Kapica M., Grabowska O., Dębowski D., Marszałek M., Tesmar A., Kamysz E., Wyrzykowski D., Samsonov S.A. Physicochemical Insights into the Interaction of Cationic Peptides (KR12 and TAT47-57) with Decavanadate: An Integrated ITC and Molecular Dynamics Study. Phys Chem Chem Phys. 2026. In press.
Grzywacz D., Nutti F., Żamojć K., Samsonov S.A., Malinowska M., Paduszyńska M., Papini A.M., Makowska J. Influence of N- and O-glycosylation on metal binding and structural properties of a C-terminal LL-37 fragment. Carbohydr Res. 2026. Vol. 563, 109872.
Le Fournis C., Maszota-Zeleniak M., Kulesza A., Chopra P., Boons G.-J., Aubrey N., Liesecke F., Samsonov S.A., Weber G. Structural determinants of glycosaminoglycan oligosaccharides as LL-37-inhibitors in breast cancer. Glycobiology. 2026. Vol. 36, cwag010.
Kapica M., Grabowska O., Kamysz E., Kamysz J., Samsonov S.A., Wyrzykowski D. Cyclodextrin and KR12-Lipopeptide Interactions: A Thermodynamic View of Binding Mechanisms and Impact on the Structure of α-Helical Peptides. J Phys Chem B. 2026. Vol. 130, 1167–1174.
Tsushima S., Seal A., Samsonov S.A., Fahmy K., Takao K. Macrocyclic and Hydroxamate Ligands for 225Ac Radiopharmaceuticals: Evaluating SSTR2-Targeting Potential. Inorg Chem. 2025. DOI
Clark J., Zykwinska A., Colliec-Jouault S., Samsonov S.A. Modeling highly sulfated Infernan. Carbohydr Res. 2025. Vol. 558, 109759. DOI
Pavan N., Grabowska O., Wyrzykowski D., Samsonov S.A. Heparin Inclusion in Cyclodextrins: A Combined MD and ITC Study. TASK Quarterly. 2025. DOI
David A., Domain R., Surback F., Vibert A., Buisson P., Maszota-Zieleniak M., Landemarre L., Schuler M., Lalmanach G., Samsonov S.A., Lopin-Bon C., Lecaille F. Deciphering minimal size of chondroitin 4-sulfate oligomers to develop innovative inhibitors of cathepsin S. Polysaccharides. 2025. Vol. 6, 99. DOI
Samsonov S.A., Frączyk T., Ufnalska I., Bal W. Molecular dynamics study of the impact of glycosylation on conformational properties of trimeric N-terminal domain of human copper transporter 1. Carbohydr Res. 2025. Vol. 558, 109708. DOI
Samsonov S.A., Ricard-Blum S. Molecular Dynamics Insights into Glycosaminoglycan Effects on the Extracellular Domains of Syndecan 2 and 4 Dimers. Carbohydr Res. 2025. Vol. 558, 109690. DOI
Clark J., Samsonov S.A. Modeling and simulation of protein-carbohydrate interaction. Comprehensive Biophysics, 2nd Ed. Editor: Zacharias. Elsevier. 2025. DOI
Grabowska O., Żamojć K., Kloska A., Niedziałkowski P., Samsonov S.A., Wyrzykowski D. An interdisciplinary study of lysozyme interactions with hexacyanoferrate(III)/(II) ions. International Journal of Molecular Sciences. 2025. Vol. 26, 8511. DOI
David A., Rigoux B., Maszota-Zieleniak M., Sinquin C., Neau C., Zykwinska A., Saidi A., Lalmanach G., Samsonov S.A., Colliec-Jouault S., Lecaille F. Selective inhibition of cathepsin S elastolytic activity by exopolysaccharides from deep-sea hydrothermal bacteria. Carbohydrate Polymers. 2025. Vol. 367, 123968. DOI
Babuty A., Zykwinska A., Samsonov S.A., Candia N., Veinstein C., Pugniere M., Ngo T. H. G., Sinquin C., Munoz-Garcia J., Colliec-Jouault S., Heymann D. Anticoagulant Potential of Modified Sulfated Exopolysaccharides from Deep-Sea Bacteria: Toward Non-Animal Heparin Alternatives. Polysaccharides. 2025. Vol. 6, 54. DOI
Grabowska O., Kogut-Günthel M., Samsonov S.A., Wyrzykowski D., Makowska J. β-CD saves lysozyme from the clutches of 1-alkylsulfonates. Journal of Molecular Liquids. 2025. Vol. 428, 127543. DOI
Kapica M., Kamysz E., Grabowska O., Tesmar A., Pająk M., Chmur K., Brzeski J., Samsonov S.A., Wyrzykowski D. Interactions of Laurylated and Myristoylated KR12 Fragment of the LL37 peptide with Polyoxidovanadates. Molecules. 2025. Vol. 30, 1589. DOI
Samsonov S.A., Marcisz M. Decrypting Glycosaminoglycan "sulfation code" with Computational Approaches. Handbook of Experimental Pharmacology - Complex Carbohydrates. Editors: Tauber, Pfengle, Pagel. Springer. 2025. 1-23. DOI
Pągielska M., Samsonov S.A. The Amazing World of Glycosaminoglycans through the Eyes of a Theoretician. Glycoforum. 2025. Vol. 27, A25. DOI
Danielsson A., Samsonov S.A., Sieradzan A.K. Implementation of the UNRES/SUGRES-1P Coarse-Grained Model of Heparin for Simulating Protein/Heparin Interactions. J Chem Theor Comp. 2024. Vol. 20: 10703-10715. DOI
Bojarski K.K., David A., Lecaille F., Samsonov S.A. In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions. Carbohydrate Research. 2024. Vol. 543: 109201. DOI
Santini B.L., Gaardløs M., Wyrzykowski D., Rothemund S., Penk A., Zacharias M., Samsonov S.A. Rational Design of Glycosaminoglycan Binding Cyclic Peptides using cPEPmatch. Computational and Structural Biotechnology. 2024. Vol. 23: 2985–2994. DOI
Mańkowska M., Krzymiński K., Wyrzykowski D., Zadykowicz B., Samsonov S.A. Why do ionic surfactants significantly alter the chemiluminogenic properties of acridinium salt? Molecules. 2024. Vol. 29: 3736. DOI
Uciechowska-Kaczmarzyk U., Frank M., Samsonov S.A., Maszota-Zieleniak M. Structural insights into the endostatin-heparan sulfate interactions by modeling approaches. Molecules. 2024. Vol. 29: 4040. DOI
Anila S., Samsonov S.A. Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. J Chem Inf Mod. 2024. Vol. 64: 1691–1703. DOI
Grabowska O., Samsonov S.A., Kogut-Günthel M., Żamojć K., Wyrzykowski D. Elucidation of binding mechanisms of bovine serum albumin and 1-alkylsulfonates with different hydrophobic chain lengths. International Journal of Biological Macromolecules. 2024. Vol. 266: 131134. DOI
Bertozo L., Tadeu H.S., Sebastian A., Maszota-Zieleniak M., Samsonov S.A., Ximenes V. A Role for Carboxylic Acid Moiety in NSAIDs: Favoring the Binding at Site II of Bovine Serum Albumin. Molecular Pharmaceutics. 2024. Vol. 21: 2501–2511. DOI
Lensink M.F. et al. (incl. Maszota-Zieleniak M., Bojarski K.K., Marcisz M., Danielsson A., Gaardløs M., Samsonov S.A.) Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment. Proteins. 2023. Vol. 91: 1658–1683.
Brzeski J., Nowicka P., Samsonov S.A. The effect of Pd(II) and Pt(II) coordination on the affinity of avibactam to OXA-48 β-lactamase. Eur J Med Chem Rep. 2023. Vol. 9: 100118. DOI
Penk A., Danielsson A., Gaardløs M., Montag C., Schöler A., Huster D., Samsonov S.A., Künze G. Detecting protein-ligand interactions with nitroxide based paramagnetic cosolutes. Chemistry - A European Journal. 2023. e202303570. DOI
Marcisz M., Anila S., Gaardløs M., Zacharias M., Samsonov S.A. Studying specificity in protein-glycosaminoglycan recognition with umbrella sampling. Beilstein Journal of Organic Chemistry. 2023. Vol. 19: 1933–1946. DOI
Schulze C., Danielsson A., Liwo A., Huster D., Samsonov S.A., Penk A. Ligand Binding of Interleukin-8: A Comparison of Glycosaminoglycans and Acidic Peptides. Phys Chem Chem Phys. 2023. Vol. 25: 24930–24947. DOI
Maszota-Zieleniak M., Samsonov S.A. Molecular dynamics simulation-based prediction of glycosaminoglycan interactions with drug molecules. Computational Drug Discovery and Design (2nd Ed.). Methods in Molecular Biology Series. Springer. 2023. 143-154. DOI
Maszota-Zieleniak M., Liwo A., Ricard-Blum S., Samsonov S.A. Interplay of heparan sulfate chains with the core proteins of syndecans 2 and 4. Proteoglycan Research. 2023. Vol. 1: e10. DOI
Danielsson A., Samsonov S.A., Liwo A., Sieradzan A.K. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theor Comp. 2023. Vol. 17: 6023–6036. DOI
Kowalska D. et al., Samsonov S.A., Maszota-Zieleniak M. et al. Insights into interaction of HSA with Ionic Liquids. Int J Biol Macromolecules. 2023. Vol. 249: 125883. DOI
Marcisz M., Samsonov S.A. Solvent models benchmark for molecular dynamics of glycosaminoglycans. J Chem Inf Mod. 2023. Vol 63: 2147–2157. DOI
Gaardløs M., Lervik A., Samsonov S.A. Computational modeling of the molecular basis for the calcium-dependence of the mannuronan C-5 epimerase AvAlgE6. Computational and Structural Biotechnology Journal. 2023. Vol. 21: 2188–2196. DOI
Gitlin-Domagalska A. et al., Samsonov S.A., Maszota-Zieleniak M. et al. Cyclic peptidic furin inhibitors developed by combinatorial chemistry. ACS Medicinal Chemistry Letters. 2023. Vol. 14: 458–465. DOI
Pągielska M., Samsonov S.A. Molecular dynamics-based comparative analysis of chondroitin and dermatan sulfates. Biomolecules. 2023. Vol. 13: 247. DOI
Bojarski K.K., Samsonov S.A. In silico insights into procathepsin S maturation mediated by glycosaminoglycans. J Mol Graph Mod. 2023. 108406. DOI
Marcisz M., Maszota-Zieleniak M., Samsonov S.A. Repulsive Scaling Replica Exchange MD in Modeling Protein-GAG Complexes. Methods in Molecular Biology. 2023. Vol. 2619. DOI
Perez S. et al. (incl. Samsonov S.A.) Glycosaminoglycans: What remains to be deciphered? JACS Au. 2023. DOI
Giatagana E-M. et al., Samsonov S.A. Rapamycin-induced autophagy in osteosarcoma cells is mediated via the biglycan/Wnt/β-catenin signaling axis. Am J Physiology-Cell Physiology. 2022. Vol. 323: C1740-C1756. DOI
Kogut M.M. et al., Samsonov S.A. Affinity and putative entrance mechanisms of alkyl sulfates into the β-CD cavity. J Mol Liq. 2022. Vol. 364: 119978. DOI
Kogut M.M., Danielsson A., Ricard-Blum S., Samsonov S.A. Impact of calcium ions on heparin oligosaccharides. Comp Biol Chem. 2022. Vol. 99: 107727. DOI
Marcisz M., Gaardløs M., Bojarski K.K., Siebenmorgen T., Zacharias M., Samsonov S.A. Explicit Solvent RS-REMD in Modeling Protein-GAG Complexes. J Comp Chem. 2022. Vol. 43: 1633–1640. DOI
Danielsson A. et al., Samsonov S.A. MD-based descriptors of 3-O-Sulfated Heparan Sulfate. Comp Biol Chem. 2022. Vol. 99: 107716. DOI
Denamur S. et al., Samsonov S.A. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L. Carbohydrate Polymers. 2022. Vol. 293: 119734. DOI
Maszota-Zieleniak M. et al., Samsonov S.A. MD Approaches Dissect Methylene Blue–GAG Interactions. Molecules. 2022. Vol. 27: 2654. DOI
Bojarski K.K. et al., Samsonov S.A. In silico and in vitro mapping of specificity patterns of GAGs towards cysteine cathepsins. J Mol Graph Mod. 2022. Vol. 113: 108153. DOI
Kogut M.M., Marcisz M., Samsonov S.A. Modeling glycosaminoglycan-protein complexes. Current Opinion in Structural Biology. 2022. Vol. 73: 102332. DOI
Marcisz M. et al., Samsonov S.A. Advanced MD to Model a Tertiary Complex APRIL/TACI with Long GAGs. Biomolecules. 2021. Vol. 11: 1349. DOI
Liwo A. et al. (incl. Samsonov S.A.) Theory and practice of coarse-grained molecular dynamics. Biomolecules. 2021. Vol. 11: 1347. DOI
Lensink M.F. et al. (incl. Samsonov S.A. et al.) Prediction of protein assemblies: The CASP14-CAPRI experiment. Proteins. 2021. DOI
Marcisz M., Zacharias M., Samsonov S.A. Modeling protein-GAG complexes: does the size matter? J Chem Inf Mod. 2021. Vol. 61: 4475–4485. DOI
Maszota-Zieleniak M., Danielsson A., Samsonov S.A. The potential role of GAGs in serum amyloid A fibril formation. Matrix Biology Plus. 2021. Vol. 12: 100008. DOI
Maszota-Zieleniak M. et al., Samsonov S.A. Heparin–small molecule interactions: stacking vs non-stacking. Carbohydrate Research. 2021. Vol. 507: 108390. DOI
Künze G., Huster D., Samsonov S.A. Investigation of regulatory proteins interacting with GAGs by combining NMR and Molecular Modeling. Biological Chemistry. 2021. DOI
Maszota-Zieleniak M., Marcisz M., Kogut M.M., Siebenmorgen T., Zacharias M., Samsonov S.A. Evaluation of RS-REMD for Docking GAGs. J Comp Chem. 2021. Vol. 42: 1040–1053. DOI
Kogut M.M., Maszota-Zieleniak M., Marcisz M., Samsonov S.A. Computational insights into the calcium ions role in protein-GAG systems. Phys Chem Chem Phys. 2021. Vol. 23: 3519–3530. DOI
Bojarski K.K., Samsonov S.A. Role of oligosaccharide chain polarity in protein-GAG interactions. J Chem Inf Mod. 2021. Vol. 61: 455–466. DOI
Zsila F., Samsonov S.A., Maszota-Zieleniak M. Thioflavin T interacts with sulfated GAGs. J Phys Chem B. 2020. Vol. 124: 11625–11633. DOI
Chazeirat T. et al., Samsonov S.A. Abnormal accumulation of heparan sulfate prevents the elastolytic activity of cathepsin V. Carbohydrate Polymers. 2020. Vol. 253: 117261. DOI
Bojarski K.K., Karczyńska A.S., Samsonov S.A. The role of GAGs in procathepsin B maturation. J Chem Inf Mod. 2020. Vol. 60: 2247–2256. DOI
Bojarski K.K. et al., Samsonov S.A. Synthesis and in silico characterization of artificially phosphorylated GAGs. J Mol Struct. 2019. Vol. 1197: 401–416. DOI
Samsonov S.A. et al. In silico analysis of heparin and chondroitin sulfate binding of berenil and pentamidine. Carb Res. 2019. 482: 107742.
Penk A. et al., Samsonov S.A. NMR and Molecular Modeling Reveal Specificity of CXCL14-GAG Interactions. Glycobiology. 2019. Vol. 29: 715–725. DOI
Kohut G. et al., Samsonov S.A. Molecular Mechanism of Structural Changes in Antimicrobial Peptide CM15 Upon Complex Formation with Suramin. Phys Chem Chem Phys. 2019. Vol. 21: 10644–10659. DOI
Uciechowska-Kaczmarzyk U. et al., Samsonov S.A. Docking software performance in protein-GAG systems. J Mol Graph Mod. 2019. Vol. 90: 42–50. DOI
Samsonov S.A. et al. Local and Long Range Potentials for Heparin-Protein Systems for CG Simulations. Biopolymers. 2019. Vol. 110: e23269. DOI
Samsonov S.A., Zacharias M., Chauvot de Beauchene I. Modeling large protein-GAG complexes using a fragment-based approach. J Comp Chem. 2019. Vol. 40: 1429–1439. DOI
Bojarski K.K., Sieradzan A.K., Samsonov S.A. MD Insights into Protein-GAG Systems from Microsecond-Scale Simulations. Biopolymers. 2019. Vol. 110: e23252. DOI
Kohut G. et al., Samsonov S.A. Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges for Flexible Systems. J Phys Chem B. 2018. Vol. 122: 7821–7827. DOI
Vallet S.D. et al., Samsonov S.A. Insights into the structure and dynamics of lysyl oxidase propeptide. Sci Rep. 2018. Vol. 8: 11768. DOI
Uciechowska-Kaczmarzyk U. et al., Samsonov S.A. MD-Based Model of VEGF-A and Its Heparin Interactions. J Mol Graph Mod. 2018. Vol. 82: 157–166. DOI
Zsila F., Samsonov S.A. Molecular interactions of ellipticine with GAGs. Carb Res. 2018. 462: 28–33. DOI
Nordsieck K. et al., Samsonov S.A. The effect of IL-8 truncations on its interactions with GAGs. Biopolymers. 2018. 109: e23103. DOI
Samsonov S.A. Computational analysis of solvent inclusion in docking studies of protein-GAG systems. Methods in Molecular Biology Series. Springer. 2018. 1762: 445–454. DOI