1
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Al-Qadhi MA, Yahya TAA, El-Nassan HB. Recent Advances in the Discovery of CK2 Inhibitors. ACS OMEGA 2024; 9:20702-20719. [PMID: 38764653 PMCID: PMC11097362 DOI: 10.1021/acsomega.3c10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
CK2 is a vital enzyme that phosphorylates a large number of substrates and thereby controls many processes in the body. Its upregulation was reported in many cancer types. Inhibitors of CK2 might have anticancer activity, and two compounds are currently under clinical trials. However, both compounds are ATP-competitive inhibitors that may have off-target side effects. The development of allosteric and dual inhibitors can overcome this drawback. These inhibitors showed higher selectivity and specificity for the CK2 enzyme compared to the ATP-competitive inhibitors. The present review summarizes the efforts exerted in the last five years in the design of CK2 inhibitors.
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Affiliation(s)
- Mustafa A. Al-Qadhi
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a, Yemen
| | - Tawfeek A. A. Yahya
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a,Yemen
| | - Hala B. El-Nassan
- Pharmaceutical
Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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2
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Bancet A, Frem R, Jeanneret F, Mularoni A, Bazelle P, Roelants C, Delcros JG, Guichou JF, Pillet C, Coste I, Renno T, Battail C, Cochet C, Lomberget T, Filhol O, Krimm I. Cancer selective cell death induction by a bivalent CK2 inhibitor targeting the ATP site and the allosteric αD pocket. iScience 2024; 27:108903. [PMID: 38318383 PMCID: PMC10838953 DOI: 10.1016/j.isci.2024.108903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/25/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Although the involvement of protein kinase CK2 in cancer is well-documented, there is a need for selective CK2 inhibitors suitable for investigating CK2 specific roles in cancer-related biological pathways and further exploring its therapeutic potential. Here, we report the discovery of AB668, an outstanding selective inhibitor that binds CK2 through a bivalent mode, interacting both at the ATP site and an allosteric αD pocket unique to CK2. Using caspase activation assay, live-cell imaging, and transcriptomic analysis, we have compared the effects of this bivalent inhibitor to representative ATP-competitive inhibitors, CX-4945, and SGC-CK2-1. Our results show that in contrast to CX-4945 or SGC-CK2-1, AB668, by targeting the CK2 αD pocket, has a distinct mechanism of action regarding its anti-cancer activity, inducing apoptotic cell death in several cancer cell lines and stimulating distinct biological pathways in renal cell carcinoma.
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Affiliation(s)
- Alexandre Bancet
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
- Kairos Discovery SAS, 36 Rue Jeanne d’Arc, 69003 Lyon, France
| | - Rita Frem
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Florian Jeanneret
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Angélique Mularoni
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
| | - Pauline Bazelle
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Caroline Roelants
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Jean-Guy Delcros
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
| | - Jean-François Guichou
- Centre de Biologie Structurale, CNRS, INSERM, University Montpellier, 34090 Montpellier, France
| | - Catherine Pillet
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Isabelle Coste
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Toufic Renno
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Christophe Battail
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Claude Cochet
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Thierry Lomberget
- University Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5246, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), COSSBA Team, Faculté de Pharmacie-ISPB, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - Odile Filhol
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Isabelle Krimm
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
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3
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Chen Y, Wang Y, Wang J, Zhou Z, Cao S, Zhang J. Strategies of Targeting CK2 in Drug Discovery: Challenges, Opportunities, and Emerging Prospects. J Med Chem 2023; 66:2257-2281. [PMID: 36745746 DOI: 10.1021/acs.jmedchem.2c01523] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CK2 (casein kinase 2) is a serine/threonine protein kinase that is ubiquitous in eukaryotic cells and plays important roles in a variety of cellular functions, including cell growth, apoptosis, circadian rhythms, DNA damage repair, transcription, and translation. CK2 is involved in cancer pathogenesis and the occurrence of many diseases. Therefore, targeting CK2 is a promising therapeutic strategy. Although many CK2-specific small-molecule inhibitors have been developed, only CX-4945 has progressed to clinical trials. In recent years, novel CK2 inhibitors have gradually become a research hotspot, which is expected to overcome the limitations of traditional inhibitors. Herein, we summarize the structure, biological functions, and disease relevance of CK2 and emphatically analyze the structure-activity relationship (SAR) and binding modes of small-molecule CK2 inhibitors. We also discuss the latest progress of novel strategies, providing insights into new drugs targeting CK2 for clinical practice.
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Affiliation(s)
- Yijia Chen
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuxi Wang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Tianfu Jincheng Laboratory, Chengdu, Sichuan 610041, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Zhilan Zhou
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shu Cao
- West China School of Stomatology Sichuan University, Chengdu, Sichuan 610064, China
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Tianfu Jincheng Laboratory, Chengdu, Sichuan 610041, China
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4
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Lin H. Substrate-selective small-molecule modulators of enzymes: Mechanisms and opportunities. Curr Opin Chem Biol 2023; 72:102231. [PMID: 36455490 PMCID: PMC9870951 DOI: 10.1016/j.cbpa.2022.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 11/29/2022]
Abstract
Small-molecule inhibitors of enzymes are widely used tools in reverse chemical genetics to probe biology and explore therapeutic opportunities. They are often compared with genetic knockdown or knockout and are expected to produce phenotypes similar to the genetic perturbations. This review aims to highlight that small molecule inhibitors of enzymes and genetic perturbations may not necessarily produce the same phenotype due to the possibility of substrate-selective or substrate-dependent effects of the inhibitors. Examples of substrate-selective inhibitors and the mechanisms for the substrate-selective effects are discussed. Substrate-selective modulators of enzymes have distinct advantages and cannot be easily replaced with biologics. Thus, they present an exciting opportunity for chemical biologists and medicinal chemists.
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Affiliation(s)
- Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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5
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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: 7] [Impact Index Per Article: 2.3] [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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6
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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: 7] [Impact Index Per Article: 2.3] [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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7
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Laufkötter O, Hu H, Miljković F, Bajorath J. Structure- and Similarity-Based Survey of Allosteric Kinase Inhibitors, Activators, and Closely Related Compounds. J Med Chem 2021; 65:922-934. [PMID: 33476146 DOI: 10.1021/acs.jmedchem.0c02076] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Allosteric kinase inhibitors are thought to have high selectivity and are prime candidates for kinase drug discovery. In addition, the exploration of allosteric mechanisms represents an attractive topic for basic research and drug design. Although the identification and characterization of allosteric kinase inhibitors is still far from being routine, X-ray structures of kinase complexes have been determined for a significant number of such inhibitors. On the basis of structural data, allosteric inhibitors can be confirmed. We report a comprehensive survey of allosteric kinase inhibitors and activators from publicly available X-ray structures, map their binding sites, and determine their distribution over binding pockets in kinases. In addition, we discuss structural features of these compounds and identify active structural analogues and high-confidence target annotations, indicating additional activities for a subset of allosteric inhibitors. This contribution aims to provide a detailed structure-based view of allosteric kinase inhibition.
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Affiliation(s)
- Oliver Laufkötter
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
| | - Huabin Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
| | - Filip Miljković
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, D-53115 Bonn, Germany
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8
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Protein kinase CK2 inhibition as a pharmacological strategy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 124:23-46. [PMID: 33632467 DOI: 10.1016/bs.apcsb.2020.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CK2 is a constitutively active Ser/Thr protein kinase which phosphorylates hundreds of substrates. Since they are primarily related to survival and proliferation pathways, the best-known pathological roles of CK2 are in cancer, where its targeting is currently being considered as a possible therapy. However, CK2 activity has been found instrumental in many other human pathologies, and its inhibition will expectably be extended to different purposes in the near future. Here, after a description of CK2 features and implications in diseases, we analyze the different inhibitors and strategies available to target CK2, and update the results so far obtained by their in vivo application.
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9
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Brear P, Ball D, Stott K, D'Arcy S, Hyvönen M. Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α. J Med Chem 2020; 63:12786-12798. [PMID: 33119282 DOI: 10.1021/acs.jmedchem.0c01173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of adenosine 5'-triphosphate (ATP)-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated them further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Rather, we report crystal structures, competitive isothermal titration calorimetry (ITC) and NMR, hydrogen-deuterium exchange (HDX) mass spectrometry, and chemoinformatic analyses that all point to these compounds binding in the ATP pocket. Comparisons of our results and experimental approach with the data presented in the original report suggest that the primary reason for the disparity is nonspecific inhibition by aggregation.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Darby Ball
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
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10
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Protopopov MV, Vdovin VS, Starosyla SA, Borysenko IP, Prykhod'ko AO, Lukashov SS, Bilokin YV, Bdzhola VG, Yarmoluk SM. Flavone inspired discovery of benzylidenebenzofuran-3(2H)-ones (aurones) as potent inhibitors of human protein kinase CK2. Bioorg Chem 2020; 102:104062. [PMID: 32683178 DOI: 10.1016/j.bioorg.2020.104062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 05/19/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022]
Abstract
In this work, we describe the design, synthesis and SAR studies of 2-benzylidenebenzofuran-3-ones (aurones), a new family of potent inhibitors of CK2. A series of aurones have been synthesized. These compounds are structurally related to the synthetic flavones and showed nanomolar activities towards CK2. Biochemical tests revealed that 20 newly synthesized compounds inhibited CK2 with IC50 values in the nanomolar range. Further property-based optimization of aurones was performed, yielding a series of CK2 inhibitors with enhanced lipophilic efficiency. The most potent compound 12m (BFO13) has CLipE = 4.94 (CLogP = 3.5; IC50 = 3.6 nM) commensurable with the best known inhibitors of CK2.
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Affiliation(s)
- M V Protopopov
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.
| | - V S Vdovin
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - S A Starosyla
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - I P Borysenko
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine; LLC Scientific and Service Firm "Otava", 117/125 Borschagivska St., Suite 79, 03056 Kyiv, Ukraine
| | - A O Prykhod'ko
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine; LLC Scientific and Service Firm "Otava", 117/125 Borschagivska St., Suite 79, 03056 Kyiv, Ukraine
| | - S S Lukashov
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Y V Bilokin
- OTAVA Ltd., 400 Applewood Crescent, Unit 100, Vaughan, Ontario L4K 0C3, Canada
| | - V G Bdzhola
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - S M Yarmoluk
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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11
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Demulder M, De Veylder L, Loris R. Crystal structure of Arabidopsis thaliana casein kinase 2 α1. Acta Crystallogr F Struct Biol Commun 2020; 76:182-191. [PMID: 32254052 PMCID: PMC7137383 DOI: 10.1107/s2053230x20004537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 11/11/2022] Open
Abstract
Casein kinase 2 (CK2) is a ubiquitous pleiotropic enzyme that is highly conserved across eukaryotic kingdoms. CK2 is singular amongst kinases as it is highly rigid and constitutively active. Arabidopsis thaliana is widely used as a model system in molecular plant research; the biological functions of A. thaliana CK2 are well studied in vivo and many of its substrates have been identified. Here, crystal structures of the α subunit of A. thaliana CK2 in three crystal forms and of its complex with the nonhydrolyzable ATP analog AMppNHp are presented. While the C-lobe of the enzyme is highly rigid, structural plasticity is observed for the N-lobe. Small but significant displacements within the active cleft are necessary in order to avoid steric clashes with the AMppNHp molecule. Binding of AMppNHp is influenced by a rigid-body motion of the N-lobe that was not previously recognized in maize CK2.
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Affiliation(s)
- Manon Demulder
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, B-9052 Ghent, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
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12
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Chen X, Li C, Wang D, Chen Y, Zhang N. Recent Advances in the Discovery of CK2 Allosteric Inhibitors: From Traditional Screening to Structure-Based Design. Molecules 2020; 25:molecules25040870. [PMID: 32079098 PMCID: PMC7070378 DOI: 10.3390/molecules25040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Protein kinase (CK2) has emerged as an attractive cancer therapeutic target and recent efforts have been made to develop its inhibitors. However, the development of selective inhibitors remains challenging because of the highly conserved ATP-binding pocket (orthosteric site) of kinase family. As an alternative strategy, allosteric inhibitors, by targeting the much more diversified allosteric site relative to the conserved ATP-binding site, achieve better pharmacological advantages than orthosteric inhibitors. Traditional serendipitous screening and structure-based design are robust tools for the discovery of CK2 allosteric inhibitors. In this review, we summarize the recent advances in the identification of CK2 allosteric inhibitors. Firstly, we briefly present the CK2 allosteric sites. Then, the allosteric inhibitors targeting the well-elucidated allosteric sites (α/β interface, αD pocket and interface between the Glycine-rich loop and αC-helix) are highlighted in the discovery process and possible binding modes with the allosteric sites are described. This study is expected to provide valuable clues for the design of CK2 allosteric inhibitors.
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Affiliation(s)
- Xiaolan Chen
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
- Correspondence: (X.C.); (N.Z.); Tel.: +86-0523-86158081 (X.C.)
| | - Chunqiong Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China;
| | - Dada Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
| | - Yu Chen
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China;
- Correspondence: (X.C.); (N.Z.); Tel.: +86-0523-86158081 (X.C.)
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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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El-Kardocy A, Mostafa YA, Mohamed NG, Abo-Zeid MN, Hassan NA, Hetta HF, Abdel-Aal ABM. CK2 inhibition, lipophilicity and anticancer activity of new N1versus N2-substituted tetrabromobenzotriazole regioisomers. NEW J CHEM 2020. [DOI: 10.1039/d0nj01194k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Both the type and position of polar group substitutions in polybrominated benzotriazoles dramatically change their lipophilicity, kinase inhibition and anticancer activity.
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Affiliation(s)
- Ahmed El-Kardocy
- Student Research Unit
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Yaser A. Mostafa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Noha G. Mohamed
- Student Research Unit
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Mohammad Nabil Abo-Zeid
- Department of Pharmaceutical Analytical Chemistry
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Nivin A. Hassan
- Cancer Biology Department
- South Egypt Cancer Institute, Assiut University
- Assiut
- Egypt
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology
- Faculty of Medicine
- Assiut University
- Assiut
- Egypt
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