1
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Shimazaki T, Tachikawa M. Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2. ACS OMEGA 2022; 7:10372-10381. [PMID: 35382271 PMCID: PMC8973106 DOI: 10.1021/acsomega.1c06976] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/09/2022] [Indexed: 05/13/2023]
Abstract
To improve virtual screening for drug discovery, we present a collaborative approach between explainable artificial intelligence (AI) and simplified chemical interaction scores to efficiently search for active ligands bound to the target receptor. In particular, we focus on cyclin-dependent kinase 2 (CDK2), which is well known as a cancer target protein. Docking simulation alone is insufficient to distinguish active ligands from decoy molecules. To identify active ligands, in this paper, machine learning is employed together with scoring functions that simplify the screened Coulomb and Lennard-Jones interactions between the ligands and residues of the target receptor. We demonstrate that these simplified interaction scores can significantly improve the classification ability of machine learning models. We also demonstrate that explainable AI together with the simplified scoring method can highlight the important residues of CDK2 for recognizing active ligands.
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Affiliation(s)
- Tomomi Shimazaki
- Graduate
School of Nanobioscience, Yokohama City
University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan
| | - Masanori Tachikawa
- Graduate
School of Data Science, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa 236-0027, Japan
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2
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Barlaam B, Casella R, Cidado J, Cook C, De Savi C, Dishington A, Donald CS, Drew L, Ferguson AD, Ferguson D, Glossop S, Grebe T, Gu C, Hande S, Hawkins J, Hird AW, Holmes J, Horstick J, Jiang Y, Lamb ML, McGuire TM, Moore JE, O'Connell N, Pike A, Pike KG, Proia T, Roberts B, San Martin M, Sarkar U, Shao W, Stead D, Sumner N, Thakur K, Vasbinder MM, Varnes JG, Wang J, Wang L, Wu D, Wu L, Yang B, Yao T. Discovery of AZD4573, a Potent and Selective Inhibitor of CDK9 That Enables Short Duration of Target Engagement for the Treatment of Hematological Malignancies. J Med Chem 2020; 63:15564-15590. [PMID: 33306391 DOI: 10.1021/acs.jmedchem.0c01754] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A CDK9 inhibitor having short target engagement would enable a reduction of Mcl-1 activity, resulting in apoptosis in cancer cells dependent on Mcl-1 for survival. We report the optimization of a series of amidopyridines (from compound 2), focusing on properties suitable for achieving short target engagement after intravenous administration. By increasing potency and human metabolic clearance, we identified compound 24, a potent and selective CDK9 inhibitor with suitable predicted human pharmacokinetic properties to deliver transient inhibition of CDK9. Furthermore, the solubility of 24 was considered adequate to allow i.v. formulation at the anticipated effective dose. Short-term treatment with compound 24 led to a rapid dose- and time-dependent decrease of pSer2-RNAP2 and Mcl-1, resulting in cell apoptosis in multiple hematological cancer cell lines. Intermittent dosing of compound 24 demonstrated efficacy in xenograft models derived from multiple hematological tumors. Compound 24 is currently in clinical trials for the treatment of hematological malignancies.
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Affiliation(s)
- Bernard Barlaam
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Robert Casella
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Justin Cidado
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Calum Cook
- Oncology R&D, AstraZeneca, Macclesfield, SK10 2NA, United Kingdom
| | - Chris De Savi
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Craig S Donald
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Lisa Drew
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Andrew D Ferguson
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Douglas Ferguson
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steve Glossop
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Tyler Grebe
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Chungang Gu
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Sudhir Hande
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Janet Hawkins
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Alexander W Hird
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Jane Holmes
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - James Horstick
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Yun Jiang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing, 100176, P. R. China
| | - Michelle L Lamb
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Jane E Moore
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Nichole O'Connell
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Andy Pike
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Kurt G Pike
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Theresa Proia
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Bryan Roberts
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | | | - Ujjal Sarkar
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Wenlin Shao
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Darren Stead
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Neil Sumner
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Kumar Thakur
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Jeffrey G Varnes
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Jianyan Wang
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Lei Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing, 100176, P. R. China
| | - Dedong Wu
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Liangwei Wu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing, 100176, P. R. China
| | - Bin Yang
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Tieguang Yao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing, 100176, P. R. China
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3
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Volkart PA, Bitencourt-Ferreira G, Souto AA, de Azevedo WF. Cyclin-Dependent Kinase 2 in Cellular Senescence and Cancer. A Structural and Functional Review. Curr Drug Targets 2019; 20:716-726. [DOI: 10.2174/1389450120666181204165344] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 02/03/2023]
Abstract
<P>Background: Cyclin-dependent kinase 2 (CDK2) has been studied due to its role in the
cell-cycle progression. The elucidation of the CDK2 structure paved the way to investigate the molecular
basis for inhibition of this enzyme, with the coordinated efforts combining crystallography with
functional studies.
</P><P>
Objective: Our goal here is to review recent functional and structural studies directed to understanding
the role of CDK2 in cancer and senescence.
</P><P>
Methods: There are over four hundreds of crystallographic structures available for CDK2, many of
them with binding affinity information. We use this abundance of data to analyze the essential features
responsible for the inhibition of CDK2 and its function in cancer and senescence.
</P><P>
Results: The structural and affinity data available CDK2 makes it possible to have a clear view of the
vital CDK2 residues involved in molecular recognition. A detailed description of the structural basis
for ligand binding is of pivotal importance in the design of CDK2 inhibitors. Our analysis shows the
relevance of the residues Leu 83 and Asp 86 for binding affinity. The recent findings revealing the
participation of CDK2 inhibition in senescence open the possibility to explore the richness of structural
and affinity data for a new era in the development of CDK2 inhibitors, targeting cellular senescence.
</P><P>
Conclusion: Here, we analyzed structural information for CDK2 in combination with inhibitors and
mapped the molecular aspects behind the strongest CDK2 inhibitors for which structures and ligandbinding
affinity data were available. From this analysis, we identified the significant intermolecular
interactions responsible for binding affinity. This knowledge may guide the future development of
CDK2 inhibitors targeting cancer and cellular senescence.</P>
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Affiliation(s)
- Priscylla Andrade Volkart
- School of Sciences - Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
| | - Gabriela Bitencourt-Ferreira
- School of Sciences - Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
| | - André Arigony Souto
- School of Sciences - Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- School of Sciences - Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
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4
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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5
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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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6
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Mahajan P, Chashoo G, Gupta M, Kumar A, Singh PP, Nargotra A. Fusion of Structure and Ligand Based Methods for Identification of Novel CDK2 Inhibitors. J Chem Inf Model 2017; 57:1957-1969. [PMID: 28723151 DOI: 10.1021/acs.jcim.7b00293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cyclin dependent kinases play a central role in cell cycle regulation which makes them a promising target with multifarious therapeutic potential. CDK2 regulates various events of the eukaryotic cell division cycle, and the pharmacological evidence indicates that overexpression of CDK2 causes abnormal cell-cycle regulation, which is directly associated with hyperproliferation of cancer cells. Therefore, CDK2 is regarded as a potential target molecule for anticancer medication. Thus, to decline CDK2 activity by potential lead compounds has proved to be an effective treatment for cancer. The availability of a large number of X-ray crystal structures and known inhibitors of CDK2 provides a gateway to perform efficient computational studies on this target. With the aim to identify new chemical entities from commercial libraries, with increased inhibitory potency for CDK2, ligand and structure based computational drug designing approaches were applied. A druglike library of 50,000 compounds from ChemDiv and ChemBridge databases was screened against CDK2, and 110 compounds were identified using the parallel application of these models. On in vitro evaluation of 40 compounds, seven compounds were found to have more than 50% inhibition at 10 μM. MD studies of the hits revealed the stability of these inhibitors and pivotal role of Glu81 and Leu83 for binding with CDK2. The overall study resulted in the identification of four new chemical entities possessing CDK2 inhibitory activity.
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Affiliation(s)
- Priya Mahajan
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Gousia Chashoo
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Monika Gupta
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Kumar
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Parvinder Pal Singh
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery Informatics, ‡Cancer Pharmacology, §Medicinal Chemistry, and ∥Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
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7
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Kettle JG, Wilson DM. Standing on the shoulders of giants: a retrospective analysis of kinase drug discovery at AstraZeneca. Drug Discov Today 2016; 21:1596-1608. [DOI: 10.1016/j.drudis.2016.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/05/2016] [Accepted: 06/07/2016] [Indexed: 11/26/2022]
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8
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Grigoroudis AI, Kontopidis G. Preparation of CDK/Cyclin Inhibitor Complexes for Structural Determination. Methods Mol Biol 2016; 1336:29-45. [PMID: 26231706 DOI: 10.1007/978-1-4939-2926-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The abundance of biochemical and structural knowledge on the Cyclin-Dependent Kinases (CDKs) has provided a comprehensive but not exhaustive insight into the molecular determinants that govern their function mechanisms. The implementation of structural and functional CDK models towards developing novel anticancer strategies that will specifically target individual or multiple CDKs remains a critical need.More than 250 CDKs crystal structures are available to-date, including truncated or whole, modified or not, active or inactive forms, co-crystallized with the cyclins and/or their respective putative inhibitors, though, to our knowledge, there is no NMR solved structure available to date. We hitherto attempt to provide a useful guide from protein production to crystallization for CDK/Inhibitors complexes based on an overview of the already elucidated CDK structures, constructs and the preferable expression vectors in each case, in order to yield the respective crystals.
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Affiliation(s)
- Asterios I Grigoroudis
- Department of Biochemistry, Veterinary School, University of Thessaly, Trikalon 224 Str., Karditsa, 43100, Greece
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9
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Elsayed NMY, Abou El Ella DA, Serya RAT, Tolba MF, Shalaby R, Abouzid KAM. Design, synthesis and biological evaluation of indazole–pyrimidine based derivatives as anticancer agents with anti-angiogenic and antiproliferative activities. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00602c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three series of novel indazole–pyrimidine based compounds were designed, synthesized and biologically evaluated as VEGFR-2 kinase inhibitors.
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Affiliation(s)
- Nevine M. Y. Elsayed
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Dalal A. Abou El Ella
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Rabah A. T. Serya
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Mai F. Tolba
- Pharmacology and Toxicology Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Raed Shalaby
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Khaled A. M. Abouzid
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
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10
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Lam F, Abbas AY, Shao H, Teo T, Adams J, Li P, Bradshaw TD, Fischer PM, Walsby E, Pepper C, Chen Y, Ding J, Wang S. Targeting RNA transcription and translation in ovarian cancer cells with pharmacological inhibitor CDKI-73. Oncotarget 2014; 5:7691-704. [PMID: 25277198 PMCID: PMC4202154 DOI: 10.18632/oncotarget.2296] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/31/2014] [Indexed: 01/09/2023] Open
Abstract
Dysregulation of cellular transcription and translation is a fundamental hallmark of cancer. As CDK9 and Mnks play pivotal roles in the regulation of RNA transcription and protein synthesis, respectively, they are important targets for drug development. We herein report the cellular mechanism of a novel CDK9 inhibitor CDKI-73 in an ovarian cancer cell line (A2780). We also used shRNA-mediated CDK9 knockdown to investigate the importance of CDK9 in the maintenance of A2780 cells. This study revealed that CDKI-73 rapidly inhibited cellular CDK9 kinase activity and down-regulated the RNAPII phosphorylation. This subsequently caused a decrease in the eIF4E phosphorylation by blocking Mnk1 kinase activity. Consistently, CDK9 shRNA was also found to down-regulate the Mnk1 expression. Both CDKI-73 and CDK9 shRNA decreased anti-apoptotic proteins Mcl-1 and Bcl-2 and induced apoptosis. The study confirmed that CDK9 is required for cell survival and that ovarian cancer may be susceptible to CDK9 inhibition strategy. The data also implied a role of CDK9 in eIF4E-mediated translational control, suggesting that CDK9 may have important implication in the Mnk-eIF4E axis, the key determinants of PI3K/Akt/mTOR- and Ras/Raf/MAPK-mediated tumorigenic activity. As such, CDK9 inhibitor drug candidate CDKI-73 should have a major impact on these pathways in human cancers.
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Affiliation(s)
- Frankie Lam
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Abdullahi Y. Abbas
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hao Shao
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Theodosia Teo
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Julian Adams
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Peng Li
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Tracey D. Bradshaw
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Peter M. Fischer
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Elisabeth Walsby
- Cardiff CLL Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Health Park, Cardiff, United Kingdom
| | - Chris Pepper
- Cardiff CLL Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Health Park, Cardiff, United Kingdom
| | - Yi Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jian Ding
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Shudong Wang
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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11
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Shao H, Shi S, Huang S, Hole A, Abbas AY, Baumli S, Liu X, Lam F, Foley D, Fischer PM, Noble M, Endicott JA, Pepper C, Wang S. Substituted 4-(thiazol-5-yl)-2-(phenylamino)pyrimidines are highly active CDK9 inhibitors: synthesis, X-ray crystal structures, structure-activity relationship, and anticancer activities. J Med Chem 2013; 56:640-59. [PMID: 23301767 PMCID: PMC3579313 DOI: 10.1021/jm301475f] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cancer cells often have a high demand for antiapoptotic proteins in order to resist programmed cell death. CDK9 inhibition selectively targets survival proteins and reinstates apoptosis in cancer cells. We designed a series of 4-thiazol-2-anilinopyrimidine derivatives with functional groups attached to the C5-position of the pyrimidine or to the C4-thiazol moiety and investigated their effects on CDK9 potency and selectivity. One of the most selective compounds, 12u inhibits CDK9 with IC(50) = 7 nM and shows over 80-fold selectivity for CDK9 versus CDK2. X-ray crystal structures of 12u bound to CDK9 and CDK2 provide insights into the binding modes. This work, together with crystal structures of selected inhibitors in complex with both enzymes described in a companion paper, (34) provides a rationale for the observed SAR. 12u demonstrates potent anticancer activity against primary chronic lymphocytic leukemia cells with a therapeutic window 31- and 107-fold over those of normal B- and T-cells.
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Affiliation(s)
- Hao Shao
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shenhua Shi
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shiliang Huang
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Alison
J. Hole
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Abdullahi Y. Abbas
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Sonja Baumli
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Xiangrui Liu
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Frankie Lam
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
- Shool of Pharmacy and Medical
Sciences, University of South Australia, Adelaide, SA 5001, Australia
| | - David
W. Foley
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Peter M. Fischer
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Martin Noble
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- Northern Institute for Cancer
Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Jane A. Endicott
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- Northern Institute for Cancer
Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Chris Pepper
- Institute of Cancer and Genetics,
School of Medicine, Cardiff University,
Heath Park, Cardiff CF14 4XN, U.K
| | - Shudong Wang
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
- Shool of Pharmacy and Medical
Sciences, University of South Australia, Adelaide, SA 5001, Australia
- Phone: +61883022372. E-mail:
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12
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Wada H, Cheng L, Jiang J, Jiang Z, Xie J, Hu T, Sanganee H, Luker T. Facile and regioselective synthesis of novel 2,4-disubstituted-5-fluoropyrimidines as potential kinase inhibitors. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.01.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Natrajan R, Mackay A, Wilkerson PM, Lambros MB, Wetterskog D, Arnedos M, Shiu KK, Geyer FC, Langerød A, Kreike B, Reyal F, Horlings HM, van de Vijver MJ, Palacios J, Weigelt B, Reis-Filho JS. Functional characterization of the 19q12 amplicon in grade III breast cancers. Breast Cancer Res 2012; 14:R53. [PMID: 22433433 PMCID: PMC3446387 DOI: 10.1186/bcr3154] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 03/04/2012] [Accepted: 03/20/2012] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION The 19q12 locus is amplified in a subgroup of oestrogen receptor (ER)-negative grade III breast cancers. This amplicon comprises nine genes, including cyclin E1 (CCNE1), which has been proposed as its 'driver'. The aim of this study was to identify the genes within the 19q12 amplicon whose expression is required for the survival of cancer cells harbouring their amplification. METHODS We investigated the presence of 19q12 amplification in a series of 313 frozen primary breast cancers and 56 breast cancer cell lines using microarray comparative genomic hybridisation (aCGH). The nine genes mapping to the smallest region of amplification on 19q12 were silenced using RNA interference in phenotypically matched breast cancer cell lines with (MDA-MB-157 and HCC1569) and without (Hs578T, MCF7, MDA-MB-231, ZR75.1, JIMT1 and BT474) amplification of this locus. Genes whose silencing was selectively lethal in amplified cells were taken forward for further validation. The effects of cyclin-dependent kinase 2 (CDK2) silencing and chemical inhibition were tested in cancer cells with and without CCNE1 amplification. RESULTS 19q12 amplification was identified in 7.8% of ER-negative grade III breast cancer. Of the nine genes mapping to this amplicon, UQCRFS1, POP4, PLEKHF1, C19ORF12, CCNE1 and C19ORF2 were significantly over-expressed when amplified in primary breast cancers and/or breast cancer cell lines. Silencing of POP4, PLEKHF1, CCNE1 and TSZH3 selectively reduced cell viability in cancer cells harbouring their amplification. Cancer cells with CCNE1 amplification were shown to be dependent on CDK2 expression and kinase activity for their survival. CONCLUSIONS The 19q12 amplicon may harbour more than a single 'driver', given that expression of POP4, PLEKHF1, CCNE1 and TSZH3 is required for the survival of cancer cells displaying their amplification. The observation that cancer cells harbouring CCNE1 gene amplification are sensitive to CDK2 inhibitors provides a rationale for the testing of these chemical inhibitors in a subgroup of patients with ER-negative grade III breast cancers.
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Affiliation(s)
- Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Alan Mackay
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Paul M Wilkerson
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Maryou B Lambros
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Daniel Wetterskog
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Monica Arnedos
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Kai-Keen Shiu
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Felipe C Geyer
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Ullernchausèen 70, Montebello, Oslo, 0310, Norway
| | - Bas Kreike
- Institute for Radiation Oncology Arnhem, Wagnerlaan 47, Arnhem 6815 AD, The Netherlands
| | - Fabien Reyal
- Department of Surgery, Institut Curie, 26 rue d'Ulm, Paris, 75005, France
| | - Hugo M Horlings
- Department of Pathology, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Jose Palacios
- Servicio de Anatomia Patologica, HHUU Virgen del Rocío, Avda. Manuel Siurot, s/n, Seville, 41013, Spain
| | - Britta Weigelt
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Jorge S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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14
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Wang F, Ma Z, Li Y, Zhu S, Xiao Z, Zhang H, Wang Y. Development of in silico models for pyrazoles and pyrimidine derivatives as cyclin-dependent kinase 2 inhibitors. J Mol Graph Model 2011; 30:67-81. [PMID: 21763166 DOI: 10.1016/j.jmgm.2011.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/03/2011] [Accepted: 06/14/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Fangfang Wang
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100,China
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15
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Wilson SC, Atrash B, Barlow C, Eccles S, Fischer PM, Hayes A, Kelland L, Jackson W, Jarman M, Mirza A, Moreno J, Nutley BP, Raynaud FI, Sheldrake P, Walton M, Westwood R, Whittaker S, Workman P, McDonald E. Design, synthesis and biological evaluation of 6-pyridylmethylaminopurines as CDK inhibitors. Bioorg Med Chem 2011; 19:6949-65. [PMID: 21982796 DOI: 10.1016/j.bmc.2011.08.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 02/07/2023]
Abstract
The cyclin-dependent kinase (CDK) inhibitor seliciclib (1, CYC202) is in phase II clinical development for the treatment of cancer. Here we describe the synthesis of novel purines with greater solubility, lower metabolic clearance, and enhanced potency versus CDKs. These compounds exhibit novel selectivity profiles versus CDK isoforms. Compound αSβR-21 inhibits CDK2/cyclin E with IC(50)=30 nM, CDK7-cyclin H with IC(50)=1.3 μM, and CDK9-cyclinT with IC(50)=0.11 μM; it (CCT68127) inhibits growth of HCT116 colon cancer cells in vitro with GI(50)=0.7 μM; and shows antitumour activity when dosed p.o. at 50mg/kg to mice bearing HCT116 solid human tumour xenografts.
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Affiliation(s)
- Stuart C Wilson
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey, UK
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16
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Böttcher J, Jestel A, Kiefersauer R, Krapp S, Nagel S, Steinbacher S, Steuber H. Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology. Methods Enzymol 2011; 493:61-89. [PMID: 21371587 DOI: 10.1016/b978-0-12-381274-2.00003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
In the past two decades, fragment-based approaches have evolved as a predominant strategy in lead discovery. The availability of structural information on the interaction geometries of binding fragments is key to successful structure-guided fragment-to-lead evolution. In this chapter, we illustrate methodological advances for protein-fragment crystal structure generation in order to offer general lessons on the importance of fragment properties and the most appropriate crystallographic setup to evaluate them. We analyze elaborate protocols, methods, and clues applied to challenging complex formation projects. The results should assist medicinal chemists to select the most promising targets and strategies for fragment-based crystallography as well as provide a tutorial to structural biologists who attempt to determine protein-fragment structures.
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Affiliation(s)
- Jark Böttcher
- Proteros biostructures GmbH, Am Klopferspitz 19, Martinsried, Germany
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18
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Cho YS, Borland M, Brain C, Chen CHT, Cheng H, Chopra R, Chung K, Groarke J, He G, Hou Y, Kim S, Kovats S, Lu Y, O’Reilly M, Shen J, Smith T, Trakshel G, Vögtle M, Xu M, Xu M, Sung MJ. 4-(Pyrazol-4-yl)-pyrimidines as Selective Inhibitors of Cyclin-Dependent Kinase 4/6. J Med Chem 2010; 53:7938-57. [DOI: 10.1021/jm100571n] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Young Shin Cho
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Maria Borland
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christopher Brain
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christine H.-T. Chen
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Hong Cheng
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajiv Chopra
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kristy Chung
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James Groarke
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Guo He
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ying Hou
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sunkyu Kim
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Steven Kovats
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yipin Lu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Marc O’Reilly
- Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Junqing Shen
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Smith
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gary Trakshel
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Markus Vögtle
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mei Xu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ming Xu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Moo Je Sung
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Gad-Elkareem MAM, El-Adasy ABAAM. Synthesis and Antibacterial Activity of Some New Ethyl Thionicotinates, Thieno[2,3-b]pyridines, Pyrido[3′,2′:4,5] thieno[3,2-d]pyrimidines, and Pyrido[3′,2′:4,5]thieno[3,2-d][1,2,3]triazines Containing Sulfonamide Moieties. PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500902800253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Zhang B, Su ZC, Tay TE, Tan VBC. Mechanism of CDK5 activation revealed by steered molecular dynamics simulations and energy calculations. J Mol Model 2009; 16:1159-68. [DOI: 10.1007/s00894-009-0629-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Accepted: 11/15/2009] [Indexed: 02/04/2023]
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Abstract
Progression of the cell cycle is controlled by various activating and inhibiting cellular factors. The subtle balance between these counteracting regulators in normal cells ensures proper cell cycle progression and facilitates cellular responses to a variety of stress stimuli. Key activators include cyclin-dependent kinases (CDKs) and, consequently, loss or inactivation of CDK inhibitors contributes to the escape of cancer cells from cell cycle control and hyperactivation of CDKs occurs in various neurodegenerative disorders. However, these adverse effects may be compensated by pharmacological counterparts. Inhibitors of CDKs representing various classes of compounds with diverse CDK inhibitory patterns have been developed, but inhibitors that have high selectivity and offer highly targeted activity against both cell cycle and transcriptional CDKs are of particular interest. This review focuses on pharmacological CDK inhibitors that have entered clinical trials and some compounds that have been evaluated preclinically. Recent discoveries in cell cycle regulation have provided rationales for clinical applications of CDK inhibitors in both monotherapeutic and combined therapeutic regimens.
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Byth KF, Thomas A, Hughes G, Forder C, McGregor A, Geh C, Oakes S, Green C, Walker M, Newcombe N, Green S, Growcott J, Barker A, Wilkinson RW. AZD5438, a potent oral inhibitor of cyclin-dependent kinases 1, 2, and 9, leads to pharmacodynamic changes and potent antitumor effects in human tumor xenografts. Mol Cancer Ther 2009; 8:1856-66. [PMID: 19509270 DOI: 10.1158/1535-7163.mct-08-0836] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Deregulation of the cell cycle has long been recognized as an essential driver of tumorigenesis, and agents that selectively target key cell cycle components continue to hold promise as potential therapeutics. We have developed AZD5438, a 4-(1-isopropyl-2-methylimidazol-5-yl)-2-(4-methylsulphonylanilino) pyrimidine, as a potent inhibitor of cyclin-dependent kinase (cdk) 1, 2, and 9 (IC(50), 16, 6, and 20 nmol/L, respectively). In vitro, AZD5438 showed significant antiproliferative activity in human tumor cell lines (IC(50) range, 0.2-1.7 micromol/L), causing inhibition of the phosphorylation of cdk substrates pRb, nucleolin, protein phosphatase 1a, and RNA polymerase II COOH-terminal domain and blocking cell cycling at G(2)-M, S, and G(1) phases. In vivo, when orally administered at either 50 mg/kg twice daily or 75 mg/kg once daily, AZD5438 inhibited human tumor xenograft growth (maximum percentage tumor growth inhibition, range, 38-153; P < 0.05). In vivo, AZD5438 reduced the proportion of actively cycling cells. Further pharmacodynamic analysis of AZD5438-treated SW620 xenografts showed that efficacious doses of AZD5438 (>40% tumor growth inhibition) maintained suppression of biomarkers, such as phospho-pRbSer(249)/Thr(252), for up to 16 hours following a single oral dose. A comparison of different schedules indicated that chronic daily oral dosing provided optimal cover to ensure antitumor efficacy. These data indicate that broad cdk inhibition may provide an effective method to impair the dysregulated cell cycle that drives tumorigenesis and AZD5438 has the pharmacologic profile that provides an ideal probe to test this premise.
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Affiliation(s)
- Kate F Byth
- AstraZeneca R&D Boston, Waltham, MA 02451, USA.
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23
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Jones CD, Andrews DM, Barker AJ, Blades K, Byth KF, Finlay MRV, Geh C, Green CP, Johannsen M, Walker M, Weir HM. Imidazole pyrimidine amides as potent, orally bioavailable cyclin-dependent kinase inhibitors. Bioorg Med Chem Lett 2008; 18:6486-9. [DOI: 10.1016/j.bmcl.2008.10.075] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/13/2008] [Accepted: 10/13/2008] [Indexed: 11/28/2022]
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24
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Jones CD, Andrews DM, Barker AJ, Blades K, Daunt P, East S, Geh C, Graham MA, Johnson KM, Loddick SA, McFarland HM, McGregor A, Moss L, Rudge DA, Simpson PB, Swain ML, Tam KY, Tucker JA, Walker M. The discovery of AZD5597, a potent imidazole pyrimidine amide CDK inhibitor suitable for intravenous dosing. Bioorg Med Chem Lett 2008; 18:6369-73. [PMID: 18996007 DOI: 10.1016/j.bmcl.2008.10.102] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/17/2008] [Accepted: 10/18/2008] [Indexed: 10/21/2022]
Abstract
The development of a novel series of imidazole pyrimidine amides as cyclin-dependent kinase (CDK) inhibitors is described. Optimisation of inhibitory potency against multiple CDK's (1, 2 and 9) resulted in imidazole pyrimidine amides with potent in vitro anti-proliferative effects against a range of cancer cell lines. Excellent physiochemical properties and large margins against inhibition of CYP isoforms and the hERG ion channel were achieved by modification of lipophilicity and amine basicity. A candidate with disease model activity in human cancer cell line xenografts and with suitable physiochemical and pharmacokinetic profiles for intravenous (i.v.) dosing was selected for further development as AZD5597.
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Affiliation(s)
- Clifford D Jones
- Cancer and Infection Research, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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