1
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Al-Qadhi MA, Yahya TAA, El-Nassan HB. Recent Advances in the Discovery of CK2 Inhibitors. ACS OMEGA 2024; 9:20702-20719. [PMID: 38764653 PMCID: PMC11097362 DOI: 10.1021/acsomega.3c10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
CK2 is a vital enzyme that phosphorylates a large number of substrates and thereby controls many processes in the body. Its upregulation was reported in many cancer types. Inhibitors of CK2 might have anticancer activity, and two compounds are currently under clinical trials. However, both compounds are ATP-competitive inhibitors that may have off-target side effects. The development of allosteric and dual inhibitors can overcome this drawback. These inhibitors showed higher selectivity and specificity for the CK2 enzyme compared to the ATP-competitive inhibitors. The present review summarizes the efforts exerted in the last five years in the design of CK2 inhibitors.
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Affiliation(s)
- Mustafa A. Al-Qadhi
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a, Yemen
| | - Tawfeek A. A. Yahya
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a,Yemen
| | - Hala B. El-Nassan
- Pharmaceutical
Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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2
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Iegre J, Krajcovicova S, Gunnarsson A, Wissler L, Käck H, Luchniak A, Tångefjord S, Narjes F, Spring DR. A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction. Chem Sci 2023; 14:10800-10805. [PMID: 37829032 PMCID: PMC10566475 DOI: 10.1039/d3sc04083f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
The disruption of the protein-protein interaction (PPI) between Nrf2 and Keap1 is an attractive strategy to counteract the oxidative stress that characterises a variety of severe diseases. Peptides represent a complementary approach to small molecules for the inhibition of this therapeutically important PPI. However, due to their polar nature and the negative net charge required for binding to Keap1, the peptides reported to date exhibit either mid-micromolar activity or are inactive in cells. Herein, we present a two-component peptide stapling strategy to rapidly access a variety of constrained and functionalised peptides that target the Nrf2/Keap1 PPI. The most promising peptide, P8-H containing a fatty acid tag, binds to Keap1 with nanomolar affinity and is effective at inducing transcription of ARE genes in a human lung epithelial cell line at sub-micromolar concentration. Furthermore, crystallography of the peptide in complex with Keap1 yielded a high resolution X-ray structure, adding to the toolbox of structures available to develop cell-permeable peptidomimetic inhibitors.
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Affiliation(s)
- Jessica Iegre
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
| | - Sona Krajcovicova
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
- Department of Organic Chemistry, Palacky University Olomouc Tr. 17. Listopadu 12 77900 Olomouc Czech Republic
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Lisa Wissler
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Anna Luchniak
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Stefan Tångefjord
- BioScience, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - David R Spring
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
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3
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Walther R, Westermann LM, Carmali S, Jackson SE, Brötz-Oesterhelt H, Spring DR. Identification of macrocyclic peptides which activate bacterial cylindrical proteases. RSC Med Chem 2023; 14:1186-1191. [PMID: 37360394 PMCID: PMC10285738 DOI: 10.1039/d3md00136a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
The caseinolytic protease complex ClpXP is an important house-keeping enzyme in prokaryotes charged with the removal and degradation of misfolded and aggregated proteins and performing regulatory proteolysis. Dysregulation of its function, particularly by inhibition or allosteric activation of the proteolytic core ClpP, has proven to be a promising strategy to reduce virulence and eradicate persistent bacterial infections. Here, we report a rational drug-design approach to identify macrocyclic peptides which increase proteolysis by ClpP. This work expands the understanding of ClpP dynamics and sheds light on the conformational control exerted by its binding partner, the chaperone ClpX, by means of a chemical approach. The identified macrocyclic peptide ligands may, in the future, serve as a starting point for the development of ClpP activators for antibacterial applications.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Linda M Westermann
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast BT9 7BL Belfast UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence Controlling Microbes to Fight Infections Germany
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
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4
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Chen Y, Wang Y, Wang J, Zhou Z, Cao S, Zhang J. Strategies of Targeting CK2 in Drug Discovery: Challenges, Opportunities, and Emerging Prospects. J Med Chem 2023; 66:2257-2281. [PMID: 36745746 DOI: 10.1021/acs.jmedchem.2c01523] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CK2 (casein kinase 2) is a serine/threonine protein kinase that is ubiquitous in eukaryotic cells and plays important roles in a variety of cellular functions, including cell growth, apoptosis, circadian rhythms, DNA damage repair, transcription, and translation. CK2 is involved in cancer pathogenesis and the occurrence of many diseases. Therefore, targeting CK2 is a promising therapeutic strategy. Although many CK2-specific small-molecule inhibitors have been developed, only CX-4945 has progressed to clinical trials. In recent years, novel CK2 inhibitors have gradually become a research hotspot, which is expected to overcome the limitations of traditional inhibitors. Herein, we summarize the structure, biological functions, and disease relevance of CK2 and emphatically analyze the structure-activity relationship (SAR) and binding modes of small-molecule CK2 inhibitors. We also discuss the latest progress of novel strategies, providing insights into new drugs targeting CK2 for clinical practice.
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Affiliation(s)
- Yijia Chen
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuxi Wang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Tianfu Jincheng Laboratory, Chengdu, Sichuan 610041, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Zhilan Zhou
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shu Cao
- West China School of Stomatology Sichuan University, Chengdu, Sichuan 610064, China
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Tianfu Jincheng Laboratory, Chengdu, Sichuan 610041, China
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5
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Ikeda A, Tsuyuguchi M, Kitagawa D, Sawa M, Nakamura S, Nakanishi I, Kinoshita T. Bivalent binding mode of an amino-pyrazole inhibitor indicates the potentials for CK2α1-selective inhibitors. Biochem Biophys Res Commun 2022; 630:30-35. [PMID: 36130444 DOI: 10.1016/j.bbrc.2022.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Casein kinase 2 (CK2) is a vital protein kinase that consists of two catalytic subunits (CK2α1 and/or CK2α2) and two regulatory subunits (CK2β). CK2α1 is a drug target for nephritis and cancers, while CK2α2 is a serious off-target because its inhibition causes testicular toxicity. High similarity between the isozymes CK2α1 and CK2α2 make it difficult to design CK2α1-specific inhibitors. Herein, the crystal structures of CK2α1 and CK2α2 complexed with a 3-amino-pyrazole inhibitor revealed the remarkable differences in the protein-inhibitor interaction modes. This inhibitor bound to the ATP binding sites of both isozymes in apparently distinct orientations. In addition, another molecule of this inhibitor bound to CK2α1, but not to CK2α2, at the CK2β protein-protein interface. Binding energy calculations and biochemical experiments suggested that this inhibitor possesses the conventional ATP-competitive characteristics with moderate allosteric function in a molecular glue mechanism. These results will assist the potential design of potent and selective CK2α1 inhibitors.
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Affiliation(s)
- Asaka Ikeda
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan
| | | | | | - Shinya Nakamura
- Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan.
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6
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Atkinson EL, Iegre J, D'Amore C, Brear P, Salvi M, Hyvönen M, Spring DR. Development of small cyclic peptides targeting the CK2α/β interface. Chem Commun (Camb) 2022; 58:4791-4794. [PMID: 35343996 PMCID: PMC9004346 DOI: 10.1039/d2cc00707j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022]
Abstract
In this work, an iterative cycle of enzymatic assays, X-ray crystallography, molecular modelling and cellular assays were used to develop a functionalisable chemical probe for the CK2α/β PPI. The lead peptide, P8C9, successfully binds to CK2α at the PPI site, is easily synthesisable and functionalisable, highly stable in serum and small enough to accommodate further optimisation.
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Affiliation(s)
- 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.
| | - Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1GA, Cambridge, UK.
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
| | - 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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Buyanova M, Pei D. Targeting intracellular protein-protein interactions with macrocyclic peptides. Trends Pharmacol Sci 2022; 43:234-248. [PMID: 34911657 PMCID: PMC8840965 DOI: 10.1016/j.tips.2021.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for traditional drug modalities. Macrocyclic peptides (MPs) prove highly effective PPI inhibitors in vitro and can be rapidly discovered against PPI targets by rational design or screening combinatorial libraries but are generally impermeable to the cell membrane. Recent advances in MP science and technology are allowing for the development of 'drug-like' MPs that potently and specifically modulate intracellular PPI targets in cell culture and animal models. In this review, we highlight recent progress in generating cell-permeable MPs that enter the mammalian cell by passive diffusion, endocytosis followed by endosomal escape, or as-yet unknown mechanisms.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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8
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Tze-Yang Ng J, Tan YS. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. J Chem Theory Comput 2022; 18:1969-1981. [PMID: 35175753 DOI: 10.1021/acs.jctc.1c01177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification and characterization of binding sites is a critical component of structure-based drug design (SBDD). Probe-based/cosolvent molecular dynamics (MD) methods that allow for protein flexibility have been developed to predict ligand binding sites. However, cryptic pockets that appear only upon ligand binding and occluded binding sites with no access to the solvent pose significant challenges to these methods. Here, we report the development of accelerated ligand-mapping MD (aLMMD), which combines accelerated MD with LMMD, for the detection of these challenging binding sites. The method was validated on five proteins with what we term "recalcitrant" cryptic pockets, which are deeply buried pockets that require extensive movement of the protein backbone to expose, and three proteins with occluded binding sites. In all the cases, aLMMD was able to detect and sample the binding sites. Our results suggest that aLMMD could be used as a general approach for the detection of such elusive binding sites in protein targets, thus providing valuable information for SBDD.
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Affiliation(s)
- Justin Tze-Yang Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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9
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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10
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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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11
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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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12
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Borgo C, D'Amore C, Cesaro L, Sarno S, Pinna LA, Ruzzene M, Salvi M. How can a traffic light properly work if it is always green? The paradox of CK2 signaling. Crit Rev Biochem Mol Biol 2021; 56:321-359. [PMID: 33843388 DOI: 10.1080/10409238.2021.1908951] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CK2 is a constitutively active protein kinase that assuring a constant level of phosphorylation to its numerous substrates supports many of the most important biological functions. Nevertheless, its activity has to be controlled and adjusted in order to cope with the varying needs of a cell, and several examples of a fine-tune regulation of its activity have been described. More importantly, aberrant regulation of this enzyme may have pathological consequences, e.g. in cancer, chronic inflammation, neurodegeneration, and viral infection. Our review aims at summarizing our current knowledge about CK2 regulation. In the first part, we have considered the most important stimuli shown to affect protein kinase CK2 activity/expression. In the second part, we focus on the molecular mechanisms by which CK2 can be regulated, discussing controversial aspects and future perspectives.
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Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neurosciences, Padova, Italy
| | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neurosciences, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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13
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Wang H, Dawber RS, Zhang P, Walko M, Wilson AJ, Wang X. Peptide-based inhibitors of protein-protein interactions: biophysical, structural and cellular consequences of introducing a constraint. Chem Sci 2021; 12:5977-5993. [PMID: 33995995 PMCID: PMC8098664 DOI: 10.1039/d1sc00165e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/07/2021] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions (PPIs) are implicated in the majority of cellular processes by enabling and regulating the function of individual proteins. Thus, PPIs represent high-value, but challenging targets for therapeutic intervention. The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices. The approach can confer significant benefits including enhanced affinity, stability and cellular penetration and is ingrained in the premise that pre-organization simultaneously pays the entropic cost of binding, prevents a peptide from adopting a protease compliant β-strand conformation and shields the hydrophilic amides from the hydrophobic membrane. This conceptual blueprint for the empirical design of peptide-based PPI inhibitors is an exciting and potentially lucrative way to effect successful PPI inhibitor drug-discovery. However, a plethora of more subtle effects may arise from the introduction of a constraint that include changes to binding dynamics, the mode of recognition and molecular properties. In this review, we summarise the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour across a range of constraining chemistries and targets, to highlight the tremendous success that has been achieved with constrained peptides alongside emerging design opportunities and challenges.
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Affiliation(s)
- Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Nanjing 210023 Jiangsu China
| | - Robert S Dawber
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Peiyu Zhang
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Martin Walko
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- Department of Applied Chemistry and Engineering, University of Science and Technology of China Hefei 230026 China
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14
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D'Amore C, Borgo C, Sarno S, Salvi M. Role of CK2 inhibitor CX-4945 in anti-cancer combination therapy - potential clinical relevance. Cell Oncol (Dordr) 2020; 43:1003-1016. [PMID: 33052585 PMCID: PMC7717057 DOI: 10.1007/s13402-020-00566-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Protein kinase CK2 inhibition has long been considered as an attractive anti-cancer strategy based on the following considerations: CK2 is a pro-survival kinase, it is frequently over-expressed in human tumours and its over-expression correlates with a worse prognosis. Preclinical evidence strongly supports the feasibility of this target and, although dozens of CK2 inhibitors have been described in the literature so far, CX-4945 (silmitasertib) was the first that entered into clinical trials for the treatment of both human haematological and solid tumours. However, kinase inhibitor monotherapies turned out to be effective only in a limited number of malignancies, probably due to the multifaceted causes that underlie them, supporting the emerging view that multi-targeted approaches to treat human tumours could be more effective. CONCLUSIONS In this review, we will address combined anti-cancer therapeutic strategies described so far which involve the use of CX-4945. Data from preclinical studies clearly show the ability of CX-4945 to synergistically cooperate with different classes of anti-neoplastic agents, thereby contributing to an orchestrated anti-tumour action against multiple targets. Overall, these promising outcomes support the translation of CX-4945 combined therapies into clinical anti-cancer applications.
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Affiliation(s)
- Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
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15
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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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16
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Tan YS, Verma CS. Straightforward Incorporation of Multiple Ligand Types into Molecular Dynamics Simulations for Efficient Binding Site Detection and Characterization. J Chem Theory Comput 2020; 16:6633-6644. [PMID: 32810406 DOI: 10.1021/acs.jctc.0c00405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Binding site identification and characterization is an important initial step in structure-based drug design. To account for the effects of protein flexibility and solvation, several cosolvent molecular dynamics (MD) simulation methods that incorporate small organic molecules into the protein's solvent box to probe for binding sites have been developed. However, most of these methods are highly inefficient, as they allow for the use of only one probe type at a time, which means that multiple sets of simulations have to be performed to map different types of binding sites. The high probe concentrations used in some of these methods also necessitate the use of artificial repulsive forces to prevent the probes from aggregating. Here, we present multiple-ligand-mapping MD (mLMMD), a method that incorporates multiple types of probes for simultaneous and efficient mapping of different types of binding sites without the need for introduction of artificial forces that may cause unintended mapping artifacts. We validate the method on a diverse set of 10 proteins and show that the mLMMD probes are able to reliably identify hydrophobic, hydrogen-bonding, charged, and cryptic binding sites in all of the test cases. Our results also highlight the potential utility of mLMMD for virtual screening and rational drug design.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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17
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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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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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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20
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Walsh SJ, Iegre J, Seki H, Bargh JD, Sore HF, Parker JS, Carroll JS, Spring DR. General dual functionalisation of biomacromolecules via a cysteine bridging strategy. Org Biomol Chem 2020; 18:4224-4230. [PMID: 32432632 DOI: 10.1039/d0ob00907e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-selective modification of peptides and proteins has resulted in the development of a host of novel tools for the study of cellular systems or the synthesis of enhanced biotherapeutics. There is a need for useful methodologies that enable site-selective modification of native peptides or proteins, which is even more prevalent when modification of the biomolecule with multiple payloads is desired. Herein, we report the development of a novel dual functional divinylpyrimidine (dfDVP) platform that enables robust and modular modification of peptides, antibody fragments and antibodies. These biomacromolecules could be easily functionalised with a range of functional payloads (e.g. fluorescent dyes, cytotoxic warheads or cell-penetrating tags). Importantly, the dual functionalised peptides and antibodies demonstrated exquisite bioactivity in a range of in vitro cellular assays, showcasing the enhanced utility of these bioactive conjugates.
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Affiliation(s)
- Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Hikaru Seki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Jonathan D Bargh
- 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.
| | - Jeremy S Parker
- Early Chemical Development, Pharmaceutical Development, R&D, AstraZeneca, Macclesfield, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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21
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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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22
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Pietsch M, Viht K, Schnitzler A, Ekambaram R, Steinkrüger M, Enkvist E, Nienberg C, Nickelsen A, Lauwers M, Jose J, Uri A, Niefind K. Unexpected CK2β-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Bioorg Chem 2020; 96:103608. [PMID: 32058103 DOI: 10.1016/j.bioorg.2020.103608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/11/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023]
Abstract
Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2α) attached to a homodimer of regulatory subunits (CK2β), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (Ki = 84 pM). In a crystal structure of ARC-3140 in complex with CK2α, three copies of the inhibitor are visible, one of them at the CK2β interface of CK2α. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2α/CK2β interaction. A structural inspection revealed that ARC-3140, unlike CK2β antagonists described so far, interferes with both sub-interfaces of the bipartite CK2α/CK2β interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2α2β2 holoenzyme.
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Affiliation(s)
- Markus Pietsch
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Alexander Schnitzler
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Ramesh Ekambaram
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Michaela Steinkrüger
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Christian Nienberg
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Miriam Lauwers
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
| | - Karsten Niefind
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany.
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23
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Kufareva I, Bestgen B, Brear P, Prudent R, Laudet B, Moucadel V, Ettaoussi M, Sautel CF, Krimm I, Engel M, Filhol O, Borgne ML, Lomberget T, Cochet C, Abagyan R. Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Sci Rep 2019; 9:15893. [PMID: 31685885 PMCID: PMC6828666 DOI: 10.1038/s41598-019-52141-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/07/2019] [Indexed: 01/06/2023] Open
Abstract
CK2 is a constitutively active protein kinase overexpressed in numerous malignancies. Interaction between CK2α and CK2β subunits is essential for substrate selectivity. The CK2α/CK2β interface has been previously targeted by peptides to achieve functional effects; however, no small molecules modulators were identified due to pocket flexibility and open shape. Here we generated numerous plausible conformations of the interface using the fumigation modeling protocol, and virtually screened a compound library to discover compound 1 that suppressed CK2α/CK2β interaction in vitro and inhibited CK2 in a substrate-selective manner. Orthogonal SPR, crystallography, and NMR experiments demonstrated that 4 and 6, improved analogs of 1, bind to CK2α as predicted. Both inhibitors alter CK2 activity in cells through inhibition of CK2 holoenzyme formation. Treatment with 6 suppressed MDA-MB231 triple negative breast cancer cell growth and induced apoptosis. Altogether, our findings exemplify an innovative computational-experimental approach and identify novel non-peptidic inhibitors of CK2 subunit interface disclosing substrate-selective functional effects.
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Affiliation(s)
- Irina Kufareva
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, 92093, USA
| | - Benoit Bestgen
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, 8 avenue Rockefeller, F-69373, Lyon, cedex 8, France.,Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany.,Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.,Ecrins Therapeutics, 5 Avenue du Grand Sablon, 38700, La Tronche, France
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Renaud Prudent
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.,Cellipse MINATEC, 7 Parvis Louis Néel, 38000, Grenoble, cedex 9, France
| | - Béatrice Laudet
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.,CHU Toulouse, Emergency Department, F-31000, Toulouse, France
| | - Virginie Moucadel
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.,BioMérieux SA, Centre Christophe Mérieux, 5 rue des Berges, 38024, Grenoble, cedex 1, France
| | - Mohamed Ettaoussi
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, 8 avenue Rockefeller, F-69373, Lyon, cedex 8, France
| | - Celine F Sautel
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.,DERMADIS, 218 avenue Marie Curie, 74160, Archamps, 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
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Odile Filhol
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France
| | - Marc Le Borgne
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, 8 avenue Rockefeller, F-69373, Lyon, cedex 8, France
| | - Thierry Lomberget
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, 8 avenue Rockefeller, F-69373, Lyon, cedex 8, France
| | - Claude Cochet
- Univ. Grenoble Alpes, Inserm U1036, CEA, BCI Laboratory, IRIG, F-38000, Grenoble, France.
| | - Ruben Abagyan
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, 92093, USA.
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24
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Ong BX, Yoo Y, Han MG, Park JB, Choi MK, Choi Y, Shin JS, Bahn YS, Cho HS. Structural analysis of fungal pathogenicity-related casein kinase α subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans. Sci Rep 2019; 9:14398. [PMID: 31591414 PMCID: PMC6779870 DOI: 10.1038/s41598-019-50678-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/16/2019] [Indexed: 12/28/2022] Open
Abstract
CK2α is a constitutively active and highly conserved serine/threonine protein kinase that is involved in the regulation of key cellular metabolic pathways and associated with a variety of tumours and cancers. The most well-known CK2α inhibitor is the human clinical trial candidate CX-4945, which has recently shown to exhibit not only anti-cancer, but also anti-fungal properties. This prompted us to work on the CK2α orthologue, Cka1, from the pathogenic fungus Cryptococcus neoformans, which causes life-threatening systemic cryptococcosis and meningoencephalitis mainly in immunocompromised individuals. At present, treatment of cryptococcosis remains a challenge due to limited anti-cryptococcal therapeutic strategies. Hence, expanding therapeutic options for the treatment of the disease is highly clinically relevant. Herein, we report the structures of Cka1-AMPPNP-Mg2+ (2.40 Å) and Cka1-CX-4945 (2.09 Å). Structural comparisons of Cka1-AMPPNP-Mg2+ with other orthologues revealed the dynamic architecture of the N-lobe across species. This may explain for the difference in binding affinities and deviations in protein-inhibitor interactions between Cka1-CX-4945 and human CK2α-CX-4945. Supporting it, in vitro kinase assay demonstrated that CX-4945 inhibited human CK2α much more efficiently than Cka1. Our results provide structural insights into the design of more selective inhibitors against Cka1.
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Affiliation(s)
- Belinda X Ong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Youngki Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Myeong Gil Han
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jun Bae Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Myung Kyung Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yeseul Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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Rational drug-design approach supported with thermodynamic studies - a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Sci Rep 2019; 9:11018. [PMID: 31358826 PMCID: PMC6662822 DOI: 10.1038/s41598-019-47404-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022] Open
Abstract
Numerous inhibitors of protein kinases act on the basis of competition, targeting the ATP binding site. In this work, we present a procedure of rational design of a bi-substrate inhibitor, complemented with biophysical assays. The inhibitors of this type are commonly engineered by combining ligands carrying an ATP-like part with a peptide or peptide-mimicking fragment that determines specificity. Approach presented in this paper led to generation of a specific system for independent screening for efficient ligands and peptides, by means of thermodynamic measurements, that assessed the ability of the identified ligand and peptide to combine into a bi-substrate inhibitor. The catalytic subunit of human protein kinase CK2 was used as the model target. Peptide sequence was optimized using peptide libraries [KGDE]-[DE]-[ST]-[DE]3-4-NH2, originated from the consensus CK2 sequence. We identified KESEEE-NH2 peptide as the most promising one, whose binding affinity is substantially higher than that of the reference RRRDDDSDDD peptide. We assessed its potency to form an efficient bi-substrate inhibitor using tetrabromobenzotriazole (TBBt) as the model ATP-competitive inhibitor. The formation of ternary complex was monitored using Differential Scanning Fluorimetry (DSF), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC).
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