Publications
2025
A Biotin-HaloTag ligand enables efficient affinity capture of protein variants from live cells. Yadav, A. K.; Jadhav, A. S.; Szczepanik, P. M.; Fagherazzi, P.; Kabelka, I.; Vácha, R.; Svenda, J.*; Polasek-Sedlackova, H.*
J. Cell Biol. 2025, accepted, doi: 10.1083/jcb.202410025
HaloTag technology represents a versatile tool for studying proteins. Fluorescent HaloTag ligands employed in sequential labeling led to the discovery of distinct protein variants for histones, cohesins, and MCM complexes. However, an efficient biochemical approach to separate the distinct protein variants to study their biological functions is missing. Principally, being a gap in technology, the HaloTag toolbox lacks affinity ligands displaying good cell permeability and efficient affinity capture. Here, we describe the design, synthesis, and validation of a new cell-permeable Biotin-HaloTag ligand, which allows rapid labeling of Halo-tagged proteins in live cells and their efficient separation using streptavidin pull-down. We provide a proof-of-concept application of how to use the herein-developed affinity ligand in sequential labeling to biochemically separate distinct protein variants and study their biological properties. This approach enables to address fundamental questions concerning essential cellular processes, including genome duplication and chromatin maintenance.
Biology and pharmacological inhibition of homeodomain-interacting protein kinases (HIPKs). Štefek, A.; Paruch, K.*
Front. Chem. Biol. 2025, 4, doi: 10.3389/fchbi.2025.1441138.
Homeodomain-interacting protein kinases (HIPKs) represent a relatively underexplored sub-family of serine/threonine protein kinases. However, the recently published studies point to the role of HIPKs in the developmental biology and etiology of pathological states, in particular cancer, and potential therapeutic applications of targeting this kinase family. This review summarizes the biology of HIPKs and their heretofore published small-molecule inhibitors.
Discovery of new inhibitors of nuclease MRE11. Nikulenkov, F.; Carbain, B.; Biswas, R.; Havel, S.; Prochazkova, J.; Sisakova, A.; Chavdarova, M.; Marini, V.; Vsiansky, V.; Weisova, V.; Slavikova, K.; Biradar, D.; Khirsariya, P.; Vitek, M.; Sedlak, D.; Bartunek, P.; Daniel, L.; Brezovsky, J.; Damborsky, J.; Paruch, K.*; Krejci, L.*
Eur. J. Med. Chem. 2025, accepted.
MRE11 nuclease is a central player in signaling and processing DNA damage, and in resolving stalled replication forks. Here, we describe the identification and characterization of new MRE11 inhibitors MU147 and MU1409. Both compounds inhibit MRE11 nuclease more specifically and effectively than the relatively weak state-of-the-art inhibitor mirin. They also abrogate double-strand break repair mechanisms that rely on MRE11 nuclease activity, without impairing ATM activation. Inhibition of MRE11 also impairs nascent strand degradation of stalled replication forks and selectively affects BRCA2-deficient cells. Herein, we illustrate that our newly discovered compounds MU147 and MU1409 can be used as chemical probes to further explore the biological role of MRE11 and support the potential clinical relevance of pharmacological inhibition of this nuclease.