1
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Al-Qadhi MA, Yahya TAA, El-Nassan HB. Recent Advances in the Discovery of CK2 Inhibitors. ACS OMEGA 2024; 9:20702-20719. [PMID: 38764653 PMCID: PMC11097362 DOI: 10.1021/acsomega.3c10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
CK2 is a vital enzyme that phosphorylates a large number of substrates and thereby controls many processes in the body. Its upregulation was reported in many cancer types. Inhibitors of CK2 might have anticancer activity, and two compounds are currently under clinical trials. However, both compounds are ATP-competitive inhibitors that may have off-target side effects. The development of allosteric and dual inhibitors can overcome this drawback. These inhibitors showed higher selectivity and specificity for the CK2 enzyme compared to the ATP-competitive inhibitors. The present review summarizes the efforts exerted in the last five years in the design of CK2 inhibitors.
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Affiliation(s)
- Mustafa A. Al-Qadhi
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a, Yemen
| | - Tawfeek A. A. Yahya
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a,Yemen
| | - Hala B. El-Nassan
- Pharmaceutical
Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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2
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Winiewska-Szajewska M, Paprocki D, Marzec E, Poznański J. Effect of histidine protonation state on ligand binding at the ATP-binding site of human protein kinase CK2. Sci Rep 2024; 14:1463. [PMID: 38233478 PMCID: PMC10794401 DOI: 10.1038/s41598-024-51905-y] [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: 05/12/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
Histidine residues contribute to numerous molecular interactions, owing to their structure with the ionizable aromatic side chain with pKa close to the physiological pH. Herein, we studied how the two histidine residues, His115 and His160 of the catalytic subunit of human protein kinase CK2, affect the binding of the halogenated heterocyclic ligands at the ATP-binding site. Thermodynamic studies on the interaction between five variants of hCK2α (WT protein and four histidine mutants) and three ionizable bromo-benzotriazoles and their conditionally non-ionizable benzimidazole counterparts were performed with nanoDSF, MST, and ITC. The results allowed us to identify the contribution of interactions involving the particular histidine residues to ligand binding. We showed that despite the well-documented hydrogen bonding/salt bridge formation dragging the anionic ligands towards Lys68, the protonated His160 also contributes to the binding of such ligands by long-range electrostatic interactions. Simultaneously, His 115 indirectly affects ligand binding, placing the hinge region in open/closed conformations.
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Affiliation(s)
- Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089, Warsaw, Poland.
| | - Daniel Paprocki
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Ewa Marzec
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland.
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3
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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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4
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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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5
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Paprocki D, Winiewska-Szajewska M, Speina E, Kucharczyk R, Poznański J. 5,6-diiodo-1H-benzotriazole: new TBBt analogue that minutely affects mitochondrial activity. Sci Rep 2021; 11:23701. [PMID: 34880390 PMCID: PMC8654832 DOI: 10.1038/s41598-021-03136-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
4,5,6,7-Tetrabromo-1H-benzotriazole is widely used as the reference ATP-competitive inhibitor of protein kinase CK2. Herein, we study its new analogs: 5,6-diiodo- and 5,6-diiodo-4,7-dibromo-1H-benzotriazole. We used biophysical (MST, ITC) and biochemical (enzymatic assay) methods to describe the interactions of halogenated benzotriazoles with the catalytic subunit of human protein kinase CK2 (hCK2α). To trace the biological activity, we measured their cytotoxicity against four reference cancer cell lines and the effect on the mitochondrial inner membrane potential. The results obtained lead to the conclusion that iodinated compounds are an attractive alternative to brominated ones. One of them retains the cytotoxicity against selected cancer cell lines of the reference TBBt with a smaller side effect on mitochondrial activity. Both iodinated compounds are candidate leaders in the further development of CK2 inhibitors.
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Affiliation(s)
- Daniel Paprocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.,Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089, Warsaw, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Róża Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
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6
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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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7
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Czapinska H, Winiewska-Szajewska M, Szymaniec-Rutkowska A, Piasecka A, Bochtler M, Poznański J. Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2. J Phys Chem B 2021; 125:2491-2503. [PMID: 33689348 PMCID: PMC8041304 DOI: 10.1021/acs.jpcb.0c10264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Binding of a family
of brominated benzotriazoles to the catalytic
subunit of human protein kinase CK2 (hCK2α) was used as a model
system to assess the contribution of halogen bonding to protein–ligand
interaction. CK2 is a constitutively active pleiotropic serine/threonine
protein kinase that belongs to the CMGC group of eukaryotic protein
kinases (EPKs). Due to the addiction of some cancer cells, CK2 is
an attractive and well-characterized drug target. Halogenated benzotriazoles
act as ATP-competitive inhibitors with unexpectedly good selectivity
for CK2 over other EPKs. We have characterized the interaction of
bromobenzotriazoles with hCK2α by X-ray crystallography, low-volume
differential scanning fluorimetry, and isothermal titration calorimetry.
Properties of free ligands in solution were additionally characterized
by volumetric and RT-HPLC measurements. Thermodynamic data indicate
that the affinity increases with bromo substitution, with greater
contributions from 5- and 6-substituents than 4- and 7-substituents.
Except for 4,7-disubstituted compounds, the bromobenzotriazoles adopt
a canonical pose with the triazole close to lysine 68, which precludes
halogen bonding. More highly substituted benzotriazoles adopt many
additional noncanonical poses, presumably driven by a large hydrophobic
contribution to binding. Some noncanonical ligand orientations allow
the formation of halogen bonds with the hinge region. Consistent with
a predominantly hydrophobic interaction, the isobaric heat capacity
decreases upon ligand binding, the more so the higher the substitution.
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Affiliation(s)
- Honorata Czapinska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | | | - Anna Piasecka
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Matthias Bochtler
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warsaw, Poland
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8
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Chojnacki K, Lindenblatt D, Wińska P, Wielechowska M, Toelzer C, Niefind K, Bretner M. Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase. Bioorg Chem 2020; 106:104502. [PMID: 33317841 DOI: 10.1016/j.bioorg.2020.104502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/06/2020] [Accepted: 11/19/2020] [Indexed: 11/26/2022]
Abstract
The new halogenated 1H-triazolo[4,5-b]pyridines and 1H-imidazo[4,5-b]pyridines were synthesised as analogues of known CK2 inhibitors: 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) and 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi). Their influence on the activity of recombinant human CK2α, CK2α' and PIM1 kinases was determined. The most active inhibitors were di- and trihalogenated 1H-triazolo[4,5-b]pyridines (4a, 5a and 10a) with IC50 values 2.56, 3.82 and 3.26 μM respectively for CK2α. Furthermore, effect on viability of cancer cell lines MCF-7 (human breast adenocarcinoma) and CCRF-CEM (T lymphoblast leukemia) of all final compounds was evaluated. Finally, three crystal structures of complexes of CK2α1-335 with inhibitors 4a, 5a and 10a were obtained. In addition, new protocol was used to obtain high-resolution crystal structures of CK2α'Cys336Ser in complex with four inhibitors (4a, 5a, 5b, 10a).
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Affiliation(s)
- K Chojnacki
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland.
| | - D Lindenblatt
- Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany
| | - P Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - M Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - C Toelzer
- Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany
| | - K Niefind
- Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany
| | - M Bretner
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
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9
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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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10
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Szymaniec-Rutkowska A, Bugajska E, Kasperowicz S, Mieczkowska K, Maciejewska AM, Poznański J. Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Rational drug-design approach supported with thermodynamic studies - a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Sci Rep 2019; 9:11018. [PMID: 31358826 PMCID: PMC6662822 DOI: 10.1038/s41598-019-47404-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022] Open
Abstract
Numerous inhibitors of protein kinases act on the basis of competition, targeting the ATP binding site. In this work, we present a procedure of rational design of a bi-substrate inhibitor, complemented with biophysical assays. The inhibitors of this type are commonly engineered by combining ligands carrying an ATP-like part with a peptide or peptide-mimicking fragment that determines specificity. Approach presented in this paper led to generation of a specific system for independent screening for efficient ligands and peptides, by means of thermodynamic measurements, that assessed the ability of the identified ligand and peptide to combine into a bi-substrate inhibitor. The catalytic subunit of human protein kinase CK2 was used as the model target. Peptide sequence was optimized using peptide libraries [KGDE]-[DE]-[ST]-[DE]3-4-NH2, originated from the consensus CK2 sequence. We identified KESEEE-NH2 peptide as the most promising one, whose binding affinity is substantially higher than that of the reference RRRDDDSDDD peptide. We assessed its potency to form an efficient bi-substrate inhibitor using tetrabromobenzotriazole (TBBt) as the model ATP-competitive inhibitor. The formation of ternary complex was monitored using Differential Scanning Fluorimetry (DSF), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC).
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12
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Santos LA, da Cunha EFF, Ramalho TC. Toward the Classical Description of Halogen Bonds: A Quantum Based Generalized Empirical Potential for Fluorine, Chlorine, and Bromine. J Phys Chem A 2017; 121:2442-2451. [DOI: 10.1021/acs.jpca.6b13112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucas A. Santos
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Elaine F. F. da Cunha
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
- Center for Basic
and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
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13
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Chojnacki K, Wińska P, Skierka K, Wielechowska M, Bretner M. Synthesis, in vitro antiproliferative activity and kinase profile of new benzimidazole and benzotriazole derivatives. Bioorg Chem 2017; 72:1-10. [PMID: 28340404 DOI: 10.1016/j.bioorg.2017.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/10/2017] [Accepted: 02/26/2017] [Indexed: 10/20/2022]
Abstract
Protein kinase 2 (CK2), a member of the serine/threonine kinase family, has been established as a promising target in anticancer therapy. New derivatives of known CK2 inhibitors 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi) and 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) bearing azide or substituted triazole groups were synthesized. Their influence on the activity of human recombinant CK2α and cytotoxicity against normal and cancer cell lines were evaluated. TBBi derivatives with triazole substituted with carboxyl substituent (7 and 10) exhibited the most potent inhibitory activity against CK2 with Ki value in the range of 1.96-0.91μM, respectively. New TBBi derivatives 2, 3, 5 and 9 have demonstrated the EC50, in the range of 12-25μM and 13-29μM respectively towards CCRF-CEM and MCF-7 cells. Derivatives TBBi decreased viability of cancer cells more efficiently than BALB cells and the biggest differences were observed for the azide substituted compounds 3 and 5. The effect of the most active compounds on the activity of eight off-target kinases was evaluated. Inhibitory efficiency of CK2-mediated p65 phosphorylation was demonstrated for the TBBi and compound 12.
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Affiliation(s)
- Konrad Chojnacki
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Patrycja Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland.
| | - Katarzyna Skierka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Monika Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Maria Bretner
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
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14
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Synthesis of polybrominated benzimidazole and benzotriazole derivatives containing a tetrazole ring and their cytotoxic activity. MONATSHEFTE FUR CHEMIE 2016; 147:1789-1796. [PMID: 27729714 PMCID: PMC5028404 DOI: 10.1007/s00706-016-1785-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/17/2016] [Indexed: 01/27/2023]
Abstract
ABSTRACT A series of new benzimidazole and benzotriazole derivatives containing a tetrazole moiety was synthesized by N-alkylation of 5-aryltetrazole with 4,5,6,7-tetrabromo-1-(3-chloropropyl)-1H-benzimidazole and 4,5,6,7-tetrabromo-2-(3-chloropropyl)-2H-benzotriazole. The reaction was regioselective and mostly 2,5-disubstituted tetrazole derivatives were obtained. The effect of all synthesized compounds on human recombinant casein kinase 2alpha subunit (rhCK2α) and cytotoxicity against human T-cell lymphoblast (CCRF-CEM) and breast adenocarcinoma (MCF-7) cell lines were evaluated. The results have shown that many of the synthesized compounds exhibit significant cytotoxicity at micromolar concentration. GRAPHICAL ABSTRACT
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Winiewska M, Kucińska K, Makowska M, Poznański J, Shugar D. Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2α. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1708-17. [PMID: 25891901 DOI: 10.1016/j.bbapap.2015.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
The interaction of human CK2α (hCK2α) with nine halogenated benzotriazoles, TBBt and its analogues representing all possible patterns of halogenation on the benzene ring of benzotriazole, was studied by biophysical methods. Thermal stability of protein-ligand complexes, monitored by calorimetric (DSC) and optical (DSF) methods, showed that the increase in the mid-point temperature for unfolding of protein-ligand complexes (i.e. potency of ligand binding to hCK2α) follow the inhibitory activities determined by biochemical assays. The dissociation constant for the ATP-hCK2α complex was estimated with the aid of microscale thermophoresis (MST) as 4.3±1.8 μM, and MST-derived dissociation constants determined for halogenated benzotriazoles, when converted according to known ATP concentrations, perfectly reconstruct IC50 values determined by the biochemical assays. Ligand-dependent quenching of tyrosine fluorescence, together with molecular modeling and DSC-derived heats of unfolding, support the hypothesis that halogenated benzotriazoles bind in at least two alternative orientations, and those that are efficient hCK2α inhibitors bind in the orientation which TBBt adopts in its complex with maize CK2α. DSC-derived apparent heat for ligand binding (ΔΔHbind) is driven by intermolecular electrostatic interactions between Lys68 and the triazole ring of the ligand, as indicated by a good correlation between ΔΔHbind and ligand pKa. Overall results, additionally supported by molecular modeling, confirm that a balance of hydrophobic and electrostatic interactions contribute predominantly (~40 kJ/mol), relative to possible intermolecular halogen/hydrogen bonding (less than 10 kJ/mol), in binding of halogenated benzotriazoles to the ATP-binding site of hCK2α. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Maria Winiewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Katarzyna Kucińska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Małgorzata Makowska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
| | - David Shugar
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
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