@article{MTMT:34567562, title = {Saturation Transfer Difference NMR and Molecular Docking Interaction Study of Aralkyl-Thiodigalactosides as Potential Inhibitors of the Human-Galectin-3 Protein}, url = {https://m2.mtmt.hu/api/publication/34567562}, author = {Hőgye, Fanni and Farkas, László Bence and Balogh, Álex Kálmán and Szilágyi, László and Alnukari, Samar and Bajza, István and Borbás, Anikó and Fehér, Krisztina and Tóthné Illyés, Tünde Zita and Timári, István}, doi = {10.3390/ijms25031742}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {25}, unique-id = {34567562}, issn = {1661-6596}, abstract = {Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3′-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3′-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation–π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3.}, keywords = {lectin; NMR spectroscopy; Galectin-3; Molecular docking; STD NMR; thiodigalactosides}, year = {2024}, eissn = {1422-0067}, orcid-numbers = {Borbás, Anikó/0000-0001-8462-4547} } @article{MTMT:33693788, title = {Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis}, url = {https://m2.mtmt.hu/api/publication/33693788}, author = {Gönczi, Mónika and Teixeira, João M. C. and Barrera-Vilarmau, Susana and Mediani, Laura and Antoniani, Francesco and Nagy, Tamás Milán and Fehér, Krisztina and Ráduly, Zsolt and Ambrus, Viktor Attila and Tőzsér, József and Barta, Endre and E Kövér, Katalin and Csernoch, László and Carra, Serena and Fuxreiter, Mónika}, doi = {10.1038/s41467-023-37017-7}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {14}, unique-id = {33693788}, issn = {2041-1723}, abstract = {During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process.}, keywords = {CELL BIOLOGY; Structural biology; Computational biology and bioinformatics}, year = {2023}, eissn = {2041-1723}, orcid-numbers = {Barta, Endre/0000-0002-6753-0714; Carra, Serena/0000-0003-0939-0140} } @article{MTMT:32707268, title = {Investigation of the Molecular Details of the Interactions of Selenoglycosides and Human Galectin-3}, url = {https://m2.mtmt.hu/api/publication/32707268}, author = {Hadháziné Raics, Mária and Balogh, Álex Kálmán and Kishor, Chandan and Timári, István and Medrano, Francisco J. and Romero, Antonio and Go, Rob Marc and Blanchard, Helen and Szilágyi, László and E Kövér, Katalin and Fehér, Krisztina}, doi = {10.3390/ijms23052494}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {23}, unique-id = {32707268}, issn = {1661-6596}, abstract = {Human galectin-3 (hGal-3) is involved in a variety of biological processes and is implicated in wide range of diseases. As a result, targeting hGal-3 for clinical applications has become an intense area of research. As a step towards the development of novel hGal-3 inhibitors, we describe a study of the binding of two Se-containing hGal-3 inhibitors, specifically that of di(β-Dgalactopyranosyl)selenide (SeDG), in which two galactose rings are linked by one Se atom and a di(β-D-galactopyranosyl)diselenide (DSeDG) analogue with a diseleno bond between the two sugar units. The binding affinities of these derivatives to hGal-3 were determined by 15N-1H HSQC NMR spectroscopy and fluorescence anisotropy titrations in solution, indicating a slight decrease in the strength of interaction for SeDG compared to thiodigalactoside (TDG), a well-known inhibitor of hGal-3, while DSeDG displayed a much weaker interaction strength. NMR and FA measurements showed that both seleno derivatives bind to the canonical S face site of hGal-3 and stack against the conserved W181 residue also confirmed by X-ray crystallography, revealing canonical properties of the interaction. The interaction with DSeDG revealed two distinct binding modes in the crystal structure which are in fast exchange on the NMR time scale in solution, explaining a weaker interaction with hGal-3 than SeDG. Using molecular dynamics simulations, we have found that energetic contributions to the binding enthalpies mainly differ in the electrostatic interactions and in polar solvation terms and are responsible for weaker binding of DSeDG compared to SeDG. Selenium-containing carbohydrate inhibitors of hGal-3 showing canonical binding modes offer the potential of becoming novel hydrolytically stable scaffolds for a new class of hGal-3 inhibitors.}, keywords = {lectin; X-RAY CRYSTALLOGRAPHY; NMR spectroscopy; molecular dynamics; Galectin-3; Selenoglycosides; Fluorescence anisotropy}, year = {2022}, eissn = {1422-0067}, orcid-numbers = {Kishor, Chandan/0000-0002-6328-1116; Romero, Antonio/0000-0002-6990-6973; Blanchard, Helen/0000-0003-3372-5027} } @article{MTMT:32603044, title = {77Se-Enriched Selenoglycoside Enables Significant Enhancement in NMR Spectroscopic Monitoring of Glycan–Protein Interactions}, url = {https://m2.mtmt.hu/api/publication/32603044}, author = {Timári, István and Balla, Sára and Fehér, Krisztina and E Kövér, Katalin and Szilágyi, László}, doi = {10.3390/pharmaceutics14010201}, journal-iso = {PHARMACEUTICS}, journal = {PHARMACEUTICS}, volume = {14}, unique-id = {32603044}, issn = {1999-4923}, abstract = {Detailed investigation of ligand–protein interactions is essential for better understanding of biological processes at the molecular level. Among these binding interactions, the recognition of glycans by lectins is of particular importance in several diseases, such as cancer; therefore, inhibition of glycan-lectin/galectin interactions represents a promising perspective towards developing therapeutics controlling cancer development. The recent introduction of 77Se NMR spectroscopy for monitoring the binding of a selenoglycoside to galectins prompted interest to optimize the sensitivity by increasing the 77Se content from the natural 7.63% abundance to 99%. Here, we report a convenient synthesis of 77Se-enriched selenodigalactoside (SeDG), which is a potent ligand of the medically relevant human galectin-3 protein, and proof of the expected sensitivity gain in 2D 1H, 77Se correlation NMR experiments. Our work opens perspectives for adding isotopically enriched selenoglycans for rapid monitoring of lectin-binding of selenated as well as non-selenated ligands and for ligand screening in competition experiments.}, keywords = {lectin; NMR spectroscopy; HSQMBC; CHEMICAL SYNTHESIS; glycan; ligand-protein binding; 77Se isotope; selenodigalactoside; TDG}, year = {2022}, eissn = {1999-4923} } @article{MTMT:32235245, title = {Conformation of Immune Stimulatory Single Stranded DNA by Biomolecular Simulations and NMR}, url = {https://m2.mtmt.hu/api/publication/32235245}, author = {Toth, Barna and Fehér, Krisztina}, doi = {10.1021/scimeetings.1c01247}, journal-iso = {BIOPHYS J}, journal = {BIOPHYSICAL JOURNAL}, volume = {120}, unique-id = {32235245}, issn = {0006-3495}, abstract = {Immunotherapies require novel type of delivery systems with specifically tailored adjuvants to activate immune responses. Among immune stimulators of microbial origin, oligodeoxynucleotides (ODNs) represent the most advanced potential adjuvants. ODNs are unmethylated single stranded DNA (ssDNA) sequences with CpG-motifs, which are able to activate the innate immune system by binding to TLR9 receptors. Adjuvant effects are optimized by maintaining ODNs and vaccine antigens in close proximity, which can be achieved by loading the immune stimulator and the antigen cargo to an appropriate carrier such as inorganic nanoparticles. Immobilisation of ODN immune stimulators onto the surface of nanoparticles while maintaining multivalent presentation to TLR9 receptors requires knowledge of their conformational properties. De novo modelling of ssDNA conformation, opposed to that of double stranded DNA, is challenging due to multiple reasons. ssDNA lacks stable structures and can only be described as an ensemble of interconverting conformations, thus methods for adequate sampling of the conformational space need to be applied. Force fields for simulation of DNAs were, however, developed by testing them mainly on duplex DNA and their ability to reproduce conformations of ssDNA is unclear. In this regard, modelling of ssDNA likely face similar challenges as modelling of Intrinsically Disordered Proteins. We set out to test the accuracy of existing DNA force fields using atomistic molecular dynamics (MD) simulations and NMR spectroscopy. Translational diffusion coefficients were obtained from diffusion experiments and compared to translational diffusion coefficients, radius of gyration and end-to-end distances calculated from MD simulations. Furthermore, we analysed secondary structure formation and descriptors of dynamic behaviour. Outcome of comparisons for different DNA force fields are discussed.}, year = {2021}, eissn = {1542-0086}, pages = {218A-218A} } @article{MTMT:32217410, title = {Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations}, url = {https://m2.mtmt.hu/api/publication/32217410}, author = {Balogh, Gábor and Gyöngyösi, Tamás and Timári, István and Herczeg, Mihály and Borbás, Anikó and Sadiq, S. Kashif and Fehér, Krisztina and E Kövér, Katalin}, doi = {10.1021/acs.jcim.1c00200}, journal-iso = {J CHEM INF MODEL}, journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING}, volume = {61}, unique-id = {32217410}, issn = {1549-9596}, year = {2021}, eissn = {1549-960X}, pages = {2926-2936}, orcid-numbers = {Herczeg, Mihály/0000-0002-7938-9789; Borbás, Anikó/0000-0001-8462-4547} } @article{MTMT:32201080, title = {The retention of Zr from potential therapeutic silica-zirconia core-shell nanoparticles in aquatic organisms}, url = {https://m2.mtmt.hu/api/publication/32201080}, author = {Sajtos, Zsófi and Fehér, Milán and Molnár, Áron and Stündl, László and Nagyné Naszályi, Lívia and Martins, José C. and Harangi, Sándor and Magyar, István and Fehér, Krisztina and Baranyai, Edina}, doi = {10.1016/j.enmm.2021.100572}, journal-iso = {ENVIRON NANOTECH MONITOR MANAG}, journal = {ENVIRONMENTAL NANOTECHNOLOGY MONITORING AND MANAGEMENT}, volume = {16}, unique-id = {32201080}, abstract = {Model experiments under laboratory conditions were carried out to assess the accumulation tendency of Zr from a silica-zirconia core-shell nanoparticles, synthesised for the assay. Acute exposition tests were conducted with Daphnia magna and Danio rerio and the accumulation tendency of the nano and the molecular form was compared. Significant elevation of Zr was found in the tissue of the test organisms treated by the NP compared to the control, however, the retention of zebrafish was lower than that of the daphnids. Increased level of bioconcentration factor and the strong correlation of the redundancy analysis data suggest accumulation tendency in D. magna, yet long-term experiments are required to prove and further assess the environmental risk of food-chain bioconcentration. The BCF results were under the REACH limit for the D. rerio groups indicating the low short-term accumulation tendency of Zr from the NP. However, Zr level was significantly higher in zebrafish individuals originating from the SiO2@ZrO2 NP exposed treatments compared to the groups supplemented by the same concentration of ZrOCl2, which did not result in the elevation of Zr in fish tissue. The trace element homeostasis of D. rerio was not affected by the acute SiO2@ZrO2 NP exposition and no lethality occurred.}, year = {2021}, eissn = {2215-1532}, orcid-numbers = {Fehér, Milán/0000-0002-4816-9329; Nagyné Naszályi, Lívia/0000-0003-2799-1150} } @article{MTMT:32164498, title = {Silica@zirconia Core@shell Nanoparticles for Nucleic Acid Building Block Sorption}, url = {https://m2.mtmt.hu/api/publication/32164498}, author = {Nagyné Naszályi, Lívia and Dhaene, Evert and Van Zele, Matthias and Mihály, Judith and Klébert, Szilvia and Varga, Zoltán and E Kövér, Katalin and De Buysser, Klaartje and Van Driessche, Isabel and Martins, José C. and Fehér, Krisztina}, doi = {10.3390/nano11092166}, journal-iso = {NANOMATERIALS-BASEL}, journal = {NANOMATERIALS}, volume = {11}, unique-id = {32164498}, abstract = {The development of delivery systems for the immobilization of nucleic acid cargo molecules is of prime importance due to the need for safe administration of DNA or RNA type of antigens and adjuvants in vaccines. Nanoparticles (NP) in the size range of 20–200 nm have attractive properties as vaccine carriers because they achieve passive targeting of immune cells and can enhance the immune response of a weakly immunogenic antigen via their size. We prepared high capacity 50 nm diameter silica@zirconia NPs with monoclinic/cubic zirconia shell by a green, cheap and up-scalable sol–gel method. We studied the behavior of the particles upon water dialysis and found that the ageing of the zirconia shell is a major determinant of the colloidal stability after transfer into the water due to physisorption of the zirconia starting material on the surface. We determined the optimum conditions for adsorption of DNA building blocks, deoxynucleoside monophosphates (dNMP), the colloidal stability of the resulting NPs and its time dependence. The ligand adsorption was favored by acidic pH, while colloidal stability required neutral-alkaline pH; thus, the optimal pH for the preparation of nucleic acid-modified particles is between 7.0–7.5. The developed silica@zirconia NPs bind as high as 207 mg dNMPs on 1 g of nanocarrier at neutral-physiological pH while maintaining good colloidal stability. We studied the influence of biological buffers and found that while phosphate buffers decrease the loading dramatically, other commonly used buffers, such as HEPES, are compatible with the nanoplatform. We propose the prepared silica@zirconia NPs as promising carriers for nucleic acid-type drug cargos.}, year = {2021}, eissn = {2079-4991}, orcid-numbers = {Nagyné Naszályi, Lívia/0000-0003-2799-1150; Dhaene, Evert/0000-0002-1604-0408; Van Zele, Matthias/0000-0001-5809-4108; Klébert, Szilvia/0000-0002-3107-3371; Varga, Zoltán/0000-0002-5741-2669; De Buysser, Klaartje/0000-0001-7462-2484; Martins, José C./0000-0001-7350-2253} } @article{MTMT:31606798, title = {Adamantane Containing Peptidoglycan Fragments Enhance RANTES and IL-6 Production in Lipopolysaccharide-Induced Macrophages}, url = {https://m2.mtmt.hu/api/publication/31606798}, author = {Manček-Keber, Mateja and Ribić, Rosana and Chain, Fernando and Sinnaeve, Davy and Martins, José C. and Jerala, Roman and Tomić, Srđanka and Fehér, Krisztina}, doi = {10.3390/molecules25163707}, journal-iso = {MOLECULES}, journal = {MOLECULES}, volume = {25}, unique-id = {31606798}, issn = {1420-3049}, abstract = {We report the enhancement of the lipopolysaccharide-induced immune response by adamantane containing peptidoglycan fragments in vitro. The immune stimulation was detected by Il-6 (interleukine 6) and RANTES (regulated on activation, normal T cell expressed and secreted) chemokine expression using cell assays on immortalized mouse bone-marrow derived macrophages. The most active compound was a α-D-mannosyl derivative of an adamantylated tripeptide with L-chirality at the adamantyl group attachment, whereby the mannose moiety assumed to target mannose receptors expressed on macrophage cell surfaces. The immune co-stimulatory effect was also influenced by the configuration of the adamantyl center, revealing the importance of specific molecular recognition event taking place with its receptor. The immunostimulating activities of these compounds were further enhanced upon their incorporation into lipid bilayers, which is likely related to the presence of the adamantyl group that helps anchor the peptidoglycan fragment into lipid nanoparticles. We concluded that the proposed adamantane containing peptidoglycan fragments act as co-stimulatory agents and are also suitable for the preparation of lipid nanoparticle-based delivery of peptidoglycan fragments.}, keywords = {mannose; immunostimulation; PEPTIDOGLYCAN; ADAMANTANE; lipid incapsulation}, year = {2020}, eissn = {1420-3049} } @article{MTMT:31495393, title = {Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface}, url = {https://m2.mtmt.hu/api/publication/31495393}, author = {Ribic, Rosana and Mancek-Keber, Mateja and Chain, Fernando and Sinnaeve, Davy and Martins, Jose C. and Jerala, Roman and Tomic, Srdanka and Fehér, Krisztina}, doi = {10.1021/acs.jpcb.0c00029}, journal-iso = {J PHYS CHEM B}, journal = {JOURNAL OF PHYSICAL CHEMISTRY B}, volume = {124}, unique-id = {31495393}, issn = {1520-6106}, abstract = {We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.}, year = {2020}, eissn = {1520-5207}, pages = {4132-4145} }