A5090289453- Computational Drug Discovery Methods
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Biochemical and Molecular Research
- Crystallography and molecular interactions
- Adenosine and Purinergic Signaling
- Protein Kinase Regulation and GTPase Signaling
- thermodynamics and calorimetric analyses
- Synthesis and Characterization of Heterocyclic Compounds
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- Cancer-related gene regulation
- RNA Research and Splicing
- Bioactive Compounds and Antitumor Agents
- Click Chemistry and Applications
- Carbohydrate Chemistry and Synthesis
- Pancreatitis Pathology and Treatment
- Peptidase Inhibition and Analysis
- Natural product bioactivities and synthesis
- Influenza Virus Research Studies
- Phosphodiesterase function and regulation
- Protein purification and stability
- Respiratory viral infections research
- Signaling Pathways in Disease
Institute of Biochemistry and Biophysics, Polish Academy of Sciences
2014-2025
University of Warsaw
2020-2024
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe syndrome in humans, which now referred to as coronavirus disease 2019 (COVID-19). Since December 2019, the new pathogen has rapidly spread globally, with over 65 million cases reported beginning of 2020, including 1.5 deaths. Unfortunately, currently, there no specific and effective treatment for COVID-19. As SARS-CoV-2 relies on its spike proteins (S) bind host cell-surface...
The binding of four bromobenzotriazoles to the catalytic subunit human protein kinase CK2 was assessed by two complementary methods: Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC). New algorithm proposed for global analysis MST pseudo-titration data enabled reliable determination affinities distinct sites, a relatively strong one with Kd order 100 nM substantially weaker (Kd > 1 μM). site determined same protein-ligand systems using ITC were in most cases...
The requirement for fast and dependable protein purification methods is constant, either functional studies of natural proteins or the production biotechnological products. original procedure has to be formulated each individual protein, this demanding task was significantly simplified by introduction affinity tags. Helicobacter pylori adenylosuccinate synthetase (AdSS) present in solution a dynamic equilibrium monomers biologically active homodimers. addition His6-tag on C-terminus...
Abstract A series of halogenated derivatives natural flavonoids: baicalein and chrysin were designed investigated as possible ligands for the catalytic subunit tumor‐associated human kinase CK2. Thermal shift assay method, in silico modeling, high‐performance liquid chromatography‐derived hydrophobicity together with IC 50 values determined biochemical used to explain ligand affinity protein Obtained results revealed that substitution halogen atom increases their binding hCK2α,...
Binding of a family brominated benzotriazoles to the catalytic subunit human protein kinase CK2 (hCK2α) was used as model system assess contribution halogen bonding protein–ligand interaction. is constitutively active pleiotropic serine/threonine that belongs CMGC group eukaryotic kinases (EPKs). Due addiction some cancer cells, an attractive and well-characterized drug target. Halogenated act ATP-competitive inhibitors with unexpectedly good selectivity for over other EPKs. We have...
Phosphodiesterase 5 (PDE5) is one of the most extensively studied phosphodiesterases that highly specific for cyclic-GMP hydrolysis. PDE5 became a target drug development based on its efficacy treatment erectile dysfunction. In present study, we synthesized four novel analogues phosphodiesterase type inhibitor—tadalafil, which differs in (i) ligand flexibility (rigid structure tadalafil vs. conformational newly compounds), (ii) stereochemistry associated with applied amino acid building...
Abstract Histidine residues contribute to numerous molecular interactions, owing their structure with the ionizable aromatic side chain pK a close physiological pH. Herein, we studied how two histidine residues, His115 and His160 of catalytic subunit human protein kinase CK2, affect binding halogenated heterocyclic ligands at ATP-binding site. Thermodynamic studies on interaction between five variants hCK2α (WT four mutants) three bromo-benzotriazoles conditionally non-ionizable...
Abstract Numerous inhibitors of protein kinases act on the basis competition, targeting ATP binding site. In this work, we present a procedure rational design bi-substrate inhibitor, complemented with biophysical assays. The type are commonly engineered by combining ligands carrying an ATP-like part peptide or peptide-mimicking fragment that determines specificity. Approach presented in paper led to generation specific system for independent screening efficient and peptides, means...
Protein kinase CK2 is a highly pleiotropic protein capable of phosphorylating hundreds substrates. It involved in numerous cellular functions, including cell viability, apoptosis, proliferation and survival, angiogenesis, or ER-stress response. As activity found perturbed many pathological states, cancers, it becomes an attractive target for the pharma. A large number low-mass ATP-competitive inhibitors have already been developed, majority them halogenated. We tested binding six series...
Purine nucleotide synthesis is realised only through the salvage pathway in pathogenic bacterium Helicobacter pylori. Therefore, enzymes of this pathway, among them also adenylosuccinate synthetase (AdSS), present potential new drug targets. This paper describes characterization His6-tagged AdSS from H. Thorough analysis 3D-structures fully ligated (in a complex with guanosine diphosphate, 6-phosphoryl-inosine monophosphate, hadacidin and Mg2+) inosine monophosphate (IMP) only, enabled...
Nudt16 is a member of the NUDIX family hydrolases that show specificity towards substrates consisting nucleoside diphosphate linked to another moiety X. Several for hNudt16 and various possible biological functions have been reported. However, some these reports contradict each other studies comparing substrate protein are limited. Therefore, we quantitatively compared affinity set previously published substrates, as well identified novel potential substrates. Here, has highest IDP GppG,...
The transient folding of domain 4 an E. coli RNA polymerase $$\sigma^{70}$$ subunit ( $$r{\text{EC}}\sigma_{4}^{70}$$ ) induced by increasing concentration 2,2,2-trifluoroethanol (TFE) in aqueous solution was monitored means CD and heteronuclear NMR spectroscopy. data, collected at a 30 % TFE, allowed the estimation population locally folded structure (CSI descriptors) local backbone dynamics (15N relaxation). spontaneous organization helical regions initially unfolded protein into...
The FTO protein is involved in a wide range of physiological processes, including adipogenesis and osteogenesis. This two-domain belongs to the AlkB family 2-oxoglutarate (2-OG)- Fe(II)-dependent dioxygenases, displaying N6-methyladenosine (N6-meA) demethylase activity. aim study was characterize relationships between structure activity FTO. effect cofactors (Fe2+/Mn2+ 2-OG), Ca2+ that do not bind at catalytic site, concentration on properties expressed either E. coli (ECFTO) or baculovirus...
New pathogens responsible for novel human disease outbreaks in the last two decades are mainly respiratory system viruses. Not different was pandemic episode, caused by infection of a severe acute syndrome coronavirus 2 (SARS-CoV-2). One extensively explored targets, recent scientific literature, as possible way rapid development COVID-19 specific drug(s) is interaction between receptor-binding domain virus' spike (S) glycoprotein and receptor angiotensin-converting enzyme (hACE2). This...
Abstract E. coli purine nucleoside phosphorylase is a homohexamer, which structure, in the apo form, can be described as trimer of dimers. Earlier studies suggested that ligand binding and kinetic properties are well by two constants sets constants. However, most crystal structures this enzyme complexes with ligands do not hold three-fold symmetry, but only two-fold one three dimers different (both active sites open conformation) from other (one site closed conformation). Our recent detailed...
Abstract 4,5,6,7-Tetrabromo-1 H -benzotriazole is widely used as the reference ATP-competitive inhibitor of protein kinase CK2. Herein, we study its new analogs: 5,6-diiodo- and 5,6-diiodo-4,7-dibromo-1 -benzotriazole. We biophysical (MST, ITC) biochemical (enzymatic assay) methods to describe interactions halogenated benzotriazoles with catalytic subunit human CK2 (hCK2α). To trace biological activity, measured their cytotoxicity against four cancer cell lines effect on mitochondrial inner...
Abstract CK2 is a member of the CMGC group eukaryotic protein kinases and cancer drug target. It can be efficiently inhibited by halogenated benzotriazoles benzimidazoles. Depending on scaffold, substitution pattern, pH, these compounds are either neutral or anionic. Their binding poses dictated hydrophobic effect (desolvation) tug war between salt bridge/hydrogen bond (to K68) halogen bonding E114 V116 backbone oxygens). Here, we test idea that might controllable pH for ligands with...
FTO is an N6-methyladenosine demethylase removing methyl groups from nucleic acids. Several studies indicate the creation of complexes with other proteins. Here, we looked for regulatory proteins recognizing parts dioxygenase region. In Calmodulin (CaM) Target Database, found C-domain potentially binding CaM, and proved this finding experimentally. The interaction was Ca2+-dependent but independent on phosphorylation. We that FTO-CaM essentially influences calcium-binding loops in indicating...