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Greco FA, Krämer A, Wahl L, Elson L, Ehret TAL, Gerninghaus J, Möckel J, Müller S, Hanke T, Knapp S. Synthesis and evaluation of chemical linchpins for highly selective CK2α targeting. Eur J Med Chem 2024; 276:116672. [PMID: 39067440 DOI: 10.1016/j.ejmech.2024.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Casein kinase-2 (CK2) are serine/threonine kinases with dual co-factor (ATP and GTP) specificity, that are involved in the regulation of a wide variety of cellular functions. Small molecules targeting CK2 have been described in the literature targeting different binding pockets of the kinase with a focus on type I inhibitors such as the recently published chemical probe SGC-CK2-1. In this study, we investigated whether known allosteric inhibitors binding to a pocket adjacent to helix αD could be combined with ATP mimetic moieties defining a novel class of ATP competitive compounds with a unique binding mode. Linking both binding sites requires a chemical linking moiety that would introduce a 90-degree angle between the ATP mimetic ring system and the αD targeting moiety, which was realized using a sulfonamide. The synthesized inhibitors were highly selective for CK2 with binding constants in the nM range and low micromolar activity. While these inhibitors need to be further improved, the present work provides a structure-based design strategy for highly selective CK2 inhibitors.
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Affiliation(s)
- Francesco A Greco
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Laurenz Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Theresa A L Ehret
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Joshua Gerninghaus
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Janina Möckel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany.
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany.
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2
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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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3
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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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4
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Zhu H, Yang J, Huang N. Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening. J Chem Inf Model 2022; 62:5485-5502. [PMID: 36268980 DOI: 10.1021/acs.jcim.2c01149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) approach was developed to assess the cross-target generalization ability of machine-learning scoring functions (MLSFs). Subsequently, 12 typical MLSFs were evaluated using random cross-validation (Random-CV), protein sequence similarity-based cross-validation (Seq-CV), and pocket Pfam-based cross-validation (Pfam-CV) methods. Surprisingly, all of the tested models showed decreased performances from Random-CV to Seq-CV to Pfam-CV experiments, not showing satisfactory generalization capacity. Our interpretable analysis suggested that the predictions on novel targets by MLSFs were dependent on buried solvent-accessible surface area (SASA)-related features of complex structures, with greater predicted binding affinities on complexes owning larger protein-ligand interfaces. By combining buried SASA-related features with target-specific patterns that were only shared among structurally similar compounds in the same cluster, the random forest (RF)-Score attained a good performance in the Random-CV test. Based on these findings, we strongly advise assessing the generalization ability of MLSFs with the Pfam-cluster approach and being cautious with the features learned by MLSFs.
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Affiliation(s)
- Hui Zhu
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China102206, China.,National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing102206, China
| | - Jincai Yang
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing102206, China
| | - Niu Huang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China102206, China.,National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing102206, China
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5
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Nipun VB, Amin KA. Recent Advances in Protein Kinase CK2, a Potential Therapeutic Target in Cancer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:919-931. [DOI: 10.1134/s1068162022050144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- V. B. Nipun
- Cancer Research Center, Shantou University Medical Collage, Shantou, Guangdong, 515041, PR China
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - K. A. Amin
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Basic and Applied Scientific Research Center, Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
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6
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Brear P, De Fusco C, Atkinson EL, Iegre J, Francis-Newton NJ, Venkitaraman AR, Hyvönen M, Spring DR. A fragment-based approach leading to the discovery of inhibitors of CK2α with a novel mechanism of action. RSC Med Chem 2022; 13:1420-1426. [DOI: 10.1039/d2md00161f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Development of a novel CK2α inhibitor from a fragment-based screen with a proposed novel mechanism of action.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1GA, Cambridge, UK
| | - Claudia De Fusco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Eleanor L. Atkinson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Jessica Iegre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Nicola J. Francis-Newton
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge CB2 0XZ, UK
| | - Ashok R. Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge CB2 0XZ, UK
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599 & DITL, IMCB, A*STAR, 8A Biomedical Grove, 138648, Singapore
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1GA, Cambridge, UK
| | - David R. Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
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7
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Synthesis of oleanolic acid hydrazide-hydrazone hybrid derivatives and investigation of their cytotoxic effects on A549 human lung cancer cells. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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8
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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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9
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Stanzione F, Giangreco I, Cole JC. Use of molecular docking computational tools in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:273-343. [PMID: 34147204 DOI: 10.1016/bs.pmch.2021.01.004] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results.
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Affiliation(s)
| | - Ilenia Giangreco
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
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10
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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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11
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Wang Y, Lv Z, Chen F, Wang X, Gou S. Discovery of 5-(3-Chlorophenylamino)benzo[ c][2,6]naphthyridine Derivatives as Highly Selective CK2 Inhibitors with Potent Cancer Cell Stemness Inhibition. J Med Chem 2021; 64:5082-5098. [PMID: 33834781 DOI: 10.1021/acs.jmedchem.1c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Multifunctional entities have recently been attractive for the development of anticancer chemotherapeutic drugs. However, such entities with concurrent CK2 along with cancer stem cell (CSC) inhibitory activities are rare in a single small molecule. Herein, a series of 5-(3-chlorophenylamino)benzo[c][2,6]naphthyridine derivatives were synthesized using a known CK2 inhibitor, silmitasertib (CX-4945), as the lead compound. Among the resulting compounds, 1c exhibited stronger CK2 inhibitory activity with higher Clk2/CK2 selectivity than CX-4945. Significantly, 1c could modulate the Akt1(ser129)-GSK-3β(ser9)-Wnt/β-catenin signaling pathway and inhibit the expression of the stemness marker ALDH1A1, CSC surface antigens, and stem genes, showing potent CSC inhibitory activity. Moreover, 1c also displayed superior pharmacokinetics and antitumor activity compared with CX-4945 sodium salt, without obvious toxicity. The favorable antiproliferative and antitumor activity of 1c, its high inhibitory selectivity for CK2, and its potent inhibition of cancer cell stemness make this molecule a candidate for the treatment of cancer.
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Affiliation(s)
- Yuanjiang Wang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Zhaodan Lv
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Feihong Chen
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Xing Wang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Shaohua Gou
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China.,Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
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12
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Spinello Z, Fregnani A, Quotti Tubi L, Trentin L, Piazza F, Manni S. Targeting Protein Kinases in Blood Cancer: Focusing on CK1α and CK2. Int J Mol Sci 2021; 22:ijms22073716. [PMID: 33918307 PMCID: PMC8038136 DOI: 10.3390/ijms22073716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
Disturbance of protein kinase activity may result in dramatic consequences that often lead to cancer development and progression. In tumors of blood origin, both tyrosine kinases and serine/threonine kinases are altered by different types of mutations, critically regulating cancer hallmarks. CK1α and CK2 are highly conserved, ubiquitously expressed and constitutively active pleiotropic kinases, which participate in multiple biological processes. The involvement of these kinases in solid and blood cancers is well documented. CK1α and CK2 are overactive in multiple myeloma, leukemias and lymphomas. Intriguingly, they are not required to the same degree for the viability of normal cells, corroborating the idea of “druggable” kinases. Different to other kinases, mutations on the gene encoding CK1α and CK2 are rare or not reported. Actually, these two kinases are outside the paradigm of oncogene addiction, since cancer cells’ dependency on these proteins resembles the phenomenon of “non-oncogene” addiction. In this review, we will summarize the general features of CK1α and CK2 and the most relevant oncogenic and stress-related signaling nodes, regulated by kinase phosphorylation, that may lead to tumor progression. Finally, we will report the current data, which support the positioning of these two kinases in the therapeutic scene of hematological cancers.
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Affiliation(s)
- Zaira Spinello
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
| | - Anna Fregnani
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
| | - Laura Quotti Tubi
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
| | - Livio Trentin
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
| | - Francesco Piazza
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
- Correspondence: (F.P.); (S.M.); Tel.: +39-049-792-3263 (F.P. & S.M.); Fax: +39-049-792-3250 (F.P. & S.M.)
| | - Sabrina Manni
- Department of Medicine, Hematology Section, University of Padova, Via N. Giustiniani 2, 35128 Padova, Italy; (Z.S.); (A.F.); (L.Q.T.); (L.T.)
- Veneto Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy
- Correspondence: (F.P.); (S.M.); Tel.: +39-049-792-3263 (F.P. & S.M.); Fax: +39-049-792-3250 (F.P. & S.M.)
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13
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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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14
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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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15
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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: 28] [Impact Index Per Article: 9.3] [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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16
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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: 13] [Impact Index Per Article: 3.3] [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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17
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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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18
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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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19
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Bancet A, Raingeval C, Lomberget T, Le Borgne M, Guichou JF, Krimm I. Fragment Linking Strategies for Structure-Based Drug Design. J Med Chem 2020; 63:11420-11435. [DOI: 10.1021/acs.jmedchem.0c00242] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Bancet
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Claire Raingeval
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Thierry Lomberget
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | - Marc Le Borgne
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | | | - Isabelle Krimm
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, 69008 Lyon, France
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20
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Kidd SL, Fowler E, Reinhardt T, Compton T, Mateu N, Newman H, Bellini D, Talon R, McLoughlin J, Krojer T, Aimon A, Bradley A, Fairhead M, Brear P, Díaz-Sáez L, McAuley K, Sore HF, Madin A, O'Donovan DH, Huber KVM, Hyvönen M, von Delft F, Dowson CG, Spring DR. Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion. Chem Sci 2020; 11:10792-10801. [PMID: 34094333 PMCID: PMC8162264 DOI: 10.1039/d0sc01232g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Organic synthesis underpins the evolution of weak fragment hits into potent lead compounds. Deficiencies within current screening collections often result in the requirement of significant synthetic investment to enable multidirectional fragment growth, limiting the efficiency of the hit evolution process. Diversity-oriented synthesis (DOS)-derived fragment libraries are constructed in an efficient and modular fashion and thus are well-suited to address this challenge. To demonstrate the effective nature of such libraries within fragment-based drug discovery, we herein describe the screening of a 40-member DOS library against three functionally distinct biological targets using X-Ray crystallography. Firstly, we demonstrate the importance for diversity in aiding hit identification with four fragment binders resulting from these efforts. Moreover, we also exemplify the ability to readily access a library of analogues from cheap commercially available materials, which ultimately enabled the exploration of a minimum of four synthetic vectors from each molecule. In total, 10-14 analogues of each hit were rapidly accessed in three to six synthetic steps. Thus, we showcase how DOS-derived fragment libraries enable efficient hit derivatisation and can be utilised to remove the synthetic limitations encountered in early stage fragment-based drug discovery.
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Affiliation(s)
- Sarah L Kidd
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Elaine Fowler
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Till Reinhardt
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Thomas Compton
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Natalia Mateu
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Hector Newman
- School of Life Sciences, University of Warwick Coventry UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Dom Bellini
- School of Life Sciences, University of Warwick Coventry UK
| | - Romain Talon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Joseph McLoughlin
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Tobias Krojer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Anthony Bradley
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Michael Fairhead
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Laura Díaz-Sáez
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Katherine McAuley
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | | | - Kilian V M Huber
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa
| | | | - David R Spring
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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21
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Alternaria toxins as casein kinase 2 inhibitors and possible consequences for estrogenicity: a hybrid in silico/in vitro study. Arch Toxicol 2020; 94:2225-2237. [PMID: 32328700 PMCID: PMC7303061 DOI: 10.1007/s00204-020-02746-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/08/2020] [Indexed: 01/05/2023]
Abstract
Emerging mycotoxins produced by Alternaria spp. were previously reported to exert cytotoxic, genotoxic, but also estrogenic effects in human cells. The involved mechanisms are very complex and not fully elucidated yet. Thus, we followed an in silico target fishing approach to extend knowledge on the possible biological targets underlying the activity of alternariol, taken as the signature compound of Alternaria toxins. Combining ligand-based screening and structure-based modeling, the ubiquitous casein kinase 2 (CK2) was identified as a potential target for the compound. This result was validated in a cell-free in vitro CK2 activity assay, where alternariol inhibited CK2 with an IC50 of 707 nM. As CK2 was recently discussed to influence estrogen receptor (ER) transcription and DNA-binding affinity, we assessed a potential impact on the mRNA levels of ERα or ERβ by qRT-PCR and on nuclear localization of the receptors by confocal microscopy, using estrogen-sensitive Ishikawa cells as a model. While AOH did not affect the transcription of ERα or ERβ, an increase in nuclear localization of ERα after incubation with 10 µM AOH was observed. However, this effect might be due to ER binding affinity and therefore estrogenicity of AOH. Furthermore, in silico docking simulation revealed not only AOH, but also a number of other Alternaria toxins as potential inhibitors of CK2, including alternariol monomethyl ether and the perylene quinone derivative altertoxin II (ATX-II). These findings were representatively confirmed in vitro for the perylene quinone derivative altertoxin II, which was found to inhibit the kinase with an IC50 of 5.1 µM. Taken together, we propose CK2 inhibition as an additional mechanism to consider in future studies for alternariol and several other Alternaria toxins.
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22
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Dalle Vedove A, Zonta F, Zanforlin E, Demitri N, Ribaudo G, Cazzanelli G, Ongaro A, Sarno S, Zagotto G, Battistutta R, Ruzzene M, Lolli G. A novel class of selective CK2 inhibitors targeting its open hinge conformation. Eur J Med Chem 2020; 195:112267. [PMID: 32283296 DOI: 10.1016/j.ejmech.2020.112267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/02/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022]
Abstract
Protein kinase CK2 sustains cancer growth, especially in hematological malignancies. Its inhibitor SRPIN803, based on a 6-methylene-5-imino-1,3,4-thiadiazolopyrimidin-7-one scaffold, showed notable specificity. Our synthesis of the initially proposed SRPIN803 resulted in its constitutional isomer SRPIN803-revised, where the 2-cyano-2-propenamide group does not cyclise and fuse to the thiadiazole ring. Its crystallographic structure in complex with CK2α identifies the structural determinants of the reported specificity. SRPIN803-revised explores the CK2 open hinge conformation, extremely rare among kinases, also interacting with side chains from this region. Its optimization lead to the more potent compound 4, which inhibits endocellular CK2, significantly affects viability of tumour cells and shows remarkable selectivity on a panel of 320 kinases.
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Affiliation(s)
- Andrea Dalle Vedove
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Francesca Zonta
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Enrico Zanforlin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padua, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149, Basovizza-Trieste, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, Division of Pharmacology, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giulia Cazzanelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, Division of Pharmacology, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padua, Italy.
| | - Roberto Battistutta
- Department of Chemical Sciences and CNR Institute of Biomolecular Chemistry, University of Padua, Via F. Marzolo 1, 35131, Padua, Italy.
| | - Maria Ruzzene
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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23
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de Souza Neto LR, Moreira-Filho JT, Neves BJ, Maidana RLBR, Guimarães ACR, Furnham N, Andrade CH, Silva FP. In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery. Front Chem 2020; 8:93. [PMID: 32133344 PMCID: PMC7040036 DOI: 10.3389/fchem.2020.00093] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Fragment-based drug (or lead) discovery (FBDD or FBLD) has developed in the last two decades to become a successful key technology in the pharmaceutical industry for early stage drug discovery and development. The FBDD strategy consists of screening low molecular weight compounds against macromolecular targets (usually proteins) of clinical relevance. These small molecular fragments can bind at one or more sites on the target and act as starting points for the development of lead compounds. In developing the fragments attractive features that can translate into compounds with favorable physical, pharmacokinetics and toxicity (ADMET-absorption, distribution, metabolism, excretion, and toxicity) properties can be integrated. Structure-enabled fragment screening campaigns use a combination of screening by a range of biophysical techniques, such as differential scanning fluorimetry, surface plasmon resonance, and thermophoresis, followed by structural characterization of fragment binding using NMR or X-ray crystallography. Structural characterization is also used in subsequent analysis for growing fragments of selected screening hits. The latest iteration of the FBDD workflow employs a high-throughput methodology of massively parallel screening by X-ray crystallography of individually soaked fragments. In this review we will outline the FBDD strategies and explore a variety of in silico approaches to support the follow-up fragment-to-lead optimization of either: growing, linking, and merging. These fragment expansion strategies include hot spot analysis, druggability prediction, SAR (structure-activity relationships) by catalog methods, application of machine learning/deep learning models for virtual screening and several de novo design methods for proposing synthesizable new compounds. Finally, we will highlight recent case studies in fragment-based drug discovery where in silico methods have successfully contributed to the development of lead compounds.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - José Teófilo Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
- Laboratory of Cheminformatics, Centro Universitário de Anápolis – UniEVANGÉLICA, Anápolis, Brazil
| | - Rocío Lucía Beatriz Riveros Maidana
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Floriano Paes Silva
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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24
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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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25
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Li C, Zhang X, Zhang N, Zhou Y, Sun G, Zhao L, Zhong R. Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening. Molecules 2020; 25:molecules25010237. [PMID: 31935979 PMCID: PMC6983002 DOI: 10.3390/molecules25010237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/19/2022] Open
Abstract
Casein kinase II (CK2) is considered as an attractive cancer therapeutic target, and recent efforts have been made to develop its ATP-competitive inhibitors. However, achieving selectivity with respect to related kinases remains challenging due to the highly conserved ATP-binding pocket of kinases. Allosteric inhibitors, by targeting the much more diversified allosteric site relative to the highly conserved ATP-binding pocket, might be a promising strategy with the enhanced selectivity and reduced toxicity than ATP-competitive inhibitors. The previous studies have highlighted the traditional serendipitousity of discovering allosteric inhibitors owing to the complicate allosteric modulation. In this current study, we identified the novel allosteric inhibitors of CK2α by combing structure-based virtual screening and biological evaluation methods. The structure-based pharmacophore model was built based on the crystal structure of CK2α-compound 15 complex. The ChemBridge fragment library was searched by evaluating the fit values of these molecules with the optimized pharmacophore model, as well as the binding affinity of the CK2α-ligand complexes predicted by Alloscore web server. Six hits forming the holistic interaction mechanism with the αD pocket were retained after pharmacophore- and Alloscore-based screening for biological test. Compound 3 was found to be the most potent non-ATP competitive CK2α inhibitor (IC50 = 13.0 μM) with the anti-proliferative activity on A549 cancer cells (IC50 = 23.1 μM). Our results provide new clues for further development of CK2 allosteric inhibitors as anti-cancer hits.
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Affiliation(s)
- Chunqiong Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Xuewen Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
- Correspondence: ; Tel.: +86-10-67392001
| | - Yue Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China;
| | - Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
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26
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Tsuyuguchi M, Nakaniwa T, Hirasawa A, Nakanishi I, Kinoshita T. Structural insights for producing CK2α1-specific inhibitors. Bioorg Med Chem Lett 2019; 30:126837. [PMID: 31859160 DOI: 10.1016/j.bmcl.2019.126837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 11/25/2022]
Abstract
Casein kinase 2 catalytic subunit (CK2α) is classified into two subtypes CK2α1 and CK2α2. CK2α1 is a drug discovery target, whereas CK2α2 is an off-target of CK2α1 inhibitors. High amino acid sequence homology between these subtypes hampers efforts to produce ATP competitive inhibitors that are highly selective to CK2α1. Hematein was identified previously as a non-ATP-competitive inhibitor for CK2α1, whereas this compound acts as an ATP competitive CK2α2 inhibitor. Crystal structures of CK2α1 and CK2α2 in complex with hematein revealed distinct binding features that provide structural insights for producing CK2α1-selective inhibitors.
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Affiliation(s)
- Masato Tsuyuguchi
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Hirasawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isao Nakanishi
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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27
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Zheng S, Zhu R, Zhou X, Chen L, Bai H, Zhang J. Synthesis and biological evaluation of calycanthaceous alkaloid analogs. Bioorg Med Chem 2019; 27:115088. [DOI: 10.1016/j.bmc.2019.115088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 11/29/2022]
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28
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Kanev GK, de Graaf C, de Esch IJP, Leurs R, Würdinger T, Westerman BA, Kooistra AJ. The Landscape of Atypical and Eukaryotic Protein Kinases. Trends Pharmacol Sci 2019; 40:818-832. [PMID: 31677919 DOI: 10.1016/j.tips.2019.09.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Kinases are attractive anticancer targets due to their central role in the growth, survival, and therapy resistance of tumor cells. This review explores the two primary kinase classes, the eukaryotic protein kinases (ePKs) and the atypical protein kinases (aPKs), and provides a structure-centered comparison of their sequences, structures, hydrophobic spines, mutation and SNP hotspots, and inhibitor interaction patterns. Despite the limited sequence similarity between these two classes, atypical kinases commonly share the archetypical kinase fold but lack conserved eukaryotic kinase motifs and possess altered hydrophobic spines. Furthermore, atypical kinase inhibitors explore only a limited number of binding modes both inside and outside the orthosteric binding site. The distribution of genetic variations in both classes shows multiple ways they can interfere with kinase inhibitor binding. This multilayered review provides a research framework bridging the eukaryotic and atypical kinase classes.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Thomas Würdinger
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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29
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Zheng S, Zhu R, Tang B, Chen L, Bai H, Zhang J. Synthesis and biological evaluations of a series of calycanthaceous analogues as antifungal agents. Nat Prod Res 2019; 35:1816-1824. [PMID: 31378086 DOI: 10.1080/14786419.2019.1644635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Starting from indole-3-acetonitrile, a total of 66 new calycanthaceous alkaloid analogues were synthesised in excellent yields. The prepared compounds were evaluated for their biological activities against a broad range of plant pathogen fungi. The results of bioassays indicated that the majority of tested compounds displayed comparable or better in vitro bioactivities than the positive control. Notably, Compound a1 displayed a significant activities against B. cereus, Escherichia sp and R. solanacearum, even better than the positive control streptomycin and Penicillin, with the same MIC value of 15.63 µg mL-1. Compound a1 displayed a broad spectrum and remarkably activities among the tested calycanthaceous analogues and might be a novel potential leading compound for further development of antifungal agents. The results obtained in the study will be very helpful for further design and structural optimisation of calycanthaceous alkaloids as potential agrochemical lead for plant disease control.
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Affiliation(s)
- Shaojun Zheng
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
| | - Rui Zhu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
| | - Bing Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
| | - Lizhuang Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
| | - Hongjin Bai
- Key Laboratory of Protection & Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps/College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Jiwen Zhang
- Key Laboratory of Botanical Pesticide R & D in Shaanxi Province, Yangling, Shaanxi, China
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30
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Pastor M, Zapico JM, Coderch C, Maslyk M, Panchuk R, de Pascual-Teresa B, Ramos A. From a MMP2/CK2 multitarget approach to the identification of potent and selective MMP13 inhibitors. Org Biomol Chem 2019; 17:916-929. [PMID: 30629065 DOI: 10.1039/c8ob02990c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this article, we describe our efforts in the search of MMP2/CK2 dual targeting inhibitors. We have followed a rational drug design approach based on our experience in the selective inhibition of these two enzymes. We have successfully obtained highly active MMP2 (10, IC50 = 70 nM; 11, IC50 = 100 nM) and CK2 (16a, IC50 = 500 nM) inhibitors. However, structural fine tuning of these small molecules to simultaneously target both enzymes turned out to be an unattainable goal. Unexpectedly, we were lucky to identify new and selective MMP13 inhibitors (10, IC50 = 3.7 nM and 11, IC50 = 5.6 nM) with a novel TBB-derived scaffold. These compounds constitute an interesting starting point for further optimization.
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Affiliation(s)
- Miryam Pastor
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28925, Alcorcón, Madrid, Spain.
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31
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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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32
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Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action. J Med Chem 2019; 62:1817-1836. [PMID: 30689946 DOI: 10.1021/acs.jmedchem.8b01765] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein CK2 has gained much interest as an anticancer drug target in the past decade. We had previously described the identification of a new allosteric site on the catalytic α-subunit, along with first small molecule ligands based on the 4-(4-phenylthiazol-2-ylamino)benzoic acid scaffold. In the present work, structure optimizations guided by a binding model led to the identification of the lead compound 2-hydroxy-4-((4-(naphthalen-2-yl)thiazol-2-yl)amino)benzoic acid (27), showing a submicromolar potency against purified CK2α (IC50 = 0.6 μM). Furthermore, 27 induced apoptosis and cell death in 786-O renal cell carcinoma cells (EC50 = 5 μM) and inhibited STAT3 activation even more potently than the ATP-competitive drug candidate CX-4945 (EC50 of 1.6 μM vs 5.3 μM). Notably, the potencies of our allosteric ligands to inhibit CK2 varied depending on the individual substrate. Altogether, the novel allosteric pocket was proved a druggable site, offering an excellent perspective to develop efficient and selective allosteric CK2 inhibitors.
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Affiliation(s)
- Benoît Bestgen
- 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, 69373 Lyon Cedex 8, France.,Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany.,Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Weiguang Seetoh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Chris Abell
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Rolf W Hartmann
- 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
| | - 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, 69373 Lyon Cedex 8, France
| | - Odile Filhol
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Claude Cochet
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - 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, 69373 Lyon Cedex 8, France
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany
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33
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Panicker RC, Chattopadhaya S, Coyne AG, Srinivasan R. Allosteric Small-Molecule Serine/Threonine Kinase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:253-278. [PMID: 31707707 DOI: 10.1007/978-981-13-8719-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deregulation of protein kinase activity has been linked to many diseases ranging from cancer to AIDS and neurodegenerative diseases. Not surprisingly, drugging the human kinome - the complete set of kinases encoded by the human genome - has been one of the major drug discovery pipelines. Majority of the approved clinical kinase inhibitors target the ATP binding site of kinases. However, the remarkable sequence and structural similarity of ATP binding pockets of kinases make selective inhibition of kinases a daunting task. To circumvent these issues, allosteric inhibitors that target sites other than the orthosteric ATP binding pocket have been developed. The structural diversity of the allosteric sites allows these inhibitors to have higher selectivity, lower toxicity and improved physiochemical properties and overcome drug resistance associated with the use of conventional kinase inhibitors. In this chapter, we will focus on the allosteric inhibitors of selected serine/threonine kinases, outline the benefits of using these inhibitors and discuss the challenges and future opportunities.
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Affiliation(s)
- Resmi C Panicker
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | | | - Anthony G Coyne
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China.
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Brear P, North A, Iegre J, Hadje Georgiou K, Lubin A, Carro L, Green W, Sore HF, Hyvönen M, Spring DR. Novel non-ATP competitive small molecules targeting the CK2 α/β interface. Bioorg Med Chem 2018; 26:3016-3020. [PMID: 29759799 PMCID: PMC6562204 DOI: 10.1016/j.bmc.2018.05.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/27/2022]
Abstract
Increased CK2 levels are prevalent in many cancers. Combined with the critical role CK2 plays in many cell-signaling pathways, this makes it a prime target for down regulation to fight tumour growth. Herein, we report a fragment-based approach to inhibiting the interaction between CK2α and CK2β at the α-β interface of the holoenzyme. A fragment, CAM187, with an IC50 of 44 μM and a molecular weight of only 257 gmol-1 has been identified as the most promising compound. Importantly, the lead fragment only bound at the interface and was not observed in the ATP binding site of the protein when co-crystallised with CK2α. The fragment-like molecules discovered in this study represent unique scaffolds to CK2 inhibition and leave room for further optimisation.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK
| | - Andrew North
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Kathy Hadje Georgiou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alexandra Lubin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Laura Carro
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - William Green
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Borysko P, Moroz YS, Vasylchenko OV, Hurmach VV, Starodubtseva A, Stefanishena N, Nesteruk K, Zozulya S, Kondratov IS, Grygorenko OO. Straightforward hit identification approach in fragment-based discovery of bromodomain-containing protein 4 (BRD4) inhibitors. Bioorg Med Chem 2018; 26:3399-3405. [DOI: 10.1016/j.bmc.2018.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
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Iegre J, Brear P, De Fusco C, Yoshida M, Mitchell SL, Rossmann M, Carro L, Sore HF, Hyvönen M, Spring DR. Second-generation CK2α inhibitors targeting the αD pocket. Chem Sci 2018; 9:3041-3049. [PMID: 29732088 PMCID: PMC5916021 DOI: 10.1039/c7sc05122k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/17/2018] [Indexed: 11/21/2022] Open
Abstract
CK2 is a critical cell cycle regulator that also promotes various anti-apoptotic mechanisms. Development of ATP-non-competitive inhibitors of CK2 is a very attractive strategy considering that the ATP binding site is highly conserved among other kinases. We have previously utilised a pocket outside the active site to develop a novel CK2 inhibitor, CAM4066. Whilst CAM4066 bound to this new pocket it was also interacting with the ATP site: herein, we describe an example of a CK2α inhibitor that binds completely outside the active site. This second generation αD-site binding inhibitor, compound CAM4712 (IC50 = 7 μM, GI50 = 10.0 ± 3.6 μM), has numerous advantages over the previously reported CAM4066, including a reduction in the number of rotatable bonds, the absence of amide groups susceptible to the action of proteases and improved cellular permeability. Unlike with CAM4066, there was no need to facilitate cellular uptake by making a prodrug. Moreover, CAM4712 displayed no drop off between its ability to inhibit the kinase in vitro (IC50) and the ability to inhibit cell proliferation (GI50).
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
| | - Paul Brear
- Department of Biochemistry , University of Cambridge , CB2 1GA , Cambridge , UK .
| | - Claudia De Fusco
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
- Structure Biophysics & FBLG , Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Masao Yoshida
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
- R&D Division , Daiichi Sankyo Co., Ltd. , 1-2-58, Hiromachi, Shinagawa-ku , Tokyo 140-8710 , Japan
| | - Sophie L Mitchell
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
| | - Maxim Rossmann
- Department of Biochemistry , University of Cambridge , CB2 1GA , Cambridge , UK .
| | - Laura Carro
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , CB2 1GA , Cambridge , UK .
| | - David R Spring
- Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK .
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Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies. Int J Mol Sci 2018; 19:ijms19010111. [PMID: 29301250 PMCID: PMC5796060 DOI: 10.3390/ijms19010111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022] Open
Abstract
Protein kinase is a novel therapeutic target for human diseases. The off-target and side effects of ATP-competitive inhibitors preclude them from the clinically relevant drugs. The compounds targeting the druggable allosteric sites outside the highly conversed ATP binding pocket have been identified as promising alternatives to overcome current barriers of ATP-competitive inhibitors. By simultaneously interacting with the αD region (new allosteric site) and sub-ATP binding pocket, the attractive compound CAM4066 was named as allosteric inhibitor of CK2α. It has been demonstrated that the rigid linker and non-ionizable substituted fragment resulted in significant decreased inhibitory activities of compounds. The molecular dynamics simulations and energy analysis revealed that the appropriate coupling between the linker and pharmacophore fragments were essential for binding of CAM4066 with CK2α. The lower flexible linker of compound 21 lost the capability of coupling fragments A and B to αD region and positive area, respectively, whereas the methyl benzoate of fragment B induced the re-orientated Pre-CAM4066 with the inappropriate polar interactions. Most importantly, the match between the optimized linker and pharmacophore fragments is the challenging work of fragment-linking based drug design. These results provide rational clues to further structural modification and development of highly potent allosteric inhibitors of CK2.
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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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