51
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Liang C, Tian D, Ren X, Ding S, Jia M, Xin M, Thareja S. The development of Bruton's tyrosine kinase (BTK) inhibitors from 2012 to 2017: A mini-review. Eur J Med Chem 2018; 151:315-326. [DOI: 10.1016/j.ejmech.2018.03.062] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/11/2018] [Accepted: 03/20/2018] [Indexed: 12/15/2022]
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52
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Xue Y, Song P, Song Z, Wang A, Tong L, Geng M, Ding J, Liu Q, Sun L, Xie H, Zhang A. Discovery of 4,7-Diamino-5-(4-phenoxyphenyl)-6-methylene-pyrimido[5,4-b]pyrrolizines as Novel Bruton’s Tyrosine Kinase Inhibitors. J Med Chem 2018; 61:4608-4627. [DOI: 10.1021/acs.jmedchem.8b00441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu Xue
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Peiran Song
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | | | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | | | - Meiyu Geng
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian Ding
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Liping Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Hua Xie
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
| | - Ao Zhang
- College of Pharmacy, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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53
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Sharma S, Galanina N, Guo A, Lee J, Kadri S, Van Slambrouck C, Long B, Wang W, Ming M, Furtado LV, Segal JP, Stock W, Venkataraman G, Tang WJ, Lu P, Wang YL. Identification of a structurally novel BTK mutation that drives ibrutinib resistance in CLL. Oncotarget 2018; 7:68833-68841. [PMID: 27626698 PMCID: PMC5356593 DOI: 10.18632/oncotarget.11932] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/15/2016] [Indexed: 12/01/2022] Open
Abstract
Ibrutinib (ibr), a first-in-class Bruton tyrosine kinase (BTK) inhibitor, has demonstrated high response rates in both relapsed/refractory and treatment naïve chronic lymphocytic leukemia (CLL). However, about 25% of patients discontinue ibrutinib therapy at a median follow-up of 20 months and many patients discontinue the treatment due to leukemia progression or Richter transformation. Mutations affecting the C481 residue of BTK disrupt ibrutinib binding and have been characterized by us and others as the most common mechanism of ibrutinib resistance. Thus far, all described BTK mutations are located in its kinase domain and mutations outside this domain have never been described. Herein, we report a patient whose CLL progressed, was salvaged with ibrutinib and then relapsed. Serial analysis of samples throughout patient's clinical course identified a structurally novel mutation (BTKT316A) in the SH2 domain, but not kinase domain, of Bruton tyrosine kinase which was associated with disease relapse. Functionally, cells carrying BTKT316A show resistance to ibrutinib at both cellular and molecular levels to a similar extent as BTKC481S. Our study lends further insight into the diverse mechanisms of ibrutinib resistance that has important implications for the development of next-generation BTK inhibitors as well as mutation detection in relapsed patients.
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Affiliation(s)
- Shruti Sharma
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Natalie Galanina
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ailin Guo
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Jimmy Lee
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Sabah Kadri
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA.,Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA
| | | | - Bradley Long
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Weige Wang
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Mei Ming
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Larissa V Furtado
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Jeremy P Segal
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Wendy Stock
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Wei-Jen Tang
- Ben-May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Pin Lu
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Yue Lynn Wang
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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54
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Chen H, Song P, Diao Y, Hao Y, Dou D, Wang W, Fang X, Wang Y, Zhao Z, Ding J, Li H, Xie H, Xu Y. Discovery and biological evaluation of N5-substituted 6,7-dioxo-6,7-dihydropteridine derivatives as potent Bruton's tyrosine kinase inhibitors. MEDCHEMCOMM 2018; 9:697-704. [PMID: 30108960 DOI: 10.1039/c8md00019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/06/2018] [Indexed: 11/21/2022]
Abstract
Bruton's tyrosine kinase (BTK) plays a critical role in B cell receptor (BCR)-mediated signaling pathways responsible for the development and function of B cells, which makes it an attractive target for the treatment of many types of B-cell malignancies. Herein, a series of N5-substituted 6,7-dioxo-6,7-dihydropteridine-based, irreversible BTK inhibitors were reported with IC50 values ranging from 1.9 to 236.6 nM in the enzymatic inhibition assay. Compounds 6 and 7 significantly inhibited the proliferation of Ramos cells which overexpress the BTK enzyme, as well as the autophosphorylation of BTK at Tyr223 and the activation of its downstream signaling molecule PLCγ2. Overall, this series of compounds could provide a promising starting point for further development of potent BTK inhibitors for B-cell malignancy treatment.
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Affiliation(s)
- Haiyang Chen
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Peiran Song
- Division of Anti-tumor Pharmacology , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China . .,University of Chinese Academy of Sciences , Beijing 100049 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Yongjia Hao
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Dou Dou
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Wanqi Wang
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Xiaoyu Fang
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Yanling Wang
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Jian Ding
- Division of Anti-tumor Pharmacology , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China .
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
| | - Hua Xie
- Division of Anti-tumor Pharmacology , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China .
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design , State Key Laboratory of Bioreactor Engineering , School of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China . ; ; ; Tel: +86 21 64250213
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55
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Pal Singh S, Dammeijer F, Hendriks RW. Role of Bruton's tyrosine kinase in B cells and malignancies. Mol Cancer 2018; 17:57. [PMID: 29455639 PMCID: PMC5817726 DOI: 10.1186/s12943-018-0779-z] [Citation(s) in RCA: 416] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/01/2018] [Indexed: 12/14/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is a non-receptor kinase that plays a crucial role in oncogenic signaling that is critical for proliferation and survival of leukemic cells in many B cell malignancies. BTK was initially shown to be defective in the primary immunodeficiency X-linked agammaglobulinemia (XLA) and is essential both for B cell development and function of mature B cells. Shortly after its discovery, BTK was placed in the signal transduction pathway downstream of the B cell antigen receptor (BCR). More recently, small-molecule inhibitors of this kinase have shown excellent anti-tumor activity, first in animal models and subsequently in clinical studies. In particular, the orally administered irreversible BTK inhibitor ibrutinib is associated with high response rates in patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and mantle-cell lymphoma (MCL), including patients with high-risk genetic lesions. Because ibrutinib is generally well tolerated and shows durable single-agent efficacy, it was rapidly approved for first-line treatment of patients with CLL in 2016. To date, evidence is accumulating for efficacy of ibrutinib in various other B cell malignancies. BTK inhibition has molecular effects beyond its classic role in BCR signaling. These involve B cell-intrinsic signaling pathways central to cellular survival, proliferation or retention in supportive lymphoid niches. Moreover, BTK functions in several myeloid cell populations representing important components of the tumor microenvironment. As a result, there is currently a considerable interest in BTK inhibition as an anti-cancer therapy, not only in B cell malignancies but also in solid tumors. Efficacy of BTK inhibition as a single agent therapy is strong, but resistance may develop, fueling the development of combination therapies that improve clinical responses. In this review, we discuss the role of BTK in B cell differentiation and B cell malignancies and highlight the importance of BTK inhibition in cancer therapy.
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Affiliation(s)
- Simar Pal Singh
- Department of Pulmonary Medicine, Room Ee2251a, Erasmus MC Rotterdam, PO Box 2040, NL 3000, CA, Rotterdam, The Netherlands.,Department of Immunology, Rotterdam, The Netherlands.,Post graduate school Molecular Medicine, Rotterdam, The Netherlands
| | - Floris Dammeijer
- Department of Pulmonary Medicine, Room Ee2251a, Erasmus MC Rotterdam, PO Box 2040, NL 3000, CA, Rotterdam, The Netherlands.,Post graduate school Molecular Medicine, Rotterdam, The Netherlands.,Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Room Ee2251a, Erasmus MC Rotterdam, PO Box 2040, NL 3000, CA, Rotterdam, The Netherlands.
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56
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von Raußendorf F, de Ruiter A, Leonard TA. A switch in nucleotide affinity governs activation of the Src and Tec family kinases. Sci Rep 2017; 7:17405. [PMID: 29234112 PMCID: PMC5727165 DOI: 10.1038/s41598-017-17703-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
The Tec kinases, closely related to Src family kinases, are essential for lymphocyte function in the adaptive immune system. Whilst the Src and Abl kinases are regulated by tail phosphorylation and N-terminal myristoylation respectively, the Tec kinases are notable for the absence of either regulatory element. We have found that the inactive conformations of the Tec kinase Itk and Src preferentially bind ADP over ATP, stabilising both proteins. We demonstrate that Itk adopts the same conformation as Src and that the autoinhibited conformation of Src is independent of its C-terminal tail. Allosteric activation of both Itk and Src depends critically on the disruption of a conserved hydrophobic stack that accompanies regulatory domain displacement. We show that a conformational switch permits the exchange of ADP for ATP, leading to efficient autophosphorylation and full activation. In summary, we propose a universal mechanism for the activation and autoinhibition of the Src and Tec kinases.
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Affiliation(s)
- Freia von Raußendorf
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Anita de Ruiter
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria.
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57
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Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain. Sci Rep 2017; 7:15604. [PMID: 29142210 PMCID: PMC5688120 DOI: 10.1038/s41598-017-10697-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinase’s solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTK’s kinase domain. Our conformational landscape links the active state to several inactive states, connected via a structurally diverse intermediate. Our calculations predict a kinome-wide conformational plasticity, and indicate the presence of several new potentially druggable BTK states. We further find that the population of these states and the kinetics of their inter-conversion are modulated by protonation of an aspartate residue, establishing the power of MD & MSMs in predicting effects of chemical perturbations.
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58
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Dittus L, Werner T, Muelbaier M, Bantscheff M. Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors. ACS Chem Biol 2017; 12:2515-2521. [PMID: 28876896 DOI: 10.1021/acschembio.7b00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoproteomics profiling of kinase inhibitors with kinobeads enables the assessment of inhibitor potency and selectivity for endogenously expressed protein kinases in cell lines and tissues. Using a small panel of targeted covalent inhibitors, we demonstrate the importance of measuring covalent target binding in live cells. We present a differential kinobeads profiling strategy for covalent kinase inhibitors where a compound is added either to live cells or to a cell extract that enables the comprehensive assessment of inhibitor selectivity for covalent and noncovalent targets. We found that Acalabrutinib, CC-292, and Ibrutinib potently and covalently bind TEC family kinases, but only Ibrutinib also potently binds to BLK. ZAK was identified as a submicromolar affinity Ibrutinib off-target due to covalent modification of Cys22. In contrast to Ibrutinib, 5Z-7-Oxozeaenol reacted with Cys150 next to the DFG loop, demonstrating an alternative route to covalent inactivation of this kinase, e.g., to inhibit canonical TGF-β dependent processes.
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Affiliation(s)
- Lars Dittus
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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59
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Goswami M, Wilke KE, Carlson EE. Rational Design of Selective Adenine-Based Scaffolds for Inactivation of Bacterial Histidine Kinases. J Med Chem 2017; 60:8170-8182. [PMID: 28933546 DOI: 10.1021/acs.jmedchem.7b01066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bacterial histidine kinases (HKs) are quintessential regulatory enzymes found ubiquitously in bacteria. Apart from their regulatory roles, they are also involved in the production of virulence factors and conferring resistance to various antibiotics in pathogenic microbes. We have previously reported compounds that inhibit multiple HKs by targeting the conserved catalytic and ATP-binding (CA) domain. Herein, we conduct a detailed structure-activity relationship assessment of adenine-based inhibitors using biochemical and docking methods. These studies have resulted in several observations. First, interaction of an inhibitor's amine group with the conserved active-site Asp is essential for activity and likely dictates its orientation in the binding pocket. Second, a N-NH-N triad in the inhibitor scaffold is highly preferred for binding to conserved Gly:Asp:Asn residues. Lastly, hydrophobic electron-withdrawing groups at several positions in the adenine core enhance potency. The selectivity of these inhibitors was tested against heat shock protein 90 (HSP90), which possesses a similar ATP-binding fold. We found that groups that target the ATP-lid portion of the catalytic domain, such as a six-membered ring, confer selectivity for HKs.
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Affiliation(s)
- Manibarsha Goswami
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
| | - Kaelyn E Wilke
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , 321 Church Street SE, Minneapolis, Minnesota 55455, United States
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60
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Musumeci F, Sanna M, Greco C, Giacchello I, Fallacara AL, Amato R, Schenone S. Pyrrolo[2,3-d]pyrimidines active as Btk inhibitors. Expert Opin Ther Pat 2017; 27:1305-1318. [DOI: 10.1080/13543776.2017.1355908] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Francesca Musumeci
- Dipartimento di Farmacia, Università degli Studi di Genova, Genova, Italy
| | - Monica Sanna
- Dipartimento di Farmacia, Università degli Studi di Genova, Genova, Italy
| | - Chiara Greco
- Dipartimento di Farmacia, Università degli Studi di Genova, Genova, Italy
| | - Ilaria Giacchello
- Dipartimento di Farmacia, Università degli Studi di Genova, Genova, Italy
| | - Anna Lucia Fallacara
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy
| | - Rosario Amato
- Dipartimento di “Scienze della Salute”, Università “Magna Graecia” di Catanzaro, Catanzaro, Italy
| | - Silvia Schenone
- Dipartimento di Farmacia, Università degli Studi di Genova, Genova, Italy
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61
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Zimmermann G, Rieder U, Bajic D, Vanetti S, Chaikuad A, Knapp S, Scheuermann J, Mattarella M, Neri D. A Specific and Covalent JNK-1 Ligand Selected from an Encoded Self-Assembling Chemical Library. Chemistry 2017; 23:8152-8155. [PMID: 28485044 PMCID: PMC5557334 DOI: 10.1002/chem.201701644] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/05/2023]
Abstract
We describe the construction of a DNA-encoded chemical library comprising 148 135 members, generated through the self-assembly of two sub-libraries, containing 265 and 559 members, respectively. The library was designed to contain building blocks potentially capable of forming covalent interactions with target proteins. Selections performed with JNK1, a kinase containing a conserved cysteine residue close to the ATP binding site, revealed the preferential enrichment of a 2-phenoxynicotinic acid moiety (building block A82) and a 4-(3,4-difluorophenyl)-4-oxobut-2-enoic acid moiety (building block B272). When the two compounds were joined by a short PEG linker, the resulting bidentate binder (A82-L-B272) was able to covalently modify JNK1 in the presence of a large molar excess of glutathione (0.5 mm), used to simulate intracellular reducing conditions. By contrast, derivatives of the individual building blocks were not able to covalently modify JNK1 in the same experimental conditions. The A82-L-B272 ligand was selective over related kinases (BTK and GAK), which also contain targetable cysteine residues in the vicinity of the active site.
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Affiliation(s)
- Gunther Zimmermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Ulrike Rieder
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland)
| | - Davor Bajic
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Sara Vanetti
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland)
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt (Germany)
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt (Germany)
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | | | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
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62
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Liu H, Qu M, Xu L, Han X, Wang C, Shu X, Yao J, Liu K, Peng J, Li Y, Ma X. Design and synthesis of sulfonamide-substituted diphenylpyrimidines (SFA-DPPYs) as potent Bruton's tyrosine kinase (BTK) inhibitors with improved activity toward B-cell lymphoblastic leukemia. Eur J Med Chem 2017; 135:60-69. [PMID: 28432946 DOI: 10.1016/j.ejmech.2017.04.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/31/2022]
Abstract
A new series of diphenylpyrimidine derivatives (SFA-DPPYs) were synthesized by introducing a functional sulfonamide into the C-2 aniline moiety of pyrimidine template, and then were biologically evaluated as potent Bruton's tyrosine kinase (BTK) inhibitors. Among these molecules, inhibitors 10c, 10i, 10j and 10k displayed high potency against the BTK enzyme, with IC50 values of 1.18 nM, 0.92 nM, 0.42 nM and 1.05 nM, respectively. In particular, compound 10c could remarkably inhibit the proliferation of the B lymphoma cell lines at concentrations of 6.49 μM (Ramos cells) and 13.2 μM (Raji cells), and was stronger than the novel agent spebrutinib. In addition, the inhibitory potency toward the normal PBMC cells showed that inhibitor 10c possesses low cell cytotoxicity. All these explorations indicated that molecule 10c could serve as a valuable inhibitor for B-cell lymphoblastic leukemia treatment.
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Affiliation(s)
- He Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Menghua Qu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Lina Xu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Xu Han
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Changyuan Wang
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Jihong Yao
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Jinyong Peng
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Yanxia Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China
| | - Xiaodong Ma
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China.
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63
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Discovery and evaluation of 1 H -pyrrolo[2,3- b ]pyridine based selective and reversible small molecule BTK inhibitors for the treatment of rheumatoid arthritis. Bioorg Med Chem Lett 2017; 27:1867-1873. [DOI: 10.1016/j.bmcl.2017.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/03/2017] [Accepted: 02/13/2017] [Indexed: 01/07/2023]
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Alfaro J, Pérez de Arce F, Belmar S, Fuentealba G, Avila P, Ureta G, Flores C, Acuña C, Delgado L, Gaete D, Pujala B, Barde A, Nayak AK, Upendra TVR, Patel D, Chauhan S, Sharma VK, Kanno S, Almirez RG, Hung DT, Chakravarty S, Rai R, Bernales S, Quinn KP, Pham SM, McCullagh E. Dual Inhibition of Bruton's Tyrosine Kinase and Phosphoinositide-3-Kinase p110 δ as a Therapeutic Approach to Treat Non-Hodgkin's B Cell Malignancies. J Pharmacol Exp Ther 2017; 361:312-321. [PMID: 28298527 DOI: 10.1124/jpet.116.238022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/10/2017] [Indexed: 02/01/2023] Open
Abstract
Although new targeted therapies, such as ibrutinib and idelalisib, have made a large impact on non-Hodgkin's lymphoma (NHL) patients, the disease is often fatal because patients are initially resistant to these targeted therapies, or because they eventually develop resistance. New drugs and treatments are necessary for these patients. One attractive approach is to inhibit multiple parallel pathways that drive the growth of these hematologic tumors, possibly prolonging the duration of the response and reducing resistance. Early clinical trials have tested this approach by dosing two drugs in combination in NHL patients. We discovered a single molecule, MDVN1003 (1-(5-amino-2,3-dihydro-1H-inden-2-yl)-3-(8-fluoro-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine), that inhibits Bruton's tyrosine kinase and phosphatidylinositol-3-kinase δ, two proteins regulated by the B cell receptor that drive the growth of many NHLs. In this report, we show that this dual inhibitor prevents the activation of B cells and inhibits the phosphorylation of protein kinase B and extracellular signal-regulated kinase 1/2, two downstream mediators that are important for this process. Additionally, MDVN1003 induces cell death in a B cell lymphoma cell line but not in an irrelevant erythroblast cell line. Importantly, we found that this orally bioavailable dual inhibitor reduced tumor growth in a B cell lymphoma xenograft model more effectively than either ibrutinib or idelalisib. Taken together, these results suggest that dual inhibition of these two key pathways by a single molecule could be a viable approach for treatment of NHL patients.
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Affiliation(s)
- Jennifer Alfaro
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Felipe Pérez de Arce
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Sebastián Belmar
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Glenda Fuentealba
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Patricio Avila
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Gonzalo Ureta
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Camila Flores
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Claudia Acuña
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Luz Delgado
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Diana Gaete
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Brahmam Pujala
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Anup Barde
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Anjan K Nayak
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - T V R Upendra
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Dhananjay Patel
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Shailender Chauhan
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Vijay K Sharma
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Stacy Kanno
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Ramona G Almirez
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - David T Hung
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Sarvajit Chakravarty
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Roopa Rai
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Sebastián Bernales
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Kevin P Quinn
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Son M Pham
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
| | - Emma McCullagh
- Translational Research Group, Fundación Ciencia y Vida, Santiago, Chile (J.A., F.P.d.A., S.Bel., G.F., P.A., G.U., C.F., C.A., L.D., D.G.); Biological Sciences Department, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Región de Valparaíso, Chile (F.P.d.A., S.Bel.); Chemistry Group, Integral BioSciences, Pvt. Ltd., Noida, India (B.P., A.B., A.K.N., T.V.R.U., D.P., S.C., V.K.S.); and Discovery Research, Medivation, Inc., now Pfizer, San Francisco, California (S.K., R.G.A., D.T.H., S.C., R.R., S.Ber., K.P.Q., S.M.P., E.M.)
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Balasubramanian PK, Balupuri A, Kang HY, Cho SJ. Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors. BMC SYSTEMS BIOLOGY 2017; 11:6. [PMID: 28361711 PMCID: PMC5374705 DOI: 10.1186/s12918-017-0385-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
BACKGROUND Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia (XLA). Btk is considered as a potential therapeutic target for treating autoimmune diseases and hematological malignancies. RESULTS In this work, a combined molecular modeling study was performed on a series of thieno [3,2-c] pyridine-4-amine derivatives as Btk inhibitors. Receptor-guided COMFA (q 2 = 0.574, NOC = 3, r 2 = 0.924) and COMSIA (q 2 = 0.646, NOC = 6, r 2 = 0.971) models were generated based on the docked conformation of the most active compound 26. All the developed models were tested for robustness using various validation techniques. Furthermore, a 5-ns molecular dynamics (MD) simulation and binding free energy calculations were carried out to determine the binding modes of the inhibitors and to identify crucial interacting residues. The rationality and stability of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM/PBSA method showed the importance of the van der Waals interaction. CONCLUSIONS A good correlation between the MD results, docking studies, and the contour map analysis were observed. The study has identified the key amino acid residues in Btk binding pocket. The results from this study can provide some insights into the development of potent, novel Btk inhibitors.
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Affiliation(s)
- Pavithra K Balasubramanian
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea
| | - Anand Balupuri
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea
| | - Hee-Young Kang
- Department of Nursing, Chosun University, Gwangju, 61452, Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea.
- Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
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Liang Q, Chen Y, Yu K, Chen C, Zhang S, Wang A, Wang W, Wu H, Liu X, Wang B, Wang L, Hu Z, Wang W, Ren T, Zhang S, Liu Q, Yun CH, Liu J. Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-carbonyl)phenyl)amino)-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl)-4-(tert-butyl)benzamide (CHMFL-BTK-01) as a highly selective irreversible Bruton's tyrosine kinase (BTK) inhibitor. Eur J Med Chem 2017; 131:107-125. [PMID: 28315597 DOI: 10.1016/j.ejmech.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 10/20/2022]
Abstract
Currently there are several irreversible BTK inhibitors targeting Cys481 residue under preclinical or clinical development. However, most of these inhibitors also targeted other kinases such as BMX, JAK3, and EGFR that bear the highly similar active cysteine residues. Through a structure-based drug design approach, we discovered a highly potent (IC50: 7 nM) irreversible BTK inhibitor compound 9 (CHMFL-BTK-01), which displayed a high selectivity profile in KINOMEscan (S score (35) = 0.00) among 468 kinases/mutants at the concentration of 1 μM. Compound 9 completely abolished BMX, JAK3 and EGFR's activity. Both X-ray crystal structure and cysteine-serine mutation mediated rescue experiment confirmed 9's irreversible binding mode. 9 also potently inhibited BTK Y223 auto-phosphorylation (EC50: <30 nM), arrested cell cycle in G0/G1 phase and induced apoptosis in U2932 and Pfeiffer cells. We believe these features would make 9 a good pharmacological tool to study the BTK related pathology.
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Affiliation(s)
- Qianmao Liang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230036, PR China; High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Yongfei Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Kailin Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Cheng Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Shouxiang Zhang
- Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China
| | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Wei Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Hong Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China
| | - Xiaochuan Liu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230036, PR China; High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Beilei Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Li Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Zhenquan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Wenchao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China
| | - Tao Ren
- Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230088, PR China
| | - Shanchun Zhang
- CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; Hefei Cosource Medicine Technology Co. LTD., 358 Ganquan Road, Hefei, Anhui 230031, PR China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230036, PR China; Precision Targeted Therapy Discovery Center, Institute of Technology Innovation, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230088, PR China
| | - Cai-Hong Yun
- Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, PR China.
| | - Jing Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Mailbox 1110, 350 Shushanhu Road, Hefei, Anhui 230031, PR China; CHMFL-HCMTC Target Therapy Joint Laboratory, 350 Shushanhu Road, Hefei, Anhui 230031, PR China.
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67
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Tiwari RK, Brown A, Sadeghiani N, Shirazi AN, Bolton J, Tse A, Verkhivker G, Parang K, Sun G. Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors. ChemMedChem 2017; 12:86-99. [PMID: 27875633 PMCID: PMC5224969 DOI: 10.1002/cmdc.201600387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/20/2016] [Indexed: 12/12/2022]
Abstract
Derivatives of the tyrosine kinase inhibitor dasatinib were synthesized by esterification with 25 carboxylic acids, including amino acids and fatty acids, thereby extending the drug to interact with more diverse sites and to improve specificity. The dasatinib-l-arginine derivative (Das-R, 7) was found to be the most potent of the inhibitors tested, with IC50 values of 4.4, <0.25, and <0.45 nm against Csk, Src, and Abl kinases, respectively. The highest selectivity ratio obtained in our study, 91.4 Csk/Src, belonged to compound 18 (Das-C10 ) with an IC50 value of 3.2 μm for Csk compared with 35 nm for Src. Furthermore, many compounds displayed increased selectivity toward Src over Abl. Compounds 15 (Das-glutamic acid) and 13 (Das-cysteine) demonstrated the largest gains (10.2 and 10.3 Abl/Src IC50 ratios). Das-R (IC50 =2.06 μm) was significantly more potent than the parent dasatinib (IC50 =26.3 μm) against Panc-1 cells, whereas both compounds showed IC50 <51.2 pm against BV-173 and K562 cells. Molecular modeling and binding free energy simulations revealed good agreements with the experimental results and rationalized the differences in selectivity among the studied compounds. Integration of experimental and computational approaches in the design and biochemical screening of dasatinib derivatives facilitated rational engineering and diversification of the dasatinib scaffold, providing useful insight into mechanisms of kinase selectivity.
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Affiliation(s)
- Rakesh K Tiwari
- Center For Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA, 92618, USA
| | - Alex Brown
- Department of Cell & Molecular Biology, University of Rhode Island, 389 CBLS Building, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Neda Sadeghiani
- Center For Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA, 92618, USA
| | - Amir Nasrolahi Shirazi
- Center For Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA, 92618, USA
| | - Jared Bolton
- Department of Cell & Molecular Biology, University of Rhode Island, 389 CBLS Building, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Amanda Tse
- Schmid College of Science and Technology Physics, Computational Science and Engineering, Chapman University, Orange, CA, 92866, USA
| | - Gennady Verkhivker
- Schmid College of Science and Technology Physics, Computational Science and Engineering, Chapman University, Orange, CA, 92866, USA
| | - Keykavous Parang
- Center For Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA, 92618, USA
| | - Gongqin Sun
- Department of Cell & Molecular Biology, University of Rhode Island, 389 CBLS Building, 120 Flagg Road, Kingston, RI, 02881, USA
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68
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Pujala B, Agarwal AK, Middya S, Banerjee M, Surya A, Nayak AK, Gupta A, Khare S, Guguloth R, Randive NA, Shinde BU, Thakur A, Patel DI, Raja M, Green MJ, Alfaro J, Avila P, Pérez de Arce F, Almirez RG, Kanno S, Bernales S, Hung DT, Chakravarty S, McCullagh E, Quinn KP, Rai R, Pham SM. Discovery of Pyrazolopyrimidine Derivatives as Novel Dual Inhibitors of BTK and PI3Kδ. ACS Med Chem Lett 2016; 7:1161-1166. [PMID: 27994757 DOI: 10.1021/acsmedchemlett.6b00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/28/2016] [Indexed: 12/13/2022] Open
Abstract
The aberrant activation of B-cells has been implicated in several types of cancers and hematological disorders. BTK and PI3Kδ are kinases responsible for B-cell signal transduction, and inhibitors of these enzymes have demonstrated clinical benefit in certain types of lymphoma. Simultaneous inhibition of these pathways could result in more robust responses or overcome resistance as observed in single agent use. We report a series of novel compounds that have low nanomolar potency against both BTK and PI3Kδ as well as acceptable PK properties that could be useful in the development of treatments against B-cell related diseases.
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Affiliation(s)
- Brahmam Pujala
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Anil K. Agarwal
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Sandip Middya
- Curadev, Pvt. Ltd., B-87, Sector 83, Noida, Uttar Pradesh 201305, India
| | - Monali Banerjee
- Curadev, Pvt. Ltd., B-87, Sector 83, Noida, Uttar Pradesh 201305, India
| | - Arjun Surya
- Curadev, Pvt. Ltd., B-87, Sector 83, Noida, Uttar Pradesh 201305, India
| | - Anjan K. Nayak
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Ashu Gupta
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Sweta Khare
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Rambabu Guguloth
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Nitin A. Randive
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Bharat U. Shinde
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Anamika Thakur
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Dhananjay I. Patel
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Mohd. Raja
- Integral BioSciences, Pvt. Ltd., C-64, Hosiery Complex Phase II Extension, Noida, Uttar Pradesh 201306, India
| | - Michael J. Green
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Jennifer Alfaro
- Fundación Ciencia y Vida, Avenida
Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Patricio Avila
- Fundación Ciencia y Vida, Avenida
Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
| | - Felipe Pérez de Arce
- Fundación Ciencia y Vida, Avenida
Zañartu 1482, Ñuñoa, Santiago 7780272, Chile
- Departamento
de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 8370146, Chile
| | - Ramona G. Almirez
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Stacy Kanno
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Sebastián Bernales
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - David T. Hung
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Sarvajit Chakravarty
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Emma McCullagh
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Kevin P. Quinn
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Roopa Rai
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
| | - Son M. Pham
- Medivation, Inc., 525 Market Street,
36th Floor, San Francisco, California 94105, United States
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69
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Ge Y, Jin Y, Wang C, Zhang J, Tang Z, Peng J, Liu K, Li Y, Zhou Y, Ma X. Discovery of Novel Bruton's Tyrosine Kinase (BTK) Inhibitors Bearing a N,9-Diphenyl-9 H-purin-2-amine Scaffold. ACS Med Chem Lett 2016; 7:1050-1055. [PMID: 27994736 DOI: 10.1021/acsmedchemlett.6b00235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Based on the pyrimidine skeleton of EGFRT790M inhibitors, a series of N,9-diphenyl-9H-purin-2-amine derivatives were identified as effective BTK inhibitors. Among these compounds, inhibitors 10d, 10i, and 10j, possessing IC50 values of 0.5, 0.5, and 0.4 nM, displayed anti-BTK kinase activity that was as potent as the reference compounds. In particular, compound 10j suppressed the proliferation of two typical B-cell leukemia cell lines expressing high levels of BTK with concentrations of 7.75 and 12.6 μM. The activity of the subject compound as determined by the CCK-8 method and apoptosis analysis validated that inhibitor 10j is slightly more potent than AVL-292 and ibrutinib. The results of these experimental explorations suggested that 10j could serve as a valuable molecule for control of leukemia pending further developments.
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Affiliation(s)
- Yang Ge
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Yue Jin
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Changyuan Wang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Jianbin Zhang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Zeyao Tang
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Jinyong Peng
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Kexin Liu
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
| | - Yanxia Li
- Respiratory
Department, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, P. R. China
| | - Youwen Zhou
- Department
of Dermatology and Skin Science, University of British Columbia, Vancouver, BC V5Z 4E8, Canada
| | - Xiaodong Ma
- College
of Pharmacy, Dalian Medical University, Dalian 116044, P. R. China
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70
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Design and synthesis of phosphoryl-substituted diphenylpyrimidines (Pho-DPPYs) as potent Bruton's tyrosine kinase (BTK) inhibitors: Targeted treatment of B lymphoblastic leukemia cell lines. Bioorg Med Chem 2016; 25:765-772. [PMID: 27956037 DOI: 10.1016/j.bmc.2016.11.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
A family of phosphoryl-substituted diphenylpyrimidine derivatives (Pho-DPPYs) were synthesized and biologically evaluated as potent BTK inhibitors in this study. Compound 7b was found to markedly inhibit BTK activity at concentrations of 0.82nmol/L, as well as to suppress the proliferations of B-cell leukemia cell lines (Ramos and Raji) expressing high levels of BTK at concentrations of 3.17μM and 6.69μM. Moreover, flow cytometry analysis results further indicated that 7b promoted cell apoptosis to a substantial degree. In a word, compound 7b is a promising BTK inhibitor for the treatment of B-cell lymphoblastic leukemia.
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71
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Zhao D, Huang S, Qu M, Wang C, Liu Z, Li Z, Peng J, Liu K, Li Y, Ma X, Shu X. Structural optimization of diphenylpyrimidine derivatives (DPPYs) as potent Bruton's tyrosine kinase (BTK) inhibitors with improved activity toward B leukemia cell lines. Eur J Med Chem 2016; 126:444-455. [PMID: 27912175 DOI: 10.1016/j.ejmech.2016.11.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/14/2022]
Abstract
A new series of diphenylpyrimidine derivatives (DPPYs) bearing various aniline side chains at the C-2 position of pyrimidine core were synthesized as potent BTK inhibitors. Most of these inhibitors displayed improved activity against B leukemia cell lines compared with lead compound spebrutinib. Subsequent studies showed that the peculiar inhibitor 7j, with IC50 values of 10.5 μM against Ramos cells and 19.1 μM against Raji cells, also displayed slightly higher inhibitory ability than the novel agent ibrutinib. Moreover, compound 7j is not sensitive to normal cells PBMC, indicating low cell cytotoxicity. In addition, flow cytometry analysis indicated that 7j significantly induced the apoptosis of Ramos cells, and arrested the cell cycle at the G0/G1 phase. These explorations provided new clues to discover pyrimidine scaffold as more effective BTK inhibitors.
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Affiliation(s)
- Dan Zhao
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Shanshan Huang
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Menghua Qu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Changyuan Wang
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Zhihao Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Zhen Li
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Jinyong Peng
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China
| | - Yanxia Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China
| | - Xiaodong Ma
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China.
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University, Dalian 116044, PR China.
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72
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Johnson AR, Kohli PB, Katewa A, Gogol E, Belmont LD, Choy R, Penuel E, Burton L, Eigenbrot C, Yu C, Ortwine DF, Bowman K, Franke Y, Tam C, Estevez A, Mortara K, Wu J, Li H, Lin M, Bergeron P, Crawford JJ, Young WB. Battling Btk Mutants With Noncovalent Inhibitors That Overcome Cys481 and Thr474 Mutations. ACS Chem Biol 2016; 11:2897-2907. [PMID: 27571029 DOI: 10.1021/acschembio.6b00480] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Bruton's tyrosine kinase (Btk) inhibitor ibrutinib has shown impressive clinical efficacy in a range of B-cell malignancies. However, acquired resistance has emerged, and second generation therapies are now being sought. Ibrutinib is a covalent, irreversible inhibitor that modifies Cys481 in the ATP binding site of Btk and renders the enzyme inactive, thereby blocking B-cell receptor signal transduction. Not surprisingly, Cys481 is the most commonly mutated Btk residue in cases of acquired resistance to ibrutinib. Mutations at other sites, including Thr474, a gatekeeper residue, have also been detected. Herein, we describe noncovalent Btk inhibitors that differ from covalent inhibitors like ibrutinib in that they do not interact with Cys481, they potently inhibit the ibrutinib-resistant Btk C481S mutant in vitro and in cells, and they are exquisitely selective for Btk. Noncovalent inhibitors such as GNE-431 also show excellent potency against the C481R, T474I, and T474M mutants. X-ray crystallographic analysis of Btk provides insight into the unique mode of binding of these inhibitors that explains their high selectivity for Btk and their retained activity against mutant forms of Btk. This class of noncovalent Btk inhibitors may provide a treatment option to patients, especially those who have acquired resistance to ibrutinib by mutation of Cys481 or Thr474.
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Affiliation(s)
- Adam R. Johnson
- Biochemical
and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Pawan Bir Kohli
- Biochemical
and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Arna Katewa
- Discovery
Immunology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Emily Gogol
- Discovery
Immunology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lisa D. Belmont
- Discovery
Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Regina Choy
- Discovery
Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elicia Penuel
- Biomarker
Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Luciana Burton
- Biomarker
Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Charles Eigenbrot
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christine Yu
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel F. Ortwine
- Computational
Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Krista Bowman
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Yvonne Franke
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christine Tam
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Alberto Estevez
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kyle Mortara
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jiansheng Wu
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Hong Li
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - May Lin
- Protein
Chemistry and Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Philippe Bergeron
- Discovery
Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - James J. Crawford
- Discovery
Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy B. Young
- Discovery
Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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73
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Zhang Y, Zhang D, Tian H, Jiao Y, Shi Z, Ran T, Liu H, Lu S, Xu A, Qiao X, Pan J, Yin L, Zhou W, Lu T, Chen Y. Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches. Mol Pharm 2016; 13:3106-18. [PMID: 27483186 DOI: 10.1021/acs.molpharmaceut.6b00302] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covalent drugs have attracted increasing attention in recent years due to good inhibitory activity and selectivity. Targeting noncatalytic cysteines with irreversible inhibitors is a powerful approach for enhancing pharmacological potency and selectivity because cysteines can form covalent bonds with inhibitors through their nucleophilic thiol groups. However, most human kinases have multiple noncatalytic cysteines within the active site; to accurately predict which cysteine is most likely to form covalent bonds is of great importance but remains a challenge when designing irreversible inhibitors. In this work, FTMap was first applied to check its ability in predicting covalent binding site defined as the region where covalent bonds are formed between cysteines and irreversible inhibitors. Results show that it has excellent performance in detecting the hot spots within the binding pocket, and its hydrogen bond interaction frequency analysis could give us some interesting instructions for identification of covalent binding cysteines. Furthermore, we proposed a simple but useful covalent fragment probing approach and showed that it successfully predicted the covalent binding site of seven targets. By adopting a distance-based method, we observed that the closer the nucleophiles of covalent warheads are to the thiol group of a cysteine, the higher the possibility that a cysteine is prone to form a covalent bond. We believe that the combination of FTMap and our distance-based covalent fragment probing method can become a useful tool in detecting the covalent binding site of these targets.
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Affiliation(s)
- Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Danfeng Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Haozhong Tian
- State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Yu Jiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Zhihao Shi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Ting Ran
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Shuai Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Anyang Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Xin Qiao
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Jing Pan
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Lingfeng Yin
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Weineng Zhou
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China
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74
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Structure-based discovery of novel 4,5,6-trisubstituted pyrimidines as potent covalent Bruton’s tyrosine kinase inhibitors. Bioorg Med Chem Lett 2016; 26:3052-3059. [DOI: 10.1016/j.bmcl.2016.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
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75
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Santos-Garcia L, Assis LC, Silva DR, Ramalho TC, da Cunha EF. QSAR analysis of nicotinamidic compounds and design of potential Bruton’s tyrosine kinase (Btk) inhibitors. J Biomol Struct Dyn 2016; 34:1421-40. [DOI: 10.1080/07391102.2015.1070750] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Letícia Santos-Garcia
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Letícia C. Assis
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Daniela R. Silva
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Elaine F.F. da Cunha
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
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76
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Chopra N, Wales TE, Joseph RE, Boyken SE, Engen JR, Jernigan RL, Andreotti AH. Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases. PLoS Comput Biol 2016; 12:e1004826. [PMID: 27010561 PMCID: PMC4807093 DOI: 10.1371/journal.pcbi.1004826] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
Bruton’s tyrosine kinase (Btk) is a Tec family non-receptor tyrosine kinase that plays a critical role in immune signaling and is associated with the immunological disorder X-linked agammaglobulinemia (XLA). Our previous findings showed that the Tec kinases are allosterically activated by the adjacent N-terminal linker. A single tryptophan residue in the N-terminal 17-residue linker mediates allosteric activation, and its mutation to alanine leads to the complete loss of activity. Guided by hydrogen/deuterium exchange mass spectrometry results, we have employed Molecular Dynamics simulations, Principal Component Analysis, Community Analysis and measures of node centrality to understand the details of how a single tryptophan mediates allostery in Btk. A specific tryptophan side chain rotamer promotes the functional dynamic allostery by inducing coordinated motions that spread across the kinase domain. Either a shift in the rotamer population, or a loss of the tryptophan side chain by mutation, drastically changes the coordinated motions and dynamically isolates catalytically important regions of the kinase domain. This work also identifies a new set of residues in the Btk kinase domain with high node centrality values indicating their importance in transmission of dynamics essential for kinase activation. Structurally, these node residues appear in both lobes of the kinase domain. In the N-lobe, high centrality residues wrap around the ATP binding pocket connecting previously described Catalytic-spine residues. In the C-lobe, two high centrality node residues connect the base of the R- and C-spines on the αF-helix. We suggest that the bridging residues that connect the catalytic and regulatory architecture within the kinase domain may be a crucial element in transmitting information about regulatory spine assembly to the catalytic machinery of the catalytic spine and active site. Bruton’s tyrosine kinase (Btk) belongs to the Tec family of protein tyrosine kinases, and plays a crucial role in the signaling pathway in B-cells. Alteration of Btk activity results in the serious immunological disorder, X-linked agammaglobulinemia. Btk is a multi-domain protein and the activity of the kinase domain is regulated by the adjacent non-catalytic domains, which mediate their effect by means of a conserved tryptophan residue. In this work, we have investigated the mechanism of regulation by this tryptophan residue, W395, in the linker preceding the Btk kinase domain. Using hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations we identify structural elements within the kinase domain that are required for function by transmitting the allosteric effects of W395. Molecular Dynamics simulations further guided us to delineate the kinase domain into dynamically correlated sets of residues using community analysis, thereby identifying the important communication nodes that connect the various elements of the kinase domain required for function. The analyses performed indicate clearly how the W395A mutant changes the communication pathway required for function.
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Affiliation(s)
- Nikita Chopra
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Raji E. Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Robert L. Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Amy H. Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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77
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Molecular modeling studies on series of Btk inhibitors using docking, structure-based 3D-QSAR and molecular dynamics simulation: a combined approach. Arch Pharm Res 2015; 39:328-39. [PMID: 26699616 DOI: 10.1007/s12272-015-0698-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/12/2015] [Indexed: 10/22/2022]
Abstract
Bruton tyrosine kinase (Btk) is a non-receptor tyrosine kinase. It is a crucial component in BCR pathway and expressed only in hematopoietic cells except T cells and Natural killer cells. BTK is a promising target because of its involvement in signaling pathways and B cell diseases such as autoimmune disorders and lymphoma. In this work, a combined molecular modeling study of molecular docking, 3D-QSAR and molecular dynamic (MD) simulation were performed on a series of 2,5-diaminopyrimidine compounds as inhibitors targeting Btk kinase to understand the interaction and key residues involved in the inhibition. A structure based CoMFA (q (2) = 0.675, NOC = 5, r (2) = 0.961) and COMSIA (q (2) = 0.704, NOC = 6, r (2) = 0.962) models were developed from the conformation obtained by docking. The developed models were subjected to various validation techniques such as leave-five-out, external test set, bootstrapping, progressive sampling and rm (2) metrics and found to have a good predictive ability in both internal and external validation. Our docking results showed the important residues that interacts in the active site residues in inhibition of Btk kinase. Furthermore, molecular dynamics simulation was employed to study the stability of the docked conformation and to investigate the binding interactions in detail. The MD simulation analyses identified several important hydrogen bonds with Btk, including the gatekeeper residue Thr474 and Met477 at the hinge region. Hydrogen bond with active site residues Leu408 and Arg525 were also recognized. A good correlation between the MD results, docking studies and the contour map analysis are observed. This indicates that the developed models are reliable. Our results from this study can provide insights in the designing and development of more potent Btk kinase inhibitors.
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78
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Tse A, Verkhivker GM. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. PLoS One 2015; 10:e0130203. [PMID: 26075886 PMCID: PMC4468085 DOI: 10.1371/journal.pone.0130203] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/17/2015] [Indexed: 12/20/2022] Open
Abstract
Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating residues. This study has outlined mechanisms by which inhibitor binding could modulate resilience and efficiency of allosteric interactions in the kinase structures, while preserving structural topology required for catalytic activity and regulation.
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Affiliation(s)
- Amanda Tse
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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79
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Zhao X, Xin M, Wang Y, Huang W, Jin Q, Tang F, Wu G, Zhao Y, Xiang H. Discovery of thieno[3,2-c]pyridin-4-amines as novel Bruton's tyrosine kinase (BTK) inhibitors. Bioorg Med Chem 2015; 23:6059-68. [PMID: 26277759 DOI: 10.1016/j.bmc.2015.05.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
A novel series of BTK inhibitors bearing thieno[3,2-c]pyridin-4-amine framework as the core scaffold were designed, synthesized and well characterized. In this paper, twenty one compounds displayed variant inhibitory activities against BTK in vitro, and compound 14 g showed the most potent inhibitory activity against BTK enzyme, with the IC50 value of 12.8 nM. Moreover, compounds 14 g displayed relatively good kinase selectivity and was subsequently evaluated in vivo for profiling its PK properties. This work identified the thieno[3,2-c]pyridin-4-amine derivatives as novel BTK inhibitors and verified the value of thieno[3,2-c]pyridin-4-amine scaffold in drug design.
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Affiliation(s)
- Xinge Zhao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, No. 24, Tongjiaxiang, Nanjing 210009, PR China; Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No 76, Yanta West Road, Xi'an 710061, PR China
| | - Yazhou Wang
- Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Wei Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Qiu Jin
- Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Feng Tang
- Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Gang Wu
- Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Yong Zhao
- Jiangsu Simcere Pharmaceutical Co. Ltd, Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research, No 699-18, Xuan Wu District, Nanjing 210042, PR China
| | - Hua Xiang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, No. 24, Tongjiaxiang, Nanjing 210009, PR China.
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80
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Bradshaw JM, McFarland JM, Paavilainen VO, Bisconte A, Tam D, Phan VT, Romanov S, Finkle D, Shu J, Patel V, Ton T, Li X, Loughhead DG, Nunn PA, Karr DE, Gerritsen ME, Funk JO, Owens TD, Verner E, Brameld KA, Hill RJ, Goldstein DM, Taunton J. Prolonged and tunable residence time using reversible covalent kinase inhibitors. Nat Chem Biol 2015; 11:525-31. [PMID: 26006010 PMCID: PMC4472506 DOI: 10.1038/nchembio.1817] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022]
Abstract
Drugs with prolonged, on-target residence time often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here, we demonstrate progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Utilizing an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, we identified potent and selective BTK inhibitors that demonstrate biochemical residence times spanning from minutes to 7 days. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK more than 18 hours after clearance from the circulation. The inverted cyanoacrylamide strategy was further utilized to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating generalizability of the approach. Targeting noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates “residence time by design”, the ability to modulate and improve the duration of target engagement in vivo.
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Affiliation(s)
| | - Jesse M McFarland
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - Ville O Paavilainen
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | | | - Danny Tam
- Principia Biopharma, South San Francisco, California, USA
| | - Vernon T Phan
- Principia Biopharma, South San Francisco, California, USA
| | | | - David Finkle
- Principia Biopharma, South San Francisco, California, USA
| | - Jin Shu
- Principia Biopharma, South San Francisco, California, USA
| | - Vaishali Patel
- Principia Biopharma, South San Francisco, California, USA
| | - Tony Ton
- Principia Biopharma, South San Francisco, California, USA
| | - Xiaoyan Li
- Principia Biopharma, South San Francisco, California, USA
| | | | - Philip A Nunn
- Principia Biopharma, South San Francisco, California, USA
| | - Dane E Karr
- Principia Biopharma, South San Francisco, California, USA
| | | | | | | | - Erik Verner
- Principia Biopharma, South San Francisco, California, USA
| | - Ken A Brameld
- Principia Biopharma, South San Francisco, California, USA
| | - Ronald J Hill
- Principia Biopharma, South San Francisco, California, USA
| | | | - Jack Taunton
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
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81
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Xiao J, Zhang S, Luo M, Zou Y, Zhang Y, Lai Y. Effective virtual screening strategy focusing on the identification of novel Bruton's tyrosine kinase inhibitors. J Mol Graph Model 2015; 60:142-54. [PMID: 26043662 DOI: 10.1016/j.jmgm.2015.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 11/18/2022]
Abstract
Dysregulation of the B-cell receptor (BCR) signaling pathway plays a vital role in the pathogenesis and development of B-cell malignancies. Bruton's tyrosine kinase (BTK), a key component in the BCR signaling, has been validated as a valuable target for the treatment of B-cell malignancies. In an attempt to find novel and potent BTK inhibitors, both ligand- and structure-based pharmacophore models were generated using Discovery Studio 2.5 and Ligandscout 3.11 with the aim of screening the ChemBridge database. The resulting hits were then subjected to sequential docking experiments using two independent docking programs, CDOCKER and Glide. Molecules displaying high glide scores and H-bond interactions with the key residue Met477 in both of the docking programs were retained. Drug-like criteria including Lipinski's rule of five and ADMET properties filters were employed for further refinement of the retrieved hits. By clustering, eight promising compounds with novel chemical scaffolds were finally selected and the top two ranking compounds were evaluated by molecular dynamics simulation. We believe that these compounds are of great potential in BTK inhibition and will be used for further investigation.
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Affiliation(s)
- Jianhu Xiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Shengping Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Minghao Luo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yi Zou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yisheng Lai
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China.
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82
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FDA-approved small-molecule kinase inhibitors. Trends Pharmacol Sci 2015; 36:422-39. [PMID: 25975227 DOI: 10.1016/j.tips.2015.04.005] [Citation(s) in RCA: 694] [Impact Index Per Article: 77.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
Abstract
Kinases have emerged as one of the most intensively pursued targets in current pharmacological research, especially for cancer, due to their critical roles in cellular signaling. To date, the US FDA has approved 28 small-molecule kinase inhibitors, half of which were approved in the past 3 years. While the clinical data of these approved molecules are widely presented and structure-activity relationship (SAR) has been reported for individual molecules, an updated review that analyzes all approved molecules and summarizes current achievements and trends in the field has yet to be found. Here we present all approved small-molecule kinase inhibitors with an emphasis on binding mechanism and structural features, summarize current challenges, and discuss future directions in this field.
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83
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Ravichandran S, Luke BT, Collins JR. Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study. J Mol Graph Model 2015; 57:36-48. [PMID: 25635590 PMCID: PMC4361267 DOI: 10.1016/j.jmgm.2014.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Cancer is a complex disease resulting from the uncontrolled proliferation of cell signaling events. Protein kinases have been identified as central molecules that participate overwhelmingly in oncogenic events, thus becoming key targets for anticancer drugs. A majority of studies converged on the idea that ligand-binding pockets of kinases retain clues to the inhibiting abilities and cross-reacting tendencies of inhibitor drugs. Even though these ideas are critical for drug discovery, validating them using experiments is not only difficult, but also in some cases infeasible. To overcome these limitations and to test these ideas at the molecular level, we present here the results of receptor-focused in-silico docking of nine marketed drugs to 19 different wild-type and mutated kinases chosen from a wide range of families. This investigation highlights the need for using relevant models to explain the correct inhibition trends and the results are used to make predictions that might be able to influence future experiments. Our simulation studies are able to correctly predict the primary targets for each drug studied in majority of cases and our results agree with the existing findings. Our study shows that the conformations a given receptor acquires during kinase activation, and their micro-environment, defines the ligand partners. Type II drugs display high compatibility and selectivity for DFG-out kinase conformations. On the other hand Type I drugs are less selective and show binding preferences for both the open and closed forms of selected kinases. Using this receptor-focused approach, it is possible to capture the observed fold change in binding affinities between the wild-type and disease-centric mutations in ABL kinase for Imatinib and the second-generation ABL drugs. The effects of mutation are also investigated for two other systems, EGFR and B-Raf. Finally, by including pathway information in the design it is possible to model kinase inhibitors with potentially fewer side-effects.
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Affiliation(s)
- Sarangan Ravichandran
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA.
| | - Brian T Luke
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA
| | - Jack R Collins
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research (FNLCR), P.O. Box B, Frederick, MD 21702, USA
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84
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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85
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Bruton's TK inhibitors: structural insights and evolution of clinical candidates. Future Med Chem 2015; 6:675-95. [PMID: 24895895 DOI: 10.4155/fmc.14.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bruton's TK (BTK) is a promising biological target for therapeutic intervention of several diseases including inflammatory diseases and cancer/B cell malignancies. Numerous research groups are actively engaged in investigating the functions of BTK, and discovering potent and selective BTK inhibitors as drug candidates. Revealed by x-ray crystal structures with ligands of diverse chemical structures, the ability of BTK kinase domain to adopt various inactive conformations offers unique opportunities to identify highly potent and exquisitely selective inhibitors. Both reversible and covalent inhibitor approaches have yielded candidates demonstrating safety profiles and efficacies in multiple preclinical models of autoimmunity and oncology. Two BTK inhibitors have entered human clinical trials for oncology indications. Ibrutinib won the US FDA approval in November 2013 to become the first-in-class BTK inhibitor for treating mantle cell lymphoma. This encouraging outcome and the other on-going human studies could ultimately expand the utility of BTK inhibitors to broader autoimmune disease areas.
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86
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Xie Q, Fulton DB, Andreotti AH. A selective NMR probe to monitor the conformational transition from inactive to active kinase. ACS Chem Biol 2015; 10:262-8. [PMID: 25248068 PMCID: PMC4301085 DOI: 10.1021/cb5004702] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Kinases control many aspects of cellular
signaling and are therefore
therapeutic targets for numerous disease states. Monitoring the conformational
changes that drive activation and inactivation of the catalytic kinase
core is a challenging experimental problem due to the dynamic nature
of these enzymes. We apply [13C] reductive methylation
to chemically introduce NMR-active nuclei into unlabeled protein kinases.
The results demonstrate that solution NMR spectroscopy can be used
to monitor specific changes in the chemical environment of structurally
important lysines in a [13C]-methylated kinase as it shifts
from the inactive to active state. This approach provides a solution
based method to complement X-ray crystallographic data and can be
applied to nearly any kinase, regardless of size or method of production.
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Affiliation(s)
- Qian Xie
- Roy J.
Carver Department
of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - D. Bruce Fulton
- Roy J.
Carver Department
of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Amy H. Andreotti
- Roy J.
Carver Department
of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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87
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88
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Badrinarayan P, Sastry GN. Specificity rendering 'hot-spots' for aurora kinase inhibitor design: the role of non-covalent interactions and conformational transitions. PLoS One 2014; 9:e113773. [PMID: 25485544 PMCID: PMC4259475 DOI: 10.1371/journal.pone.0113773] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors.
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Affiliation(s)
- Preethi Badrinarayan
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
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89
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Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol 2014; 9:1894-905. [PMID: 24946274 PMCID: PMC4136698 DOI: 10.1021/cb500371g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Multidomain protein kinases, central
controllers of signal transduction,
use regulatory domains to modulate catalytic activity in a complex
cellular environment. Additionally, these domains regulate noncatalytic
functions, including cellular localization and protein–protein
interactions. Src-family kinases (SFKs) are promising therapeutic
targets for a number of diseases and are an excellent model for studying
the regulation of multidomain kinases. Here, we demonstrate that the
regulatory domains of the SFKs Src and Hck are divergently affected
by ligands that stabilize two distinct inactive ATP-binding site conformations.
Conformation-selective, ATP-competitive inhibitors differentially
modulate the ability of the SH3 and SH2 domains of Src and Hck to
engage in intermolecular interactions and the ability of the kinase–inhibitor
complex to undergo post-translational modification by effector enzymes.
This surprising divergence in regulatory domain behavior by two classes
of inhibitors that each stabilize inactive ATP-binding site conformations
is found to occur through perturbation or stabilization of the αC
helix. These studies provide insight into how conformation-selective,
ATP-competitive inhibitors can be designed to modulate domain interactions
and post-translational modifications distal to the ATP-binding site
of kinases.
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Affiliation(s)
- Stephen E. Leonard
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A. C. Register
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ratika Krishnamurty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriel J. Brighty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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90
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Ponader S, Burger JA. Bruton's tyrosine kinase: from X-linked agammaglobulinemia toward targeted therapy for B-cell malignancies. J Clin Oncol 2014; 32:1830-9. [PMID: 24778403 PMCID: PMC5073382 DOI: 10.1200/jco.2013.53.1046] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Discovery of Bruton's tyrosine kinase (BTK) mutations as the cause for X-linked agammaglobulinemia was a milestone in understanding the genetic basis of primary immunodeficiencies. Since then, studies have highlighted the critical role of this enzyme in B-cell development and function, and particularly in B-cell receptor signaling. Because its deletion affects mostly B cells, BTK has become an attractive therapeutic target in autoimmune disorders and B-cell malignancies. Ibrutinib (PCI-32765) is the most advanced BTK inhibitor in clinical testing, with ongoing phase III clinical trials in patients with chronic lymphocytic leukemia and mantle-cell lymphoma. In this article, we discuss key discoveries related to BTK and clinically relevant aspects of BTK inhibitors, and we provide an outlook into clinical development and open questions regarding BTK inhibitor therapy.
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Affiliation(s)
- Sabine Ponader
- All authors: The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jan A Burger
- All authors: The University of Texas MD Anderson Cancer Center, Houston, TX.
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91
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Hutchinson CV, Dyer MJS. Breaking good: the inexorable rise of BTK inhibitors in the treatment of chronic lymphocytic leukaemia. Br J Haematol 2014; 166:12-22. [PMID: 24749490 DOI: 10.1111/bjh.12895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although expressed in several haematological lineages and involved in multiple different signalling pathways, Bruton tyrosine kinase (BTK) plays an indispensible role in B cells in signalling from the B cell receptor (BCR) for antigen. Many B cell malignancies remain dependent on constitutive BCR signalling, making BTK a functional therapeutic target. Several BTK inhibitors (BTKi) with different kinomes and modes of action are being assessed clinically. This review documents the efficacy and toxicity of BTKi in chronic lymphocytic leukaemia (CLL). Clinically, the furthest in development is ibrutinib (trade name, Imbruvica), an irreversible BTKi, which has shown spectacular preliminary efficacy, with rapid reductions in lymph nodes accompanied by peripheral blood lymphocytosis. The lymphocytosis resolves slowly and most patients do not enter a complete remission. Nevertheless, it is possible to maintain many CLL patients, even those with adverse cytogenetic features, on drug for many months with minimal toxicities, thus potentially transforming the therapeutic paradigms for CLL. The efficacy, lack of toxicity and oral administration of BTKi will ensure their adoption in a wide range of B cell malignancies. An outstanding challenge is to incorporate BTKi with other precision medicines in a mechanism-based manner in order to dispense with conventional chemotherapy.
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Affiliation(s)
- Claire V Hutchinson
- Department of of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK; The Ernest and Helen Scott Haematological Research Institute, University of Leicester
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92
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Structure-functional prediction and analysis of cancer mutation effects in protein kinases. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:653487. [PMID: 24817905 PMCID: PMC4000980 DOI: 10.1155/2014/653487] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 12/31/2013] [Accepted: 02/28/2014] [Indexed: 12/17/2022]
Abstract
A central goal of cancer research is to discover and characterize the functional effects of mutated genes that contribute to tumorigenesis. In this study, we provide a detailed structural classification and analysis of functional dynamics for members of protein kinase families that are known to harbor cancer mutations. We also present a systematic computational analysis that combines sequence and structure-based prediction models to characterize the effect of cancer mutations in protein kinases. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinase-inactivating mutations that decrease activity. Mapping of cancer mutations onto the conformational mobility profiles of known crystal structures demonstrated that activating mutations could reduce a steric barrier for the movement from the basal “low” activity state to the “active” state. According to our analysis, the mechanism of activating mutations reflects a combined effect of partial destabilization of the kinase in its inactive state and a concomitant stabilization of its active-like form, which is likely to drive tumorigenesis at some level. Ultimately, the analysis of the evolutionary and structural features of the major cancer-causing mutational hotspot in kinases can also aid in the correlation of kinase mutation effects with clinical outcomes.
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93
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Jongco AM, Gough JD, Sarnataro K, Rosenthal DW, Moreau J, Ponda P, Bonagura VR. X-linked agammaglobulinemia presenting as polymicrobial pneumonia, including Pneumocystis jirovecii. Ann Allergy Asthma Immunol 2013; 112:74-75.e2. [PMID: 24331399 DOI: 10.1016/j.anai.2013.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Artemio M Jongco
- Laboratory of Host Defense, Center for Immunology and Inflammation, Feinstein Institute for Medical Research, Manhasset, New York; Division of Allergy and Immunology, Hofstra North Shore-LIJ School of Medicine, Great Neck, New York.
| | - Jonathan D Gough
- Department of Chemistry and Biochemistry, Long Island University, Brooklyn, New York
| | - Kyle Sarnataro
- Laboratory of Host Defense, Center for Immunology and Inflammation, Feinstein Institute for Medical Research, Manhasset, New York
| | - David W Rosenthal
- Laboratory of Host Defense, Center for Immunology and Inflammation, Feinstein Institute for Medical Research, Manhasset, New York; Division of Allergy and Immunology, Hofstra North Shore-LIJ School of Medicine, Great Neck, New York
| | - Joanne Moreau
- Division of Allergy and Immunology, Hofstra North Shore-LIJ School of Medicine, Great Neck, New York
| | - Punita Ponda
- Division of Allergy and Immunology, Hofstra North Shore-LIJ School of Medicine, Great Neck, New York
| | - Vincent R Bonagura
- Laboratory of Host Defense, Center for Immunology and Inflammation, Feinstein Institute for Medical Research, Manhasset, New York; Division of Allergy and Immunology, Hofstra North Shore-LIJ School of Medicine, Great Neck, New York
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94
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Kitagawa D, Gouda M, Kirii Y. Quick Evaluation of Kinase Inhibitors by Surface Plasmon Resonance Using Single-Site Specifically Biotinylated Kinases. ACTA ACUST UNITED AC 2013; 19:453-61. [DOI: 10.1177/1087057113506051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In evaluating kinase inhibitors, kinetic parameters such as association/dissociation rate constants are valuable information, as are equilibrium parameters KD and IC50 values. Surface plasmon resonance (SPR) is a powerful technique to investigate these parameters. However, results are often complicated because of impaired conformations by inappropriate conditions required for protein immobilization and/or heterogeneity of the orientation of immobilization. In addition, conventional SPR experiments are generally time-consuming. Here we introduce the use of single-site specifically biotinylated kinases combined with a multichannel SPR device to improve such problems. Kinetic parameters of four compounds—staurosporine, dasatinib, sunitinib, and lapatinib—against six kinases were determined by the ProteOn XPR36 system. The very slow off-rate of lapatinib from the epidermal growth factor receptor and dasatinib from Bruton’s tyrosine kinase and colony stimulating factor 1 receptor (CSF1R) were confirmed. Furthermore, IC50 values were determined by an activity-based assay. Evaluating both physicochemical and biochemical properties would help to understand the detailed character of the compound.
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95
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Joseph RE, Kleino I, Wales TE, Xie Q, Fulton DB, Engen JR, Berg LJ, Andreotti AH. Activation loop dynamics determine the different catalytic efficiencies of B cell- and T cell-specific tec kinases. Sci Signal 2013; 6:ra76. [PMID: 23982207 DOI: 10.1126/scisignal.2004298] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Itk (interleukin-2-inducible T cell kinase) and Btk (Bruton's tyrosine kinase) are nonreceptor tyrosine kinases of the Tec family that signal downstream of the T cell receptor (TCR) and B cell receptor (BCR), respectively. Despite their high sequence similarity and related signaling roles, Btk is a substantially more active kinase than Itk. We showed that substitution of 6 of the 619 amino acid residues of Itk with the corresponding residues of Btk (and vice versa) was sufficient to completely switch the activities of Itk and Btk. The substitutions responsible for the swap in activity are all localized to the activation segment of the kinase domain. Nuclear magnetic resonance and hydrogen-deuterium exchange mass spectrometry analyses revealed that Itk and Btk had distinct protein dynamics in this region, which could explain the differences in catalytic efficiency between these kinases. Introducing Itk with enhanced activity into T cells led to enhanced and prolonged TCR signaling compared to that in cells with wild-type Itk. These findings imply that evolutionary pressures have led to Tec kinases having distinct enzymatic properties, depending on the cellular context. We suggest that the weaker catalytic activities of T cell-specific kinases serve to regulate cellular activation and prevent aberrant immune responses.
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Affiliation(s)
- Raji E Joseph
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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96
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Ibrutinib is an irreversible molecular inhibitor of ITK driving a Th1-selective pressure in T lymphocytes. Blood 2013; 122:2539-49. [PMID: 23886836 DOI: 10.1182/blood-2013-06-507947] [Citation(s) in RCA: 601] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given its critical role in T-cell signaling, interleukin-2-inducible kinase (ITK) is an appealing therapeutic target that can contribute to the pathogenesis of certain infectious, autoimmune, and neoplastic diseases. Ablation of ITK subverts Th2 immunity, thereby potentiating Th1-based immune responses. While small-molecule ITK inhibitors have been identified, none have demonstrated clinical utility. Ibrutinib is a confirmed irreversible inhibitor of Bruton tyrosine kinase (BTK) with outstanding clinical activity and tolerability in B-cell malignancies. Significant homology between BTK and ITK alongside in silico docking studies support ibrutinib as an immunomodulatory inhibitor of both ITK and BTK. Our comprehensive molecular and phenotypic analysis confirms ITK as an irreversible T-cell target of ibrutinib. Using ibrutinib clinical trial samples along with well-characterized neoplastic (chronic lymphocytic leukemia), parasitic infection (Leishmania major), and infectious disease (Listeria monocytogenes) models, we establish ibrutinib as a clinically relevant and physiologically potent ITK inhibitor with broad therapeutic utility. This trial was registered at www.clinicaltrials.gov as #NCT01105247 and #NCT01217749.
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97
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Brigham JL, Perera BGK, Maly DJ. A hexylchloride-based catch-and-release system for chemical proteomic applications. ACS Chem Biol 2013; 8:691-9. [PMID: 23305300 DOI: 10.1021/cb300623a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioorthogonal ligation methods that allow the selective conjugation of fluorophores or biotin to proteins and small molecule probes that contain inert chemical handles are an important component of many chemical proteomic strategies. Here, we present a new catch-and-release enrichment strategy that utilizes a hexylchloride group as a bioorthogonal chemical handle. Proteins and small molecules that contain a hexylchloride tag can be efficiently captured by an immobilized version of the self-labeling protein HaloTag. Furthermore, by using a HaloTag fusion protein that contains a protease cleavage site, captured proteins can be selectively eluted under mild conditions. We demonstrate the utility of the hexylchloride-based catch-and-release strategy by enriching protein kinases that are covalently and noncovalently bound to ATP-binding site-directed probes from mammalian cell lysates. Our catch-and-release system creates new possibilities for profiling enzyme families and for the identification of the cellular targets of bioactive small molecules.
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Affiliation(s)
- Jennifer L. Brigham
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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98
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Abstract
Bruton’s tyrosine kinase (Btk) is intimately involved in multiple signal-transduction pathways regulating survival, activation, proliferation, and differentiation of B-lineage lymphoid cells. Btk is overexpressed and constitutively active in several B-lineage lymphoid malignancies. Btk has emerged as a new antiapoptotic molecular target for treatment of B-lineage leukemias and lymphomas. Preclinical and early clinical results indicate that Btk inhibitors may be useful in the treatment of leukemias and lymphomas.
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Affiliation(s)
- Osmond J D'Cruz
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
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99
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Krishnamurty R, Brigham JL, Leonard SE, Ranjitkar P, Larson ET, Dale EJ, Merritt EA, Maly DJ. Active site profiling reveals coupling between domains in SRC-family kinases. Nat Chem Biol 2012; 9:43-50. [PMID: 23143416 PMCID: PMC3522794 DOI: 10.1038/nchembio.1118] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/01/2012] [Indexed: 12/14/2022]
Abstract
Protein kinases, key regulators of intracellular signal transduction, have emerged as an important class of drug targets. Chemical proteomic tools that facilitate the functional interrogation of protein kinase active sites are powerful reagents for studying the regulation of this large enzyme family and for performing inhibitor selectivity screens. Here we describe a new crosslinking strategy that enables rapid and quantitative profiling of protein kinase active sites in lysates and live cells. Applying this methodology to the SRC-family kinases (SFKs) SRC and HCK led to the identification of a series of conformation-specific, ATP-competitive inhibitors that display a distinct preference for autoinhibited forms of these kinases. Furthermore, we show that ligands that demonstrate this selectivity are able to modulate the ability of the regulatory domains of SRC and HCK to engage in intermolecular binding interactions. These studies provide insight into the regulation of this important family of tyrosine kinases.
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100
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Clinical perspectives for irreversible tyrosine kinase inhibitors in cancer. Biochem Pharmacol 2012; 84:1388-99. [PMID: 22885287 DOI: 10.1016/j.bcp.2012.07.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/21/2022]
Abstract
Irreversible inhibitors provide potent and selective inhibition of tyrosine kinase enzymes. Use of such inhibitors has proved promising in overcoming the tumor resistance encountered with reversible tyrosine kinase inhibitors. Irreversible inhibitors inactivate their protein target through covalent interaction with a nucleophilic cysteine residue within the nucleotide binding pocket of the kinase domain. Different irreversible tyrosin kinase inhibitors directed against epidermal growth factor receptor (EGFR), Bruton's tyrosine kinase (BTK), vascular endothelial growth factor receptor (VEGFR) and fibroblast growth factor receptor tyrosine kinase (FGFR) have been developed and some of them have been employed clinically as anticancer agents. This review focuses on recent preclinical and clinical progress with currently available irreversible tyrosine kinase inhibitors. The chemical structures of the candidates, structure-activity relationships, biological activities and results of current clinical investigations are described.
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