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Latosińska M, Latosińska JN. Serine/Threonine Protein Kinases as Attractive Targets for Anti-Cancer Drugs-An Innovative Approach to Ligand Tuning Using Combined Quantum Chemical Calculations, Molecular Docking, Molecular Dynamic Simulations, and Network-like Similarity Graphs. Molecules 2024; 29:3199. [PMID: 38999151 PMCID: PMC11243552 DOI: 10.3390/molecules29133199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Serine/threonine protein kinases (CK2, PIM-1, RIO1) are constitutively active, highly conserved, pleiotropic, and multifunctional kinases, which control several signaling pathways and regulate many cellular functions, such as cell activity, survival, proliferation, and apoptosis. Over the past decades, they have gained increasing attention as potential therapeutic targets, ranging from various cancers and neurological, inflammation, and autoimmune disorders to viral diseases, including COVID-19. Despite the accumulation of a vast amount of experimental data, there is still no "recipe" that would facilitate the search for new effective kinase inhibitors. The aim of our study was to develop an effective screening method that would be useful for this purpose. A combination of Density Functional Theory calculations and molecular docking, supplemented with newly developed quantitative methods for the comparison of the binding modes, provided deep insight into the set of desirable properties responsible for their inhibition. The mathematical metrics helped assess the distance between the binding modes, while heatmaps revealed the locations in the ligand that should be modified according to binding site requirements. The Structure-Binding Affinity Index and Structural-Binding Affinity Landscape proposed in this paper helped to measure the extent to which binding affinity is gained or lost in response to a relatively small change in the ligand's structure. The combination of the physico-chemical profile with the aforementioned factors enabled the identification of both "dead" and "promising" search directions. Tests carried out on experimental data have validated and demonstrated the high efficiency of the proposed innovative approach. Our method for quantifying differences between the ligands and their binding capabilities holds promise for guiding future research on new anti-cancer agents.
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Affiliation(s)
- Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-814 Poznań, Poland
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Wińska P, Wielechowska M, Koronkiewicz M, Borowiecki P. Synthesis and Anticancer Activity of Novel Dual Inhibitors of Human Protein Kinases CK2 and PIM-1. Pharmaceutics 2023; 15:1991. [PMID: 37514177 PMCID: PMC10385865 DOI: 10.3390/pharmaceutics15071991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
CK2 and PIM-1 are serine/threonine kinases involved in the regulation of many essential processes, such as proliferation, differentiation, and apoptosis. Inhibition of CK2 and PIM-1 kinase activity has been shown to significantly reduce the viability of cancer cells by inducing apoptosis. A series of novel amino alcohol derivatives of parental DMAT were designed and synthesized as potent dual CK2/PIM-1 inhibitors. Concomitantly with the inhibition studies toward recombinant CK2 and PIM-1, the influence of the obtained compounds on the viability of three human carcinoma cell lines, i.e., acute lymphoblastic leukemia (CCRF-CEM), human chronic myelogenous leukemia (K-562), and breast cancer (MCF-7), as well as non-cancerous cells (Vero), was evaluated using an MTT assay. Induction of apoptosis and cell cycle progression after treatment with the most active compound and a lead compound were studied by flow-cytometry-based assay. Additionally, autophagy induction in K-562 cells and intracellular inhibition of CK2 and PIM-1 in all the tested cell lines were evaluated by qualitative/quantitative fluorescence-based assay and Western blot method, respectively. Among the newly developed inhibitors, 1,1,1-trifluoro-3-[(4,5,6,7-tetrabromo-1H-benzimidazol-2-yl)amino]propan-2-ol demonstrates the highest selectivity and the most prominent proapoptotic properties towards the studied cancer cells, especially towards acute lymphoblastic leukemia, in addition to inducing autophagy in K-562 cells.
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Affiliation(s)
- Patrycja Wińska
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Monika Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | | | - Paweł Borowiecki
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
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Koronkiewicz M, Kazimierczuk Z, Orzeszko A. Antitumor activity of the protein kinase inhibitor 1-(β-D-2'-deoxyribofuranosyl)-4,5,6,7-tetrabromo- 1H-benzimidazole in breast cancer cell lines. BMC Cancer 2022; 22:1069. [PMID: 36243702 PMCID: PMC9571492 DOI: 10.1186/s12885-022-10156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background The protein kinases CK2 and PIM-1 are involved in cell proliferation and survival, the cell cycle, and drug resistance, and they are found overexpressed in virtually all types of human cancer, including breast cancer. In this study, we investigated the antitumor activity of a deoxynucleoside derivative, the protein kinase inhibitor compound 1-(β-D-2′-deoxyribofuranosyl)-4,5,6,7-tetrabromo-1H-benzimidazole (K164, also termed TDB), inter alia CK2 and PIM-1, on breast cancer cell lines (MDA-MB-231, MCF-7, and SK-BR-3). Methods An evaluation of the cytotoxic and proapoptotic effects, mitochondrial membrane potential (ΔΨm), and cell cycle progression was performed using an MTT assay, flow cytometry, and microscopic analysis. The Western blotting method was used to analyze the level of proteins important for the survival of breast cancer cells and proteins phosphorylated by the CK2 and PIM-1 kinases. Results The examined compound demonstrated the inhibition of cell viability in all the tested cell lines and apoptotic activity, especially in the MCF-7 and SK-BR-3 cells. Changes in the mitochondrial membrane potential (ΔΨm), cell cycle progression, and the level of the proteins studied were also observed. Conclusions The investigated CK2 and PIM-1 kinase inhibitor K164 is a promising compound that can be considered a potential agent in targeted therapy in selected types of breast cancer; therefore, further research is necessary. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10156-8.
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Affiliation(s)
- Mirosława Koronkiewicz
- Department of Biomedical Research, National Medicines Institute, Chełmska St. 30/34, 00-725, Warsaw, Poland.
| | - Zygmunt Kazimierczuk
- Institute of Chemistry, Warsaw University of Life Sciences, Nowoursynowska St. 159C, 02-787, Warsaw, Poland
| | - Andrzej Orzeszko
- Institute of Chemistry, Warsaw University of Life Sciences, Nowoursynowska St. 159C, 02-787, Warsaw, Poland
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Ali AM, Tawfik SS, Mostafa AS, Massoud MAM. Benzimidazole-Based Protein Kinase Inhibitors: Current Perspectives in Targeted Cancer Therapy. Chem Biol Drug Des 2022; 100:656-673. [PMID: 35962624 DOI: 10.1111/cbdd.14130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/31/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022]
Abstract
Targeted therapy has emerged to be the cornerstone of advanced cancer treatment, allowing for more selectivity and avoiding the common drug toxicity and resistance. Identification of potential targets having vital role in growth and survival of cancer cells got much easier with the aid of the recent advances in high throughput screening approaches. Various protein kinases came into focus as valuable targets in cancer therapy. Meanwhile, benzimidazole-based scaffolds have gained significant attention as promising protein kinase inhibitors with high potency and varied selectivity. Great diversity of these scaffolds has inspired the medicinal chemists to inspect the effect of structural changes upon inhibitory activity on the molecular level through modeling studies. The present review gathers all the considerable attempts to develop benzimidazole-based compounds; designed as protein kinase inhibitors with anticancer activity since 2015; that target aurora kinase, CDK, CK2, EGFR, FGFR, and VEGFR-2; to allow further development and progression regarding benzimidazoles.
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Affiliation(s)
- Alaa M Ali
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Samar S Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Amany S Mostafa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohammed A M Massoud
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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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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Akhtar MJ, Yar MS, Sharma VK, Khan AA, Ali Z, Haider MDR, Pathak A. Recent Progress of Benzimidazole Hybrids for Anticancer Potential. Curr Med Chem 2021; 27:5970-6014. [PMID: 31393240 DOI: 10.2174/0929867326666190808122929] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/16/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
This review presents the detailed account of factors leading to cancer and design strategy for the synthesis of benzimidazole derivatives as anticancer agents. The recent survey for cancer treatment in Cancer facts and figures 2017 American Chemical Society has shown progressive development in fighting cancer. Researchers all over the world in both developed and developing countries are in a continuous effort to tackle this serious concern. Benzimidazole and its derivatives showed a broad range of biological activities due to their resemblance with naturally occurring nitrogenous base i.e. purine. The review discussed benzimidazole derivatives showing anticancer properties through a different mechanism viz. intercalation, alkylating agents, topoisomerases, DHFR enzymes, and tubulin inhibitors. Benzimidazole derivatives act through a different mechanism and the substituents reported from the earlier and recent research articles are prerequisites for the synthesis of targeted based benzimidazole derivatives as anticancer agents. The review focuses on an easy comparison of the substituent essential for potency and selectivity through SAR presented in figures. This will further provide a better outlook or fulfills the challenges faced in the development of novel benzimidazole derivatives as anticancer.
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Affiliation(s)
- Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India,Department of Pharmaceutical Chemistry, Indo Soviet Friendship College of Pharmacy, Ghal Kalan, Ferozpur G.T. Road MOGA-142001, Punjab, India
| | - Mohammad Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India
| | - Vinod Kumar Sharma
- School of Pharmacy, Bharat Institute of Technology, NH58, Partapur Bypass Meerut-250103, India
| | - Ahsan Ahmed Khan
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India
| | - Zulphikar Ali
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India
| | - M D Rafi Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India
| | - Ankita Pathak
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Hamdard University,
Hamdard Nagar, New Delhi-110062, India
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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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Chen ZL, Zou BQ, Qin QP, Wang ZF, Tan MX, Huang XL, Liang CJ, Liang H. Cyclometallated iridium(III)-5-bromo-8-quinolinol complexes as mitochondria-targeted anticancer agents. INORG CHEM COMMUN 2020. [DOI: 10.1016/j.inoche.2020.107854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zhang WY, Wang YJ, Du F, He M, Gu YY, Bai L, Yang LL, Liu YJ. Evaluation of anticancer effect in vitro and in vivo of iridium(III) complexes on gastric carcinoma SGC-7901 cells. Eur J Med Chem 2019; 178:401-416. [DOI: 10.1016/j.ejmech.2019.06.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/04/2023]
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Karataş MO, Tekin S, Alici B, Sandal S. Cytotoxic effects of coumarin substituted benzimidazolium salts against human prostate and ovarian cancer cells. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1647-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Chojnacki K, Wińska P, Wielechowska M, Łukowska-Chojnacka E, Tölzer C, Niefind K, Bretner M. Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases. Bioorg Chem 2018; 80:266-275. [PMID: 29966873 DOI: 10.1016/j.bioorg.2018.06.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 11/30/2022]
Abstract
The new aminoalkyl-substituted derivatives of known CK2 inhibitors 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi) and 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) were synthesized, and their influence on the activity of recombinant human CK2 α, CK2 holoenzyme and PIM1 kinases was evaluated. All derivatives inhibited the activity of studied kinases and the most efficient were aminopropyl-derivatives 8b and 14b. These compounds also exerted inhibition of cancer cell lines - CCRF-CEM (acute lymphoblastoid leukemia), MCF-7 (human breast cancer), and PC-3 (prostate cancer) proliferation and their EC50 is comparable with the value for clinically studied CK2 inhibitor CX-4945. Preliminary structure activity relationship analysis indicated that the spacer length affected antitumor potency, and two to three methylene units were more favorable. The complex of CK2 α1-335/8b was crystallized, both under high-salt conditions and under low-salt conditions giving crystals which diffracted X-rays to about 2.4 Å resolution, what enabled the determination of the corresponding 3D-structures.
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Affiliation(s)
- K Chojnacki
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - P Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - M Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - E Łukowska-Chojnacka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - C Tölzer
- 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 3, 00-664 Warsaw, Poland.
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