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Synthesis of new nucleosides as potential inhibitors of flaviviral replication
Horkelová, Simona ; Nencka, Radim (advisor) ; Janeba, Zlatko (referee)
Viruses of the Flaviviridae family are the causative agents of many dangerous diseases for which we currently have no known cure, and research into new drugs against them therefore represents one of the major challenges for modern medicinal chemistry. Targeting the proteins encoded by viruses is the most common approach to combat them. For flaviviruses, the non- structural protein NS5 exhibiting methyltransferase (MTase) and RNA-dependent-RNA polymerase (RdRp) enzyme activity appears to be one of the most suitable molecular targets. This bachelor thesis deals with the synthesis of new potential drugs capable of inhibition skill of flaviviral RdRp. C-nucleoside analogues were prepared, containing 2 types of heterocyclical base: 3-fluoropicolamide modified in positions 5 or 6 and pyrido[3,2-d]pyrimidine-4-amine modified in positions 6 or 7 using aryl or heteroaromatic substituent Key words: C-nucleosides, polymerase, flaviviruses, Tick-borne encephalitis virus, Suzuki reaction, Grignard reaction
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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Structural and functional characterization of a flaviviral methyltransferase.
Todd, Matthew Zagorey ; Bouřa, Evžen (advisor) ; Honzejková, Karolína (referee)
Genus flavivirus, member of the Flaviviridae family, is a wide-spread group of viral pathogens that pose a global threat to human health. Infections result in neurological and other diseases such as encephalitis, meningitis, microcephaly or haemorrhagic fever with direct anti-viral treatment restricted to only a few members including Yellow Fever Virus (YFV) and Japanese Encephalitis Virus (JEV). The flaviviral genome consists of a positive sense single-strand RNA, translated into a long viral polyprotein cleaved by host and viral proteases into structural and non-structural proteins. Non-structural protein 5 (NS5) is a highly conserved viral protein consisting of a C-terminal RNA-dependent RNA-polymerase (RdRp) and N-terminal methyltransferase (MTase) domain. Flaviviral MTases catalyse the final step of genomic RNA cap formation, that plays a crucial role in viral translation, replication and host immune system evasion. Due to its conservative nature, the flaviviral MTase is a promising drug target. It's structural analysis is needed for the development of broad-spectrum inhibitors and anti-viral treatment. Key words Flavivirus, St. Louis Encephalitis Virus, Flaviviral methyltransferase (MTase), N-7 methylation, 2'-O methylation.
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Structural and functional characterization of a flaviviral methyltransferase
Kúdelová, Veronika ; Bouřa, Evžen (advisor) ; Faltová, Lenka (referee)
Recently, non-cellular viral agents became the focus of a large number of scientific groups. A prominent and widespread group of these viruses are flaviviruses, which include, for example, Zika virus, Dengue fever virus, tick-borne encephalitis virus and West Nile virus. There is a considerable diversity among these viruses, however, highly conserved proteins can be found throughout this viral genus. The largest and most conserved protein encoded by flaviviruses is the nonstructural NS5 protein. Its N-terminal domain bears the methyltransferase (MTase) activity. Thanks to the methylation of its genome, it allows the virus to initiate translation and at the same time mask it from the host's immune system. By blocking the active site of this enzyme with a small molecule, viral infection could be stopped not only in one flavivirus, but, due to the high conservation of MTases, in all other flaviviruses. This diploma thesis deals with the aforementioned MTase domain of the NS5 protein, specifically of the West Nile virus (WNV). After designing an insert encoding the WNV MTase domain, amplifying it and ligating it into the vector, the MTase domain was prepared by a recombinant expression, followed by purification. Subsequently, complexes of the protein with small molecules (MTase ligands) were formed, in...
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Structural and functional study of viral RNA polymerases
Dubánková, Anna
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Structural and functional study of viral RNA polymerases
Dubánková, Anna
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Preparation of fluorinated carbocyclic derivatives of nucleosides as potential viral replication inhibitors
Štefek, Milan ; Nencka, Radim (advisor) ; Šimák, Ondřej (referee)
This master thesis is dedicated to the preparation of fluorinated derivatives of carbocyclic nucleosides, that may serve as flaviviral replication inhibitors. Preparation of both monofluorinated as well as gem-difluorinated analogs of ribo and 2'-deoxyribonucleoside was attempted. While a suitable and reliable route for the preparation of monofluorinated compounds way found, synthesis of gem-difluorinated turned out to be rather challenging. Although most of the presented work dealt with compounds bearing adenine as a nucleobase, the universal applicability of the developed procedures, demonstrated on the preparation of a guanosine-type molecule, suggests that after slight optimization larger series of this type of compounds could be prepared.
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Interakce viru klíšťové encefalitidy s cytoskeletem hostitelských buněk
PRANČLOVÁ, Veronika
This thesis is focused on the role of host cytoskeleton, primarily microtubules and microfilaments, during tick-borne encephalitis virus infection in human neuroblastoma cell line SK-N-SH and tick cell line IRE/CTVM19. The importance of cytoskeletal integrity and dynamics to the viral replication cycle were examined using specific chemical inhibitors showing the virus utilizes studied structures in both cell lines. Immunofluorescence microscopy revealed structural changes in the actin cytoskeleton during late infection in SK-N-SH cells. Moreover, differences in expression of cytoskeleton-associated genes in both cell lines were compared. Several genes with up-regulated expression in SK-N-SH cells were identified during late infection.
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Synthesis of novel prodrugs for antiviral therapy
Štefek, Milan ; Nencka, Radim (advisor) ; Janeba, Zlatko (referee)
This bachelor thesis is dedicated to preparation of prodrugs derived from 2'-C- methyladenosine, which is a potent inhibitor of the RNA dependent RNA polymerase of flaviviruses. Prodrugs modifying 3' and 5' hydroxy groups able to deliver the drug to brain and were prepared. As targeting moieties tropine and the redox system trigonelline/1,4- dihydrotrigonelline were used. In the case of tropine a suitable method for the preparation of prodrugs was developed. Reliable procedure for performing the last step of synthesis of compounds utilizing the trigonelline redox system is yet to be discovered.
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