1
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Kolonko-Adamska M, Zawadzka-Kazimierczuk A, Bartosińska-Marzec P, Koźmiński W, Popowicz G, Krężel A, Ożyhar A, Greb-Markiewicz B. Interaction patterns of methoprene-tolerant and germ cell-expressed Drosophila JH receptors suggest significant differences in their functioning. Front Mol Biosci 2023; 10:1215550. [PMID: 37654797 PMCID: PMC10465699 DOI: 10.3389/fmolb.2023.1215550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Methoprene-tolerant (Met) and germ cell-expressed (Gce) proteins were shown to be juvenile hormone (JH) receptors of Drosophila melanogaster with partially redundant functions. We raised the question of where the functional differentiation of paralogs comes from. Therefore, we tested Met and Gce interaction patterns with selected partners. In this study, we showed the ability of Gce and its C-terminus (GceC) to interact with 14-3-3 in the absence of JH. In contrast, Met or Met C-terminus (MetC) interactions with 14-3-3 were not observed. We also performed a detailed structural analysis of Met/Gce interactions with the nuclear receptor fushi tarazu factor-1 (Ftz-F1) ligand-binding domain. We showed that GceC comprising an Ftz-F1-binding site and full-length protein interacts with Ftz-F1. In contrast to Gce, only MetC (not full-length Met) can interact with Ftz-F1 in the absence of JH. We propose that the described differences result from the distinct tertiary structure and accessibility of binding sites in the full-length Met/Gce. Moreover, we hypothesize that each interacting partner can force disordered MetC and GceC to change the structure in a partner-specific manner. The observed interactions seem to determine the subcellular localization of Met/Gce by forcing their translocation between the nucleus and the cytoplasm, which may affect the activity of the proteins. The presented differences between Met and Gce can be crucial for their functional differentiation during D. melanogaster development and indicate Gce as a more universal and more active paralog. It is consistent with the theory indicating gce as an ancestor gene.
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Affiliation(s)
- M. Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - A. Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - P. Bartosińska-Marzec
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - W. Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - G. Popowicz
- Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - A. Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - A. Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - B. Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
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2
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Czarna A, Plewka J, Kresik L, Matsuda A, Karim A, Robinson C, O'Byrne S, Cunningham F, Georgiou I, Wilk P, Pachota M, Popowicz G, Wyatt PG, Dubin G, Pyrć K. Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity. Structure 2022; 30:1050-1054.e2. [PMID: 35609600 PMCID: PMC9125827 DOI: 10.1016/j.str.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
During RNA replication, coronaviruses require proofreading to maintain the integrity of their large genomes. Nsp14 associates with viral polymerase complex to excise the mismatched nucleotides. Aside from the exonuclease activity, nsp14 methyltransferase domain mediates cap methylation, facilitating translation initiation and protecting viral RNA from recognition by the innate immune sensors. The nsp14 exonuclease activity is modulated by a protein co-factor nsp10. While the nsp10/nsp14 complex structure is available, the mechanistic basis for nsp10-mediated modulation remains unclear in the absence of the nsp14 structure. Here, we provide a crystal structure of nsp14 in an apo-form. Comparative analysis of the apo- and nsp10-bound structures explain the modulatory role of the co-factor protein and reveal the allosteric nsp14 control mechanism essential for drug discovery. Further, the flexibility of the N-terminal lid of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp14 structure presented in this study rationalizes the recently proposed idea of nsp14/nsp10/nsp16 ternary complex.
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Affiliation(s)
- Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Jacek Plewka
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Leanid Kresik
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Abdulkarim Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, Kirkuk Road, 44002 Erbil, Kurdistan Region, Iraq; Department of Community Health, College of Health Technology, Cihan University-Erbil, 100 Street, 44001 Erbil, Kurdistan Region, Iraq
| | - Colin Robinson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DDI 5EH, UK
| | - Sean O'Byrne
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DDI 5EH, UK
| | - Fraser Cunningham
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DDI 5EH, UK
| | - Irene Georgiou
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DDI 5EH, UK
| | - Piotr Wilk
- Structural Biology Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Magdalena Pachota
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Grzegorz Popowicz
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Paul Graham Wyatt
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DDI 5EH, UK.
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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3
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Olguín-Contreras LF, Mendler AN, Popowicz G, Hu B, Noessner E. Double Strike Approach for Tumor Attack: Engineering T Cells Using a CD40L:CD28 Chimeric Co-Stimulatory Switch Protein for Enhanced Tumor Targeting in Adoptive Cell Therapy. Front Immunol 2021; 12:750478. [PMID: 34912334 PMCID: PMC8666660 DOI: 10.3389/fimmu.2021.750478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/01/2021] [Indexed: 12/24/2022] Open
Abstract
Activation of co-stimulatory pathways in cytotoxic T lymphocytes expressing chimeric antigen receptors (CARs) have proven to boost effector activity, tumor rejection and long-term T cell persistence. When using antigen-specific T cell receptors (TCR) instead of CARs, the lack of co-stimulatory signals hampers robust antitumoral response, hence limiting clinical efficacy. In solid tumors, tumor stroma poses an additional hurdle through hindrance of infiltration and active inhibition. Our project aimed at generating chimeric co-stimulatory switch proteins (CSP) consisting of intracellular co-stimulatory domains (ICD) fused to extracellular protein domains (ECD) for which ligands are expressed in solid tumors. The ECD of CD40L was selected for combination with the ICD from the CD28 protein. With this approach, it was expected to not only provide co-stimulation and strengthen the TCR signaling, but also, through the CD40L ECD, facilitate the activation of tumor-resident antigen-presenting cells (APCs), modulate activation of tumor endothelium and induce TCR-MHC independent apoptotic effect on tumor cells. Since CD28 and CD40L belong to different classes of transmembrane proteins (type I and type II, respectively), creating a chimeric protein presented a structural and functional challenge. We present solutions to this challenge describing different CSP formats that were successfully expressed in human T cells along with an antigen-specific TCR. The level of surface expression of the CSPs depended on their distinct design and the state of T cell activation. In particular, CSPs were upregulated by TCR stimulation and downregulated following interaction with CD40 on target cells. Ligation of the CSP in the context of TCR-stimulation modulated intracellular signaling cascades and led to improved TCR-induced cytokine secretion and cytotoxicity. Moreover, the CD40L ECD exhibited activity as evidenced by effective maturation and activation of B cells and DCs. CD40L:CD28 CSPs are a new type of switch proteins designed to exert dual beneficial antitumor effect by acting directly on the gene-modified T cells and simultaneously on tumor cells and tumor-supporting cells of the TME. The observed effects suggest that they constitute a promising tool to be included in the engineering process of T cells to endow them with complementary features for improved performance in the tumor milieu.
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Affiliation(s)
| | - Anna N. Mendler
- Institute of Molecular Immunology, Helmholtz Center Munich, Munich, Germany
| | - Grzegorz Popowicz
- Institute of Structural Biology, Helmholtz Center Munich, Munich, Germany
| | - Bin Hu
- Institute of Molecular Immunology, Helmholtz Center Munich, Munich, Germany
| | - Elfriede Noessner
- Institute of Molecular Immunology, Helmholtz Center Munich, Munich, Germany
- Immunoanalytics Research Group - Tissue Control of Immunocytes, Helmholtz Center Munich, Munich, Germany
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4
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Kolonko M, Bystranowska D, Taube M, Kozak M, Bostock M, Popowicz G, Ożyhar A, Greb-Markiewicz B. The intrinsically disordered region of GCE protein adopts a more fixed structure by interacting with the LBD of the nuclear receptor FTZ-F1. Cell Commun Signal 2020; 18:180. [PMID: 33153474 PMCID: PMC7643343 DOI: 10.1186/s12964-020-00662-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
The Drosophila melanogaster Germ cell-expressed protein (GCE) is a paralog of the juvenile hormone (JH) receptor - Methoprene tolerant protein (MET). Both proteins mediate JH function, preventing precocious differentiation during D. melanogaster development. Despite that GCE and MET are often referred to as equivalent JH receptors, their functions are not fully redundant and show tissue specificity. Both proteins belong to the family of bHLH-PAS transcription factors. The similarity of their primary structure is limited to defined bHLH and PAS domains, while their long C-terminal fragments (GCEC, METC) show significant differences and are expected to determine differences in GCE and MET protein activities. In this paper we present the structural characterization of GCEC as a coil-like intrinsically disordered protein (IDP) with highly elongated and asymmetric conformation. In comparison to previously characterized METC, GCEC is less compacted, contains more molecular recognition elements (MoREs) and exhibits a higher propensity for induced folding. The NMR shifts perturbation experiment and pull-down assay clearly demonstrated that the GCEC fragment is sufficient to form an interaction interface with the ligand binding domain (LBD) of the nuclear receptor Fushi Tarazu factor-1 (FTZ-F1). Significantly, these interactions can force GCEC to adopt more fixed structure that can modulate the activity, structure and functions of the full-length receptor. The discussed relation of protein functionality with the structural data of inherently disordered GCEC fragment is a novel look at this protein and contributes to a better understanding of the molecular basis of the functions of the C-terminal fragments of the bHLH-PAS family. Video abstract.
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Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
| | - Mark Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Grzegorz Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
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5
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Denis M, Softley C, Giuntini S, Gentili M, Ravera E, Parigi G, Fragai M, Popowicz G, Sattler M, Luchinat C, Cerofolini L, Nativi C. The Photocatalyzed Thiol-ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins. Chemphyschem 2020; 21:863-869. [PMID: 32092218 PMCID: PMC7384118 DOI: 10.1002/cphc.202000071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Indexed: 11/18/2022]
Abstract
Paramagnetic restraints have been used in biomolecular NMR for the last three decades to elucidate and refine biomolecular structures, but also to characterize protein-ligand interactions. A common technique to generate such restraints in proteins, which do not naturally contain a (paramagnetic) metal, consists in the attachment to the protein of a lanthanide-binding-tag (LBT). In order to design such LBTs, it is important to consider the efficiency and stability of the conjugation, the geometry of the complex (conformational exchanges and coordination) and the chemical inertness of the ligand. Here we describe a photo-catalyzed thiol-ene reaction for the cysteine-selective paramagnetic tagging of proteins. As a model, we designed an LBT with a vinyl-pyridine moiety which was used to attach our tag to the protein GB1 in fast and irreversible fashion. Our tag T1 yields magnetic susceptibility tensors of significant size with different lanthanides and has been characterized using NMR and relaxometry measurements.
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Affiliation(s)
- Maxime Denis
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
| | - Charlotte Softley
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Stefano Giuntini
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Matteo Gentili
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Giacomo Parigi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Marco Fragai
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Grzegorz Popowicz
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Michael Sattler
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
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6
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Denis M, Softley C, Giuntini S, Gentili M, Ravera E, Parigi G, Fragai M, Popowicz G, Sattler M, Luchinat C, Cerofolini L, Nativi C. Cover Feature: The Photocatalyzed Thiol‐ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins (ChemPhysChem 9/2020). Chemphyschem 2020. [DOI: 10.1002/cphc.202000286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Maxime Denis
- Giotto Biotech, S.R.L Via Madonna del piano 6 50019 Sesto Fiorentino (FI) Italy
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
| | - Charlotte Softley
- Biomolecular NMR, Department ChemieTechnical University of Munich Lichtenbergstrasse 4 85747 Garching Germany
- Institute of Structural BiologyHelmholtz Center Munich Neuherberg Germany
| | - Stefano Giuntini
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Matteo Gentili
- Giotto Biotech, S.R.L Via Madonna del piano 6 50019 Sesto Fiorentino (FI) Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Giacomo Parigi
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Marco Fragai
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Grzegorz Popowicz
- Institute of Structural BiologyHelmholtz Center Munich Neuherberg Germany
| | - Michael Sattler
- Biomolecular NMR, Department ChemieTechnical University of Munich Lichtenbergstrasse 4 85747 Garching Germany
- Institute of Structural BiologyHelmholtz Center Munich Neuherberg Germany
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P) Via L. Sacconi 6 50019 Sesto FIorentino (FI) Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI), Italy
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7
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Ratkova EL, Dawidowski M, Napolitano V, Dubin G, Fino R, Ostertag MS, Sattler M, Popowicz G, Tetko IV. Water envelope has a critical impact on the design of protein–protein interaction inhibitors. Chem Commun (Camb) 2020; 56:4360-4363. [DOI: 10.1039/c9cc07714f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We show that a water envelope network plays a critical role in protein–protein interactions (PPI).
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Affiliation(s)
- Ekaterina L. Ratkova
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Medicinal Chemistry, Cardiovascular, Renal and Metabolic Diseases
| | - Maciej Dawidowski
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Department of Drug Technology and Pharmaceutical Biotechnology
| | - Valeria Napolitano
- Faculty of Biochemistry, Biophysics and Biotechnology and Malopolska Centre of Biotechnology
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology and Malopolska Centre of Biotechnology
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Roberto Fino
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Michael S. Ostertag
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Michael Sattler
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR
| | - Grzegorz Popowicz
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Igor V. Tetko
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- BIGCHEM GmbH
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8
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Abstract
We present a Focused Library Generator that is able to create from scratch new molecules with desired properties. After training the Generator on the ChEMBL database, transfer learning was used to switch the generator to producing new Mdmx inhibitors that are a promising class of anticancer drugs. Lilly medicinal chemistry filters, molecular docking, and a QSAR IC50 model were used to refine the output of the Generator. Pharmacophore screening and molecular dynamics (MD) simulations were then used to further select putative ligands. Finally, we identified five promising hits with equivalent or even better predicted binding free energies and IC50 values than known Mdmx inhibitors. The source code of the project is available on https://github.com/bigchem/online-chem.
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Affiliation(s)
- Zhonghua Xia
- Institute of Structural Biology, Helmholtz Zentrum München - Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Pavel Karpov
- Institute of Structural Biology, Helmholtz Zentrum München - Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- BigChem GmbH, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München - Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Igor V Tetko
- Institute of Structural Biology, Helmholtz Zentrum München - Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- BigChem GmbH, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
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9
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Bolz C, Bach NC, Meyer H, Müller G, Dawidowski M, Popowicz G, Sieber SA, Skerra A, Gerhard M. Comparison of enzymatic properties and small molecule inhibition of γ-glutamyltranspeptidases from pathogenic and commensal bacteria. Biol Chem 2017; 398:341-357. [PMID: 27636829 DOI: 10.1515/hsz-2016-0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/24/2016] [Indexed: 01/06/2023]
Abstract
Helicobacter pylori infects the stomach of 50% of the population worldwide, thus causing chronic gastritis. Although this infection can be cured by antibiotic treatment, therapeutic options are increasingly limited due to the development of resistances. The γ-glutamyl-transpeptidase (gGT) of H. pylori (HpgGT) is a virulence factor important for colonization and contributes to bacterial immune evasion. Therefore, this enzyme is a potential target for developing new anti-infectives. As species specificity of such compounds is required in order to avoid off-target or adverse effects, comparative analysis of the gGTs from different organisms is a prerequisite for drug development. To allow detailed biochemical and enzymatic characterization, recombinant gGTs from five different bacteria as well as Homo sapiens were characterized and compared. Investigation of the enzymatic activity, the binding modes of known inhibitors to the catalytic center, and a high resolution X-ray structure of the HpgGT provided a starting point for the identification of new inhibitory substances targeting HpgGT. Inhibitors with Ki values in the nm to mm range were identified and their binding modes were analyzed by mass spectrometry. The results of this study provide a basis for the development of species-specific lead compounds with anti-infective potential by effectively inhibiting HpgGT.
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10
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Corvino A, Severino B, Fiorino F, Frecentese F, Magli E, Perissutti E, Santagada V, Bucci M, Cirino G, Kelly G, Servillo L, Popowicz G, Pastore A, Caliendo G. Fragment-based de novo design of a cystathionine γ-lyase selective inhibitor blocking hydrogen sulfide production. Sci Rep 2016; 6:34398. [PMID: 27708394 PMCID: PMC5052628 DOI: 10.1038/srep34398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022] Open
Abstract
Hydrogen sulfide is an essential catabolite that intervenes in the pathophysiology of several diseases from hypertension to stroke, diabetes and pancreatitis. It is endogenously synthesized mainly by two pyridoxal-5′-phosphate-dependent enzymes involved in L-cysteine metabolism: cystathionine-ß-synthase (CBS) and cystathionine-γ-lyase (CSE). Research in this field is currently impaired by the lack of pharmacological tools such as selective enzymatic inhibitors that could target specifically only one of these pathways. We used a novel approach based on a hybrid method that includes drug design, synthetic biology, metabolomics and pharmacological assays to rationally design a new inhibitor selective for the CSE enzyme. The identification of this compound opens new frontiers towards a better understanding of the role of CSE over CBS in the pathophysiology of diseases where a role for the H2S pathway has been proposed and the development of new lead compounds that could target the CSE enzyme.
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Affiliation(s)
- Angela Corvino
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy.,Department of Neuroscience, Wohl Institute, King's College London, Denmark Hill Campus, London SE5, UK
| | - Beatrice Severino
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Ferdinando Fiorino
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Francesco Frecentese
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Elisa Magli
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Elisa Perissutti
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Vincenzo Santagada
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
| | - Geoff Kelly
- MRC Biomedical NMR Centre, NIMR, NW7 1AA, London
| | - Luigi Servillo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Italy
| | | | - Annalisa Pastore
- Department of Neuroscience, Wohl Institute, King's College London, Denmark Hill Campus, London SE5, UK
| | - Giuseppe Caliendo
- Department of Pharmacy, University of Naples "Federico II" - Via D. Montesano, 49, 80131-Napoli, Italy
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11
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Pustelny K, Zdzalik M, Stach N, Stec-Niemczyk J, Cichon P, Czarna A, Popowicz G, Mak P, Drag M, Salvesen GS, Wladyka B, Potempa J, Dubin A, Dubin G. Staphylococcal SplB serine protease utilizes a novel molecular mechanism of activation. J Biol Chem 2014; 289:15544-53. [PMID: 24713703 DOI: 10.1074/jbc.m113.507616] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylococcal SplB protease belongs to the chymotrypsin family. Chymotrypsin zymogen is activated by proteolytic processing at the N terminus, resulting in significant structural rearrangement at the active site. Here, we demonstrate that the molecular mechanism of SplB protease activation differs significantly and we characterize the novel mechanism in detail. Using peptide and protein substrates we show that the native signal peptide, or any N-terminal extension, has an inhibitory effect on SplB. Only precise N-terminal processing releases the full proteolytic activity of the wild type analogously to chymotrypsin. However, comparison of the crystal structures of mature SplB and a zymogen mimic show no rearrangement at the active site whatsoever. Instead, only the formation of a unique hydrogen bond network, distant form the active site, by the new N-terminal glutamic acid of mature SplB is observed. The importance of this network and influence of particular hydrogen bond interactions at the N terminus on the catalytic process is demonstrated by evaluating the kinetics of a series of mutants. The results allow us to propose a consistent model where changes in the overall protein dynamics rather than structural rearrangement of the active site are involved in the activation process.
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Affiliation(s)
- Katarzyna Pustelny
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Michal Zdzalik
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Natalia Stach
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Justyna Stec-Niemczyk
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Przemyslaw Cichon
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Anna Czarna
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the NMR Group, Max-Planck Institute for Biochemistry, 82 152 Martinsried, Germany
| | - Grzegorz Popowicz
- the NMR Group, Max-Planck Institute for Biochemistry, 82 152 Martinsried, Germany, the Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Pawel Mak
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Malopolska Centre of Biotechnology, 30 387 Krakow, Poland
| | - Marcin Drag
- the Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, 50 370 Wroclaw, Poland, the Program in Cell Death Research, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Guy S Salvesen
- the Program in Cell Death Research, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Benedykt Wladyka
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Malopolska Centre of Biotechnology, 30 387 Krakow, Poland
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Center of Oral Health and Systemic Disease, School of Dentistry, University of Louisville, Louisville, Kentucky 40202, and
| | - Adam Dubin
- From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland
| | - Grzegorz Dubin
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Malopolska Centre of Biotechnology, 30 387 Krakow, Poland
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12
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Burchacka E, Zdzalik M, Niemczyk JS, Pustelny K, Popowicz G, Wladyka B, Dubin A, Potempa J, Sienczyk M, Dubin G, Oleksyszyn J. Development and binding characteristics of phosphonate inhibitors of SplA protease from Staphylococcus aureus. Protein Sci 2013; 23:179-89. [PMID: 24375505 DOI: 10.1002/pro.2403] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/27/2013] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
Staphylococcus aureus is responsible for a variety of human infections, including life-threatening, systemic conditions. Secreted proteome, including a range of proteases, constitutes the major virulence factor of the bacterium. However, the functions of individual enzymes, in particular SplA protease, remain poorly characterized. Here, we report development of specific inhibitors of SplA protease. The design, synthesis, and activity of a series of α-aminoalkylphosphonate diaryl esters and their peptidyl derivatives are described. Potent inhibitors of SplA are reported, which may facilitate future investigation of physiological function of the protease. The binding modes of the high-affinity compounds Cbz-Phe(P) -(OC6 H4 -4-SO2 CH3 )2 and Suc-Val-Pro-Phe(P) -(OC6 H5 )2 are revealed by high-resolution crystal structures of complexes with the protease. Surprisingly, the binding mode of both compounds deviates from previously characterized canonical interaction of α-aminoalkylphosphonate peptidyl derivatives and family S1 serine proteases.
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Affiliation(s)
- Ewa Burchacka
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
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13
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Czarna A, Beck B, Srivastava S, Popowicz G, Wolf S, Huang Y, Bista M, Holak TA, Dömling A. Robust generation of lead compounds for protein-protein interactions by computational and MCR chemistry: p53/Hdm2 antagonists. Angew Chem Int Ed Engl 2010; 49:5352-6. [PMID: 20575124 PMCID: PMC3772515 DOI: 10.1002/anie.201001343] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Czarna
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Barbara Beck
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Stuti Srivastava
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Grzegorz Popowicz
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Siglinde Wolf
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yijun Huang
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Michal Bista
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tad A. Holak
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Dömling
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
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14
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Mavoungou C, Israel L, Rehm T, Ksiazek D, Krajewski M, Popowicz G, Noegel AA, Schleicher M, Holak TA. NMR structural characterization of the N-terminal domain of the adenylyl cyclase-associated protein (CAP) from Dictyostelium discoideum. J Biomol NMR 2004; 29:73-84. [PMID: 15017141 DOI: 10.1023/b:jnmr.0000019513.86120.98] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cyclase-associated proteins (CAPs) are highly conserved, ubiquitous actin binding proteins that are involved in microfilament reorganization. The N-termini of CAPs play a role in Ras signaling and bind adenylyl cyclase; the C-termini bind to G-actin. We report here the NMR characterization of the amino-terminal domain of CAP from Dictyostelium discoideum (CAP(1-226)). NMR data, including the steady state (1)H-(15)N heteronuclear NOE experiments, indicate that the first 50 N-terminal residues are unstructured and that this highly flexible serine-rich fragment is followed by a stable, folded core starting at Ser 51. The NMR structure of the folded core is an alpha-helix bundle composed of six antiparallel helices, in a stark contrast to the recently determined CAP C-terminal domain structure, which is solely built by beta-strands.
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15
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Dubin G, Popowicz G, Krajewski M, Potempa J, Dubin A, Holak TA. 1H, 15N and 13C NMR resonance assignments of staphostatin A, a specific Staphylococcus aureus cysteine proteinase inhibitor. J Biomol NMR 2004; 28:295-296. [PMID: 14752262 DOI: 10.1023/b:jnmr.0000013681.37659.24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The increasing antibiotic resistance of an important human pathogen Staphylococcus aureus calls for the development of new therapeutic strategies. Staphylococcal cysteine proteases have been suggested as targets for such therapies. The recent discovery of staphostatins, specific protein inhibitors of these enzymes, gives prospects for the design and production of synthetic, low molecular weight analogs which might become drugs. We have decided to structurally characterize staphostatin A, a representative inhibitor of staphylococcal cysteine proteases, and to assess its binding mode to the target protease with the view of clarifying the specificity determinants. Here we report the (1)H, (15)N and (13)C NMR resonance assignments of staphostatin A.
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16
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Dubin G, Krajewski M, Popowicz G, Stec-Niemczyk J, Bochtler M, Potempa J, Dubin A, Holak TA. A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus. Biochemistry 2004; 42:13449-56. [PMID: 14621990 DOI: 10.1021/bi035310j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of secreted proteases are included among the virulence factors documented for Staphylococcus aureus. In light of increasing antibiotic resistance of this dangerous human pathogen, these proteases are considered as suitable targets for the development of novel therapeutic strategies. The recent discovery of staphostatins, endogenous, highly specific, staphylococcal cysteine protease inhibitors, opened a possibility for structure-based design of low molecular weight analogues. Moreover, the crystal structure of staphostatin B revealed a distinct folding pattern and an unexpected, substrate-like binding mode. The solution structure of staphostatin A reported here confirms that staphostatins constitute a novel, distinct class of cysteine protease inhibitors. In addition, the structure knowledge-based mutagenesis studies shed light on individual structural features of staphostatin A, the inhibition mechanism, and the determinants of distinct specificity of staphostatins toward their target proteases.
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Affiliation(s)
- Grzegorz Dubin
- Faculty of Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland.
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