1
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Bojko M, Węgrzyn K, Sikorska E, Ciura P, Battin C, Steinberger P, Magiera-Mularz K, Dubin G, Kulesza A, Sieradzan AK, Spodzieja M, Rodziewicz-Motowidło S. Peptide-based inhibitors targeting the PD-1/PD-L1 axis: potential immunotherapeutics for cancer. Transl Oncol 2024; 42:101892. [PMID: 38359715 PMCID: PMC10877416 DOI: 10.1016/j.tranon.2024.101892] [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: 09/29/2023] [Revised: 12/20/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The PD-1/PD-L1 complex belongs to the group of inhibitory immune checkpoints and plays a critical role in immune regulation. The PD-1/PD-L1 axis is also responsible for immune evasion of cancer cells, and this complex is one of the main targets of immunotherapies used in oncology. Treatment using immune checkpoint inhibitors is mainly based on antibodies. This approach has great therapeutic potential; however, it also has major drawbacks and can induce immune-related adverse events. Thus, there is a strong need for alternative, non-antibody-based therapies using small molecules, peptides, or peptidomimetics. In the present study, we designed, synthesized, and evaluated a set of PD-1-targeting peptides based on the sequence and structure of PD-L1. The binding of these peptides to PD-1 was investigated using SPR and ELISA. We also assessed their ability to compete with PD-L1 for binding to PD-1 and their inhibitory properties against the PD-1/PD-L1 complex at the cellular level. The best results were obtained for the peptide PD-L1(111-127)(Y112C-I126C), named (L11), which displaced PD-L1 from binding to PD-1 in the competitive assay and inhibited the formation of the PD-1/PD-L1 complex. The (L11) peptide also exhibited strong affinity for PD-1. NMR studies revealed that (L11) does not form a well-defined secondary structure; however, MD simulation indicated that (L11) binds to PD-1 at the same place as PD-L1. After further optimization of the structure, the peptide inhibitor obtained in this study could also be used as a potential therapeutic compound targeting the PD-1/PD-L1 axis.
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Affiliation(s)
- Magdalena Bojko
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Katarzyna Węgrzyn
- University of Gdańsk, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Emilia Sikorska
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Piotr Ciura
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Claire Battin
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, Lazarettgasse 19, 1090 Vienna, Austria
| | - Peter Steinberger
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, Lazarettgasse 19, 1090 Vienna, Austria
| | - Katarzyna Magiera-Mularz
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Kraków, Poland
| | - Grzegorz Dubin
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Adam Kulesza
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K Sieradzan
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Marta Spodzieja
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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2
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Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones AN, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz GM, Pyrć K, Czarna A. Despite the odds: formation of the SARS-CoV-2 methylation complex. Nucleic Acids Res 2024:gkae165. [PMID: 38499483 DOI: 10.1093/nar/gkae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.
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Affiliation(s)
- Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-387 Kraków, Poland
| | - Jacek Plewka
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - André Mourão
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Leanid Kresik
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Kinga Lis
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemical Engineering and Technology, Kraków University of Technology, 31-155 Kraków, Poland
| | - Alisha N Jones
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Magdalena Pachota
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Abdulkarim Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, 44002 Erbil, Kurdistan Region, Iraq
- Department of Community Health, College of Health Technology, Cihan University-Erbil, 44001 Erbil, Kurdistan Region, Iraq
| | - Kinga Hartman
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Ravi Sonani
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Igor Minia
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Markus Landthaler
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michael Sattler
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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3
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Chykunova Y, Plewka J, Wilk P, Torzyk K, Sienczyk M, Dubin G, Pyrc K. Autoinhibition of suicidal capsid protease from O'nyong'nyong virus. Int J Biol Macromol 2024; 262:130136. [PMID: 38354926 DOI: 10.1016/j.ijbiomac.2024.130136] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Alphaviruses pose a significant threat to public health. Capsid protein encoded in the alphaviral genomes constitutes an interesting therapy target, as it also serves as a protease (CP). Remarkably, it undergoes autoproteolysis, leading to the generation of the C-terminal tryptophan that localizes to the active pocket, deactivating the enzyme. Lack of activity hampers the viral replication cycle, as the virus is not capable of producing the infectious progeny. We investigated the structure and function of the CP encoded in the genome of O'nyong'nyong virus (ONNV), which has instigated outbreaks in Africa. Our research provides a high-resolution crystal structure of the ONNV CP in its active state and evaluates the enzyme's activity. Furthermore, we demonstrated a dose-dependent reduction in ONNV CP proteolytic activity when exposed to indole, suggesting that tryptophan analogs may be a promising basis for developing small molecule inhibitors. It's noteworthy that the capsid protease plays an essential role in virus assembly, binding viral glycoproteins through its glycoprotein-binding hydrophobic pocket. We showed that non-aromatic cyclic compounds like dioxane disrupt this vital interaction. Our findings provide deeper insights into ONNV's biology, and we believe they will prove instrumental in guiding the development of antiviral strategies against arthritogenic alphaviruses.
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Affiliation(s)
- Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Piotr Wilk
- Structural Biology Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Karolina Torzyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Sienczyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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4
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Kitel R, Surmiak E, Borggräfe J, Kalinowska-Tluscik J, Golik P, Czub M, Uzar W, Musielak B, Madej M, Popowicz GM, Dubin G, Holak TA. Discovery of Inhibitory Fragments That Selectively Target Spire2-FMN2 Interaction. J Med Chem 2023; 66:15715-15727. [PMID: 38039505 PMCID: PMC10726347 DOI: 10.1021/acs.jmedchem.3c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Here, we report the fragment-based drug discovery of potent and selective fragments that disrupt the Spire2-FMN2 but not the Spire1-FMN2 interaction. Hit fragments were identified in a differential scanning fluorimetry-based screen of an in-house library of 755 compounds and subsequently validated in multiple orthogonal biophysical assays, including fluorescence polarization, microscale thermophoresis, and 1H-15N HSQC nuclear magnetic resonance. Extensive structure-activity relationships combined with molecular docking followed by chemical optimization led to the discovery of compound 13, which exhibits micromolar potency and high ligand efficiency (LE = 0.38). Therefore, this fragment represents a validated starting point for the future development of selective chemical probes targeting the Spire2-FMN2 interaction.
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Affiliation(s)
- Radoslaw Kitel
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Jan Borggräfe
- Institute
of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian
NMR Center, School of Natural Sciences, Technical University of Munich Garching, 85748 München, Germany
| | | | - Przemyslaw Golik
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Miroslawa Czub
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Wiktor Uzar
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Prof. S.
Lojasiewicza 11, 30-348 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Mariusz Madej
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Grzegorz M. Popowicz
- Institute
of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian
NMR Center, School of Natural Sciences, Technical University of Munich Garching, 85748 München, Germany
| | - Grzegorz Dubin
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
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5
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Pustelny K, Grygier P, Barzowska A, Pucelik B, Matsuda A, Mrowiec K, Slugocka E, Popowicz GM, Dubin G, Czarna A. Binding mechanism and biological effects of flavone DYRK1A inhibitors for the design of new antidiabetics. Sci Rep 2023; 13:18114. [PMID: 37872245 PMCID: PMC10593742 DOI: 10.1038/s41598-023-44810-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The selective inhibition of kinases from the diabetic kinome is known to promote the regeneration of beta cells and provide an opportunity for the curative treatment of diabetes. The effect can be achieved by carefully tailoring the selectivity of inhibitor toward a particular kinase, especially DYRK1A, previously associated with Down syndrome and Alzheimer's disease. Recently DYRK1A inhibition has been shown to promote both insulin secretion and beta cells proliferation. Here, we show that commonly available flavones are effective inhibitors of DYRK1A. The observed biochemical activity of flavone compounds is confirmed by crystal structures solved at 2.06 Å and 2.32 Å resolution, deciphering the way inhibitors bind in the ATP-binding pocket of the kinase, which is driven by the arrangement of hydroxyl moieties. We also demonstrate antidiabetic properties of these biomolecules and prove that they could be further improved by therapy combined with TGF-β inhibitors. Our data will allow future structure-based optimization of the presented scaffolds toward potent, bioavailable and selective anti-diabetic drugs.
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Affiliation(s)
- Katarzyna Pustelny
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Przemyslaw Grygier
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Agata Barzowska
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Barbara Pucelik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Alex Matsuda
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Krzysztof Mrowiec
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Emilia Slugocka
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Anna Czarna
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland.
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6
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Malicki S, Książek M, Sochaj Gregorczyk A, Kamińska M, Golda A, Chruścicka B, Mizgalska D, Potempa J, Marti HP, Kozieł J, Wieczorek M, Pieczykolan J, Mydel P, Dubin G. Identification and characterization of aptameric inhibitors of human neutrophil elastase. J Biol Chem 2023; 299:104889. [PMID: 37286041 PMCID: PMC10359491 DOI: 10.1016/j.jbc.2023.104889] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
Human neutrophil elastase (HNE) plays a pivotal role in innate immunity, inflammation, and tissue remodeling. Aberrant proteolytic activity of HNE contributes to organ destruction in various chronic inflammatory diseases including emphysema, asthma, and cystic fibrosis. Therefore, elastase inhibitors could alleviate the progression of these disorders. Here, we used the systematic evolution of ligands by exponential enrichment to develop ssDNA aptamers that specifically target HNE. We determined the specificity of the designed inhibitors and their inhibitory efficacy against HNE using biochemical and in vitro methods, including an assay of neutrophil activity. Our aptamers inhibit the elastinolytic activity of HNE with nanomolar potency and are highly specific for HNE and do not target other tested human proteases. As such, this study provides lead compounds suitable for the evaluation of their tissue-protective potential in animal models.
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Affiliation(s)
- Stanisław Malicki
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mirosław Książek
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alicja Sochaj Gregorczyk
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marta Kamińska
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | - Anna Golda
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Barbara Chruścicka
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Joanna Kozieł
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maciej Wieczorek
- Innovative Drugs R&D Department, Celon Pharma Inc, Lomianki, Poland
| | | | - Piotr Mydel
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | - Grzegorz Dubin
- Protein Crystallography Research, Group Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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7
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Magoch M, McEwen AG, Napolitano V, Władyka B, Dubin G. Crystal Structure of Staphopain C from Staphylococcus aureus. Molecules 2023; 28:molecules28114407. [PMID: 37298883 DOI: 10.3390/molecules28114407] [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: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Staphylococcus aureus is a common opportunistic pathogen of humans and livestock that causes a wide variety of infections. The success of S. aureus as a pathogen depends on the production of an array of virulence factors including cysteine proteases (staphopains)-major secreted proteases of certain strains of the bacterium. Here, we report the three-dimensional structure of staphopain C (ScpA2) of S. aureus, which shows the typical papain-like fold and uncovers a detailed molecular description of the active site. Because the protein is involved in the pathogenesis of a chicken disease, our work provides the foundation for inhibitor design and potential antimicrobial strategies against this pathogen.
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Affiliation(s)
- Malgorzata Magoch
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Alastair G McEwen
- CNRS, INSERM, Université de Strasbourg, IGBMC UMR 7104-UMR-S 1258, F-67400 Illkirch, France
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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8
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Grygier P, Pustelny K, Nowak J, Golik P, Popowicz GM, Plettenburg O, Dubin G, Menezes F, Czarna A. Silmitasertib (CX-4945), a Clinically Used CK2-Kinase Inhibitor with Additional Effects on GSK3β and DYRK1A Kinases: A Structural Perspective. J Med Chem 2023; 66:4009-4024. [PMID: 36883902 PMCID: PMC10041529 DOI: 10.1021/acs.jmedchem.2c01887] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A clinical casein kinase 2 inhibitor, CX-4945 (silmitasertib), shows significant affinity toward the DYRK1A and GSK3β kinases, involved in down syndrome phenotypes, Alzheimer's disease, circadian clock regulation, and diabetes. This off-target activity offers an opportunity for studying the effect of the DYRK1A/GSK3β kinase system in disease biology and possible line extension. Motivated by the dual inhibition of these kinases, we solved and analyzed the crystal structures of DYRK1A and GSK3β with CX-4945. We built a quantum-chemistry-based model to rationalize the compound affinity for CK2α, DYRK1A, and GSK3β kinases. Our calculations identified a key element for CK2α's subnanomolar affinity to CX-4945. The methodology is expandable to other kinase selectivity modeling. We show that the inhibitor limits DYRK1A- and GSK3β-mediated cyclin D1 phosphorylation and reduces kinase-mediated NFAT signaling in the cell. Given the CX-4945's clinical and pharmacological profile, this inhibitory activity makes it an interesting candidate with potential for application in additional disease areas.
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Affiliation(s)
- Przemyslaw Grygier
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Katarzyna Pustelny
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Jakub Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | | | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Institute of Organic Chemistry, Centre of Biomolecular Drug Research (BMWZ) and Laboratory of Nano and Quantum Engineering (LNQE), Leibniz University Hannover, Schneiderberg 1b, Hannover 30167, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Institute of Lung Health (ILH), Aulweg 130, Giessen 35392, Germany
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Filipe Menezes
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Anna Czarna
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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9
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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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10
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Hoyer M, Crevenna AH, Kitel R, Willems K, Czub M, Dubin G, Van Dorpe P, Holak TA, Lamb DC. Analysis tools for single-monomer measurements of self-assembly processes. Sci Rep 2022; 12:4682. [PMID: 35304498 PMCID: PMC8933434 DOI: 10.1038/s41598-022-08245-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 11/29/2022] Open
Abstract
Protein assembly plays an important role throughout all phyla of life, both physiologically and pathologically. In particular, aggregation and polymerization of proteins are key-strategies that regulate cellular function. In recent years, methods to experimentally study the assembly process on a single-molecule level have been developed. This progress concomitantly has triggered the question of how to analyze this type of single-filament data adequately and what experimental conditions are necessary to allow a meaningful interpretation of the analysis. Here, we developed two analysis methods for single-filament data: the visitation analysis and the average-rate analysis. We benchmarked and compared both approaches with the classic dwell-time-analysis frequently used to study microscopic association and dissociation rates. In particular, we tested the limitations of each analysis method along the lines of the signal-to-noise ratio, the sampling rate, and the labeling efficiency and bleaching rate of the fluorescent dyes used in single-molecule fluorescence experiments. Finally, we applied our newly developed methods to study the monomer assembly of actin at the single-molecule-level in the presence of the class II nucleator Cappuccino and the WH2 repeats of Spire. For Cappuccino, our data indicated fast elongation circumventing a nucleation phase whereas, for Spire, we found that the four WH2 motifs are not sufficient to promote de novo nucleation of actin.
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Affiliation(s)
- Maria Hoyer
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany
| | - Alvaro H Crevenna
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany.,Epigenetics and Neurobiology Unit, EMBL Rome, Monterotondo, Italy
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | | | - Miroslawa Czub
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | | | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany.
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11
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Sonani RR, Blat A, Dubin G. Crystal structures of apo- and FAD-bound human peroxisomal acyl-CoA oxidase provide mechanistic basis explaining clinical observations. Int J Biol Macromol 2022; 205:203-210. [PMID: 35149097 DOI: 10.1016/j.ijbiomac.2022.02.008] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/27/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022]
Abstract
Peroxisomal acyl-CoA oxidase 1a (ACOX1a) catalyzes the first and rate-limiting step of fatty acid oxidation, the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The dysfunction of human ACOX1a (hACOX1a) leads to deterioration of the nervous system manifesting in myeloneuropathy, hypotonia and convulsions. Crystal structures of hACOX1a in apo- and cofactor (FAD)-bound forms were solved at 2.00 and 2.09 Å resolution, respectively. hACOX1a exists as a homo-dimer with solvation free energy gain (ΔGo) of -44.7 kcal mol-1. Two FAD molecules bind at the interface of protein monomers completing the active sites. The substrate binding cleft of hACOX1a is wider compared to mitochondrial very-long chain specific acyl-CoA dehydrogenase. Mutations (p.G178C, p.M278V and p.N237S) reported to cause dysfunctionality of hACOX1a are analyzed on its 3D-structure to understand structure-function related perturbations and explain the associated phenotypes.
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Affiliation(s)
- Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Artur Blat
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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12
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Pustelny K, Kuska K, Gorecki A, Musielak B, Dobosz E, Wladyka B, Koziel J, Czarna A, Holak T, Dubin G. Mechanism of MyD88S mediated signal termination. Cell Commun Signal 2022; 20:10. [PMID: 35057808 PMCID: PMC8772076 DOI: 10.1186/s12964-021-00811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Background A universal adaptor protein, MyD88, orchestrates the innate immune response by propagating signals from toll-like receptors (TLRs) and interleukin-1 receptor (IL-1R). Receptor activation seeds MyD88 dependent formation of a signal amplifying supramolecular organizing center (SMOC)—the myddosome. Alternatively spliced variant MyD88S, lacking the intermediate domain (ID), exhibits a dominant negative effect silencing the immune response, but the mechanistic understanding is limited. Methods Luciferase reporter assay was used to evaluate functionality of MyD88 variants and mutants. The dimerization potential of MyD88 variants and myddosome nucleation process were monitored by co-immunoprecipitation and confocal microscopy. The ID secondary structure was characterized in silico employing I-TASSER server and in vitro using nuclear magnetic resonance (NMR) and circular dichroism (CD). Results We show that MyD88S is recruited to the nucleating SMOC and inhibits its maturation by interfering with incorporation of additional components. Biophysical analysis suggests that important functional role of ID is not supported by a well-defined secondary structure. Mutagenesis identifies Tyr116 as the only essential residue within ID required for myddosome nucleation and signal propagation (NF-κB activation). Conclusions Our results argue that the largely unstructured ID of MyD88 is not only a linker separating toll-interleukin-1 receptor (TIR) homology domain and death domain (DD), but contributes intermolecular interactions pivotal in MyD88-dependent signaling. The dominant negative effect of MyD88S relies on quenching the myddosome nucleation and associated signal transduction. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00811-1.
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13
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Napolitano V, Dabrowska A, Schorpp K, Mourão A, Barreto-Duran E, Benedyk M, Botwina P, Brandner S, Bostock M, Chykunova Y, Czarna A, Dubin G, Fröhlich T, Hölscher M, Jedrysik M, Matsuda A, Owczarek K, Pachota M, Plettenburg O, Potempa J, Rothenaigner I, Schlauderer F, Slysz K, Szczepanski A, Greve-Isdahl Mohn K, Blomberg B, Sattler M, Hadian K, Popowicz GM, Pyrc K. Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses. Cell Chem Biol 2022; 29:774-784.e8. [PMID: 35021060 PMCID: PMC8751734 DOI: 10.1016/j.chembiol.2021.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has been socially and economically devastating. Despite an unprecedented research effort and available vaccines, effective therapeutics are still missing to limit severe disease and mortality. Using high-throughput screening, we identify acriflavine (ACF) as a potent papain-like protease (PLpro) inhibitor. NMR titrations and a co-crystal structure confirm that acriflavine blocks the PLpro catalytic pocket in an unexpected binding mode. We show that the drug inhibits viral replication at nanomolar concentration in cellular models, in vivo in mice and ex vivo in human airway epithelia, with broad range activity against SARS-CoV-2 and other betacoronaviruses. Considering that acriflavine is an inexpensive drug approved in some countries, it may be immediately tested in clinical trials and play an important role during the current pandemic and future outbreaks.
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Affiliation(s)
- Valeria Napolitano
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Agnieszka Dabrowska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Kenji Schorpp
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - André Mourão
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Emilia Barreto-Duran
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Malgorzata Benedyk
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Pawel Botwina
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Stefanie Brandner
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Mark Bostock
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tony Fröhlich
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Michael Hölscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstrasse 5, 80802 Munich, Germany
| | - Malwina Jedrysik
- 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
| | - Katarzyna Owczarek
- Virogenetics Laboratory of Virology, 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; Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Oliver Plettenburg
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Centre of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, Hannover, Germany; Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Jan Potempa
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Ina Rothenaigner
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Florian Schlauderer
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Klaudia Slysz
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Artur Szczepanski
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | | | | | - Michael Sattler
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Kamyar Hadian
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Grzegorz Maria 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.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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14
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Barzowska A, Pucelik B, Pustelny K, Matsuda A, Martyniak A, Stępniewski J, Maksymiuk A, Dawidowski M, Rothweiler U, Dulak J, Dubin G, Czarna A. DYRK1A Kinase Inhibitors Promote β-Cell Survival and Insulin Homeostasis. Cells 2021; 10:2263. [PMID: 34571911 PMCID: PMC8467532 DOI: 10.3390/cells10092263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/06/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022] Open
Abstract
The rising prevalence of diabetes is threatening global health. It is known not only for the occurrence of severe complications but also for the SARS-Cov-2 pandemic, which shows that it exacerbates susceptibility to infections. Current therapies focus on artificially maintaining insulin homeostasis, and a durable cure has not yet been achieved. We demonstrate that our set of small molecule inhibitors of DYRK1A kinase potently promotes β-cell proliferation, enhances long-term insulin secretion, and balances glucagon level in the organoid model of the human islets. Comparable activity is seen in INS-1E and MIN6 cells, in isolated mice islets, and human iPSC-derived β-cells. Our compounds exert a significantly more pronounced effect compared to harmine, the best-documented molecule enhancing β-cell proliferation. Using a body-like environment of the organoid, we provide a proof-of-concept that small-molecule-induced human β-cell proliferation via DYRK1A inhibition is achievable, which lends a considerable promise for regenerative medicine in T1DM and T2DM treatment.
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Affiliation(s)
- Agata Barzowska
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
| | - Barbara Pucelik
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
| | - Katarzyna Pustelny
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
| | - Alex Matsuda
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
| | - Alicja Martyniak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.M.); (J.S.); (J.D.)
| | - Jacek Stępniewski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.M.); (J.S.); (J.D.)
| | - Anna Maksymiuk
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warszawa, Poland; (A.M.); (M.D.)
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warszawa, Poland; (A.M.); (M.D.)
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway;
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.M.); (J.S.); (J.D.)
| | - Grzegorz Dubin
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
| | - Anna Czarna
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; (A.B.); (B.P.); (K.P.); (A.M.); (G.D.)
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15
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Zyla E, Dubin G. Structural characteristics of macrocyclic peptide as a potent modulator of PD‐1/PD‐L1 immune checkpoint axis. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.05146] [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: 11/11/2022]
Affiliation(s)
- Edyta Zyla
- MCB Jagiellonian UniversityKraków
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityKraków
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16
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Sonani RR, Kurpiewska K, Lewiński K, Dubin G. Distinct sequence and structural feature of trypanosoma malate dehydrogenase. Biochem Biophys Res Commun 2021; 557:288-293. [PMID: 33894416 DOI: 10.1016/j.bbrc.2021.04.033] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Glycosomal malate dehydrogenase from Trypanosoma cruzi (tcgMDH) catalyzes the oxidation/reduction of malate/oxaloacetate, a crucial step of the glycolytic process occurring in the glycosome of the human parasite. Inhibition of tcgMDH is considered a druggable trait for the development of trypanocidal drugs. Sequence comparison of MDHs from different organisms revealed a distinct insertion of a prolin rich 9-mer (62-KLPPVPRDP-70) in tcgMDH as compared to other eukaryotic MDHs. Crystal structure of tcgMDH is solved here at 2.6 Å resolution with Rwork/Rfree values of 0.206/0.216. The tcgMDH forms homo-dimer with the solvation free energy (ΔGo) gain of -9.77 kcal/mol. The dimeric form is also confirmed in solution by biochemical assays, chemical-crosslinking and dynamic light scattering. The inserted 9-mer adopts a structure of a solvent accessible loop in the vicinity of NAD+ binding site. The distinct sequence and structural feature of tcgMDH, revealed in the present report, provides an anchor point for the development of inhibitors specific for tcgMDH, possible trypanocidal agents of the future.
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Affiliation(s)
- Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.
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17
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Niedziałkowski P, Bojko M, Ryl J, Wcisło A, Spodzieja M, Magiera-Mularz K, Guzik K, Dubin G, Holak TA, Ossowski T, Rodziewicz-Motowidło S. Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode. Bioelectrochemistry 2021; 139:107742. [PMID: 33517203 DOI: 10.1016/j.bioelechem.2021.107742] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/22/2023]
Abstract
This work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10-18 to 10-8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10-14 M for PD-L1 (S/N = 3.3) and at a concentration of 10-14 M via cyclic voltammetry (CV). Additionally, high-resolution X-ray photoelectron spectroscopy (XPS), contact angle, and surface free energy measurements were applied to confirm the functionalization of the electrode. We investigated the selectivity of the electrode for other proteins: Programmed Death-1 (PD-1), cluster of differentiation 160 (CD160), and B- and T-lymphocyte attenuator (BTLA) at concentrations of 10-8 M. Differentiation between PD-L1 and PD-1 was achieved based on the analysis of the capacitance effect frequency dispersion at the surface of the modified Au electrode with BMS-8 after incubation at various concentrations of PD-L1 and PD-1 proteins in the range of 10-18 to 10-8 M. Significant differences were observed in the heterogeneity of PD-L1 and PD-1. The results of the quasi-capacitance studies demonstrate that BMS-8 strongly and specifically interacts with the PD-L1 protein.
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Affiliation(s)
- Paweł Niedziałkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Magdalena Bojko
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jacek Ryl
- Department of Electrochemistry, Corrosion and Materials Engineering, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-233, Poland
| | - Anna Wcisło
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Spodzieja
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | - Katarzyna Guzik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tadeusz Ossowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylwia Rodziewicz-Motowidło
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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18
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Bonar E, Chlebicka K, Dubin G, Wladyka B. Application of Two-Dimensional Difference Gel Electrophoresis in Identification of Factors Responsible for Virulence of Staphylococcus aureus. Methods Mol Biol 2020; 2069:139-154. [PMID: 31523772 DOI: 10.1007/978-1-4939-9849-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Staphylococcus aureus is a dangerous opportunistic pathogen of humans and animals. Highly virulent and multi-antibiotic-resistant strains are of particular concern due to high invasiveness and limited array of useful treatment options. Proteomics allows identification and investigation of staphylococcal virulence factors to better understand and treat the related disease. Two-dimensional difference gel electrophoresis (2D DIGE) is a powerful method for identification of differences in staphylococcal proteomes, both intracellular and secretory. Not only the presence of particular proteins and their quantities may be determined, but also each modification changing the molecular mass and/or isoelectric point of a protein is trackable. Especially, 2D DIGE allows for detection of posttranslational modifications, including processing and degradation by proteases. For differential analysis, protein samples are labeled with spectrally distinguishable fluorescent dyes, mixed and separated according to their isoelectric point (first dimension), and then electrophoresed in the presence of sodium dodecyl sulfate according to their molecular mass (second dimension). Exceptional resolution of 2D DIGE allows to obtain focused and sharp protein spots, and identify a large number of differentiating proteins. Here we provide protocols for TRI Reagent-based preparation of high-quality samples for 2D DIGE, sample separation, and ways of handling differentiating protein spots which lead to samples ready for protein identification using MS.
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Affiliation(s)
- Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kinga Chlebicka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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19
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Janczak M, Hyz K, Bukowski M, Lyzen R, Hydzik M, Wegrzyn G, Szalewska-Palasz A, Grudnik P, Dubin G, Wladyka B. Chromosomal localization of PemIK toxin-antitoxin system results in the loss of toxicity - Characterization of pemIK Sa1-Sp from Staphylococcus pseudintermedius. Microbiol Res 2020; 240:126529. [PMID: 32622987 DOI: 10.1016/j.micres.2020.126529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 11/20/2022]
Abstract
Toxin-antitoxin (TA) systems are ubiquitous in bacteria and on numerous occasions have been postulated to play a role in virulence of pathogens. Some Staphylococcus aureus strains carry a plasmid, which encodes the highly toxic PemIKSa TA system involved in maintenance of the plasmid but also implicated in modulation of gene expression. Here we showed that pemIKSa1-Sp TA system, homologous to the plasmid-encoded PemIKSa, is present in virtually each chromosome of S. pseudintermedius strain, however exhibits sequence heterogeneity. This results in two length variants of the PemKSa1-Sp toxin. The shorter (96 aa), C-terminally truncated toxin is enzymatically inactive, whereas the full length (112 aa) variant is an RNase, though nontoxic to the host cells. The lack of toxicity of the active PemKSa-Sp2 toxin is explained by increased substrate specificity. The pemISa1-Sp antitoxin gene seems pseudogenized, however, the whole pemIKSa1-Sp system is transcriptionally active. When production of N-terminally truncated antitoxins using alternative start codons is assumed, there are five possible length variants. Here we showed that even substantially truncated antitoxins are able to interact with PemKSa-Sp2 toxin and inhibit its RNase activity. Moreover, the antitoxins can rescue bacterial cells from toxic effects of overexpression of plasmid-encoded PemKSa toxin. Collectively, our data indicates that, contrary to the toxic plasmid-encoded PemIKSa TA system, location of pemIKSa1-Sp in the chromosome of S. pseudintermedius results in the loss of its toxicity. Interestingly, the retained RNase activity of PemKSa1-Sp2 toxin and functionality of the putative, N-terminally truncated antitoxins suggest the existence of evolutionary pressure for alleviation/mitigation of the toxin's toxicity and retention of the inhibitory activity of the antitoxin, respectively.
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Affiliation(s)
- Monika Janczak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Hyz
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Lyzen
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdansk, Gdansk, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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20
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Encarnação JC, Napolitano V, Opassi G, Danielson UH, Dubin G, Popowicz GM, Munier-Lehmann H, Buijs J, Andersson K, Björkelund H. A real-time cell-binding assay reveals dynamic features of STxB-Gb3 cointernalization and STxB-mediated cargo delivery into cancer cells. FEBS Lett 2020; 594:2406-2420. [PMID: 32473599 DOI: 10.1002/1873-3468.13847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/23/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022]
Abstract
The interaction between the Shiga toxin B-subunit (STxB) and its globotriaosylceramide receptor (Gb3) has a high potential for being exploited for targeted cancer therapy. The primary goal of this study was to evaluate the capacity of STxB to carry small molecules and proteins as cargo into cells. For this purpose, an assay was designed to provide real-time information about the StxB-Gb3 interaction as well as the dynamics and mechanism of the internalization process. The assay revealed the ability to distinguish the process of binding to the cell surface from internalization and presented the importance of receptor and STxB clustering for internalization. The overall setup demonstrated that the binding mechanism is complex, and the concept of affinity is difficult to apply. Hence, time-resolved methods, providing detailed information about the interaction of STxB with cells, are critical for the optimization of intracellular delivery.
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Affiliation(s)
- João Crispim Encarnação
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Giulia Opassi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | | | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Garching, Germany
| | - Hélène Munier-Lehmann
- Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR3523, Paris, France
| | - Jos Buijs
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl Andersson
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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21
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Pęcak A, Skalniak Ł, Pels K, Książek M, Madej M, Krzemień D, Malicki S, Władyka B, Dubin A, Holak TA, Dubin G. Anti-CD44 DNA Aptamers Selectively Target Cancer Cells. Nucleic Acid Ther 2020; 30:289-298. [PMID: 32379519 DOI: 10.1089/nat.2019.0833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/12/2022] Open
Abstract
CD44 is a type I transmembrane glycoprotein interacting with a number of extracellular components, including hyaluronic acid (HA). CD44-HA axis is involved in a variety of processes, including adhesion, migration, differentiation, trafficking, and others. CD44 is overexpressed in several cancers where binding of HA induces signal transduction leading to activation of antiapoptotic proteins and factors linked to drug resistance. As such, CD44 has been implicated in cancer growth, progression, and metastasis. It has been convincingly demonstrated that blocking CD44-HA interaction decreases cancer cell survival and metastasis. In this study, using in vitro selection, we have developed DNA aptamers recognizing a HA-binding domain of CD44 with high affinity and specificity. The aptamers bind to CD44 with nanomolar affinities and efficiently inhibit the growth of leukemic cancer cells characterized by high expression of CD44. The selectivity is demonstrated by an irrelevant effect on cells characterized by low CD44 levels. The obtained aptamers broaden the existing landscape of potential approaches to the development of antitumor strategies based on inhibition of the CD44 axis.
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Affiliation(s)
- Aleksandra Pęcak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Łukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Katarzyna Pels
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mirosław Książek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mariusz Madej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dobrosława Krzemień
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Stanisław Malicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Władyka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Adam Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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22
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Dawidowski M, Kalel VC, Napolitano V, Fino R, Schorpp K, Emmanouilidis L, Lenhart D, Ostertag M, Kaiser M, Kolonko M, Tippler B, Schliebs W, Dubin G, Mäser P, Tetko IV, Hadian K, Plettenburg O, Erdmann R, Sattler M, Popowicz GM. Structure-Activity Relationship in Pyrazolo[4,3- c]pyridines, First Inhibitors of PEX14-PEX5 Protein-Protein Interaction with Trypanocidal Activity. J Med Chem 2020; 63:847-879. [PMID: 31860309 DOI: 10.1021/acs.jmedchem.9b01876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trypanosoma protists are pathogens leading to a spectrum of devastating infectious diseases. The range of available chemotherapeutics against Trypanosoma is limited, and the existing therapies are partially ineffective and cause serious adverse effects. Formation of the PEX14-PEX5 complex is essential for protein import into the parasites' glycosomes. This transport is critical for parasite metabolism and failure leads to mislocalization of glycosomal enzymes, with fatal consequences for the parasite. Hence, inhibiting the PEX14-PEX5 protein-protein interaction (PPI) is an attractive way to affect multiple metabolic pathways. Herein, we have used structure-guided computational screening and optimization to develop the first line of compounds that inhibit PEX14-PEX5 PPI. The optimization was driven by several X-ray structures, NMR binding data, and molecular dynamics simulations. Importantly, the developed compounds show significant cellular activity against Trypanosoma, including the human pathogen Trypanosoma brucei gambiense and Trypanosoma cruzi parasites.
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Affiliation(s)
- Maciej Dawidowski
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany.,Department of Drug Technology and Pharmaceutical Biotechnology , Medical University of Warsaw , Banacha 1 , 02-097 Warszawa , Poland
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Valeria Napolitano
- Faculty of Biochemistry, Biophysics and Biotechnology , Jagiellonian University , Gronostajowa 7 , Krakow 30-387 , Poland.,Małopolska Center of Biotechnology , Jagiellonian University in Kraków , Gronostajowa 7 , Kraków 30-387 , Poland
| | - Roberto Fino
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | | | - Leonidas Emmanouilidis
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Dominik Lenhart
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Michael Ostertag
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , 4001 Basel , Switzerland
| | - Marta Kolonko
- Department of Biochemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Bettina Tippler
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Grzegorz Dubin
- Małopolska Center of Biotechnology , Jagiellonian University in Kraków , Gronostajowa 7 , Kraków 30-387 , Poland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , 4001 Basel , Switzerland
| | | | | | - Oliver Plettenburg
- Institute of Organic Chemistry , Leibniz Universität Hannover , Schneiderberg 1b , Hannover 30167 , Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Grzegorz M Popowicz
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
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23
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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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24
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Aroso RT, Calvete MJ, Pucelik B, Dubin G, Arnaut LG, Pereira MM, Dąbrowski JM. Photoinactivation of microorganisms with sub-micromolar concentrations of imidazolium metallophthalocyanine salts. Eur J Med Chem 2019; 184:111740. [DOI: 10.1016/j.ejmech.2019.111740] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
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25
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Zak KM, Kalińska M, Wątor E, Kuśka K, Krutyhołowa R, Dubin G, Popowicz GM, Grudnik P. Crystal Structure of Kluyveromyces lactis Glucokinase ( KlGlk1). Int J Mol Sci 2019; 20:ijms20194821. [PMID: 31569356 PMCID: PMC6801647 DOI: 10.3390/ijms20194821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 11/30/2022] Open
Abstract
Glucose phosphorylating enzymes are crucial in the regulation of basic cellular processes, including metabolism and gene expression. Glucokinases and hexokinases provide a pool of phosphorylated glucose in an adenosine diphosphate (ADP)- and ATP-dependent manner to shape the cell metabolism. The glucose processing enzymes from Kluyveromyces lactis are poorly characterized despite the emerging contribution of this yeast strain to industrial and laboratory scale biotechnology. The first reports on K. lactis glucokinase (KlGlk1) positioned the enzyme as an essential component required for glucose signaling. Nevertheless, no biochemical and structural information was available until now. Here, we present the first crystal structure of KlGlk1 together with biochemical characterization, including substrate specificity and enzyme kinetics. Additionally, comparative analysis of the presented structure and the prior structures of lactis hexokinase (KlHxk1) demonstrates the potential transitions between open and closed enzyme conformations upon ligand binding.
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Affiliation(s)
- Krzysztof M Zak
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Magdalena Kalińska
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Elżbieta Wątor
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Katarzyna Kuśka
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland.
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland.
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland.
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
| | - Przemysław Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
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26
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Sułek A, Pucelik B, Kuncewicz J, Dubin G, Dąbrowski JM. Sensitization of TiO2 by halogenated porphyrin derivatives for visible light biomedical and environmental photocatalysis. Catal Today 2019. [DOI: 10.1016/j.cattod.2019.02.070] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Rembacz KP, Zrubek KM, Golik P, Michalik K, Bogusz J, Wladyka B, Romanowska M, Dubin G. Crystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK) in complex with dorsomorphin (Compound C). Arch Biochem Biophys 2019; 671:1-7. [PMID: 31108049 DOI: 10.1016/j.abb.2019.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 12/21/2018] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 11/16/2022]
Abstract
Maternal Embryonic Leucine Zipper Kinase (MELK) is overexpressed in various tumors which has been convincingly linked to tumor cell survival. As such, MELK became an interesting target for pharmacological intervention. In this study we present the crystal structure of MELK in complex with dorsomorphin, an inhibitor of VEGFR and AMPK. By defining the mechanistic details of ligand recognition we identify a key residue (Cys89) at the hinge region of MELK responsible for positioning of the ligand at the catalytic pocket. This conclusion is supported by kinetic characterization of Cys89 mutants which show decreased affinity towards both ATP and dorsomorphin. The detailed binding mode of dorsomorphin characterized in this study defines a minimal requirement for MELK ligands, a valuable information for future rational design of inhibitors based on entirely new scaffolds.
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Affiliation(s)
- Krzysztof P Rembacz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Karol M Zrubek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Przemyslaw Golik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | | | - Jozefina Bogusz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Benedykt Wladyka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Malgorzata Romanowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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28
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Malicki S, Ksiazek M, Majewski P, Pecak A, Mydel P, Grudnik P, Dubin G. Development of a novel, high-affinity ssDNA trypsin inhibitor. J Enzyme Inhib Med Chem 2019; 34:638-643. [PMID: 30727784 PMCID: PMC6366424 DOI: 10.1080/14756366.2019.1569648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Inhibitors of serine proteases are not only extremely useful in the basic research but are also applied extensively in clinical settings. Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) approach we developed a family of novel, single-stranded DNA aptamers capable of specific trypsin inhibition. Our most potent candidate (T24) and its short version (T59) were thoroughly characterised in terms of efficacy. T24 and T59 efficiently inhibited bovine trypsin with Ki of 176 nM and 475 nM, respectively. Interestingly, in contrast to the majority of known trypsin inhibitors, the selected aptamers have superior specificity and did not interact with porcine trypsin or any human proteases tested. These included plasmin and thrombin characterised by trypsin-like substrate specificity. Our results demonstrate that SELEX may be successfully employed in the development of potent and specific DNA based protease inhibitors.
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Affiliation(s)
- Stanislaw Malicki
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Miroslaw Ksiazek
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland.,c Department of Oral Immunology and Infectious Diseases , University of Louisville School of Dentistry , Kentucky , USA
| | - Pawel Majewski
- b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Aleksandra Pecak
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Piotr Mydel
- b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland.,d Department of Clinical Science , Broegelmann Research Laboratory, University of Bergen , Bergen , Norway
| | - Przemyslaw Grudnik
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland
| | - Grzegorz Dubin
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
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29
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Skalniak L, Twarda-Clapa A, Neochoritis CG, Surmiak E, Machula M, Wisniewska A, Labuzek B, Ali AM, Krzanik S, Dubin G, Groves M, Dömling A, Holak TA. A fluorinated indole-based MDM2 antagonist selectively inhibits the growth of p53 wt osteosarcoma cells. FEBS J 2019; 286:1360-1374. [PMID: 30715803 DOI: 10.1111/febs.14774] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/15/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Abstract
The p53 protein is engaged in the repair of DNA mutations and elimination of heavily damaged cells, providing anticancer protection. Dysregulation of p53 activity is a crucial step in carcinogenesis. This dysregulation is often caused by the overexpression of negative regulators of p53, among which MDM2 is the most prominent one. Antagonizing MDM2 with small molecules restores the activity of p53 in p53 wild-type (p53wt ) cells and thus provides positive outcomes in the treatment of p53wt cancers. Previously, we have reported the discovery of a panel of fluoro-substituted indole-based antagonists of MDM2. Here, we demonstrate the biological activity and stereoselectivity of the most active compound from this series. Both enantiomers of the esterified form of the compound, as well as its corresponding carboxylic acids, were found active in fluorescence polarization (FP) assay, nuclear magnetic resonance (NMR) and microscale thermophoresis (MST) assay, with Ki and KD values around 1 μm. From these four compounds, the esterified enantiomer (R)-5a was active in cells, which was evidenced by the increase of p53 levels, the induced expression of p53-target genes (CDKN1A and MDM2), the selective induction of cell cycle arrest, and selective growth inhibition of p53wt U-2 OS and SJSA-1 compared to p53del SAOS-2 cells. The analysis of the crystal structure of human MDM2 in complex with the compound (R)-6a (carboxylic acid of the active (R)-5a compound) revealed the classical three-finger binding mode. Altogether, our data demonstrate the activity of the compound and provide the structural basis for further structure optimization.
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Affiliation(s)
- Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | | | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Monika Machula
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ameena M Ali
- Department of Drug Design, University of Groningen, The Netherlands
| | - Sylwia Krzanik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Drug Design, University of Groningen, The Netherlands
| | | | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
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30
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Bonar EA, Bukowski M, Hydzik M, Jankowska U, Kedracka-Krok S, Groborz M, Dubin G, Akkerboom V, Miedzobrodzki J, Sabat AJ, Friedrich AW, Wladyka B. Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains. Front Cell Infect Microbiol 2018; 8:313. [PMID: 30237986 PMCID: PMC6136393 DOI: 10.3389/fcimb.2018.00313] [Citation(s) in RCA: 9] [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: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that S. aureus strains exhibiting virulent (VIR) and non-virulent (NVIR) phenotypes in a chicken embryo infection model genetically fall into two separate groups, with the VIR group being much more cohesive than the NVIR group. Significantly, the genes encoding known staphylococcal virulence factors, such as clumping factors, are either found in different allelic variants in the genomes of NVIR strains (compared to VIR strains) or are inactive pseudogenes. Moreover, the pyruvate carboxylase and gamma-aminobutyrate permease genes, which were previously linked with virulence, are pseudogenized in NVIR strain ch22. Further, we use comprehensive proteomics tools to characterize strains that show opposing phenotypes in a chicken embryo virulence model. VIR strain CH21 had an elevated level of diapolycopene oxygenase involved in staphyloxanthin production (protection against free radicals) and expressed a higher level of immunoglobulin-binding protein Sbi on its surface compared to NVIR strain ch22. Furthermore, joint genomic and proteomic approaches linked the elevated production of superoxide dismutase and DNA-binding protein by NVIR strain ch22 with gene duplications.
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Affiliation(s)
- Emilia A Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Groborz
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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31
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Grudnik P, Kamiński MM, Rembacz KP, Kuśka K, Madej M, Potempa J, Dawidowski M, Dubin G. Structural basis for ADP-dependent glucokinase inhibition by 8-bromo-substituted adenosine nucleotide. J Biol Chem 2018; 293:11088-11099. [PMID: 29784881 DOI: 10.1074/jbc.ra117.001562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/19/2017] [Revised: 05/18/2018] [Indexed: 01/01/2023] Open
Abstract
In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose 6-phosphate. In contrast to canonical hexokinases, which use ATP, ADP-dependent glucokinase (ADPGK) catalyzes noncanonical phosphorylation of glucose to glucose 6-phosphate using ADP as a phosphate donor. Initially discovered in Archaea, the human homolog of ADPGK was described only recently. ADPGK's involvement in modified bioenergetics of activated T cells has been postulated, and elevated ADPGK expression has been reported in various cancer tissues. However, the physiological role of ADPGK is still poorly understood, and effective ADPGK inhibitors still await discovery. Here, we show that 8-bromo-substituted adenosine nucleotide inhibits human ADPGK. By solving the crystal structure of archaeal ADPGK in complex with 8-bromoadenosine phosphate (8-Br-AMP) at 1.81 Å resolution, we identified the mechanism of inhibition. We observed that 8-Br-AMP is a competitive inhibitor of ADPGK and that the bromine substitution induces marked structural changes within the protein's active site by engaging crucial catalytic residues. The results obtained using the Jurkat model of activated human T cells suggest its moderate activity in a cellular setting. We propose that our structural insights provide a critical basis for rational development of novel ADPGK inhibitors.
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Affiliation(s)
- Przemysław Grudnik
- From the Faculty of Biochemistry, Biophysics and Biotechnology and .,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Marcin M Kamiński
- the Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, and
| | | | - Katarzyna Kuśka
- From the Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Mariusz Madej
- From the Faculty of Biochemistry, Biophysics and Biotechnology and.,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Jan Potempa
- From the Faculty of Biochemistry, Biophysics and Biotechnology and.,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Maciej Dawidowski
- the Faculty of Pharmacy, Warsaw Medical University, Banacha 1 Street, 02-097 Warsaw, Poland
| | - Grzegorz Dubin
- From the Faculty of Biochemistry, Biophysics and Biotechnology and .,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
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32
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Twarda-Clapa A, Labuzek B, Krzemien D, Musielak B, Grudnik P, Dubin G, Holak TA. Crystal structure of the FAS1 domain of the hyaluronic acid receptor stabilin-2. Acta Crystallogr D Struct Biol 2018; 74:695-701. [PMID: 29968679 DOI: 10.1107/s2059798318007271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/14/2018] [Indexed: 11/11/2022]
Abstract
Recent research has identified a potential role of the hyaluronic acid receptor stabilin-2 (Stab2) in cancer metastasis. Stab2 belongs to a group of scavenger receptors and is responsible for the clearance of more than ten ligands, including hyaluronic acid (HA). In vivo experiments on mice have shown that the absence of Stab2, or its blocking by an antibody, effectively opposes cancer metastasis, which is accompanied by an increase in the level of circulating HA. Knowledge of ligand recognition and signal transduction by Stab2 is limited and no three-dimensional structures of any protein fragments of this receptor have been solved to date. Here, a high-resolution X-ray structure of the seventh FAS1 domain of Stab2 is reported. This structure provides the first insight into the Stab2 structure.
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Affiliation(s)
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
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33
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Skalniak L, Kocik J, Guzik K, Dubin G, Holak T. PO-432 Small molecules, peptides and antibodies – the comparison of PD-1/PD-L1 blocking potential in an in vitro immune checkpoint blockade assay. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Zak KM, Grudnik P, Magiera K, Dömling A, Dubin G, Holak TA. Structural Biology of the Immune Checkpoint Receptor PD-1 and Its Ligands PD-L1/PD-L2. Structure 2018; 25:1163-1174. [PMID: 28768162 DOI: 10.1016/j.str.2017.06.011] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [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: 03/01/2017] [Revised: 05/23/2017] [Accepted: 06/16/2017] [Indexed: 12/30/2022]
Abstract
Cancer cells can avoid and suppress immune responses through activation of inhibitory immune checkpoint proteins, such as PD-1, PD-L1, and CTLA-4. Blocking the activities of these proteins with monoclonal antibodies, and thus restoring T cell function, has delivered breakthrough therapies against cancer. In this review, we describe the latest work on structural characterization of the checkpoint proteins, their interactions with cognate ligands and with therapeutic antibodies. Structures of the extracellular portions of these proteins reveal that they all have a similar modular structure, composed of small domains similar in topology to the domains found in antibodies. Structural basis for blocking the PD-1/PD-L1 interaction by small molecules is illustrated with the compound BMS-202 that binds to and induces dimerization of PD-L1.
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Affiliation(s)
- Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV 9713 Groningen, the Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland; Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany.
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35
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Tomala MD, Magiera-Mularz K, Kubica K, Krzanik S, Zieba B, Musielak B, Pustula M, Popowicz GM, Sattler M, Dubin G, Skalniak L, Holak TA. Identification of small-molecule inhibitors of USP2a. Eur J Med Chem 2018. [PMID: 29529503 DOI: 10.1016/j.ejmech.2018.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 12/15/2022]
Abstract
USP2a is a deubiquitinating protease that rescues its target proteins from destruction by the proteasome by reversing the process of protein ubiquitination. USP2a shows oncogenic properties in vivo and has been found to be a specific activator of cyclin D1. Many types of cancers are addicted to cyclin D1 expression. Targeting USP2a is a promising strategy for cancer therapy but little progress has been made in the field of inhibition of USP2a. Using NMR-based fragment screening and biophysical binding assays, we have discovered small molecules that bind to USP2a. Iterations of fragment combination and structure-driven design identified two 5-(2-thienyl)-3-isoxazoles as the inhibitors of the USP2a-ubiquitin protein-protein interaction. The affinity of these molecules for the catalytic domain of USP2a parallels their ability to interfere with USP2a binding to ubiquitin in vitro. Altogether, our results establish the 5-(2-thienyl)-3-isoxazole pharmacophore as an attractive starting point for lead optimization.
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Affiliation(s)
- Marcin D Tomala
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | | | - Katarzyna Kubica
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Sylwia Krzanik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bartosz Zieba
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Marcin Pustula
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
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36
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Tokarz P, Wiśniewska M, Kamiński MM, Dubin G, Grudnik P. Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism. Protein Sci 2018; 27:790-797. [PMID: 29352744 DOI: 10.1002/pro.3377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 10/11/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 11/11/2022]
Abstract
ADP-dependent glucokinase (ADPGK) is an alternative novel glucose phosphorylating enzyme in a modified glycolysis pathway of hyperthermophilic Archaea. In contrast to classical ATP-dependent hexokinases, ADPGK utilizes ADP as a phosphoryl group donor. Here, we present a crystal structure of archaeal ADPGK from Methanocaldococcus jannaschii in complex with an inhibitor, 5-iodotubercidin, d-glucose, inorganic phosphate, and a magnesium ion. Detailed analysis of the architecture of the active site allowed for confirmation of the previously proposed phosphorylation mechanism and the crucial role of the invariant arginine residue (Arg197). The crystal structure shows how the phosphate ion, while mimicking a β-phosphate group, is positioned in the proximity of the glucose moiety by arginine and the magnesium ion, thus providing novel insights into the mechanism of catalysis. In addition, we demonstrate that 5-iodotubercidin inhibits human ADPGK-dependent T cell activation-induced reactive oxygen species (ROS) release and downstream gene expression, and as such it may serve as a model compound for further screening for hADPGK-specific inhibitors.
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Affiliation(s)
- Piotr Tokarz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Magdalena Wiśniewska
- Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Marcin M Kamiński
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Przemysław Grudnik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
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37
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Pucelik B, Paczyński R, Dubin G, Pereira MM, Arnaut LG, Dąbrowski JM. Correction: Properties of halogenated and sulfonated porphyrins relevant for the selection of photosensitizers in anticancer and antimicrobial therapies. PLoS One 2018; 13:e0191777. [PMID: 29352293 PMCID: PMC5774837 DOI: 10.1371/journal.pone.0191777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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38
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Maciejewska B, Źrubek K, Espaillat A, Wiśniewska M, Rembacz KP, Cava F, Dubin G, Drulis-Kawa Z. Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Sci Rep 2017; 7:14501. [PMID: 29109551 PMCID: PMC5674055 DOI: 10.1038/s41598-017-14797-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 01/19/2023] Open
Abstract
Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we present a comprehensive characterization of phage AP3 modular endolysin (AP3gp15) containing cell wall binding domain and an enzymatic domain (DUF3380 by BLASTP), both widespread and conservative. Our structural analysis demonstrates the low similarity of an enzymatic domain to known lysozymes and an unusual catalytic centre characterized by only a single glutamic acid residue and no aspartic acid. Thus, our findings suggest distinguishing a novel class of muralytic enzymes having the activity and catalytic centre organization of DUF3380. The lack of amino acid sequence homology between AP3gp15 and other known muralytic enzymes may reflect the evolutionary convergence of analogous glycosidases. Moreover, the broad antibacterial spectrum, lack of cytotoxic effect on human cells and the stability characteristics of AP3 endolysin advocate for its future application development.
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Affiliation(s)
- Barbara Maciejewska
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Karol Źrubek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Magdalena Wiśniewska
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Krzysztof P Rembacz
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland.
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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Nowakowski M, Jaremko Ł, Wladyka B, Dubin G, Ejchart A, Mak P. Spatial attributes of the four-helix bundle group of bacteriocins - The high-resolution structure of BacSp222 in solution. Int J Biol Macromol 2017; 107:2715-2724. [PMID: 29107139 DOI: 10.1016/j.ijbiomac.2017.10.158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 08/21/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022]
Abstract
BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues. In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns. Although the amino acid sequence of BacSp222 has no significant similarity to any known peptide or protein, a 3D structure similarity search indicates a close relation to other four-helix bundle-motif bacteriocins, such as aureocin A53, lacticin Q and enterocins 7A/7B. Assuming similar functions, biology, structure and physicochemical properties, we propose to distinguish the four-helix bundle bacteriocins as a new Type A in subclass IId of bacteriocins, containing linear, non-pediocin-like peptides.
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Affiliation(s)
- Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Kraków, Poland.
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysiscs, Polish Academy of Science, Laboratory of Biological NMR, Pawińskiego 5A, 02-106 Warszawa, Poland.
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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40
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Pucelik B, Paczyński R, Dubin G, Pereira MM, Arnaut LG, Dąbrowski JM. Properties of halogenated and sulfonated porphyrins relevant for the selection of photosensitizers in anticancer and antimicrobial therapies. PLoS One 2017; 12:e0185984. [PMID: 29016698 PMCID: PMC5634595 DOI: 10.1371/journal.pone.0185984] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/24/2017] [Indexed: 01/10/2023] Open
Abstract
The impact of substituents on the photochemical and biological properties of tetraphenylporphyrin-based photosensitizers for photodynamic therapy of cancer (PDT) as well as photodynamic inactivation of microorganisms (PDI) was examined. Spectroscopic and physicochemical properties were related with therapeutic efficacy in PDT of cancer and PDI of microbial cells in vitro. Less polar halogenated, sulfonamide porphyrins were most readily taken up by cells compared to hydrophilic and anionic porphyrins. The uptake and PDT of a hydrophilic porphyrin was significantly enhanced with incorporation in polymeric micelles (Pluronic L121). Photodynamic inactivation studies were performed against Gram-positive (S. aureus, E. faecalis), Gram-negative bacteria (E. coli, P. aeruginosa, S. marcescens) and fungal yeast (C. albicans). We observed a 6 logs reduction of S. aureus after irradiation (10 J/cm2) in the presence of 20 μM of hydrophilic porphyrin, but this was not improved with incorporation in Pluronic L121. A 2–3 logs reduction was obtained for E. coli using similar doses, and a decrease of 3–4 logs was achieved for C. albicans. Rational substitution of tetraphenylporphyrins improves their photodynamic properties and informs on strategies to obtain photosensitizers for efficient PDT and PDI. However, the design of the photosensitizers must be accompanied by the development of tailored drug formulations.
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Affiliation(s)
- Barbara Pucelik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, Poland
| | - Robert Paczyński
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Luis G. Arnaut
- Chemistry Department, University of Coimbra, Coimbra, Portugal
| | - Janusz M. Dąbrowski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, Poland
- * E-mail:
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41
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Murphy J, Ramezanpour M, Stach N, Dubin G, Psaltis AJ, Wormald PJ, Vreugde S. Staphylococcus Aureus V8 protease disrupts the integrity of the airway epithelial barrier and impairs IL-6 production in vitro. Laryngoscope 2017; 128:E8-E15. [PMID: 28994126 DOI: 10.1002/lary.26949] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/03/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Staphylococcus aureus (S. aureus) infection is known to contribute to the severity and recalcitrance of chronic rhinosinusitis (CRS), and its secreted products have been shown to alter the airway barrier. Extracellular proteases secreted by S. aureus are thought to be important in epithelial infection and immune evasion; however, their effect on airway mucosal barrier function is not known. METHODS To investigate the impact of extracellular proteases on airway epithelial integrity, the purified S. aureus proteases V8 protease, Staphopain A, Staphopain B, Exfoliative toxin A, and serine protease-like A-F were applied to human nasal epithelial cell air-liquid interface (HNEC-ALI) cultures. Transepithelial electrical resistance (TEER), permeability (Papp) measurements, and immuno-localization of the tight junction proteins claudin-1 and ZO-1 were used to assess barrier integrity. Effects of the proteases on inflammation and cell viability were measured using interleukin-6 (IL-6) ELISA and a lactate dehydrogenase assay. RESULTS Application of V8 protease to HNEC-ALI cultures caused a significant concentration and time-dependent decrease in TEER (22.67%, P < 0.0001), a reciprocal Papp increase (20.14-fold, P < 0.05), and a discontinuous ZO-1 immuno-localization compared to control. IL-6 production was significantly reduced in V8 protease-treated cells (153.5 pg/mL, P = 0.0069) compared to control (548.3 pg/mL), whereas no difference in cell viability was observed. CONCLUSION S. aureus V8 protease causes dysfunction of mucosal barrier structure and function indicative of a leaky barrier. A reduction in IL-6 levels suggests that the mucosal immunity is impaired by this protease and thus has the potential to contribute to CRS recalcitrance. LEVEL OF EVIDENCE NA. Laryngoscope, 128:E8-E15, 2018.
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Affiliation(s)
- Jae Murphy
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Mahnaz Ramezanpour
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Natalia Stach
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alkis James Psaltis
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Sarah Vreugde
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
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42
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Magiera-Mularz K, Skalniak L, Zak KM, Musielak B, Rudzinska-Szostak E, Berlicki Ł, Kocik J, Grudnik P, Sala D, Zarganes-Tzitzikas T, Shaabani S, Dömling A, Dubin G, Holak TA. Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Angew Chem Int Ed Engl 2017; 56:13732-13735. [PMID: 28881104 DOI: 10.1002/anie.201707707] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [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: 07/28/2017] [Indexed: 11/05/2022]
Abstract
Blockade of the immunoinhibitory PD-1/PD-L1 pathway using monoclonal antibodies has shown impressive results with durable clinical antitumor responses. Anti-PD-1 and anti-PD-L1 antibodies have now been approved for the treatment of a number of tumor types, whereas the development of small molecules targeting immune checkpoints lags far behind. We characterized two classes of macrocyclic-peptide inhibitors directed at the PD-1/PD-L1 pathway. We show that these macrocyclic compounds act by directly binding to PD-L1 and that they are capable of antagonizing PD-L1 signaling and, similarly to antibodies, can restore the function of T-cells. We also provide the crystal structures of two of these small-molecule inhibitors bound to PD-L1. The structures provide a rationale for the checkpoint inhibition by these small molecules, and a description of their small molecule/PD-L1 interfaces provides a blueprint for the design of small-molecule inhibitors of the PD-1/PD-L1 pathway.
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Affiliation(s)
- Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Ewa Rudzinska-Szostak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Dominik Sala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Tryfon Zarganes-Tzitzikas
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Shabnam Shaabani
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Alexander Dömling
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland.,Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152, Martinsried, Germany
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43
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Magiera-Mularz K, Skalniak L, Zak KM, Musielak B, Rudzinska-Szostak E, Berlicki Ł, Kocik J, Grudnik P, Sala D, Zarganes-Tzitzikas T, Shaabani S, Dömling A, Dubin G, Holak TA. Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katarzyna Magiera-Mularz
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Krzysztof M. Zak
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Bogdan Musielak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Ewa Rudzinska-Szostak
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Justyna Kocik
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Dominik Sala
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Tryfon Zarganes-Tzitzikas
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Shabnam Shaabani
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Alexander Dömling
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Tad A. Holak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
- Max Planck Institute for Biochemistry; Am Klopferspitz 18a 82152 Martinsried Germany
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Skalniak L, Zak KM, Guzik K, Magiera K, Musielak B, Pachota M, Szelazek B, Kocik J, Grudnik P, Tomala M, Krzanik S, Pyrc K, Dömling A, Dubin G, Holak TA. Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells. Oncotarget 2017; 8:72167-72181. [PMID: 29069777 PMCID: PMC5641120 DOI: 10.18632/oncotarget.20050] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [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: 06/14/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
Antibodies targeting the PD-1/PD-L1 immune checkpoint achieved spectacular success in anticancer therapy in the recent years. In contrast, no small molecules with cellular activity have been reported so far. Here we provide evidence that small molecules are capable of alleviating the PD-1/PD-L1 immune checkpoint-mediated exhaustion of Jurkat T-lymphocytes. The two optimized small-molecule inhibitors of the PD-1/PD-L1 interaction, BMS-1001 and BMS-1166, developed by Bristol-Myers Squibb, bind to human PD-L1 and block its interaction with PD-1, when tested on isolated proteins. The compounds present low toxicity towards tested cell lines and block the interaction of soluble PD-L1 with the cell surface-expressed PD-1. As a result, BMS-1001 and BMS-1166 alleviate the inhibitory effect of the soluble PD-L1 on the T-cell receptor-mediated activation of T-lymphocytes. Moreover, the compounds were effective in attenuating the inhibitory effect of the cell surface-associated PD-L1. We also determined the X-ray structures of the complexes of BMS-1001 and BMS-1166 with PD-L1, which revealed features that may be responsible for increased potency of the compounds compared to their predecessors. Further development may lead to the design of an anticancer therapy based on the orally delivered immune checkpoint inhibition.
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Affiliation(s)
- Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Katarzyna Guzik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Magdalena Pachota
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bozena Szelazek
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Marcin Tomala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Sylwia Krzanik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Krzysztof Pyrc
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
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45
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Witkowska J, Giżyńska M, Grudnik P, Golik P, Karpowicz P, Giełdoń A, Dubin G, Jankowska E. Crystal structure of a low molecular weight activator Blm-pep with yeast 20S proteasome - insights into the enzyme activation mechanism. Sci Rep 2017; 7:6177. [PMID: 28733623 PMCID: PMC5522460 DOI: 10.1038/s41598-017-05997-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 01/25/2017] [Accepted: 06/28/2017] [Indexed: 11/22/2022] Open
Abstract
Proteasomes are responsible for protein turnover in eukaryotic cells, degrading short-lived species but also removing improperly folded or oxidatively damaged ones. Dysfunction of a proteasome results in gradual accumulation of misfolded/damaged proteins, leading to their aggregation. It has been postulated that proteasome activators may facilitate removal of such aggregation-prone proteins and thus prevent development of neurodegenerative disorders. However, the discovery of pharmacologically relevant compounds is hindered by insufficient structural understanding of the activation process. In this study we provide a model peptidic activator of human proteasome and analyze the structure-activity relationship within this novel scaffold. The binding mode of the activator at the relevant pocket within the proteasome has been determined by X-ray crystallography. This crystal structure provides an important basis for rational design of pharmacological compounds. Moreover, by providing a novel insight into the proteasome gating mechanism, our results allow the commonly accepted model of proteasome regulation to be revisited.
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Affiliation(s)
- Julia Witkowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Małgorzata Giżyńska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Przemysław Grudnik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Przemysław Golik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Przemysław Karpowicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
| | - Elżbieta Jankowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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46
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Czardybon W, Windak R, Gołas A, Gałęzowski M, Sabiniarz A, Dolata I, Salwińska M, Guzik P, Zawadzka M, Gabor-Worwa E, Winnik B, Żurawska M, Kolasińska E, Wincza E, Bugaj M, Danielewicz M, Dubin G, Jabłońska E, Szydłowski M, Sewastianik T, Puła B, Szumera-Ciećkiewicz A, Prochorec-Sobieszek M, Mądro E, Lech-Marańda E, Warzocha K, Tamburini J, Juszczyński P, Brzózka K. Abstract 4087: Development of a potent, dual pan-PIM/FLT3 inhibitor for the treatment of heme malignancies. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite huge effort spent on understanding the pathogenesis of acute myeloid leukemia (AML), current standards of care are still based on the same chemotherapy agents as two decades ago - combinational treatment of cytarabine with an anthracycline. Fms-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD) is one of the most common genetic lesions in AML. Although FLT3 inhibitors initially exhibit clinical activity, resistance to treatment inevitably occurs within months. PIM kinases are thought to be major drivers of the resistance phenotype and their inhibition in relapsed samples restores cell sensitivity to FLT3 inhibitors. Thus, simultaneous PIM and FLT3 inhibition represents a promising strategy in AML therapy. Selvita has developed a potent and selective first-in-class, dual PIM/FLT3 kinase inhibitor, the SEL24-B489 compound, and profiled its activity for in vitro and in vivo AML models showing significantly broader anti-tumor activity of SEL24-B489 than selective FLT3-ITD or PIM inhibitors. We compared SEL24-B489 head-to-head with a selective PIM inhibitor (AZD1208) and a selective FLT3-ITD inhibitor (AC220) in a panel of AML cell lines with FLT3-ITD or unmutated kinase (FLT3-WT) as well as peripheral AML cells and CD34+ bone marrow blasts. SEL24-B489 exhibited a significantly broader activity, irrespective of FLT3 status, than either of the selective inhibitors. Since PIM kinases have emerged as important mediators of FLT3-inhibitor resistance, we hypothesized that the dual specificity of SEL24-B489 might overcome the phenotype of resistance. We utilized previously developed MOLM-14 cells transduced with either FLT3-WT or FLT3 alleles containing TKD point mutations to show that neither of the these mutations decreased the cellular sensitivity to SEL24-B489. Higher cellular activity and biomarker response of SEL24-B489 than competitive inhibitors was shown by inhibition of specific biomarkers such as S6 and STAT5 phosphorylation at nanomolar concentrations in both FLT3-ITD positive and FLT3-WT cell lines in vitro. We have also demonstrated SEL24-B489 superior potency of SEL24-B489 in xenograft models in vivo. Consistent with the experiments in vitro showing marked synergy between SEL24-B489 and AraC, a combination of these agents resulted in almost completely blocked tumor growth in vivo. Most importantly, SEL24-B489 has been selected as a clinical candidate and is currently in phase I clinical trials.
Citation Format: Wojciech Czardybon, Renata Windak, Aniela Gołas, Michał Gałęzowski, Aleksandra Sabiniarz, Izabela Dolata, Magdalena Salwińska, Paweł Guzik, Magdalena Zawadzka, Ewelina Gabor-Worwa, Bożena Winnik, Małgorzata Żurawska, Ewa Kolasińska, Ewelina Wincza, Marta Bugaj, Monika Danielewicz, Grzegorz Dubin, Ewa Jabłońska, Maciej Szydłowski, Tomasz Sewastianik, Bartosz Puła, Anna Szumera-Ciećkiewicz, Monika Prochorec-Sobieszek, Elżbieta Mądro, Ewa Lech-Marańda, Krzysztof Warzocha, Jerome Tamburini, Przemysław Juszczyński, Krzysztof Brzózka. Development of a potent, dual pan-PIM/FLT3 inhibitor for the treatment of heme malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4087. doi:10.1158/1538-7445.AM2017-4087
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ewa Jabłońska
- 3Instytut Hematologii i Transfuzjologii, Warszawa, Poland
| | | | | | - Bartosz Puła
- 3Instytut Hematologii i Transfuzjologii, Warszawa, Poland
| | | | | | - Elżbieta Mądro
- 3Instytut Hematologii i Transfuzjologii, Warszawa, Poland
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47
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Guzik K, Zak KM, Grudnik P, Magiera K, Musielak B, Törner R, Skalniak L, Dömling A, Dubin G, Holak TA. Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1. J Med Chem 2017; 60:5857-5867. [PMID: 28613862 DOI: 10.1021/acs.jmedchem.7b00293] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Blockade of the PD-1/PD-L1 immune checkpoint pathway with monoclonal antibodies has provided significant advances in cancer treatment. The antibody-based immunotherapies carry a number of disadvantages such as the high cost of the antibodies, their limited half-life, and immunogenicity. Development of small-molecule PD-1/PD-L1 inhibitors that could overcome these drawbacks is slow because of the incomplete structural information for this pathway. The first chemical PD-1/PD-L1 inhibitors have been recently disclosed by Bristol-Myers Squibb. Here we present NMR and X-ray characterization for the two classes of these inhibitors. The X-ray structures of the PD-L1/inhibitor complexes reveal one inhibitor molecule located at the center of the PD-L1 homodimer, filling a deep hydrophobic channel-like pocket between two PD-L1 molecules. Derivatives of (2-methyl-3-biphenylyl)methanol exhibit the structures capped on one side of the channel, whereas the compounds based on [3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methylphenyl]methanol induce an enlarged interaction interface that results in the open "face-back" tunnel through the PD-L1 dimer.
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Affiliation(s)
- Katarzyna Guzik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Krzysztof M Zak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Przemyslaw Grudnik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Ricarda Törner
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department for Drug Design, University of Groningen , A. Deusinglaan 9, AV 9713 Groningen, The Netherlands
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
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48
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Twarda-Clapa A, Krzanik S, Kubica K, Guzik K, Labuzek B, Neochoritis CG, Khoury K, Kowalska K, Czub M, Dubin G, Dömling A, Skalniak L, Holak TA. 1,4,5-Trisubstituted Imidazole-Based p53–MDM2/MDMX Antagonists with Aliphatic Linkers for Conjugation with Biological Carriers. J Med Chem 2017; 60:4234-4244. [DOI: 10.1021/acs.jmedchem.7b00104] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Sylwia Krzanik
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Katarzyna Guzik
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Beata Labuzek
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Constantinos G. Neochoritis
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kareem Khoury
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kaja Kowalska
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Miroslawa Czub
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Lukasz Skalniak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
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49
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Magiera K, Tomala M, Kubica K, De Cesare V, Trost M, Zieba BJ, Kachamakova-Trojanowska N, Les M, Dubin G, Holak TA, Skalniak L. Lithocholic Acid Hydroxyamide Destabilizes Cyclin D1 and Induces G 0/G 1 Arrest by Inhibiting Deubiquitinase USP2a. Cell Chem Biol 2017; 24:458-470.e18. [PMID: 28343940 PMCID: PMC5404848 DOI: 10.1016/j.chembiol.2017.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 09/26/2016] [Accepted: 03/01/2017] [Indexed: 12/29/2022]
Abstract
USP2a is a deubiquitinase responsible for stabilization of cyclin D1, a crucial regulator of cell-cycle progression and a proto-oncoprotein overexpressed in numerous cancer types. Here we report that lithocholic acid (LCA) derivatives are inhibitors of USP proteins, including USP2a. The most potent LCA derivative, LCA hydroxyamide (LCAHA), inhibits USP2a, leading to a significant Akt/GSK3β-independent destabilization of cyclin D1, but does not change the expression of p27. This leads to the defects in cell-cycle progression. As a result, LCAHA inhibits the growth of cyclin D1-expressing, but not cyclin D1-negative cells, independently of the p53 status. We show that LCA derivatives may be considered as future therapeutics for the treatment of cyclin D1-addicted p53-expressing and p53-defective cancer types.
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Affiliation(s)
- Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Marcin Tomala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bartosz J Zieba
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Neli Kachamakova-Trojanowska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Marcin Les
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
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50
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Surmiak E, Twarda-Clapa A, Zak KM, Musielak B, Tomala MD, Kubica K, Grudnik P, Madej M, Jablonski M, Potempa J, Kalinowska-Tluscik J, Dömling A, Dubin G, Holak TA. A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction. ACS Chem Biol 2016; 11:3310-3318. [PMID: 27709883 DOI: 10.1021/acschembio.6b00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction opens up a prospect for a nongenotoxic anticancer therapy. Here, we present the syntheses, activities, and crystal structures of two novel classes of Mdm2-p53 inhibitors that are based on the 3-pyrrolin-2-one and 2-furanone scaffolds. The structures of the complexes formed by these inhibitors and Mdm2 reveal the dimeric protein molecular organization that has not been observed in the small-molecule/Mdm2 complexes described until now. In particular, the 6-chloroindole group does not occupy the usual Trp-23 pocket of Mdm2 but instead is engaged in dimerization. This entirely unique binding mode of the compounds opens new possibilities for optimization of the Mdm2-p53 interaction inhibitors.
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Affiliation(s)
- Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Krzysztof M. Zak
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marcin D. Tomala
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Przemyslaw Grudnik
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Mariusz Madej
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Mateusz Jablonski
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Jan Potempa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | | | - Alexander Dömling
- Faculty
of Mathematics and Natural Sciences, Department of Pharmacy, University of Groningen, 9713AV Groningen, The Netherlands
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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