51
|
Barletta GP, Hasenahuer MA, Fornasari MS, Parisi G, Fernandez-Alberti S. Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase. J Comput Chem 2018; 39:2472-2480. [PMID: 30298935 DOI: 10.1002/jcc.25590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/06/2018] [Accepted: 08/19/2018] [Indexed: 12/29/2022]
Abstract
Epidermal growth factor receptor (EGFR) is a prototypical cell-surface receptor that plays a key role in the regulation of cellular signaling, proliferation and differentiation. Mutations of its kinase domain have been associated with the development of a variety of cancers and, therefore, it has been the target of drug design. Single amino acid substitutions (SASs) in this domain have been proven to alter the equilibrium of pre-existing conformer populations. Despite the advances in structural descriptions of its so-called active and inactive conformations, the associated dynamics aspects that characterize them have not been thoroughly studied yet. As the dynamic behaviors and molecular motions of proteins are important for a complete understanding of their structure-function relationships we present a novel procedure, using (or based on) normal mode analysis, to identify the collective dynamics shared among different conformers in EGFR kinase. The method allows the comparison of patterns of low-frequency vibrational modes defining representative directions of motions. Our procedure is able to emphasize the main similarities and differences between the collective dynamics of different conformers. In the case of EGFR kinase, two representative directions of motions have been found as dynamics fingerprints of the active conformers. Protein motion along both directions reveals to have a significant impact on the cavity volume of the main pocket of the active site. Otherwise, the inactive conformers exhibit a more heterogeneous distribution of collective motions. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- German P Barletta
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Marcia Anahi Hasenahuer
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Sebastian Fernandez-Alberti
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| |
Collapse
|
52
|
Design, synthesis, biological evaluation and cellular imaging of imidazo[4,5-b]pyridine derivatives as potent and selective TAM inhibitors. Bioorg Med Chem 2018; 26:5510-5530. [PMID: 30309671 DOI: 10.1016/j.bmc.2018.09.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 12/14/2022]
Abstract
The TAM kinase family arises as a new effective and attractive therapeutic target for cancer therapy, autoimmune and viral diseases. A series of 2,6-disubstituted imidazo[4,5-b]pyridines were designed, synthesized and identified as highly potent TAM inhibitors. Despite remarkable structural similarities within the TAM family, compounds 28 and 25 demonstrated high activity and selectivity in vitro against AXL and MER, with IC50 value of 0.77 nM and 9 nM respectively and a 120- to 900-fold selectivity. We also observed an unexpected nuclear localization for compound 10Bb, thanks to nanoSIMS technology, which could be correlated to the absence of cytotoxicity on three different cancer cell lines being sensitive to TAM inhibition.
Collapse
|
53
|
Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S. Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism. Biochemistry 2018; 57:6387-6390. [PMID: 30339352 DOI: 10.1021/acs.biochem.8b00729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.
Collapse
Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Lisa G Lippert
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Titu Devamani
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Benjamin Levy
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sangbae Lee
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Manbir Sandhu
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| |
Collapse
|
54
|
Raab M, Sanhaji M, Pietsch L, Béquignon I, Herbrand AK, Süß E, Gande SL, Caspar B, Kudlinzki D, Saxena K, Sreeramulu S, Schwalbe H, Strebhardt K, Biondi RM. Modulation of the Allosteric Communication between the Polo-Box Domain and the Catalytic Domain in Plk1 by Small Compounds. ACS Chem Biol 2018; 13:1921-1931. [PMID: 29927572 DOI: 10.1021/acschembio.7b01078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Polo-like kinases (Plks) are an evolutionary conserved family of Ser/Thr protein kinases that possess, in addition to the classical kinase domain at the N-terminus, a C-terminal polo-box domain (PBD) that binds to phosphorylated proteins and modulates the kinase activity and its localization. Plk1, which regulates the formation of the mitotic spindle, has emerged as a validated drug target for the treatment of cancer, because it is required for numerous types of cancer cells but not for the cell division in noncancer cells. Here, we employed chemical biology methods to investigate the allosteric communication between the PBD and the catalytic domain of Plk1. We identified small compounds that bind to the catalytic domain and inhibit or enhance the interaction of Plk1 with the phosphorylated peptide PoloBoxtide in vitro. In cells, two new allosteric Plk1 inhibitors affected the proliferation of cancer cells in culture and the cell cycle but had distinct phenotypic effects on spindle formation. Both compounds inhibited Plk1 signaling, indicating that they specifically act on Plk1 in cultured cells.
Collapse
Affiliation(s)
- Monika Raab
- Department of Gynecology , Goethe-University , 60323 Frankfurt , Germany
| | - Mourad Sanhaji
- Department of Gynecology , Goethe-University , 60323 Frankfurt , Germany
| | - Larissa Pietsch
- Research Group PhosphoSites, Medizinische Klinik 1 , Universitätsklinikum Frankfurt , Frankfurt am Main , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Isabelle Béquignon
- Research Group PhosphoSites, Medizinische Klinik 1 , Universitätsklinikum Frankfurt , Frankfurt am Main , Germany
| | - Amanda K Herbrand
- Research Group PhosphoSites, Medizinische Klinik 1 , Universitätsklinikum Frankfurt , Frankfurt am Main , Germany
| | - Evelyn Süß
- Research Group PhosphoSites, Medizinische Klinik 1 , Universitätsklinikum Frankfurt , Frankfurt am Main , Germany
| | - Santosh L Gande
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Birgit Caspar
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance , Johann Wolfgang Goethe University , 60438 Frankfurt , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Klaus Strebhardt
- Department of Gynecology , Goethe-University , 60323 Frankfurt , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Ricardo M Biondi
- Research Group PhosphoSites, Medizinische Klinik 1 , Universitätsklinikum Frankfurt , Frankfurt am Main , Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society , Buenos Aires C1425FQD , Argentina
| |
Collapse
|
55
|
New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors. Biochem J 2018; 475:2435-2455. [PMID: 29934490 PMCID: PMC6094398 DOI: 10.1042/bcj20180266] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/14/2018] [Accepted: 06/21/2018] [Indexed: 12/11/2022]
Abstract
Protein tyrosine sulfation is a post-translational modification best known for regulating extracellular protein–protein interactions. Tyrosine sulfation is catalysed by two Golgi-resident enzymes termed tyrosylprotein sulfotransferases (TPSTs) 1 and 2, which transfer sulfate from the cofactor PAPS (3′-phosphoadenosine 5′-phosphosulfate) to a context-dependent tyrosine in a protein substrate. A lack of quantitative tyrosine sulfation assays has hampered the development of chemical biology approaches for the identification of small-molecule inhibitors of tyrosine sulfation. In the present paper, we describe the development of a non-radioactive mobility-based enzymatic assay for TPST1 and TPST2, through which the tyrosine sulfation of synthetic fluorescent peptides can be rapidly quantified. We exploit ligand binding and inhibitor screens to uncover a susceptibility of TPST1 and TPST2 to different classes of small molecules, including the anti-angiogenic compound suramin and the kinase inhibitor rottlerin. By screening the Published Kinase Inhibitor Set, we identified oxindole-based inhibitors of the Ser/Thr kinase RAF (rapidly accelerated fibrosarcoma) as low-micromolar inhibitors of TPST1 and TPST2. Interestingly, unrelated RAF inhibitors, exemplified by the dual BRAF/VEGFR2 inhibitor RAF265, were also TPST inhibitors in vitro. We propose that target-validated protein kinase inhibitors could be repurposed, or redesigned, as more-specific TPST inhibitors to help evaluate the sulfotyrosyl proteome. Finally, we speculate that mechanistic inhibition of cellular tyrosine sulfation might be relevant to some of the phenotypes observed in cells exposed to anionic TPST ligands and RAF protein kinase inhibitors.
Collapse
|
56
|
Ribaudo G, Zanforlin E, Zagotto G. Overcoming resistance in non-small-cell lung cancer: A practical lesson for the medicinal chemist. Arch Pharm (Weinheim) 2018; 351:e1800037. [PMID: 30101528 DOI: 10.1002/ardp.201800037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/25/2022]
Abstract
The introduction of tyrosine kinase inhibitors (TKIs) in the clinical management of oncological patients spread the light on the use of selective, rationally designed small molecules for the treatment of cancer. First-generation TKIs bared high response against these malignancies, although the unavoidable shadow of resistance limits their long-term efficacy. Non-small-cell lung cancer (NSCLC) accounts for 85% of lung cancer cases, and it is the first cause of cancer deaths worldwide for men and women. Traditional chemotherapy is marginally effective against this form, and erlotinib and gefitinib were introduced as first-line treatments based on the observation that the epidermal growth factor receptor (EGFR), a receptor tyrosine kinase (RTK), is mutated in several cases and, thus, represents a druggable target. EGFR-mutant and anaplastic lymphoma kinase (ALK)-positive patients are more responsive to these treatments, even if secondary mutations causing resistance soon emerged. The efforts of medicinal chemists are currently oriented toward the development of new generations of TKIs overcoming these obstacles. We here overview the novel strategies from the point of view of the medicinal chemist: the rational structure-based drug design that led to the development of irreversible and non-ATP-competitive inhibitors. Such improvements parallel the novel therapeutic strategies adopted in the clinic, which are also discussed.
Collapse
Affiliation(s)
- Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Enrico Zanforlin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| |
Collapse
|
57
|
Anborgh PH, Lee DJ, Stam PF, Tuck AB, Chambers AF. Role of osteopontin as a predictive biomarker for anti-EGFR therapy in triple-negative breast cancer. Expert Opin Ther Targets 2018; 22:727-734. [DOI: 10.1080/14728222.2018.1502272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Danny J. Lee
- London Regional Cancer Program, London, Ontario, Canada
| | | | - Alan B. Tuck
- London Regional Cancer Program, London, Ontario, Canada
- Departments of Oncology and of Pathology, University of Western Ontario, London, Ontario, Canada
| | - Ann F. Chambers
- London Regional Cancer Program, London, Ontario, Canada
- Departments of Oncology and of Pathology, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
58
|
Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Syst 2018; 7:161-179.e14. [PMID: 30007540 DOI: 10.1016/j.cels.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation.
Collapse
|
59
|
Ōmura S, Asami Y, Crump A. Staurosporine: new lease of life for parent compound of today's novel and highly successful anti-cancer drugs. J Antibiot (Tokyo) 2018; 71:688-701. [PMID: 29934602 DOI: 10.1038/s41429-018-0029-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
Abstract
Staurosporine, together with such examples as penicillin, aspirin, ivermectin and sildenafil, exemplifies the role that serendipity has in drug discovery and why 'finding things without actually searching for them' retains a prominent role in drug discovery. Hitherto not clinically useful, due to its potency and promiscuity, new delivery technology is opening up new horizons for what was previously just the parent compound of innovative, highly-successful anti-cancer agents.
Collapse
Affiliation(s)
- Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan.
| | - Yukihiro Asami
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Andy Crump
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| |
Collapse
|
60
|
Ajani H, Jansa J, Köprülüoğlu C, Hobza P, Kryštof V, Lyčka A, Lepsik M. Imidazo[1,2-c
]pyrimidin-5(6H
)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring. J Mol Recognit 2018; 31:e2720. [DOI: 10.1002/jmr.2720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Josef Jansa
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Department of Organic Chemistry, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University and Institute of Experimental Botany; Olomouc Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Faculty of Science; University of Hradec Králové; Hradec Králové Czech Republic
| | | |
Collapse
|
61
|
Malki WH, Gouda AM, Ali HEA, Al-Rousan R, Samaha D, Abdalla AN, Bustamante J, Abd Elmageed ZY, Ali HI. Structural-based design, synthesis, and antitumor activity of novel alloxazine analogues with potential selective kinase inhibition. Eur J Med Chem 2018; 152:31-52. [PMID: 29684708 DOI: 10.1016/j.ejmech.2018.04.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 01/09/2023]
Abstract
Protein kinases are promising therapeutic targets for cancer therapy. Here, we applied multiple approaches to optimize the potency and selectivity of our reported alloxazine scaffold. Flexible moieties at position 2 of the hetero-tricyclic system were incorporated to fit into the ATP binding site and extend to the adjacent allosteric site and selectively inhibit protein kinases. This design led to potential selective inhibition of ABL1, CDK1/Cyclin A1, FAK, and SRC kinase by 30-59%. Cytotoxicity was improved by ∼50 times for the optimized lead (10b; IC50 = 40 nM) against breast cancer (MCF-7) cells. Many compounds revealed potential cytotoxicity against ovarian (A2780) and colon carcinoma (HCT116) cells of ∼10-30 time improvement (IC50 5-17 nM). The results of the Annexin-V/PI apoptotic assay demonstrated that many compounds induced significantly early (89-146%) and a dramatically late (556-1180%) cell death in comparison to the vehicle control of MCF-7 cells. SAR indicated that 5-deazaalloxazines have a higher selectivity for Abl-1 and FAK kinases than alloxazines. The correlations between GoldScore fitness into FAK and SRC kinases and IC50 against MCF-7 and A2780 cells were considerable (R2: 0.86-0.98).
Collapse
Affiliation(s)
- Waleed H Malki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, KSA
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, College of Pharmacy, Umm Al-Qura University, KSA; Department of Medicinal Chemistry, College of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Hamdy E A Ali
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Rabaa Al-Rousan
- The Ben and Maytee Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX 75799, United States
| | - Doaa Samaha
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, Berlin 12489, Germany; Department of Pharmaceutical Chemistry, College of Pharmacy, Helwan University, Cairo 11795, Egypt
| | - Ashraf N Abdalla
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, KSA
| | - Juan Bustamante
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Zakaria Y Abd Elmageed
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Hamed I Ali
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States; Department of Pharmaceutical Chemistry, College of Pharmacy, Helwan University, Cairo 11795, Egypt.
| |
Collapse
|
62
|
Takada M, Parys M, Gregory-Bryson E, Vilar Saavedra P, Kiupel M, Yuzbasiyan-Gurkan V. A novel canine histiocytic sarcoma cell line: initial characterization and utilization for drug screening studies. BMC Cancer 2018; 18:237. [PMID: 29490634 PMCID: PMC5831740 DOI: 10.1186/s12885-018-4132-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/14/2018] [Indexed: 12/15/2022] Open
Abstract
Background Histiocytic sarcoma is a rare disorder in humans, however it is seen with appreciable frequency in certain breeds of dogs, such as Bernese mountain dog. The purpose of this study was to fully characterize a novel canine histiocytic sarcoma cell line, and utilize it as a tool to screen for potential therapeutic drugs. Methods The histiocytic sarcoma cell line was characterized by expression of cellular markers as determined by immunohistochemistry and flow cytometry techniques. The neoplastic cells were also evaluated for their capability of phagocytizing beads particles, and their potential to grow as xenograft in an immunodeficient mouse. We investigated the in vitro cytotoxic activity of a panel of thirteen compounds using the MTS proliferation assay. Inhibitory effects of different drugs were compared using one-way ANOVA, and multiple means were compared using Tukey’s test. Results Neoplastic cells expressed CD11c, CD14, CD18, CD45, CD172a, CD204, MHC I, and vimentin. Expression of MHC II was upregulated after exposure to LPS. Furthermore, the established cell line clearly demonstrated phagocytic activity similar to positive controls of macrophage cell line. The xenograft mouse developed a palpable subcutaneous soft tissue mass after 29 days of inoculation, which histologically resembled the primary neoplasm. Dasatinib, a tyrosine kinase pan-inhibitor, significantly inhibited the growth of the cells in vitro within a clinically achievable and tolerable plasma concentration. The inhibitory response to dasatinib was augmented when combined with doxorubicin. Conclusions In the present study we demonstrated that a novel canine histiocytic sarcoma cell line presents a valuable tool to evaluate novel treatment approaches. The neoplastic cell line favorably responded to dasatinib, which represents a promising anticancer strategy for the treatment of this malignancy in dogs and similar disorders in humans. Electronic supplementary material The online version of this article (10.1186/s12885-018-4132-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marilia Takada
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maciej Parys
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Present address: Royal (Dick) School of Veterinary Studies and the Roslin Institute, Roslin, Midlothian, UK
| | - Emmalena Gregory-Bryson
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Paulo Vilar Saavedra
- Small Animal Clinical Science, Michigan State University, East Lansing, 48824, MI, USA
| | - Matti Kiupel
- Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, 48824, USA
| | - Vilma Yuzbasiyan-Gurkan
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
63
|
Barletta GP, Fernandez-Alberti S. Protein Fluctuations and Cavity Changes Relationship. J Chem Theory Comput 2018; 14:998-1008. [PMID: 29262685 DOI: 10.1021/acs.jctc.7b00744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein cavities and tunnels are critical for function. Ligand recognition and binding, transport, and enzyme catalysis require cavities rearrangements. Therefore, the flexibility of cavities should be guaranteed by protein vibrational dynamics. Molecular dynamics simulations provide a framework to explore conformational plasticity of protein cavities. Herein, we present a novel procedure to characterize the dynamics of protein cavities in terms of their volume gradient vector. For this purpose, we make use of algorithms for calculation of the cavity volume that result robust for numerical differentiations. Volume gradient vector is expressed in terms of principal component analysis obtained from equilibrated molecular dynamics simulations. We analyze contributions of principal component modes to the volume gradient vector according to their frequency and degree of delocalization. In all our test cases, we find that low frequency modes play a critical role together with minor contributions of high frequency modes. These modes involve concerted motions of significant fractions of the total residues lining the cavities. We make use of variations of the potential energy of a protein in the direction of the volume gradient vector as a measure of flexibility of the cavity. We show that proteins whose collective low frequency fluctuations contribute the most to changes of cavity volume exhibit more flexible cavities.
Collapse
Affiliation(s)
- German P Barletta
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352, B1876BXD Bernal, Argentina
| | | |
Collapse
|
64
|
Meine R, Becker W, Falke H, Preu L, Loaëc N, Meijer L, Kunick C. Indole-3-Carbonitriles as DYRK1A Inhibitors by Fragment-Based Drug Design. Molecules 2018; 23:E64. [PMID: 29364148 PMCID: PMC6017736 DOI: 10.3390/molecules23020064] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a potential drug target because of its role in the development of Down syndrome and Alzheimer's disease. The selective DYRK1A inhibitor 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid (KuFal194), a large, flat and lipophilic molecule, suffers from poor water solubility, limiting its use as chemical probe in cellular assays and animal models. Based on the structure of KuFal194, 7-chloro-1H-indole-3-carbonitrile was selected as fragment template for the development of smaller and less lipophilic DYRK1A inhibitors. By modification of this fragment, a series of indole-3-carbonitriles was designed and evaluated as potential DYRK1A ligands by molecular docking studies. Synthesis and in vitro assays on DYRK1A and related protein kinases identified novel double-digit nanomolar inhibitors with submicromolar activity in cell culture assays.
Collapse
Affiliation(s)
- Rosanna Meine
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.
- Zentrum für Pharmaverfahrenstechnik (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35A, 38106 Braunschweig, Germany.
| | - Walter Becker
- Institute of Pharmacology and Toxicology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany.
| | - Hannes Falke
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.
| | - Lutz Preu
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.
| | - Nadège Loaëc
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, France.
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, France.
| | - Conrad Kunick
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.
- Zentrum für Pharmaverfahrenstechnik (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35A, 38106 Braunschweig, Germany.
| |
Collapse
|
65
|
Strategies to overcome resistance mutations of Bruton's tyrosine kinase inhibitor ibrutinib. Future Med Chem 2018; 10:343-356. [PMID: 29347836 DOI: 10.4155/fmc-2017-0145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ibrutinib, as the first Bruton's tyrosine kinase (Btk) inhibitor, has been shown to have clinically significant activity in leukemias and lymphomas. However, the initially responsive tumors will develop resistance during the process of treatment in few patients. Here, we summarized the mechanism of acquired resistance and suggested the next-generation Btk inhibitors that override the target resistance. Moreover, the development of combination of selective antagonists or inhibitors targeting to multiple protein kinases have increased therapeutic potency to reduce the risk of the emergence of kinases inhibitor resistance. Thus, the reported combination of therapeutic drugs as an alternative therapy to overcome ibrutinib collapse or reduce the risk of the emergence of Btk inhibitor resistance also has been reviewed.
Collapse
|
66
|
Wilson LJ, Linley A, Hammond DE, Hood FE, Coulson JM, MacEwan DJ, Ross SJ, Slupsky JR, Smith PD, Eyers PA, Prior IA. New Perspectives, Opportunities, and Challenges in Exploring the Human Protein Kinome. Cancer Res 2017; 78:15-29. [DOI: 10.1158/0008-5472.can-17-2291] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 11/16/2022]
|
67
|
Hasenahuer MA, Barletta GP, Fernandez-Alberti S, Parisi G, Fornasari MS. Pockets as structural descriptors of EGFR kinase conformations. PLoS One 2017; 12:e0189147. [PMID: 29228029 PMCID: PMC5724837 DOI: 10.1371/journal.pone.0189147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
Epidermal Growth Factor Receptor (EGFR), a tyrosine kinase receptor, is one of the main tumor markers in different types of cancers. The kinase native state is mainly composed of two populations of conformers: active and inactive. Several sequence variations in EGFR kinase region promote the differential enrichment of conformers with higher activity. Some structural characteristics have been proposed to differentiate kinase conformations, but these considerations could lead to ambiguous classifications. We present a structural characterisation of EGFR kinase conformers, focused on active site pocket comparisons, and the mapping of known pathological sequence variations. A structural based clustering of this pocket accurately discriminates active from inactive, well-characterised conformations. Furthermore, this main pocket contains, or is in close contact with, ≈65% of cancer-related variation positions. Although the relevance of protein dynamics to explain biological function has been extensively recognised, the usage of the ensemble of conformations in dynamic equilibrium to represent the functional state of proteins and the importance of pockets, cavities and/or tunnels was often neglected in previous studies. These functional structures and the equilibrium between them could be structurally analysed in wild type as well as in sequence variants. Our results indicate that biologically important pockets, as well as their shape and dynamics, are central to understanding protein function in wild-type, polymorphic or disease-related variations.
Collapse
Affiliation(s)
- Marcia Anahi Hasenahuer
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - German Patricio Barletta
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| |
Collapse
|
68
|
Cazzamalli S, Corso AD, Neri D. Targeted Delivery of Cytotoxic Drugs: Challenges, Opportunities and New Developments. Chimia (Aarau) 2017; 71:712-715. [PMID: 29070415 PMCID: PMC5844459 DOI: 10.2533/chimia.2017.712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cytotoxic drugs, which are commonly used for the pharmacotherapy of many forms of cancer, often cause substantial toxicity to the patient without being able to induce long-lasting remissions. Ligands specific to accessible tumor-associated targets, capable of selective localization at the neoplastic site, may facilitate the preferential delivery of anti-cancer drugs, boosting activity and helping spare normal organs. In this article, we present a critical analysis of the limitation of conventional anti-cancer drugs and we contrast monoclonal antibodies and small organic ligands, as vehicles for pharmacodelivery applications.
Collapse
Affiliation(s)
- Samuele Cazzamalli
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zurich) Vladimir-Prelog-Weg 4, CH-8093 Zurich
| | - Alberto Dal Corso
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zurich) Vladimir-Prelog-Weg 4, CH-8093 Zurich
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zurich) Vladimir-Prelog-Weg 4, CH-8093 Zurich;,
| |
Collapse
|
69
|
Gomez-Gutierrez P, Rubio-Martinez J, Perez JJ. Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase. J Chem Inf Model 2017; 57:2566-2574. [DOI: 10.1021/acs.jcim.7b00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Patricia Gomez-Gutierrez
- Allinky
Biopharma, Madrid Scientific Park, Faraday, 7, 28049 Madrid, Spain
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department
of Physical Chemistry, Faculty of Chemistry, Universitat de Barcelona and Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Marti i Franques 1-3, 08028 Barcelona, Spain
| | - Juan J. Perez
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
| |
Collapse
|
70
|
Changeux JP, Christopoulos A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Diabetes Obes Metab 2017; 19 Suppl 1:4-21. [PMID: 28880476 DOI: 10.1111/dom.12959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.
Collapse
MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Binding Sites/drug effects
- Dimerization
- Drug Discovery/trends
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacology
- Humans
- Ligand-Gated Ion Channels/agonists
- Ligand-Gated Ion Channels/antagonists & inhibitors
- Ligand-Gated Ion Channels/chemistry
- Ligand-Gated Ion Channels/metabolism
- Ligands
- Models, Molecular
- Protein Conformation/drug effects
- Protein Multimerization/drug effects
- Receptor Protein-Tyrosine Kinases/agonists
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Voltage-Gated Sodium Channels/chemistry
- Voltage-Gated Sodium Channels/metabolism
Collapse
Affiliation(s)
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, VIC 3052 Parkville, Australia
| |
Collapse
|
71
|
Beretta GL, Cassinelli G, Pennati M, Zuco V, Gatti L. Overcoming ABC transporter-mediated multidrug resistance: The dual role of tyrosine kinase inhibitors as multitargeting agents. Eur J Med Chem 2017; 142:271-289. [PMID: 28851502 DOI: 10.1016/j.ejmech.2017.07.062] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
Resistance to conventional and target specific antitumor drugs still remains one of the major cause of treatment failure and patience death. This condition often involves ATP-binding cassette (ABC) transporters that, by pumping the drugs outside from cancer cells, attenuate the potency of chemotherapeutics and negatively impact on the fate of anticancer therapy. In recent years, several tyrosine kinase inhibitors (TKIs) (e.g., imatinib, nilotinib, dasatinib, ponatinib, gefitinib, erlotinib, lapatinib, vandetanib, sunitinib, sorafenib) have been reported to interact with ABC transporters (e.g., ABCB1, ABCC1, ABCG2, ABCC10). This finding disclosed a very complex scenario in which TKIs may behave as substrates or inhibitors depending on the expression of specific pumps, drug concentration, affinity for transporters and types of co-administered agents. In this context, in-depth investigation on TKI chemosensitizing functions might provide a strong rationale for combining TKIs and conventional therapeutics in specific malignancies. The reposition of TKIs as antagonists of ABC transporters opens a new way towards anticancer therapy and clinical strategies aimed at counteracting drug resistance. This review will focus on some paradigmatic examples of the complex and not yet fully elucidated interaction between clinical available TKIs (e.g. BCR-ABL, EGFR, VEGFR inhibitors) with the main ABC transporters implicated in multidrug resistance.
Collapse
Affiliation(s)
- Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano, Italy.
| | - Giuliana Cassinelli
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano, Italy.
| | - Marzia Pennati
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano, Italy.
| | - Valentina Zuco
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano, Italy.
| | - Laura Gatti
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano, Italy.
| |
Collapse
|
72
|
Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM. Progress towards a public chemogenomic set for protein kinases and a call for contributions. PLoS One 2017; 12:e0181585. [PMID: 28767711 PMCID: PMC5540273 DOI: 10.1371/journal.pone.0181585] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/03/2017] [Indexed: 01/01/2023] Open
Abstract
Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.
Collapse
Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Andrews
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge, United Kingdom
| | - Richard Angell
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephen J. Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan M. Elkins
- Structural Genomics Consortium, Universidade Estadual de Campinas—UNICAMP, Campinas, Sao Paulo, Brazil
| | | | - Mathias Frederiksen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Opher Gileadi
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nathanael Gray
- Harvard Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Alice Hooper
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Stefan Laufer
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, Tübingen, Germany
| | - Ulrich Luecking
- Bayer Pharma AG, Drug Discovery, Müllerstrasse 178, Berlin, Germany
| | - Michael Michaelides
- Oncology Chemistry, AbbVie, 1 North Waukegan Road, North Chicago, Illinois, United States of America
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - R. Aldrin Denny
- Worldwide Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts, United States of America
| | - Kumar S. Saikatendu
- Global Research Externalization, Takeda California, Inc., 10410 Science Center Drive, San Diego, California, United States of America
| | | | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
73
|
Abstract
OBJECTIVE We aimed to identify key principles of targeted therapy of protein kinases and their application to the management of solid tumors. BACKGROUND Concurrent advances in tumor genomic analysis and molecular inhibitor development have dramatically impacted the diagnosis and treatment of solid tumors, and common themes regarding the use of kinase inhibitors are developing. METHODS The list of kinase inhibitors that have been approved by the US Food and Drug Administration was reviewed and articles related to the agents were searched in the PubMed database up until December 2015. We included pivotal, randomized controlled phase 2 and 3 trials, and also pertinent preclinical studies. RESULTS Small molecule inhibitors targeted against driver kinases, overactive in selected subsets of solid tumors, elicit improved response rates and survival compared with standard chemotherapy. Disease control has been proven in the metastatic and, to a limited extent, the adjuvant setting. However, tumor eradication is rare, and duration of treatment response is limited by the development of drug resistance. CONCLUSIONS Kinase inhibitors induce response in diverse types of solid tumors. Although the agents are often effective in defined molecular subsets, cure is rare and resistance is common. This broad review provides rationale for further investigation of multimodality therapy combining kinase inhibitors with additional systemic and local therapies, including surgery.
Collapse
|
74
|
Nishiguchi GA, Rico A, Tanner H, Aversa RJ, Taft BR, Subramanian S, Setti L, Burger MT, Wan L, Tamez V, Smith A, Lou Y, Barsanti PA, Appleton BA, Mamo M, Tandeske L, Dix I, Tellew JE, Huang S, Mathews Griner LA, Cooke VG, Van Abbema A, Merritt H, Ma S, Gampa K, Feng F, Yuan J, Wang Y, Haling JR, Vaziri S, Hekmat-Nejad M, Jansen JM, Polyakov V, Zang R, Sethuraman V, Amiri P, Singh M, Lees E, Shao W, Stuart DD, Dillon MP, Ramurthy S. Design and Discovery of N-(2-Methyl-5′-morpholino-6′-((tetrahydro-2H-pyran-4-yl)oxy)-[3,3′-bipyridin]-5-yl)-3-(trifluoromethyl)benzamide (RAF709): A Potent, Selective, and Efficacious RAF Inhibitor Targeting RAS Mutant Cancers. J Med Chem 2017; 60:4869-4881. [DOI: 10.1021/acs.jmedchem.6b01862] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gisele A. Nishiguchi
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alice Rico
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Huw Tanner
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert J. Aversa
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Benjamin R. Taft
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lina Setti
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Matthew T. Burger
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lifeng Wan
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Victoriano Tamez
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aaron Smith
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yan Lou
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Paul A. Barsanti
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Laura Tandeske
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ina Dix
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Werk Klybeck, Postfach, CH-4002 Basel, Switzerland
| | - John E. Tellew
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Shenlin Huang
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Lesley A. Mathews Griner
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vesselina G. Cooke
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anne Van Abbema
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Hanne Merritt
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sylvia Ma
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kalyani Gampa
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fei Feng
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jing Yuan
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yingyun Wang
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jacob R. Haling
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Sepideh Vaziri
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Mohammad Hekmat-Nejad
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Richard Zang
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Vijay Sethuraman
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Payman Amiri
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mallika Singh
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Emma Lees
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenlin Shao
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Darrin D. Stuart
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael P. Dillon
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Savithri Ramurthy
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| |
Collapse
|
75
|
Uitdehaag JCM, de Man J, Willemsen-Seegers N, Prinsen MBW, Libouban MAA, Sterrenburg JG, de Wit JJP, de Vetter JRF, de Roos JADM, Buijsman RC, Zaman GJR. Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity. J Mol Biol 2017; 429:2211-2230. [PMID: 28539250 DOI: 10.1016/j.jmb.2017.05.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/10/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
Abstract
The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the first TTK inhibitors have entered clinical trials, little is known about how the inhibition of TTK with small-molecule compounds affects cellular activity. We studied the selective TTK inhibitor NTRC 0066-0, which was developed in our own laboratory, together with 11 TTK inhibitors developed by other companies, including Mps-BAY2b, BAY 1161909, BAY 1217389 (Bayer), TC-Mps1-12 (Shionogi), and MPI-0479605 (Myrexis). Parallel testing shows that the cellular activity of these TTK inhibitors correlates with their binding affinity to TTK and, more strongly, with target residence time. TTK inhibitors are therefore an example where target residence time determines activity in in vitro cellular assays. X-ray structures and thermal stability experiments reveal that the most potent compounds induce a shift of the glycine-rich loop as a result of binding to the catalytic lysine at position 553. This "lysine trap" disrupts the catalytic machinery. Based on these insights, we developed TTK inhibitors, based on a (5,6-dihydro)pyrimido[4,5-e]indolizine scaffold, with longer target residence times, which further exploit an allosteric pocket surrounding Lys553. Their binding mode is new for kinase inhibitors and can be classified as hybrid Type I/Type III. These inhibitors have very potent anti-proliferative activity that rivals classic cytotoxic therapy. Our findings will open up new avenues for more applications for TTK inhibitors in cancer treatment.
Collapse
Affiliation(s)
- Joost C M Uitdehaag
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Jos de Man
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | | | - Martine B W Prinsen
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Marion A A Libouban
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Jan Gerard Sterrenburg
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Joeri J P de Wit
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Judith R F de Vetter
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Jeroen A D M de Roos
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Rogier C Buijsman
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands
| | - Guido J R Zaman
- Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands.
| |
Collapse
|
76
|
Saijo K, Imai H, Chikamatsu S, Narita K, Katoh T, Ishioka C. Antitumor activity and pharmacologic characterization of the depsipeptide analog as a novel histone deacetylase/ phosphatidylinositol 3-kinase dual inhibitor. Cancer Sci 2017; 108:1469-1475. [PMID: 28406576 PMCID: PMC5497724 DOI: 10.1111/cas.13255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/26/2017] [Accepted: 04/07/2017] [Indexed: 01/10/2023] Open
Abstract
Histone deacetylase (HDAC)/phosphatidylinositol 3-kinase (PI3K) dual inhibition is a promising strategy for the treatment of intractable cancers because of the advantages of overcoming potential resistance and showing synergistic effects. Therefore, development of an HDAC/PI3K dual inhibitor is reasonably attractive. Romidepsin (FK228, depsipeptide) is a potent HDAC inhibitor. We previously reported that depsipeptide and its analogs have an additional activity as PI3K inhibitors and are defined as HDAC/PI3K dual inhibitors. Subsequently, we identified FK-A11 as the most potent analog and reported its biochemical, biological, and structural properties as an HDAC/PI3K dual inhibitor. In this study, we reveal the in vitro and in vivo efficacy of FK-A11 in HT1080 fibrosarcoma and PC3 prostate cancer cell xenograft mouse models. FK-A11 showed in vivo antitumor activity by both i.v. and i.p. administration in a dose-dependent manner. In both xenograft models, FK-A11 showed superior antitumor effects compared to other depsipeptide analogs in accordance with in vitro anti-cell proliferation effects and the potency of HDAC/PI3K dual inhibition. In addition, we showed evidence of HDAC/PI3K dual inhibition accompanying antitumor efficacy in xenograft tumor tissues by immunohistochemistry. We also detailed pharmacokinetic characterization of FK-A11 in mice. These findings will be essential for guiding further preclinical and clinical studies.
Collapse
Affiliation(s)
- Ken Saijo
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hiroo Imai
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Sonoko Chikamatsu
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Koichi Narita
- Laboratory of Synthetic and Medicinal Chemistry, Department of Chemical Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Tadashi Katoh
- Laboratory of Synthetic and Medicinal Chemistry, Department of Chemical Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| |
Collapse
|
77
|
Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
Collapse
Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| |
Collapse
|
78
|
Brocklesby KL, Waby JS, Cawthorne C, Smith G. An alternative synthesis of Vandetanib (Caprelsa™) via a microwave accelerated Dimroth rearrangement. Tetrahedron Lett 2017; 58:1467-1469. [PMID: 28413233 PMCID: PMC5381755 DOI: 10.1016/j.tetlet.2017.02.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 11/24/2022]
Abstract
Vandetanib is an orally available tyrosine kinase inhibitor used in the treatment of cancer. The current synthesis proceeds via an unstable 4-chloroquinazoline, using harsh reagents, in addition to requiring sequential protection and deprotection steps. In the present work, use of the Dimroth rearrangement in the key quinazoline forming step enabled the synthesis of Vandetanib in nine steps (compared to the previously reported 12-14).
Collapse
Affiliation(s)
- Kayleigh L. Brocklesby
- Hull-York Medical School, University of York, Heslington, York YO10 5DD, UK
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London SW7 3RP, UK
| | - Jennifer S. Waby
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - Chris Cawthorne
- PET Research Centre, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - Graham Smith
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London SW7 3RP, UK
| |
Collapse
|
79
|
Miners JO, Chau N, Rowland A, Burns K, McKinnon RA, Mackenzie PI, Tucker GT, Knights KM, Kichenadasse G. Inhibition of human UDP-glucuronosyltransferase enzymes by lapatinib, pazopanib, regorafenib and sorafenib: Implications for hyperbilirubinemia. Biochem Pharmacol 2017; 129:85-95. [DOI: 10.1016/j.bcp.2017.01.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/04/2017] [Indexed: 01/11/2023]
|
80
|
Halekotte J, Witt L, Ianes C, Krüger M, Bührmann M, Rauh D, Pichlo C, Brunstein E, Luxenburger A, Baumann U, Knippschild U, Bischof J, Peifer C. Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1δ and Their Structural Relation to p38α MAPK. Molecules 2017; 22:molecules22040522. [PMID: 28338621 PMCID: PMC6154583 DOI: 10.3390/molecules22040522] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer’s disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications. Consequently, only few potent and selective CK1δ inhibitors have been reported so far and structurally divergent approaches are urgently needed in order to establish SAR that might enable complete discrimination of CK1 isoforms and related p38α MAPK. In this study we report on design and characterization of optimized 4,5-diarylimidazoles as highly effective ATP-competitive inhibitors of CK1δ with compounds 11b (IC50 CK1δ = 4 nM, IC50 CK1ε = 25 nM), 12a (IC50 CK1δ = 19 nM, IC50 CK1ε = 227 nM), and 16b (IC50 CK1δ = 8 nM, IC50 CK1ε = 81 nM) being among the most potent CK1δ-targeting agents published to date. Inhibitor compound 11b, displaying potential as a pharmacological tool, has further been profiled over a panel of 321 protein kinases exhibiting high selectivity. Cellular efficacy has been evaluated in human pancreatic cancer cell lines Colo357 (EC50 = 3.5 µM) and Panc89 (EC50 = 1.5 µM). SAR is substantiated by X-ray crystallographic analysis of 16b in CK1δ and 11b in p38α.
Collapse
Affiliation(s)
- Jakob Halekotte
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
| | - Lydia Witt
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
| | - Chiara Ianes
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Marc Krüger
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Mike Bührmann
- Institute of Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany.
| | - Daniel Rauh
- Institute of Chemical Biology, Dortmund University of Technology, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany.
| | - Christian Pichlo
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Elena Brunstein
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Andreas Luxenburger
- The Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Lower Hutt P.O. Box 33-436, New Zealand.
| | - Ulrich Baumann
- Department for Chemistry, University of Cologne, Otto-Fischer-Straße 12-14, D-50674 Cologne, Germany.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Joachim Bischof
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Christian Peifer
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany.
| |
Collapse
|
81
|
Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
Collapse
Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
| |
Collapse
|
82
|
Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
Collapse
Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
| |
Collapse
|
83
|
Sarvagalla S, Coumar MS. Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most of the developed kinase inhibitor drugs are ATP competitive and suffer from drawbacks such as off-target kinase activity, development of resistance due to mutation in the ATP binding pocket and unfavorable intellectual property situations. Besides the ATP binding pocket, protein kinases have binding sites that are involved in Protein-Protein Interactions (PPIs); these PPIs directly or indirectly regulate the protein kinase activity. Of recent, small molecule inhibitors of PPIs are emerging as an alternative to ATP competitive agents. Rational design of inhibitors for kinase PPIs could be carried out using molecular modeling techniques. In silico tools available for the prediction of hot spot residues and cavities at the PPI sites and the means to utilize this information for the identification of inhibitors are discussed. Moreover, in silico studies to target the Aurora B-INCENP PPI sites are discussed in context. Overall, this chapter provides detailed in silico strategies that are available to the researchers for carrying out structure-based drug design of PPI inhibitors.
Collapse
|
84
|
Abstract
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
Collapse
Affiliation(s)
- Ashwani Kumar
- Guru Jambheshwar University of Science and Technology, India
| | - Ruchika Goyal
- Guru Jambheshwar University of Science and Technology, India
| | - Sandeep Jain
- Guru Jambheshwar University of Science and Technology, India
| |
Collapse
|
85
|
Yamada K, Zhang JH, Xie X, Reinhardt J, Xie AQ, LaSala D, Kohls D, Yowe D, Burdick D, Yoshisue H, Wakai H, Schmidt I, Gunawan J, Yasoshima K, Yue QK, Kato M, Mogi M, Idamakanti N, Kreder N, Drueckes P, Pandey P, Kawanami T, Huang W, Yagi YI, Deng Z, Park HM. Discovery and Characterization of Allosteric WNK Kinase Inhibitors. ACS Chem Biol 2016; 11:3338-3346. [PMID: 27712055 DOI: 10.1021/acschembio.6b00511] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinases are known for their highly conserved adenosine triphosphate (ATP)-binding site, rendering the discovery of selective inhibitors a major challenge. In theory, allosteric inhibitors can achieve high selectivity by targeting less conserved regions of the kinases, often with an added benefit of retaining efficacy under high physiological ATP concentration. Although often overlooked in favor of ATP-site directed approaches, performing a screen at high ATP concentration or stringent hit triaging with high ATP concentration offers conceptually simple methods of identifying inhibitors that bind outside the ATP pocket. Here, we applied the latter approach to the With-No-Lysine (K) (WNK) kinases to discover lead molecules for a next-generation antihypertensive that requires a stringent safety profile. This strategy yielded several ATP noncompetitive WNK1-4 kinase inhibitors, the optimization of which enabled cocrystallization with WNK1, revealing an allosteric binding mode consistent with the observed exquisite specificity for WNK1-4 kinases. The optimized compound inhibited rubidium uptake by sodium chloride cotransporter 1 (NKCC1) in HT29 cells, consistent with the reported physiology of WNK kinases in renal electrolyte handling.
Collapse
Affiliation(s)
- Ken Yamada
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Ji-Hu Zhang
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Xiaoling Xie
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Juergen Reinhardt
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Amy Qiongshu Xie
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Daniel LaSala
- Novartis Institutes for BioMedical Research, Novartis
Pharmaceuticals Corporation, East
Hanover, New Jersey 07936-1080, United States
| | - Darcy Kohls
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - David Yowe
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Debra Burdick
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Hajime Yoshisue
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Hiromichi Wakai
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Isabel Schmidt
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Jason Gunawan
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Kayo Yasoshima
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Q. Kimberley Yue
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Mitsunori Kato
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Muneto Mogi
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Neeraja Idamakanti
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Natasha Kreder
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Peter Drueckes
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Pramod Pandey
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Toshio Kawanami
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Waanjeng Huang
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Yukiko I. Yagi
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Zhan Deng
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Hyi-Man Park
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| |
Collapse
|
86
|
Gomez-Gutierrez P, Campos PM, Vega M, Perez JJ. Identification of a Novel Inhibitory Allosteric Site in p38α. PLoS One 2016; 11:e0167379. [PMID: 27898710 PMCID: PMC5127581 DOI: 10.1371/journal.pone.0167379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022] Open
Abstract
In the present study, we report the discovery of a novel allosteric inhibitory site for p38α, a subclass of the mitogen-activated protein kinases (MAPK) family. The putative site was discovered after inspection of the crystallographic structure of the p38α-MK2 complex. MK2 (MAPK-activated protein kinase 2) is an interesting protein playing a dual role as modulator and substrate of p38α. This intriguing behavior is due to the ability of the two proteins to form distinctive heterodimers when p38α is phosphorylated or not. We hypothesized that the regulatory action of MK2 is due to its capability to keep p38α in an inactive conformation and consequently, we investigated the atomic structure of the p38α-MK2 complex to understand such regulatory behavior at the molecular level. After inspection of the complex structure, two peptides designed from the MK2 regulatory loop in contact with p38α with sequences Tyr1-Ser2-Asn3-His4-Gly5-Leu6 (peptide-1) and [Phe0]-peptide-1 (peptide-2) in their zwitterionic form were investigated for their phosphorylation inhibitory capability in vitro. Since both peptides exhibited inhibitory capability of the p38α kinase mediated phosphorylation of MEF2A, in a subsequent step we pursued the discovery of small molecule peptidomimetics. For this purpose we characterized in detail the peptide-p38α interaction using molecular dynamics simulations, leading to the definition of a pharmacophore for the peptide-protein interaction. This hypothesis was used as query for a in silico screening, leading to the discovery of a fused ring compound with micromolar inhibitory activity. Site-directed mutagenesis studies support that the compound binds to the putative novel allosteric site in p38α.
Collapse
Affiliation(s)
- Patricia Gomez-Gutierrez
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
- Dept. of Chemical Engineering. Universitat Politecnica de Catalunya. ETSEIB. Av. Diagonal, Spain
| | - Pedro M. Campos
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
| | - Miguel Vega
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
| | - Juan J. Perez
- Dept. of Chemical Engineering. Universitat Politecnica de Catalunya. ETSEIB. Av. Diagonal, Spain
- * E-mail:
| |
Collapse
|
87
|
Ebiike H, Taka N, Matsushita M, Ohmori M, Takami K, Hyohdoh I, Kohchi M, Hayase T, Nishii H, Morikami K, Nakanishi Y, Akiyama N, Shindoh H, Ishii N, Isobe T, Matsuoka H. Discovery of [5-Amino-1-(2-methyl-3H-benzimidazol-5-yl)pyrazol-4-yl]-(1H-indol-2-yl)methanone (CH5183284/Debio 1347), An Orally Available and Selective Fibroblast Growth Factor Receptor (FGFR) Inhibitor. J Med Chem 2016; 59:10586-10600. [DOI: 10.1021/acs.jmedchem.6b01156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirosato Ebiike
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Naoki Taka
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Masayuki Matsushita
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masayuki Ohmori
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kyoko Takami
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Ikumi Hyohdoh
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masami Kohchi
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Tadakatsu Hayase
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hiroki Nishii
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kenji Morikami
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Yoshito Nakanishi
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Nukinori Akiyama
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hidetoshi Shindoh
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Nobuya Ishii
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Takehito Isobe
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Hiroharu Matsuoka
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| |
Collapse
|
88
|
Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PLoS One 2016; 11:e0166583. [PMID: 27861609 PMCID: PMC5115767 DOI: 10.1371/journal.pone.0166583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment.
Collapse
|
89
|
Gande SL, Saxena K, Sreeramulu S, Linhard V, Kudlinzki D, Heinzlmeir S, Reichert AJ, Skerra A, Kuster B, Schwalbe H. Expression and Purification of EPHA2 Tyrosine Kinase Domain for Crystallographic and NMR Studies. Chembiochem 2016; 17:2257-2263. [DOI: 10.1002/cbic.201600483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Santosh L. Gande
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Stephanie Heinzlmeir
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
- Chair of Proteomics and Bioanalytics; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Andreas J. Reichert
- Chair of Biological Chemistry; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Arne Skerra
- Chair of Biological Chemistry; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
- Chair of Proteomics and Bioanalytics; Technical University of Munich; Emil-Erlenmeyer-Forum 5 85354 Freising Germany
- Center for integrated Protein Science Munich (CIPSM); Technical University of Munich; Arcisstrasse 21 80333 München Germany
- Bavarian Biomolecular Mass Spectrometry Center; Technical University of Munich; Gregor-Mendel-Strasse 4 85354 Freising Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ); Institute for Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe-Universität; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium (DKTK); In Neuenheimer Feld 280 69120 Heidelberg Germany
- German Cancer Research Center (DKFZ); In Neuenheimer Feld 280 69120 Heidelberg Germany
| |
Collapse
|
90
|
Cutillas PR. Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry. Methods Enzymol 2016; 585:245-268. [PMID: 28109432 DOI: 10.1016/bs.mie.2016.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein phosphorylation encodes information on the activity of kinase-driven signaling pathways that regulate cell biology. This chapter discusses an approach, named TIQUAS (targeted in-depth quantification of signaling), to quantify cell signaling comprehensively and without bias. The workflow-based on mass spectrometry (MS) and computational science-consists of targeting the analysis of phosphopeptides previously identified by shotgun liquid chromatography tandem MS (LC-MS/MS) across the samples that are being compared. TIQUAS therefore takes advantage of concepts derived from both targeted (data-independent) and data-dependent acquisition methods; phosphorylation sites are quantified in all experimental samples regardless of whether or not these phosphopeptides were identified by MS/MS in all runs. As a result, datasets are obtained containing quantitative information on several thousand phosphorylation sites in as many samples and replicates as required in the experimental design, and these rich datasets are devoid of a significant number of missing data points. This chapter discussed the biochemical, analytical, and computational procedures required to apply the approach and for obtaining a biological interpretation of the data in the context of our understanding of cell signaling regulation and kinase-substrate relationships.
Collapse
Affiliation(s)
- P R Cutillas
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom.
| |
Collapse
|
91
|
Zhang J, Deng X, Kahle KT. Leveraging unique structural characteristics of WNK kinases to achieve therapeutic inhibition. Sci Signal 2016; 9:e3. [PMID: 27811182 DOI: 10.1126/scisignal.aaj2227] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The with-no-lysine (K) WNK kinases are master regulators of the Na+-(K+)-Cl- cotransporters, including the renal-specific NCC and NKCC2 cotransporters. The discovery of WNK463, an orally bioavailable pan-WNK kinase inhibitor that exploits unique structural properties of the WNK catalytic domain to achieve high affinity and kinase selectivity, illustrates a strategy of leveraging distinct kinase features to develop specific inhibitors and validates the genetic predictions of the in vivo pharmacology of WNK inhibition.
Collapse
Affiliation(s)
- Jinwei Zhang
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kristopher T Kahle
- Department of Cellular and Molecular Physiology and Centers for Mendelian Genomics, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
92
|
Allosteric Modulation as a Unifying Mechanism for Receptor Function and Regulation. Cell 2016; 166:1084-1102. [DOI: 10.1016/j.cell.2016.08.015] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/13/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
|
93
|
cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry. Biochem J 2016; 473:3159-75. [PMID: 27444646 PMCID: PMC5095912 DOI: 10.1042/bcj20160648] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.
Collapse
|
94
|
Psarra V, Fousteris MA, Hennig L, Bantzi M, Giannis A, Nikolaropoulos SS. Identification of azepinone fused tetracyclic heterocycles as new chemotypes with protein kinase inhibitory activities. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
95
|
Olszewska DA, Lynch T. New Light Shed on Leucine-Rich Repeat Kinase 2 (LRRK2) Kinase Inhibitors in Parkinson's Disease. Mov Disord Clin Pract 2016; 3:241-242. [DOI: 10.1002/mdc3.12333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/31/2015] [Accepted: 01/09/2016] [Indexed: 11/09/2022] Open
Affiliation(s)
- Diana A. Olszewska
- Dublin Neurological Institute at the Mater Misericordiae University Hospital; Dublin Ireland
| | - Tim Lynch
- Dublin Neurological Institute at the Mater Misericordiae University Hospital; Dublin Ireland
| |
Collapse
|
96
|
Brábek J, Rosel D, Fernandes M. Pragmatic medicine in solid cancer: a translational alternative to precision medicine. Onco Targets Ther 2016; 9:1839-55. [PMID: 27103822 PMCID: PMC4827419 DOI: 10.2147/ott.s103832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The precision medicine (PM) initiative is a response to the dismal outlook in solid cancer. Despite heterogeneity, common mechanistic denominators may exist across the spectrum of solid cancer. A shift from conventional research and development (R&D) toward PM will require conceptual and structural change. As individuals and as a society, we welcome innovation, but question change. We ask: In solid cancer, does PM identify and address the causes of prior failures, and, if so, are the proposed solutions feasible? And, when may we expect safer, more effective and affordable drugs in the clinic? Considerations that prompt a pragmatic rethink include a failure analysis of translational R&D in solid cancer suggesting that trials and regulations need to be aligned with the natural history of the disease. In successful therapeutic interventions in chronic, complex disease, surrogate markers and endpoints should be consistent with the Prentice's criteria. In solid cancer, drug induced tumor shrinkage, is a drug effect and not a disease response; tumor shrinkage does not reflect nor predict interruption of the disease. Overall, we support a pragmatic, multidisciplinary, and collaborative R&D, and suggest that direction be set by clinical need and utility, and by questions, not answers. PM will prove worthwhile if it could improve clinical outcomes. The lag in therapeutics relative to diagnostics is a cause for confusion. Overdiagnosis adds to fear and harm, especially in the absence of effective interventions. A revised initiative that prioritizes metastasis research could replicate the successful HIV/AIDS model in solid cancer. A pragmatic approach may further translational efforts toward meaningfully effective, generally available, and affordable solutions.
Collapse
Affiliation(s)
- Jan Brábek
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Daniel Rosel
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | | |
Collapse
|
97
|
Zhao Z, Xie L, Xie L, Bourne PE. Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. J Med Chem 2016; 59:4326-41. [PMID: 26929980 DOI: 10.1021/acs.jmedchem.5b02041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Targeted polypharmacology of kinases has emerged as a promising strategy to design efficient and safe therapeutics. Here, we perform a systematic study of kinase-ligand binding modes for the human structural kinome at scale (208 kinases, 1777 unique ligands, and their complexes) by integrating chemical genomics and structural genomics data and by introducing a functional site interaction fingerprint (Fs-IFP) method. New insights into kinase-ligand binding modes were obtained. We establish relationships between the features of binding modes, the ligands, and the binding pockets, respectively. We also drive the intrinsic binding specificity and which correlation with amino acid conservation. Third, we explore the landscape of the binding modes and highlight the regions of "selectivity pocket" and "selectivity entrance". Finally, we demonstrate that Fs-IFP similarity is directly correlated to the experimentally determined profile. These improve our understanding of kinase-ligand interactions and contribute to the design of novel polypharmacological therapies targeting kinases.
Collapse
Affiliation(s)
- Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland 20894, United States
| | - Li Xie
- Scripps Ranch , San Diego, California 92131, United States
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York , New York, New York 10065, United States.,The Graduate Center, The City University of New York , New York, New York 10016, United States
| | - Philip E Bourne
- Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
98
|
Verkhivker GM. Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation. MOLECULAR BIOSYSTEMS 2016; 12:3146-65. [DOI: 10.1039/c6mb00298f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The computational analysis of residue interaction networks dissects the allosteric effects of inhibitor-induced BRAF kinase dimerization and paradoxical activation.
Collapse
Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Sciences
- Schmid College of Science and Technology
- Chapman University
- Orange
| |
Collapse
|
99
|
|
100
|
Tiligada E, Ishii M, Riccardi C, Spedding M, Simon HU, Teixeira MM, Landys Chovel Cuervo M, Holgate ST, Levi-Schaffer F. The expanding role of immunopharmacology: IUPHAR Review 16. Br J Pharmacol 2015; 172:4217-27. [PMID: 26173913 PMCID: PMC4556463 DOI: 10.1111/bph.13219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/05/2015] [Accepted: 05/20/2015] [Indexed: 02/06/2023] Open
Abstract
Drugs targeting the immune system such as corticosteroids, antihistamines and immunosuppressants have been widely exploited in the treatment of inflammatory, allergic and autoimmune disorders during the second half of the 20th century. The recent advances in immunopharmacological research have made available new classes of clinically relevant drugs. These comprise protein kinase inhibitors and biologics, such as monoclonal antibodies, that selectively modulate the immune response not only in cancer and autoimmunity but also in a number of other human pathologies. Likewise, more effective vaccines utilizing novel antigens and adjuvants are valuable tools for the prevention of transmissible infectious diseases and for allergen-specific immunotherapy. Consequently, immunopharmacology is presently considered as one of the expanding fields of pharmacology. Immunopharmacology addresses the selective regulation of immune responses and aims to uncover and exploit beneficial therapeutic options for typical and non-typical immune system-driven unmet clinical needs. While in the near future a number of new agents will be introduced, improving the effectiveness and safety of those currently in use is imperative for all researchers and clinicians working in the fields of immunology, pharmacology and drug discovery. The newly formed ImmuPhar (http://iuphar.us/index.php/sections-subcoms/immunopharmacology) is the Immunopharmacology Section of the International Union of Basic and Clinical Pharmacology (IUPHAR, http://iuphar.us/). ImmuPhar provides a unique international expert-lead platform that aims to dissect and promote the growing understanding of immune (patho)physiology. Moreover, it challenges the identification and validation of drug targets and lead candidates for the treatment of many forms of debilitating disorders, including, among others, cancer, allergies, autoimmune and metabolic diseases.
Collapse
Affiliation(s)
- Ekaterini Tiligada
- Department of Pharmacology, Medical School, University of AthensAthens, Greece
- Allergy Unit ‘D. Kalogeromitros’, 2nd Department of Dermatology and Venereology, ‘Attikon’ General University Hospital, Medical School, University of AthensAthens, Greece
| | - Masaru Ishii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka UniversityOsaka, Japan
| | - Carlo Riccardi
- Department of Medicine, University of PerugiaPerugia, Italy
| | | | - Hans-Uwe Simon
- Institute of Pharmacology, University of BernBern, Switzerland
| | | | | | | | - Francesca Levi-Schaffer
- Pharmacology Unit, Faculty of Medicine, School of Pharmacy Institute for Drug Research, Hebrew University of JerusalemJerusalem, Israel
| |
Collapse
|