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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [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: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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Zhang P, Shi C, Dong T, Song J, Du G. The anticancer therapeutic potential of pyrimidine-sulfonamide hybrids. Future Med Chem 2024; 16:905-924. [PMID: 38624011 PMCID: PMC11249161 DOI: 10.4155/fmc-2024-0010] [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: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Cancer as a devastating malignancy, seriously threatens human life and health, but most chemotherapeutics have long been criticized for unsatisfactory therapeutic efficacy due to drug resistance and severe off-target toxicity. Pyrimidines, including fused pyrimidines, are privileged scaffolds for various biological cancer targets and are the most important class of metalloenzyme carbonic anhydrase inhibitors. Pyrimidine-sulfonamide hybrids can act on different targets in cancer cells simultaneously and possess potent activity against various cancers, revealing that hybridization of pyrimidine with sulfonamide is a promising approach to generate novel effective anticancer candidates. This review aims to summarize the recent progress of pyrimidine-sulfonamide hybrids with anticancer potential, covering papers published from 2020 to present, to facilitate further rational design of more effective candidates.
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Affiliation(s)
- Peng Zhang
- Emergency Intensive Care Medicine Department, Zibo 148 Hospital, China RongTong Medical Healthcare Group Co. Ltd, Zibo, Shandong Province, 255000, PR China
| | - Congcong Shi
- Zibo Vocational Institute College of Medical Technology, Zibo, Shandong Province, 255000, PR China
| | - Tongbao Dong
- Zibo Vocational Institute College of Medical Technology, Zibo, Shandong Province, 255000, PR China
| | - Juntao Song
- Hematology & Oncology Department, Zibo 148 Hospital, China RongTong Medical Healthcare Group Co. Ltd, Zibo, Shandong Province, 255000, PR China
| | - Gang Du
- Emergency Intensive Care Medicine Department, Zibo 148 Hospital, China RongTong Medical Healthcare Group Co. Ltd, Zibo, Shandong Province, 255000, PR China
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3
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Wang H, Ba J, Kang Y, Gong Z, Liang T, Zhang Y, Qi J, Wang J. Recent Progress in CDK4/6 Inhibitors and PROTACs. Molecules 2023; 28:8060. [PMID: 38138549 PMCID: PMC10745860 DOI: 10.3390/molecules28248060] [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: 10/31/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cell division in eukaryotes is a highly regulated process that is critical to the life of a cell. Dysregulated cell proliferation, often driven by anomalies in cell Cyclin-dependent kinase (CDK) activation, is a key pathological mechanism in cancer. Recently, selective CDK4/6 inhibitors have shown clinical success, particularly in treating advanced-stage estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. This review provides an in-depth analysis of the action mechanism and recent advancements in CDK4/6 inhibitors, categorizing them based on their structural characteristics and origins. Furthermore, it explores proteolysis targeting chimers (PROTACs) targeting CDK4/6. We hope that this review could be of benefit for further research on CDK4/6 inhibitors and PROTACs.
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Affiliation(s)
| | | | | | | | | | | | - Jianguo Qi
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
| | - Jianhong Wang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
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Yang B, Quan Y, Zhao W, Ji Y, Yang X, Li J, Li Y, Liu X, Wang Y, Li Y. Design, synthesis and biological evaluation of 2-((4-sulfamoylphenyl)amino)-pyrrolo[2,3-d]pyrimidine derivatives as CDK inhibitors. J Enzyme Inhib Med Chem 2023; 38:2169282. [PMID: 36656085 PMCID: PMC9858427 DOI: 10.1080/14756366.2023.2169282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
To explore the potential use of CDK inhibitors in pancreatic ductal adenocarcinoma (PDAC) therapy, a series of novel 2-((4-sulfamoylphenyl)amino)-pyrrolo[2,3-d]pyrimidine derivatives was designed, synthesised, and investigated for inhibition on both CDK kinase activity and cellular proliferation of pancreatic cancer. Most of new sulphonamide-containing derivatives demonstrated strong inhibitory activity on CDK9 and obvious anti-proliferative activity in cell culture. Moreover, two new compounds suppressed cell proliferation of multiple human pancreatic cancer cell lines. The most potent compound 2g inhibited cancer cell proliferation by blocking Rb phosphorylation and induced apoptosis via downregulation of CDK9 downstream proteins Mcl-1 and c-Myc in MIA PaCa-2 cells. CDK9 knockdown experiment suggests its anti-proliferative activity is mainly mediated by CDK9. Additionally, 2g displayed moderate tumour inhibition effect in AsPC-1 derived xenograft mice model. Altogether, this study provided a new start for further optimisation to develop potential CDK inhibitor candidates for PDAC treatment by alone or combination use.
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Affiliation(s)
- Bo Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yanni Quan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wuli Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yingjie Ji
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaotang Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jianrui Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiujun Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ying Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Ying Wang Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, China
| | - Yanping Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,CONTACT Yanping Li
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Komkov AV, Sukhanova AА, Menchikov LG, Zavarzin IV. о-Aminopyrimidine Aldehydes and Ketones: Synthesis and use as Precursors to Fused Pyrimidines. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Fedotov VV, Valieva MI, Taniya OS, Aminov SV, Kharitonov MA, Novikov AS, Kopchuk DS, Slepukhin PA, Zyryanov GV, Ulomsky EN, Rusinov VL, Charushin VN. 4-(Aryl)-Benzo[4,5]imidazo[1,2- a]pyrimidine-3-Carbonitrile-Based Fluorophores: Povarov Reaction-Based Synthesis, Photophysical Studies, and DFT Calculations. Molecules 2022; 27:8029. [PMID: 36432130 PMCID: PMC9698514 DOI: 10.3390/molecules27228029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
A series of novel 4-(aryl)-benzo[4,5]imidazo[1,2-a]pyrimidine-3-carbonitriles were obtained through the Povarov (aza-Diels-Alder) and oxidation reactions, starting from benzimidazole-2-arylimines. Based on the literature data and X-ray diffraction analysis, it was discovered that during the Povarov reaction, [1,3] sigmatropic rearrangement leading to dihydrobenzimidazo[1,2-a]pyrimidines took place. The structures of all the obtained compounds were confirmed based on the data from 1H- and 13C-NMR spectroscopy, IR spectroscopy, and elemental analysis. For all the obtained compounds, their photophysical properties were studied. In all the cases, a positive emission solvatochromism with Stokes shifts from 120 to 180 nm was recorded. Aggregation-Induced Emission (AIE) has been illustrated for compound 6c using different water fractions (fw) in THF. The compounds 6c and 6f demonstrated changes in emission maxima or/and intensities after mechanical stimulation.
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Affiliation(s)
- Victor V. Fedotov
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Maria I. Valieva
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Olga S. Taniya
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Semen V. Aminov
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Mikhail A. Kharitonov
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
| | - Dmitry S. Kopchuk
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Pavel A. Slepukhin
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Grigory V. Zyryanov
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Evgeny N. Ulomsky
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Vladimir L. Rusinov
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
| | - Valery N. Charushin
- Chemical Engineering Institute, Ural Federal University, 19 Mira St., 620002 Yekaterinburg, Russia
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Yadav TT, Moin Shaikh G, Kumar MS, Chintamaneni M, YC M. A Review on Fused Pyrimidine Systems as EGFR Inhibitors and Their Structure–Activity Relationship. Front Chem 2022; 10:861288. [PMID: 35769445 PMCID: PMC9234326 DOI: 10.3389/fchem.2022.861288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/28/2022] [Indexed: 01/05/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) belongs to the family of tyrosine kinase that is activated when a specific ligand binds to it. The EGFR plays a vital role in the cellular proliferation process, differentiation, and apoptosis. In the case of cancer, EGFR undergoes uncontrolled auto-phosphorylation that results in increased cellular proliferation and decreased apoptosis, causing cancer promotion. From the literature, it shows that pyrimidine is one of the most commonly studied heterocycles for its antiproliferative activity against EGFR inhibition. The authors have collated some interesting results in the heterocycle-fused pyrimidines that have been studied using different cell lines (sensitive and mutational) and in animal models to determine their activity and potency. It is quite clear that the fused systems are highly effective in inhibiting EGFR activity in cancer cells. Therefore, the structure–activity relationship (SAR) comes into play in determining the nature of the heterocycle and the substituents that are responsible for the increased activity and toxicity. Understanding the SAR of heterocycle-fused pyrimidines will help in getting a better overview of the molecules concerning their activity and potency profile as future EGFR inhibitors.
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Affiliation(s)
| | | | | | | | - Mayur YC
- *Correspondence: Mayur YC, mayur
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