National Repository of Grey Literature 9 records found  Search took 0.00 seconds. 
Noncovalent Interactions of Biologically Active Compounds
Osifová, Zuzana ; Dračínský, Martin (advisor) ; Lyčka, Antonín (referee) ; Sýkora, Jan (referee)
This thesis deals with the employment of nuclear magnetic resonance (NMR) spectroscopy in the studies of non-covalent interactions of biologically active compounds. The introduction serves as a brief overview of the literature, pointing out the milestones in determining and studying the most common non-covalent interactions - hydrogen bonding, π-π stacking and halogen bonding - by NMR spectroscopy. This part also includes the basics of this method to ensure that the results presented and the principles used will also be understandable for readers outside the field. Similarly, the employment and limitations of theoretical calculations are shortly discussed. The thesis aimed to determine the role of non-covalent interactions in biologically active compounds, including hydrogen bonding of modified nucleobases, interactions influencing ketoenol-diketo tautomerism of pharmacologically active curcuminoids, and the role of hydrogen bonding and amino acid sequence in the adoption of secondary structure in short peptides. Methylation and oxidation are nucleobases' most common natural modifications, causing changes in their hydrogen bonding pattern and preferences. We found that N-methylation of adenine residue stabilises its hydrogen-bonded base pairs with thymine and that these base pairs tend to adopt...
Interactions of modified nucleobases studied by NMR spectroscopy
Štoček, Jakub Radek ; Kuneš, Jiří (advisor) ; Lyčka, Antonín (referee)
(EN) Nucleic acids are among the largest and most complex compounds in nature and without a doubt the most important molecules for the existence of life. Understanding the chemical behaviour and thermodynamic parameters of their building components enables us to make ever so increasingly accurate predictions of nucleic acid structures, reactions and functions. These predictions in turn provide great help in research fields such as DNA nanotechnology, nucleic acid targeted drug development and DNA material sciences. My research work targeting nucleobases and their analogues is focused on exploring effects of their conformational isomers and tautomers on the thermodynamics of intermolecular complexes that these compounds can theoretically form with each other through hydrogen bonds. Doc. RNDr. Martin Dračínský, Ph.D. and I have conducted two separate studies concerning this topic at the NMR department of the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences. The first research project concentrated on developing a method for the determination of nucleobase-pairing free energies from rotamer equilibria of various 2-(methylamino)pyrimidines [1], while the second project aimed to shed light on the tautomerism of guanine analogues [2]. Keywords Nuclear Magnetic Resonance...
Chiral metallocomplex synthons of α-amino acids. Synthesis, physical-chemical properties and applications
Popkov, Alexandr ; Lyčka, Antonín (advisor) ; Kotora, Martin (referee) ; Růžička, Aleš (referee) ; Pour, Milan (referee)
CONCLUSIONS Study of chiral amino acids synthons resulted in: I a deeper understanding of the intramolecular interactions affecting the stereochemistry of alkylation of the metallocomplex o_amino acids synthons. The interactions are a valuable tool for evaluation of the stereochemistry of the complexes; the disclosure of new phenomena in NMR spectroscopy (unexpected long-range couphngs.); 3 synthesis ofthe stereospecific synthon ofglycine; 4 the continuing development of diagnostic tools for the clinical diagnostic of some tumours. 5 the development of an envrronmentally_friendly procedure for multikilogram-scale preparatlon of starting metallocomplex chiral synthons ofo_amino acids.
Interactions of modified nucleobases studied by NMR spectroscopy
Štoček, Jakub Radek ; Kuneš, Jiří (advisor) ; Lyčka, Antonín (referee)
(EN) Nucleic acids are among the largest and most complex compounds in nature and without a doubt the most important molecules for the existence of life. Understanding the chemical behaviour and thermodynamic parameters of their building components enables us to make ever so increasingly accurate predictions of nucleic acid structures, reactions and functions. These predictions in turn provide great help in research fields such as DNA nanotechnology, nucleic acid targeted drug development and DNA material sciences. My research work targeting nucleobases and their analogues is focused on exploring effects of their conformational isomers and tautomers on the thermodynamics of intermolecular complexes that these compounds can theoretically form with each other through hydrogen bonds. Doc. RNDr. Martin Dračínský, Ph.D. and I have conducted two separate studies concerning this topic at the NMR department of the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences. The first research project concentrated on developing a method for the determination of nucleobase-pairing free energies from rotamer equilibria of various 2-(methylamino)pyrimidines [1], while the second project aimed to shed light on the tautomerism of guanine analogues [2]. Keywords Nuclear Magnetic Resonance...
Complexes of cyclen-based macrocyclic ligands with a phosphinate pendant arm
Urbanovský, Peter ; Hermann, Petr (advisor) ; Lyčka, Antonín (referee) ; Pinkas, Jiří (referee)
Lanthanide(III) complexes of DOTA derivatives are utilized in the medical imaging techniques such as magnetic resonance imaging (MRI), magnetic resonance angiography (MRA), and magnetic resonance spectroscopy (MRS), nuclear imaging (PET and SPECT), or optical methods (luminescence). It has been shown that relaxometric parameters of the Gd(III) complexes of DOTA derivatives with a phosphinic acid pendant arm (Gd-DO3APR ) can reach optimal values (e.g. water residence time, τM, being close to ~10 ns). The relaxometric parameters can be further modified through the phosphorus substituents. It is also known that the complexes possess a high thermodynamic stability and they are kinetically inert. The main goal of this Thesis is an investigation of the effect of pendant amino group protonation in substituents bound to the phosphorus atom on properties of the complexes. Thus in this Thesis, DOTA derivatives with the phosphinic acid pendant arm with an amino group and their complexes were prepared and characterized. The complexes are intended as contrast agents for molecular imaging techniques (mainly for MRI and 31 P MRS). The first part of the Thesis introduces two new versatile "phospha-Mannich" protocols performed under mild conditions. Amino-H-phosphinic acids (AHPAs) were synthesized with excess of...
Interactions of modified nucleobases studied by NMR spectroscopy
Štoček, Jakub Radek ; Kuneš, Jiří (advisor) ; Lyčka, Antonín (referee)
(EN) Nucleic acids are among the largest and most complex compounds in nature and without a doubt the most important molecules for the existence of life. Understanding the chemical behaviour and thermodynamic parameters of their building components enables us to make ever so increasingly accurate predictions of nucleic acid structures, reactions and functions. These predictions in turn provide great help in research fields such as DNA nanotechnology, nucleic acid targeted drug development and DNA material sciences. My research work targeting nucleobases and their analogues is focused on exploring effects of their conformational isomers and tautomers on the thermodynamics of intermolecular complexes that these compounds can theoretically form with each other through hydrogen bonds. Doc. RNDr. Martin Dračínský, Ph.D. and I have conducted two separate studies concerning this topic at the NMR department of the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences. The first research project concentrated on developing a method for the determination of nucleobase-pairing free energies from rotamer equilibria of various 2-(methylamino)pyrimidines [1], while the second project aimed to shed light on the tautomerism of guanine analogues [2]. Keywords Nuclear Magnetic Resonance...
Chiral metallocomplex synthons of α-amino acids. Synthesis, physical-chemical properties and applications
Popkov, Alexandr ; Lyčka, Antonín (advisor) ; Kotora, Martin (referee) ; Růžička, Aleš (referee) ; Pour, Milan (referee)
CONCLUSIONS Study of chiral amino acids synthons resulted in: I a deeper understanding of the intramolecular interactions affecting the stereochemistry of alkylation of the metallocomplex o_amino acids synthons. The interactions are a valuable tool for evaluation of the stereochemistry of the complexes; the disclosure of new phenomena in NMR spectroscopy (unexpected long-range couphngs.); 3 synthesis ofthe stereospecific synthon ofglycine; 4 the continuing development of diagnostic tools for the clinical diagnostic of some tumours. 5 the development of an envrronmentally_friendly procedure for multikilogram-scale preparatlon of starting metallocomplex chiral synthons ofo_amino acids.
Synthesis of ellipticine derivatives and study of their interactions with DNA
Dračínský, Martin ; Sejbal, Jan (advisor) ; Klinot, Jiří (referee) ; Lyčka, Antonín (referee) ; Rosenberg, Ivan (referee)
CONCLUSIONS t New strategy for ellipticine synthesis was proposed' The yields of the synthesis are very hígh and pure product is obtained. The strategy was verified with the synthesis of other ellipticine derivatives' rBenzylicoxidationsoťellipticineandl,4-dimethylcarbazolewerestudiedand13. hydroxyellipticine was slnthesised' ' Three empirical potentials were compared with reference ab initio data of ellipticine derivative - DNA base patr' . The ernpirical potentials calculate interaction energies of the complexes quite well (espeglallytheA-ffE6andtheLHpotentials)buttheyfailinthesearchofglobal energy minima geometri es' .Interactionsofellipticineandg.hydroxyellipticinewithtwooligonucleotideswerc studiedintwobuffers(weaklyacidicandneutral,ellipticineisprotonatedintlro acidic buffer). Using two-dimensional NMR techniques assignment of all hydrogen signals of oligonucleotides CGCTAGCG and ATAGCTAT was done. The most important interaction of the ellipticine derivatives with the oligonucleotides is intercalation, but in the acidic buffer ellipticine can form also non-intercalative (bond to the minor or to the major groove) complexes with the oligonucleotides. Both ellipticine derivatives destabilised the duplex structuÍe of the oligonucleotide ATAGCTAT in acidic environment. ln the neutral buffer the life-time...
Struktura a vlastnosti modifikovaných složek nukleových kyselin
Procházková, Eliška ; Dračínský, Martin (advisor) ; Lyčka, Antonín (referee) ; Hrabal, Richard (referee)
Modified nucleic acid components (nucleotides, nucleosides, nucleobases) display a wide range of biological activities such as antiviral, cytostatic, antimicrobial or antioxidative. Many of them are successfully used in clinical practice, for instance as anti-HIV drugs or in hepatitis B treatment. The first precondition for understanding biological effects is to evaluate the chemical structure as well as the conformation of the studied compounds correctly. For this purpose, solution-state nuclear magnetic resonance (NMR) spectroscopy in combination with mass spectrometry is the most frequently used method. Not only the structure, but also physico- chemical properties can be investigated using NMR spectroscopy, for instance, conformational changes, tautomeric forms, protonation sites, acido-basic properties, non-covalent interactions, isotopic exchanges or interactions with biomolecules. Similarly to solutions, NMR spectroscopy can be employed in studies of nucleic acid components (NACs) in solid state. This technique found assertion after computational-chemistry methods development during the last decades. Different solid-state structures (polymorphic forms) or dynamics of these compounds can be established by solid-state NMR spectroscopy in combination with quantum-chemical calculations. In this...

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5 Lyčka, Aleš
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