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  • The development of a high-affinity conformation-sensitive antibody mimetic using a biocompatible copolymer carrier (iBody) JOURNAL OF BIOLOGICAL CHEMISTRY Blazkova, K., Beranova, J., Hradilek, M., Kostka, L., Subr, V., Etrych, T., Sacha, P., Konvalinka, J. 2021; 297 (5): 101342


    Peptide display methods are a powerful tool for discovering new ligands of pharmacologically relevant targets. However, the selected ligands often suffer from low affinity. Using phage display, we identified a new bicyclic peptide binder of prostate-specific membrane antigen (PSMA), a metalloprotease frequently overexpressed in prostate cancer. We show that linking multiple copies of a selected low-affinity peptide to a biocompatible water-soluble N-(2-hydroxypropyl)methacrylamide copolymer carrier (iBody) improved binding of the conjugate by several orders of magnitude. Furthermore, using ELISA, enzyme kinetics, confocal microscopy, and other approaches, we demonstrate that the resulting iBody can distinguish between different conformations of the target protein. The possibility to develop stable, fully synthetic, conformation-selective antibody mimetics has potential applications for molecular recognition, diagnosis and treatment of many pathologies. This strategy could significantly contribute to more effective drug discovery and design.

    View details for DOI 10.1016/j.jbc.2021.101342

    View details for Web of Science ID 000723119000013

    View details for PubMedID 34710374

    View details for PubMedCentralID PMC8600089

  • Identification of Protein Targets of Bioactive Small Molecules Using Randomly Photomodified Probes ACS CHEMICAL BIOLOGY Simon, P., Knedlik, T., Blazkova, K., Dvorakova, P., Brezinova, A., Kostka, L., Subr, V., Konvalinka, J., Sacha, P. 2018; 13 (12): 3333-3342


    Identifying protein targets of bioactive small molecules often requires complex, lengthy development of affinity probes. We present a method for stochastic modification of small molecules of interest with a photoactivatable phenyldiazirine linker. The resulting isomeric mixture is conjugated to a hydrophilic copolymer decorated with biotin and a fluorophore. We validated this approach using known inhibitors of several medicinally relevant enzymes. At least a portion of the stochastic derivatives retained their binding to the target, enabling target visualization, isolation, and identification. Moreover, the mix of stochastic probes could be separated into fractions and tested for binding affinity. The structure of the active probe could be determined and the probe resynthesized to improve binding efficiency. Our approach can thus enable rapid target isolation, identification, and visualization, while providing information required for subsequent synthesis of an optimized probe.

    View details for DOI 10.1021/acschembio.8b00791

    View details for Web of Science ID 000454568000015

    View details for PubMedID 30489064

  • Polymers as tools for studying the internalization of membrane protein glutamate carboxypeptidase II Kostka, L., Sedlak, F., Blazkova, K., Etrych, T., Sacha, P., Subr, V., Konvalinka, J. ELSEVIER SCIENCE BV. 2017: E81-E82
  • In Vivo Performance and Properties of Tamoxifen Metabolites for CreERT2 Control PLOS ONE Felker, A., Nieuwenhuize, S., Dolbois, A., Blazkova, K., Hess, C., Low, L. L., Burger, S., Samson, N., Carney, T. J., Bartunek, P., Nevado, C., Mosimann, C. 2016; 11 (4): e0152989


    Mutant Estrogen Receptor (ERT2) ligand-binding domain fusions with Cre recombinase are a key tool for spatio-temporally controlled genetic recombination with the Cre/lox system. CreERT2 is efficiently activated in a concentration-dependent manner by the Tamoxifen metabolite trans-4-OH-Tamoxifen (trans-4-OHT). Reproducible and efficient Cre/lox experimentation is hindered by the gradual loss of CreERT2 induction potency upon prolonged storage of dissolved trans-4-OHT, which potentially results from gradual trans-to-cis isomerization or degradation. Here, we combined zebrafish CreERT2 recombination experiments and cell culture assays to document the gradual activity loss of trans-4-OHT and describe the alternative Tamoxifen metabolite Endoxifen as more stable alternative compound. Endoxifen retains potent activation upon prolonged storage (3 months), yet consistently induces half the ERT2 domain fusion activity compared to fresh trans-4-OHT. Using 1H-NMR analysis, we reveal that trans-4-OHT isomerization is undetectable upon prolonged storage in either DMSO or Ethanol, ruling out isomer transformation as cause for the gradual loss of trans-4-OHT activity. We further establish that both trans-4-OHT and Endoxifen are insensitive to light exposure under regular laboratory handling conditions. We attribute the gradual loss of trans-4-OHT potency to precipitation over time, and show that heating of aged trans-4-OHT aliquots reinstates their CreERT2 induction potential. Our data establish Endoxifen as potent and reproducible complementary compound to 4-OHT to control ERT2 domain fusion proteins in vivo, and provide a framework for efficient chemically controlled recombination experiments.

    View details for DOI 10.1371/journal.pone.0152989

    View details for Web of Science ID 000374131700016

    View details for PubMedID 27077909

    View details for PubMedCentralID PMC4831813