|
|
Development of pharmacophore-guided molecular docking protocol for design of SARS-CoV-2 main protease inhibitors
Klenor, Mikuláš ; Lepšík, Martin (advisor) ; Riedlová, Kamila (referee)
Covid-19 is a highly contagious potentially life-threatening disease caused by the SARS-CoV-2 coronavirus. The virus is responsible for a global pandemic and has claimed over 6 million human lives between years 2020 and 2022. To limit the spread of SARS-CoV-2, numerous vaccines have been developed and applied. For already infected individuals, antiviral drugs are applied. An important validated target is the main protease of SARS-CoV-2 (Mpro ). Although thousands of inhibitors have been prepared and one is used in clinical practice (sold under the name of Paxlovid), improved computational protocols to design new active compounds are needed. The computational approach used here is based on pharmacophores. By curating and inspecting 298 structures of Mpro /inhibitors complexes retrieved from the Protein Data Bank (PDB), we have generated six distinct pharmacophores featuring different binding modes. With their aid, we have carried out molecular docking, whose effectiveness was evaluated by measuring root-mean-square deviation (RMSD) of the generated poses with respect to the native conformations. The routine captured 177 out of 213 ligands naturally binding to the active site of the protein with 127 (72% of the captured) generated with RMSD within 2 Å relative to the native conformation....
|
|
|
Extraction of spontaneously occurring activity patterns from an electrophysiological signal
Voldřich, Matěj ; Korvasová, Karolína (advisor) ; Riedlová, Kamila (referee)
To be able to elicit desired percepts using a cortical visual prosthesis, is it essential to understand the functional structure of the neural network under the implant. However, in a blind individual the functional proper- ties of neurons cannot be measured by recording responses to visual stimuli and information can only be extracted from spontaneous activity. Spon- taneous activity in the primary visual cortex (V1) of anesthetized primates has been shown to encode information about local functional architecture of the neural network. Particularly, inference of the orientation-preference map from spontaneous activity has been achieved in non-human animals using in- vasive imaging techniques that are not intended for applications in humans. Whether the same inference is possible with spatially sparse electrophysiolo- gical recordings from a micro-electrode array that is currently used as a cortical visual prosthesis remains unknown. The aim of this thesis is to use automatic spatial pattern detection algorithm for orientation preference map inference from spontaneous activity and compare outcomes using four differ- ent variables extracted from signal recorded with intracranial micro-electrode arrays in awake macaque monkeys. 1
|
|
|
Counterion condensation on a polyelectrolyte: A fluorescence quenching study
Riedlová, Kamila ; Štěpánek, Miroslav (advisor) ; Humpolíčková, Jana (referee)
In this thesis, we studied the counterion condensation on the polyelectrolyte chain by means of the fluorescence quenching technique, using poly(methacrylic acid) (PMAA) labelled by the naphthyl group either at the end or in the middle of the chain and cesium ions as counterions which act as the fluorescence quencher. Both polymer samples were characterized by dynamic light scattering. The interaction of Cs+ ions with the polyelectrolyte was studied in solvents differing in the dielectric permittivity, using mixtures of water with 1,4-dioxane. The results confirm that fluorescence quenching is enhanced by the counterion condensation and that this process is more pronounced in the case of the naphthyl moiety localized in the middle of the PMAA chain.
|
|
|
Determination of the structure of pore-forming colicins
Riedlová, Kamila ; Fišer, Radovan (advisor) ; Barvík, Ivan (referee)
6 Abstract This master's thesis provides study of individual helixes from C-terminal pore-forming domain (CTD) of colicin U and their behavior in lipid bilayer on atomic level. For this purpose the all-atom molecular simulation method was used. Later the study was extended an applied on CTD of published structures of other pore-forming colicins. On the base of study extension the ability of disruption of lipid bilayer integrity by helixes H1 and H10 was successfully observed. Helix H1 was synthesized and its activity was experimentally proved on black lipid membranes. The other helixes are often too short to be able to keep position in lipid bilayer and their behavior could be affected by artificial termini, therefore they were not synthesized. The MD simulations of pairs of helixes show that structure stability and their ability to stay in the membrane depends on binding partners. The results of the thesis show the importance of H10 for colicin pore-formation, which has not been observed yet. The results also support the toroidal pore model suggested previously for colicin E1. The results prove that colicins contain specific secondary structures, which are able to disrupt the inner bacterial membrane not only in its native form but also when artificially separated from the rest of the protein. Klíčová...
|
|
|
Counterion condensation on a polyelectrolyte: A fluorescence quenching study
Riedlová, Kamila ; Štěpánek, Miroslav (advisor) ; Humpolíčková, Jana (referee)
In this thesis, we studied the counterion condensation on the polyelectrolyte chain by means of the fluorescence quenching technique, using poly(methacrylic acid) (PMAA) labelled by the naphthyl group either at the end or in the middle of the chain and cesium ions as counterions which act as the fluorescence quencher. Both polymer samples were characterized by dynamic light scattering. The interaction of Cs+ ions with the polyelectrolyte was studied in solvents differing in the dielectric permittivity, using mixtures of water with 1,4-dioxane. The results confirm that fluorescence quenching is enhanced by the counterion condensation and that this process is more pronounced in the case of the naphthyl moiety localized in the middle of the PMAA chain.
|
|
|
Simulation of the interaction of steroid allosteric modulators of NMDA receptors with membrane
Riedlová, Kamila ; Konopásek, Ivo (advisor) ; Novák, Josef (referee)
Molecular dynamics (MD) method allows the real-time monitoring of the system composed of molecules and atoms, such as phospholipid bilayer or biomolecule. Applications of MD are very common in drug design where the real experimental procedures could be much more financially- and time-consuming or even impossible. The aim of this project is to explain the applications and advantages of MD method in case of studies of lipid membranes, with a special emphasis on a study od neurosteriod behaviour in lipid bilayer. Properly designed and synthesized neurosteroids could be used for the treatment of the serious neurological diseases. This work also included the experimental data obtained by MD simulations for two neurosteroids - pregnanolone glutamate and pregnanolone sulphate. Behaviour of this molecules in model membranes was observed and analyzed by MD simulations. Key words: molecular dynamics simulation, model membrane, lipid bilayer, NMDA receptor, neurosteroids, pregnanolone glutamate, pregnanolone sulfate
|
guest ::
RSS feed.