Molecular simulations of potential agents and targets of Alzheimer’s disease
- Authors: Carlisle, Tanya
- Date: 2020
- Subjects: Alzheimer's disease -- Treatment , Alzheimer's disease -- Molecular aspects , Amyloid beta-protein precurs , Amyloid beta-protein
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140025 , vital:37825
- Description: The World Alzheimer Report statedin 2016 that approximately 46.8 million people were living with dementia and this figure is expected to triple by 2050. Alzheimer’s Disease was discovered to be a precursor to dementia in 1976 and since then efforts to understand Alzheimer’s have been prioritized. To date, there are very few effective forms of treatment for Alzheimer’s, many are known to offer only mild calming of the symptoms and have side effects such as diarrhea, nausea, loss of appetite and sleep disturbances. This has been due to lack of understanding on how Alzheimer’s is caused. With the two main hallmarks of the disease now being more understood it has opened the doorway into the discovery of new treatments for this disease. This study focuses on the hallmark involving the aggregation of the β-amyloid protein to form plaques surrounding the neurons of the brain. Copper, Zinc and Iron have also been found in high concentrations in and surrounding these plaques. This study focused on the screening of the South African Natural Compound database (SANCDB) to discover hits that have potential destabilizing action against the Beta-amyloid aggregate. If one of these compounds could prove to have destabilizing action on the aggregate it could open the doorway to new potential forms of treatment. Over 700 SANCDB compounds were docked, and the top hits were taken to molecular dynamics to further study the interactions of the compounds and the aggregate. However, the hits identified had strong binding to the aggregate causing it to become stable instead of the desired effect of destabilizing the structure. This information, however, does not rule out the possibility of these compounds preventing the formation of the aggregates. Further, interactions of copper with β-amyloid and copper were determined by solubilizing the aggregate and introducing copper ions in a dynamics simulation. Possible interactions between copper and the methionine residues were visualised.
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Molecular simulations of potential agents and targets of Alzheimer’s disease
- Authors: Joli, Luxolo
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Ligands (Biochemistry) , Proteins -- Chemistry , Molecular dynamics -- Simulation methods
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146411 , vital:38523
- Description: Alzheimer's Disease (AD) is a neurodegenerative brain disorder that was first discovered in 1901 by Dr Aloïs Alzheimer and was later reported publicly in 1906. The German doctor had a 51-yearold woman patient called Auguste Deter, who was suffering from a rare brain disorder with early signs of memory loss and cognition. Alzheimer's Disease is the most common type of dementia that affects people with the age of 65 years and older. There is no single known cause of Alzheimer’s disease however, amyloid β-peptide (Aβ1–40/42) was found to be at the centre of AD pathogenesis and this connection was referred as “amyloid hypothesis”. It is suspected that an accumulation of amyloid β-peptide is a major contributor to neuronal dysfunction and degeneration. Alzheimer’s disease is complex and therefore, currently there is no medication available that treats the disease. However, there are approaches that focus on helping people maintain mental function, manage behavioral symptoms, and slow down the symptoms of disease. According to South Africa’s 2011 census, there are approximately 2.2 million people in South Africa with some form of dementia and therefore there is a need to find a treatment for the disease. This study aims to find agents and targets of Alzheimer’s Disease by using different computational techniques such as molecular modelling. The study will use compounds from the South African Compounds Database (SANCDB) and the following therapeutic targets α-, β- and γ-secretase, acetylcholinesterase, tau protein and neprilysin. A successful High-throughput Virtual Screening (HTVS) study to determine lead compounds was performed using a computational program called KNIME. Molecular docking was achieved with GLIDE as it allows for exhaustive ligand flexibility. The docking calculations were carried out using the high level of precision XP (extra precision) for enhanced docking accuracy. The binding affinities (docking scores) for the best bound ligands obtained from docking were in the order of -5 kcal/mol or less. The ligandSANC00370 was the best binding ligand against the protein 1J1C_B and had the best binding energy of -13.94 kcal/mol compared to others. The receptor-ligand complexes were analyzed using the interaction diagrams obtained from the Discovery Studio Visualizer and Maestro programs. Molecular Dynamics simulations were performed on the complexes obtained from docking to help in optimizing their interactions. The simulations were performed using the Desmond tool with the OPLS3 force field. 100 ns simulations were performed for six systems with the best docking score results epresenting each of the therapeutic targets and for the other complex systems, 50 ns simulations were performed. The Desmond simulations were analyzed using the Simulations Interaction Diagrams such as PL-RMSD, L-RMSF, P-RMSF, L-Torsions, P-SSE, LP-Contacts and L-Properties. Maestro was used to visualize the stability of the ligands in the active site during the simulation. All 13 Desmond simulations were successful however, there were 9 simulations which produced satisfactory results while the others were nsatisfactory. Based on the molecular docking and Molecular Dynamics results of this study, 9 potential targets and 6 potential agents were obtained successfully and can be studied further as therapeutics for Alzheimer’s Disease.
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Structure and interaction studies of beta-amyloid in the search for new lead compounds for the treatment of Alzheimer’s disease
- Authors: Mtini, Onke
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Amyloid beta-protein , Oxidative stress , Protein binding , South African Natural Compounds Database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167574 , vital:41493
- Description: Alzheimer’s disease (AD) is the most devastating neurodegenerative disorder that effects the aging population worldwide. In this study three hypotheses of AD are explored, the β-amyloid cascade hypothesis, the β-amyloid metal binding hypothesis and the oxidative stress hypothesis are explored. In the first case compounds from the South African Natural Compounds Database (SANCDB) are docked to models of β-amyloid fibrils and the properties of these fibrils under pulling simulations are compared to a known small molecule disruptor of β-amyloid, wgx-50. In these simulations SANCDB compounds are identified that disrupt β-amyloid in a similar manner to wgx-50. In these simulations the disruption to the free energy of binding of chains to the fibrils is quantified. For metal binding and oxidative stress hypotheses, problems in simulation arise due to only fragments of β-amyloid being present in the Research Collaboratory for Structural Bioinformatics protein data bank (RCSB PDB), as determined from NMR experiments. In this work, β-amyloid is set up under periodic boundary conditions to simulate a fibril under reasonable computational time. Within these periodic boundary conditions, β-amyloid has been solvated in copper and zinc rich environments and diffusion of these metals around the fibrils has been explored. The localization of these metals (in simulation only using van der Waal’s and electrostatic terms) around the fibril has led us to explore other possible metal binding sites. Metal bound to the infinite fibril has been optimized at the QM/MM level and some of the reactive oxygen species in the presence of the fibril are quantified.
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An investigation into the neuroprotective effects of estrogen and progesterone in a model of homocysteine-induced neurodegeration
- Authors: Wu, Wing Man
- Date: 2006
- Subjects: Homocysteine , Estrogen , Estrogen -- Therapeutic use , Progesterone , Hormone receptors , Methyl aspartate , Oxidative stress , Alzheimer's disease -- Treatment , Nervous system -- Degeneration -- Prevention
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3806 , http://hdl.handle.net/10962/d1003284 , Homocysteine , Estrogen , Estrogen -- Therapeutic use , Progesterone , Hormone receptors , Methyl aspartate , Oxidative stress , Alzheimer's disease -- Treatment , Nervous system -- Degeneration -- Prevention
- Description: Homocysteine (Hcy) is a sulfur containing amino acid and is a potent neurotoxin. It has been shown that elevated levels of Hcy, termed hyperhomocysteinemia, plays a role in the pathologies of Alzheimer’s disease (AD) and age-related cognitive decline. Hcy is a glutamate agonist, which causes in increase in Ca[superscript (2+)] influx via the activation of NMDA class of excitatory amino acid receptors, which results in neuronal cell death and apoptosis. Estrogen and progesterone are female hormones that are responsible for reproduction and maternal behaviour. However, in the last decade, it is evident that both female hormones have neuroprotective properties in many animal models of neurodegeneration. Collectively, both estrogen and progesterone reduce the consequences of the oxidative stress by enhancing the antioxidant defence mechanisms, reducing excitotoxicity by altering glutamate receptor activity and reducing the damage caused by lipid peroxidation. However, the mechanisms by which estrogen and progesterone provide such neuroprotection probably depend on the type and concentration of hormone present. Moreover, numerous studies have shown that hormone replacement therapy (HRT, estrogen and progestins) or estrogen-only replacement therapy (ERT) may prevent or delay the onset of AD and improve cognition for women with AD. Clinical trials have also shown that women taking HRT may modify the effects of Hcy levels on cognitive functioning. Oxidative stress increases in the aging brain and thus has a powerful effect on enhanced susceptibility to neurodegenerative disease. The detection and measurement of lipid peroxidation and superoxide anion radicals in the brain tissue supports the involvement of free radical reactions in neurotoxicity and in neurodegenerative disorders. The hippocampus is an important region of the brain responsible for the formation of memory. However, agents that induce stress in this area have harmful effects and could lead to dementia. This study aims to investigate and clarify the neuroprotective effects of estrogen and progesterone, using Hcy-induced neurodegenerative models. The initial studies demonstrate that estrogen and progesterone have the ability to scavenge potent free radicals. Histological studies undertaken reveal that both estrogen and progesterone protect against Hcy-induced neuronal cell death. In addition, immunohistochemical investigations show that Hcy-induced apoptosis in the hippocampus can be inhibited by both estrogen and progesterone. However, estrogen also acts at the NMDA receptor as an agonist, while progesterone blocks at the NMDA receptor. These mechanisms reduce the ability of Hcy to cause damage to neurons, since Hcy-induced neurotoxicity is dependent on the overstimulation of the NMDA receptor. SOD and GPx are important enzymatic antioxidants which can react with ROS and neutralize them before these inflict damage in the brain. Hcy can increase oxidative stress by inhibiting expression and function of these antioxidants. However, it has been shown that the antioxidant abilities of both estrogen and progesterone can up-regulate the activities of SOD and GPx. These results provide further evidence that estrogen and progesterone act as antioxidants and are free radical scavengers. The discovery of neuroprotective agents is becoming important as accumulating evidence indicates the protective role of both estrogen and progesterone in Hcy-induced neurodegeneration. Thus further work in clinical trials is needed to examine whether reducing Hcy levels with HRT can become the treatment of neurodegenerative disorders, such as Alzheimer’s disease.
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An investigation into the possible neuroprotective or neurotoxic properties of metrifonate
- Authors: Ramsunder, Adrusha
- Date: 2005 , 2013-06-11
- Subjects: Nervous system -- Degeneration -- Treatment , Neurotoxic agents , Alzheimer's disease -- Treatment , Metrifonate
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3833 , http://hdl.handle.net/10962/d1007560 , Nervous system -- Degeneration -- Treatment , Neurotoxic agents , Alzheimer's disease -- Treatment , Metrifonate
- Description: Alzheimer's disease is a progressive neurodegenerative disorder, in which there is a marked decline in neurotransmitters, especially those of the cholinergic pathways. One of the approaches to the symptomatic treatment of Alzheimer's disease is the inhibition of the breakdown of the neurotransmitter acetylcholine, using an acetylcholinesterase inhibitor. One such drug tested, is the organophosphate, metrifonate. Any drug used for the treatment of neurodegenerative disorders should preferably not induce further neurological damage. Thus, in the present study, we investigated whether or not metrifonate is neuroprotective. The in vivo and in vitro effect of this drug on free radicals generation shows that metrifonate increases the level ofthese reactive species. Lipid peroxidation induced using quinolinic acid (QA) and iron (II) and show that metrifonate increased the peroxidative damage induced by using quinolinic acid. Metrifonate is also able to induce lipid peroxidation both in vivo and in vitro. This was reduced in vitro in the presence of melatonin. Using iron (II), in vi/ro, there was no significant difference in the level of lipid peroxidation in the presence of this drug. An investigation of the activity of the mitochondrial electron transport chain and complex I of the electron transport chain in the presence of metrifonate revealed that metrifonate reduces the activity of the electron transport chain at the level of complex I. The activity of the mitochondrial electron transport chain was restored in the presence of melatonin. Pineal organ culture showed that metrifonate does not increase melatonin production. Histological and apoptosis studies show that tissue necrosis and apoptosis respectively, occur in the presence of this agent, which is reduced in the presence of melatonin. Metal binding studies were performed USing ultraviolet spectroscopy, and electrochemical analysis to examine the interaction of metrifonate with iron (II) and iron (III). No shift in the peak was observed in the ultraviolet spectrum when iron (ll) was added to metrifonate. Electrochemical studies show that there may be a very weak or no ligand formed between the metal and drug. This study shows that while drugs such as metrifonate may be beneficial in restoring cognitive function in Alzheimer's disease, it could also have the potential to enhance neurodegeneration, thus worsening the condition, in the long term. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
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Cimetidine as a free radical scavenger
- Authors: Lambat, Zaynab Yusuf
- Date: 2003
- Subjects: Cimetidine , Cimetidine -- Physiological effect , Cimetidine -- Therapeutic use , Alzheimer's disease -- Treatment , Cancer -- Treatment , Free radicals (Chemistry) -- Physiological effect
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3766 , http://hdl.handle.net/10962/d1003244 , Cimetidine , Cimetidine -- Physiological effect , Cimetidine -- Therapeutic use , Alzheimer's disease -- Treatment , Cancer -- Treatment , Free radicals (Chemistry) -- Physiological effect
- Description: The present study was undertaken to determine the effects and possible mechanism of action of cimetidine in cancer and Alzheimer’s disease (AD). Throughout this study emphasis is placed on free radical levels since the magnitude of the relationship between diseases and the levels of free radicals vary from one disease to another. Studies were carried out to examine the effect of cimetidine on free radical levels using superoxide formation and lipid peroxidation as indicators of free radical levels. The experiments revealed that addition of cimetidine, especially in high concentrations (0.5 and 1.0 x10-6 M) significantly inhibited WHCO6 cancer cell growth rather than cancer cell growth, as no normal control was available. Free radical formation as well as hydroxyl radical formation were reduced in the deoxyribose assay. In addition, cimetidine exhibits properties of binding to metals such as copper and iron. To maintain consistency in the experiments, a WHCO6 (Wits Human Carcinoma of the Oesophagus) cell line was used to investigate the effect of cimetidine in cancer. Neurodegeneration was induced in the rat brain using neurotoxins such as cyanide to investigate the relationship between cimetidine in AD. A decrease in cancer cell growth was accompanied by a concomitant decrease in the levels of free radicals and lipid peroxidation, suggesting that the growth-inhibitory effects of cimetidine on WHCO6 cancer cells in vitro may be due to free radical scavenging properties. This proposal was further strengthened by determination of free radical levels in the rat brain. After treatment with neurotoxins to induce neurodegeneration, the levels of free radicals in the rat brain suggest that addition of cimetidine reduces free radical levels in the rat brain in a dosedependent manner. Further experiments were done in an attempt to uncover the underlying mechanism by which cimetidine exhibits free radical scavenging properties. Metal binding studies were done using electrochemical, HPLC and UV/Vis studies. The results show that cimetidine binds iron and copper. These metals have been implicated in free radical production via the Fenton reaction. By binding with cimetidine the metals become unavailable to produce free radicals and hence cimetidine indirectly reduces the formation of free radicals. The final experiment was the determination of cimetidine as a hydroxyl radical scavenger in the deoxyribose assay. Cimetidine was shown to act as a potent hydroxyl radical scavenger, thereby confirming its activity as a free radical scavenger. In addition, cimetidine protects against damage to the deoxyribose sugar, a component of DNA. Whilst there are many theories that explain the therapeutic role of cimetidine in degenerative disease, the actual mechanism of the role of cimetidine is emphasized as a free radical scavenger. Regardless of the mechanism of action, cimetidine does inhibit tumour growth according to this study and also reduce free radical levels in neurodegeneration, which suggests a role for cimetidine as a possible additive in treatment of patients with such disease states. These findings have important clinical implications, and needs to be investigated further.
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