TY - JOUR AB - Dual-specificity tyrosine-phosphorylation-regulated kinase 1B (DYRK1B) has recently emerged as a critical therapeutic target in oncology and non-alcoholic fatty liver disease. As a kinase, DYRK1B plays key roles in regulating cellular survival pathways; however, the lack of structural information has impeded the development of selective inhibitors. In this study, we implemented multi-method framework: recombinant expression and stability profiling, cellular target engagement, enzyme inhibition, biophysical thermodynamics, cell-based pathway readout, X-ray crystallography, quantum-mechanical and molecular-dynamics analyses. We report the crystal structure of DYRK1B in complex with the small-molecule inhibitor AZ191. For comparative purposes, we also present the structure of the closely related kinase, DYRK1A, bound to the same ligand. While a structural overlay of the two kinase domains reveals overall negligible differences, detailed inspection highlights distinct features within the hinge-binding region of DYRK1B that are pivotal for achieving kinase selectivity. Moreover, detailed evaluation of the active site architecture reveals a notable difference in the accessibility of the catalytic lysine residue between DYRK1B and DYRK1A, suggesting potential strategies to distinguish selective binders. Overall, these findings provide important macromolecular insights into the DYRK1B structure and offer a structural framework to guide medicinal chemistry efforts towards improved inhibitor selectivity with minimized off-target activity. AU - Grygier, P.* AU - Pustelny, K.* AU - Cardoso Micu Menezes, F.M. AU - Jemiola-Rzeminska, M.* AU - Suder, P.* AU - Dubin, G.* AU - Czarna, A.* C1 - 75743 C2 - 58156 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Structural perspective on the design of selective DYRK1B inhibitors. JO - Int. J. Biol. Macromol. VL - 330 PB - Elsevier PY - 2025 SN - 0141-8130 ER - TY - JOUR AB - BACKGROUND: SARS-CoV-2 disrupts lung vascular endothelial integrity, contributing to severe COVID-19 complications. However, the molecular mechanisms driving endothelial dysfunction remain underexplored, and targeted therapeutic strategies are lacking. OBJECTIVE: This study investigates Naringenin-7-O-glucoside (N7G) as a multi-target therapeutic candidate for modulating vascular integrity and immune response by inhibiting MMP1, MMP7, and SERPINE1-key regulators of extracellular matrix (ECM) remodeling and inflammation. METHODS & RESULTS: RNA-set analysis of COVID-19 lung tissues identified 17 upregulated N7G targets, including MMP1, MMP7, and SERPINE1, with the latter exhibiting the highest expression. PPI network analysis linked these targets to ECM degradation, IL-17, HIF-1, and AGE-RAGE signaling pathways, and endothelial dysfunction. Disease enrichment associated these genes with idiopathic pulmonary fibrosis and asthma. Molecular docking, 200 ns MD simulations (triplicate), and MMGBSA calculations confirmed N7G's stable binding affinity to MMP1, MMP7, and SERPINE1. Immune profiling revealed increased neutrophils and activated CD4+ T cells, alongside reduced mast cells, NK cells, and naïve B cells, indicating immune dysregulation. Correlation analysis linked MMP1, MMP7, and SERPINE1 to distinct immune cell populations, supporting N7G's immunomodulatory role. CONCLUSION: These findings suggest that N7G exhibits multi-target therapeutic potential by modulating vascular integrity, ECM remodeling, and immune dysregulation, positioning it as a promising candidate for mitigating COVID-19-associated endothelial dysfunction. AU - Mishra, V.K.* AU - Agrawal, S.* AU - Malik, D.* AU - Mishra, D.* AU - Bhavya, B.* AU - Pathak, E. AU - Mishra, R.* C1 - 73577 C2 - 57112 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Targeting Matrix Metalloproteinase-1, Matrix Metalloproteinase-7, and Serine Protease Inhibitor E1: Implications in preserving lung vascular endothelial integrity and immune modulation in COVID-19. JO - Int. J. Biol. Macromol. VL - 306 PB - Elsevier PY - 2025 SN - 0141-8130 ER - TY - JOUR AB - Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a debilitating neurodegenerative disorder linked to CGG trinucleotide repeat expansions in the FMR1 gene. These expanded repeats produce toxic FMR1poly-Glycine (FMR1polyG) proteins in neurons through mechanisms such as Repeat-Associated Non-AUG (RAN) translation and RNA foci formation, driving disease progression. In this study, we investigate the potential of Nitazoxanide (NTZ), a broad-spectrum antiparasitic and antiviral medication, as a therapeutic agent for FXTAS by targeting CGG repeat-associated toxicity. This comprehensive approach utilizing biophysical techniques, bioinformatic studies, cellular assays, and Drosophila models reveals NTZ's remarkable ability to bind specifically to toxic CGG repeat RNA, particularly GG mismatches, and to inhibit FMR1polyG aggregation. Biophysical methods, including Circular Dichroism (CD), Isothermal Titration Calorimetry (ITC), Electrophoretic Mobility Shift assays (EMSA), and Nuclear Magnetic Resonance (NMR) spectroscopy, accompanied with Molecular Docking, confirmed that NTZ effectively binds to CGG repeat RNA and mitigates its toxicity. Moreover, treatment with NTZ significantly reduced FMR1polyG-associated toxicity, corrected the splicing defects in FXTAS cell models, and improved different phenotypes in the Drosophila model of FXTAS. These compelling findings position NTZ as a promising candidate for neuroprotection in FXTAS, indicating its remarkable therapeutic potential and paving the way for future clinical applications to improve outcomes for the affected patients. AU - Singh, K.* AU - Shukla, S.* AU - Kumari, A.P.* AU - Qurashi, A.* AU - Verma, A.K. AU - Kumar, A.* C1 - 75644 C2 - 58219 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Repurposing Nitazoxanide to target the expanded r(CGG)n repeat RNA for therapeutic intervention in fragile-X tremor/Ataxia syndrome. JO - Int. J. Biol. Macromol. VL - 329 PB - Elsevier PY - 2025 SN - 0141-8130 ER - TY - JOUR AB - Peroxisomal protein import has been identified as a valid target in trypanosomiases, an important health threat in Central and South America. The importomer is built of multiple peroxins (Pex) and structural characterization of these proteins facilitates rational inhibitor development. We report crystal structures of the Trypanosoma brucei and T. cruzi tetratricopeptide repeat domain (TPR) of the cytoplasmic peroxisomal targeting signal 1 (PTS1) receptor Pex5. The structure of the TPR domain of TbPex5 represents an apo-form of the receptor which, together with the previously determined structure of the complex of TbPex5 TPR and PTS1 demonstrate significant receptor dynamics associated with signal peptide recognition. The structure of the complex of TPR domain of TcPex5 with PTS1 provided in this study details the molecular interactions that guide signal peptide recognition at the atomic level in the pathogenic species currently perceived as the most relevant among Trypanosoma. Small - angle X - ray scattering (SAXS) data obtained in solution supports the crystallographic findings on the compaction of the TPR domains of TbPex5 and TcPex5 upon interaction with the cargo. AU - Banasik, M.* AU - Napolitano, V.* AU - Blat, A.* AU - Abdulkarim, K.* AU - Plewka, J.* AU - Czaplewski, C.* AU - Gieldon, A.* AU - Kozak, M.* AU - Wladyka, B.* AU - Popowicz, G.M. AU - Dubin, G.* C1 - 71792 C2 - 56430 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma. JO - Int. J. Biol. Macromol. VL - 280 PB - Elsevier PY - 2024 SN - 0141-8130 ER - TY - JOUR AB - Combining a Sodium-Glucose-Cotransporter-2-inhibitor (SGLT2i) with metformin is recommended for managing hyperglycemia in patients with type 2 diabetes (T2D) who have cardio-renal complications. Our study aimed to investigate the metabolic effects of SGLT2i and metformin, both individually and synergistically. We treated leptin receptor-deficient (db/db) mice with these drugs for two weeks and conducted metabolite profiling, identifying 861 metabolites across kidney, liver, muscle, fat, and plasma. Using linear regression and mixed-effects models, we identified two SGLT2i-specific metabolites, X-12465 and 3-hydroxybutyric acid (3HBA), a ketone body, across all examined tissues. The levels of 3HBA were significantly higher under SGLT2i monotherapy compared to controls and were attenuated when combined with metformin. We observed similar modulatory effects on metabolites involved in protein catabolism (e.g., branched-chain amino acids) and gluconeogenesis. Moreover, combination therapy significantly raised pipecolate levels, which may enhance mTOR1 activity, while modulating GSK3, a common target of SGLT2i and 3HBA inhibition. The combination therapy also led to significant reductions in body weight and lactate levels, contrasted with monotherapies. Our findings advocate for the combined approach to better manage muscle loss, and the risks of DKA and lactic acidosis, presenting a more effective strategy for T2D treatment. AU - Harada, M. AU - Han, S. AU - Shi, M. AU - Ge, J. AU - Yu, S. AU - Adam, J. AU - Adamski, J. AU - Scheerer, M.F. AU - Neschen, S. AU - Hrabě de Angelis, M. AU - Wang-Sattler, R. C1 - 70313 C2 - 55226 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Metabolic effects of SGLT2i and metformin on 3-hydroxybutyric acid and lactate in db/db mice. JO - Int. J. Biol. Macromol. VL - 265 IS - Pt 1 PB - Elsevier PY - 2024 SN - 0141-8130 ER - TY - JOUR AB - The main protease (Mpro) of SARS-CoV-2 is critical in the virus's replication cycle, facilitating the maturation of polyproteins into functional units. Due to its conservation across taxa, Mpro is a promising target for broad-spectrum antiviral drugs. Targeting Mpro with small molecule inhibitors, such as nirmatrelvir combined with ritonavir (Paxlovid™), which the FDA has approved for post-exposure treatment and prophylaxis, can effectively interrupt the replication process of the virus. A key aspect of Mpro's function is its ability to form a functional dimer. However, the mechanics of dimerization and its influence on proteolytic activity remain less understood. In this study, we utilized biochemical, structural, and molecular modelling approaches to explore Mpro dimerization. We evaluated critical residues, specifically Arg4 and Arg298, that are essential for dimerization. Our results show that changes in the oligomerization state of Mpro directly affect its enzymatic activity and dimerization propensity. We discovered a synergistic relationship influencing dimer formation, involving both intra- and intermolecular interactions. These findings highlight the potential for developing allosteric inhibitors targeting Mpro, offering promising new directions for therapeutic strategies. AU - Lis, K.* AU - Plewka, J.* AU - Cardoso Micu Menezes, F.M. AU - Bielecka, E.* AU - Chykunova, Y.* AU - Pustelny, K.* AU - Niebling, S.* AU - Garcia, A.S.* AU - Garcia-Alai, M.* AU - Popowicz, G.M. AU - Czarna, A.* AU - Kantyka, T.* AU - Pyrc, K.* C1 - 70423 C2 - 55613 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - SARS-CoV-2 Mpro oligomerization as a potential target for therapy. JO - Int. J. Biol. Macromol. VL - 267 PB - Elsevier PY - 2024 SN - 0141-8130 ER - TY - JOUR AB - The authors regret that the name of one of the contributing author was inadvertently omitted from the publication. The correct list of authors should include Jakub S. Nowak from the Malopolska Centre of Biotechnology at Jagiellonian University along with the original authors. Dr Nowak made substantial contributions to the research, particularly in Mpro affinity analyses and preliminary studies on dimerization. His input is integral to the overall findings of the article. The authors would like to apologise for any inconvenience caused. AU - Lis, K.* AU - Plewka, J.* AU - Cardoso Micu Menezes, F.M. AU - Bielecka, E.* AU - Chykunova, Y.* AU - Pustelny, K.* AU - Niebling, S.* AU - Garcia, A.S.* AU - Garcia-Alai, M.* AU - Popowicz, G.M. AU - Nowak, J.S.* AU - Czarna, A.* AU - Kantyka, T.* AU - Pyrc, K.* C1 - 71229 C2 - 55955 TI - Corrigendum to "SARS-CoV-2 Mpro oligomerization as a potential target for therapy" [Int. J. Biol. Macromol. 267 (Part 1) (May 2024) 131392]. JO - Int. J. Biol. Macromol. VL - 276 IS - Pt 1 PY - 2024 SN - 0141-8130 ER - TY - JOUR AB - Chronic non-healing diabetic wounds and ulcers can be fatal, lead to amputations, and remain a major challenge to medical, and health care sectors. Susceptibility to infection and impaired angiogenesis are two central reasons for the clinical consequences associated with chronic non-healing diabetic wounds. Herein, we successfully developed calcium ion (Ca2+) cross-linked sodium alginate (SA) hydrogels with both pro-angiogenesis and antibacterial properties. Our results demonstrated that deferoxamine (DFO) and copper nanoparticles (Cu-NPs) worked synergistically to enhance the proliferation, migration, and angiogenesis of human umbilical venous endothelial cells in vitro. Results of colony formation assay indicated Cu-NPs were effective against E. coli and S. aureus in a dose-dependent manner in vitro. An SA hydrogel containing both DFO and Cu-NPs (SA-DFO/Cu) was prepared using a Ca2+ cross-linking method. Cytotoxicity assay and colony formation assay indicated that the hydrogel exhibited beneficial biocompatible and antibacterial properties in vitro. Furthermore, SA-DFO/Cu significantly accelerated diabetic wound healing, improved angiogenesis and reduced long-lasting inflammation in a mouse model of diabetic wound. Mechanistically, DFO and Cu-NPs synergistically stimulated the levels of hypoxia-inducible factor 1α and vascular endothelial growth factor in vivo. Given the pro-angiogenesis, antibacterial and healing properties, the hydrogel possesses high potential for clinical application in refractory wounds. AU - Li, S.* AU - Wang, X.* AU - Chen, J.* AU - Guo, J.* AU - Yuan, M.* AU - Wan, G.* AU - Yan, C.* AU - Li, W.* AU - Machens, H.G.* AU - Rinkevich, Y. AU - Yang, X.* AU - Song, H.* AU - Chen, Z.* C1 - 64203 C2 - 52106 SP - 657-670 TI - Calcium ion cross-linked sodium alginate hydrogels containing deferoxamine and copper nanoparticles for diabetic wound healing. JO - Int. J. Biol. Macromol. VL - 202 PY - 2022 SN - 0141-8130 ER -