Group of Proteases of Human Pathogens ****************************************************************************************** * ****************************************************************************************** "We offer a multidisciplinary approach to in vitro and cellular assays development and ada as testing compounds of interest with subsequent advanced analyses of interaction target p ****************************************************************************************** * Offer ****************************************************************************************** *========================================================================================= * Ibodies *========================================================================================= iBodies are fully syntetic antibody mimetics based on pHPMA scaff old which is decorated w - small molecule targeting ligand - affinity anchor and - fluorescence labelling. iBodies are useful various biochemical assays: - ELISA - surface plasmon resonance (SPR) - flow cytometry - fluorescence microscopy etc. ****************************************************************************************** * Know-how & Technologies ****************************************************************************************** - We use iBodies for reveling binders/receptors/enzymes of biologically active compounds w targets - We set up the stochastic modification of those active small molecules to attach the hand possible sites on small mollecules, conjugate it to iBodies and after pull-down we identif mass spectrometry - We routinely use iBody against GCPII (PSMA), FAP, aspartic proteases, His-tagged protein are in development "From ligands of proteases to future first-class early lead compounds." *========================================================================================= * Main Capabilities *========================================================================================= - Protein expression and purification - Small molecule inhibitor design - Assay development in vitro and ex vivo ****************************************************************************************** * Content of Research ****************************************************************************************** - In the viral proteases research, we integrate the tools of classical biochemistry and st biology with methods of cellular and molecular biology for in house development of in vitr enzymological assays for search of early lead compounds with non-canonical mechanisms of a - In the field of proteases participating in cancer development, we characterized Prostate membrane antigen (PSMA) and fibroblast activated protein (FAP) in terms of 3D structure, s specificity and inhibitor design. - We study viral proteases is focused mainly to HIV, Zika and Dengue NS2B-NS3 proteins as proteases autoactivation and activity modulation. We also study proteases involved in mali FAP and others). - We develop novel assays for enzyme detection and characterization. ****************************************************************************************** * Key Research Equipment ****************************************************************************************** Konvalinka’s lab is a joint laboratory between the Department of Proteases of Human Pathog Institute of Organic Chemistry and Biochemistry of the Academy of Science (IOCB) and Depar Biochemistry. Extensive set of instrumentation at IOCB is available to interested collabor state of the art FPLC instrument, protein microcalorimetry, SPR, qPCR equipment, protein c and others. ****************************************************************************************** * Partnerships & Collaborations ****************************************************************************************** *========================================================================================= * Academic Partners *========================================================================================= - Hans-Georg Kräusslich: Department of Virology, University of Heidelberg, Heidelberg, Ger analysis of polyprotein processing, culture testing of protease inhibitors) - Alex Wlodawer: National Institutes of Health, Bethesda, USA (Structural biology of HIV P mutants) - Monique Nijhuis: Eijkman-Winklar Centre for Medical Microbiology, Infectious Diseases an *========================================================================================= * Private and Public Sector *========================================================================================= - AIDS Center, Clinic of Infectious Diseases, Faculty Hospital Bulovka: Long term clinical development of resistance against antiretroviral treatment in HIV positive patients *========================================================================================= * Main Projects *========================================================================================= - 2012–2018: Controlling Structure and Function of Biomolecules at the Molecular Scale: Th Experiment. Grant Agency of the Czech Republic; project P208/12/G016 (principal coinvestig - 2012–2014: Glutamate carboxypeptidase II and its role in tumor development. Grant Agency Republic; project P304/12/0847 (principal investigator) - 2013–2015: Assembly of HIV virions as a therapeutic target. Grant Agency of the Czech Re GA13-19561S (principal investigator) ****************************************************************************************** * Achievements ****************************************************************************************** - Šimon, P., Knedlík, T., Blažková, K., Dvořáková, P., Březinová, A., Kostka. L., Šubr, V. J. and Šácha, P. (2018) Identification of Protein Targets of Bioactive Small Molecules Usi Photomodified Probes, ACS Chem. Biol. 13, 3333–3342 - Humpolíčková, J., Weber, J., Starková, J., Mašínová, E., Günterová, J., Flaisigová, I., J.,and Majerová, T. (2018) Inhibition of the precursor and mature forms of HIV-1 protease drug evaluation, Scientific Reports 8, 10438 - Tretyachenko V, Vymetal J, Bednarova L, Kopecky V, Jr., Hofbauerova K, Jindrova H, Hubal R, Konvalinka J, Vondrasek J, Hlouchova K (2017). Random protein sequences can form define structures and are well-tolerated in vivo. Sci Rep.7, 15449 - Dvořáková P, Bušek P, Knedlík T, Schimer J, Etrych T, Kostka L, Stollinová Šromová L, Šu P, Šedo A, Konvalinka J. (2017) Inhibitor-Decorated Polymer Conjugates Targeting Fibroblas Protein. J Med Chem. 60, 8385–8393 - Machara A., Lux V., Kožíšek M., Grantz Šašková K., Štěpánek O., Kotora M., Parkan K., Pá B., Sehr P., Lewis J., Müller B., Kräusslich H.G., Konvalinka J. (2016) Specific Inhibitor Assembly Binding to the C-Terminal Domain of the Capsid Protein: Evaluation of 2-Arylquina Potential Antiviral Compounds. Journal of Medicinal Chemistry 59: 545–558 - Šácha P., Knedlík T., Schimer J., Tykvart J., Parolek J., Navrátil V., Dvořáková P., Sed K., Strohalm J., Majer P., Šubr V., Konvalinka J. (2016) iBodies: modular synthetic antibo based on hydrophilic polymers decorated with functional moieties. Angewandte Chemie Intern Online: January 8 - Vorlová B., Nachtigallová D., Jirásková-Vaníčková J., Ajani H., Jansa P., Řezáč J., Fanf M., Hobza P., Konvalinka J., Lepšík M. (2015) Malonate-based inhibitors of mammalian serin Kinetic characterization and structure-based computational study. European Journal of Medi 89: 189–197 - Schimer J., Pávová M., Anders M., Pachl P., Šácha P., Cígler P., Weber J., Majer P., Řez Krausslich H.G., Muller B., Konvalinka J. (2015) Triggering HIV polyprotein processing by photodegradation of a tight-binding protease inhibitor. Nature Communications 6: 6461 - Tykvart J., Bařinka C., Svoboda M., Navrátil V., Souček R., Hradílek M., Šácha P., Lubko Konvalinka J. (2015) Structural and biochemical characterization of human N-acetylated alp dipeptidase-like (NAALADase L) protein, a novel aminopeptidase from human intestine. Journ Chemistry 290: 11321–11336 - Tykvart J., Schimer J., Jančařík A., Bařinková J., Navrátil V., Starková J., Šrámková K. J., Majer P., Šácha P. (2015) Design of Highly Potent Urea-Based, Exosite-Binding Inhibito Glutamate Carboxypeptidase II. Journal of Medicinal Chemistry 58: 4357–4363 ****************************************************************************************** * Are you interested in this expertisa? ****************************************************************************************** Please contact CPPT UK Web: www.cppt.cuni.cz/ [ URL "https://cppt.cuni.cz/"] Mail: transfer@cuni.cz Tel.: +420 224 491 255 ****************************************************************************************** * Experts and their department ****************************************************************************************** Assoc. Prof. RNDr. Jan Konvalinka, CSc. Department of Biochemistry Web: https://twitter.com/konvalinka_lab [ URL "https://twitter.com/konvalinka_lab"]