dramatically improved the survival rates of HIV positive children maturing into adulthood. However, HIV-associated neurocognitive decline still persists in the era of ARVs. Within the framework of brain plasticity, a number of researchers have begun to assess the feasibility of cognitive rehabilitation therapy as a complement to ARVs to reverse neurocognitive decline as a result of HIV (e.g., Becker et al., 2012). Only one study has been conducted in South Africa, by Zondo & Mulder (2014), assessing the efficacy of cognitive rehabilitation in a paediatric sample. The current research builds on the above mentioned study by implementing an experimental approach to examine the effect of cognitive rehabilitation in a sample of both HIV positive and HIV negative children. Five HIV positive and six HIV negative children were assigned to either an experimental or control group. The experimental group underwent two months of cognitive rehabilitation therapy remediating sustained attention, whereas the control group took part in placebo activities. Sustained attention measures were taken before and after the intervention training sessions, using a sustained attention subtest from the Test of Everyday Attention for Children (TEA-CH). A Mann Whitney U Test revealed that the experimental group (Mdn=38.50) did not differ significantly from the control group (Mdn = 37.00) after the cognitive rehabilitation intervention, U=12.00, z= -.55, p= .66, r= -.17. But a Wilcoxon Signed Rank Test found that there was a significant improvement from pretest scores (Mdn=31.00) to posttest scores (Mdn=38.00) following the rehabilitation for HIV positive participants in the sample, T=15.00, z = -2.02, p= .04, r= -.90. This raises the possibility that cognitive rehabilitation could be used as a low cost intervention in underdeveloped contexts
  • Full Text:
  • Date Issued: 2015

Influence of non-synonymous sequence mutations on the architecture of HIV-1 clade C protease receptor site : docking and molecular dynamics studies

  • Authors: Onywera, David Harris
  • Date: 2014
  • Subjects: HIV (Viruses) -- Research , HIV infections -- Treatment -- Research , HIV infections -- Chemotherapy , Protease inhibitors -- Research , Viruses -- Effect of drugs on -- Research , Antiretroviral agents
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4116 , http://hdl.handle.net/10962/d1013133
  • Description: Despite the current interventions to avert contagions and AIDS-related deaths, sub-Saharan Africa is still the region most severely affected by the HIV/AIDS pandemic, where clade C is the dominant circulating HIV-1 strain. The pol-encoded HIV-1 protease enzyme has been extensively exploited as a drug target. Protease inhibitors have been engineered within the framework of clade B, the commonest in America, Europe and Australia. Recent studies have attested the existence of sequence and catalytic disparities between clades B and C proteases that could upset drug susceptibilities. Emergence of drug-resistant associated mutations and combinatorial explosions due to recombination thwarts the attempt to stabilize the current highly active antiretroviral therapy (HAART) baseline. The project aimed at identifying the structural and molecular mechanisms hired by mutants to affect the efficacies of both FDA approved and Rhodes University (RU)-synthesized inhibitors, in order to define how current and or future drugs ought to be modified or synthesized with the intent of combating drug resistance. The rationale involved the generation of homology models of the HIV-1 sequences from the South African infants failing treatment with two protease inhibitors: lopinavir and ritonavir (as monitored by alterations in surrogate markers: CD4 cell count decline and viral load upsurge). Consistent with previous studies, we established nine polymorphisms: 12S, 15V, 19I, 36I, 41K, 63P, 69K, 89M, and 93L, linked to subtype C wild-type; some of which are associated with protease treatment in clade B. Even though we predicted two occurrence patterns of M46I, I54V and V82A mutations as V82A→I54V→M46I and I54V→V82A→M46V, other possibilities might exist. Mutations either caused a protracted or contracted active site cleft, which enforced differential drug responses. The in silico docking indicated susceptibility discordances between clades B and C in certain polymorphisms and non-polymorphisms. The RU-synthesized ligands displayed varied efficacies that were below those of the FDA approved protease inhibitors. The flaps underwent a wide range of structural motions to accommodate and stabilize the ligands. Computational analyses unravelled the need for these potential drugs to be restructured by (de novo) drug engineers to improve their binding fits, affinities, energies and interactions with multiple key protease residues in order to target resilient HIV-1 assemblages. Accumulating evidences on contrasting drug-choice interpretations from the Stanford HIVdb should act as an impetus for the customization of a HIVdb for the sub-Saharan subcontinent.
  • Full Text:
  • Date Issued: 2014

Prevention of mother to child transmission (PMTCT) of HIV/AIDS: a review of using PMTCT services in South Africa

  • Authors: Jumare, Fadila
  • Date: 2012
  • Subjects: AIDS (Disease) in pregnancy -- South Africa -- Prevention , AIDS (Disease) -- South Africa -- Prevention , HIV infections -- Transmission -- South Africa , Antiretroviral agents
  • Language: English
  • Type: Thesis , Masters , MA
  • Identifier: vital:9091 , http://hdl.handle.net/10948/d1011508 , AIDS (Disease) in pregnancy -- South Africa -- Prevention , AIDS (Disease) -- South Africa -- Prevention , HIV infections -- Transmission -- South Africa , Antiretroviral agents
  • Description: Despite good intentions and commitment from health providers, it is difficult for HIV positive pregnant women to access Prevention of Mother to Child Transmission of HIV (PMTCT) services (Skinner et al 2005:115). The aim of this research was to find out the extent to which socio-economic and cultural factors influence access to and utilization of PMTCT services. It appeared that despite having a legal plan and framework to ensure that PMTCT services are available and free, the realities confronting HIV positive women in South Africa as suggested by the literature contradicted this objective. Inevitably, these contradictions were identified as some of the main factors contributing to lack of access and inadequate utilization of PMTCT services. These factors were identified through a review of fifteen studies selected based on their relevance to the research aim. The findings were presented according to the following themes: Functioning of clinics, adherence to ART, uptake of VCT and infant feeding practices. According to research evidence, the major socio-cultural factors influencing access and utilization of PMTCT services include fear of stigma and discrimination which are related to cultural norms and practices. The socio-economic factors include transport costs, lack of food, medicines and formula milk which are all related to poverty and unemployment. The research also found that health system constraints such as long waiting times in clinics, stock-outs of formula milk, medicines and test kits influenced the utilization of PMTCT services by HIV positive women.
  • Full Text:
  • Date Issued: 2012

African traditional medicine-antiretroviral interactions : effects of Sutherlandia frutescens on the pharmacokinetics of Atazanavir

  • Authors: Müller, Adrienne Carmel
  • Date: 2011 , 2011-03-28
  • Subjects: Antiretroviral agents , Medicinal plants , Traditional medicine , AIDS (Disease) -- Treatment , HIV infections -- Drug therapy , Drug interactions , Pharmacokinetics
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:3859 , http://hdl.handle.net/10962/d1013373
  • Description: In response to the urgent call for investigations into antiretroviral (ARV)-African traditional medicine (ATM) interactions, this research was undertaken to ascertain whether chronic administration of the ATM, Sutherlandia frutescens (SF) may alter the bioavailability of the protease inhibitor (PI), atazanavir (ATV), which may impact on the safety or efficacy of the ARV. Prior to investigating a potential interaction between ATV and SF in vitro and in vivo, a high performance liquid chromatography method with ultraviolet detection (HPLC-UV) was developed and validated for the bioanalysis of ATV in human plasma and liver microsomes. An improved and efficient analytical method with minimal use of solvents and short run time was achieved in comparison to methods published in the literature. In addition, the method was selective, linear, accurate and precise for quantitative analysis of ATV in these studies. Molecular docking studies were conducted to compare the binding modes and affinities of ATV and two major SF constituents, Sutherlandioside B and Sutherlandin C, with the efflux transporter, P-glycoprotein (P-gp) and the CYP450 isoenzyme, CYP3A4 to determine the potential for these phytochemicals to competitively inhibit the binding of ATV to these two proteins, which are mediators of absorption and metabolism. These studies revealed that modulation of P-gp transport of ATV by Sutherlandioside B and Sutherlandin C was not likely to occur via competitive inhibition. The results further indicated that weak competitive inhibition of CYP3A4 may possibly occur in the presence of either of these two SF constituents. The Caco-2 cell line was used as an in vitro model of human intestinal absorption. Accumulation studies in these cells were conducted to ascertain whether extracts and constituents of SF have the ability to alter the absorption of ATV. The results showed that the aqueous extract of SF significantly reduced ATV accumulation, suggesting decreased ATV absorption, whilst a triterpenoid glycoside fraction isolated from SF exhibited an opposing effect. Analogous responses were elicited by the aqueous extract and a triterpenoid glycoside fraction in similar accumulation studies in P-gp overexpressing Madin–Darby Canine Kidney Strain II cells (MDCKII-MDR1), which signified that the effects of this extract and component on ATV transport in the Caco-2 cells were P-gp-mediated. The quantitative analysis of ATV in human liver microsomes after co-incubation with extracts and components of SF was conducted to determine the effects of SF on the metabolism of ATV. The aqueous and methanolic extracts of SF inhibited ATV metabolism, whilst the triterpenoid glycoside fraction had a converse effect. Analogous effects by the extracts were demonstrated in experiments conducted in CYP3A4-transfected microsomes, suggesting that the inhibition of ATV metabolism in the liver microsomes by these SF extracts was CYP3A4-mediated. A combination of Sutherlandiosides C and D also inhibited CYP3A4-mediated ATV metabolism, which was in contrast to the response elicited by the triterpenoid fraction in the liver microsomes, where other unidentified compounds, shown to be present therein, may have contributed to the activation of ATV metabolism. The in vitro studies revealed the potential for SF to alter the bioavailability of ATV, therefore a clinical study in which the effect of a multiple dose regimen of SF on the pharmacokinetics (PK) of a single dose of ATV was conducted in healthy male volunteers. The statistical analysis showed that the 90 % confidence intervals around the geometric mean ratios (ATV + SF/ATV alone) for both Cmax and AUC0-24 hours, fell well below the lower limit of the "no-effect" boundary of 0.8 – 1.25, implying that the bioavailability of ATV was significantly reduced in this cohort of subjects. It may thus be concluded that if the reduction in bioavailability observed in this clinical study is found to be clinically relevant, co-administration of SF commercial dosage forms and ATV in HIV/AIDS patients may potentially result in subtherapeutic ATV levels, which may in turn contribute to ATV resistance and/or treatment failure. This research has therefore highlighted the potential risk for toxicity or lack of efficacy of ARV regimens which may result when ATMs and PIs are used concurrently and that patients and health care practitioners alike should be aware of these perils.
  • Full Text:
  • Date Issued: 2011

A chemo-enzymatic process for the production of beta-thymidine, a key intermediate in antiretrovirol manufacture

  • Authors: Gordon, Gregory Ernest Robert
  • Date: 2010
  • Subjects: HIV infections -- Treatment -- South Africa , HIV infections -- South Africa -- Prevention , Antiretroviral agents
  • Language: English
  • Type: Thesis , Doctoral , DTech
  • Identifier: vital:10423 , http://hdl.handle.net/10948/d1016217
  • Description: The socio-economic impact of HIV/AIDS on South Africa has resulted in lower gross domestic product, loss of skills in key sectors such as education, and increased health-care costs in providing access to treatment. Currently active pharmaceutical ingredients (API’s) such as stavudine (d4T) and azidothymidine (AZT) are imported from India and China, while formulation is conducted locally. A strategy was initiated between CSIR Biosciences and LIFElab under the auspices of Arvir Technologies to investigate the feasibility of local antiretroviral manufacture (d4T and AZT) or the manufacture of a key intermediate such as β- thymidine (dT). Several advantages associated with successful implementation of this strategy include ensuring a local supply of API’s, thus reducing reliance on procurement from foreign sources and reducing the effect of foreign exchange rate fluctuations on providing cost effective access to treatment. A local supply source would also reduce the imports and thus aid the balance of payments deficit, and in addition to this, provide stimulus in the local pharmaceutical manufacturing industry (which has been in decline for several decades), resulting in increased skills and employment opportunities. This thesis describes the development of a superior chemo-enzymatic process for the production of β-thymidine (72 percent yield, prior to isolation), a key intermediate in the preparation of anti-retrovirals. Alternative processes based purely on chemical or bioprocess transformations to prepare either 5-methyluridine (5-MU) or dT suffer from several disadvantages: lengthy transformations due to protection/deprotection strategies, low selectivties and product yields (30 percent in the chemical process) and isolation of the product from dilute process streams requiring the use of large uneconomical reactors (bioprocesss). This contributes significantly to the cost of d4T and AZT manufacture. Our novel chemoenzymatic process comprises of a biocatalytic reaction for the production of 5-MU, with subsequent chemical transformation into dT (3 steps) negating and circumventing the limitations of the chemical or bioprocess routes. During the course of this project development, the β-thymidine selling price declined from 175 $/kg (2005) to 100 $/kg (2008). However, the process described in this work is still competitive based on the current β- thymidine selling price of 100 $/kg. The process economics show that with further optimization and increasing the isolated dT yield from 70 percent to 90 percent, the variable cost decreases from 136 $/kg to 110 $/kg. The increase in isolated yield is highly probable, based on solubility data of β-thymidine. The decrease in β-thymidine selling price and technological improvement in dT manufacture should translate into lower API manufacture costs and more cost effective access to treatment. Our novel biocatalytic process producing 5-MU uses a coupled enzyme system employing PNP, Purine Nucleoside Phosphorylase and PyNP, Pyrimidine Nucleoside Phosphorylase. The overall transglycosylation reaction may be decoupled into the phosphorolysis reaction (PNP) and synthesis reaction (PyNP). During the phosphorolysis reaction, guanosine is converted into guanine and ribose-1-phosphate (R-1-P) in the presence of PNP enzyme. The reaction intermediate R-1-P is then coupled to thymine in the presence of PyNP enzyme during the synthesis reaction, producing 5-MU. The process was scaled up from lab-scale to bench-scale (10 - 20 L) and demonstrated to be robust and reproducible. This is evident from the average guanosine conversion (94.7 percent ± 2.03) and 5-MU yield (88.2 percent ± 6.21) and mole balance (104 percent ± 7.61) which were obtained at bench-scale (3 replicates, 10 L). The reaction was carried out at reactor productivities of between 7 – 11 g.L-1.h-1. The integration of the biocatalytic process and chemical processes was successfully carried out, showing that 5-MU produced using our novel biocatalytic process behaved similarly to commercially available 5- MU (ex. Dayang Chemicals, China). A PCT patent application (Ref. No. P44422PC01) on this chemo-enzymatic process has been filed and currently public private partnerships are being explored through Arvir Technologies to evaluate and validate this technology at one ton scale.
  • Full Text:
  • Date Issued: 2010

Implementation of the dual therapy prevention of mother-to-child transmission protocol

  • Authors: Singh, Vikesh
  • Date: 2010
  • Subjects: HIV infections -- Transmission -- South Africa , AIDS (Disease) in pregnancy -- Prevention -- South Africa , Antiretroviral agents
  • Language: English
  • Type: Thesis , Masters , MPharm
  • Identifier: vital:10138 , http://hdl.handle.net/10948/1374 , HIV infections -- Transmission -- South Africa , AIDS (Disease) in pregnancy -- Prevention -- South Africa , Antiretroviral agents
  • Description: Antiretroviral drugs taken during pregnancy, reduce the rates of mother-to-child transmission from 35 percent to as low as 1 to 2 percent (UNAIDS, 2009). In 2002, the Prevention of Mother-to-Child Transmission (PMTCT) programme was implemented in South Africa. Studies on the implementation of the PMTCT programme have shown that understaffed and under-developed health care facilities were key barriers to the provision of PMTCT services (Health Systems Trust, 2002: 6; Skinner et al., 2003). The aim of this study was to assess the challenges experienced by health care workers working in public sector facilities in the Nelson Mandela Metropole after implementation of the dual therapy PMTCT programme. Four areas were investigated: Infrastructure; Drug Supply Management; Clinic Procedures and Staffing. A quantitative descriptive study was conducted in August 2009 at nine public health care facilities in the Nelson Mandela Metropole, South Africa. Questionnaires were issued to 81 nurses and 41 pharmacy personnel (pharmacists and pharmacist assistants). Checklist audit forms were issued to the Facility Manager of each facility and completed with the researcher. The key findings for Infrastructure were lack of space at patient waiting rooms (9; 100 percent n=9), counselling area (5; 55.5 percent; n=9), nurse consultation rooms (6; 66.6 percent; n=9), storage areas (5; 55.5 percent; n=9) and filing areas (7; 77.7 percent; n=9). The key findings for Drug Supply Management were none of the dispensaries (0 percent; n=10) were fully compliant with Good Pharmacy Practice, pharmacy personnel indicated that there were no stock cards for medication (13; 31.7 percent; n=41); there was less than two weeks supply of buffer stock kept for zidovudine and nevirapine (13; 35.1percent; n=37) and medication orders were placed without any reference to minimum and maximum levels of medication (15; 36.5 percent; n=41) . The key findings for Clinic Procedures were only two facilities followed up on patients that had missed appointments (22.2 percent; n=9) and four facilities (44.4 percent; n=9) had a tracking system for patients that had defaulted. Of the nine facilities only three (33.3 percent; n=9) updated patient demographic details regularly. The key findings for Staffing were a shortage of doctors, nurses, counsellors and pharmacists at the facilities. One of the major challenges identified was the lack of training offered on new PMTCT protocols with 56.2 percent (45; n=80) of the nurses stating that no training was provided on the dual PMTCT protocol. Only 54.3 percent (44; n=81) of nurses stated that they knew the criteria to start the mother on dual PMTCT therapy. In conclusion there is an urgent need for barriers such as lack of staff, lack of space, lack of training on PMTCT and standard procedures for follow up of patients to be addressed in order to ensure the successful scaling up of PMTCT.
  • Full Text:
  • Date Issued: 2010
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