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Article ; Online: Silver Ion High-Performance Liquid Chromatography-Atmospheric Pressure Chemical Ionization Mass Spectrometry: A Tool for Analyzing Cuticular Hydrocarbons.

Vrkoslav, Vladimír / Horká, Petra / Jindřich, Jindřich / Buděšínský, Miloš / Cvačka, Josef

2023 Volume 28, Issue 9

Abstract: Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of ... ...

Abstract	Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of decomposition at high temperatures. MALDI cannot distinguish between isomeric HCs. An alternative approach based on silver ion high-performance liquid chromatography (Ag-HPLC) is shown here. The separation of HC standards and cuticular HCs was accomplished using two ChromSpher Lipids columns connected in series. A gradient elution of the analytes was optimized using mobile phases prepared from hexane (or isooctane) and acetonitrile, 2-propanol, or toluene. HCs were detected by atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Good separation of the analytes according to the number of double bonds, cis/trans geometry, and position of double bonds was achieved. The retention times increased with the number of double bonds, and trans isomers eluted ahead of cis isomers. The mobile phase significantly affected the mass spectra of HCs. Depending on the mobile phase composition, deprotonated molecules, molecular ions, protonated molecules, and various solvent-related adducts of HCs were observed. The optimized Ag-HPLC/APCI-MS was applied for characterizing cuticular HCs from a flesh fly,
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; Silver/chemistry ; Gas Chromatography-Mass Spectrometry ; Hydrocarbons ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Atmospheric Pressure
Chemical Substances	Silver (3M4G523W1G) ; Hydrocarbons
Language	English
Publishing date	2023-04-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28093794
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Article ; Online: Spirostanol Saponins from Flowers of

Harmatha, Juraj / Buděšínský, Miloš / Zídek, Zdeněk / Kmoníčková, Eva

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 21

Abstract: Saponins, a diverse group of natural compounds, offer an interesting pool of derivatives with biomedical application. In this study, three structurally related spirostanol saponins were isolated and identified from the leek flowers ... ...

Abstract	Saponins, a diverse group of natural compounds, offer an interesting pool of derivatives with biomedical application. In this study, three structurally related spirostanol saponins were isolated and identified from the leek flowers of
MeSH term(s)	Allium/chemistry ; Animals ; Cell Line ; Cell Survival/drug effects ; Flowers/chemistry ; Lipopolysaccharides/antagonists & inhibitors ; Lipopolysaccharides/pharmacology ; Macrophages, Peritoneal/drug effects ; Macrophages, Peritoneal/metabolism ; Mice ; Mice, Inbred C57BL ; Molecular Conformation ; Nitric Oxide/antagonists & inhibitors ; Nitric Oxide/biosynthesis ; Saponins/chemistry ; Saponins/isolation & purification ; Saponins/pharmacology ; Spirostans/chemistry ; Spirostans/isolation & purification ; Spirostans/pharmacology
Chemical Substances	Lipopolysaccharides ; Saponins ; Spirostans ; Nitric Oxide (31C4KY9ESH)
Language	English
Publishing date	2021-10-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26216533
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Article ; Online: Acid-Stable Ester Linkers for the Solid-Phase Synthesis of Immobilized Peptides.

Pícha, Jan / Buděšínský, Miloš / Mitrová, Katarína / Jiráček, Jiří

ChemPlusChem

2020 Volume 85, Issue 6, Page(s) 1297–1306

Abstract: A series of N-terminally Fmoc-protected linkers of the general formula Fmoc-X-CO-O-Y-COOH have been prepared, where X is -NH- ... ...

Abstract	A series of N-terminally Fmoc-protected linkers of the general formula Fmoc-X-CO-O-Y-COOH have been prepared, where X is -NH-CH
MeSH term(s)	Esters/chemical synthesis ; Esters/chemistry ; Immobilized Proteins/chemical synthesis ; Indicators and Reagents/chemical synthesis ; Indicators and Reagents/chemistry ; Peptides/chemical synthesis ; Solid-Phase Synthesis Techniques/methods
Chemical Substances	Esters ; Immobilized Proteins ; Indicators and Reagents ; Peptides
Language	English
Publishing date	2020-08-05
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2192-6506
ISSN (online)	2192-6506
DOI	10.1002/cplu.202000246
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Article ; Online: Electrochemistry of Tetrathiafulvalene Ligands Assembled on the Surface of Gold Nanoparticles.

Janoušek, Jiří / Rybáček, Jiří / Buděšínský, Miloš / Pospíšil, Lubomír / Stará, Irena G / Starý, Ivo

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 21

Abstract: The synthesis of a tetrathiafulvalene (TTF) derivative, ...

Abstract	The synthesis of a tetrathiafulvalene (TTF) derivative,
MeSH term(s)	Gold/chemistry ; Electrochemistry/methods ; Ligands ; Metal Nanoparticles/chemistry
Chemical Substances	Gold (7440-57-5) ; tetrathiafulvalene (HY1EN16W9T) ; Ligands
Language	English
Publishing date	2022-11-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27217639
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Article ; Online: Modulation of the antagonistic properties of an insulin mimetic peptide by disulfide bridge modifications.

Lubos, Marta / Pícha, Jan / Selicharová, Irena / Žák, Jíří / Buděšínský, Miloš / Mitrová, Katarína / Žáková, Lenka / Jiráček, Jiří

Journal of peptide science : an official publication of the European Peptide Society

2023 Volume 29, Issue 7, Page(s) e3478

Abstract: Insulin is a peptide responsible for regulating the metabolic homeostasis of the organism; it elicits its effects through binding to the transmembrane insulin receptor (IR). Insulin mimetics with agonistic or antagonistic effects toward the receptor are ... ...

Abstract	Insulin is a peptide responsible for regulating the metabolic homeostasis of the organism; it elicits its effects through binding to the transmembrane insulin receptor (IR). Insulin mimetics with agonistic or antagonistic effects toward the receptor are an exciting field of research and could find applications in treating diabetes or malignant diseases. We prepared five variants of a previously reported 20-amino acid insulin-mimicking peptide. These peptides differ from each other by the structure of the covalent bridge connecting positions 11 and 18. In addition to the peptide with a disulfide bridge, a derivative with a dicarba bridge and three derivatives with a 1,2,3-triazole differing from each other by the presence of sulfur or oxygen in their staples were prepared. The strongest binding to IR was exhibited by the peptide with a disulfide bridge. All other derivatives only weakly bound to IR, and a relationship between increasing bridge length and lower binding affinity can be inferred. Despite their nanomolar affinities, none of the prepared peptide mimetics was able to activate the insulin receptor even at high concentrations, but all mimetics were able to inhibit insulin-induced receptor activation. However, the receptor remained approximately 30% active even at the highest concentration of the agents; thus, the agents behave as partial antagonists. An interesting observation is that these mimetic peptides do not antagonize insulin action in proportion to their binding affinities. The compounds characterized in this study show that it is possible to modulate the functional properties of insulin receptor peptide ligands using disulfide mimetics.
MeSH term(s)	Insulin/metabolism ; Receptor, Insulin ; Disulfides/chemistry ; Peptides/chemistry
Chemical Substances	Insulin ; Receptor, Insulin (EC 2.7.10.1) ; Disulfides ; Peptides
Language	English
Publishing date	2023-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	1234416-3
ISSN	1099-1387 ; 1075-2617
ISSN (online)	1099-1387
ISSN	1075-2617
DOI	10.1002/psc.3478
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Article ; Online: Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy.

Štěpánová, Sille / Andris, Erik / Gutten, Ondrej / Buděšínský, Miloš / Dejmek, Milan / Břehová, Petra / Rulíšek, Lubomír / Kašička, Václav

Electrophoresis

2023 Volume 45, Issue 7-8, Page(s) 687–705

Abstract: Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and ... ...

Abstract	Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pK
MeSH term(s)	Electrophoresis, Capillary/methods ; Hydrogen-Ion Concentration ; Protons ; Magnetic Resonance Spectroscopy/methods ; Dinucleoside Phosphates/chemistry ; Thermodynamics ; Density Functional Theory
Chemical Substances	Protons ; Dinucleoside Phosphates
Language	English
Publishing date	2023-12-07
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.202300232
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Article ; Online: Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments.

Gutten, Ondrej / Jurečka, Petr / Aliakbar Tehrani, Zahra / Buděšínský, Miloš / Řezáč, Jan / Rulíšek, Lubomír

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 12, Page(s) 7280–7294

Abstract: Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR ... ...

Abstract	Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters.
MeSH term(s)	Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Nucleotides, Cyclic/chemistry ; Solutions ; Thermodynamics
Chemical Substances	Nucleotides, Cyclic ; Solutions
Language	English
Publishing date	2021-03-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp05993e
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Article ; Online: The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The

Fukal, Jiří / Buděšínský, Miloš / Páv, Ondřej / Jurečka, Petr / Zgarbová, Marie / Šebera, Jakub / Sychrovský, Vladimír

Journal of computational chemistry

2021 Volume 43, Issue 2, Page(s) 132–143

Abstract: A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of ... ...

Abstract	A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the
MeSH term(s)	DNA/chemistry ; Density Functional Theory ; Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Phosphorus
Chemical Substances	Phosphorus (27YLU75U4W) ; DNA (9007-49-2)
Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.26778
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Article: Synthesis of phosphonate derivatives of 2′-deoxy-2′-fluorotetradialdose d-nucleosides and tetradialdose d-nucleosides

Lášek, Tomáš / Dobiáš, Juraj / Buděšínský, Miloš / Kozák, Jaroslav / Lapuníková, Barbora / Rosenberg, Ivan / Birkuš, Gabriel / Páv, Ondřej

Tetrahedron. 2021 June 04, v. 89

2021

Abstract: Analogs of nucleosides and nucleotides represent a promising pool of potential therapeutics. This work describes a new synthetic route leading to 2′-deoxy-2′-fluorotetradialdose D-nucleoside phosphonates. Moreover, a new universal synthetic route leading ...

Abstract	Analogs of nucleosides and nucleotides represent a promising pool of potential therapeutics. This work describes a new synthetic route leading to 2′-deoxy-2′-fluorotetradialdose D-nucleoside phosphonates. Moreover, a new universal synthetic route leading to tetradialdose d-nucleosides bearing purine nucleobases is also described. All new compounds were tested as triphosphate analogs for inhibitory potency against a variety of viral polymerases. The fluorinated nucleosides were transformed to phosphoramidate prodrugs and evaluated in cell cultures against various viruses including influenza and SARS-CoV-2.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; influenza ; nucleobases ; nucleosides ; nucleotides ; phosphonates ; therapeutics
Language	English
Dates of publication	2021-0604
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	204285-x
ISSN	1464-5416 ; 0040-4020 ; 0563-2064
ISSN (online)	1464-5416
ISSN	0040-4020 ; 0563-2064
DOI	10.1016/j.tet.2021.132159
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Functional stapled fragments of human preptin of minimised length.

Lubos, Marta / Mrázková, Lucie / Gwozdiaková, Petra / Pícha, Jan / Buděšínský, Miloš / Jiráček, Jiří / Kaminský, Jakub / Žáková, Lenka

Organic & biomolecular chemistry

2022 Volume 20, Issue 12, Page(s) 2446–2454

Abstract: Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological ... ...

Abstract	Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological activities of six shortened analogues of human preptin. Eight- and nine-amino-acid-long peptide amides corresponding to the C-terminal part of human preptin were stabilised by two types of staples to induce a higher proportion of helicity in their secondary structure. We monitored the secondary structure of the stapled peptides using circular dichroism. The biological effect of the structural changes was determined afterwards by the ability of peptides to stimulate the release of intracellular calcium ions. We confirmed the previous observation that the stabilisation of the disordered conformation of human preptin has a deleterious effect on biological potency. However, surprisingly, one of our preptin analogues, a nonapeptide stabilised by olefin metathesis between positions 3 and 7 of the amino acid chain, had a similar ability to stimulate calcium ions' release to the full-length human preptin. Our findings could open up new ways to design new preptin analogues, which may have potential as drugs for the treatment of diabetes and osteoporosis.
MeSH term(s)	Bone and Bones ; Calcium ; Humans ; Insulin-Like Growth Factor II/chemistry ; Peptide Fragments/chemistry ; Peptides
Chemical Substances	Peptide Fragments ; Peptides ; preptin ; Insulin-Like Growth Factor II (67763-97-7) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d1ob02193a
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