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Design and evaluation of potential viral methyltransferase inhibitors
Kocek, Hugo ; Nencka, Radim (advisor) ; Grantz Šašková, Klára (referee)
A global pandemic of SARS-CoV-2 confirmed the pandemic potential of the Coronaviridae family and pointed out the need for novel antiviral drugs. The SARS-CoV-2 pandemic has been tamed thanks to mRNA vaccines; however, monoclonal antibodies and small molecules such as nirmatrelvir (protease inhibitor), remdesivir (polymerase inhibitor), or molnupiravir (mutagen) are currently also available. It is worth noting that remdesivir and molnupiravir were previously investigated as antivirals against different pathogens. SARS-CoV-2 encodes 16 non-structural proteins, and two of them - methyltransferases (MTases) nsp14 and nsp16 - participate in RNA capping as the virus must mimic the host's mRNA to evade the cellular antiviral sensors (e.g., IFIT1) and replicate. These MTases are structurally very similar to those of SARS-Co-V; therefore, we might expect that inhibitors of SARS-CoV-2 MTases could be used in the future against different coronaviruses. For the reasons mentioned above, this thesis focuses on developing novel MTase inhibitors targeting SARS-CoV-2 nsp14 and nsp16. The design was based on S-adenosyl-L-homocysteine (SAH; endogenous inhibitor of MTases) and an in silico compound library was constructed with various replacements for SAH's amino acid moiety. The potential inhibitory activity was...
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Synthesis of novel viral methyltransferase inhibitors
Kocek, Hugo ; Nencka, Radim (advisor) ; Česnek, Michal (referee)
Methyltransferases (MTases) are a class of enzymes that catalyze methylation of their substrates. These enzymes are found in all living organisms (including some viruses) as methylations are involved in numerous biological processes. Therefore, MTases are attractive targets for medicinal chemistry. Currently, only inhibitors of human MTases are used in medicine, for example, 5-azacytidine targeting DNA-MTase. However, viral MTases are potential drug targets as well. They enable viruses to escape the immune system and to use the host's translation machinery. As a consequence of the SARS-CoV-2 pandemic, coronaviral MTases became the center of attention, followed by the Mpox virus, which spread in the population in 2022. This thesis is focused on the synthesis of potential MTase inhibitors derived from adenosine-5'-carboxylic acid. The primary target is SARS-CoV-2 nsp14, however, the compound library will be used for screening against other MTases as well. Key words: methyltransferase; inhibitor; SARS-CoV-2; medicinal chemistry
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Viral proteins that facilitate RNA replication
Černý, Prokop ; Bouřa, Evžen (advisor) ; Faltová, Lenka (referee)
In recent years, the pathogenic human coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has caused a global pandemic of highly infectious disease COVID--19 (coronavirus disease 2019). According to the World Health Organization, as of August 20, 2023, there have been nearly 770 million confirmed cases and nearly 7 million deaths associated with the disease. However, only a small number of effective antiviral drugs are currently known to help treat the disease in already infected patients. Therefore, in this work, the interaction of host 14-3-3 proteins with the nucleocapsid protein of SARS-CoV-2 was studied as a potential biological target for the rational design of new antiviral drugs. The importance of this interaction in the virus life cycle has not been fully elucidated, but it probably has an important regulatory function affecting multiple processes in the infected cell. The SARS-CoV-2 N protein contains several binding motifs for 14-3-3 proteins in its sequence, two of which (at positions S197 and T205), most likely responsible for the protein- protein interaction, were studied in this work. Microscale thermophoresis was performed to determine the affinity of each of these phosphorylation sites on the nucleoprotein for the 14-3-3ζ protein. The key phosphorylated residue...
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The effect of the COVID 19 infection on the respiratory and cardiovascular system, physical stress during the course of the disease
Doležalová, Anna ; Heller, Jan (advisor) ; Šteffl, Michal (referee)
Title: Impact of the COVID 19 infection on the respiratory and cardiovascular system, physical strain during the course of the disease Aims: The primary aim of this thesis is to find and study the latest relevant findings regarding the impact of COVID 19 infection on the respiratory system, cardiovascular system and the effect of physical strain on the course of this disease. Subsequently, to write down a critical review on the topic. Methods: A literature review on the impact of COVID 19 infection on the respiratory system, the cardiovascular system and the effect of physical strain on the course of the disease. Results: The impact of the COVID 19 infection on the respiratory system is considerable. The disease can be asymptomatic or with only mild symptoms, typically shortness of breath and cough. The main manifestation of a developed infection is bilateral covid pneumonia, which progresses to ARDS in approximately 20-30% of hospitalized patients. The impact of the disease on the cardiovascular system is increasingly debated. Sources describe elevation of troponin in the serum, as an indicator of myocardial damage, in up to 12% of all cases. It can manifest as myocarditis, arrhythmias, myocardial infarction, cardiogenic shock or even heart failure. The infection of COVID 19 is a multisystem...
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Spatial-temporal epidemiologic models of Covid-19
Schubert, Richard ; Ředina, Richard (referee) ; Mézl, Martin (advisor)
This work aims to establish a fundamental framework for studying spatially diffusive models that describe the dynamics of infectious disease spread with constant parameters in a homogeneous domain. Initially, compartmental models and their extension to spatial domains are examined, followed by the theory of metapopulation models, where the degree of coupling between populations and the overall reproductive number R0 is discussed. Furthermore, the relationship between R0 and the shape of the spatial distribution of infected individuals in a simple diffusive SIR model is modeled. The influence of Neumann boundary conditions versus Dirichlet boundary conditions on R0 is demonstrated. In the second part of the work, selected findings and conclusions of studies that applied models in the spatiotemporal domain to analyze and predict the COVID-19 pandemic are summarized. In the third part of the work, a model with diffusive and metapopulation elements is fitted to epidemiological data from Lombardy in 2020, and the suitability of this approach is discussed.
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Analysis and possibilities of support for health care workers during the current crisis situation with Covid-19
MRÁZKOVÁ, Vendula
COVID-19 disease is caused by a new type of coronavirus SARS-CoV-2. On 1. 12. 2021 the Czech Republic was in the 5th degree of emergency or in a critical state of the anti-epidemic system. The critical situation means that the capacity of the hospital inpatient and intensive care system is beginning to approach its limit, the number of people infected in the population is high and there is a community spread of the disease. On 8th of December 2021, statistics shown 19 482 new cases of COVID-19, a total of 2 282 212 confirmed cases, 6 670 hospitalized residents, 1 963 455 cured, 14 031 605 reported vaccines and 34 034 deaths in Czech republic. As of 20 January 2023, the WHO has published a total of 663 640 386 confirmed cases with COVID-19 and 6 713 093 deaths in the world between 31. 12. 2019 and 16. 1. 2023. The current coronavirus disease has a global impact, but healthcare professionals play a vital role and are one of the most exposed groups. Stress in mental health of nursing has long been recognized as an impact on individual performance, illness and job retention. Since the beginning of the pandemic, health professionals have struggled to work harder, are at risk of transmitting the infection to themselves and their loved ones, so they are often separated from them. They experience discomfort due to the use of more protective equipment. Further more, they are exposed to stressful situations, when a large number of young and older people die due to insufficient capacity of beds and ventilators, they decide on human lives, and who will be given priority care. Therefore, it is natural for employees, that they are getting to be depressed, scared, anxious, irritable, sleep deprived or use alcohol.
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Simulation of Spread of Infectious Diseases in Human Population
Křištof, Jiří ; Šimek, Václav (referee) ; Strnadel, Josef (advisor)
The aim of this work is to develop an epidemiological model to simulate the spread of the infectious disease covid-19. The developed SVLIHDRS model builds on compartmental models and is implemented as a Markov chain with continuous time. For the implementation, the UPPAAL tool is used. By comparing the simulation outputs with the observed data, the Spearman coefficients are 0.8940 for infectious individuals and 0.9987 for deceased individuals, the mean bias errors are 12510.7285 and 316.2697, respectively. The results of this thesis are useful for making long-term predictions of the epidemic evolution of covid-19 infection.
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Studies of precursor forms of SARS-CoV-2 3-CL protease
Nováková, Veronika ; Majerová, Taťána (advisor) ; Novotný, Marian (referee)
The SARS-CoV-2 virus (Severe acute respiratory syndrome coronavirus 2), the causative agent of the disease COVID-19 (coronavirus disease 2019), is an enveloped virus with a positive RNA genome. After the binding of the virus to the cell receptor and the release of the genome into the cytoplasm, the viral genome is immediately translated. It is translated into a polyprotein consisting of non-structural proteins necessary for viral replication. A part of this polyprotein is also protease 3-CL, which autocatalytically cleaves itself out from this polyprotein and further releases (and thus activates) individual proteins. Due to this key function in virus replication, 3-CL protease has become an important target for the design of specific antiviral drugs. As part of this thesis, we focused on the study of the precursor form of this protease, i.e. the protease that is still embedded in the polyprotein. The precursor form of the 3-CL protease was mimicked by attaching a 100 amino acid extramembrane C-terminal fragment of the nsp4 protein to the N-terminus of the mature form of the protease. The aim was to find out, how the sequence added to the N-terminus of the matured protease affects its enzymatic characteristics. As a part of this work, mutations of the N-terminal autoprocessing site were identified,...
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Spatial-temporal epidemiologic models of Covid-19
Schubert, Richard ; Ředina, Richard (referee) ; Mézl, Martin (advisor)
This work aims to establish a fundamental framework for studying spatially diffusive models that describe the dynamics of infectious disease spread with constant parameters in a homogeneous domain. Initially, compartmental models and their extension to spatial domains are examined, followed by the theory of metapopulation models, where the degree of coupling between populations and the overall reproductive number R0 is discussed. Furthermore, the relationship between R0 and the shape of the spatial distribution of infected individuals in a simple diffusive SIR model is modeled. The influence of Neumann boundary conditions versus Dirichlet boundary conditions on R0 is demonstrated. In the second part of the work, selected findings and conclusions of studies that applied models in the spatiotemporal domain to analyze and predict the COVID-19 pandemic are summarized. In the third part of the work, a model with diffusive and metapopulation elements is fitted to epidemiological data from Lombardy in 2020, and the suitability of this approach is discussed.
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Monogenic susceptibility to infectious pathogens
Bloomfield, Markéta ; Šedivá, Anna (advisor) ; Koziar Vašáková, Martina (referee) ; Litzman, Jiří (referee)
(ENG) The modern approach to studies of monogenic inborn errors of immunity, driven by unprecedented advances of genetic tools, opens vast undiscovered areas of immune system components and functions. In particular, the diseases with striking clinical phenotypes with normal or near normal baseline immunophenotype, such as disorders of innate and intrinsic immunity with susceptibility to single pathogen, provide a unique window into the host-pathogen interactions. This thesis covers various novel aspects of immunopathology, genetics and clinical facets behind some such diseases, namely chronic mucocutaneous candidiasis due to hypermorphic (gain-of-function, GOF) STAT1 mutations, which hamper Th17-associated immune activities, and Mendelian susceptibility to mycobacterial diseases (MSMD) due to impairment of IL-12, IL-23/IFNγ signalling pathway. Moreover, it contributes to the mounting evidence that IL- 6 signalling is non-redundant in anti-staphylococcal immunity. Finally, it explores the novel Paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS- TS) as a single pathogen-driven life-threatening immunopathology, which most likely develops due to individual, yet unknown, genetic predisposition. The findings presented in this thesis were in several cases translated...
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