Proteolysis-targeting strategies in bacterial systems for functional studies of proteins and improvement of antibiotics

Principal Investigator: Maria Górna (Project partners: Ben Luisi and WPD Pharmaceuticals).

Proteolysis-Targeting Chimeras (PROTACs) are heterobifunctional molecules targeting proteins for degradation. Eukaryotic PROTACs exploiting ligands of E3 ubiquitin ligases emerged as very potent drugs, due to their irreversible and recyclable mode of action. However, this approach has not yet been employed in bacteria, which lack the ubiquitin-proteasome pathway. We will establish whether an induced-proteolysis approach would be effective to down-regulate target endogenous proteins in bacteria, and engineer the chemical tools needed to do so. We will screen for suitable bacterial proteases and ligands, including known adaptor tags and protease ligands. Identified compounds will be validated in vitro and in bacteria. The resulting tool compounds will enable regulation of gene expression on the protein level for studies of protein function and drug action. Bacterial PROTACs could pave the way to create novel antibiotics, which is crucial in the era of increasing antimicrobial resistance.

Funding sources: FIRST TEAM 5/2018, Foundation for Polish Science

Post-transcriptional regulators from the Fas-activated serine/threonine kinase protein family

Principal Investigators: Maria Górna, Daria Dawidziak

We are especially interested in mitochondrial proteins, since the mitochondrion is an essential organelle that is the main source of ATP and has fundamental roles in all aspects of cell biology, ranging from cell death to growth, differentiation and inflammation. Unsurprisingly, mitochondrial malfunction is associated with a plethora of diseases including cancer, diabetes, neurodegenerative diseases and inflammatory disorders. Proteins which are involved in pathological processes constitute therapy targets and their structures may be used in drug design. In addition, mitochondrion is an intriguing study subject due to its origin in endosymbiosis of a prokaryotic ancestor. Mitochondrial proteins often combine elements of the prokaryotic and eukaryotic worlds or offer an opportunity to discover new protein architectures. One such intriguing group of proteins is the Fas-activated serine/threonine kinase (FASTK) family which participates in the regulation of mitochondrial RNA metabolism. Excitingly, FASTK family members contain putative novel RNA-binding domains of unknown structure, including a potentially new type of helical repeats.

In the latest extension of this project, we also study non-mitochondrial roles of FASTK in alternative splicing and stress response. Due to its involvement in the alternative splicing of Fas mRNA, FASTK is also a putative target for anti-inflammatory therapeuticals. Once the structure of FASTK becomes available, it may enable us to design drugs against this protein which could help treat asthma or rheumathoid arthritis.

Funding sources:
SONATA 8, PRELUDIUM 19, National Science Centre, Poland;
the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 655075

Antiviral effectors from the Interferon-induced proteins with tetratricopeptide repeats (IFIT) protein family

Principal Investigator: Maria Górna

Our additional topic of interest are the Interferon-induced proteins with tetratricopeptide repeats (IFIT). IFITs are antiviral proteins which are expressed in vertebrate cells in response to viral infection, where they act as innate immune effectors that sequester viral transcripts and inhibit their translation. Building on the previous work on the structure and interactions of human IFITs , we investigate the structure and function of higher order IFIT complexes and their specificity for RNA. We hope to elucidate further the mode of RNA recognition by IFITs and their interplay with the cellular machinery in antiviral defense, as well as to find some medical applications of IFITs in diagnostics of infectious diseases.

Funding sources: R&D work: LIDER 6, National Centre for research and devlopment, Poland;
Basic research: TRIBIOcHEM PHD programme, Operational Project Knowledge Education Development 2014-2020 cofinanced by European Social Fund

Past funded projects:

Hydrogen bonding variability in protein structures

Principal Investigator: Matthew Merski

Hydrogen bonding is one of the most fundamental physical interactions in proteins. Hydrogen bonds play a critical role in proteins in forming three dimensional structures, binding ligands and catalyzing enzymatic reactions. We are investigating which hydrogen bonds are conserved in proteins which have been multiply solved and reported in the protein database (PDB). We will use this information to better define the physical principles which govern hydrogen bonding energetics in proteins. Understanding how these patterns are conserved by evolution will also impact our ability to improve rational structure-based drug design and protein engineering.

Funding sources: Miniatura 1, National Science Centre, Poland;

USP family of deubiquitinases

Principal Investigator: Marcin Ziemniak

USP proteins are deubiquitinases that remove ubiquitin from proteins; alteration of this activity may be detrimental to health, leading to cancer. Recently, USPs have emerged as promising targets in anticancer therapy. There have been a number of inhibition studies of these enzymes although to our knowledge none have focused on structural biology. In this project we plan to perform structural studies on a set of selected inhibitors of USP1 and USP7 proteins using X-ray crystallography. After initial biochemical evaluation, we will select the most potent inhibitors and subject them to structural studies in order to understand the atomic details of the interactions between USP proteins and their inhibitors. This will enable us to develop better inhibitors as well as molecular probes to study the ubiquitin-proteasome system (UPS).

Funding sources: SONATinA 1, National Science Centre, Poland;