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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Teo T, Kasirzadeh S, Albrecht H, Sykes MJ, Yang Y, Wang S. An Overview of CDK3 in Cancer: Clinical Significance and Pharmacological Implications. Pharmacol Res 2022; 180:106249. [DOI: 10.1016/j.phrs.2022.106249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
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3
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El-Sattar NEAA, Badawy EHK, AbdEl-Hady WH, Abo-Alkasem MI, Mandour AA, Ismail NSM. Design and Synthesis of New CDK2 Inhibitors Containing Thiazolone and Thiazolthione Scafold with Apoptotic Activity. Chem Pharm Bull (Tokyo) 2021; 69:106-117. [PMID: 33390512 DOI: 10.1248/cpb.c20-00714] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cyclin dependent kinase 2 (CDK2) inhibition is a well-established strategy for treating cancer. Different series of novel thiazolone (1, 7-9) together with fused thiazolthione (2-6, and 10) derivatives were designed, then synthesized and evaluated for their biological inhibitory activity against CDK2. Additionally, the cytotoxicity of the new compounds was explored against breast and colon cancer cell lines. The novel thiazolone and the fused thiazolthione derivatives exhibited potent CDK2/cyclin A2 inhibitory effect of an IC50 values ranging 105.39-742.78 nM. Amongst them compounds 4 and 6 revealed highest IC50 of 105.39 and 139.27 nM, respectively. Most compounds showed significant inhibition on both breast cancer and colon cancer cell lines with IC50 range 0.54-5.26 and 0.83-278 µM, respectively. Further investigations involved flow cytometry analysis on MCF-7 cancer cell line for compounds 5 and 7 which resulted in arrest cell-cycle at two phases Pre G1/G2-M and re-enforced apoptosis via activation of caspase-7. Molecular modeling simulation of the designed compounds revealed that they were well fitted into CDK2 active site and their complexes were stabilized through the essential hydrogen bonding. Three dimensional quantitative structure activity relationship (3D QSAR) pharmacophore, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were also carried out showing proper pharmacokinetic and drug-likeness which aided in the prediction of the structure requirements responsible for the observed antitumor activity.
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Affiliation(s)
- Nour E A Abd El-Sattar
- Department of Chemistry, Organic Labs, and Computational Chemistry Lab, Faculty of Science, Ain Shams University
| | - Eman H K Badawy
- Department of Chemistry, Organic Labs, and Computational Chemistry Lab, Faculty of Science, Ain Shams University
| | - Wafaa H AbdEl-Hady
- Department of Chemistry, Organic Labs, and Computational Chemistry Lab, Faculty of Science, Ain Shams University
| | - Mohamed I Abo-Alkasem
- Department of chemistry of Natural and Microbial Products, National Research Center.,Biotechnology and genetic Engineering Pilot Plant Unit, National Research Centre
| | - Asmaa A Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt (FUE)
| | - Nasser S M Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Future University in Egypt (FUE)
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4
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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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5
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Jorda R, Hendrychová D, Voller J, Řezníčková E, Gucký T, Kryštof V. How Selective Are Pharmacological Inhibitors of Cell-Cycle-Regulating Cyclin-Dependent Kinases? J Med Chem 2018; 61:9105-9120. [PMID: 30234987 DOI: 10.1021/acs.jmedchem.8b00049] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclin-dependent kinases (CDKs) are an important and emerging class of drug targets for which many small-molecule inhibitors have been developed. However, there is often insufficient data available on the selectivity of CDK inhibitors (CDKi) to attribute the effects on the presumed target CDK to these inhibitors. Here, we highlight discrepancies between the kinase selectivity of CDKi and the phenotype exhibited; we evaluated 31 CDKi (claimed to target CDK1-4) for activity toward CDKs 1, 2, 4, 5, 7, 9 and for effects on the cell cycle. Our results suggest that most CDKi should be reclassified as pan-selective and should not be used as a tool. In addition, some compounds did not even inhibit CDKs as their primary cellular targets; for example, NU6140 showed potent inhibition of Aurora kinases. We also established an online database of commercially available CDKi for critical evaluation of their utility as molecular probes. Our results should help researchers select the most relevant chemical tools for their specific applications.
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Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Denisa Hendrychová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Jiří Voller
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Eva Řezníčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Tomáš Gucký
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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6
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Ye L, Guo L, He Z, Wang X, Lin C, Zhang X, Wu S, Bao Y, Yang Q, Song L, Lin H. Upregulation of E2F8 promotes cell proliferation and tumorigenicity in breast cancer by modulating G1/S phase transition. Oncotarget 2018; 7:23757-71. [PMID: 26992224 PMCID: PMC5029661 DOI: 10.18632/oncotarget.8121] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/25/2016] [Indexed: 01/04/2023] Open
Abstract
E2F transcription factors are involved in cell cycle regulation and synthesis of DNA in mammalian cells, and simultaneously play important roles in the development and progression of cancer when dysregulated. E2F8, a novel identified E2F family member, was found to be associated with the progression of several human cancers; however, the biological role and clinical significance of E2F8 in breast cancer remain to be further elucidated. Herein, we report that E2F8 is robustly elevated in breast cancer cell lines and clinical breast cancer tissue samples, respectively. The high expression level of E2F8 significantly correlates with clinical progression (P = 0.001), poor patient survival (P < 0.001) and a high Ki67 staining index (P = 0.008) in 187 human breast cancer specimens. Furthermore, we find that overexpressing E2F8 promotes, whereas silencing E2F8 suppresses, the proliferation and tumorigenicity of breast cancer cells both in vitro and in vivo. We further demonstrate that E2F8 transcriptionally upregulates CCNE1 and CCNE2 via directly interacting with their respective gene promoter, which accelerates the transition of G1 to S phase of breast cancer cells. Taken together, these findings uncover a novel biologic role and regulatory mechanism of E2F8 responsible for the progression of breast cancer, indicating E2F8 may represent a novel prognostic biomarker and therapeutic target against breast cancer.
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Affiliation(s)
- Liping Ye
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Ling Guo
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Zhenyu He
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Xi Wang
- Department of Breast Surgery, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Xin Zhang
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Shu Wu
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Yong Bao
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Qi Yang
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Huanxin Lin
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
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7
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Selective inhibition reveals cyclin-dependent kinase 2 as another kinase that phosphorylates the androgen receptor at serine 81. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:354-363. [DOI: 10.1016/j.bbamcr.2017.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022]
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8
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Bacevic K, Noble R, Soffar A, Wael Ammar O, Boszonyik B, Prieto S, Vincent C, Hochberg ME, Krasinska L, Fisher D. Spatial competition constrains resistance to targeted cancer therapy. Nat Commun 2017; 8:1995. [PMID: 29222471 PMCID: PMC5722825 DOI: 10.1038/s41467-017-01516-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/25/2017] [Indexed: 01/08/2023] Open
Abstract
Adaptive therapy (AT) aims to control tumour burden by maintaining therapy-sensitive cells to exploit their competition with resistant cells. This relies on the assumption that resistant cells have impaired cellular fitness. Here, using a model of resistance to a pharmacological cyclin-dependent kinase inhibitor (CDKi), we show that this assumption is valid when competition between cells is spatially structured. We generate CDKi-resistant cancer cells and find that they have reduced proliferative fitness and stably rewired cell cycle control pathways. Low-dose CDKi outperforms high-dose CDKi in controlling tumour burden and resistance in tumour spheroids, but not in monolayer culture. Mathematical modelling indicates that tumour spatial structure amplifies the fitness penalty of resistant cells, and identifies their relative fitness as a critical determinant of the clinical benefit of AT. Our results justify further investigation of AT with kinase inhibitors. Adaptive therapy aims to control tumours by exploiting competition between therapy-sensitive and resistant cells. Here, the authors show that tumour spatial structure is a critical parameter for adaptive therapy as competition for space increases fitness differentials, allowing suppression of resistance with low-dose treatments.
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Affiliation(s)
- Katarina Bacevic
- IGMM, CNRS, University of Montpellier, 34090, Montpellier, France
| | - Robert Noble
- ISEM, University of Montpellier, 34090, Montpellier, France.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Ahmed Soffar
- IGMM, CNRS, University of Montpellier, 34090, Montpellier, France.,Division of Molecular Biology, Department of Zoology, Faculty of Science Alexandria University, 21526, Alexandria, Egypt
| | | | | | - Susana Prieto
- IGMM, CNRS, University of Montpellier, 34090, Montpellier, France
| | | | - Michael E Hochberg
- ISEM, University of Montpellier, 34090, Montpellier, France.,Santa Fe Institute, Santa Fe, NM, 87501, USA
| | | | - Daniel Fisher
- IGMM, CNRS, University of Montpellier, 34090, Montpellier, France.
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9
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Coxon C, Anscombe E, Harnor SJ, Martin MP, Carbain B, Golding BT, Hardcastle IR, Harlow LK, Korolchuk S, Matheson CJ, Newell DR, Noble MEM, Sivaprakasam M, Tudhope SJ, Turner DM, Wang LZ, Wedge SR, Wong C, Griffin RJ, Endicott JA, Cano C. Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines. J Med Chem 2017; 60:1746-1767. [PMID: 28005359 PMCID: PMC6111440 DOI: 10.1021/acs.jmedchem.6b01254] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Indexed: 02/08/2023]
Abstract
Purines and related heterocycles substituted at C-2 with 4'-sulfamoylanilino and at C-6 with a variety of groups have been synthesized with the aim of achieving selectivity of binding to CDK2 over CDK1. 6-Substituents that favor competitive inhibition at the ATP binding site of CDK2 were identified and typically exhibited 10-80-fold greater inhibition of CDK2 compared to CDK1. Most impressive was 4-((6-([1,1'-biphenyl]-3-yl)-9H-purin-2-yl)amino) benzenesulfonamide (73) that exhibited high potency toward CDK2 (IC50 0.044 μM) but was ∼2000-fold less active toward CDK1 (IC50 86 μM). This compound is therefore a useful tool for studies of cell cycle regulation. Crystal structures of inhibitor-kinase complexes showed that the inhibitor stabilizes a glycine-rich loop conformation that shapes the ATP ribose binding pocket and that is preferred in CDK2 but has not been observed in CDK1. This aspect of the active site may be exploited for the design of inhibitors that distinguish between CDK1 and CDK2.
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Affiliation(s)
- Christopher
R. Coxon
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Elizabeth Anscombe
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Suzannah J. Harnor
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Mathew P. Martin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Benoit Carbain
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Bernard T. Golding
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Ian R. Hardcastle
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lisa K. Harlow
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Svitlana Korolchuk
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Christopher J. Matheson
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - David R. Newell
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Martin E. M. Noble
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mangaleswaran Sivaprakasam
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Susan J. Tudhope
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - David M. Turner
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lan Z. Wang
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Stephen R. Wedge
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Christopher Wong
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Roger J. Griffin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Jane A. Endicott
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Céline Cano
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
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10
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Beale G, Haagensen EJ, Thomas HD, Wang LZ, Revill CH, Payne SL, Golding BT, Hardcastle IR, Newell DR, Griffin RJ, Cano C. Combined PI3K and CDK2 inhibition induces cell death and enhances in vivo antitumour activity in colorectal cancer. Br J Cancer 2016; 115:682-90. [PMID: 27529512 PMCID: PMC5023777 DOI: 10.1038/bjc.2016.238] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/31/2016] [Accepted: 07/14/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The phosphatidylinositol-3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway is commonly deregulated in human cancer, hence many PI3K and mTOR inhibitors have been developed and have now reached clinical trials. Similarly, CDKs have been investigated as cancer drug targets. METHODS We have synthesised and characterised a series of 6-aminopyrimidines identified from a kinase screen that inhibit PI3K and/or mTOR and/or CDK2. Kinase inhibition, tumour cell growth, cell cycle distribution, cytotoxicity and signalling experiments were undertaken in HCT116 and HT29 colorectal cancer cell lines, and in vivo HT29 efficacy studies. RESULTS 2,6-Diaminopyrimidines with an O(4)-cyclohexylmethyl substituent and a C-5-nitroso or cyano group (1,2,5) induced cell cycle phase alterations and were growth inhibitory (GI50<20 μM). Compound 1, but not 2 or 5, potently inhibits CDK2 (IC50=0.1 nM) as well as PI3K, and was cytotoxic at growth inhibitory concentrations. Consistent with kinase inhibition data, compound 1 reduced phospho-Rb and phospho-rS6 at GI50 concentrations. Combination of NU6102 (CDK2 inhibitor) and pictilisib (GDC-0941; pan-PI3K inhibitor) resulted in synergistic growth inhibition, and enhanced cytotoxicity in HT29 cells in vitro and HT29 tumour growth inhibition in vivo. CONCLUSIONS These studies identified a novel series of mixed CDK2/PI3K inhibitors and demonstrate that dual targeting of CDK2 and PI3K can result in enhanced antitumour activity.
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Affiliation(s)
- Gary Beale
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Emma J Haagensen
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Huw D Thomas
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Lan-Zhen Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Charlotte H Revill
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Sara L Payne
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Ian R Hardcastle
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
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11
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Anscombe E, Meschini E, Mora-Vidal R, Martin MP, Staunton D, Geitmann M, Danielson UH, Stanley WA, Wang LZ, Reuillon T, Golding BT, Cano C, Newell DR, Noble MEM, Wedge SR, Endicott JA, Griffin RJ. Identification and Characterization of an Irreversible Inhibitor of CDK2. CHEMISTRY & BIOLOGY 2015; 22:1159-64. [PMID: 26320860 PMCID: PMC4579270 DOI: 10.1016/j.chembiol.2015.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2015] [Accepted: 07/24/2015] [Indexed: 01/04/2023]
Abstract
Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.
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Affiliation(s)
- Elizabeth Anscombe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elisa Meschini
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Regina Mora-Vidal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - David Staunton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - U Helena Danielson
- Beactica AB, Box 567, 751 22 Uppsala, Sweden; Department of Chemistry-BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Will A Stanley
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lan Z Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Tristan Reuillon
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin E M Noble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen R Wedge
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Carbain B, Paterson DJ, Anscombe E, Campbell AJ, Cano C, Echalier A, Endicott JA, Golding BT, Haggerty K, Hardcastle IR, Jewsbury PJ, Newell DR, Noble MEM, Roche C, Wang LZ, Griffin RJ. 8-Substituted O(6)-cyclohexylmethylguanine CDK2 inhibitors: using structure-based inhibitor design to optimize an alternative binding mode. J Med Chem 2014; 57:56-70. [PMID: 24304238 DOI: 10.1021/jm401555v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Evaluation of the effects of purine C-8 substitution within a series of CDK1/2-selective O(6)-cyclohexylmethylguanine derivatives revealed that potency decreases initially with increasing size of the alkyl substituent. Structural analysis showed that C-8 substitution is poorly tolerated, and to avoid unacceptable steric interactions, these compounds adopt novel binding modes. Thus, 2-amino-6-cyclohexylmethoxy-8-isopropyl-9H-purine adopts a "reverse" binding mode where the purine backbone has flipped 180°. This provided a novel lead chemotype from which we have designed more potent CDK2 inhibitors using, in the first instance, quantum mechanical energy calculations. Introduction of an ortho-tolyl or ortho-chlorophenyl group at the purine C-8 position restored the potency of these "reverse" binding mode inhibitors to that of the parent 2-amino-6-cyclohexylmethoxy-9H-purine. By contrast, the corresponding 8-(2-methyl-3-sulfamoylphenyl)-purine derivative exhibited submicromolar CDK2-inhibitory activity by virtue of engineered additional interactions with Asp86 and Lys89 in the reversed binding mode, as confirmed by X-ray crystallography.
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Affiliation(s)
- Benoit Carbain
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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