1
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Paprocki D, Winiewska-Szajewska M, Speina E, Kucharczyk R, Poznański J. 5,6-diiodo-1H-benzotriazole: new TBBt analogue that minutely affects mitochondrial activity. Sci Rep 2021; 11:23701. [PMID: 34880390 PMCID: PMC8654832 DOI: 10.1038/s41598-021-03136-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
4,5,6,7-Tetrabromo-1H-benzotriazole is widely used as the reference ATP-competitive inhibitor of protein kinase CK2. Herein, we study its new analogs: 5,6-diiodo- and 5,6-diiodo-4,7-dibromo-1H-benzotriazole. We used biophysical (MST, ITC) and biochemical (enzymatic assay) methods to describe the interactions of halogenated benzotriazoles with the catalytic subunit of human protein kinase CK2 (hCK2α). To trace the biological activity, we measured their cytotoxicity against four reference cancer cell lines and the effect on the mitochondrial inner membrane potential. The results obtained lead to the conclusion that iodinated compounds are an attractive alternative to brominated ones. One of them retains the cytotoxicity against selected cancer cell lines of the reference TBBt with a smaller side effect on mitochondrial activity. Both iodinated compounds are candidate leaders in the further development of CK2 inhibitors.
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Affiliation(s)
- Daniel Paprocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.,Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089, Warsaw, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Róża Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
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2
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Lindenblatt D, Applegate V, Nickelsen A, Klußmann M, Neundorf I, Götz C, Jose J, Niefind K. Molecular Plasticity of Crystalline CK2α' Leads to KN2, a Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity. J Med Chem 2021; 65:1302-1312. [PMID: 34323071 DOI: 10.1021/acs.jmedchem.1c00063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CK2α and CK2α' are paralogous catalytic subunits of CK2, which belongs to the eukaryotic protein kinases. CK2 promotes tumorigenesis and the spread of pathogenic viruses like SARS-CoV-2 and is thus an attractive drug target. Efforts to develop selective CK2 inhibitors binding offside the ATP site had disclosed the αD pocket in CK2α; its occupation requires large conformational adaptations of the helix αD. As shown here, the αD pocket is accessible also in CK2α', where the necessary structural plasticity can be triggered with suitable ligands even in the crystalline state. A CK2α' structure with an ATP site and an αD pocket ligand guided the design of the bivalent CK2 inhibitor KN2. It binds to CK2 with low nanomolar affinity, is cell-permeable, and suppresses the intracellular phosphorylation of typical CK2 substrates. Kinase profiling revealed a high selectivity of KN2 for CK2 and emphasizes the selectivity-promoting potential of the αD pocket.
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Affiliation(s)
- Dirk Lindenblatt
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Violetta Applegate
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Merlin Klußmann
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Ines Neundorf
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Claudia Götz
- Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg/Saar, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Karsten Niefind
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
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3
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Iegre J, Atkinson EL, Brear PD, Cooper BM, Hyvönen M, Spring DR. Chemical probes targeting the kinase CK2: a journey outside the catalytic box. Org Biomol Chem 2021; 19:4380-4396. [PMID: 34037044 DOI: 10.1039/d1ob00257k] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CK2 is a protein kinase that plays important roles in many physio-pathological cellular processes. As such, the development of chemical probes for CK2 has received increasing attention in the past decade with more than 40 lead compounds developed. In this review, we aim to provide the reader with a comprehensive overview of the chemical probes acting outside the highly-conserved ATP-site developed to date. Such probes belong to different classes of molecules spanning from small molecules to peptides, act with a range of mechanisms of action and some of them present themselves as promising tools to investigate the biology of CK2 and therefore develop therapeutics for many disease areas including cancer and COVID-19.
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Eleanor L Atkinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Paul D Brear
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Bethany M Cooper
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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4
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Atkinson EL, Iegre J, Brear PD, Zhabina EA, Hyvönen M, Spring DR. Downfalls of Chemical Probes Acting at the Kinase ATP-Site: CK2 as a Case Study. Molecules 2021; 26:1977. [PMID: 33807474 PMCID: PMC8037657 DOI: 10.3390/molecules26071977] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Protein kinases are a large class of enzymes with numerous biological roles and many have been implicated in a vast array of diseases, including cancer and the novel coronavirus infection COVID-19. Thus, the development of chemical probes to selectively target each kinase is of great interest. Inhibition of protein kinases with ATP-competitive inhibitors has historically been the most widely used method. However, due to the highly conserved structures of ATP-sites, the identification of truly selective chemical probes is challenging. In this review, we use the Ser/Thr kinase CK2 as an example to highlight the historical challenges in effective and selective chemical probe development, alongside recent advances in the field and alternative strategies aiming to overcome these problems. The methods utilised for CK2 can be applied to an array of protein kinases to aid in the discovery of chemical probes to further understand each kinase's biology, with wide-reaching implications for drug development.
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Affiliation(s)
- Eleanor L. Atkinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (E.L.A.); (J.I.)
| | - Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (E.L.A.); (J.I.)
| | - Paul D. Brear
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (P.D.B.); (E.A.Z.); (M.H.)
| | - Elizabeth A. Zhabina
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (P.D.B.); (E.A.Z.); (M.H.)
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (P.D.B.); (E.A.Z.); (M.H.)
| | - David R. Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (E.L.A.); (J.I.)
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5
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Czapinska H, Winiewska-Szajewska M, Szymaniec-Rutkowska A, Piasecka A, Bochtler M, Poznański J. Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2. J Phys Chem B 2021; 125:2491-2503. [PMID: 33689348 PMCID: PMC8041304 DOI: 10.1021/acs.jpcb.0c10264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Binding of a family
of brominated benzotriazoles to the catalytic
subunit of human protein kinase CK2 (hCK2α) was used as a model
system to assess the contribution of halogen bonding to protein–ligand
interaction. CK2 is a constitutively active pleiotropic serine/threonine
protein kinase that belongs to the CMGC group of eukaryotic protein
kinases (EPKs). Due to the addiction of some cancer cells, CK2 is
an attractive and well-characterized drug target. Halogenated benzotriazoles
act as ATP-competitive inhibitors with unexpectedly good selectivity
for CK2 over other EPKs. We have characterized the interaction of
bromobenzotriazoles with hCK2α by X-ray crystallography, low-volume
differential scanning fluorimetry, and isothermal titration calorimetry.
Properties of free ligands in solution were additionally characterized
by volumetric and RT-HPLC measurements. Thermodynamic data indicate
that the affinity increases with bromo substitution, with greater
contributions from 5- and 6-substituents than 4- and 7-substituents.
Except for 4,7-disubstituted compounds, the bromobenzotriazoles adopt
a canonical pose with the triazole close to lysine 68, which precludes
halogen bonding. More highly substituted benzotriazoles adopt many
additional noncanonical poses, presumably driven by a large hydrophobic
contribution to binding. Some noncanonical ligand orientations allow
the formation of halogen bonds with the hinge region. Consistent with
a predominantly hydrophobic interaction, the isobaric heat capacity
decreases upon ligand binding, the more so the higher the substitution.
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Affiliation(s)
- Honorata Czapinska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | | | - Anna Piasecka
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Matthias Bochtler
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland
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6
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Lee S, Kim J, Jo J, Chang JW, Sim J, Yun H. Recent advances in development of hetero-bivalent kinase inhibitors. Eur J Med Chem 2021; 216:113318. [PMID: 33730624 DOI: 10.1016/j.ejmech.2021.113318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Identifying a pharmacological agent that targets only one of more than 500 kinases present in humans is an important challenge. One potential solution to this problem is the development of bivalent kinase inhibitors, which consist of two connected fragments, each bind to a dissimilar binding site of the bisubstrate enzyme. The main advantage of bivalent (type V) kinase inhibitors is generating more interactions with target enzymes that can enhance the molecules' selectivity and affinity compared to single-site inhibitors. Earlier type V inhibitors were not suitable for the cellular environment and were mostly used in in vitro studies. However, recently developed bivalent compounds have high kinase affinity, high biological and chemical stability in vivo. This review summarized the hetero-bivalent kinase inhibitors described in the literature from 2014 to the present. We attempted to classify the molecules by serine/threonine and tyrosine kinase inhibitors, and then each target kinase and its hetero-bivalent inhibitor was assessed in depth. In addition, we discussed the analysis of advantages, limitations, and perspectives of bivalent kinase inhibitors compared with the monovalent kinase inhibitors.
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Affiliation(s)
- Seungbeom Lee
- College of Pharmacy, CHA University, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jae Won Chang
- Department of Pharmacology & Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Hematology & Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA; Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jaehoon Sim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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7
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Schnitzler A, Niefind K. Structural basis for the design of bisubstrate inhibitors of protein kinase CK2 provided by complex structures with the substrate-competitive inhibitor heparin. Eur J Med Chem 2021; 214:113223. [PMID: 33571828 DOI: 10.1016/j.ejmech.2021.113223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022]
Abstract
The Ser/Thr kinase CK2, a member of the superfamily of eukaryotic protein kinases, has an acidophilic substrate profile with the substrate recognition sequence S/T-D/E-X-D/E, and it is inhibited by polyanionic substances like heparin. The latter, a highly sulphated glucosamino glycan composed mainly of repeating 2-O-sulpho-α-l-idopyranuronic acid/N,O6-disulpho-α-d-glucosamine disaccharide units, is the longest known substrate-competitive CK2 inhibitor. The structural basis of CK2's preference for anionic substrates and substrate-competitive inhibitors is only vaguely known which limits the value of the substrate-binding region for the structure-based development of CK2 bisubstrate inhibitors. Here, a tetragonal and a monoclinic co-crystal structure of CK2α, the catalytic subunit of CK2, with a decameric heparin fragment are described. In the tetragonal structure, the heparin molecule binds to the polybasic stretch at the beginning of CK2α's helix αC, whereas in the monoclinic structure it occupies the central substrate-recognition region around the P+1 loop. Together, the structures rationalize the inhibitory efficacy of heparin fragments as a function of chain length. The monoclinic CK2α/heparin structure, in which the heparin fragment is particularly well defined, is the first CK2 structure with an anionic inhibitor of considerable size at the central part of the substrate-recognition site. The bound heparin fragment is so close to the binding site of ATP-competitive inhibitors that it can guide the design of linkers and pave the way to efficient CK2 bisubstrate inhibitors in the future.
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Affiliation(s)
- Alexander Schnitzler
- Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Straße 47, D-50674 Köln, Germany
| | - Karsten Niefind
- Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Straße 47, D-50674 Köln, Germany.
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8
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Lindenblatt D, Nickelsen A, Applegate VM, Jose J, Niefind K. Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2. J Med Chem 2020; 63:7766-7772. [DOI: 10.1021/acs.jmedchem.0c00587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dirk Lindenblatt
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Violetta M. Applegate
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Karsten Niefind
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
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9
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Pietsch M, Viht K, Schnitzler A, Ekambaram R, Steinkrüger M, Enkvist E, Nienberg C, Nickelsen A, Lauwers M, Jose J, Uri A, Niefind K. Unexpected CK2β-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Bioorg Chem 2020; 96:103608. [PMID: 32058103 DOI: 10.1016/j.bioorg.2020.103608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/11/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023]
Abstract
Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2α) attached to a homodimer of regulatory subunits (CK2β), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (Ki = 84 pM). In a crystal structure of ARC-3140 in complex with CK2α, three copies of the inhibitor are visible, one of them at the CK2β interface of CK2α. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2α/CK2β interaction. A structural inspection revealed that ARC-3140, unlike CK2β antagonists described so far, interferes with both sub-interfaces of the bipartite CK2α/CK2β interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2α2β2 holoenzyme.
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Affiliation(s)
- Markus Pietsch
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Alexander Schnitzler
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Ramesh Ekambaram
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Michaela Steinkrüger
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Christian Nienberg
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Miriam Lauwers
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
| | - Karsten Niefind
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany.
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10
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Rational drug-design approach supported with thermodynamic studies - a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Sci Rep 2019; 9:11018. [PMID: 31358826 PMCID: PMC6662822 DOI: 10.1038/s41598-019-47404-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022] Open
Abstract
Numerous inhibitors of protein kinases act on the basis of competition, targeting the ATP binding site. In this work, we present a procedure of rational design of a bi-substrate inhibitor, complemented with biophysical assays. The inhibitors of this type are commonly engineered by combining ligands carrying an ATP-like part with a peptide or peptide-mimicking fragment that determines specificity. Approach presented in this paper led to generation of a specific system for independent screening for efficient ligands and peptides, by means of thermodynamic measurements, that assessed the ability of the identified ligand and peptide to combine into a bi-substrate inhibitor. The catalytic subunit of human protein kinase CK2 was used as the model target. Peptide sequence was optimized using peptide libraries [KGDE]-[DE]-[ST]-[DE]3-4-NH2, originated from the consensus CK2 sequence. We identified KESEEE-NH2 peptide as the most promising one, whose binding affinity is substantially higher than that of the reference RRRDDDSDDD peptide. We assessed its potency to form an efficient bi-substrate inhibitor using tetrabromobenzotriazole (TBBt) as the model ATP-competitive inhibitor. The formation of ternary complex was monitored using Differential Scanning Fluorimetry (DSF), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC).
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11
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Bestgen B, Krimm I, Kufareva I, Kamal AAM, Seetoh WG, Abell C, Hartmann RW, Abagyan R, Cochet C, Le Borgne M, Engel M, Lomberget T. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem 2019; 62:1803-1816. [PMID: 30689953 DOI: 10.1021/acs.jmedchem.8b01766] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CK2 is a ubiquitous Ser/Thr protein kinase involved in the control of various signaling pathways and is known to be constitutively active. In the present study, we identified aryl 2-aminothiazoles as a novel class of CK2 inhibitors, which displayed a non-ATP-competitive mode of action and stabilized an inactive conformation of CK2 in solution. Enzyme kinetics studies, STD NMR, circular dichroism spectroscopy, and native mass spectrometry experiments demonstrated that the compounds bind in an allosteric pocket outside the ATP-binding site. Our data, combined with molecular docking studies, strongly suggested that this new binding site was located at the interface between the αC helix and the flexible glycine-rich loop. A first hit optimization led to compound 7, exhibiting an IC50 of 3.4 μM against purified CK2α in combination with a favorable selectivity profile. Thus, we identified a novel class of CK2 inhibitors targeting an allosteric pocket, offering great potential for further optimization into anticancer drugs.
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Affiliation(s)
- Benoît Bestgen
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany.,Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France.,Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, Commissariat à l'Energie Atomique, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Lyon 1, ENS Lyon 5, Rue de la Doua , 69100 Villeurbanne , France
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ahmed Ashraf Moustafa Kamal
- Pharmaceutical and Medicinal Chemistry, Saarland University, and Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus C2.3, 66123 Saarbrücken , Germany
| | - Wei-Guang Seetoh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Chris Abell
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Rolf W Hartmann
- Pharmaceutical and Medicinal Chemistry, Saarland University, and Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus C2.3, 66123 Saarbrücken , Germany
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Claude Cochet
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, Commissariat à l'Energie Atomique, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Marc Le Borgne
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany
| | - Thierry Lomberget
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France
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12
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Thiazole- and selenazole-comprising high-affinity inhibitors possess bright microsecond-scale photoluminescence in complex with protein kinase CK2. Bioorg Med Chem 2018; 26:5062-5068. [PMID: 30217463 DOI: 10.1016/j.bmc.2018.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 12/14/2022]
Abstract
A previously disclosed protein kinase (PK) CK2-selective inhibitor 4-(2-amino-1,3-thiazol-5-yl)benzoic acid (ATB) and its selenium-containing counterpart (ASB) revealed remarkable room temperature phosphorescence when bound to the ATP pocket of the protein kinase CK2. Conjugation of these fragments with a mimic of CK2 substrate peptide resulted in bisubstrate inhibitors with increased affinity towards the kinase. Attachment of the fluorescent acceptor dye 5-TAMRA to the conjugates led to significant enhancement of intensity of long-lifetime (microsecond-scale) photoluminescence of both sulfur- and selenium-containing compounds. The developed photoluminescent probes make possible selective determination of the concentration of CK2 in cell lysates and characterization of CK2 inhibitors by means of time-gated measurement of photoluminescence.
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13
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Hochscherf J, Lindenblatt D, Witulski B, Birus R, Aichele D, Marminon C, Bouaziz Z, Le Borgne M, Jose J, Niefind K. Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2α and Its Paralog CK2α'. Pharmaceuticals (Basel) 2017; 10:ph10040098. [PMID: 29236079 PMCID: PMC5748653 DOI: 10.3390/ph10040098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Protein kinase CK2, a member of the eukaryotic protein kinase superfamily, is associated with cancer and other human pathologies and thus an attractive drug target. The indeno[1,2-b]indole scaffold is a novel lead structure to develop ATP-competitive CK2 inhibitors. Some indeno[1,2-b]indole-based CK2 inhibitors additionally obstruct ABCG2, an ABC half transporter overexpressed in breast cancer and co-responsible for drug efflux and resistance. Comprehensive derivatization studies revealed substitutions of the indeno[1,2-b]indole framework that boost either the CK2 or the ABCG2 selectivity or even support the dual inhibition potential. The best indeno[1,2-b]indole-based CK2 inhibitor described yet (IC50 = 25 nM) is 5-isopropyl-4-(3-methylbut-2-enyl-oxy)-5,6,7,8-tetrahydroindeno[1,2-b]indole-9,10-dione (4p). Herein, we demonstrate the membrane permeability of 4p and describe co-crystal structures of 4p with CK2α and CK2α′, the paralogs of human CK2 catalytic subunit. As expected, 4p occupies the narrow, hydrophobic ATP site of CK2α/CK2α′, but surprisingly with a unique orientation: its hydrophobic substituents point towards the solvent while its two oxo groups are hydrogen-bonded to a hidden water molecule. An equivalent water molecule was found in many CK2α structures, but never as a critical mediator of ligand binding. This unexpected binding mode is independent of the interdomain hinge/helix αD region conformation and of the salt content in the crystallization medium.
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Affiliation(s)
- Jennifer Hochscherf
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.
| | - Dirk Lindenblatt
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.
| | - Benedict Witulski
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.
| | - Robin Birus
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany.
| | - Dagmar Aichele
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany.
| | - Christelle Marminon
- EA4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453-INSERM US7, Faculté de Pharmacie-ISPB, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, F-69373 Lyon CEDEX 8, France.
| | - Zouhair Bouaziz
- EA4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453-INSERM US7, Faculté de Pharmacie-ISPB, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, F-69373 Lyon CEDEX 8, France.
| | - Marc Le Borgne
- EA4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453-INSERM US7, Faculté de Pharmacie-ISPB, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, F-69373 Lyon CEDEX 8, France.
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany.
| | - Karsten Niefind
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.
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Rahnel H, Viht K, Lavogina D, Mazina O, Haljasorg T, Enkvist E, Uri A. A Selective Biligand Inhibitor of CK2 Increases Caspase-3 Activity in Cancer Cells and Inhibits Platelet Aggregation. ChemMedChem 2017; 12:1723-1736. [PMID: 28837260 DOI: 10.1002/cmdc.201700457] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 11/08/2022]
Abstract
Cancer cells express high levels of CK2, and its inhibition leads to apoptosis. CK2 has therefore emerged as a new drug target for cancer therapy. A biligand inhibitor ARC-772 was constructed by conjugating 4-(2-amino-1,3-thiazol-5-yl)benzoic acid and a carboxylate-rich peptoid. ARC-772 was found to bind CK2 with a Kd value of 0.3 nm and showed remarkable CK2 inhibitory selectivity in a panel of 140 protein kinases (Gini coefficient: 0.75 at c=100 nm). ARC-775, the acetoxymethyl ester prodrug of ARC-772, was efficiently taken up by cells. Once internalized, the inhibitor is activated by cellular esterase activity. In HeLa cancer cells ARC-775 was found to activate caspase-3 (an apoptosis marker) at sub-micromolar concentrations (EC50 =0.3 μm), a 20-fold lower extracellular concentration than CX-4945, the only CK2 inhibitor under clinical trials. At micromolar concentrations, ARC-775 was also found to inhibit ADP-induced aggregation of human platelets. The overall results of this study demonstrate that oligo-anionic biligand inhibitors have good potential for drug development.
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Affiliation(s)
- Hedi Rahnel
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Darja Lavogina
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Olga Mazina
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Tõiv Haljasorg
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
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15
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Vahter J, Viht K, Uri A, Enkvist E. Oligo-aspartic acid conjugates with benzo[c][2,6]naphthyridine-8-carboxylic acid scaffold as picomolar inhibitors of CK2. Bioorg Med Chem 2017; 25:2277-2284. [PMID: 28274673 DOI: 10.1016/j.bmc.2017.02.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/22/2017] [Accepted: 02/25/2017] [Indexed: 12/20/2022]
Abstract
Structurally diverse inhibitors of the protein kinase CK2 are required for regulation of this ubiquitous protein to establish biological roles of the enzyme which catalyzes the phosphorylation of a vast number of substrate proteins. In this article we disclose a series of new bisubstrate inhibitors of CK2 that are structurally represented by the oligo(l-Asp) peptide conjugates of benzo[c][2,6]naphthyridine-8-carboxylic acid. This fragment originated from CX-4945, the first in class inhibitor taken to clinical trials. The most potent conjugates possessed two-digit picomolar affinity and clear selectivity for CK2α in a panel of 140 protein kinases. Labeling of the inhibitors with a fluorescent dye yielded probes for a fluorescence anisotropy-based binding/displacement assay which can be used for analysis of CK2 and precise determination of affinity of the highly potent (tight-binding) CK2-targeting inhibitors.
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Affiliation(s)
- Jürgen Vahter
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
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16
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Abstract
INTRODUCTION The conventional term 'casein kinase' (CK) denotes three classes of kinases - CK1, CK2 and Golgi-CK (G-CK)/Fam20C (family with sequence similarity 20, member C) - sharing the ability to phoshorylate casein in vitro, but otherwise unrelated to each other. All CKs have been reported to be implicated in human diseases, and reviews individually dealing with the druggability of CK1 and CK2 are available. Our aim is to provide a comparative analysis of the three classes of CKs as therapeutic targets. AREAS COVERED CK2 is the CK for which implication in neoplasia is best documented, with the survival of cancer cells often relying on its overexpression. An ample variety of cell-permeable CK2 inhibitors have been developed, with a couple of these now in clinical trials. Isoform-specific CK1 inhibitors that are expected to play a beneficial role in oncology and neurodegeneration have been also developed. In contrast, the pathogenic potential of G-CK/Fam20C is caused by its loss of function. Activators of Fam20C, notably sphingolipids and their analogs, may prove beneficial in this respect. EXPERT OPINION Optimization of CK2 and CK1 inhibitors will prove useful to develop new therapeutic strategies for treating cancer and neurodegenerative disorders, while the design of potent activators of G-CK/Fam20C will provide a new tool in the fields of bio-mineralization and hypophosphatemic diseases.
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Affiliation(s)
- Giorgio Cozza
- a 1 University of Padova, Department of Biomedical Sciences , Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Lorenzo A Pinna
- a 1 University of Padova, Department of Biomedical Sciences , Via Ugo Bassi 58B, 35131 Padova, Italy .,b 2 University of Padova, Department of Biomedical Sciences and CNR Institute of Neurosciences , Padova, Italy ;
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Viht K, Saaver S, Vahter J, Enkvist E, Lavogina D, Sinijärv H, Raidaru G, Guerra B, Issinger OG, Uri A. Acetoxymethyl Ester of Tetrabromobenzimidazole-Peptoid Conjugate for Inhibition of Protein Kinase CK2 in Living Cells. Bioconjug Chem 2015; 26:2324-35. [PMID: 26559659 DOI: 10.1021/acs.bioconjchem.5b00383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CK2 is a ubiquitous serine/threonine protein kinase, which has the potential to catalyze the generation of a large proportion of the human phosphoproteome. Due to its role in numerous cellular functions and general anti-apoptotic activity, CK2 is an important target of research with therapeutic potential. This emphasizes the need for cell-permeable highly potent and selective inhibitors and photoluminescence probes of CK2 for investigating the protein phosphorylation networks in living cells. Previously, we had developed bisubstrate inhibitors for CK2 (CK2-targeted ARCs) that showed remarkable affinity (KD < 1 nM) and selectivity, but lacked proteolytic stability and plasma membrane permeability. In this report, the structures of CK2-targeted ARCs were modified for the application in live cells. Based on structure-activity studies, proteolytically stable achiral oligoanionic peptoid conjugates of 4,5,6,7-tetrabromo-1H-benzimidazole (TBBz) were constructed. Affinity of the conjugates toward CK2 reached subnanomolar range. Acetoxymethyl (AM) prodrug strategy was applied for loading TBBz-peptoid conjugates into living cells. The uptake of inhibitors was visualized by live cell imaging and the reduction of the phosphorylation levels of two CK2-related phosphosites, Cdc37 pSer13 and NFκB pSer529, was demonstrated by Western blot analysis.
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Affiliation(s)
- Kaido Viht
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Siiri Saaver
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Jürgen Vahter
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Darja Lavogina
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Hedi Sinijärv
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Gerda Raidaru
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Barbara Guerra
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
| | - Olaf-Georg Issinger
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.,KinaseDetect Aps , Skovvej 22, 6340 Kruså, Denmark
| | - Asko Uri
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
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18
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Design, validation and efficacy of bisubstrate inhibitors specifically affecting ecto-CK2 kinase activity. Biochem J 2015; 471:415-30. [PMID: 26349539 DOI: 10.1042/bj20141127] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 09/08/2015] [Indexed: 11/17/2022]
Abstract
By derivatizing the purely competitive CK2 inhibitor N1-(4,5,6,7-tetrabromo-1H-benzimidazol-2-yl)-propane-1,3-diamine (K137) at its 3-amino position with a peptidic fragment composed of three or four glutamic or aspartic acid residues, a new family of bisubstrate inhibitors has been generated whose ability to simultaneously interact with both the ATP and the phosphoacceptor substrate-binding sites has been probed by running mixed competition kinetics and by mutational mapping of the kinase residues implicated in substrate recognition. The most effective bisubstrate inhibitor, K137-E4, interacts with three functional regions of the kinase: the hydrophobic pocket close to the ATP-binding site, the basic residues of the p+1 loop that recognizes the acidic determinant at position n+1 and the basic residues of α-helixC that recognize the acidic determinant at position n+3. Compared with the parent inhibitor (K137), K137-E4 is severalfold more potent (IC50 25 compared with 130 nM) and more selective, failing to inhibit any other kinase as drastically as CK2 out of 140 enzymes, whereas 35 kinases are inhibited more potently than CK2 by K137. K137-E4 is unable to penetrate the cell and to inhibit endogenous CK2, its pro-apoptotic efficacy being negligible compared with cell-permeant inhibitors; however, it readily inhibits ecto-CK2 on the outer cell surface, reducing the phosphorylation of several external phosphoproteins. Inhibition of ecto-CK2 by K137-E4 is accompanied by a slower migration of cancer cells as judged by wound healing assays. On the basis of the cellular responses to K137-E4, we conclude that ecto-CK2 is implicated in cell motility, whereas its contribution to the pro-survival role of CK2 is negligible.
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19
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Manoharan GB, Enkvist E, Kasari M, Viht K, Zenn M, Prinz A, Filhol O, Herberg FW, Uri A. FRET-based screening assay using small-molecule photoluminescent probes in lysate of cells overexpressing RFP-fused protein kinases. Anal Biochem 2015; 481:10-7. [PMID: 25866074 DOI: 10.1016/j.ab.2015.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/16/2015] [Accepted: 04/07/2015] [Indexed: 01/08/2023]
Abstract
An assay was developed for the characterization of protein kinase inhibitors in lysates of mammalian cells based on the measurement of FRET between overexpressed red fluorescent protein (TagRFP)-fused protein kinases (PKs) and luminophore-labeled small-molecule inhibitors (ARC-Photo probes). Two types of the assay, one using TagRFP as the photoluminescence donor together with ARC-Photo probes containing a red fluorophore dye as acceptor, and the other using TagRFP as the acceptor fluorophore in combination with a terbium cryptate-based long-lifetime photoluminescence donor, were used for FRET-based measurements in lysates of the cells overexpressing TagRFP-fused PKs. The second variant of the assay enabled the performance of the measurements under time-resolved conditions that led to substantially higher values of the signal/background ratio and further improved the reliability of the assay.
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Affiliation(s)
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | - Marje Kasari
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | - Michael Zenn
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Anke Prinz
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Odile Filhol
- Institut National de la Santé et de la Recherche Médicale, U1036, Grenoble, France; Commisariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche, S1036, Grenoble, France
| | | | - Asko Uri
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia.
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Kim SW, Hasanuzzaman M, Cho M, Heo YR, Ryu MJ, Ha NY, Park HJ, Park HY, Shin JG. Casein Kinase 2 (CK2)-mediated Phosphorylation of Hsp90β as a Novel Mechanism of Rifampin-induced MDR1 Expression. J Biol Chem 2015; 290:17029-40. [PMID: 25995454 DOI: 10.1074/jbc.m114.624106] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 12/15/2022] Open
Abstract
The P-glycoprotein (P-gp) encoded by the MDR1 gene is a drug-exporting transporter located in the cellular membrane. P-gp induction is regarded as one of the main mechanisms underlying drug-induced resistance. Although there is great interest in the regulation of P-gp expression, little is known about its underlying regulatory mechanisms. In this study, we demonstrate that casein kinase 2 (CK2)-mediated phosphorylation of heat shock protein 90β (Hsp90β) and subsequent stabilization of PXR is a key mechanism in the regulation of MDR1 expression. Furthermore, we show that CK2 is directly activated by rifampin. Upon exposure to rifampin, CK2 catalyzes the phosphorylation of Hsp90β at the Ser-225/254 residues. Phosphorylated Hsp90β then interacts with PXR, causing a subsequent increase in its stability, leading to the induction of P-gp expression. In addition, inhibition of CK2 and Hsp90β enhances the down-regulation of PXR and P-gp expression. The results of this study may facilitate the development of new strategies to prevent multidrug resistance and provide a plausible mechanism for acquired drug resistance by CK2-mediated regulation of P-gp expression.
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Affiliation(s)
- So Won Kim
- From the Department of Pharmacology and the Institute for Clinical and Translational Research, Catholic Kwandong University College of Medicine, Gangneung 210-701, Korea, the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea, the Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 614-735, Korea
| | - Md Hasanuzzaman
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea
| | - Munju Cho
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea
| | - Ye Rang Heo
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea
| | - Min-Jung Ryu
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea
| | - Na-Young Ha
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea
| | - Hyun June Park
- the Bio-MAX Institute, Seoul National University, Seoul 151-742, Korea, and
| | - Hyung-Yeon Park
- the Agriculture and Biotechnology Department, Noroo Holdings Co. Ltd., Seoul 135-983, Korea
| | - Jae-Gook Shin
- the Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Korea, the Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 614-735, Korea,
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21
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Guerra B, Hochscherf J, Jensen NB, Issinger OG. Identification of a novel potent, selective and cell permeable inhibitor of protein kinase CK2 from the NIH/NCI Diversity Set Library. Mol Cell Biochem 2015; 406:151-61. [PMID: 25963666 DOI: 10.1007/s11010-015-2433-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/05/2015] [Indexed: 01/06/2023]
Abstract
The anti-apoptotic protein kinase CK2 increasingly becomes an attractive target in cancer research with great therapeutic potential. Here, we have performed an in vitro screening of the Diversity Set III of the DTP program from the NCI/NIH, comprising 1600 compounds. We have identified 1,3-Dichloro-6-[(E)-((4-methoxyphenyl)imino)methyl] dibenzo(b,d) furan-2,7-diol (referred to as D11) to be a potent and selective inhibitor of protein kinase CK2. The D11 compound was tested against 354 eukaryotic protein kinases. By setting the threshold for inhibition to <2% remaining kinase activity, only DYRK1B, IRAK1 and PIM3 were inhibited to an extent as the tetrameric CK2 holoenzyme and its catalytic subunits α and α'. The IC50 values for the CK2α and CK2α' were on average 1-2 nM in comparison to the DYRK1B, IRAK1 and PIM3 kinases, which ranged from 18 to 49 nM. Cell permeability and efficacy of D11 were tested with cells in culture. In MIA PaCa-2 cells (human pancreatic carcinoma cell line), the phosphorylation of the CK2 biomarker CDC37 at S13 was almost completely inhibited in the presence of D11. This was observed both under normoxia and hypoxia. In the case of the human non-small cell lung carcinoma cell line, H1299, increasing amounts of D11 led to an inhibition of S380/T382/383 phosphorylation in PTEN, another biomarker for CK2 activity.
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Affiliation(s)
- Barbara Guerra
- Department of Biochemistry and Molecular Biology, Biomedical Research Group, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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22
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Winiewska M, Kucińska K, Makowska M, Poznański J, Shugar D. Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2α. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1708-17. [PMID: 25891901 DOI: 10.1016/j.bbapap.2015.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
The interaction of human CK2α (hCK2α) with nine halogenated benzotriazoles, TBBt and its analogues representing all possible patterns of halogenation on the benzene ring of benzotriazole, was studied by biophysical methods. Thermal stability of protein-ligand complexes, monitored by calorimetric (DSC) and optical (DSF) methods, showed that the increase in the mid-point temperature for unfolding of protein-ligand complexes (i.e. potency of ligand binding to hCK2α) follow the inhibitory activities determined by biochemical assays. The dissociation constant for the ATP-hCK2α complex was estimated with the aid of microscale thermophoresis (MST) as 4.3±1.8 μM, and MST-derived dissociation constants determined for halogenated benzotriazoles, when converted according to known ATP concentrations, perfectly reconstruct IC50 values determined by the biochemical assays. Ligand-dependent quenching of tyrosine fluorescence, together with molecular modeling and DSC-derived heats of unfolding, support the hypothesis that halogenated benzotriazoles bind in at least two alternative orientations, and those that are efficient hCK2α inhibitors bind in the orientation which TBBt adopts in its complex with maize CK2α. DSC-derived apparent heat for ligand binding (ΔΔHbind) is driven by intermolecular electrostatic interactions between Lys68 and the triazole ring of the ligand, as indicated by a good correlation between ΔΔHbind and ligand pKa. Overall results, additionally supported by molecular modeling, confirm that a balance of hydrophobic and electrostatic interactions contribute predominantly (~40 kJ/mol), relative to possible intermolecular halogen/hydrogen bonding (less than 10 kJ/mol), in binding of halogenated benzotriazoles to the ATP-binding site of hCK2α. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Maria Winiewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Katarzyna Kucińska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Małgorzata Makowska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
| | - David Shugar
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
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23
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Development of a high-throughput screening-compatible assay to identify inhibitors of the CK2α/CK2β interaction. Anal Biochem 2015; 468:4-14. [DOI: 10.1016/j.ab.2014.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/22/2014] [Accepted: 09/05/2014] [Indexed: 01/10/2023]
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Swider R, Masłyk M, Zapico JM, Coderch C, Panchuk R, Skorokhyd N, Schnitzler A, Niefind K, de Pascual-Teresa B, Ramos A. Synthesis, biological activity and structural study of new benzotriazole-based protein kinase CK2 inhibitors. RSC Adv 2015. [DOI: 10.1039/c5ra12114k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new series of TBB-derivatives was synthesized and characterized as CK2 inhibitors. Crystallographic analysis and docking studies were used to understand the mode of binding.
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Synthesis of novel chiral TBBt derivatives with hydroxyl moiety. Studies on inhibition of human protein kinase CK2α and cytotoxicity properties. Eur J Med Chem 2014; 84:364-74. [PMID: 25036794 DOI: 10.1016/j.ejmech.2014.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/26/2014] [Accepted: 07/06/2014] [Indexed: 11/20/2022]
Abstract
The efficient method for the synthesis of novel 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) derivatives bearing a single stereogenic center has been developed. New compounds with a variety of substituents at the meta- and para-position of the phenyl ring are reported. All of the presented compounds were obtained using classical synthetic methods, such as bromination of benzotriazole, and its subsequent alkylation by monotosylated arylpropane-1,3-diols, which in turn have been synthesized through reduction of the corresponding prochiral β-keto esters, and the selective monotosylation of the primary hydroxyl group. The influence of the new and previously reported N-hydroxyalkyl TBBt derivatives on the activity of human protein kinase CK2α catalytic subunit was examined. The most active were derivatives with N-hydroxyalkyl substituents (IC50 in 0.80-7.35 μM range). A binding mode of (R)-1-(4,5,6,7-tetrabromo-2H-benzotriazol-2-yl)butan-3-ol 7b to hCK2α has been proposed based on in silico docking studies. Additionally, MTT-based cytotoxicity tests demonstrated high activities of novel 1-aryl-3-TBBt-propan-1-ol and 3-TBBt-propan-1,2-diol derivatives against human peripheral blood T lymphoblast (CCRF-CEM), and moderate anti-tumor activities against human breast adenocarcinoma (MCF7) cell lines.
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Zhang X. A Computational Study of Allene Synthesis via the ZnI2-Promoted Alleylation of Terminal Alkynes (ATA Reaction). ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201300251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ekambaram R, Enkvist E, Manoharan GB, Ugandi M, Kasari M, Viht K, Knapp S, Issinger OG, Uri A. Benzoselenadiazole-based responsive long-lifetime photoluminescent probes for protein kinases. Chem Commun (Camb) 2014; 50:4096-8. [DOI: 10.1039/c3cc49198f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Benzoselenadiazole was used as a novel scaffold for construction of microsecond scale responsive photoluminescent probes for protein kinases.
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Affiliation(s)
| | - Erki Enkvist
- Institute of Chemistry
- University of Tartu
- 50411 Tartu, Estonia
| | | | - Mihkel Ugandi
- Institute of Chemistry
- University of Tartu
- 50411 Tartu, Estonia
| | - Marje Kasari
- Institute of Chemistry
- University of Tartu
- 50411 Tartu, Estonia
| | - Kaido Viht
- Institute of Chemistry
- University of Tartu
- 50411 Tartu, Estonia
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine
- Structural Genomics Consortium and Target Discovery Institute (TDI) University of Oxford
- Oxford OX3 7BN, UK
| | - Olaf-Georg Issinger
- Institut for Biokemi og Molekylær Biologi
- Syddansk Universitet
- DK-5230 Odense, Denmark
| | - Asko Uri
- Institute of Chemistry
- University of Tartu
- 50411 Tartu, Estonia
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Ekambaram R, Enkvist E, Vaasa A, Kasari M, Raidaru G, Knapp S, Uri A. Selective bisubstrate inhibitors with sub-nanomolar affinity for protein kinase Pim-1. ChemMedChem 2013; 8:909-13. [PMID: 23616352 DOI: 10.1002/cmdc.201300042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/05/2013] [Indexed: 11/06/2022]
Abstract
Potent and selective: The unique nature of the ATP binding pocket structure of Pim family protein kinases (PKs) was used for the development of bisubstrate inhibitors and a fluorescent probe with sub-nanomolar affinity. Conjugates of arginine-rich peptides with two ATP mimetic scaffolds were synthesized and tested as inhibitors of Pim-1. Against a panel of 124 protein kinases, a novel ARC-PIM conjugate selectively inhibited PKs of the Pim family.
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