Publications

 Arising from Independent Career

Ptacek J, Nedvedova J, Navratil M, Havlinova B, Konvalinka J, Barinka C*: The calcium-binding site of human glutamate carboxypeptidase II is critical for dimerization, thermal stability and enzymatic activity. Prot Sci, 2018, accepted  ico-link

Kutil Z, Novakova Z, Meleshin M, Mikesova J, Schutkowski M, Barinka C*: Histone deacetylase 11 is a fatty-acid deacylase. ACS Chem Biol, 2018, 13(3):685-693.  ico-link

Skultetyova L, Ustinova K, Kutil Z, Novakova Z, Pavlicek J, Mikesova J, Trapl D, Baranova P, Havlinova B, Hubalek M, Lansky Z, Barinka C*: Human histone deacetylase 6 shows strong preference for tubulin dimers over assembled microtubules. Sci Rep, 2017 7(1):11547-515.  ico-link  ico-pdf

Tavares MT, Shen S, Knox T, Hadley M, Kutil Z, Barinka C, Villagra A, Kozikowski AP: Synthesis and Pharmacological Evaluation of Selective Histone Deacetylase 6 Inhibitors in Melanoma Models. ACS Med Chem Lett, 2017 8(10):1031-1036.  ico-link

Kopka K, Benešová M, Barinka C, Haberkorn U, Babich J: Glu-Ureido–Based Inhibitors of Prostate-Specific Membrane Antigen: Lessons Learned During the Development of a Novel Class of Low-Molecular-Weight Theranostic Radiotracers. J Nucl Med, 2017 58:17S-26S.  ico-link ico-pdf

Rais R, Vávra J, Tichý T, Dash RP, Gadiano AJ, Tenora L, Monincova L, Barinka C, Alt J, Zimmermann SC, Slusher CE, Wu Y, Wozniak K, Majer P, Tsukamoto T, Slusher BS: Discovery of a para-acetoxy-benzyl ester prodrug of a hydroxamate-based Glutamate Carboxypeptidase II inhibitor as oral therapy for neuropathic pain. J Med Chem. 2017 60(18):7799-7809.  ico-link ico-pdf

Lv W, Zhang G, Barinka C, Eubanks JH, Kozikowski AP: Design and Synthesis of Mercaptoacetamides as Potent, Selective, and Brain Permeable Histone Deacetylase 6 Inhibitors. ACS Med Chem Lett, 2017 8(5):510-515.  ico-link ico-pdf

Novakova Z, Foss C, Copeland B, Morath V, Baranova P, Havlinova B, Skerra A, Pomper M, Barinka C*: Novel monoclonal antibodies recognizing human prostate-specific membrane antigen (PSMA) as research and theranostic tools. The Prostate. 2017, 77(7):749-764.  ico-link

Conway RE, Rojas C, Alt J, Nováková Z, Richardson SM, Rodrick TC, Fuentes JL, Richardson NH, Attalla J, Stewart S, Fahmy B, Barinka C, Ghosh M, Shapiro LH, Slusher BS: Prostate-specific membrane antigen (PSMA)-mediated laminin proteolysis generates a pro-angiogenic peptide. Angiogenesis. 2016, 19(4): 487 – 500.  ico-link  ico-pdf

Dannoon S, Ganguly T, Cahaya H, Geruntho JJ, Galliher MS, Beyer SK, Choy CJ, Hopkins MR, Regan M, Blecha JE, Skultetyova L, Drake CR, Jivan S, Barinka C, Jones EF, Berkman CE, VanBrocklin HF: Structure-Activity Relationship of 18F-labeled phosphoramidate peptidomimetic Prostate-Specific Membrane Antigen (PSMA)-targeted inhibitor analogues for PET imaging of prostate cancer. J Med Chem. 2016, 59(12): 5684 – 5694.  ico-link  ico-pdf

Novakova Z, Wozniak K, Jancarik A, Rais R, Wu Y, Pavlicek J, Ferraris DV, Havlinova B, Ptacek J, Vavra J, Hin N, Rojas C, Majer P, Slusher BS, Tsukamoto T, Barinka C*: Unprecedented binding mode of hydroxamate-based inhibitors of glutamate carboxypeptidase II: structural characterization and biological activity. J Med Chem. 2016, 59(10): 4539 – 4550.  ico-link   ico-pdf

Bumba L, Masin J, Macek P, Wald T, Motlova L, Bibova I, Klimova N, Bednarova L, Veverka V, Kachala M, Svergun DI, Barinka C, Sebo P: Calcium-driven folding of RTX domain β-rolls ratchets translocation of RTX proteins through type I secretion ducts. Mol Cell. 2016, 62(1): 47 – 62.  ico-link  ico-pdf

Barinka C*, Ptacek J, Richter A, Novakova Z, Morath V, Skerra A*: Selection and characterization of Anticalins targeting human prostate-specific membrane antigen (PSMA). Protein Eng Des Sel. 2016, 29(3): 105 – 115.  ico-link  ico-pdf

Novakova Z, Cerny J, Choy CJ, Nedrow J, Choi JK, Lubkowski J, Berkman CE, Barinka C*: Design of composite inhibitor targeting glutamate carboxypetidease II: the importance of effector functionalities. FEBS J. 2016, 283(1): 130 – 143.  ico-link  ico-pdf

Youn S, Kim K, Ptacek J, Ok K, Novakova Z, Kim J, Koo J, Barinka C*, Byun Y*: Carborane-containing urea-based inhibitors of glutamate carboxypepitdase II: Synthesis and structural characterization. Bioorg Med Chem Lett. 2015, 25(22): 5232 – 5236.  ico-link  ico-pdf

Ganguly T, Dannoon S, Hopkins MR, Murphy S, Cahaya H, Blecha JE, Jivan S, Drake CR, Bařinka C, Jones EF, VanBrocklin HF, Berkman CE: A high-affinity [(18)F]-labeled phosphoramidate peptidomimetic PSMA-targeted inhibitor for PET imaging of prostate cancer.  Nucl Med Biol. 2015, 42(10): 780- 787.  ico-link  ico-pdf

Tykvart J, Bařinka C, Svoboda M, Navrátil M, Souček R,  Hubálek M, Hradílek M, Šácha P, Lubkowski J, Konvalinka J: Structural and biochemical characterization of a novel aminopeptidase from human intestine. J Biol Chem. 2015, 290(18): 11321- 11336. ico-link ico-pdf             

Tykvart J, Navrátil M, Sedlák F, Corey E, Colombatti M,  Fracasso G, Koukolík F, Bařinka C, Šácha P, Konvalinka J: Comparative analysis of monoclonal antibodies against prostate-specific membrane antigen (PSMA). Prostate. 2014, 74(16): 1674 – 1690.  ico-link  ico-pdf

Navrátil M, Ptáček J, Šácha P. Starková J, Lubkowski J, Bařinka C, Konvalinka J: Structural and Biochemical Characterization of the Folyl-poly-γ-L-glutamate Hydrolyzing Activity of Human Glutamate Carboxypeptidase II. FEBS J. 2014, 281(14):3228-3242.  ico-link  ico-pdf

Pavlíček J, Ptáček J, Černý J, Byun Y, Škultétyová L, Pomper MG, Lubkowski J, and Bařinka C*: Structural characterization of P1′-diversified urea-based inhibitors of glutamate carboxypeptidase II.  Bioorg Med Chem Lett. 2014, 24(10):2340-2345.   ico-link  ico-pdf

Alquicer G, Sedlák D, Byun Y, Pavlíček J, Stathis M, Rojas C, Slusher B, Pomper MG, Bartůněk P, and Bařinka C*: Development of a high-throughput fluorescence polarization assay to identify novel ligands of glutamate carboxypeptidase II. J Biomol Screening 2012, 17:1030-1040.  ico-link  ico-pdf

Tykvart J, Sacha P, Barinka C, Knedlik T, Starkova J, Lubkowski J, Konvalinka J: Efficient and versatile one-step affinity purification of in vivo biotinylated proteins: expression, characterization and structure analysis of recombinant human glutamate carboxypeptidase II. Protein Expr Purif 2012, 82:106-115.  ico-link  ico-pdf

Pavlicek J, Ptacek J, Barinka C*: Glutamate Carboxypeptidase II: An Overview of Structural Studies and Their Importance for Structure-Based Drug Design and Deciphering the Reaction Mechanism of the Enzyme. Curr Med Chem 2012, 19:1300-1309.  ico-link  ico-pdf

Barinka C*, Rojas C, Slusher B, Pomper M: Glutamate Carboxypeptidase II in Diagnosis and Treatment of Neurologic Disorders and Prostate Cancer. Curr Med Chem 2012, 19:856-870.  ico-link  ico-pdf

Plechanovova A, Byun Y, Alquicer G, Skultetyova L, Mlcochova P, Nemcova A, Kim HJ, Navratil M, Mease R, Lubkowski J, Pomper MG, Konvalinka J, Rulisek L, Barinka C*: Novel substrate-based inhibitors of human glutamate carboxypeptidase II with enhanced lipophilicity. J Med Chem 2011, 54:7535-7546.  ico-link  ico-pdf

Zhang AX, Murelli RP, Barinka C, Michel J, Cocleaza A, Jorgensen WL, Lubkowski J, Spiegel DA: A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules. J Am Chem Soc 2010, 132:12711-12716.  ico-link  ico-pdf

 

Arising from Graduate/Postdoctoral Work

Zhang Y, Doherty T, Li J, Lu W, Barinka C, Lubkowski J, Hong M: Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR. J Mol Biol 2010, 397:408-422.  ico-link  ico-pdf

Wang H, Byun Y, Barinka C, Pullambhatla M, Bhang HE, Fox JJ, Lubkowski J, Mease RC, Pomper MG: Bioisosterism of urea-based GCPII inhibitors: Synthesis and structure-activity relationship studies. Bioorg Med Chem Lett 2010, 20:392-397.  ico-link  ico-pdf

Mlcochova P, Barinka C, Tykvart J, Sacha P, Konvalinka J: Prostate-specific membrane antigen and its truncated form PSM’. Prostate 2009, 69:471-479.  ico-link  ico-pdf

Klusak V#, Barinka C#, Plechanovova A, Mlcochova P, Konvalinka J, Rulisek L, Lubkowski J: Reaction mechanism of glutamate carboxypeptidase II revealed by mutagenesis, X-ray crystallography, and computational methods. Biochemistry 2009, 48:4126-4138.  ico-link  ico-pdf

Hlouchova K, Barinka C, Konvalinka J, Lubkowski J: Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III. FEBS J 2009, 276:4448-4462.  ico-link  ico-pdf

Rovenska M, Hlouchova K, Sacha P, Mlcochova P, Horak V, Zamecnik J, Barinka C, Konvalinka J: Tissue expression and enzymologic characterization of human prostate specific membrane antigen and its rat and pig orthologs. Prostate 2008, 68:171-182.  ico-link  ico-pdf

Barinka C, Prahl A, Lubkowski J: Structure of human monocyte chemoattractant protein 4 (MCP-4/CCL13). Acta Crystallogr D Biol Crystallogr 2008, 64:273-278.  ico-link 

Barinka C*, Hlouchova K, Rovenska M, Majer P, Dauter M, Hin N, Ko YS, Tsukamoto T, Slusher BS, Konvalinka J, Lubkowski J.: Structural basis of interactions between human glutamate carboxypeptidase II and its substrate analogs. J Mol Biol 2008, 376:1438-1450.  ico-link  ico-pdf

Barinka C, Byun Y, Dusich CL, Banerjee SR, Chen Y, Castanares M, Kozikowski AP, Mease RC, Pomper MG, Lubkowski J: Interactions between human glutamate carboxypeptidase II and urea-based inhibitors: structural characterization. J Med Chem 2008, 51:7737-7743.  ico-link  ico-pdf

Sacha P, Zamecnik J, Barinka C, Hlouchova K, Vicha A, Mlcochova P, Hilgert I, Eckschlager T, Konvalinka J: Expression of glutamate carboxypeptidase II in human brain. Neuroscience 2007, 144:1361-1372.  ico-link  ico-pdf

Mlcochova P, Plechanovova A, Barinka C, Mahadevan D, Saldanha JW, Rulisek L, Konvalinka J: Mapping of the active site of glutamate carboxypeptidase II by site-directed mutagenesis. FEBS J 2007, 274:4731-4741.  ico-link  ico-pdf

Hlouchova K, Barinka C, Klusak V, Sacha P, Mlcochova P, Majer P, Rulisek L, Konvalinka J: Biochemical characterization of human glutamate carboxypeptidase III. J Neurochem 2007, 101:682-696.  ico-link  ico-pdf

Barinka C*, Starkova J, Konvalinka J, Lubkowski J: A high-resolution structure of ligand-free human glutamate carboxypeptidase II. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007, 63:150-153.  ico-link  ico-pdf

Barinka C, Rovenska M, Mlcochova P, Hlouchova K, Plechanovova A, Majer P, Tsukamoto T, Slusher BS, Konvalinka J, Lubkowski J: Structural insight into the pharmacophore pocket of human glutamate carboxypeptidase II. J Med Chem 2007, 50:3267-3273.  ico-link  ico-pdf

Mesters JR#, Barinka C#, Li W, Tsukamoto T, Majer P, Slusher BS, Konvalinka J, Hilgenfeld R: Structure of glutamate carboxypeptidase II, a drug target in neuronal damage and prostate cancer. EMBO J 2006, 25:1375-1384.  ico-link  ico-pdf

Barinka C, Parry G, Callahan J, Shaw DE, Kuo A, Bdeir K, Cines DB, Mazar A, Lubkowski J: Structural basis of interaction between urokinase-type plasminogen activator and its receptor. J Mol Biol 2006, 363:482-495.  ico-link  ico-pdf

Caffrey CR, Placha L, Barinka C, Hradilek M, Dostal J, Sajid M, McKerrow JH, Majer P, Konvalinka J, Vondrasek J: Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors. Biol Chem 2005, 386:339-349.  ico-link  ico-pdf

Barinka C, Sacha P, Sklenar J, Man P, Bezouska K, Slusher BS, Konvalinka J: Identification of the N-glycosylation sites on glutamate carboxypeptidase II necessary for proteolytic activity. Protein Sci 2004, 13:1627-1635.  ico-link  ico-pdf

Barinka C, Mlcochova P, Sacha P, Hilgert I, Majer P, Slusher BS, Horejsi V, Konvalinka J: Amino acids at the N- and C-termini of human glutamate carboxypeptidase II are required for enzymatic activity and proper folding. Eur J Biochem 2004, 271:2782-2790.  ico-link  ico-pdf

Strisovsky K, Jiraskova J, Barinka C, Majer P, Rojas C, Slusher BS, Konvalinka J: Mouse brain serine racemase catalyzes specific elimination of L-serine to pyruvate. FEBS Lett 2003, 535:44-48.  ico-link  ico-pdf

Barinka C, Rinnova M, Sacha P, Rojas C, Majer P, Slusher BS, Konvalinka J: Substrate specificity, inhibition and enzymological analysis of recombinant human glutamate carboxypeptidase II. J Neurochem 2002, 80:477-487.  ico-link  ico-pdf

Rinnova M, Hradilek M, Barinka C, Weber J, Soucek M, Vondrasek J, Klimkait T, Konvalinka J: A picomolar inhibitor of resistant strains of human immunodeficiency virus protease identified by a combinatorial approach. Arch Biochem Biophys 2000, 382:22-30.  ico-link  ico-pdf