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Large-Scale Analysis of the Ligand Transport and Docking inside of the Protein Tunels
Ježík, Andrej ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis discusses large-scale analysis of the ligand transport and docking inside of the protein tunnels. Protein-ligand interactions are involved in processes such as cell signalling, transport, metabolism, regulation, gene expression, and enzyme activity. To understand the interaction between these molecules is vitally important for the research for new pharmaceuticals. The procedure of protein-ligand docking involves the following steps: (i) finding the structures of proteins (receptors) and ligands, (ii) identifying ligand binding sites, (iii) considering receptor/ligand flexibility, and (iv) computing interaction energy between the receptor and the ligand. Additional functionality will be implemented to allow CaverWeb to test a complete set of pre-processed drug ligands on a protein, in an effort to enhance the efficiency of the procedure for large sets of ligands, which will allow a much smoother workflow.
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Studium konformačních efektů vazby ligandu na proteinovou strukturu
Šefců, Oskar ; Novotný, Marian (advisor) ; Hexnerová, Rozálie (referee)
This bachelor thesis aims to provide a comprehensive overview of the effects of ligand binding on the 3D structure of proteins. The focus will be on examples where ligand binding causes a significant conformational change between the structure without the ligand (apo structure) and the structure with the ligand (holo-structure). The thesis will discuss various techniques used to determine the structural changes caused by ligand binding, including X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. Furthermore, the thesis will provide insight into the structural and functional implications of ligand-induced conformational changes in proteins. Overall, this thesis will serve as a resource for understanding the role of ligand binding in modulating the 3D structure of proteins. Keywords: apo, holo, ligand, conformational change, IDP
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Design and synthesis of a potential orexin receptor OX2R modulator with the use of in silico methods
Kárová, Barbora ; Doležal, Rafael (advisor) ; Kolář, Karel (referee)
Orexinergic nervous system is a complex of neurons playing a significant role in managing sleep cycle and food intake. Orexin neurons situated in the lateral hypothalamus produce orexin neuropeptides A and B, which interact with two orexin receptors in a broad range of neurons in the brain. A reduced production of these neuropeptides due to the loss of orexin neurons is the cause of a specific and rare disease narcolepsy, which is currently incurable. A significant milestone in terms of drug research and development against narcolepsy is a study of Takashi Nagaraha's scientific group (2015), which was the first one to synthesize a non-peptidic agonist of the orexin 2 receptor (OX2R) that has inspired further design of new drug candidates with an increased chance to reach the clinical practice. This Bachelor Thesis is focused on the design and organic synthesis of a novel OX2R agonist with a 2-deoxystreptamine substructure and follows the Nagahara's study using rational and computer-aided drug design. The theoretical part is dedicated to the literature review of this issue, the practical part focuses on the design of 11 ligands using in silico and medicinal chemistry methods. The organic synthesis was then proposed, based on a retrosynthetic analysis, for the final candidate with the optimal...
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Screening of selected alkaloids of Fumariaceae and Amaryllidaceae families on Farnesoid X receptor and the G protein-coupled bile acid receptor 1
Hutníková, Miriama ; Pávek, Petr (advisor) ; Chlebek, Jakub (referee)
Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Miriama Hutníková Supervisor: Prof. PharmDr. Petr Pávek, PhD. Title of diploma thesis: Screening of selected alkaloids of Fumariaceae and Amaryllidaceae families on the farnesoid X receptor and the G protein coupled receptor 1 Farnesoid X receptor (FXR) and bile acid receptor associated with G protein 1 (TGR5) significantly affect metabolic processes in the human body. The role of FXR in neuronal apoptosis in Alzheimer's disease (AD) has also been discovered. The possible structural similarity of the small lipophilic molecules binding to these receptors and the alkaloids found in the plants Corydalis cava and Narcissus pseudonarcissus, as well as the richoften use of these plants in traditional medicine, represent a potential therapeutic intervention for these molecules. In our screening methods, we performed tests using a luciferase gene reporter assay to determine the ability of the alkaloids to interact with FXR and TGR5 in the HepG2 cell line. Many derivatives have shown a strong ability to antagonize FXR and TGR5 activated by obethicholic (OCA) or litocholic (LCA) acids in this assay. Some of the compounds also demonstrated the ability to potentiate the effects of OCA or LCA. Cytotoxicity...
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Screening of selected alkaloids of Fumariaceae and Amaryllidaceae families on Farnesoid X receptor and the G protein-coupled bile acid receptor 1
Hutníková, Miriama ; Pávek, Petr (advisor) ; Chlebek, Jakub (referee)
Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Miriama Hutníková Supervisor: Prof. PharmDr. Petr Pávek, PhD. Title of diploma thesis: Screening of selected alkaloids of Fumariaceae and Amaryllidaceae families on the farnesoid X receptor and the G protein coupled receptor 1 Farnesoid X receptor (FXR) and bile acid receptor associated with G protein 1 (TGR5) significantly affect metabolic processes in the human body. The role of FXR in neuronal apoptosis in Alzheimer's disease (AD) has also been discovered. The possible structural similarity of the small lipophilic molecules binding to these receptors and the alkaloids found in the plants Corydalis cava and Narcissus pseudonarcissus, as well as the richoften use of these plants in traditional medicine, represent a potential therapeutic intervention for these molecules. In our screening methods, we performed tests using a luciferase gene reporter assay to determine the ability of the alkaloids to interact with FXR and TGR5 in the HepG2 cell line. Many derivatives have shown a strong ability to antagonize FXR and TGR5 activated by obethicholic (OCA) or litocholic (LCA) acids in this assay. Some of the compounds also demonstrated the ability to potentiate the effects of OCA or LCA. Cytotoxicity...
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Bifunctional chelators for selective copper(II) binding
Paúrová, Monika ; Kotek, Jan (advisor) ; Vojtíšek, Pavel (referee)
Title: Bifunctional chelators for selective copper(II) binding Autor: Bc. Monika Paúrová Department: Department of Inorganic Chemistry, Faculty of Science Supervisor: doc. RNDr. Jan Kotek, Ph.D. Supervisor's e-mail: modrej@natur.cuni.cz Abstract: In this Master thesis, cyclam bifunctional derivatives bearing pendant phosphinate groups (4-methyl-11-p-aminobenzyl-1,4,8,11-tetraazacyclotetradecane-1,8- bis(methylenephosphinic acid)) and phosphonate groups (4-methyl-11-p-aminobenzyl- 1,4,8,11-tetraazacyclotetradecane-1,8-bis(methylenephosphonic acid)), were prepared and studied as potential ligands for complexation of divalent copper. These ligands are suitable for binding to a macromolecular carrier. Keywords: radiomedicine, copper, cyclam, chelating agent, phosphinate, phosphonate, kinetic inertness, kinetic lability, thermodynamic stability
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Large-Scale Analysis of the Ligand Transport and Docking inside of the Protein Tunels
Ježík, Andrej ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis discusses large-scale analysis of the ligand transport and docking inside of the protein tunnels. Protein-ligand interactions are involved in processes such as cell signalling, transport, metabolism, regulation, gene expression, and enzyme activity. To understand the interaction between these molecules is vitally important for the research for new pharmaceuticals. The procedure of protein-ligand docking involves the following steps: (i) finding the structures of proteins (receptors) and ligands, (ii) identifying ligand binding sites, (iii) considering receptor/ligand flexibility, and (iv) computing interaction energy between the receptor and the ligand. Additional functionality will be implemented to allow CaverWeb to test a complete set of pre-processed drug ligands on a protein, in an effort to enhance the efficiency of the procedure for large sets of ligands, which will allow a much smoother workflow.
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Interaction of a surface marker of immune cells with low-molecular weight ligands and their polymer conjugates
Šimonová, Lenka ; Konvalinka, Jan (advisor) ; Obšil, Tomáš (referee)
Millions of people worldwide die of cancer every year. In the last decade, im- munotherapy offered new treatment options achieving long-lasting remissions in a number of patients. Several new immunotherapy-based drugs have been ap- proved by Food and Drug Administration. However, majority of patients either do not respond or soon relapse. Combination of therapies as well as exploring new immune checkpoints seems promising. This thesis focuses on the new immunotherapeutic target CD73. CD73 is membrane ectonucleotidase, widely expressed on the regulatory leukocytes and on cancer cells. The enzymatically active CD73 contributes to the tumour mi- croenvironment by production of immunosuppressive adenosine. This novel im- mune checkpoint is being intensively studied. This thesis aims on development of new approaches for targeting and inhibition of CD73. Soluble recombinant CD73 (rhCD73) was prepared in mammalian expression system and transfectants stably expressing membrane-bound CD73 were prepared as well. Inhibitors necessary for both of my goals have been designed based on published inhibitor of CD73. Development and evaluation of novel antibody mimetic for CD73 characteri- sation was done. The so-called iBody, HPMA polymer conjugate decorated with CD73 inhibitor for targeting, fluorophore for...
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Interaction of a surface marker of immune cells with low-molecular weight ligands and their polymer conjugates
Šimonová, Lenka ; Konvalinka, Jan (advisor) ; Obšil, Tomáš (referee)
Millions of people worldwide die of cancer every year. In the last decade, im- munotherapy offered new treatment options achieving long-lasting remissions in a number of patients. Several new immunotherapy-based drugs have been ap- proved by Food and Drug Administration. However, majority of patients either do not respond or soon relapse. Combination of therapies as well as exploring new immune checkpoints seems promising. This thesis focuses on the new immunotherapeutic target CD73. CD73 is membrane ectonucleotidase, widely expressed on the regulatory leukocytes and on cancer cells. The enzymatically active CD73 contributes to the tumour mi- croenvironment by production of immunosuppressive adenosine. This novel im- mune checkpoint is being intensively studied. This thesis aims on development of new approaches for targeting and inhibition of CD73. Soluble recombinant CD73 (rhCD73) was prepared in mammalian expression system and transfectants stably expressing membrane-bound CD73 were prepared as well. Inhibitors necessary for both of my goals have been designed based on published inhibitor of CD73. Development and evaluation of novel antibody mimetic for CD73 characteri- sation was done. The so-called iBody, HPMA polymer conjugate decorated with CD73 inhibitor for targeting, fluorophore for...
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Determination of binding constants of human insulin complexes with serotonin, dopamine, arginine, and phenol by pressure assisted partial filling affinity capillary electrophoresis
Šolínová, Veronika ; Žáková, Lenka ; Jiráček, Jiří ; Kašička, Václav
A new method, pressure assisted partial filling affinity capillary electrophoresis (PF-ACE), has been developed to study noncovalent interactions of the hexamer of human insulin (HI) with cationic ligands, such as phenolic neurotransmitters serotonin and dopamine, and amino acid arginine, or with anionic ligand phenol, in alkaline aqueous solutions. The apparent binding constants, Kb, of the HI-ligand complexes were determined from the dependence of the effective migration time changes of the above ligands on the variable zone lengths of HI dissolved in the background electrolyte and hydrodynamically introduced into the bare fused silica capillary close to the UV detector. The HI interactions with the above ligands were found to be moderately strong, with Kb values in the range 385-1314 L/mol.
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