A5021047504- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- RNA Research and Splicing
- RNA modifications and cancer
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Research Data Management Practices
- Machine Learning in Materials Science
- Gene expression and cancer classification
- Microbial Natural Products and Biosynthesis
- Ionic liquids properties and applications
- Invertebrate Immune Response Mechanisms
- Protein Structure and Dynamics
- Advanced biosensing and bioanalysis techniques
- Studies on Chitinases and Chitosanases
- Protein Degradation and Inhibitors
- interferon and immune responses
- Chemical Synthesis and Reactions
- Phosphodiesterase function and regulation
- Cholinesterase and Neurodegenerative Diseases
- Conducting polymers and applications
- Supercapacitor Materials and Fabrication
- Ubiquitin and proteasome pathways
- Cytokine Signaling Pathways and Interactions
- Biocrusts and Microbial Ecology
International Institute of Molecular and Cell Biology
2015-2024
Celon Pharma (Poland)
2014-2022
OncoArendi Therapeutics (Poland)
2017
Poznań University of Technology
2005-2009
First Technical University
2005
The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of ribonucleosides, their biosynthetic pathways, location residues in RNA sequences, RNA-modifying enzymes. Over years, prompted by accumulation new knowledge types data, been updated with functionalities. In this release, we have created catalog modifications...
The MODOMICS database was updated with recent data and now includes new types related to RNA modifications. Changes the include an expanded modification catalog, encompassing both natural synthetic residues identified in structures. This addition aids representing sequences from RCSB PDB more effectively. To manage increased number of modifications, adjustments nomenclature system were made. Updates section reintroduction sequence alignments for tRNAs rRNAs. protein connected structures...
RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed these prediction purposes, such molecular docking or scoring functions, are parametrized protein targets. The performance methods, when applied to RNA-ligand systems, insufficient. To overcome problems, we AnnapuRNA, a knowledge-based function designed evaluate complex structures, generated any method. We also...
Abstract E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, web server that searches degrons and maps them to nearby residues can undergo ubiquitination disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment degron conservation, the also reports on...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
Electropolymerizable functional and cross-linking monomers were used to prepare conducting molecularly imprinted polymer film with improved surface area the help of a sacrificial metal-organic framework (MOF). Subsequent dissolution MOF layer resulted in developed MIP film. This enlargement increased analyte accessibility molecular cavities. Application porous as recognition unit an extended-gate field effect transistor (EG-FET) chemosensor effectively enhanced analytical current signals...
Abstract Staphylococcus simulans lysostaphin cleaves pentaglycine cross-bridges between stem peptides in the peptidoglycan of susceptible staphylococci, including S. aureus . This enzyme consists an N-terminal catalytic domain and a cell wall binding (SH3b), which anchors protein to peptidoglycan. Although structures SH3bs from are available, modes these domains still unclear. We have solved crystal structure SH3b complex with peptide representing cross-bridge. The identifies groove β1 β2...
Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform 3D structure analysis folding trajectories based the SimRNA method. employs a coarse-grained model, Monte Carlo sampling statistical potentials to explore conformational space, optionally guided by spatial restraints. Recognized its accuracy in...
Abstract We present a new class of solvents containing nonfluorous, well‐established, nontoxic organoanions that can be used as “green” alternatives to volatile organic in variety applications such solvent extraction, antielectrostatic agents, and electrolytes solar‐cell applications. The acesulfamate anion is an effective substitute for very expensive bis(trifluoromethylsulfonyl)imide (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Ribonucleic acids (RNAs) play crucial roles in living organisms and some of them, such as bacterial ribosomes precursor messenger RNA, are targets small molecule drugs, whereas others, e.g. riboswitches or viral RNA motifs considered potential therapeutic targets. Thus, the continuous discovery new functional increases demand for developing compounds targeting them methods analyzing RNA-small interactions. We recently developed fingeRNAt-a software detecting non-covalent bonds formed within...
Toxicity evaluation of newly synthesized or used compounds is one the main challenges during product development in many areas industry. For example, toxicity second reason - after lack efficacy for failure preclinical and clinical studies drug candidates. To avoid attrition at late stage process, analyses are employed early stages a discovery pipeline, along with activity selectivity enhancing. Although assays screening vitro available, their massive application not always time cost...
RNArchitecture is a database that provides comprehensive description of relationships between known families structured non-coding RNAs, with focus on structural similarities. The classification hierarchical and similar to the system used in SCOP CATH databases protein structures. Its central level Family, which builds Rfam catalog gathers closely related RNAs. Consensus structures Families are described reduced secondary structure representation. Evolutionarily grouped into Superfamilies....
Acidic mammalian chitinase (AMCase) and chitotriosidase-1 (CHIT1) are two enzymatically active proteins produced by mammals capable of cleaving the glycosidic bond in chitin. Based on clinical findings animal model studies, involvement chitinases has been suggested several respiratory system diseases including asthma, COPD, idiopathic pulmonary fibrosis. Exploration structure–activity relationships within series 1-(3-amino-1H-1,2,4-triazol-5-yl)-piperidin-4-amines, which was earlier...
The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in metabolism. In humans, cap formation includes post-transcriptional modification of the first transcribed nucleotide by cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards substrates with highly structured 5′ termini. We found binds ATP-dependent DHX15 helicase and this interaction, mediated G-patch domain CMTr1, has an advantageous effect on substrates....
Computational methods play a pivotal role in drug discovery and are widely applied virtual screening, structure optimization, compound activity profiling. Over the last decades, almost all attention medicinal chemistry has been directed to protein-ligand binding, computational tools have created with this target mind. With novel discoveries of functional RNAs their possible applications, gained considerable as potential targets. However, availability bioinformatics for nucleic acids is...
Ribonucleic acid (RNA) molecules serve as master regulators of cells by encoding their biological function in the ribonucleotide sequence, particularly ability to interact with other molecules. To understand how RNA perform tasks and design new sequences specific functions, it is great benefit be able computationally predict folds interacts cellular environment. Our workflow for computational modeling 3D structures its interactions uses a set methods developed our laboratory, including...
Abstract RNA molecules play key roles in all living cells. Knowledge of the structural characteristics allows for a better understanding mechanisms their action. chemical probing us to study susceptibility nucleotides modification, and information obtained can be used guide secondary structure prediction. These experimental results analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization reactivities visualization results),...
Computational methods play a pivotal role in the early stages of small molecule drug discovery and are widely applied virtual screening, structure optimization, compound activity profiling. Over past half century medicinal chemistry, almost all attention has been directed to protein–ligand binding computational tools were created with such targets mind. However, growing discoveries functional RNAs their possible applications, RNA macromolecules have gained considerable as targets. This flow...
Human acidic mammalian chitinase (hAMCase) is one of two true chitinases in humans, the function which remains elusive. In addition to defense against highly antigenic chitin and chitin-containing pathogens gastric intestinal contents, AMCase has been implicated asthma, allergic inflammation, ocular pathologies. Potent selective small-molecule inhibitors this enzyme have not identified date. Here we describe structural modifications compound OAT-177, a previously developed inhibitor mouse...
We developed a cell sensor that detects the liver cancer-specific microRNA MIR92b-3p, involved in hepatocellular carcinoma development and hepatitis C virus infection. To validate our small-molecule screen employs Huh7 human hepatoma line stably transfected with pmirGLO vector containing dual luciferase reporters, we used i) MIR92b-3p antisense or mimicking agent (concentrations from 0.1 pM to 100 nM), ii) expression of XIST, long non-coding RNA is cellular target MIR92b, iii) ectopic Luc2...