1
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Diao AJ, Su BG, Vos SM. Pause Patrol: Negative Elongation Factor's Role in Promoter-Proximal Pausing and Beyond. J Mol Biol 2024:168779. [PMID: 39241983 DOI: 10.1016/j.jmb.2024.168779] [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: 06/28/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
RNA polymerase (Pol) II is highly regulated to ensure appropriate gene expression. Early transcription elongation is associated with transient pausing of RNA Pol II in the promoter-proximal region. In multicellular organisms, this pausing is stabilized by the association of transcription elongation factors DRB-sensitivity inducing factor (DSIF) and Negative Elongation Factor (NELF). DSIF is a broadly conserved transcription elongation factor whereas NELF is mostly restricted to the metazoan lineage. Mounting evidence suggests that NELF association with RNA Pol II serves as checkpoint for either release into rapid and productive transcription elongation or premature termination at promoter-proximal pause sites. Here we summarize NELF's roles in promoter-proximal pausing, transcription termination, DNA repair, and signaling based on decades of cell biological, biochemical, and structural work and describe areas for future research.
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Affiliation(s)
- Annette J Diao
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States
| | - Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States; Howard Hughes Medical Institute, United States.
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2
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González-Arzola K. The nucleolus: Coordinating stress response and genomic stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195029. [PMID: 38642633 DOI: 10.1016/j.bbagrm.2024.195029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain.
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3
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Nishiwaki K, Nakatani S, Nakamura S, Yoshioka K, Nakagawa E, Tsuyuguchi M, Kinoshita T, Nakanishi I. Enhanced inhibitory activity of compounds containing purine scaffolds compared to protein kinase CK2α considering crystalline water. RSC Med Chem 2024; 15:1274-1282. [PMID: 38665825 PMCID: PMC11042117 DOI: 10.1039/d3md00755c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/21/2024] [Indexed: 04/28/2024] Open
Abstract
We recently reported novel purine-based CK2α inhibitors using the solvent ordering-based method as virtual screening. Among these, the X-ray crystal structure of a complex with CK2α was determined. The results showed that the crystalline water molecules observed in many previously reported complex structures of CK2α and its inhibitors had been eliminated. We then proposed a structure-based drug design. Since the removal of water molecules would be detrimental to inhibitor binding, new groups of compounds were designed by changing the position of the carboxy group located at the point where a water molecule would be present so as not to eliminate it. Compounds with (E)-2-carboxyethenyl and 3-carboxyphenyl substituted at the 2-position on the purine scaffold showed much higher inhibitory potency than 4-carboxyphenyl derivatives. Furthermore, in the presence of a 4-fluorophenyl group at the 9-position on the purine scaffold, the inhibitory activity of the 3-carboxyphenyl derivative against CK2α was 0.18 μM, a 167-fold improvement compared to the 4-carboxyphenyl derivative. The strategy of leaving crystalline water can significantly increase inhibitory activity.
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Affiliation(s)
- Keiji Nishiwaki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
| | - Shiori Nakatani
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
| | - Shinya Nakamura
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
| | - Kenji Yoshioka
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
| | - Eri Nakagawa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
- Antiaging Center, Kindai University 3-4-1 Kowakae Higashiosaka Osaka 577-8502 Japan
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4
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de Oliveira Souza JE, Gomes SMR, Lima AKC, de Souza Brito AC, Da-Silva SAG, de Carvalho Santos Lopes AH, Silva-Neto MAC, Atella GC, Dutra PML. Influence of CK2 protein kinase activity on the interaction between Trypanosoma cruzi and its vertebrate and invertebrate hosts. Parasitol Res 2024; 123:80. [PMID: 38163833 DOI: 10.1007/s00436-023-08085-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Chagas disease, endemic from Latin America, is caused by Trypanosoma cruzi and is transmitted by triatomine feces. This parasite undergoes complex morphological changes through its life cycle, promoted by significant changes in signal transduction pathways. The activity of protein kinase CK2 has been described in trypanosomatids. Using a specific peptide and radioactive ATP, we identified CK2 activity on the cellular surface and the cytoplasmic content in Trypanosoma cruzi, apart from the secreted form. Dephosphorylated casein promoted an increase of 48% in the secreted CK2 activity. Total extract of peritoneal macrophages from BALB/c and inactivated human serum promoted an increase of 67% and 36%, respectively, in this activity. The protein secreted by parasites was purified by HPLC and had shown compatibility with the catalytic subunit of mammalian CK2. Incubation of the parasites with CK2 inhibitors, added to the culture medium, prevented their growth. The opposite was observed when CK2 activators were used. Results of interaction between Trypanosoma cruzi and the gut of the vector have revealed that, in the presence of CK2 inhibitors, there is a reduction in the association rate. A similar inhibition profile was seen in the Trypanosoma cruzi-macrophages interaction, confirming the importance of this enzyme in the life cycle of this protozoan.
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Affiliation(s)
- Joyce Eliza de Oliveira Souza
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Shayane Martins Rodrigues Gomes
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Karina Castro Lima
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andréia Carolinne de Souza Brito
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Silvia Amaral Gonçalves Da-Silva
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Geórgia Correa Atella
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Maria Lourenço Dutra
- Discipline of Parasitology, Department of Microbiology, Immunology and Parasitology (FCM), State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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5
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Patel S, Vyas VK, Sharma M, Ghate M. Structure-guided discovery of adenosine triphosphate-competitive casein kinase 2 inhibitors. Future Med Chem 2023; 15:987-1014. [PMID: 37307219 DOI: 10.4155/fmc-2023-0005] [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] [Indexed: 06/14/2023] Open
Abstract
Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic serine-threonine kinase. CK2 has been identified as a potential drug target for the treatment of cancer and related disorders. Several adenosine triphosphate-competitive CK2 inhibitors have been identified and have progressed at different levels of clinical trials. This review presents details of CK2 protein, structural insights into adenosine triphosphate binding pocket, current clinical trial candidates and their analogues. Further, it includes the emerging structure-based drug design approaches, chemistry, structure-activity relationship and biological screening of potent and selective CK2 inhibitors. The authors tabulated the details of CK2 co-crystal structures because these co-crystal structures facilitated the structure-guided discovery of CK2 inhibitors. The narrow hinge pocket compared with related kinases provides useful insights into the discovery of CK2 inhibitors.
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Affiliation(s)
- Shivani Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manjunath Ghate
- School of Pharmacy, National Forensic Science University, Gandhinagar, Gujarat, 382007, India
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6
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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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7
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Nishiwaki K, Nakamura S, Yoshioka K, Nakagawa E, Nakatani S, Tsuyuguchi M, Kinoshita T, Nakanishi I. Design, Synthesis and Structure-Activity Relationship Studies of Protein Kinase CK2 Inhibitors Containing a Purine Scaffold. Chem Pharm Bull (Tokyo) 2023; 71:558-565. [PMID: 37394605 DOI: 10.1248/cpb.c23-00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein kinase CK2 (CK2) is involved in the suppression of gene expression, protein synthesis, cell proliferation, and apoptosis, thus making it a target protein for the development of therapeutics toward cancer, nephritis, and coronavirus disease 2019. Using the solvent dipole ordering-based method for virtual screening, we identified and designed new candidate CK2α inhibitors containing purine scaffolds. Virtual docking experiments supported by experimental structure-activity relationship studies identified the importance of the 4-carboxyphenyl group at the 2-position, a carboxamide group at the 6-position, and an electron-rich phenyl group at the 9-position of the purine scaffold. Docking studies based on the crystal structures of CK2α and inhibitor (PDBID: 5B0X) successfully predicted the binding mode of 4-(6-carbamoyl-8-oxo-9-phenyl-8,9-dihydro-7H-purin-2-yl) benzoic acid (11), and the results were used to design stronger small molecule targets for CK2α inhibition. Interaction energy analysis suggested that 11 bound around the hinge region without the water molecule (W1) near Trp176 and Glu81 that is frequently reported in crystal structures of CK2α inhibitor complexes. X-ray crystallographic data for 11 bound to CK2α was in very good agreement with the docking experiments, and consistent with activity. From the structure-activity relationship (SAR) studies presented here, 4-(6-Carbamoyl-9-(4-(dimethylamino)phenyl)-8-oxo-8,9-dihydro-7H-purin-2-yl) benzoic acid (12) was identified as an improved active purine-based CK2α inhibitor with an IC50 of 4.3 µM. These active compounds with an unusual binding mode are expected to inspire new CK2α inhibitors and the development of therapeutics targeting CK2 inhibition.
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Affiliation(s)
- Keiji Nishiwaki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
| | - Shinya Nakamura
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
| | - Kenji Yoshioka
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
| | - Eri Nakagawa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
| | - Shiori Nakatani
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
| | | | | | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University
- Antiaging Center, Kindai University
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8
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Winiewska-Szajewska M, Czapinska H, Kaus-Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J. Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes. Sci Rep 2022; 12:18964. [PMID: 36347916 PMCID: PMC9641685 DOI: 10.1038/s41598-022-23611-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
CK2 is a member of the CMGC group of eukaryotic protein kinases and a cancer drug target. It can be efficiently inhibited by halogenated benzotriazoles and benzimidazoles. Depending on the scaffold, substitution pattern, and pH, these compounds are either neutral or anionic. Their binding poses are dictated by a hydrophobic effect (desolvation) and a tug of war between a salt bridge/hydrogen bond (to K68) and halogen bonding (to E114 and V116 backbone oxygens). Here, we test the idea that binding poses might be controllable by pH for ligands with near-neutral pKa, using the conditionally anionic 5,6-DBBt and constitutively anionic TBBt as our models. We characterize the binding by low-volume Differential Scanning Fluorimetry (nanoDSF), Isothermal Calorimetry (ITC), Hydrogen/Deuterium eXchange (HDX), and X-ray crystallography (MX). The data indicate that the ligand pose away from the hinge dominates for the entire tested pH range (5.5-8.5). The insensitivity of the binding mode to pH is attributed to the perturbation of ligand pKa upon binding that keeps it anionic in the ligand binding pocket at all tested pH values. However, a minor population of the ligand, detectable only by HDX, shifts towards the hinge in acidic conditions. Our findings demonstrate that electrostatic (ionic) interactions predominate over halogen bonding.
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Affiliation(s)
- Maria Winiewska-Szajewska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | - Honorata Czapinska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena Kaus-Drobek
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Fricke
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Kinga Mieczkowska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Michał Dadlez
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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9
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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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10
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Pucko EB, Ostrowski RP. Inhibiting CK2 among Promising Therapeutic Strategies for Gliomas and Several Other Neoplasms. Pharmaceutics 2022; 14:331. [PMID: 35214064 PMCID: PMC8877581 DOI: 10.3390/pharmaceutics14020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
In gliomas, casein kinase 2 (CK2) plays a dominant role in cell survival and tumour invasiveness and is upregulated in many brain tumours. Among CK2 inhibitors, benzimidazole and isothiourea derivatives hold a dominant position. While targeting glioma tumour cells, they show limited toxicity towards normal cells. Research in recent years has shown that these compounds can be suitable as components of combined therapies with hyperbaric oxygenation. Such a combination increases the susceptibility of glioma tumour cells to cell death via apoptosis. Moreover, researchers planning on using any other antiglioma investigational pharmaceutics may want to consider using these agents in combination with CK2 inhibitors. However, different compounds are not equally effective when in such combination. More research is needed to elucidate the mechanism of treatment and optimize the treatment regimen. In addition, the role of CK2 in gliomagenesis and maintenance seems to have been challenged recently, as some compounds structurally similar to CK2 inhibitors do not inhibit CK2 while still being effective at reducing glioma viability and invasion. Furthermore, some newly developed inhibitors specific for CK2 do not appear to have strong anticancer properties. Further experimental and clinical studies of these inhibitors and combined therapies are warranted.
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Affiliation(s)
| | - Robert P. Ostrowski
- Department of Experimental and Clinical Neuropathology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego St., 02-106 Warsaw, Poland;
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11
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Lorenz R, Wu J, Herberg FW, Taylor SS, Engh RA. Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics. Biochemistry 2021; 60:3470-3484. [PMID: 34370450 DOI: 10.1021/acs.biochem.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1984, Japanese researchers led by the biochemist Hiroyoshi Hidaka described the first synthetic protein kinase inhibitors based on an isoquinoline sulfonamide structure (Hidaka et al. Biochemistry, 1984 Oct 9; 23(21): 5036-41. doi: 10.1021/bi00316a032). These led to the first protein kinase inhibitor approved for medical use (fasudil), an inhibitor of the AGC subfamily Rho kinase. With potencies strong enough to compete against endogenous ATP, the isoquinoline compounds established the druggability of the ATP binding site. Crystal structures of their protein kinase complexes, including with cAMP-dependent protein kinase (PKA), showed interactions that, on the one hand, could mimic ATP but, on the other hand, could be optimized for high potency binding, kinase selectivity, and diversification away from adenosine. They also showed the flexibility of the glycine-rich loop, and PKA became a major prototype for crystallographic and nuclear magnetic resonance (NMR) studies of protein kinase mechanism and dynamic activity control. Since fasudil, more than 70 kinase inhibitors have been approved for clinical use, involving efforts that progressively have introduced new paradigms of data-driven drug discovery. Publicly available data alone comprise over 5000 protein kinase crystal structures and hundreds of thousands of binding data. Now, new methods, including artificial intelligence techniques and expansion of protein kinase targeting approaches, together with the expiration of patent protection for optimized inhibitor scaffolds, promise even greater advances in drug discovery. Looking back to the time of the first isoquinoline hinge binders brings the current state-of-the-art into stark contrast. Appropriately for this Perspective article, many of the milestone papers during this time were published in Biochemistry (now ACS Biochemistry).
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø 9012, Norway
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12
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Mohibi S, Zhang J, Chen M, Chen X. Mice Deficient in the RNA-Binding Protein Zfp871 Are Prone to Early Death and Steatohepatitis in Part through the p53-Mdm2 Axis. Mol Cancer Res 2021; 19:1751-1762. [PMID: 34257081 DOI: 10.1158/1541-7786.mcr-21-0239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/11/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
p53 transcription factor is activated upon exposure to various cellular stresses, leading to growth suppression. However, aberrant activation of p53 can lead to defects in embryonic development and other abnormalities. Here, we identified zinc finger protein Zfp871 as a p53 target gene. We showed that as an RNA-binding protein, Zfp871 binds to Mdm2 3'UTR and stabilizes Mdm2 mRNA, which in turn suppresses p53 expression through increased expression of Mdm2 E3 ubiquitin ligase. Consistently, Zfp871 deficiency increases p53 expression, leading to growth suppression in a p53-dependent manner. To determine the role of Zfp871 in the p53 pathway, we used Zfp871-deficient mouse model and found that Zfp871-null mice were prone to embryonic/pre-weaning lethality, which can be partially rescued by simultaneous deletion of Trp53. We also found that mice heterozygous for Zfp871 had a short lifespan and were susceptible to steatohepatitis but not to spontaneous tumors. To determine the underlying mechanism, RNA-seq analysis was performed and showed that an array of genes involved in development, lipid metabolism, and inflammation is regulated by Zfp871 in conjunction with p53. Taken together, we conclude that the Zfp871-Mdm2-p53 pathway plays a critical role in tumor-free survival and development. IMPLICATIONS: A fine equilibrium of p53 is required for preventing damaging effects of aberrant p53 expression. We identify the Zfp871-Mdm2-p53 pathway that plays a critical role in development of mice and steatohepatitis.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, California.
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13
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Garton CS, DeRose NK, Dominguez D, Turbi-Henderson ML, Lehr AL, Padilla AD, Twining SD, Casas S, Alozie CO, Gucwa AL, Elshaer MR, De Castro M. Synthesis and Antiproliferative Evaluation of 2-Deoxy- N-glycosylbenzotriazoles/imidazoles. Molecules 2021; 26:molecules26123742. [PMID: 34205324 PMCID: PMC8234545 DOI: 10.3390/molecules26123742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
A series of 2-deoxy-2-iodo-α-d-mannopyranosylbenzotriazoles was synthesized using the benzyl, 4,6-benzylidene and acetyl protected D-glucal in the presence of N-iodosuccinimide (NIS). Subsequent removal of the iodine at the C-2 position using tributyltin hydride under free radical conditions afforded the 2-deoxy-α-d-glucopyranosylbenzotriazoles in moderate to high yields. This method was extended to the preparation of substituted 2-deoxy-β-d-glucopyranosylimidazoles as well. The stereoselectivity of the addition reaction and the effect of the protecting group and temperature on anomer distribution of the benzotriazole series were also investigated. The anticancer properties of the newly synthesized compounds were evaluated in a series of viability studies using HeLa (human cervical adenocarcinoma), human breast and lung cancer cell lines. The N-[3,4,6-tri-O-benzyl-2-deoxy-α-d-glucopyranosyl]-1H-benzotriazole and the N-[3,4,6-tri-O-acetyl-2-deoxy-α-d-glucopyranosyl]-2H-benzotriazole were found to be the most potent cancer cell inhibitors at 20 µM concentrations across all four cell lines.
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Affiliation(s)
- Caleigh S. Garton
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Noelle K. DeRose
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Dylan Dominguez
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Maria L. Turbi-Henderson
- Department of Biology, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (M.L.T.-H.); (A.D.P.); (A.L.G.)
| | - Ashley L. Lehr
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Ashley D. Padilla
- Department of Biology, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (M.L.T.-H.); (A.D.P.); (A.L.G.)
| | - Scott D. Twining
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Stephanie Casas
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Chidozie O. Alozie
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
| | - Azad L. Gucwa
- Department of Biology, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (M.L.T.-H.); (A.D.P.); (A.L.G.)
| | - Mohammed R. Elshaer
- Department of Chemistry, Biochemistry and Physics, Fairleigh Dickinson University, Madison, NJ 07940, USA
- Correspondence: (M.R.E.); (M.D.C.)
| | - Michael De Castro
- Department of Chemistry, Farmingdale State College-SUNY, 2350 Broadhollow Rd, Farmingdale, NY 11735, USA; (C.S.G.); (N.K.D.); (D.D.); (A.L.L.); (S.D.T.); (S.C.); (C.O.A.)
- Correspondence: (M.R.E.); (M.D.C.)
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14
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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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15
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Winiewska-Szajewska M, Maciejewska AM, Speina E, Poznański J, Paprocki D. Synthesis of Novel Halogenated Heterocycles Based on o-Phenylenediamine and Their Interactions with the Catalytic Subunit of Protein Kinase CK2. Molecules 2021; 26:molecules26113163. [PMID: 34070615 PMCID: PMC8198750 DOI: 10.3390/molecules26113163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 01/07/2023] Open
Abstract
Protein kinase CK2 is a highly pleiotropic protein kinase capable of phosphorylating hundreds of protein substrates. It is involved in numerous cellular functions, including cell viability, apoptosis, cell proliferation and survival, angiogenesis, or ER-stress response. As CK2 activity is found perturbed in many pathological states, including cancers, it becomes an attractive target for the pharma. A large number of low-mass ATP-competitive inhibitors have already been developed, the majority of them halogenated. We tested the binding of six series of halogenated heterocyclic ligands derived from the commercially available 4,5-dihalo-benzene-1,2-diamines. These ligand series were selected to enable the separation of the scaffold effect from the hydrophobic interactions attributed directly to the presence of halogen atoms. In silico molecular docking was initially applied to test the capability of each ligand for binding at the ATP-binding site of CK2. HPLC-derived ligand hydrophobicity data are compared with the binding affinity assessed by low-volume differential scanning fluorimetry (nanoDSF). We identified three promising ligand scaffolds, two of which have not yet been described as CK2 inhibitors but may lead to potent CK2 kinase inhibitors. The inhibitory activity against CK2α and toxicity against four reference cell lines have been determined for eight compounds identified as the most promising in nanoDSF assay.
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16
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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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17
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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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18
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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19
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Husain K, Williamson TT, Nelson N, Ghansah T. Protein kinase 2 (CK2): a potential regulator of immune cell development and function in cancer. Immunol Med 2020; 44:159-174. [PMID: 33164702 DOI: 10.1080/25785826.2020.1843267] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein kinase CK2, formally known as casein kinase II, is ubiquitously expressed and highly conserved serine/threonine or tyrosine kinase enzyme that regulates diverse signaling pathways responsible for cellular processes (i.e., cell proliferation and apoptosis) via interactions with over 500 known substrates. The enzyme's physiological interactions and cellular functions have been widely studied, most notably in the blood and solid malignancies. CK2 has intrinsic role in carcinogenesis as overexpression of CK2 subunits (α, α`, and β) and deregulation of its activity have been linked to various forms of cancers. CK2 also has extrinsic role in cancer stroma or in the tumor microenvironment (TME) including the immune cells. However, very few research studies have focused on extrinsic role of CK2 in regulating immune responses as a therapeutic alternative for cancer. The following review discusses CK2's regulation of key signaling events [Nuclear factor kappa B (NF-κB), Janus kinase/signal transducer and activators of transcription (JAK/STAT), Hypoxia inducible factor-1alpha (HIF-1α), Cyclooygenase-2 (COX-2), Extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK), Notch, Protein kinase B/AKT, Ikaros and Wnt] that can influence the development and function of immune cells in cancer. Potential clinical trials using potent CK2 inhibitors will facilitate and improve the treatment of human malignancies.
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Affiliation(s)
- Kazim Husain
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Tanika T Williamson
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Nadine Nelson
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Tomar Ghansah
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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20
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Marzec E, Poznański J, Paprocki D. Thermodynamic contribution of iodine atom to the binding of heterogeneously polyhalogenated benzotriazoles by the catalytic subunit of human protein kinase CK2. IUBMB Life 2020; 72:1203-1210. [PMID: 32083806 DOI: 10.1002/iub.2257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/09/2020] [Indexed: 12/29/2022]
Abstract
A series of novel benzotriazole derivatives containing iodine atom(s) were synthesized. The binding of these compounds to the catalytic subunit of human protein kinase CK2 was evaluated using differential scanning fluorimetry. The obtained thermodynamic data were compared with those determined previously for the brominated and chlorinated benzotriazole analogues to get a deeper insight into the thermodynamic contribution of iodine substitution to the free energy of ligand binding. We have shown that iodine atom(s) attached to the benzene ring of benzotriazole enhance(s) its binding by the target protein. This effect is the strongest when two iodine atoms are attached at positions peripheral to the triazole ring, which according to the structures deposited in protein data bank may be indicative for the formation of the halogen bond between iodine and carbonyl groups of residues located in the hinge region of the protein. Finally, quantitative structure-activity relationship analysis pointed the solute hydrophobicity as the main factor contributing to the binding affinity.
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Affiliation(s)
- Ewa Marzec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Daniel Paprocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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21
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Pinna LA. IPK2019: David Shugar and the genesis of the IPK conferences. IUBMB Life 2020; 72:1097-1102. [PMID: 32031322 DOI: 10.1002/iub.2245] [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: 12/18/2019] [Accepted: 01/24/2020] [Indexed: 11/07/2022]
Abstract
A short biographical sketch of Professor David Shugar, the "father of the IPK conferences," is presented, focusing on the growing interest of this eminent scientist for protein kinases and his farsighted perception of the extraordinary therapeutic potential of protein kinase inhibitors, after his discovery in 1986 that 5,6-dichloro-1-(beta-D-ribofuranosyl)benzimidazole effects are mediated by inhibition of protein kinase CK2. This led David Shugar to conceive the idea of organizing a periodic international conference on protein kinase inhibitors ("IPK conference"). The first conference was held in 1998 and the 10th one under the auspices of International Union of Biochemistry and Molecular Biology in September 2019. David Shugar died at the age of 100 in 2015, shortly after having organized the eight IPK conference.
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Affiliation(s)
- Lorenzo A Pinna
- Department of Biomedical Sciences, The University of Padua, and CNR Institute of Neurosciences, Padova, Italy
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22
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Zhang J, Kong X, Zhang Y, Sun W, Xu E, Chen X. Mdm2 is a target and mediator of IRP2 in cell growth control. FASEB J 2019; 34:2301-2311. [PMID: 31907996 DOI: 10.1096/fj.201902278rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 12/26/2022]
Abstract
Iron is an essential element to all living organisms and plays a vital role in many cellular processes, such as DNA synthesis and energy production. The Mdm2 oncogene is an E3 ligase and known to promote tumor growth. However, the role of Mdm2 in iron homeostasis is not certain. Here, we showed that Mdm2 expression was increased by iron depletion but decreased by iron repletion. We also showed that Iron Regulatory Protein 2 (IRP2) mediated iron-regulated Mdm2 expression. Specifically, Mdm2 expression was increased by ectopic IRP2 but decreased by knockdown or knockout of IRP2 in human cancer cells as well as in mouse embryonic fibroblasts. In addition, we showed that IRP2-regulated Mdm2 expression was independent of tumor suppressor p53. Mechanistically, we found that IRP2 stabilized Mdm2 transcript via binding to an iron response element (IRE) in the 3'UTR of Mdm2 mRNA. Finally, we showed that Mdm2 is required for IRP2-mediated cell proliferation and Mdm2 expression is highly associated with IRP2 in both the normal and cancerous liver tissues. Together, we uncover a novel regulation of Mdm2 by IRP2 via mRNA stability and that the IRP2-Mdm2 axis may play a critical role in cell growth.
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Affiliation(s)
- Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xiangmudong Kong
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Yanhong Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Wenqiang Sun
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Enshun Xu
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, Davis, California
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23
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Small molecule modulators targeting protein kinase CK1 and CK2. Eur J Med Chem 2019; 181:111581. [DOI: 10.1016/j.ejmech.2019.111581] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022]
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24
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Shahraki A, Ebrahimi A. Binding of ellagic acid and urolithin metabolites to the CK2 protein, based on the ONIOM method and molecular docking calculations. NEW J CHEM 2019. [DOI: 10.1039/c9nj03508g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Using three-layer ONIOM and molecular docking calculations to investigate the binding of urolithins to the active site of the CK2 protein.
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Affiliation(s)
- Asiyeh Shahraki
- Department of Chemistry
- Computational Quantum Chemistry Laboratory
- University of Sistan and Baluchestan
- Zahedan
- Iran
| | - Ali Ebrahimi
- Department of Chemistry
- Computational Quantum Chemistry Laboratory
- University of Sistan and Baluchestan
- Zahedan
- Iran
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25
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Abe KI, Funaya S, Tsukioka D, Kawamura M, Suzuki Y, Suzuki MG, Schultz RM, Aoki F. Minor zygotic gene activation is essential for mouse preimplantation development. Proc Natl Acad Sci U S A 2018; 115:E6780-E6788. [PMID: 29967139 PMCID: PMC6055165 DOI: 10.1073/pnas.1804309115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mice, transcription initiates at the mid-one-cell stage and transcriptional activity dramatically increases during the two-cell stage, a process called zygotic gene activation (ZGA). Associated with ZGA is a marked change in the pattern of gene expression that occurs after the second round of DNA replication. To distinguish ZGA before and after the second-round DNA replication, the former and latter are called minor and major ZGA, respectively. Although major ZGA are required for development beyond the two-cell stage, the function of minor ZGA is not well understood. Transiently inhibiting minor ZGA with 5, 6-dichloro-1-β-d-ribofuranosyl-benzimidazole (DRB) resulted in the majority of embryos arresting at the two-cell stage and retention of the H3K4me3 mark that normally decreases. After release from DRB, at which time major ZGA normally occurred, transcription initiated with characteristics of minor ZGA but not major ZGA, although degradation of maternal mRNA normally occurred. Thus, ZGA occurs sequentially starting with minor ZGA that is critical for the maternal-to-zygotic transition.
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Affiliation(s)
- Ken-Ichiro Abe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Dai Tsukioka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 277-0882 Kashiwa, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan;
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26
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Zhang J, Xu E, Ren C, Yang HJ, Zhang Y, Sun W, Kong X, Zhang W, Chen M, Huang E, Chen X. Genetic Ablation of Rbm38 Promotes Lymphomagenesis in the Context of Mutant p53 by Downregulating PTEN. Cancer Res 2018; 78:1511-1521. [PMID: 29330147 DOI: 10.1158/0008-5472.can-17-2457] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/16/2017] [Accepted: 01/09/2018] [Indexed: 11/16/2022]
Abstract
Mutant p53 exerts gain-of-function effects that drive metastatic progression and therapeutic resistance, but the basis for these effects remain obscure. The RNA binding protein RBM38 limits translation of mutant p53 and is often altered in tumors harboring it. Here we show how loss of Rbm38 significantly alters cancer susceptibility in mutant p53 knock-in mice by shortening lifespan, altering tumor incidence, and promoting T-cell lymphomagenesis. Loss of Rbm38 enhanced mutant p53 expression and decreased expression of the tumor suppressor Pten, a key regulator of T-cell development. Furthermore, Rbm38 was required for Pten expression via stabilization of Pten mRNA through an AU-rich element in its 3'UTR. Our results suggest that Rbm38 controls T-cell lymphomagenesis by jointly modulating mutant p53 and Pten, with possible therapeutic implications for treating T-cell malignancies.Significance: An RNA-binding protein controls T-cell lymphomagenesis by jointly modulating mutant p53 and PTEN, with possible therapeutic implications for treating T-cell malignancies. Cancer Res; 78(6); 1511-21. ©2018 AACR.
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Affiliation(s)
- Jin Zhang
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California.
| | - Enshun Xu
- College of Agriculture, Nanjing Agriculture University, Nanjing, China
| | - Cong Ren
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hee Jung Yang
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California
| | - Yanhong Zhang
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California
| | - Wenqiang Sun
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California
| | - Xiangmudong Kong
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California
| | - Weici Zhang
- Division of Rheumatology/Allergy and Clinical Immunology, School of Medicine, University of California at Davis, California
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Eric Huang
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California at Davis, California
| | - Xinbin Chen
- Department of Surgical and Radiological Sciences, Schools of Veterinary Medicine and Medicine, University of California at Davis, California.
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27
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Buontempo F, McCubrey JA, Orsini E, Ruzzene M, Cappellini A, Lonetti A, Evangelisti C, Chiarini F, Evangelisti C, Barata JT, Martelli AM. Therapeutic targeting of CK2 in acute and chronic leukemias. Leukemia 2017; 32:1-10. [PMID: 28951560 PMCID: PMC5770594 DOI: 10.1038/leu.2017.301] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 12/22/2022]
Abstract
CK2 is a ubiquitously expressed, constitutively active Ser/Thr protein kinase, which is considered the most pleiotropic protein kinase in the human kinome. Such a pleiotropy explains the involvement of CK2 in many cellular events. However, its predominant roles are stimulation of cell growth and prevention of apoptosis. High levels of CK2 messenger RNA and protein are associated with CK2 pathological functions in human cancers. Over the last decade, basic and translational studies have provided evidence of CK2 as a pivotal molecule driving the growth of different blood malignancies. CK2 overexpression has been demonstrated in nearly all the types of hematological cancers, including acute and chronic leukemias, where CK2 is a key regulator of signaling networks critical for cell proliferation, survival and drug resistance. The findings that emerged from these studies suggest that CK2 could be a valuable therapeutic target in leukemias and supported the initiation of clinical trials using CK2 antagonists. In this review, we summarize the recent advances on the understanding of the signaling pathways involved in CK2 inhibition-mediated effects with a particular emphasis on the combinatorial use of CK2 inhibitors as novel therapeutic strategies for treating both acute and chronic leukemia patients.
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Affiliation(s)
- F Buontempo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - J A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - E Orsini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - M Ruzzene
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - A Cappellini
- Department of Human, Social and Health Sciences, University of Cassino, Cassino, Italy
| | - A Lonetti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - C Evangelisti
- Institute of Molecular Genetics, National Research Council, Bologna, Italy.,Cell and Molecular Biology Laboratory, Rizzoli Orthopedic Institute, Bologna, Italy
| | - F Chiarini
- Institute of Molecular Genetics, National Research Council, Bologna, Italy.,Cell and Molecular Biology Laboratory, Rizzoli Orthopedic Institute, Bologna, Italy
| | - C Evangelisti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - J T Barata
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - A M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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28
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The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design. Pharmaceuticals (Basel) 2017; 10:ph10010026. [PMID: 28230762 PMCID: PMC5374430 DOI: 10.3390/ph10010026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Casein kinase II (CK2) is an ubiquitous and pleiotropic serine/threonine protein kinase able to phosphorylate hundreds of substrates. Being implicated in several human diseases, from neurodegeneration to cancer, the biological roles of CK2 have been intensively studied. Upregulation of CK2 has been shown to be critical to tumor progression, making this kinase an attractive target for cancer therapy. Several CK2 inhibitors have been developed so far, the first being discovered by "trial and error testing". In the last decade, the development of in silico rational drug design has prompted the discovery, de novo design and optimization of several CK2 inhibitors, active in the low nanomolar range. The screening of big chemical libraries and the optimization of hit compounds by Structure Based Drug Design (SBDD) provide telling examples of a fruitful application of rational drug design to the development of CK2 inhibitors. Ligand Based Drug Design (LBDD) models have been also applied to CK2 drug discovery, however they were mainly focused on methodology improvements rather than being critical for de novo design and optimization. This manuscript provides detailed description of in silico methodologies whose applications to the design and development of CK2 inhibitors proved successful and promising.
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29
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Chua MMJ, Ortega CE, Sheikh A, Lee M, Abdul-Rassoul H, Hartshorn KL, Dominguez I. CK2 in Cancer: Cellular and Biochemical Mechanisms and Potential Therapeutic Target. Pharmaceuticals (Basel) 2017; 10:E18. [PMID: 28134850 PMCID: PMC5374422 DOI: 10.3390/ph10010018] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/23/2017] [Accepted: 01/23/2017] [Indexed: 01/09/2023] Open
Abstract
CK2 genes are overexpressed in many human cancers, and most often overexpression is associated with worse prognosis. Site-specific expression in mice leads to cancer development (e.g., breast, lymphoma) indicating the oncogenic nature of CK2. CK2 is involved in many key aspects of cancer including inhibition of apoptosis, modulation of signaling pathways, DNA damage response, and cell cycle regulation. A number of CK2 inhibitors are now available and have been shown to have activity against various cancers in vitro and in pre-clinical models. Some of these inhibitors are now undergoing exploration in clinical trials as well. In this review, we will examine some of the major cancers in which CK2 inhibition has promise based on in vitro and pre-clinical studies, the proposed cellular and signaling mechanisms of anti-cancer activity by CK2 inhibitors, and the current or recent clinical trials using CK2 inhibitors.
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Affiliation(s)
- Melissa M J Chua
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Charina E Ortega
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Ayesha Sheikh
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Migi Lee
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Hussein Abdul-Rassoul
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Kevan L Hartshorn
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
| | - Isabel Dominguez
- Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA.
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30
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Kubiński K, Masłyk M, Orzeszko A. Benzimidazole inhibitors of protein kinase CK2 potently inhibit the activity of atypical protein kinase Rio1. Mol Cell Biochem 2016; 426:195-203. [PMID: 27909846 PMCID: PMC5290066 DOI: 10.1007/s11010-016-2892-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022]
Abstract
Benzimidazole derivatives of 5,6-dichlorobenzimidazole 1-β-d-ribofuranoside (DRB) comprise the important class of protein kinase CK2 inhibitors. Depending on the structure, benzimidazoles inhibit CK2 with different selectivity and potency. Besides CK2, the compounds can inhibit, with similar activity, other classical eukaryotic protein kinases (e.g. PIM, DYRK, and PKD). The present results show that a majority of the most common CK2 inhibitors can affect the atypical kinase Rio1 in a nanomolar range. Kinetic data confirmed the mode of action of benzimidazoles as typical ATP-competitive inhibitors. In contrast to toyocamycin—the first discovered small-molecule inhibitor of Rio1—the most potent representative of benzimidazoles TIBI (IC50 = 0.09 µM, Ki = 0.05 µM) does not influence the oligomeric state of the Rio1 kinase. Docking studies revealed that TIBI can occupy the ATP-binding site of Rio1 in a manner similar to toyocamycin, and enhances the thermostability of the enzyme.
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Affiliation(s)
- Konrad Kubiński
- Department of Molecular Biology, Institute of Biotechnology, The John Paul II Catholic University of Lublin, ul. Konstantynów 1i, 20-708, Lublin, Poland
| | - Maciej Masłyk
- Department of Molecular Biology, Institute of Biotechnology, The John Paul II Catholic University of Lublin, ul. Konstantynów 1i, 20-708, Lublin, Poland.
| | - Andrzej Orzeszko
- Institute of Chemistry, Warsaw Life Sciences University, ul. Nowoursynowska 159c, 02-787, Warsaw, Poland
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31
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Gosselin G, Périgaud C, Bergogne MC, Balzarini J, De Clercq E, Imbach JL. Synthesis and Biological Evaluation of New 5,6-dichlorobenzimidazole Nucleoside Derivatives. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Novel 5,6-dichlorobenzimidazole nucleoside analogues structurally related to the well-known riboside DRB have been synthesized. The 1′,2′- trans nucleosides were prepared by condensation of peracylated sugars with 5,6-dichlorobenzimidazole, whereas the 1′,2′- cis β-D-arabinofuranosyl and β-D-lyxofuranosyl nucleosides were obtained by inversion of configuration on the sugar moiety. Chiral acyclic derivatives were stereospecifically prepared by ring-opening of furano- or pyrano-nucleosides by means of periodate oxidation, followed by borohydride reduction. The in vitro activities against a range of DNA and RNA viruses, as well as the cytotoxicities in human T-lymphocyte MT-4 cells, have been determined for these novel compounds and for DRB. No truly selective activity (i.e. clearly below the cytotoxic concentration) was observed against any of the viruses used. Some of the compounds, including DRB, were cytotoxic to MT-4 cells at CC50 values of less than 10 μg ml−1.
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Affiliation(s)
- G. Gosselin
- Laboratoire de Chimie Bioorganique, URA 488 du CNRS, case courrier 008, Université de Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
| | - C. Périgaud
- Laboratoire de Chimie Bioorganique, URA 488 du CNRS, case courrier 008, Université de Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
| | - M.-C. Bergogne
- Laboratoire de Chimie Bioorganique, URA 488 du CNRS, case courrier 008, Université de Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
| | - J. Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - E. De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - J.-L. Imbach
- Laboratoire de Chimie Bioorganique, URA 488 du CNRS, case courrier 008, Université de Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
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32
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Todd MAM, Huh MS, Picketts DJ. The sub-nucleolar localization of PHF6 defines its role in rDNA transcription and early processing events. Eur J Hum Genet 2016; 24:1453-9. [PMID: 27165002 PMCID: PMC5027685 DOI: 10.1038/ejhg.2016.40] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/12/2016] [Indexed: 12/20/2022] Open
Abstract
Ribosomal RNA synthesis occurs in the nucleolus and is a tightly regulated process that is targeted in some developmental diseases and hyperactivated in multiple cancers. Subcellular localization and immunoprecipitation coupled mass spectrometry demonstrated that a proportion of plant homeodomain (PHD) finger protein 6 (PHF6) protein is localized within the nucleolus and interacts with proteins involved in ribosomal processing. PHF6 sequence variants cause Börjeson–Forssman–Lehmann syndrome (BFLS, MIM#301900) and are also associated with a female-specific phenotype overlapping with Coffin–Siris syndrome (MIM#135900), T-cell acute lymphoblastic leukemia (MIM#613065), and acute myeloid leukemia (MIM#601626); however, very little is known about its cellular function, including its nucleolar role. HEK 293T cells were treated with RNase A, DNase I, actinomycin D, or 5,6-dichloro-β-D-ribofuranosylbenzimadole, followed by immunocytochemistry to determine PHF6 sub-nucleolar localization. We observed RNA-dependent localization of PHF6 to the sub-nucleolar fibrillar center (FC) and dense fibrillar component (DFC), at whose interface rRNA transcription occurs. Subsequent ChIP-qPCR analysis revealed strong enrichment of PHF6 across the entire rDNA-coding sequence but not along the intergenic spacer (IGS) region. When rRNA levels were quantified in a PHF6 gain-of-function model, we observed an overall decrease in rRNA transcription, accompanied by a modest increase in repressive promoter-associated RNA (pRNA) and a significant increase in the expression levels of the non-coding IGS36RNA and IGS39RNA transcripts. Collectively, our results demonstrate a role for PHF6 in carefully mediating the overall levels of ribosome biogenesis within a cell.
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Affiliation(s)
- Matthew A M Todd
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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33
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Ostrynska OV, Balanda AO, Bdzhola VG, Golub AG, Kotey IM, Kukharenko OP, Gryshchenko AA, Briukhovetska NV, Yarmoluk SM. Design and synthesis of novel protein kinase CK2 inhibitors on the base of 4-aminothieno[2,3-d]pyrimidines. Eur J Med Chem 2016; 115:148-60. [PMID: 27017545 DOI: 10.1016/j.ejmech.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 01/20/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
Abstract
An extension of our previous research work has resulted in a number of new ATP-competitive CK2 inhibitors that have been identified among 4-aminothieno[2,3-d]pyrimidine derivatives. The most active compounds obtained in the course of the research are 3-(5-p-tolyl-thieno[2,3-d]pyrimidin-4-ylamino)-benzoic acid, 5e (NHTP23, IC50 = 0.01 μM), 3-(5-phenyl-thieno[2,3-d]pyrimidin-4-ylamino)-benzoic acid, 5g (NHTP25, IC50 = 0.065 μM) and 3-(6-methyl-5-phenyl-thieno[2,3-d]pyrimidin-4-ylamino)-benzoic acid, 5n (NHTP33, IC50 = 0.008 μM). Structure-activity relationships of the tested 4-aminothieno[2,3-d]pyrimidine derivatives have been studied and their binding mode with ATP-acceptor site of CK2 has been proposed. A negative effect of intramolecular hydrogen bonding in the compounds' structure is discussed.
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Affiliation(s)
- Olga V Ostrynska
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Anatoliy O Balanda
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Andriy G Golub
- Otava Ltd, 400 Applewood Crescent, Unit 100, Vaughan, Ontario L4K 0C3, Canada
| | - Igor M Kotey
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Olexander P Kukharenko
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Andrii A Gryshchenko
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Nadiia V Briukhovetska
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680 Kyiv, Ukraine.
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34
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Huang S, Xu X, Wang G, Lu G, Xie W, Tao W, Zhang H, Jiang Q, Zhang C. DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation. J Cell Sci 2016; 129:1429-40. [PMID: 26872786 DOI: 10.1242/jcs.178723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/06/2016] [Indexed: 01/28/2023] Open
Abstract
RNA-polymerase-I-dependent ribosomal DNA (rDNA) transcription is fundamental to rRNA processing, ribosome assembly and protein synthesis. However, how this process is initiated during the cell cycle is not fully understood. By performing a proteomic analysis of transcription factors that bind RNA polymerase I during rDNA transcription initiation, we identified that the DNA replication initiator Cdc6 interacts with RNA polymerase I and its co-factors, and promotes rDNA transcription in G1 phase in an ATPase-activity-dependent manner. We further showed that Cdc6 is targeted to the nucleolus during late mitosis and G1 phase in a manner that is dependent on B23 (also known as nucleophosmin, NPM1), and preferentially binds to the rDNA promoter through its ATP-binding domain. Overexpression of Cdc6 increases rDNA transcription, whereas knockdown of Cdc6 results in a decreased association of both RNA polymerase I and the RNA polymerase I transcription factor RRN3 with rDNA, and a reduction of rDNA transcription. Furthermore, depletion of Cdc6 impairs the interaction between RRN3 and RNA polymerase I. Taken together, our data demonstrate that Cdc6 also serves as a regulator of rDNA transcription initiation, and indicate a mechanism by which initiation of rDNA transcription and DNA replication can be coordinated in cells.
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Affiliation(s)
- Shijiao Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaowei Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Guopeng Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Guoliang Lu
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wenbing Xie
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Tao
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hongyin Zhang
- Cancer Research Center, Peking University Hospital, Peking University, Beijing 100871, China
| | - Qing Jiang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Chuanmao Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
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35
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Liu ZL, Zhang RM, Meng QG, Zhang XC, Sun Y. Discovery of new protein kinase CK2 inhibitors with 1,3-dioxo-2,3-dihydro-1H-indene core. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00189k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein kinase CK2 (CK2) serves as an attractive anticancer target. Herein new CK2 inhibitors with a 1,3-dioxo-2,3-dihydro-1H-indene core are reported.
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Affiliation(s)
- Zong-liang Liu
- School of Pharmacy
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University)
- Ministry of Education
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong
- Yantai University
| | - Ren-mei Zhang
- School of Pharmacy
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University)
- Ministry of Education
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong
- Yantai University
| | - Qing-guo Meng
- School of Pharmacy
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University)
- Ministry of Education
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong
- Yantai University
| | - Xiao-chen Zhang
- School of Pharmacy
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University)
- Ministry of Education
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong
- Yantai University
| | - Yuan Sun
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
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36
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Abstract
INTRODUCTION The conventional term 'casein kinase' (CK) denotes three classes of kinases - CK1, CK2 and Golgi-CK (G-CK)/Fam20C (family with sequence similarity 20, member C) - sharing the ability to phoshorylate casein in vitro, but otherwise unrelated to each other. All CKs have been reported to be implicated in human diseases, and reviews individually dealing with the druggability of CK1 and CK2 are available. Our aim is to provide a comparative analysis of the three classes of CKs as therapeutic targets. AREAS COVERED CK2 is the CK for which implication in neoplasia is best documented, with the survival of cancer cells often relying on its overexpression. An ample variety of cell-permeable CK2 inhibitors have been developed, with a couple of these now in clinical trials. Isoform-specific CK1 inhibitors that are expected to play a beneficial role in oncology and neurodegeneration have been also developed. In contrast, the pathogenic potential of G-CK/Fam20C is caused by its loss of function. Activators of Fam20C, notably sphingolipids and their analogs, may prove beneficial in this respect. EXPERT OPINION Optimization of CK2 and CK1 inhibitors will prove useful to develop new therapeutic strategies for treating cancer and neurodegenerative disorders, while the design of potent activators of G-CK/Fam20C will provide a new tool in the fields of bio-mineralization and hypophosphatemic diseases.
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Affiliation(s)
- Giorgio Cozza
- a 1 University of Padova, Department of Biomedical Sciences , Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Lorenzo A Pinna
- a 1 University of Padova, Department of Biomedical Sciences , Via Ugo Bassi 58B, 35131 Padova, Italy .,b 2 University of Padova, Department of Biomedical Sciences and CNR Institute of Neurosciences , Padova, Italy ;
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37
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Briguglio I, Piras S, Corona P, Gavini E, Nieddu M, Boatto G, Carta A. Benzotriazole: An overview on its versatile biological behavior. Eur J Med Chem 2015; 97:612-48. [PMID: 25293580 PMCID: PMC7115563 DOI: 10.1016/j.ejmech.2014.09.089] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 09/25/2014] [Accepted: 09/28/2014] [Indexed: 12/13/2022]
Abstract
Discovered in late 1960, azoles are heterocyclic compounds class which constitute the largest group of available antifungal drugs. Particularly, the imidazole ring is the chemical component that confers activity to azoles. Triazoles are obtained by a slight modification of this ring and similar or improved activities as well as less adverse effects are reported for triazole derivatives. Consequently, it is not surprising that benzimidazole/benzotriazole derivatives have been found to be biologically active. Since benzimidazole has been widely investigated, this review is focused on defining the place of benzotriazole derivatives in biomedical research, highlighting their versatile biological properties, the mode of action and Structure Activity Relationship (SAR) studies for a variety of antimicrobial, antiparasitic, and even antitumor, choleretic, cholesterol-lowering agents.
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Affiliation(s)
- I Briguglio
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - S Piras
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - P Corona
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - E Gavini
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - M Nieddu
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - G Boatto
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy
| | - A Carta
- Department of Chemistry and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy.
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CK2 Secreted by Leishmania braziliensis Mediates Macrophage Association Invasion: A Comparative Study between Virulent and Avirulent Promastigotes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:167323. [PMID: 26120579 PMCID: PMC4450227 DOI: 10.1155/2015/167323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/28/2014] [Indexed: 01/03/2023]
Abstract
CK2 is a protein kinase distributed in different compartments of Leishmania braziliensis: an externally oriented ecto-CK2, an intracellular CK2, and a secreted CK2. This latter form is constitutively secreted from the parasite (CsCK2), but such secretion may be highly enhanced by the association of specific molecules, including enzyme substrates, which lead to a higher enzymatic activity, called inductively secreted CK2 (IsCK2). Here, we examined the influence of secreted CK2 (sCK2) activity on the infectivity of a virulent L. braziliensis strain. The virulent strain presented 121-fold higher total CK2 activity than those found in an avirulent strain. The use of specific CK2 inhibitors (TBB, DRB, or heparin) inhibited virulent parasite growth, whereas no effect was observed in the avirulent parasites. When these inhibitors were added to the interaction assays between the virulent L. braziliensis strain and macrophages, association index was drastically inhibited. Polyamines enhanced sCK2 activity and increased the association index between parasites and macrophages. Finally, sCK2 and the supernatant of the virulent strain increased the association index between the avirulent strain and macrophages, which was inhibited by TBB. Thus, the kinase enzyme CK2 seems to be important to invasion mechanisms of L. braziliensis.
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Nakanishi I, Murata K, Nagata N, Kurono M, Kinoshita T, Yasue M, Miyazaki T, Takei Y, Nakamura S, Sakurai A, Iwamoto N, Nishiwaki K, Nakaniwa T, Sekiguchi Y, Hirasawa A, Tsujimoto G, Kitaura K. Identification of protein kinase CK2 inhibitors using solvent dipole ordering virtual screening. Eur J Med Chem 2015; 96:396-404. [PMID: 25912672 DOI: 10.1016/j.ejmech.2015.04.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 01/15/2023]
Abstract
Novel protein kinase CK2 inhibitors were identified using the solvent dipole ordering virtual screening method. A total of 26 compounds categorized in 15 distinct scaffold classes inhibited greater than 50% of enzyme activity at 50 μM, and eight exhibited IC50 values less than 10 μM. Most of the identified compounds are lead-like and dissimilar to known inhibitors. The crystal structures of two of the CK2 complexes revealed the high accuracy of the predicted binding modes.
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Affiliation(s)
- Isao Nakanishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Katsumi Murata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoya Nagata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masakuni Kurono
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Misato Yasue
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takako Miyazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshinori Takei
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Nakamura
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Atsushi Sakurai
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Nobuko Iwamoto
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Keiji Nishiwaki
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Tetsuko Nakaniwa
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Yusuke Sekiguchi
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Akira Hirasawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Gozoh Tsujimoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Cozza G, Girardi C, Ranchio A, Lolli G, Sarno S, Orzeszko A, Kazimierczuk Z, Battistutta R, Ruzzene M, Pinna LA. Cell-permeable dual inhibitors of protein kinases CK2 and PIM-1: structural features and pharmacological potential. Cell Mol Life Sci 2014; 71:3173-85. [PMID: 24442476 PMCID: PMC11113908 DOI: 10.1007/s00018-013-1552-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 12/05/2013] [Accepted: 12/30/2013] [Indexed: 11/28/2022]
Abstract
It has been proposed that dual inhibitors of protein kinases CK2 and PIM-1 are tools particularly valuable to induce apoptosis of cancer cells, a property, however, implying cell permeability, which is lacking in the case of selective CK2/PIM-1 inhibitors developed so far. To fill this gap, we have derivatized the scaffold of the promiscuous CK2 inhibitor TBI with a deoxyribose moiety, generating TDB, a selective, cell-permeable inhibitor of CK2 and PIM-1. Here, we shed light on the structural features underlying the potency and narrow selectivity of TDB by exploiting a number of TDB analogs and by solving the 3D structure of the TDB/CK2 complex at 1.25 Å resolution, one of the highest reported so far for this kinase. We also show that the cytotoxic efficacy of TDB is almost entirely due to apoptosis, is accompanied by parallel inhibition of cellular CK2 and PIM-1, and is superior to both those observed combining individual inhibitors of CK2 and PIM-1 and by treating cells with the CK2 inhibitor CX4945. These data, in conjunction with the observations that cancer cells are more susceptible than non-cancer cells to TDB and that such a sensitivity is maintained in a multi-drug resistance background, highlight the pharmacological potential of this compound.
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Affiliation(s)
- Giorgio Cozza
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Cristina Girardi
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Alessandro Ranchio
- Department of Chemical Sciences and Venetian Institute of Molecular Medicine (VIMM), University of Padova, Padua, Italy
| | - Graziano Lolli
- Department of Chemical Sciences and Venetian Institute of Molecular Medicine (VIMM), University of Padova, Padua, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Andrzej Orzeszko
- Institute of Chemistry, Warsaw Life Sciences University, Warsaw, Poland
| | | | - Roberto Battistutta
- Department of Chemical Sciences and Venetian Institute of Molecular Medicine (VIMM), University of Padova, Padua, Italy
| | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Lorenzo A. Pinna
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- CNR, Institute of Neuroscience, University of Padova, Padua, Italy
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Perera Y, Toro ND, Gorovaya L, Fernandez-DE-Cossio J, Farina HG, Perea SE. Synergistic interactions of the anti-casein kinase 2 CIGB-300 peptide and chemotherapeutic agents in lung and cervical preclinical cancer models. Mol Clin Oncol 2014; 2:935-944. [PMID: 25279177 DOI: 10.3892/mco.2014.338] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/13/2014] [Indexed: 11/06/2022] Open
Abstract
CIGB-300 is a novel clinical-stage synthetic peptide that impairs the casein kinase 2 (CK2)-mediated phosphorylation of B23/nucleophosmin in different experimental settings and cancer models. As a single agent, CIGB-300 induces apoptosis in vitro and in vivo and modulates an array of proteins that are mainly involved in drug resistance, cell proliferation and apoptosis, as determined by proteomic analysis. However, the clinical oncology practice and cumulative knowledge on tumor biology suggest that drug combinations are more likely to cope with tumor complexity compared to single agents. In this study, we investigated the antiproliferative effect of CIGB-300 when combined with different anticancer drugs, such as cisplatin (alkylating), paclitaxel (antimitotic), doxorubicin (antitopoisomerase II) or 5-fluorouracil (DNA/RNA antimetabolite) in cell lines derived from lung and cervical cancer. Of note, using a Latin square design and subsequent analysis by CalcuSyn software, we observed that paclitaxel and cisplatin exhibited the best synergistic/additive profile when combined with CIGB-300, according to the combination and dose reduction indices. Such therapeutically favorable profiles may be explained by a direct cytotoxic effect and also by the observed cell cycle impairment following incubation of tumor cells with selected drug combinations. Importantly, on in vivo dose-finding schedules in human cervical tumors xenografted in nude mice, we observed that concomitant administration of CIGB-300 and cisplatin increased mice survival compared to single-agent treatment. Collectively, these findings provide a rationale for combining the anti-CK2 CIGB-300 peptide with currently available anticancer agents in the clinical setting and indicate platins and taxanes as compounds with major perspectives.
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Affiliation(s)
- Yasser Perera
- Laboratory of Molecular Oncology, Division of Pharmaceuticals, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba
| | - Neylen Del Toro
- Laboratory of Molecular Oncology, Division of Pharmaceuticals, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba
| | - Larisa Gorovaya
- Animal Facility Unit, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba
| | - Jorge Fernandez-DE-Cossio
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba
| | - Hernan G Farina
- Laboratory of Molecular Oncology, Quilmes National University, Bernal, Buenos Aires B1876BXD, Argentina
| | - Silvio E Perea
- Laboratory of Molecular Oncology, Division of Pharmaceuticals, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba
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Alexander SPH, Benson HE, Faccenda E, Pawson AJ, Sharman JL, Spedding M, Peters JA, Harmar AJ. The Concise Guide to PHARMACOLOGY 2013/14: enzymes. Br J Pharmacol 2013; 170:1797-867. [PMID: 24528243 PMCID: PMC3892293 DOI: 10.1111/bph.12451] [Citation(s) in RCA: 415] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. Enzymes are one of the seven major pharmacological targets into which the Guide is divided, with the others being G protein-coupled receptors, ligand-gated ion channels, ion channels, nuclear hormone receptors, catalytic receptors and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors and Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and the Guide to Receptors and Channels, providing a permanent, citable, point-in-time record that will survive database updates.
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Affiliation(s)
- Stephen PH Alexander
- School of Life Sciences, University of Nottingham Medical SchoolNottingham, NG7 2UH, UK
| | - Helen E Benson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Elena Faccenda
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Adam J Pawson
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | - Joanna L Sharman
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
| | | | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of DundeeDundee, DD1 9SY, UK
| | - Anthony J Harmar
- The University/BHF Centre for Cardiovascular Science, University of EdinburghEdinburgh, EH16 4TJ, UK
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Su H, Kodiha M, Lee S, Stochaj U. Identification of novel markers that demarcate the nucleolus during severe stress and chemotherapeutic treatment. PLoS One 2013; 8:e80237. [PMID: 24223222 PMCID: PMC3819286 DOI: 10.1371/journal.pone.0080237] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/01/2013] [Indexed: 01/08/2023] Open
Abstract
The nucleolus, the ribosomal factory of the cell, has emerged as a key player that regulates many aspects of cell biology. Several thousand proteins associate at least transiently with nucleoli, thereby generating a highly dynamic compartment with a protein profile which is sensitive to changes in cell physiology and pharmacological agents. Powerful tools that reliably demarcate the nucleoli are a prerequisite to measure their composition and activities. Previously, we developed quantitative methods to measure fluorescently labeled molecules in nucleoli. While these tools identify nucleoli under control and mild stress conditions, the accurate detection of nucleolar boundaries under harsh experimental conditions is complicated by the lack of appropriate markers for the nucleolar compartment. Using fluorescence microscopy we have now identified new marker proteins to detect nucleoli upon (a) severe stress and (b) drug treatments that trigger a pronounced reorganization of nucleoli. Our results demonstrate that nucleolin is an ideal marker to delimit nucleoli when cells are exposed to heat or oxidative stress. Furthermore, we show for the first time that cellular apoptosis susceptibility protein (CAS) and human antigen R protein (HuR) are excluded from nucleoli and can be employed to delimit these compartments under severe conditions that redistribute major nucleolar proteins. As proof-of-principle, we used these markers to demarcate nucleoli in cells treated with pharmacological compounds that disrupt the nucleolar organization. Furthermore, to gain new insights into the biology of the nucleolus, we applied our protocols and quantified stress- and drug-induced changes in nucleolar organization and function. Finally, we show that CAS, HuR and nucleolin not only identify nucleoli in optical sections, but are also suitable to demarcate the nucleolar border following 3D reconstruction. Taken together, our studies present novel marker proteins that delimit nucleoli with high confidence under a variety of experimental settings.
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Affiliation(s)
- Haitong Su
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Mohamed Kodiha
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Sunghoon Lee
- McGill University, Department of Physiology, Montreal, Quebec, Canada
| | - Ursula Stochaj
- McGill University, Department of Physiology, Montreal, Quebec, Canada
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Kinoshita T, Nakaniwa T, Sekiguchi Y, Sogabe Y, Sakurai A, Nakamura S, Nakanishi I. Crystal structure of human CK2α at 1.06 Å resolution. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:974-9. [PMID: 24121351 PMCID: PMC3795567 DOI: 10.1107/s0909049513020785] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/25/2013] [Indexed: 05/24/2023]
Abstract
The Ser/Thr kinase CK2 consists of two catalytic subunits (CK2α) and a dimer of the regulatory subunits (CK2β), and is a ubiquitous enzyme that regulates growth, proliferation and the survival of cells. CK2 is a remarkable drug target for potentially treating a wide variety of tumours and glomerulonephritis. The purified CK2α protein was crystallized using ethylene glycol as a precipitant. The crystal structure of CK2α with 21 loci of alternative conformations, including a niacin, 19 ethylene glycols and 346 waters, was determined at 1.06 Å resolution to an Rwork of 14.0% (Rfree = 16.5%). The alternative ensemble in the internal hydrophobic core underpins the plasticity of the αD-helix responsible for the regulation of ATP/GTP binding. The clear density map indicates that a niacin molecule, contained in the Escherichia coli culture medium, binds to the ATP binding site. An ethylene glycol molecule binds in the hydrophobic pocket lateral to the αD-helix forming the rim of the active site. The other ethylene glycol molecules occupy physiologically significant sites, including the CK2β binding interface and substrate binding site, as well as the gap in the crystal packing. Together with water molecules in the active site, these structural insights should facilitate drug discovery.
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Affiliation(s)
- Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Tetsuko Nakaniwa
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yusuke Sekiguchi
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Yuri Sogabe
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Atsushi Sakurai
- Department of Pharmaceutical Sciences, Kinki Univeristy, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shinya Nakamura
- Department of Pharmaceutical Sciences, Kinki Univeristy, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kinki Univeristy, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
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Sun H, Xu X, Wu X, Zhang X, Liu F, Jia J, Guo X, Huang J, Jiang Z, Feng T, Chu H, Zhou Y, Zhang S, Liu Z, You Q. Discovery and design of tricyclic scaffolds as protein kinase CK2 (CK2) inhibitors through a combination of shape-based virtual screening and structure-based molecular modification. J Chem Inf Model 2013; 53:2093-102. [PMID: 23937544 DOI: 10.1021/ci400114f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinase CK2 (CK2), a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates, serves as an attractive anticancer target. One of its most potent inhibitors, CX-4945, has entered a phase I clinical trial. Herein we present an integrated workflow combining shape-based virtual screening for the identification of novel CK2 inhibitors. A shape-based model derived from CX-4945 was built, and the subsequent virtual screening led to the identification of several novel scaffolds with high shape similarity to that of CX-4945. Among them two tricyclic scaffolds named [1,2,4]triazolo[4,3-c]quinazolin and [1,2,4]triazolo[4,3-a]quinoxalin attracted us the most. Combining strictly chemical similarity analysis, a second-round shape-based screening was performed based on the two tricyclic scaffolds, leading to 28 derivatives. These compounds not only targeted CK2 with potent and dose-dependent activities but also showed acceptable antiproliferative effects against a series of cancer cell lines. Our workflow supplies a high efficient strategy in the identification of novel CK2 inhibitors. Compounds reported here can serve as ideal leads for further modifications.
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Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Cozza G, Sarno S, Ruzzene M, Girardi C, Orzeszko A, Kazimierczuk Z, Zagotto G, Bonaiuto E, Di Paolo ML, Pinna LA. Exploiting the repertoire of CK2 inhibitors to target DYRK and PIM kinases. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1402-9. [PMID: 23360763 DOI: 10.1016/j.bbapap.2013.01.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
Advantage has been taken of the relative promiscuity of commonly used inhibitors of protein kinase CK2 to develop compounds that can be exploited for the selective inhibition of druggable kinases other than CK2 itself. Here we summarize data obtained by altering the scaffold of CK2 inhibitors to give rise to novel selective inhibitors of DYRK1A and to a powerful cell permeable dual inhibitor of PIM1 and CK2. In the former case one of the new compounds, C624 (naphto [1,2-b]benzofuran-5,9-diol) displays a potency comparable to that of the first-in-class DYRK1A inhibitor, harmine, lacking however the drawback of drastically inhibiting monoamine oxidase-A (MAO-A) as harmine does. On the other hand the promiscuous CK2 inhibitor 4,5,6,7-tetrabromo-1H-benzimidazole (TBI,TBBz) has been derivatized with a sugar moiety to generate a 1-(β-D-2'-deoxyribofuranosyl)-4,5,6,7-tetrabromo-1H-benzimidazole (TDB) compound which inhibits PIM1 and CK2 with comparably high efficacy (IC50 values<100nM) and remarkable selectivity. TDB, unlike other dual PIM1/CK2 inhibitors described in the literature is readily cell permeable and displays a cytotoxic effect on cancer cells consistent with concomitant inhibition of both its onco-kinase targets. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Giorgio Cozza
- Department of Biomedical Sciences and CNR, Institute of Neuroscience, University of Padua, Viale G. Colombo 3 35131, Padova, Italy
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Abstract
INTRODUCTION CK2 is a pleiotropic, ubiquitous and constitutively active protein kinase, localized in both cytosolic and nuclear compartments, where it catalyzes the phosphorylation of hundreds of proteins. CK2 is generally described as a tetramer composed of two catalytic (α and/or α') and two regulatory subunits (β), however, the free α/α' subunits are catalytically active by themselves. CK2 plays a key role in several physiological and pathological processes and has been connected to many neoplastic, inflammatory, autoimmune and infectious disorders. In the last 20 years, several inhibitors of CK2 have been discovered though only one of these, CX-4945, has recently entered into Phase II clinical trials as potential anticancer drug. AREAS COVERED The main objective of the present review is to describe the development of CK2 activity modulators over the years according to the timeline of their patent registration. EXPERT OPINION CK2 was discovered in 1954, but the first patent on CK2 modulators was deposited only 50 years later, in 2004. However, in the last 5 years an increasing number of patents on CK2 inhibitors have been registered, reflecting an increased interest in this kind of drug candidates and their possible therapeutic applications.
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Affiliation(s)
- Giorgio Cozza
- University of Padova, Department of Biomedical Sciences, Padova 35121, Italy
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Hundsdörfer C, Hemmerling HJ, Götz C, Totzke F, Bednarski P, Le Borgne M, Jose J. Indeno[1,2-b]indole derivatives as a novel class of potent human protein kinase CK2 inhibitors. Bioorg Med Chem 2012; 20:2282-9. [PMID: 22377675 DOI: 10.1016/j.bmc.2012.02.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/31/2012] [Accepted: 02/04/2012] [Indexed: 10/28/2022]
Abstract
Herein we describe the synthesis and properties of indeno[1,2-b]indole derivatives as a novel class of potent inhibitors of the human protein kinase CK2. A set of 19 compounds was obtained using a convenient and straightforward synthesis protocol. The compounds were tested for inhibition of human protein kinase CK2, which was recombinantly expressed in Escherichia coli. New inhibitors with IC(50) in the micro- and sub-micromolar range were identified. Compound 4b (5-isopropyl-7,8-dihydroindeno[1,2-b]indole-9,10(5H,6H)-dione) inhibited human CK2 with an IC(50) of 0.11 μM and did not significantly inhibit 22 other human protein kinases, suggesting selectivity towards CK2. ATP-competitive inhibition by compound 4b was shown and a K(i) of 0.06 μM was determined. Our findings indicate that indeno[1,2-b]indoles are a promising starting point for further development and optimization of human protein kinase CK2 inhibitors.
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Affiliation(s)
- Claas Hundsdörfer
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Hittorfstraße 58-62, 48149 Münster, Germany
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49
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Synthesis and biological evaluation of benzo[d]imidazole derivatives as potential anti-cancer agents. Bioorg Med Chem Lett 2011; 22:1317-21. [PMID: 22225635 DOI: 10.1016/j.bmcl.2011.12.088] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/14/2011] [Accepted: 12/16/2011] [Indexed: 11/21/2022]
Abstract
We herein report the synthesis, biological activity and structure-activity relationship of derivatives of 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole and benzo[d]imidazole. A lead compound 6o demonstrates potent anti-proliferative activity and the ability to induce cancer cell apoptosis.
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50
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Kinoshita T, Sekiguchi Y, Fukada H, Nakaniwa T, Tada T, Nakamura S, Kitaura K, Ohno H, Suzuki Y, Hirasawa A, Nakanishi I, Tsujimoto G. A detailed thermodynamic profile of cyclopentyl and isopropyl derivatives binding to CK2 kinase. Mol Cell Biochem 2011; 356:97-105. [PMID: 21735094 DOI: 10.1007/s11010-011-0960-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 06/24/2011] [Indexed: 12/12/2022]
Abstract
The detailed understanding of the molecular features of a ligand binding to a target protein, facilitates the successful design of potent and selective inhibitors. We present a case study of ATP-competitive kinase inhibitors that include a pyradine moiety. These compounds have similar chemical structure, except for distinct terminal hydrophobic cyclopentyl or isopropyl groups, and block kinase activity of casein kinase 2 subunit α (CK2α), which is a target for several diseases, such as cancer and glomerulonephritis. Although these compounds display similar inhibitory potency against CK2α, the crystal structures reveal that the cyclopentyl derivative gains more favorable interactions compared with the isopropyl derivative, because of the additional ethylene moiety. The structural observations and biological data are consistent with the thermodynamic profiles of these inhibitors in binding to CK2α, revealing that the enthalpic advantage of the cyclopentyl derivative is accompanied with a lower entropic loss. Computational analyses indicated that the relative enthalpic gain of the cyclopentyl derivative arises from an enhancement of a wide range of van der Waals interactions from the whole complex. Conversely, the relative entropy loss of the cyclopentyl derivative arises from a decrease in the molecular fluctuation and higher conformational restriction in the active site of CK2α. These structural insights, in combination with thermodynamic and computational observations, should be helpful in developing potent and selective CK2α inhibitors.
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Affiliation(s)
- Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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