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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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2
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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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3
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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4
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Nakamura S, Akaki T, Nishiwaki K, Nakatani M, Kawase Y, Takahashi Y, Nakanishi I. System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study. J Comput Chem 2023; 44:824-831. [PMID: 36444861 DOI: 10.1002/jcc.27044] [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: 08/07/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
The fragment molecular orbital (FMO) method is a fast quantum-mechanical method that divides systems into pieces of fragments and performs ab initio calculations. The system truncation enables further speed improvement. In this article, we systematically study the effects of system truncations on binding affinity calculations obtained with FMO in combination with either the polarizable continuum model (FMO/PCM) or in combination with the Møller-Plesset method (FMO-MP2). We have used five protein complexes with ligands of several charged states. The calculated binding energies of the size variants of the truncated system, including only a restricted number of atoms around the ligand, are compared to the energy obtained from a full system. The result shows that the systems could be truncated to a radius of 8 Å from neutral ligands within an error of 0.7 kcal/mol, and 12 Å from charged ligands within an error of 1.1 kcal/mol for calculating the binding energy in solution.
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Affiliation(s)
- Shinya Nakamura
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Tatsuo Akaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Keiji Nishiwaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Midori Nakatani
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuji Kawase
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuki Takahashi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Isao Nakanishi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
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5
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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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6
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Ikeda A, Tsuyuguchi M, Kitagawa D, Sawa M, Nakamura S, Nakanishi I, Kinoshita T. Bivalent binding mode of an amino-pyrazole inhibitor indicates the potentials for CK2α1-selective inhibitors. Biochem Biophys Res Commun 2022; 630:30-35. [PMID: 36130444 DOI: 10.1016/j.bbrc.2022.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Casein kinase 2 (CK2) is a vital protein kinase that consists of two catalytic subunits (CK2α1 and/or CK2α2) and two regulatory subunits (CK2β). CK2α1 is a drug target for nephritis and cancers, while CK2α2 is a serious off-target because its inhibition causes testicular toxicity. High similarity between the isozymes CK2α1 and CK2α2 make it difficult to design CK2α1-specific inhibitors. Herein, the crystal structures of CK2α1 and CK2α2 complexed with a 3-amino-pyrazole inhibitor revealed the remarkable differences in the protein-inhibitor interaction modes. This inhibitor bound to the ATP binding sites of both isozymes in apparently distinct orientations. In addition, another molecule of this inhibitor bound to CK2α1, but not to CK2α2, at the CK2β protein-protein interface. Binding energy calculations and biochemical experiments suggested that this inhibitor possesses the conventional ATP-competitive characteristics with moderate allosteric function in a molecular glue mechanism. These results will assist the potential design of potent and selective CK2α1 inhibitors.
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Affiliation(s)
- Asaka Ikeda
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan
| | | | | | - Shinya Nakamura
- Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Metropolitan University, Sakai, 599-8531, Japan.
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7
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Modrić M, Božičević M, Odak I, Talić S, Barić D, Mlakić M, Raspudić A, Škorić I. The structure–activity relationship and computational studies of 1,3-thiazole derivatives as cholinesterase inhibitors with anti-inflammatory activity. CR CHIM 2022. [DOI: 10.5802/crchim.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Wang Q, Hu X, Shi W, Long H, Wang H. Design, synthesis and biological evaluation of chromone derivatives as novel protein kinase CK2 inhibitors. Bioorg Med Chem Lett 2022; 69:128799. [PMID: 35580724 DOI: 10.1016/j.bmcl.2022.128799] [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: 03/28/2022] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 11/02/2022]
Abstract
Protein kinase CK2 is a potential target for the discovery of anticancer drugs. Flavonoids are reported to be effective CK2 inhibitors. Herein, based on structural trimming of flavonoids, a series of chromone-2-aminothiazole derivatives (1a-d, 2a-g, 4a-j, 5a-k) were designed and synthesized by hybridizing the chromone skeleton with 2-aminothiazole scaffold. Among these compounds, compound 5i was the most effective CK2 inhibitor (IC50 = 0.08 μM) and possessed potent anti-proliferative activity against HL-60 tumor cells (IC50 = 0.25 μM). Cellular thermal shift assay (CESTA) confirmed that 5i directly bound to the CK2, and the possible binding mode of 5i toward CK2 was also simulated. Further studies showed that 5i induced the apoptosis of HL-60 cells and arrested the cell cycle. Finally, western-blot analysis showed that 5i could inhibit the downstream of CK2, including α-catenin/Akt pathway and PARP/Survivin pathway.
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Affiliation(s)
- Quan Wang
- State Key Laboratory of Natural Medicines, Department of TCM Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - XiaoLong Hu
- State Key Laboratory of Natural Medicines, Department of TCM Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Wei Shi
- State Key Laboratory of Natural Medicines, Department of TCM Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Huan Long
- State Key Laboratory of Natural Medicines, Department of TCM Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, Department of TCM Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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9
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Modrić M, Božičević M, Faraho I, Bosnar M, Škorić I. Design, synthesis and biological evaluation of new 1,3-thiazole derivatives as potential anti-inflammatory agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Brear P, Ball D, Stott K, D'Arcy S, Hyvönen M. Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α. J Med Chem 2020; 63:12786-12798. [PMID: 33119282 DOI: 10.1021/acs.jmedchem.0c01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of adenosine 5'-triphosphate (ATP)-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated them further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Rather, we report crystal structures, competitive isothermal titration calorimetry (ITC) and NMR, hydrogen-deuterium exchange (HDX) mass spectrometry, and chemoinformatic analyses that all point to these compounds binding in the ATP pocket. Comparisons of our results and experimental approach with the data presented in the original report suggest that the primary reason for the disparity is nonspecific inhibition by aggregation.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Darby Ball
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
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11
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He ZX, Gong YP, Zhang X, Ma LY, Zhao W. Pyridazine as a privileged structure: An updated review on anticancer activity of pyridazine containing bioactive molecules. Eur J Med Chem 2020; 209:112946. [PMID: 33129590 DOI: 10.1016/j.ejmech.2020.112946] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/26/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
Identification of potent anticancer agents with high selectivity and low toxicity remains on the way to human health. Pyridazine featuring advantageous physicochemical properties and antitumor potential usually is regarded as a central core in numerous anticancer derivatives. There are several approved pyridazine-based drugs in the market and analogues currently going through different clinical phases or registration statuses, suggesting pyridazine as a promising drug-like scaffold. The current review is intended to provide a comprehensive and updated overview of pyridazine derivatives as potential anticancer agents. In particular, we focused on their structure-activity relationship (SAR) studies, design strategies, binding modes and biological activities in the hope of offering novel insights for further rational design of more active and less toxic anticancer drugs.
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Affiliation(s)
- Zhang-Xu He
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yun-Peng Gong
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xin Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Li-Ying Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Wen Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
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12
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Zonouzi A, Kakeshpour A, Ranjbar PR, Moradi A. Computational studies on the conformational preference of
N
‐(Thiazol‐2‐yl) benzamide. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201900277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Afsaneh Zonouzi
- School of Chemistry, College of Science University of Tehran Tehran Iran
- Pharmaceutical and Cosmetic Research Center (PCRC) University of Tehran Tehran Iran
| | - Ali Kakeshpour
- School of Chemistry, College of Science University of Tehran Tehran Iran
| | | | - Ashraf Moradi
- School of Chemistry, University College of Science University of Zabol Zabol Iran
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13
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Krämer A, Kurz CG, Berger BT, Celik IE, Tjaden A, Greco FA, Knapp S, Hanke T. Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor. Eur J Med Chem 2020; 208:112770. [PMID: 32883634 DOI: 10.1016/j.ejmech.2020.112770] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/09/2020] [Accepted: 08/15/2020] [Indexed: 12/13/2022]
Abstract
Casein kinase 2 (CK2) is a constitutively expressed serine/threonine kinase that has a large diversity of cellular substrates. Thus, CK2 has been associated with a plethora of regulatory functions and dysregulation of CK2 has been linked to disease development in particular to cancer. The broad implications in disease pathology makes CK2 an attractive target. To date, the most advanced CK2 inhibitor is silmitasertib, which has been investigated in clinical trials for treatment of various cancers, albeit several off-targets for silmitasertib have been described. To ascertain the role of CK2 inhibition in cancer, other disease and normal physiology the development of a selective CK2 inhibitor would be highly desirable. In this study we explored the pyrazolo [1,5-a]pyrimidine hinge-binding moiety for the development of selective CK2 inhibitors. Optimization of this scaffold, which included macrocyclization, led to IC20 (31) a compound that displayed high in vitro potency for CK2 (KD = 12 nM) and exclusive selectivity for CK2. X-ray analysis revealed a canonical type-I binding mode for IC20 (31). However, the polar carboxylic acid moiety that is shared by many CK2 inhibitors including silmitasertib was required for potency but limits the cellular activity of IC20 (31) and the cellular IC50 dropped to the low micromolar range. In summary, IC20 (31) represents a highly selective and potent inhibitor of CK2, which can be used as a tool compound to study CK2 biology and potential new applications for the treatment of diseases.
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Affiliation(s)
- Andreas Krämer
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany; Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, 60596, Frankfurt Am Main, Germany
| | - Christian Georg Kurz
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Ibrahim Ethem Celik
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Francesco Aleksy Greco
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany; German Translational Cancer Network (DKTK) Site Frankfurt/Mainz, Germany; Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, 60596, Frankfurt Am Main, Germany.
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany.
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14
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Tsuyuguchi M, Nakaniwa T, Hirasawa A, Nakanishi I, Kinoshita T. Structural insights for producing CK2α1-specific inhibitors. Bioorg Med Chem Lett 2019; 30:126837. [PMID: 31859160 DOI: 10.1016/j.bmcl.2019.126837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 11/25/2022]
Abstract
Casein kinase 2 catalytic subunit (CK2α) is classified into two subtypes CK2α1 and CK2α2. CK2α1 is a drug discovery target, whereas CK2α2 is an off-target of CK2α1 inhibitors. High amino acid sequence homology between these subtypes hampers efforts to produce ATP competitive inhibitors that are highly selective to CK2α1. Hematein was identified previously as a non-ATP-competitive inhibitor for CK2α1, whereas this compound acts as an ATP competitive CK2α2 inhibitor. Crystal structures of CK2α1 and CK2α2 in complex with hematein revealed distinct binding features that provide structural insights for producing CK2α1-selective inhibitors.
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Affiliation(s)
- Masato Tsuyuguchi
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Hirasawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isao Nakanishi
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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15
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Feng J, He H, Zhou Y, Guo X, Liu H, Cai M, Wang F, Feng L, He H. Design, synthesis and biological evaluation of novel inhibitors against cyanobacterial pyruvate dehydrogenase multienzyme complex E1. Bioorg Med Chem 2019; 27:2413-2420. [DOI: 10.1016/j.bmc.2019.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 01/06/2023]
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16
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Bestgen B, Krimm I, Kufareva I, Kamal AAM, Seetoh WG, Abell C, Hartmann RW, Abagyan R, Cochet C, Le Borgne M, Engel M, Lomberget T. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem 2019; 62:1803-1816. [PMID: 30689953 DOI: 10.1021/acs.jmedchem.8b01766] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CK2 is a ubiquitous Ser/Thr protein kinase involved in the control of various signaling pathways and is known to be constitutively active. In the present study, we identified aryl 2-aminothiazoles as a novel class of CK2 inhibitors, which displayed a non-ATP-competitive mode of action and stabilized an inactive conformation of CK2 in solution. Enzyme kinetics studies, STD NMR, circular dichroism spectroscopy, and native mass spectrometry experiments demonstrated that the compounds bind in an allosteric pocket outside the ATP-binding site. Our data, combined with molecular docking studies, strongly suggested that this new binding site was located at the interface between the αC helix and the flexible glycine-rich loop. A first hit optimization led to compound 7, exhibiting an IC50 of 3.4 μM against purified CK2α in combination with a favorable selectivity profile. Thus, we identified a novel class of CK2 inhibitors targeting an allosteric pocket, offering great potential for further optimization into anticancer drugs.
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Affiliation(s)
- Benoît Bestgen
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany.,Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France.,Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, Commissariat à l'Energie Atomique, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Lyon 1, ENS Lyon 5, Rue de la Doua , 69100 Villeurbanne , France
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ahmed Ashraf Moustafa Kamal
- Pharmaceutical and Medicinal Chemistry, Saarland University, and Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus C2.3, 66123 Saarbrücken , Germany
| | - Wei-Guang Seetoh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Chris Abell
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Rolf W Hartmann
- Pharmaceutical and Medicinal Chemistry, Saarland University, and Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus C2.3, 66123 Saarbrücken , Germany
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Claude Cochet
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, Commissariat à l'Energie Atomique, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Marc Le Borgne
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany
| | - Thierry Lomberget
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France
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17
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Thiazole- and selenazole-comprising high-affinity inhibitors possess bright microsecond-scale photoluminescence in complex with protein kinase CK2. Bioorg Med Chem 2018; 26:5062-5068. [PMID: 30217463 DOI: 10.1016/j.bmc.2018.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 12/14/2022]
Abstract
A previously disclosed protein kinase (PK) CK2-selective inhibitor 4-(2-amino-1,3-thiazol-5-yl)benzoic acid (ATB) and its selenium-containing counterpart (ASB) revealed remarkable room temperature phosphorescence when bound to the ATP pocket of the protein kinase CK2. Conjugation of these fragments with a mimic of CK2 substrate peptide resulted in bisubstrate inhibitors with increased affinity towards the kinase. Attachment of the fluorescent acceptor dye 5-TAMRA to the conjugates led to significant enhancement of intensity of long-lifetime (microsecond-scale) photoluminescence of both sulfur- and selenium-containing compounds. The developed photoluminescent probes make possible selective determination of the concentration of CK2 in cell lysates and characterization of CK2 inhibitors by means of time-gated measurement of photoluminescence.
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18
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Protopopov MV, Ostrynska OV, Starosyla SA, Vodolazhenko MA, Sirko SM, Gorobets NY, Bdzhola V, Desenko SM, Yarmoluk SM. Dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-ones as a new class of CK2 inhibitors. Mol Divers 2018; 22:991-998. [PMID: 29845490 DOI: 10.1007/s11030-018-9836-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 05/14/2018] [Indexed: 01/08/2023]
Abstract
Identification of new small molecules inhibiting protein kinase CK2 is highly required for the study of this protein's functions in cell and for the further development of novel pharmaceuticals against a variety of disorders associated with CK2 activity. In this article, a virtual screening of a random small-molecule library was performed and 12 compounds were initially selected for biochemical tests toward CK2. Among them, the most active compound 1 ([Formula: see text]) belonged to dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-ones. The complex of this compound with CK2 was analyzed, and key ligand-enzyme interactions were determined. Then, a virtual screening of 231 dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-one derivatives was performed and 37 compounds were chosen for in vitro testing. It was found that 32 compounds inhibit CK2 with [Formula: see text] values from 2.5 to 7.5 [Formula: see text]. These results demonstrate that dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-4-one is a novel class of CK2 inhibitors.
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Affiliation(s)
- Mykola V Protopopov
- Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kiev, 01601, Ukraine.,Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo Street, Kiev, 03143, Ukraine
| | - Olga V Ostrynska
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo Street, Kiev, 03143, Ukraine
| | - Sergiy A Starosyla
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo Street, Kiev, 03143, Ukraine
| | - Maria A Vodolazhenko
- Department of Organic and Bioorganic Chemistry, SSI "Institute for Single Crystals" of NAS of Ukraine, 60 Nauky Ave., Kharkiv, 61072, Ukraine.,Department of Medical and Bioorganic Chemistry, Kharkiv National Medical University, 4 Nauky Ave., Kharkiv, 61022, Ukraine
| | - Svetlana M Sirko
- Department of Organic and Bioorganic Chemistry, SSI "Institute for Single Crystals" of NAS of Ukraine, 60 Nauky Ave., Kharkiv, 61072, Ukraine
| | - Nikolay Yu Gorobets
- Department of Organic and Bioorganic Chemistry, SSI "Institute for Single Crystals" of NAS of Ukraine, 60 Nauky Ave., Kharkiv, 61072, Ukraine.,Department of Organic Chemistry, V. N. Karazin Kharkiv National University, Svobody Sq. 4, Kharkiv, 61077, Ukraine
| | - Volodymyr Bdzhola
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo Street, Kiev, 03143, Ukraine
| | - Sergey M Desenko
- Department of Organic and Bioorganic Chemistry, SSI "Institute for Single Crystals" of NAS of Ukraine, 60 Nauky Ave., Kharkiv, 61072, Ukraine.,Department of Organic Chemistry, V. N. Karazin Kharkiv National University, Svobody Sq. 4, Kharkiv, 61077, Ukraine
| | - Sergiy M Yarmoluk
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo Street, Kiev, 03143, Ukraine.
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19
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Srivastava A, Hirota T, Irle S, Tama F. Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition. Proteins 2017; 86:344-353. [PMID: 29243286 DOI: 10.1002/prot.25444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/03/2017] [Accepted: 12/13/2017] [Indexed: 01/31/2023]
Abstract
Protein kinase, casein kinase II (CK2), is ubiquitously expressed and highly conserved protein kinase that shows constitutive activity. It phosphorylates a diverse set of proteins and plays crucial role in several cellular processes. The catalytic subunit of this enzyme (CK2α) shows remarkable flexibility as evidenced in numerous crystal structures determined till now. Here, using analysis of multiple crystal structures and long timescale molecular dynamics simulations, we explore the conformational flexibility of CK2α. The enzyme shows considerably higher flexibility in the solution as compared to that observed in crystal structure ensemble. Multiple conformations of hinge region, located near the active site, were observed during the dynamics. We further observed that among these multiple conformations, the most populated conformational state was inadequately represented in the crystal structure ensemble. The catalytic spine, was found to be less dismantled in this state as compared to the "open" hinge/αD state crystal structures. The comparison of dynamics in unbound (Apo) state and inhibitor (CX4945) bound state exhibits inhibitor induced suppression in the overall dynamics of the enzyme. This is especially true for functionally important glycine-rich loop above the active site. Together, this work gives novel insights into the dynamics of CK2α in solution and relates it to the function. This work also explains the effect of inhibitor on the dynamics of CK2α and paves way for development of better inhibitors.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,PRESTO, JST, Nagoya, Japan
| | - Stephan Irle
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,Computational Structural Biology Research Unit, RIKEN Advanced Institute of Computational Science, Kobe, Japan
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20
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Exploring the Pivotal Role of the CK2 Hinge Region Sub-Pocket in Binding with Tricyclic Quinolone Analogues by Computational Analysis. Molecules 2017; 22:molecules22050840. [PMID: 28534839 PMCID: PMC6154313 DOI: 10.3390/molecules22050840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/12/2017] [Accepted: 05/17/2017] [Indexed: 11/21/2022] Open
Abstract
Protein kinase CK2 has been considered as an attractive therapeutic target of cancer therapy. The tricyclic quinoline compound CX-4945 is the first representative of CK2 inhibitors used in human clinical trials. The binding of non-2,6-naphtyridine substituted compounds 27e (IC50 > 500 nM) and 27h (IC50 > 1000 nM) to CK2 is abolished. However, the unbinding mechanisms due to the key pharmacophore group replacement of compounds 27e and 27h are unveiled. In the present work, combined computational analysis was performed to investigate the underlying structural basis of the low-affinity of two systems. As indicated in the results, the loss of hydrogen bonds between the non-2,6-naphtyridine and the hinge region destroyed the proper recognition of the two complexes. Besides, the allosteric mechanisms between the deviated ligands and the changed regions (G-loop, C-loop and β4/β5 loop) are proposed. Furthermore, energetic analysis was evaluated by detailed energy calculation and residue-based energy decomposition. More importantly, the summary of known polar pharmacophore groups elucidates the pivotal roles of hinge region sub-pocket in the binding of CK2 inhibitors. These results provide rational clues to the fragment-based design of more potent CK2 inhibitors.
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21
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Zhang N, Zhao H. Enriching screening libraries with bioactive fragment space. Bioorg Med Chem Lett 2016; 26:3594-7. [PMID: 27311891 DOI: 10.1016/j.bmcl.2016.06.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/05/2016] [Accepted: 06/06/2016] [Indexed: 02/04/2023]
Abstract
By deconvoluting 238,073 bioactive molecules in the ChEMBL library into extended Murcko ring systems, we identified a set of 2245 ring systems present in at least 10 molecules. These ring systems belong to 2221 clusters by ECFP4 fingerprints with a minimum intracluster similarity of 0.8. Their overlap with ring systems in commercial libraries was further quantified. Our findings suggest that success of a small fragment library is driven by the convergence of effective coverage of bioactive ring systems (e.g., 10% coverage by 1000 fragments vs. 40% by 2million HTS compounds), high enrichment of bioactive ring systems, and low molecular complexity enhancing the probability of a match with the protein targets. Reconciling with the previous studies, bioactive ring systems are underrepresented in screening libraries. As such, we propose a library of virtual fragments with key functionalities via fragmentation of bioactive molecules. Its utility is exemplified by a prospective application on protein kinase CK2, resulting in the discovery of a series of novel inhibitors with the most potent compound having an IC50 of 0.5μM and a ligand efficiency of 0.41kcal/mol per heavy atom.
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Affiliation(s)
- Na Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Hongtao Zhao
- Lephar Research, Rindögatan 21, 11558 Stockholm, Sweden.
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