Papers by Jaroslav Sebestik
Progress in Drug Research, 2017
Usually, the moderate binding of acridines to nucleic acid cannot compete with tight binding of t... more Usually, the moderate binding of acridines to nucleic acid cannot compete with tight binding of transcription factors. Thus, other explanations for acridine biological activities are necessary. Biological activities of acridines can be significantly caused by direct interactions with proteins. Acridines interact with proteins both directly or as a component of nucleic acid-acridine complex. Acridines influence the living system by direct interaction with receptors, and also on genetic or epigenetic levels where more prolonged effects can be achieved. Influence of acridines on many kinases alters the signaling pathway and regulates apoptosis. Structural aspects of interactions with proteins are useful hints to design enzyme inhibitors involved in treatment of cancer , inflammation, and neurodegenerative diseases.
Journal of the American Chemical Society, 2005
Progress in Drug Research
Hallmark of neurodegenerative disorders such as Alzheimer’s, Parkinson’s, and prion diseases is a... more Hallmark of neurodegenerative disorders such as Alzheimer’s, Parkinson’s, and prion diseases is aggregation of various proteins, which accumulate in the brain. The early stages of aggregation are responsible for toxicity of the protein to neurons. Later, the protein precipitates out from the system and can be unavailable for its original purpose. The diseases are accompanied with higher oxidative stress and accumulation of various metals. Since acridines can interact with proteins, they can influence the aggregation process or lead to dissociation of the aggregates. Furthermore, acridines can inhibit various enzymes involved in neurodegenerative diseases. In order to tackle multiple factors involved in neurodegenerative diseases, acridine conjugates with anti-oxidants, metal chelators, or anion binders are constructed. Moreover, the reader can see how subtle alterations of acridine structure can serve for detection of prion strains i.e. most probably various conformations of pathogenic proteins.
Amino Acids
Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins... more Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm −1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.
Progress in Drug Research
The Journal of Physical Chemistry B
Raman optical activity (ROA) spectroscopy combined with quantum-chemical simulations is a sensiti... more Raman optical activity (ROA) spectroscopy combined with quantum-chemical simulations is a sensitive method to determine the absolute configuration and conformation of chiral molecules in solutions. However, the precision of this approach varies for different systems. In the present study, the reliability and numerical stability of decomposing experimental spectra into calculated subspectra is tested on the Ala-Ala dipeptide. Molecular dynamics (MD) snapshots of Ala-Ala/water clusters are averaged to account for solvent effects and molecular flexibility. Multiple experiments with protonated, zwitterionic, and deprotonated dipeptide forms and natural and d 2-and d 8-isotopically labeled dipeptides are used to verify the results and estimate the overall accuracy. Although the precision is still limited by experimental noise and computational error, a very close match between the observed and theoretical spectral shapes has been achieved. This enabled quantitative determination of conformer populations with a typical dispersion of 10%. The spectroscopy also demonstrated how the conformation depends on pH. The ROA results were more consistent than the Raman ones. Typically, the ROA analysis was more resistant to artifacts in the experiment, such as incomplete baseline subtraction. Conformer ratios predicted by MD agree fairly but not fully with the experimental ones. This indicates minor deficiencies in the Amber force field, particularly for the protonated dipeptide. Overall, the combination of ROA experiment and computational chemistry appears to be a robust tool providing deep insight into molecular structure.
Chemical biology & drug design, 2017
Quinacrine-the drug based on 9-aminoacridine-failed in clinical trials for prion diseases, wherea... more Quinacrine-the drug based on 9-aminoacridine-failed in clinical trials for prion diseases, whereas it was active in in vitro studies. We hypothesize that aromatic nucleophilic substitution at C9 could be contributing factor responsible for this failure because of the transfer of acridine moiety from quinacrine to abundant glutathione. Here, we described the semi-large-scale synthesis of the acridinylated glutathione and the consequences of its formation on biological and biophysical activities. The acridinylated glutathione is one order of magnitude weaker prion protein binder than the parent quinacrine. Moreover, according to log DpH 7.4 , the glutathione conjugate is two orders of magnitude more hydrophilic than quinacrine. Its higher hydrophilicity and higher dsDNA binding potency will significantly decrease its bioavailability in membrane-like environment. The glutathione deactivates quinacrine not only directly but also decreases its bioavailability. Furthermore, the conjugate ...
ChemPhysChem, 2016
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular ... more The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data.
Chem. Commun., 2016
A large induction of solvent chirality was observed in Raman optical activity spectra of a helqua... more A large induction of solvent chirality was observed in Raman optical activity spectra of a helquat dye in nitrile solvents.
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
Angewandte Chemie (International ed. in English), Jan 25, 2014
Raman optical activity (ROA) detects the intensity difference between right and left circularly p... more Raman optical activity (ROA) detects the intensity difference between right and left circularly polarized scattered light, and thus brings about enhanced information about the molecules under investigation. The difference is quite small and the technique is mostly constrained to the condensed phase. For NO2 in the presence of a static magnetic field, however, the ROA signal with high ROA/Raman intensity ratio was observed. The signal is so strong owing to molecular paramagnetism and a pre-resonance signal enhancement. The spectral shape was explained on the basis of the Fermi golden rule and rotational wave functions expanded to a spherical top basis. The results indicate that the technique can be immediately used to obtain information about molecular properties, such as polarizability components. It also has a potential to detect other paramagnetic gases and discriminate among them.
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
It is a difficult task to create a simple, universal, clear, unambiguous, logical, and generally ... more It is a difficult task to create a simple, universal, clear, unambiguous, logical, and generally applicable classification or even nomenclature of different sorts of dendrimers. In general, dendrimers contain a core, branches, and surface functional groups. Sometimes the core is missing (e.g., MAPs), or the branches are missing (RAFTs). The classification can stress either the shape of the core, branches, or surface groups (linear, cyclic) or the chemical nature of the core (fullerene, porphyrin, calixarene, cyclodextrin, RAFT, etc.) or branches (peptide, carbohydrate, PEG, PAMAM, etc.) Another way of classification is in accord with globular structure, cluster effect, and polyvalency. Our classification is limited mainly to peptide-, glyco-, and glycopeptide dendrimers. It is necessary to explain three partly overlapping terms: core, scaffold, and cluster. Nearly all molecules exhibiting at least two copies of a reactive group can theoretically serve as core or scaffold for the synthesis of different sorts of dendrimers [9
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
Dendrimers have been utilized for regulating intracellular signaling pathways. Series of dendrime... more Dendrimers have been utilized for regulating intracellular signaling pathways. Series of dendrimers harboring tetrapeptide sequences containing an immunoreceptor tyrosine-based activation motif (ITAM) phosphotyrosine motif, which were synthesized and conjugated to dendrimers via click chemistry to create a series of functional phosphopeptide-containing dendrimers, have been shown to activate spleen tyrosine kinase (Syk) through binding of their tandem Src homology 2 (SH2) domains [3]. Syk is known to be activated through its divalent interactions of each SH2 domain to a diphosphorylated ITAM. The specific tetra-and octavalent dendrimers harboring ITAM tetrapeptide sequences have been shown to display high affinity in the nanomolar range, using surface plasmon resonance competition experiments. The effect of multivalency was demonstrated by comparative analysis in which tetra-and octavalent dendrimers displayed higher K d than the divalent or monovalent constructs. Bone marrow-derived mesenchymal stem cells (MSCs) represent a population of self-renewing, multipotent cells that are able to differentiate upon different stimulations into a number of phenotypes, such as osteogenic, chondrogenic, adipogenic, cardiomyogenic, and neurogenic lineages. Their commitment can be regulated by the intercellular signals. It has been found that alterations in small signaling G protein Rho family GTPase activities derived from cytoskeletal formation can lead to guidance of cardiomyogenic differentiation of human mesenchymal stem cells (hMSCs) in vitro. A dendrimer-immobilized substrate that displayed glucose was employed to regulate the cytoskeletal formation of hMSCs [2]. It has been shown that active migration of cells during the culture, accompanied by their morphological changes of stretching and contracting, correlated with an increase in the dendrimer generation number. The most dramatic effects on Rho family GTPase activities, RhoA down-regulation and Rac1 (another small signaling G protein of the Rac subfamily of Rho family) upregulation, were observed when the G5 dendrimer surface was used. This was associated with altered cellular morphology and migration. Cell aggregation was promoted on this surface indicating that an increase in N-cadherin-mediated cell-cell contacts and Wnt signaling regulates hMSC differentiation toward cardiomyocyte-like cells.
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
Before 1984, three classes of macromolecular architecture (i.e., linear, cross-linked, and branch... more Before 1984, three classes of macromolecular architecture (i.e., linear, cross-linked, and branched) were widely accepted for construction of relatively polydisperse products of different molecular weights [13, 19, 32, 49, 57]. Since that year, the "dendritic state" is acknowledged as a new, fourth class of polymer architecture. It can be divided to five subclasses: random hyperbranched polymers, dendrigrafts,
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
Dendrimers and Bacteria Peptide, glyco, and glycopeptide dendrimers, capable of binding bacterial... more Dendrimers and Bacteria Peptide, glyco, and glycopeptide dendrimers, capable of binding bacterial polysaccharides, represent attractive tools both for the therapy and for the diagnostics of the diseases of bacterial etiology. Finding new antibacterial drugs, as well as diagnostic tools, is nowadays of particular importance due to enhanced resistance of bacteria toward common antimicrobial agents. Indeed, the resistant microorganisms caused severe diseases with dramatic impact on mortality, disability, and economics. Attractive targets are bacterial lectins; some of them initiate infection by their interaction with the host cell glycoconjugates [49]. Free saccharides bind to the bacterial lectins with low affinity which is an obstacle for their therapeutic or diagnostic use. Notably, this can be overcome by their attachment to polymeric carriers or presentation as dendrimers resulting in strong multivalent binding. A critical overview about achievements in exploring the potential of dendrimers (PAMAM, PPI) as bactericides, as well as, an analysis of the factors influencing their biocidal activity was described [5]. 15.1 Escherichia coli Food contamination with Escherichia coli pathogenic strains results in frequent outbreaks of infections. Therefore, rapid and reliable detection of pathogenic bacteria is a key step in avoiding the spread of contamination. The carbohydratebinding proteins on the bacteria surface are responsible for binding to host cells. Importantly, invasive strains of E. coli display high levels of mannose-binding proteins (lectins). These cell-surface molecules can represent targets both for novel diagnostic agents and for antibiotics. For example, E. coli and several other enterobacteria use type 1 fimbriae-30 kDa lectin-like subunit FimH-for mannosemediated specific binding during anchoring to the host [6
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
This chapter deals with applications of dendrimers for treatment of Alzheimer's (AD) and Parkinso... more This chapter deals with applications of dendrimers for treatment of Alzheimer's (AD) and Parkinson's diseases (PD), as well as the diseases which involve the prion proteins such as scrapie, bovine spongiform encephalopathy (BSE), Gerstmann-Straüssler-Scheinker's syndrome (GSS), Creutzfeldt-Jakob's disease (CJD), and its new variant (nvCJD). These neurodegenerative diseases include at least one stage where the formation of amyloidogenic plaques takes place [39, 43, 49]. The accumulation of peptides or proteins with propensity toˇ-sheet aggregation leads to viscous gel formation and suppression of cellular trophic functions. The neurodegenerative diseases are accompanied with cell damage caused by accumulation of these toxic and pathological proteins [42]. In AD and PD, the aggregation of Aˇpeptide and˛-synuclein is related to its organism of origin [43], whereas, in prion diseases, it is believed that the misfolded protein is a causative agent of transmissible encephalopathies and can act in an organism different from that of its origin [1, 22, 49]. Whether the seed propagation is responsible for disease transmission is still not clear [43]. Recently, the interactions between Aˇand prions have been described and attributed to certain role during the pathogenesis [7, 36]. 23.1 Dendrimers as Anti-prion Agents In prion-related neurodegenerative diseases, the cellular prion protein (PrP C) is converted from soluble˛-helical rich protein to partially insoluble,ˇ-sheet rich, and resistant protein (scrapie form, PrP Sc) toward proteases [1,22,49]. PrP Sc aggregates are accumulated in neuronal tissue as a constant feature of all prion diseases. PrP Sc is the sole causative agent of the prion diseases [1, 22, 49]. Natural and synthetic prion proteins were studied by X-ray fiber diffraction [73]. PrP Sc is very stable toward many chemical and physical treatments [72]; however, its infectivity is completely suppressed when it is exposed to high concentrations of protein denaturants like guanidinium and thiocyanate ions [50]. Since PrP Sc inactivation and dissociation proceed via a solubilization of PrP Sc ,
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
The word "nano(s)" means a dwarf in Greek. One nanometer corresponds to one-billionth of a meter,... more The word "nano(s)" means a dwarf in Greek. One nanometer corresponds to one-billionth of a meter, 10 9 m. This is approximately four and half times of the diameter of an individual carbon atom. Width of DNA is roughly 2.5 nm and size of protein molecules is in the range of 1-20 nm. Since nanotechnologies include the design, production, characterization, and application of structures, devices, and systems for management of size and shape at nanometer scale, they can handle and form materials at the atomic scale [42, 83, 88]. Nanotechnology provides useful materials, devices, and systems via the manipulation of tiny matter with at least one dimension smaller than 100 nm. Nanotechnology is an interdisciplinary science spreading to almost all hard sciences including physics, chemistry, biology, and medicine. Nanoscale devices are three to five orders of magnitude smaller than human cells. This means that their size corresponds to large biological molecules, such as enzymes and receptors, as shown in Fig. 12.1 [83, 88]. Their diameter in the range of 1-100 nm corresponds to molecular mass in the interval 10 4-10 7 Da and a number of atoms within 10 3-10 9 atoms [99]. These nanodimensions allowed nanoscale systems to act both on the cell surface and in inner parts of cells. Therefore, nanoscale systems can detect diseases and deliver the cargo to the exact target in a way unknown so far. The tailored artificial nanostructures can serve for sensing and repair of damaged parts of human body. In this way, their function can resemble or outperform naturally occurring biological systems, e.g., the white blood cells [88]. Due to nanoscale size of dendrimers, the multidisciplinary field of dendrimers and nanotechnology have many similar features and overlaps [5
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
Delivery of nucleic acids to target cells can be achieved by both viral and nonviral delivery sys... more Delivery of nucleic acids to target cells can be achieved by both viral and nonviral delivery systems [7,8,18,20,22,32]. Both of these methods have distinct advantages and disadvantages. In contrast to viral vectors, the nonviral ones provide the advantage of safety and flexibility. The disadvantage of nonviral carriers is their low efficiency. Inherent properties of dendritic nanoscale devices provide an ideal tool for development of synthetic (nonviral) carriers for delivery of nucleic acids [7]. Among these properties, the defined architecture, high ratio of surface groups to molecular volume, and difference of hydropathic properties of interior and exterior are the most important for drug and gene delivery. Dendrimeric structures have been suggested to be used in gene therapy as potent carriers capable to, sometimes specifically, deliver DNA or RNA into the cells. Dendrimers are able to form complexes with many types of nucleic acids, such as plasmid DNA, antisense oligonucleotides, and RNA. Due to their defined architecture and a high ratio of multivalent surface moieties to molecular volume, they have become very important for the development of synthetic vectors for nucleic acid delivery [7]. Indeed, dendrimer-based transfection agents have become routine tools for many molecular and cell biologists, but the therapeutic delivery of nucleic acids complexed with dendrimer should be further investigated. The cationic dendrimers interact with the anionic backbone of nucleic acids mainly electrostatically. Complexed DNA is protected against degradation and the net positive charge of the dendrimer nucleic acid complex determines the transfection efficiency. However, highly cationic complexes are cytotoxic. Their properties can be tuned by many factors such as concentration of dendrimer amines and nucleic acid phosphates, salt concentration, stoichiometry, bulk solvent properties like pH, and buffer strength [7, 8]. For a development of dendriplex complexes with nucleic acids which can be used in gene therapy or, in general, as transfection reagents, knowledge of their transfection efficiencies and cytotoxicities is crucial. For transfection efficacy of reporter genes, standard techniques have been summarized [25] such as luciferase reporter assay,ˇ-galactosidase assay, or green fluorescent protein microscopy. The cytotoxicity is usually determined by standard MTT test.
Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 2012
The vast majority of signal transduction processes in most living organisms are caused by four so... more The vast majority of signal transduction processes in most living organisms are caused by four sorts of biomolecules: nucleic acids, proteins, glycoconjugates, and lipids. The sequence and structure of nucleic acids as well as peptides and proteins have been extensively studied, including different sorts of interactions and functions (
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Papers by Jaroslav Sebestik