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Modified ribonucleotides as building blocks for enzymatic construction of functionalized RNA or as antiviral compounds
Milisavljević, Nemanja ; Hocek, Michal (advisor) ; Baszczyňski, Ondřej (referee) ; Krečmerová, Marcela (referee)
The aim of this thesis was to study the steric influence of the base-modified nucleoside triphosphates (NTPs) on the enzymatic incorporation into RNA, as well as to study their inhibitory effect on different viral RNA polymerases in vitro. Their parent nucleosides and prodrug derivatives were also prepared and their antiviral activity evaluated. In the first part of the thesis, NTPs bearing groups varying in size from small methyl and ethynyl substituents via medium-size phenyl and benzofuryl groups, up to large dibenzofuran ring were prepared. Aromatic substituents were installed via Suzuki coupling on iodinated triphosphates or, in the case of modified guanosines, by the phosphorylation of modified nucleosides. Methyl and ethynyl NTPs were prepared via Pd-catalyzed coupling with AlMe3 and Sonogashira coupling, respectively, followed by the phosphorylation of modified nucleoside. To examine their incorporation into RNA by T7 RNA polymerase, templates coding for 35mer RNA containing one, three or seven modifications were designed. Modified pyrimidine triphosphates worked well for all the sequences, while the biggest dibenzofuryl group was not accepted in the difficult sequence with seven modifications. In the case of AR TPs dibenzofuryl modification did not incorporate at all, while other...
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Study of redox reactions and adsorption of 4-nitrophenyl triazole labeled nucleosides and cresols on boron doped diamond electrodes for development of electroanalytical methods
Vosáhlová, Jana ; Schwarzová, Karolina (advisor) ; Havran, Luděk (referee) ; Navrátil, Tomáš (referee)
In this work, the application of boron-doped diamond electrodes with various surface pre- treatment were tested on selected oxidizable and reducible model compounds, specifically para and ortho cresols and 2'-deoxycytidine and 7-deazaadenosine labeled by 4-nitrophenyl triazole. The aim of the study was the investigation of electrochemical and adsorptive processes with respect to the development of electroanalytical methods of detection of the selected compounds, or utilization of boron-doped diamond electrodes as detectors in liquid-flow systems. Cresols were used as the model oxidizable compound. On O-terminated and polished boron- doped diamond electrodes, cresols provide oxidation signal owing to their oxidation to methylphenoxy radical at comparable potentials as on other carbon-based electrodes used as a reference in this work, i.e., glassy carbon electrode, pyrolytic graphite electrode, and carbon paste electrode. These carbon electrode materials show relatively high propensity to adsorption of reaction products, while such adsorption is minimal on boron-doped diamond. In situ anodic activation allows for a rapid regeneration of boron-doped diamond surface prior to each scan. A differential pulse voltammetric method that was developed with a detection limit of 0.61 mol∙l-1 to 2.97 mol∙l-1...
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Synthesis of fluorinated nucleosides
Nguyen, Van Hai ; Hocek, Michal (advisor) ; Baszczyňski, Ondřej (referee)
The key intermediate 6-amino-7-iodo-7-deazapurine 3'-deoxy-3'-fluororibonucleoside was synthesized using multistep sequence of several reactions, which started from the commercially available D-xylose and 6-chloro-7-deazapurine. The synthetic strategy was based on fluorination of sugar and glycosylation with corresponding nucleobase afterwards. The fluorination of 5-protected-1,2-isopropylidine xylose with different protecting groups at position 5 always led to elimination. It was later discovered that isopropylidine forces the conformation, which is unfavorable for substitution. During the extensive optimization it was also found out that DAST appears to be an optimal fluorinating agent. Fluorination was performed on 2,3-unprotected xylose, which was subsequently used for glycosylation. After several unsuccessful attempts on "protection group free" glycosylation, Vorbrüggen glycosylation was successful and gave desired 3'-fluoro nucleoside in good yield. However, benzoyl group had to be introduced into position 2'. The protected nucleoside was then aminated and simultaneously deproctected with solution of aqueous NH3 and 1,4-dioxane. The obtained key intermediate was used for synthesis of a small series of desired 6-amino-7-hetaryl nucleoside using Pd-catalyzed Suzuki reaction under aqueous...
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Development of new glycosylation methods for the synthesis of nucleosides
Downey, Alan Michael ; Hocek, Michal (advisor) ; Křen, Vladimír (referee) ; Kočovský, Pavel (referee)
As they make up DNA and RNA, nucleosides are considered the key to life. Synthetic nucleosides also constitute many drugs that treat viral infections and cancer. As a result, more efficient methods to access these crucial molecules would have implications that extend beyond a synthetic chemist's benchtop and into medicinal chemistry and medical research. One of the most challenging steps in the synthesis of nucleosides is the glycosylation step between the acceptor heterocycle (nucleobase) and the saccharide-based donor. Often to obtain satisfactory yield of this step with good regio- and stereochemical control the extensive use of protecting groups must be employed to squelch reactivity at unwanted reactive groups. Consequently, this process of protection−glycosylation−deprotection is laborious, inefficient, and often requires the use of toxic reagents. It would be, therefore, highly welcomed if new methodology to effect this glycosylation step was designed that reduces or removes the need to use protecting groups, but would still provide nucleosides in good yield, regio- and stereoselectively. Herein, this thesis presents my efforts into achieving this end. By employing modified Mitsunobu conditions, I determined that it is possible to directly glycosylate a nucleobase with D-ribose to afford...
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Modified nucleosides derived from pyrimido[4,5-b]indole
Konč, Juraj ; Hocek, Michal (advisor) ; Jindřich, Jindřich (referee)
Syntheses of two series of 2'-sugar-modified pyrimido[4,5-b]indole nucleosides were developed. The synthetic strategy was based on functional group transformations of the 2'-hydroxy group of the 3',5'-protected ribonucleoside. The key intermediate was prepared via stereoselective nucleobase anion glycosylation of the known 4,6-dichloropyrimido[4,5-b]indole nucleobase with 2,3-O-isopropylidene- 5-O-TBS-protected halogenose, subsequent deprotection under acidic conditions and protection of 3'- and 5'-hydroxy groups with Markiewicz reagent. Pyrimidoindole arabinonucleoside was then synthesized using a sequence of oxidation-reduction reactions of the 2'-hydroxy stereocenter. The synthesis of pyrimidoindole 2'-deoxy- 2'-fluororibonucleoside was achieved by stereoselective SN2 fluorination of the THP-protected arabinoside followed by acidic deprotection. For the biological activity testing, two series of 4-substituted arabinonucleosides and 2'-deoxy- 2'-fluororibonucleosides were synthesized employing nucleophilic substitution or Pd-catalyzed cross-coupling reactions.
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Synthesis of novel C-nucleosides with modified sugar
Havlíček, Vojtěch ; Hocek, Michal (advisor) ; Janeba, Zlatko (referee)
In this bachelor thesis, a new method of preparation of C-nukleosides with 2'-deoxy-2',2'-difluoro modified sugar part was developed. During the research, nucleophilic addition on furanolacton was used and for this modification, the method of modular approach was developed. Using this method, it is possible to prepare a series of structurally similar compounds. We succeeded in preparing two C-nukleosides, potentially biologically active substances.
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Synthesis of novel cytostatic deazapurine nucleosides and pronucleotides
Perlíková, Pavla ; Hocek, Michal (advisor) ; Jindřich, Jindřich (referee) ; Hlaváč, Jan (referee)
The synthetic routes to three types of phosphate prodrugs of 6-hetaryl-7-deazapurine ribonucleosides based on palladium-catalyzed cross-coupling reactions have been developed. CycloSal- and phosphoramidate pronucleotides and octadecyl phosphates derived from 6- hetaryl-7-deazapurine ribonucleosides were screened for their in vitro cytostatic activity. It was shown that cytostatic activity of cycloSal phosphates was similar or slightly lower compared to the parent nucleosides. Significant drop of cytostatic activity was observed in phosphoramidate pronucleotides. Octadecyl phosphates were devoid of any cytostatic activity. 6-Hetaryl-7-deazapurine ribonucleosides with bulky groups in position 6 showed very strong and selective inhibition of adenosine kinase from Mycobacterium tuberculosis. 2'-Modified 6-hetaryl-7-deazapurine nucleosides: 2'-O-methylribonucleosides, arabinonucleosides and 2'- deoxy-2'-fluororibonucleosides, were prepared by multistep functional group transformations from a ribonucleoside. The synthesis of 2'-deoxy-2',2'-difluoro-erythro-pentofuranosyl nucleosides was based on a glycosylation of 6-chloro-7-deazapurine with a sugar synthon followed by palladium-catalyzed cross-coupling reaction and deprotection. Despite the low yields and laborious separation of the anomers,...
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