National Repository of Grey Literature 88 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Synthesis of 9-deazaguanine derivatives as potential inhibitors of tRNA-guanine transglycosylase (TGT)
Chylíková, Barbora ; Hocek, Michal (advisor) ; Smrček, Stanislav (referee)
Shigellosis is an acute diarrheal disease caused by enterobacteria of the genus Shigella. Worldwide, these bacteria are responsible for about 1 million deaths out of 165 million cases of the disease yearly, of which children under the age of 5 from developing countries are the most vulnerable group. The enzyme tRNA-guanine transglycolase (TGT for short) has been identified as essential for the effective pathogenesis of Shigella bacteria and therefore becomes a potential target for the selective treatment of shigellosis. This bachelor thesis describes the optimization of the preparation of a key intermediate for the synthesis of potential TGT inhibitors based on 8-aryl-9-deazaguanine structure. The synthesis starts from commercially available 2,6-dichloro-9-deazapurine. The main steps of the synthesis are the hydrolysis at position 6, the nucleophilic aromatic substitution of the chlorine group for the amino group in position 2, further the iodation and the introduction of the 3-thienyl group in position 8 by Suzuki coupling.
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...
Study of azaphthalocyanines as fluorescence quenchers in oligodeoxynucleotide probes
Demuth, Jiří ; Nováková, Veronika (advisor) ; Hocek, Michal (referee) ; Vávrová, Kateřina (referee)
Charles University, Faculty of Pharmacy in Hradec Kralove Department: Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Author: Mgr. Jiří Demuth Supervisor: doc. PharmDr. Veronika Nováková, Ph.D. Consultant: prof. PharmDr. Petr Zimčík, Ph.D. Doctoral Thesis: Study of azaphthalocyanines suitable for quenching of fluorescence in oligodeoxynucleotide probes Phthalocyanines (Pcs) and azaphthalocyanines (AzaPcs) are planar macrocyclic compounds. These synthetic compounds are derived from naturally occurring dyes - porphyrins. Pcs and AzaPcs have very interesting photophysical properties due to their extensive 18 -electron conjugated system. They are used in electrotechnics, material industry or in medicinal applications. Octaalkylamino substituted tetrapyrazinoporphyrazines (TPyzPzs), which belong to AzaPc family, can quench fluorescence of other molecules due to the ultrafast intramolecular charge transfer. This thesis studies this quenching ability of TPyzPzs with the aim to develop efficient fluorescence probes. Such probes could find application in a variety of experiments across scientific disciplines i.e. - biochemistry, forensic or genetic analysis. Synthetic part of dissertation thesis is a continuation of previous investigation of TPyzPzs in our research group. It describes...
Construction of modified DNAs with selected reactive or protective groups
Vaníková, Zuzana ; Hocek, Michal (advisor) ; Křen, Vladimír (referee) ; Zimčík, Petr (referee)
This PhD thesis is focused on the synthesis of DNA modified with photocleavable 2- nitrobenzyl protecting groups in major groove and its applications in the regulation of gene expression in the level of transcription. In the first part of my thesis, the synthesis of photocaged 2'-deoxyribonucleosides triphosphates and their photolysis to unprotected 5-hydroxymethylated nucleotides is described. All prepared nucleoside triphosphates were good substrates for their enzymatic incorporation into DNA. Synthesized 5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine-5'- monophosphate (dUNBMP) and DNA with one 5-(2-nitrobenzyloxy)methyl- modification in the sequence were used for the detailed kinetic studies of photocleavage reactions. In the second part of the thesis, the series of modified DNAs with specific sequences were prepared by primer extension (PEX) and/or polymerase chain reaction (PCR). A cleavage of prepared modified DNAs was studied by selected restriction endonucleases (REs). In all cases, the nitrobenzylated DNA fully resist the cleavage by REs. The deprotection/ photocleavage conditions for nitrobenzylated DNA were studied in the case of DNAs with positive restriction endonuclease digestion of hydroxymethylated DNA. The resulting photocleaved DNA was fully digested by REs, therefore 2-nitrobenzyl...
Phenotyping of proteolytic activities enabled by fluorogenic libraries
Pospíšil, Šimon ; Míšek, Jiří (advisor) ; Hocek, Michal (referee)
This work deals with the preparation of combinatorial libraries of peptides serving as platforms for proteolytic phenotyping. The primary objective was to prepare a solid phase fluorogenic peptide library and screen proteases by fluorescence. Further, the possibility of preparing solid phase DNA-encoded libraries was studied. Due to the non-reactivity of the specific proteases with the solid phase peptides, the solid phase was completely abandoned and DNA-encoded peptide library was prepared in the solution. Using this model of DNA-encoded dipeptide with terminal biotin, the new principle of testing proteolytic activities of proteases was verified. A combinatorial library of DNA-encoded hexapeptides was also prepared. Despite the low yield of the library, the possibility of DNA encoding, the amplifiability of the prepared molecules and the possibility of biotin-based separation were verified. The integrity of the hexapeptide sequence and the protease testing is the subject of further study.
New redox labels for DNA
Simonova, Anna ; Hocek, Michal (advisor) ; Urban, Milan (referee) ; Vyskočil, Vlastimil (referee)
The aim of my thesis was the synthesis of the modified 2'-deoxyribonucleoside triphosphates (dNTPs) bearing electrochemically oxidizable labels and their incorporation into DNA for the application in bioanalysis. In the first part of my thesis, I developed the synthesis of modified dNTPs bearing 2,3- dihydrobenzofuran (DHB) or 2-methoxyphenol (MOP) labels at 5-position of 2'- deoxycytidine 5'-O-triphosphate and at the 7-position of 7-deaza-2'-deoxyadenosine 5'-O- triphosphate by Suzuki-Miyaura cross-coupling reactions. Then modified dNTPs were used as substrates for DNA polymerases in enzymatic synthesis of modified DNA by PCR and primer extension. Electrochemical properties of the DHB and MOP-labeled nucleosides, dNTPs and DNA were studied by using of a square-wave voltammetry (SWV) at the pyrolytic graphite electrode (PGE) giving signals of MOP oxidation around 0.5 V and DHB oxidation around 0.85 V. The use of DHB group in combination with other electrochemical active labels was limited by close position of its oxidation peak to the signals of oxidation of natural nucleobases, whereas MOP moiety was successfully used for redox coding of nucleobases in combination with aminophenyl or benzofurazane label giving two independently readable redox signals in each case. In the second part of this...
Study of cyclization of tetrazolopyrimidines for synthesis of tricyclic nucleobases
Grúlová, Kristýna ; Hocek, Michal (advisor) ; Smrček, Stanislav (referee)
This bachelor thesis describes a study of cyclization reaction of substituted tetrazolopyrimidines, which were obtained by a three-step synthesis starting from 4,6-dichloropyrimidine, which was first zincated and then submitted to Negishi coupling with corresponding heteroaryl iodide followed by nucleophilic substitution with sodium azide. The previously known unexpected fluorescent product produced by the cyclization of the 2-thiophenyl derivative was resynthesized. An analogous product was obtained by cyclization of the 3-thiophenyl derivative. In contrast, the cyclization of the phenyl, 1-naphthyl and 2-furyl derivatives gave the expected tricyclic product resulting from the cyclization of the azide. Key words: heterocycles, cyclizations, nucleobases
Synthesis of Purine - Amino Acid Conjugates
Čapek, Petr ; Hocek, Michal (advisor) ; Kotora, Martin (referee) ; Dvořák, Dalimil (referee) ; Mazal, Ctibor (referee)
4. Conclusions A simple and efficient approach to the synthesis of (purin-6-yl)alanines based on Negishi cross-coupling reactions of 6-iodopurines and iodozinc- alanines applicable to the synthesis of both racemic and optically pure compounds was developed. Though analogous reactions were used before for the synthesis of some simple aryl- or hetarylaranines, this was the first successful use in the functionalization ofprotected nucleobases and nucleosides. A practical method for synthesis of enantiomerically pure (purin-6_ yl)phenylalanines by palladium catalyzeď, copper mediated Stille cross-coupling reactions ofprotected 4-(trimethylstanyl)phenylalanines and 6-iodopurines was developed. This method was used in the synthesis of series of (purin_6_ yl)phenylalanines (bases and nucleosides) varying in substitution in position 9 of purine scaffold and in absolute configuration on o-carbon ofphenylalanine. The shaughnessy method for the Suzuki cross-coupling reactions in aqueous media was further optimized and applied to the single-step synthesis of novel optically pure (adenin-8-yl)phenylalanines and (purine_6_yl)phenyl_ alanines. wide tolerance of this methodology towards variety of functionalities and its applicability to 1abile systems was demonstrated particularly by the very first examples of couplings...
Acyclic nucleoside phosphonates with expanded purine bases
Čapková, Kateřina ; Holý, Antonín (advisor) ; Černý, Miloslav (referee) ; Kefurt, Karel (referee) ; Hocek, Michal (referee)
Univerzita Karlova Příro dovědecká fakulta Katedra organické a jaderné chemie Akademie věd Ceské Republiky Ústav organické chemie a biochemie S tirrltrffi[n Acyklické nukleo sidfo sfon áty rozšířenoupurinovou bazí Kateřina Čapková Shrnutí disertačnípráce Praha 2006 -tt ai-''- ffi-'.--.-/ /{ía' s Acyklické nukleosid fosfonáty předstalují velice zajimavou skupinu nukleotidových analogů s protivirovými, cýostatickj.rni a antiprotozoá|ními účinky.Jsou aktivní nejen proti širokému spektru DNA viru (herpesviry, poxviry, adenoviry, papillomaviry), ale i proti retrovirům (virus hepatitidy B, HIV). Nejvýznamnějšími představiteli celé skupiny jsou PMEA (adefovir, v klinické praxi ve formě adefovir dipivoxil), schválený pro léčbuhepatitidy B (HepseraTM), dále (fi).PMPA (teno-Qvir. v klinické praxi jako tenofovir disoproxil fumarát), schválený pro léčbuAIDS (Viread.'u') a (S)-HPMPC (cidofovir),-schválený pro léčbucýomegalovirové retinitidy u imunosuprimovaných pacientů (VistideTM). 1 V rámci hledání nových potenciálních virostatik a cýostatik bylo mým úkolem připravit série několika nových typůmodifikovaných acyklických nukleosid fosfonátů, konkrétně s tricyklickou bazi odvozenou od původnípurinové baze. Tricyk|ické baze23 ;so., zajímavé předevšímkvůli své fluorescencí,která umoŽňuje snadnou detekci a sledování osudu...

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