The influenza RNA-dependent RNA polymerase harbours an endonuclease subunit characterized by a catalytic site housing two divalent metal ions. By effectively chelating both Mg2+ and Mn2+ ions, a small-molecule inhibitor with a metal-binding pharmacophore can halt endonuclease activity. Herein, two 3'-dehydroxypurpurogallin-4-carboxamide series, namely twelve C-4' unsubstituted and twelve C-4' phenyl substituted congeners were designed and prepared to be tested as inhibitors of the metal-dependent viral enzyme. These inhibitors were accessed through the chemoenzymatic reaction of gallic acid with either pyrocatechol or phenylpyrocatechol moderated by laccase, followed by amidation. Experimental IC50 values were determined using AlphaScreen technology, with the most potent inhibitors exhibiting IC50 values around 0.35 μM. Using X-ray crystallography, we analyzed structure of the endonuclease in complex with one potent 3'-dehydroxypurpurogallin-carboxamide at 2.0 Å resolution, revealing the coordination of the compound's triad of oxygen atoms with the two metal ions in the influenza A endonuclease active site.
- Klíčová slova
- Chemical synthesis, Endonuclease, Enzyme inhibition, Influenza, Metalloenzymes,
- MeSH
- amidy chemie farmakologie chemická syntéza MeSH
- antivirové látky * farmakologie chemická syntéza chemie MeSH
- endonukleasy * antagonisté a inhibitory metabolismus MeSH
- inhibitory enzymů * chemie chemická syntéza farmakologie MeSH
- katalytická doména MeSH
- krystalografie rentgenová MeSH
- mikrobiální testy citlivosti MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- virus chřipky A účinky léků enzymologie MeSH
- vztah mezi dávkou a účinkem léčiva MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- amidy MeSH
- antivirové látky * MeSH
- endonukleasy * MeSH
- inhibitory enzymů * MeSH
Ion channels represent a druggable family of transmembrane pore-forming proteins with important (patho)physiological functions. While electrophysiological measurement (manual patch clamp) remains the only direct method for detection of ion currents, it is a labor-intensive technique. Although automated patch clamp instruments have become available to date, their high costs limit their use to large pharma companies or commercial screening facilities. Therefore, fluorescence-based assays are particularly important for initial screening of compound libraries. Despite their numerous disadvantages, they are highly amenable to high-throughput screening and in many cases, no sophisticated instrumentation or materials are required. These features predispose them for implementation in early phases of drug discovery pipelines (hit identification), even in an academic environment. This review summarizes the advantages and pitfalls of individual methodological approaches for identification of ion channel modulators employing fluorescent probes (i. e., membrane potential and ion flux assays) with emphasis on practical aspects of their adaptation to high-throughput format.
- Klíčová slova
- Fluorescence-based assay, Fluorescent probes, High-throughput screening, Ion channels,
- MeSH
- fluorescence MeSH
- fluorescenční barviva * chemie farmakologie chemická syntéza MeSH
- iontové kanály * metabolismus antagonisté a inhibitory MeSH
- lidé MeSH
- objevování léků * MeSH
- rychlé screeningové testy * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- fluorescenční barviva * MeSH
- iontové kanály * MeSH
The extent to which electrophores covalently bridged by a saturated linker are electrochemically independent was investigated considering the charge/spin duality of the electron and functionality of the electrophore as a spin carrier upon reduction. By combining computational modeling with electrochemical experiments, we investigated the mechanism by which tethered electrophores react together within 4,4'-oligo[n]methylene-bipyridinium assemblies (with n=2 to 5). We show that native dicationic electrophores (redox state Z=+2) are folded prior to electron injection into the system, allowing the emergence of supra-molecular orbitals (supra-MOs) likely to support the process of the reductive σ bond formation giving cyclomers. Indeed, for Z=+2, London Dispersion (LD) forces contribute to flatten the potential energy surface such that all-trans and folded conformers are approximately isoenergetic. Then, upon one-electron injection, for radical cations (Z=+1), LD forces significantly stabilize the folded conformers, except for the ethylene derivative deprived of supra-MOs. For radical cations equipped with supra-MOs, the unpaired electron is delocalized over both heterocycles through space. Cyclomer completion (Z=0) upon the second electron transfer occurs according to the inversion of redox potentials. This mechanism explains why intramolecular reactivity is favored and why pyridinium electrophores are not independent.
- Klíčová slova
- London dispersion forces, computational chemistry, molecular electrochemistry, pyridinium, structure–activity relationship,
- Publikační typ
- časopisecké články MeSH
The binding process of insulin to its transmembrane receptor entails a sophisticated interplay between two proteins, each possessing two binding sites. Given the difficulties associated with the use of insulin in the treatment of diabetes, despite its remarkable efficacy, there is interest in smaller and more stable compounds than the native hormone that would effectively activate the receptor. Our study adopts a strategy focused on synthesizing extensive combinatorial libraries of bipodal compounds consisting of two distinct peptides linked to a molecular scaffold. These constructs, evaluated in a resin bead-bound format, were designed to assess their binding to the insulin receptor. Despite notable nonspecific binding, our approach successfully generated and tested millions of compounds. Rigorous evaluations via flow cytometry and specific antibodies revealed peptide sequences with specific interactions at either receptor binding Site 1 or 2. Notably, these sequences bear similarity to peptides discovered through phage display by other researchers. This convergence of chemical and biological methods underscores nature's beauty, revealing general principles in peptide binding to the insulin receptor. Overall, our study deepens the understanding of molecular interactions in ligand binding to the insulin receptor, highlighting the challenges of targeting large proteins with small synthetic peptides.
- Klíčová slova
- insulin, library, peptide, receptor, scaffold,
- MeSH
- inzulin metabolismus chemie MeSH
- knihovny malých molekul chemie farmakologie chemická syntéza MeSH
- lidé MeSH
- ligandy MeSH
- molekulární struktura MeSH
- peptidová knihovna MeSH
- peptidy chemie metabolismus chemická syntéza MeSH
- receptor inzulinu * metabolismus chemie MeSH
- techniky kombinatorické chemie * MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- inzulin MeSH
- knihovny malých molekul MeSH
- ligandy MeSH
- peptidová knihovna MeSH
- peptidy MeSH
- receptor inzulinu * MeSH
Kainate receptors play a crucial role in mediating synaptic transmission within the central nervous system. However, the lack of selective pharmacological tool compounds for the GluK3 subunit represents a significant challenge in studying these receptors. Recently presented compound 1 stands out as a potent antagonist of GluK3 receptors, exhibiting nanomolar affinity at GluK3 receptors and strongly inhibiting glutamate-induced currents at homomeric GluK1 and GluK3 receptors in HEK293 cells with Kb values of 65 and 39 nM, respectively. This study presents the synthesis of two potent GluK3-preferring iodine derivatives of compound 1, serving as precursors for radiolabelling. Furthermore, we demonstrate the optimisation of dehalogenation conditions using hydrogen and deuterium, resulting in [2H]-1, and demonstrate the efficient synthesis of the radioligand [3H]-1 with a specific activity of 1.48 TBq/mmol (40.1 Ci/mmol). Radioligand binding studies conducted with [3H]-1 as a radiotracer at GluK1, GluK2, and GluK3 receptors expressed in Sf9 and rat P2 membranes demonstrated its potential applicability for selectively studying native GluK3 receptors in the presence of GluK1 and 2-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor-blocking ligands.
- Klíčová slova
- ionotropic glutamate receptors, quinoxaline‐2,3‐diones, tritium labelling,
- MeSH
- AMPA receptory chemie metabolismus MeSH
- deuterium MeSH
- HEK293 buňky MeSH
- krysa rodu Rattus MeSH
- kyselina glutamová * MeSH
- lidé MeSH
- receptory kyseliny kainové * chemie metabolismus MeSH
- tritium MeSH
- zvířata MeSH
- Check Tag
- krysa rodu Rattus MeSH
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- AMPA receptory MeSH
- deuterium MeSH
- kyselina glutamová * MeSH
- receptory kyseliny kainové * MeSH
- tritium MeSH
Hybrid taxa from the genus Pelophylax can propagate themselves in a modified way of sexual reproduction called hybridogenesis ensuring the formation of clonal gametes containing the genome of only one parental (host) species. Pelophylax grafi from South-Western Europe is a hybrid composed of P. ridibundus and P. perezi genomes and it lives with a host species P. perezi (P-G system). Yet it is unknown, whether non-Mendelian inheritance is fully maintained in such populations. In this study, we characterize P. perezi and P. grafi somatic karyotypes by using comparative genomic hybridization, genomic in situ hybridization, fluorescent in situ hybridization, and actinomycin D-DAPI. Here, we show the homeology of P. perezi and P. grafi somatic karyotypes to other Pelophylax taxa with 2n = 26 and equal contribution of ridibundus and perezi chromosomes in P. grafi which supports F1 hybrid genome constitution as well as a hemiclonal genome inheritance. We show that ridibundus chromosomes have larger regions of interstitial (TTAGGG)n repeats flanking the nucleolus organizing region on chromosome no. 10 and a high quantity of AT pairs in the centromeric regions. In P. perezi, we found species-specific sequences in metaphase chromosomes and marker structures in lampbrush chromosomes. Pericentromeric RrS1 repeat sequence was present in perezi and ridibundus chromosomes, but the blocks were stronger in ridibundus. Various cytogenetic techniques applied to the P-G system provide genome discrimination between ridibundus and perezi chromosomal sets. They could be used in studies of germ-line cells to explain patterns of clonal gametogenesis in P. grafi and broaden the knowledge about reproductive strategies in hybrid animals.
- Klíčová slova
- Pelophylax grafi, Pelophylax perezi, comparative genomic hybridization, fluorescent in situ hybridization, hybridogenesis, karyotype,
- MeSH
- centromera * genetika MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- Ranidae * genetika MeSH
- srovnávací genomová hybridizace MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Specific biomarker molecules are increasingly being used for detection and quantification in plant and soil samples of arbuscular mycorrhizal (AM) fungi, an important and widespread microbial guild heavily implicated in transfers of nutrients and carbon between plants and soils and in the maintenance of soil physico-chemical properties. Yet, concerns have previously been raised as to the validity of a range of previously used approaches (e.g., microscopy, AM-specific fatty acids, sterols, glomalin-like molecules, ribosomal DNA sequences), justifying further research into novel biomarkers for AM fungal abundance and/or functioning. Here, we focused on complex polar lipids contained in pure biomass of Rhizophagus irregularis and in nonmycorrhizal and mycorrhizal roots of chicory (Cichorium intybus), leek (Allium porrum), and big bluestem (Andropogon gerardii). The lipids were analyzed by shotgun lipidomics using a high-resolution hybrid mass spectrometer. Size range between 1350 and 1550 Da was chosen for the detection of potential biomarkers among cardiolipins (1,3-bis(sn-3'-phosphatidyl)-sn-glycerols), a specific class of phospholipids. The analysis revealed a variety of molecular species, including cardiolipins containing one or two polyunsaturated fatty acids with 20 carbon atoms each, i.e., arachidonic and/or eicosapentaenoic acids, some of them apparently specific for the mycorrhizal samples. Although further verification using a greater variety of AM fungal species and samples from various soils/ecosystems/environmental conditions is needed, current results suggest the possibility to identify novel biochemical signatures specific for AM fungi within mycorrhizal roots. Whether they could be used for quantification of both root and soil colonization by the AM fungi merits further scrutiny.
- Klíčová slova
- Biomarker, Cardiolipins, Extraradical mycelium, Quantification, Root colonization, Shotgun lipidomics,
- MeSH
- česneky MeSH
- ekosystém MeSH
- houby MeSH
- kardiolipiny MeSH
- kořeny rostlin mikrobiologie MeSH
- mykorhiza * MeSH
- půda chemie MeSH
- rostliny MeSH
- uhlík MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kardiolipiny MeSH
- půda MeSH
- uhlík MeSH
Insulin is a key hormone involved in the regulation of overall energetic homeostasis of the organism. The dimeric character of the receptor for insulin evokes ideas about its activation or inhibition with peptide dimers that could either trigger or block the structural transition of the insulin receptor, leading to its activation. Herewith, we present the chemical engineering and biological characterization of several series of insulin dimers or dimers of specific peptides that should be able to bind receptors for insulin or insulin growth factor 1. The hormones or peptides in the dimers were interconnected with different linkers, consisting of triazole moieties and 3, 6, 8, 11, or 23 polyethylene glycol units. The prepared dimers were weaker in binding to insulin receptors than human insulin. However, some of the insulin dimers showed preferential binding specificity toward the isoform A of the insulin receptor, and the insulin dimers also stimulated the insulin receptor more strongly than would be consistent with their binding affinities. Our results suggest that designing insulin dimers may be a promising strategy for modulating the ability of the hormone to activate the receptor or to alter its specificity toward insulin receptor isoforms.
- Klíčová slova
- conjugation, dimer, insulin, peptide hormone, receptor, synthesis,
- MeSH
- inzulin metabolismus MeSH
- lidé MeSH
- peptidy * chemie MeSH
- polyethylenglykoly MeSH
- protein - isoformy MeSH
- receptor inzulinu * metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- inzulin MeSH
- peptidy * MeSH
- polyethylenglykoly MeSH
- protein - isoformy MeSH
- receptor inzulinu * MeSH
In bio-nanocomposites with a poly(lactic acid) (PLA)/poly(ε-caprolactone) (PCL) matrix with neat and polydopamine (PDA)-coated cellulose nanocrystals (CNCd), the use of different mixing protocols with masterbatches prepared by solution casting led to marked variation of localization, as well as reinforcing and structure-directing effects, of cellulose nanocrystals (CNC). The most balanced mechanical properties were found with an 80/20 PLA/PCL ratio, and complex PCL/CNC structures were formed. In the nanocomposites with a bicontinuous structure (60/40 and 40/60 PLA/PCL ratios), pre-blending the CNC and CNCd/PLA caused a marked increase in the continuity of mechanically stronger PLA and an improvement in related parameters of the system. On the other hand, improved continuity of the PCL phase when using a PCL masterbatch may lead to the reduction in or elimination of reinforcing effects. The PDA coating of CNC significantly changed its behavior. In particular, a higher affinity to PCL and ordering of PLA led to dissimilar structures and interface transformations, while also having antagonistic effects on mechanical properties. The negligible differences in bulk crystallinity indicate that alteration of mechanical properties may have originated from differences in crystallinity at the interface, also influenced by presence of CNC in this area. The complex effect of CNC on bio-nanocomposites, including the potential of PDA coating to increase thermal stability, is worthy of further study.
- Klíčová slova
- cellulose nanocrystals, poly(lactic acid), poly(ε-caprolactone), polydopamine coating,
- Publikační typ
- časopisecké články MeSH
All four iodinated 2'-deoxyribonucleoside triphosphates (dNTPs) derived from 5-iodouracil, 5-iodocytosine, 7-iodo-7-deazaadenine and 7-iodo-7-deazaguanine were prepared and studied as substrates for KOD XL DNA polymerase. All of the nucleotides were readily incorporated by primer extension and by PCR amplification to form DNA containing iodinated nucleobases. Systematic study of the Suzuki-Miyaura cross-coupling reactions with two bulkier arylboronic acids revealed that the 5-iodopyrimidines were more reactive and gave cross-coupling products both in the terminal or internal position in single-stranded oligonucleotides (ssONs) and in the terminal position of double-stranded DNA (dsDNA), whereas the 7-iodo-7-deazapurines were less reactive and gave cross-coupling products only in the terminal position. None of the four iodinated bases reacted in an internal position of dsDNA. These findings are useful for the use of the iodinated nucleobases for post-synthetic modification of DNA with functional groups for various applications.
- Klíčová slova
- DNA, bioconjugations, cross-coupling reactions, nucleotides, oligonucleotides,
- MeSH
- DNA-dependentní DNA-polymerasy metabolismus MeSH
- DNA chemie MeSH
- halogenace MeSH
- molekulární konformace MeSH
- nukleosidy chemická syntéza chemie MeSH
- puriny chemická syntéza chemie MeSH
- pyrimidiny chemická syntéza chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- 7-deazapurine MeSH Prohlížeč
- DNA-dependentní DNA-polymerasy MeSH
- DNA MeSH
- nukleosidy MeSH
- puriny MeSH
- pyrimidine MeSH Prohlížeč
- pyrimidiny MeSH
