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Institute of Chemistry> People> Stanislav KOZMON>
Stanislav KOZMON, PhD
Research Scientist


Tel.: +421-2-59410324
Fax: +421-2-59410222
Research Interests
  • theoretical/computational chemistry
  • application of molecular modeling methods (force field and quantum chemical methods) to study organic, pharmaceutical chemistry or biochemistry relevant topics
  • applications of high-level ab initio (HF, MPn, CC) and density functional theory (DFT) methods
  • molecular mechanics (MM), molecular dynamics (MD)
  • combined quantum mechanics and molecular mechanics (QM/MM) methods, QM/MM ab initio MD or metadynamics (MTD)
  • docking studies of the small molecules as enzyme inhibitors
Publications
  1. Tvaroska, I., Kozmon, S. & Kona, J.:
    Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review
    Cells-Basel 12, (2023).
  2. Stratilova, B., Sestak, S., Stratilova, E., Vadinova, K., Kozmon, S. & Hrmova, M.:
    Engineering of substrate specificity in a plant cell-wall modifying enzyme through alterations of carboxyl-terminal amino acid residues
    Plant J 116, 1529-1544 (2023).
  3. Stratilova, B., Kozmon, S., Stratilova, E. & Hrmova, M. in Glycoside Hydrolases: Biochemistry, Biophysics, and Biotechnology Vol. (ed^(eds Ch. 213-242 (Elsevier, 2023).
  4. Pancik, F., Pakanova, Z., Nemcovic, M., Kveton, F., Salingova, A., Hlavata, A., Kozmon, S. & Barath, P.:
    Application of MALDI-TOF Mass Spectrometry for Non-invasive Diagnostics of Mucopolysaccharidosis IIIA
    Journal of Inborn Errors of Metabolism and Screening 11, (2023).
  5. Stratilova, B., Stratilova, E., Hrmova, M. & Kozmon, S.:
    Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry
    Int. J. Mol. Sci. 23, (2022).
  6. Pancik, F., Pakanova, Z., Mecarova, J., Cizova, A., Bystricky, S., Kozmon, S. & Barath, P.:
    Fragmentation analysis of O-specific polysaccharide from bacteria Vibrio cholerae O139 by MALDI-TOF and LC/ESI-MS/MS
    Eur J Mass Spectrom 28, 47-55 (2022).
  7. Savkova, K., Huszar, S., Barath, P., Pakanova, Z., Kozmon, S., Vancova, M., Tesarova, M., Blasko, J., Kalinak, M., Singh, V., Kordulakova, J. & Mikusova, K.:
    An ABC transporter Wzm-Wzt catalyzes translocation of lipid-linked galactan across the plasma membrane in mycobacteria
    P Natl Acad Sci USA 118, (2021).
  8. Houser, J., Kozmon, S., Mishra, D., Hammerova, Z., Wimmerova, M. & Koca, J.:
    The analysis of CH-p interaction in protein-carbohydrate binding
    Acta Crystallogr A 77, C689-C689 (2021).
  9. Stratilova, B., Sestak, S., Mravec, J., Garajova, S., Pakanova, Z., Vadinova, K., Kucerova, D., Kozmon, S., Schwerdt, J. G., Shirley, N., Stratilova, E. & Hrmova, M.:
    Another building block in the plant cell wall: Barley xyloglucan xyloglucosyl transferases link covalently xyloglucan and anionic oligosaccharides derived from pectin
    Plant J 104, 752-767 (2020).
  10. Stratilova, B., Kozmon, S., Stratilova, E. & Hrmova, M.:
    Plant Xyloglucan Xyloglucosyl Transferases and the Cell Wall Structure: Subtle but Significant
    Molecules 25, (2020).
  11. Barath, M., Jakubcinova, J., Konyarikova, Z., Kozmon, S., Mikusova, K. & Bella, M.:
    Synthesis, docking study and biological evaluation of D-fructofuranosyl and D-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2
    Beilstein J Org Chem 16, 1853-1862 (2020).
  12. Houser, J., Kozmon, S., Mishra, D., Hammerova, Z., Wimmerova, M. & Koca, J.:
    The CH-pi interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification
    Chemistry – A European Journal, (2020).
  13. Jakubcinova, J., Kozmon, S., Sestak, S. & Barath, M.:
    Novel 1-O-Sulfono-alpha-d-Fructofuranosyl Sulfones as Possible Inhibitors of Human GnT-I Enzyme
    Chemistryselect 5, 4967-4972 (2020).
  14. Konyarikova, Z., Savkova, K., Kozmon, S. & Mikusova, K.:
    Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target?
    Antibiotics-Basel 9, (2020).
  15. Stratilova, B., Rehulka, P., Garajova, S., Rehulkova, H., Stratilova, E., Hrmova, M. & Kozmon, S.:
    Structural characterization of the Pet c 1.0201 PR-10 protein isolated from roots of Petroselinum crispum (Mill.) Fuss
    Phytochemistry 175, (2020).
  16. Hammerova, Z., Houser, J., Kozmon, S., Mishra, D., Wimmerova, M. & Koca, J.:
    Interactions of carbohydrate and aromatic amino acid in protein binding sites
    Febs Open Bio 9, 251-252 (2019).
  17. Mastihuba, V., Potocka, E. K., Uhliarikova, I., Kis, P., Kozmon, S. & Mastihubova, M.:
    Reaction mechanism of beta-apiosidase from Aspergillus aculeatus
    Food Chem 274, 543-546 (2019).
  18. Stratilova, B., Firakova, Z., Klaudiny, J., Sestak, S., Kozmon, S., Strouhalova, D., Garajova, S., Ait-Mohand, F., Horvathova, A., Farkas, V., Stratilova, E. & Hrmova, M.:
    Engineering the acceptor substrate specificity in the xyloglucan endotransglycosylase TmXET6.3 from nasturtium seeds (Tropaeolum majus L.)
    Plant Mol.Biol. 100, 181-197 (2019).
  19. Janos, P., Kozmon, S., Tvaroska, I. & Koca, J.:
    How Mycobacterium tuberculosis Galactofuranosyl Transferase2 (GlfT2) Generates Alternating beta-(1-6) and beta-(1-5) Linkages: AQM/MM Molecular Dynamics Study of the Chemical Steps
    Chem-Eur J 24, 7051-7059 (2018).
  20. Stratilova, B., Klaudiny, J., Rehulka, P., Stratilova, E., Meszarosova, C., Garajova, S., Pavlatovska, B., Rehulkova, H., Kozmon, S., Sestak, S., Firakova, Z. & Vadkertiova, R.:
    Characterization of a long-chain alpha-galactosidase from Papiliotrema flavescens
    World J Microb Biot 34, (2018).
  21. Suchova, K., Kozmon, S., Puchart, V., Malovikova, A., Hoff, T., Morkeberg Krogh, K. B. R. & Biely, P.:
    Glucuronoxylan recognition by GH 30 xylanases: A study with enzyme and substrate variants
    Archives of Biochemistry and Biophysics 643, 42-49 (2018).
  22. Zufanova, Z., Houser, J., Kozmon, S., Mishra, D., Wimmerova, M. & Koca, J.:
    Importance of CH-pi stacking interaction in carbohydrate-protein complexes
    Febs Open Bio 8, 385-385 (2018).
  23. Bella, M., Yan, S., Sestak, S., Kozmon, S., Lin, C.-H., Mucha, J. & Koos, M.:
    Synthesis of a β-d-Psicofuranosyl Sulfone and Inhibitory-Activity Evaluation Against N-Acetylglucosaminyltransferase I
    European Journal of Organic Chemistry 2017, 6179-6191 (2017).
  24. Houser, J., Kozmon, S., Mishra, D., Mishra, S. K., Romano, P. R., Wimmerova, M. & Koca, J.:
    Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL
    Plos One 12, e0189375 (2017).
  25. Janos, P., Kozmon, S., Tvaroska, I. & Koca, J.:
    Three-dimensional homologymodel of GlcNAc-TV glycosyltransferase
    Glycobiology 26, 757-771 (2016).
  26. Janos, P., Trnka, T., Kozmon, S., Tvaroska, I. & Koca, J.:
    Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2
    Journal of Chemical Theory and Computation 12, 6062-6076 (2016).
  27. Kozmon, S. & Tvaroska, I.:
    Molecular dynamic studies of amyloid-beta interactions with curcumin and Cu2+ ions
    Chem. Pap. 69, 1262-1276 (2015).
  28. Kumari, M., Kozmon, S., Kuhanek, P., Stepan, J., Tvaroska, I. & Koca, J.:
    Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study
    J. Phys. Chem. B 119, 4371-4381 (2015).
  29. Trnka, T., Kozmon, S., Tvaroska, I. & Koca, J.:
    Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
    PLoS Comput Biol 11, e1004061 (2015).
  30. Tvaroska, I., Kozmon, S., Wimmerova, M. & Koca, J.:
    A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta 1,6-N-Acetylglucosaminyltransferase
    Chem-Eur J 19, 8153-8162 (2013).
  31. Nagy, V., Felfoldi, N., Konya, B., Praly, J. P., Docsa, T., Gergely, P., Chrysina, E. D., Tiraidis, C., Kosmopoulou, M. N., Alexacou, K. M., Konstantakaki, M., Leonidas, D. D., Zographos, S. E., Oikonomakos, N. G., Kozmon, S., Tvaroska, I. & Somsak, L.:
    N-(4-Substituted-benzoyl)-N '-(beta-D-glucopyranosyl)ureas as inhibitors of glycogen phosphorylase: Synthesis and evaluation by kinetic, crystallographic, and molecular modelling methods
    Bioorgan Med Chem 20, 1801-1816 (2012).
  32. Tvaroska, I., Kozmon, S., Wimmerova, M. & Koca, J.:
    Substrate-assisted catalytic mechanism of O-GlcNAc transferase discovered by quantum mechanics/molecular mechanics investigation
    Journal of the American Chemical Society 134, 15563-15571 (2012).
  33. Wimmerova, M., Kozmon, S., Necasova, I., Mishra, S. K., Komarek, J. & Koca, J.:
    Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
    Plos One 7, (2012).
  34. Both, P., Sobczak, L., Breton, C., Hann, S., Nobauer, K., Paschinger, K., Kozmon, S., Mucha, J. & Wilson, I. B. H.:
    Distantly related plant and nematode core alpha 1,3-fucosyltransferases display similar trends in structure-function relationships
    Glycobiology 21, 1401-1415 (2011).
  35. Kozmon, S., Matuska, R., Spiwok, V. & Koca, J.:
    Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH-pi interaction additive properties
    Phys. Chem. Chem. Phys. 13, 14215-14222 (2011).
  36. Kozmon, S., Matuska, R., Spiwok, V. & Koca, J.:
    Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/pi Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods
    Chem-Eur J 17, 5680-5690 (2011).
  37. Nurisso, A., Kozmon, S. & Imberty, A.:
    Comparison of docking methods for carbohydrate binding in calcium-dependent lectins and prediction of the carbohydrate binding mode to sea cucumber lectin CEL-III
    Mol. Simul. 34, 469-479 (2008).
  38. Sihelnikova, L., Kozmon, S. & Tvaroska, I.:
    DFT and docking study of potential transition state analogue inhibitors of glycosyltransferases
    Collect. Czech. Chem. Commun. 73, 591-607 (2008).
  39. Kozmon, S. & Tvaroska, I.:
    Catalytic mechanism of glycosyltransferases: Hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I
    Journal of the American Chemical Society 128, 16921-16927 (2006).
  40. Kozmon, S. & Tvaroska, I.:
    DFT study on 3-substituted tetrahydropyran-2-yl radicals
    Collect. Czech. Chem. Commun. 71, 1453-1469 (2006).
  41. Kona, J., Zahradnik, P., Kozmon, S. & Fabian, W. M. F.:
    Role of solvent effects on nucleophilic substitution of 4H-pyran-4-one and its 2,6-dimethyl derivative with hydroxide ion in aqueous solution: ab initio and density functional theory studies on a supermolecular reaction model
    J Mol Struc-Theochem 728, 117-122 (2005).
  42. Raab, M., Kozmon, S. & Tvaroska, I.:
    Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior
    Carbohydr. Res. 340, 1051-1057 (2005).
Institute of Chemistry
Slovak Academy of Sciences
webmaster@chem.sk
2017