1
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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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2
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Liu R, Li W, Yao Y, Wu Y, Luo HB, Li Z. Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function. J Chem Inf Model 2023; 63:7755-7767. [PMID: 38048439 DOI: 10.1021/acs.jcim.3c01670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
The accurate prediction of the binding affinities between small molecules and biological macromolecules plays a fundamental role in structure-based drug design, which is still challenging. The free energy perturbation-based absolute binding free energy (FEP-ABFE) approach has shown potential in its reliability. To correctly calculate the energy related to the ligand being restrained by the receptor, additional restraints between the ligand and the receptor are needed. However, determining the restraint parameters for individual ligands empirically is too trivial to be automated, and usually gives rise to numerical instabilities, which set back the applications of FEP-ABFE. To address these issues, we derived the analytical expression for the probability distribution of energy differences, P(ΔU), during the process of restraint addition, which is called the RED-E (restraint energy distribution at equilibrium position) function. Simulations indicated that the RED-E function can accurately describe P(ΔU) when restraints are added at the equilibrium position. Based on the RED-E function, an automatic restraint selection method was proposed to select the best restraint. With this method, there is a high phase-space overlap between the free and restrained states, such that using a 2-λ perturbation can accurately calculate the free energy of the restraint addition, which is a nearly 6 times acceleration compared with current widely used 12-λ perturbation method. The RED-E function gives insight into the non-Gaussian behavior of the sampled P(ΔU) in certain FEP processes in an analytical way. The highly automated and accelerated restraint selection also makes it possible for the large-scale application of FEP-ABFE in real drug discovery practices.
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Affiliation(s)
- Runduo Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenchao Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yufen Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yinuo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan 570228, China
- Song Li' Academician Workstation of Hainan University (School of Pharmaceutical Sciences), Yazhou Bay, Sanya 572000, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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3
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Discovery of novel benzofuro[3,2-b]quinoline derivatives as dual CDK2/Topo I inhibitors. Bioorg Chem 2022; 126:105870. [DOI: 10.1016/j.bioorg.2022.105870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 12/31/2022]
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4
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Eco-friendly sequential one-pot synthesis, molecular docking, and anticancer evaluation of arylidene-hydrazinyl-thiazole derivatives as CDK2 inhibitors. Bioorg Chem 2021; 108:104615. [PMID: 33484942 DOI: 10.1016/j.bioorg.2020.104615] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/19/2020] [Accepted: 12/28/2020] [Indexed: 11/20/2022]
Abstract
One current approach in the treatment of cancer is the inhibition of cyclin dependent kinase (CDK) enzymes with small molecules. CDK are a class of enzymes, which catalyze the transfer of the terminal phosphate of a molecule of ATP to a protein that acts as a substrate. Among CDK enzymes, CDK2 has been implicated in a variety of cancers, supporting its potential as a novel target for cancer therapy across many tumor types. Here the discovery and development of arylidene-hydrazinyl-thiazole as a potentially CDK2 inhibitors is described, including details of the design and successful synthesis of the series analogs (27a-r) using one-pot approach under eco-friendly ultrasound and microwave conditions. Most of the newly synthesized compounds showed good growth inhibition when assayed for their in-vitro anti-proliferative activity against three cancer cell lines (HepG2, MCF-7 and HCT-116) compared to the reference drug roscovitine, with little toxicity on the normal fibroblast cell lines (WI-38). Furthermore, the compounds exhibiting the highest anti-proliferative activities were tested against a panel of kinase enzymes. These derivatives displayed an outstanding CDK2 inhibitory potential with varying degree of inhibition in the range of IC50 0.35-1.49 μM when compared with the standard inhibitor roscovitine having an IC50 value 0.71 μM. The most promising CDK2 inhibitor (27f) was selected for further studies to determine its effect on the cell cycle progression and apoptosis in HepG2 cell line. The results indicated that this compound implied inhibition in the G2/M phase of the cell cycle, and it is a good apoptotic agent. Finally, Molecular docking study was performed to identify the structural elements which involved in the inhibitory activity with the prospective target, CDK2, and to rationalize the structure-activity relationship (SAR).
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5
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Wu F, Zhuo L, Wang F, Huang W, Hao G, Yang G. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead. iScience 2020; 23:101179. [PMID: 32498019 PMCID: PMC7267738 DOI: 10.1016/j.isci.2020.101179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Motivated by the growing demand for reducing the chemical optimization burden of H2L, we developed auto in silico ligand directing evolution (AILDE, http://chemyang.ccnu.edu.cn/ccb/server/AILDE), an efficient and general approach for the rapid identification of drug leads in accessible chemical space. This computational strategy relies on minor chemical modifications on the scaffold of a hit compound, and it is primarily intended for identifying new lead compounds with minimal losses or, in some cases, even increases in ligand efficiency. We also described how AILDE greatly reduces the chemical optimization burden in the design of mesenchymal-epithelial transition factor (c-Met) kinase inhibitors. We only synthesized eight compounds and found highly efficient compound 5g, which showed an ∼1,000-fold improvement in in vitro activity compared with the hit compound. 5g also displayed excellent in vivo antitumor efficacy as a drug lead. We believe that AILDE may be applied to a large number of studies for rapid design and identification of drug leads. AILDE was developed for the rapid identification of drug leads A potent drug lead targeted to c-Met was found by synthesizing only eight compounds
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Linsheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Gefei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, P. R. China.
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6
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Cheng W, Yang Z, Wang S, Li Y, Wei H, Tian X, Kan Q. Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures. Eur J Med Chem 2019; 164:615-639. [PMID: 30639897 DOI: 10.1016/j.ejmech.2019.01.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases that display crucial effects in regulation of cell cycle and transcription. While the excessive expression of CDKs is intimate related to the development of diseases including cancers, which provides opportunities for disease treatment. A large number of small molecules are explored targeting CDKs. CDK/inhibitor co-crystal structures play an important role during the exploration of inhibitors. So far nine kinds of CDK/inhibitor co-crystals have been determined, they account for the highest proportion among the Protein Data Bank (PDB) deposited crystal structures. Herein, we review main co-crystals of CDKs in complex with corresponding inhibitors reported in recent years, focusing our attention on the binding models and the pharmacological activities of inhibitors.
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Affiliation(s)
- Weiyan Cheng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ying Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Han Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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7
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Tadesse S, Caldon EC, Tilley W, Wang S. Cyclin-Dependent Kinase 2 Inhibitors in Cancer Therapy: An Update. J Med Chem 2018; 62:4233-4251. [PMID: 30543440 DOI: 10.1021/acs.jmedchem.8b01469] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) drives the progression of cells into the S- and M-phases of the cell cycle. CDK2 activity is largely dispensable for normal development, but it is critically associated with tumor growth in multiple cancer types. Although the role of CDK2 in tumorigenesis has been controversial, emerging evidence proposes that selective CDK2 inhibition may provide a therapeutic benefit against certain tumors, and it continues to appeal as a strategy to exploit in anticancer drug development. Several small-molecule CDK2 inhibitors have progressed to the clinical trials. However, a CDK2-selective inhibitor is yet to be discovered. Here, we discuss the latest understandings of the role of CDK2 in normal and cancer cells, review the core pharmacophores used to target CDK2, and outline strategies for the rational design of CDK2 inhibitors. We attempt to provide an outlook on how CDK2-selective inhibitors may open new avenues for cancer therapy.
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Affiliation(s)
- Solomon Tadesse
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
| | - Elizabeth C Caldon
- The Kinghorn Cancer Centre , Garvan Institute of Medical Research , Darlinghurst , NSW 2010 , Australia.,St Vincent's Clinical School, UNSW Medicine , UNSW Sydney , Darlinghurst , NSW 2010 , Australia
| | - Wayne Tilley
- Adelaide Medical School , University of Adelaide , Adelaide , SA 5000 , Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
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8
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Zhang G, Ren Y. Molecular Modeling and Design Studies of Purine Derivatives as Novel CDK2 Inhibitors. Molecules 2018; 23:molecules23112924. [PMID: 30423939 PMCID: PMC6278423 DOI: 10.3390/molecules23112924] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential target for treating cancer. Purine heterocycles have attracted particular attention as the scaffolds for the development of CDK2 inhibitors. To explore the interaction mechanism and the structure–activity relationship (SAR) and to design novel candidate compounds as potential CDK2 inhibitors, a systematic molecular modeling study was conducted on 35 purine derivatives as CDK2 inhibitors by combining three-dimensional quantitative SAR (3D-QSAR), virtual screening, molecular docking, and molecular dynamics (MD) simulations. The predictive CoMFA model (q2 = 0.743, rpred2 = 0.991), the CoMSIA model (q2 = 0.808, rpred2 = 0.990), and the Topomer CoMFA model (q2 = 0.779, rpred2 = 0.962) were obtained. Contour maps revealed that the electrostatic, hydrophobic, hydrogen bond donor and steric fields played key roles in the QSAR models. Thirty-one novel candidate compounds with suitable predicted activity (predicted pIC50 > 8) were designed by using the results of virtual screening. Molecular docking indicated that residues Asp86, Glu81, Leu83, Lys89, Lys33, and Gln131 formed hydrogen bonds with the ligand, which affected activity of the ligand. Based on the QSAR model prediction and molecular docking, two candidate compounds, I13 and I60 (predicted pIC50 > 8, docking score > 10), with the most potential research value were further screened out. MD simulations of the corresponding complexes of these two candidate compounds further verified their stability. This study provided valuable information for the development of new potential CDK2 inhibitors.
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Affiliation(s)
- Gaomin Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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9
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Ruíz-Pérez KM, Quiroz-García B, Hernández-Rodríguez M. Prolinamides of Aminouracils, Organocatalyst Modifiable by Complementary Modules. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Karen M. Ruíz-Pérez
- Instituto de Química; Universidad Nacional Autónoma de México. Circuito Exterior; Ciudad Universitaria, Del. Coyoacán, C.P. 04510 México Cd. Mx. México
| | - Beatriz Quiroz-García
- Instituto de Química; Universidad Nacional Autónoma de México. Circuito Exterior; Ciudad Universitaria, Del. Coyoacán, C.P. 04510 México Cd. Mx. México
| | - Marcos Hernández-Rodríguez
- Instituto de Química; Universidad Nacional Autónoma de México. Circuito Exterior; Ciudad Universitaria, Del. Coyoacán, C.P. 04510 México Cd. Mx. México
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10
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Havel V, Sadilová T, Šindelář V. Unsubstituted Bambusurils: Post-Macrocyclization Modification of Versatile Intermediates. ACS OMEGA 2018; 3:4657-4663. [PMID: 31458686 PMCID: PMC6641224 DOI: 10.1021/acsomega.8b00497] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/19/2018] [Indexed: 06/10/2023]
Abstract
A new bambusuril derivative, (H)BU[6], lacking substituents on the ureidic nitrogen atoms, has been isolated and characterized. This macrocycle was prepared by the deprotection of bambusuril (PMB)BU[6]. (H)BU[6] is attractive for use as a starting compound for the preparation of other bambusuril derivatives, which was demonstrated via propargylation and the copper-catalyzed click reaction performed on the macrocycle.
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Affiliation(s)
- Václav Havel
- Department
of Chemistry, Faculty of Science, and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tereza Sadilová
- Department
of Chemistry, Faculty of Science, and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vladimír Šindelář
- Department
of Chemistry, Faculty of Science, and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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11
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Wang Y, Zhi Y, Jin Q, Lu S, Lin G, Yuan H, Yang T, Wang Z, Yao C, Ling J, Guo H, Li T, Jin J, Li B, Zhang L, Chen Y, Lu T. Discovery of 4-((7H-Pyrrolo[2,3-d]pyrimidin-4-yl)amino)-N-(4-((4-methylpiperazin-1-yl)methyl)phenyl)-1H-pyrazole-3-carboxamide (FN-1501), an FLT3- and CDK-Kinase Inhibitor with Potentially High Efficiency against Acute Myelocytic Leukemia. J Med Chem 2018; 61:1499-1518. [DOI: 10.1021/acs.jmedchem.7b01261] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yue Wang
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yanle Zhi
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Qiaomei Jin
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Shuai Lu
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Guowu Lin
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Haoliang Yuan
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Taotao Yang
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Zhanwei Wang
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Chao Yao
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jun Ling
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hao Guo
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Tonghui Li
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jianlin Jin
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Baoquan Li
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Li Zhang
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yadong Chen
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Tao Lu
- School
of Sciences and ‡State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
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12
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Trisubstituted purine inhibitors of PDGFRα and their antileukemic activity in the human eosinophilic cell line EOL-1. Bioorg Med Chem 2017; 25:6523-6535. [PMID: 29089259 DOI: 10.1016/j.bmc.2017.10.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/12/2017] [Accepted: 10/20/2017] [Indexed: 12/26/2022]
Abstract
Inhibition of protein kinases is a validated concept for pharmacological intervention in cancers. Many kinase inhibitors have been approved for clinical use, but their practical application is often limited. Here, we describe a collection of 23 novel 2,6,9-trisubstituted purine derivatives with nanomolar inhibitory activities against PDGFRα, a receptor tyrosine kinase often found constitutively activated in various tumours. The compounds demonstrated strong and selective cytotoxicity in the human eosinophilic leukemia cell line EOL-1, whereas several other cell lines were substantially less sensitive. The cytotoxicity in EOL-1, which is known to express the FIP1L1-PDGFRA fusion gene encoding an oncogenic kinase, correlated significantly with PDGFRα inhibition. EOL-1 cells treated with the compounds also exhibited dose-dependent inhibition of PDGFRα autophosphorylation and suppression of its downstream signaling pathways with concomitant G1 phase arrest, confirming the proposed mechanism of action. Our results show that substituted purines can be used as platforms for preparing tyrosine kinase inhibitors with specific activity towards eosinophilic leukemia.
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13
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Anthony NG, Baiget J, Berretta G, Boyd M, Breen D, Edwards J, Gamble C, Gray AI, Harvey AL, Hatziieremia S, Ho KH, Huggan JK, Lang S, Llona-Minguez S, Luo JL, McIntosh K, Paul A, Plevin RJ, Robertson MN, Scott R, Suckling CJ, Sutcliffe OB, Young LC, Mackay SP. Inhibitory Kappa B Kinase α (IKKα) Inhibitors That Recapitulate Their Selectivity in Cells against Isoform-Related Biomarkers. J Med Chem 2017; 60:7043-7066. [PMID: 28737909 PMCID: PMC5578373 DOI: 10.1021/acs.jmedchem.7b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Indexed: 01/01/2023]
Abstract
IKKβ plays a central role in the canonical NF-kB pathway, which has been extensively characterized. The role of IKKα in the noncanonical NF-kB pathway, and indeed in the canonical pathway as a complex with IKKβ, is less well understood. One major reason for this is the absence of chemical tools designed as selective inhibitors for IKKα over IKKβ. Herein, we report for the first time a series of novel, potent, and selective inhibitors of IKKα. We demonstrate effective target engagement and selectivity with IKKα in U2OS cells through inhibition of IKKα-driven p100 phosphorylation in the noncanonical NF-kB pathway without affecting IKKβ-dependent IKappa-Bα loss in the canonical pathway. These compounds represent the first chemical tools that can be used to further characterize the role of IKKα in cellular signaling, to dissect this from IKKβ and to validate it in its own right as a target in inflammatory diseases.
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Affiliation(s)
- Nahoum G. Anthony
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jessica Baiget
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Giacomo Berretta
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Marie Boyd
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - David Breen
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Joanne Edwards
- Wolfson Wohl Cancer Research Centre, Institute
of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland, United Kingdom
| | - Carly Gamble
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alexander I. Gray
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alan L. Harvey
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Sophia Hatziieremia
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Ka Ho Ho
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Judith K. Huggan
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Stuart Lang
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Sabin Llona-Minguez
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jia Lin Luo
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Kathryn McIntosh
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Andrew Paul
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Robin J. Plevin
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Murray N. Robertson
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Rebecca Scott
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Colin J. Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Oliver B. Sutcliffe
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Louise C. Young
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Simon P. Mackay
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
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14
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Xu X, Yao Q. Scaffold Hopping Approach to a New Series of Pyridine Derivatives as Potent Inhibitors of CDK2. Arch Pharm (Weinheim) 2016; 349:224-31. [DOI: 10.1002/ardp.201500335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojuan Xu
- School of Chemistry and Chemical Engineering; Yancheng Teachers University; Yancheng China
| | - Qizheng Yao
- Department of Medicinal Chemistry, School of Pharmacy; China Pharmaceutical University; Nanjing China
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15
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Efficient functionalization of 2-amino-6-chloropurine derivatives at C-8 via 8-lithiated species. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.09.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Tanneeru K, Balla AR, Guruprasad L. In silico3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase. J Biomol Struct Dyn 2014; 33:1710-9. [DOI: 10.1080/07391102.2014.968622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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