1
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Lin TE, Sung LC, Chao MW, Li M, Zheng JH, Sung TY, Hsieh JH, Yang CR, Lee HY, Cho EC, Hsu KC. Structure-based virtual screening and biological evaluation of novel small-molecule BTK inhibitors. J Enzyme Inhib Med Chem 2021; 37:226-235. [PMID: 34894949 PMCID: PMC8667945 DOI: 10.1080/14756366.2021.1999237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bruton tyrosine kinase (BTK) is linked to multiple signalling pathways that regulate cellular survival, activation, and proliferation. A covalent BTK inhibitor has shown favourable outcomes for treating B cell malignant leukaemia. However, covalent inhibitors require a high reactive warhead that may contribute to unexpected toxicity, poor selectivity, or reduced effectiveness in solid tumours. Herein, we report the identification of a novel noncovalent BTK inhibitor. The binding interactions (i.e. interactions from known BTK inhibitors) for the BTK binding site were identified and incorporated into a structure-based virtual screening (SBVS). Top-rank compounds were selected and testing revealed a BTK inhibitor with >50% inhibition at 10 µM concentration. Examining analogues revealed further BTK inhibitors. When tested across solid tumour cell lines, one inhibitor showed favourable inhibitory activity, suggesting its potential for targeting BTK malignant tumours. This inhibitor could serve as a basis for developing an effective BTK inhibitor targeting solid cancers.
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Affiliation(s)
- Tony Eight Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Master Program in Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Li-Chin Sung
- Division of Cardiology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan., School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Min-Wu Chao
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Min Li
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jia-Huei Zheng
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Ying Sung
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Jui-Hua Hsieh
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Chia-Ron Yang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Er-Chieh Cho
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, ROC
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, ROC.,Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, ROC.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,TMU Research Center of Drug Discovery, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
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2
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Lu C, Fan L, Zhang PF, Tao WW, Yang CB, Shang EX, Chen FY, Che CT, Cheng HB, Duan JA, Zhao M. A novel P38α MAPK activator Bruceine A exhibits potent anti-pancreatic cancer activity. Comput Struct Biotechnol J 2021; 19:3437-3450. [PMID: 34194669 PMCID: PMC8220105 DOI: 10.1016/j.csbj.2021.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Bruceine A displays potent anti-pancreatic cancer activity in vitro and in vivo. Phosphoproteomic analyses identify bruceine A induces phosphorylation of p38α MAPK. Octet system and microscale thermophoresis reveal p38α MAPK has high affinity for bruceine A. Molecular simulations illustrate determinants of bruceine A binding with p38α MAPK.
Pancreatic cancer remains one of the cancers with the poorest prognosis bearing an overall 5-year survival rate of about 5%. Efficient new chemotherapic drugs are still highly desired. Here, bruceine A, a quassinoid identified from the dried fruits of Brucea javanica (L.) Merr., displayed the most potent anti-proliferation activity against pancreatic cancer in vitro and in vivo. Phosphoproteomic analysis revealed p38α MAPK phosphorylation was involved in bruceine A’s action in MIA PaCa-2 cells. Utilizing fortebio octet system and microscale thermophoresis, we found p38α MAPK had high affinity for bruceine A. Molecular docking and molecular dynamic simulations showed that bruceine A widely bound to residues (Leu171, Ala172, Met179, Thr180, Val183) in P-loop of p38α MAPK. Key determinants of bruceine A binding with P-loop of p38α MAPK were 19-C
Created by potrace 1.16, written by Peter Selinger 2001-2019
]]>O, 22-CH3, 32-CH3, and 34-CH3. Taken together, our findings demonstrate that bruceine A binds directly to p38α MAPK, which can be used to probe the role of p38α MAPK phosphorylation in pancreatic cancer progression, and as a novel lead compound for pancreatic cancer therapy.
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Affiliation(s)
- Cai Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lu Fan
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Peng-Fei Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wei-Wei Tao
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cheng-Bin Yang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Er-Xin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Fei-Yan Chen
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chun-Tao Che
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hai-Bo Cheng
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing 210023, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
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3
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Ariey-Bonnet J, Carrasco K, Le Grand M, Hoffer L, Betzi S, Feracci M, Tsvetkov P, Devred F, Collette Y, Morelli X, Ballester P, Pasquier E. In silico molecular target prediction unveils mebendazole as a potent MAPK14 inhibitor. Mol Oncol 2020; 14:3083-3099. [PMID: 33021050 PMCID: PMC7718943 DOI: 10.1002/1878-0261.12810] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/27/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
The concept of polypharmacology involves the interaction of drug molecules with multiple molecular targets. It provides a unique opportunity for the repurposing of already-approved drugs to target key factors involved in human diseases. Herein, we used an in silico target prediction algorithm to investigate the mechanism of action of mebendazole, an antihelminthic drug, currently repurposed in the treatment of brain tumors. First, we confirmed that mebendazole decreased the viability of glioblastoma cells in vitro (IC50 values ranging from 288 nm to 2.1 µm). Our in silico approach unveiled 21 putative molecular targets for mebendazole, including 12 proteins significantly upregulated at the gene level in glioblastoma as compared to normal brain tissue (fold change > 1.5; P < 0.0001). Validation experiments were performed on three major kinases involved in cancer biology: ABL1, MAPK1/ERK2, and MAPK14/p38α. Mebendazole could inhibit the activity of these kinases in vitro in a dose-dependent manner, with a high potency against MAPK14 (IC50 = 104 ± 46 nm). Its direct binding to MAPK14 was further validated in vitro, and inhibition of MAPK14 kinase activity was confirmed in live glioblastoma cells. Consistent with biophysical data, molecular modeling suggested that mebendazole was able to bind to the catalytic site of MAPK14. Finally, gene silencing demonstrated that MAPK14 is involved in glioblastoma tumor spheroid growth and response to mebendazole treatment. This study thus highlighted the role of MAPK14 in the anticancer mechanism of action of mebendazole and provides further rationale for the pharmacological targeting of MAPK14 in brain tumors. It also opens new avenues for the development of novel MAPK14/p38α inhibitors to treat human diseases.
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Affiliation(s)
- Jeremy Ariey-Bonnet
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Kendall Carrasco
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Marion Le Grand
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Laurent Hoffer
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Stéphane Betzi
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Mikael Feracci
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Philipp Tsvetkov
- CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Pharm, Aix Marseille Université, France
| | - Francois Devred
- CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Pharm, Aix Marseille Université, France
| | - Yves Collette
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Xavier Morelli
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Pedro Ballester
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
| | - Eddy Pasquier
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université, France
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4
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Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. J Med Chem 2020; 63:7559-7568. [PMID: 32543856 DOI: 10.1021/acs.jmedchem.0c00403] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.
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Affiliation(s)
- Charlie Nichols
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Joseph Ng
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Annika Keshu
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Geoff Kelly
- NMR Facility, The Francis Crick Institute, London NW1 1AT, U.K
| | - Maria R Conte
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Michael S Marber
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K
| | - Franca Fraternali
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Gian F De Nicola
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
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5
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Bartolini D, Bührmann M, Barreca ML, Manfroni G, Cecchetti V, Rauh D, Galli F. Co-crystal structure determination and cellular evaluation of 1,4-dihydropyrazolo[4,3-c] [1,2] benzothiazine 5,5-dioxide p38α MAPK inhibitors. Biochem Biophys Res Commun 2019; 511:579-586. [DOI: 10.1016/j.bbrc.2019.02.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022]
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6
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Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X, Huang N. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. J Med Chem 2017; 60:8552-8564. [PMID: 28945083 DOI: 10.1021/acs.jmedchem.7b01075] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To explore novel kinase hinge-binding scaffolds, we carried out structure-based virtual screening against p38α MAPK as a model system. With the assistance of developed kinase-specific structural filters, we identify a novel lead compound that selectively inhibits a panel of kinases with threonine as the gatekeeper residue, including BTK and LCK. These kinases play important roles in lymphocyte activation, which encouraged us to design novel kinase inhibitors as drug candidates for ameliorating inflammatory diseases and cancers. Therefore, we chemically modified our substituted triazole-class lead compound to improve the binding affinity and selectivity via a "minimal decoration" strategy, which resulted in potent and selective kinase inhibitors against LCK (18 nM) and BTK (8 nM). Subsequent crystallographic experiments validated our design. These rationally designed compounds exhibit potent on-target inhibition against BTK in B cells or LCK in T cells, respectively. Our work demonstrates that structure-based virtual screening can be applied to facilitate the development of novel chemical entities in crowded chemical space in the field of kinase inhibitor discovery.
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Affiliation(s)
- Yanli Wang
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuze Sun
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ran Cao
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Dan Liu
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuting Xie
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Li Li
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Niu Huang
- National Institute of Biological Sciences, Beijing , No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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7
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Bührmann M, Wiedemann BM, Müller MP, Hardick J, Ecke M, Rauh D. Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK. PLoS One 2017; 12:e0184627. [PMID: 28892510 PMCID: PMC5593189 DOI: 10.1371/journal.pone.0184627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/28/2017] [Indexed: 12/27/2022] Open
Abstract
In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings. Here, we present the structure-based design and synthesis of a focused library of 2-arylquinazoline derivatives to target the lipophilic C-terminal binding pocket in p38α MAPK, for which a clear biological function has yet to be identified. The interactions of the ligands with p38α MAPK was analyzed by SPR measurements and validated by protein X-ray crystallography.
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Affiliation(s)
- Mike Bührmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Bianca M. Wiedemann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Matthias P. Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Maria Ecke
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- * E-mail:
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8
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Bassi R, Burgoyne JR, DeNicola GF, Rudyk O, DeSantis V, Charles RL, Eaton P, Marber MS. Redox-dependent dimerization of p38α mitogen-activated protein kinase with mitogen-activated protein kinase kinase 3. J Biol Chem 2017; 292:16161-16173. [PMID: 28739872 PMCID: PMC5625047 DOI: 10.1074/jbc.m117.785410] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/13/2017] [Indexed: 11/08/2022] Open
Abstract
The kinase p38α MAPK (p38α) plays a pivotal role in many biological processes. p38α is activated by canonical upstream kinases that phosphorylate the activation region. The purpose of our study was to determine whether such activation may depend on redox-sensing cysteines within p38α. p38α was activated and formed a disulfide-bound heterodimer with MAP2K3 (MKK3) in rat cardiomyocytes and isolated hearts exposed to H2O2. This disulfide heterodimer was sensitive to reduction by mercaptoethanol and was enhanced by the thioredoxin-reductase inhibitor auranofin. We predicted that Cys-119 or Cys-162 of p38α, close to the known MKK3 docking domain, were relevant for these redox characteristics. The C119S mutation decreased whereas the C162S mutation increased the dimer formation, suggesting that these two Cys residues act as vicinal thiols, consistent with C119S/C162S being incapable of sensing H2O2. Similarly, disulfide heterodimer formation was abolished in H9C2 cells expressing both MKK3 and p38α C119S/C162S and subjected to simulated ischemia and reperfusion. However, the p38α C119S/C162S mutants did not exhibit appreciable alteration in activating dual phosphorylation. In contrast, the anti-inflammatory agent 10-nitro-oleic acid (NO2-OA), a component of the Mediterranean diet, reduced p38α activation and covalently modified Cys-119/Cys-162, probably obstructing MKK3 access. Moreover, NO2-OA reduced the dephosphorylation of p38α by hematopoietic tyrosine phosphatase (HePTP). Furthermore, steric obstruction of Cys-119/Cys-162 by NO2-OA pretreatment in Langendorff-perfused murine hearts prevented the p38-MKK3 disulfide dimer formation and attenuated H2O2-induced contractile dysfunction. Our findings suggest that cysteine residues within p38α act as redox sensors that can dynamically regulate the association between p38 and MKK3.
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Affiliation(s)
- Rekha Bassi
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Joseph R Burgoyne
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Gian F DeNicola
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Olena Rudyk
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Vittorio DeSantis
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Rebecca L Charles
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Philip Eaton
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - Michael S Marber
- From the King's College London British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom
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9
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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.
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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.
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10
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Shafiee F, Rabbani M, Jahanian-Najafabadi A. Optimization of the Expression of DT386-BR2 Fusion Protein in Escherichia coli using Response Surface Methodology. Adv Biomed Res 2017; 6:22. [PMID: 28349025 PMCID: PMC5353773 DOI: 10.4103/2277-9175.201334] [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] [Indexed: 12/02/2022] Open
Abstract
Background: The aim of this study was to determine the best condition for the production of DT386-BR2 fusion protein, an immunotoxin consisting of catalytic and translocation domains of diphtheria toxin fused to BR2, a cancer specific cell penetrating peptide, for targeted eradication of cancer cells, in terms of the host, cultivation condition, and culture medium. Materials and Methods: Recombinant pET28a vector containing the codons optimized for the expression of the DT386-BR2 gene was transformed to different strains of Escherichia coli (E. coli BL21 DE3, E. coli Rosetta DE3 and E. coli Rosetta-gami 2 DE3), followed by the induction of expression using 1 mM IPTG. Then, the strain with the highest ability to produce recombinant protein was selected and used to determine the best expression condition using response surface methodology (RSM). Finally, the best culture medium was selected. Results: Densitometry analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the expressed fusion protein showed that E. coli Rosetta DE3 produced the highest amounts of the recombinant fusion protein when quantified by 1 mg/ml bovine serum albumin (178.07 μg/ml). Results of RSM also showed the best condition for the production of the recombinant fusion protein was induction with 1 mM IPTG for 2 h at 37°C. Finally, it was established that terrific broth could produce higher amounts of the fusion protein when compared to other culture media. Conclusion: In this study, we expressed the recombinant DT386-BR2 fusion protein in large amounts by optimizing the expression host, cultivation condition, and culture medium. This fusion protein will be subjected to purification and evaluation of its cytotoxic effects in future studies.
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Affiliation(s)
- Fatemeh Shafiee
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Rabbani
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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11
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Vinh NB, Devine SM, Munoz L, Ryan RM, Wang BH, Krum H, Chalmers DK, Simpson JS, Scammells PJ. Design, Synthesis, and Biological Evaluation of Tetra-Substituted Thiophenes as Inhibitors of p38α MAPK. ChemistryOpen 2014; 4:56-64. [PMID: 25861571 PMCID: PMC4380954 DOI: 10.1002/open.201402076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 12/30/2022] Open
Abstract
p38α mitogen-activated protein kinase (MAPK) plays a role in several cellular processes and consequently has been a therapeutic target in inflammatory diseases, cancer, and cardiovascular disease. A number of known p38α MAPK inhibitors contain vicinal 4-fluorophenyl/4-pyridyl rings connected to either a 5- or 6-membered heterocycle. In this study, a small library of substituted thiophene-based compounds bearing the vicinal 4-fluorophenyl/4-pyridyl rings was designed using computational docking as a visualisation tool. Compounds were synthesised and evaluated in a fluorescence polarisation binding assay. The synthesised analogues had a higher binding affinity to the active phosphorylated form of p38α MAPK than the inactive nonphosphorylated form of the protein. 4-(2-(4-fluorophenyl)thiophen-3-yl)pyridine had a Ki value of 0.6 μm to active p38α MAPK highlighting that substitution of the core ring to a thiophene retains affinity to the enzyme and can be utilised in p38α MAPK inhibitors. This compound was further elaborated using a substituted phenyl ring in order to probe the second hydrophobic pocket. Many of these analogues exhibited low micromolar affinity to active p38α MAPK. The suppression of neonatal rat fibroblast collagen synthesis was also observed suggesting that further development of these compounds may lead to potential therapeutics having cardioprotective properties.
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Affiliation(s)
- Natalie B Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Shane M Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Lenka Munoz
- Discipline of Pharmacology, School of Medical Sciences and Bosch Institute, The University of Sydney Sydney, NSW 2006 (Australia)
| | - Renae M Ryan
- Discipline of Pharmacology, School of Medical Sciences and Bosch Institute, The University of Sydney Sydney, NSW 2006 (Australia)
| | - Bing H Wang
- Centre of Cardiovascular Research and Education in Therapeutics, Department of Epidemiology and Preventative Medicine, Monash University 99 Commercial Road, Melbourne, VIC 3004 (Australia)
| | - Henry Krum
- Centre of Cardiovascular Research and Education in Therapeutics, Department of Epidemiology and Preventative Medicine, Monash University 99 Commercial Road, Melbourne, VIC 3004 (Australia)
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Jamie S Simpson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville, VIC 3052 (Australia)
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12
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Piala AT, Moon TM, Akella R, He H, Cobb MH, Goldsmith EJ. Chloride sensing by WNK1 involves inhibition of autophosphorylation. Sci Signal 2014; 7:ra41. [PMID: 24803536 DOI: 10.1126/scisignal.2005050] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
WNK1 [with no lysine (K)] is a serine-threonine kinase associated with a form of familial hypertension. WNK1 is at the top of a kinase cascade, leading to phosphorylation of several cotransporters, in particular those transporting sodium, potassium, and chloride (NKCC), sodium and chloride (NCC), and potassium and chloride (KCC). The responsiveness of NKCC, NCC, and KCC to changes in extracellular chloride parallels their phosphorylation state, provoking the proposal that these transporters are controlled by a chloride-sensitive protein kinase. We found that chloride stabilizes the inactive conformation of WNK1, preventing kinase autophosphorylation and activation. Crystallographic studies of inactive WNK1 in the presence of chloride revealed that chloride binds directly to the catalytic site, providing a basis for the unique position of the catalytic lysine. Mutagenesis of the chloride-binding site rendered the kinase less sensitive to inhibition of autophosphorylation by chloride, validating the binding site. Thus, these data suggest that WNK1 functions as a chloride sensor through direct binding of a regulatory chloride ion to the active site, which inhibits autophosphorylation.
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Affiliation(s)
- Alexander T Piala
- 1Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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13
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Wongtrakul J, Janphen K, Saisawang C, Ketterman AJ. Interaction of Omega, Sigma, and Theta glutathione transferases with p38b mitogen-activated protein kinase from the fruit fly, Drosophila melanogaster. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:60. [PMID: 25373207 PMCID: PMC4207522 DOI: 10.1093/jis/14.1.60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/22/2012] [Indexed: 06/04/2023]
Abstract
Glutathione S-transferases (GSTs) are a diverse family of phase II detoxification enzymes found in almost all organisms. Besides playing a major role in the detoxification of xenobiotic and toxic compounds, GSTs are also involved in the regulation of mitogen activated protein (MAP) kinase signal transduction by interaction with proteins in the pathway. An in vitro study was performed for Theta, Omega, Sigma GSTs and their interaction with MAP kinase p38b protein from the fruit fly Drosophila melanogaster Meigen (Diptera: Drosophilidae). The study included the effects of all five Omega class GSTs (DmGSTO1, DmGSTO2a, DmGSTO2b, DmGSTO3, DmGSTO4), all five Theta class GSTs (DmGSTT1, DmGSTT2, DmGSTT3a, DmGSTT3b, DmGSTT4), and one Sigma class glutathione transferase on the activity of Drosophila p38b, including the reciprocal effect of this kinase protein on glutathione transferase activity. It was found that DmGSTT2, DmGSTT3b, DmGSTO1, and DmGSTO3 activated p38b significantly. Substrate specificities of GSTs were also altered after co-incubation with p38b. Although p38b activated DmGSTO1, DmGSTO2a, and DmGSTT2, it inhibited DmGSTT3b and DmGSTO3 activity toward xenobiotic and physiological substrates tested. These results suggest a novel link between Omega and Theta GSTs with the p38b MAP kinase pathway.
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Affiliation(s)
- J Wongtrakul
- Research Institute for Health Sciences (RIHES), Chiang Mai University, P.O.BOX 80 CMU, Chiang Mai, Thailand 50200
| | - K Janphen
- Research Institute for Health Sciences (RIHES), Chiang Mai University, P.O.BOX 80 CMU, Chiang Mai, Thailand 50200
| | - C Saisawang
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand 73170
| | - A J Ketterman
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand 73170
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14
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DeNicola GF, Martin ED, Chaikuad A, Bassi R, Clark J, Martino L, Verma S, Sicard P, Tata R, Atkinson RA, Knapp S, Conte MR, Marber MS. Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1. Nat Struct Mol Biol 2013; 20:1182-90. [PMID: 24037507 PMCID: PMC3822283 DOI: 10.1038/nsmb.2668] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/02/2013] [Indexed: 11/09/2022]
Abstract
p38α mitogen-activated protein kinase (p38α) is activated by a variety of mechanisms, including autophosphorylation initiated by TGFβ-activated kinase 1 binding protein 1 (TAB1) during myocardial ischemia and other stresses. Chemical-genetic approaches and coexpression in mammalian, bacterial and cell-free systems revealed that mouse p38α autophosphorylation occurs in cis by direct interaction with TAB1(371-416). In isolated rat cardiac myocytes and perfused mouse hearts, TAT-TAB1(371-416) rapidly activates p38 and profoundly perturbs function. Crystal structures and characterization in solution revealed a bipartite docking site for TAB1 in the p38α C-terminal kinase lobe. TAB1 binding stabilizes active p38α and induces rearrangements within the activation segment by helical extension of the Thr-Gly-Tyr motif, allowing autophosphorylation in cis. Interference with p38α recognition by TAB1 abolishes its cardiac toxicity. Such intervention could potentially circumvent the drawbacks of clinical pharmacological inhibitors of p38 catalytic activity.
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Affiliation(s)
- Gian Felice DeNicola
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Eva Denise Martin
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Apirat Chaikuad
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK
| | - Rekha Bassi
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - James Clark
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Sharwari Verma
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Pierre Sicard
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Renée Tata
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK
- Department of Biochemistry and Molecular Biology, George Washington University, Washington, DC 20037, USA
- University of Oxford, Nuffield Department of Clinical Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Michael S Marber
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
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15
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Humphreys JM, Piala AT, Akella R, He H, Goldsmith EJ. Precisely ordered phosphorylation reactions in the p38 mitogen-activated protein (MAP) kinase cascade. J Biol Chem 2013; 288:23322-30. [PMID: 23744074 PMCID: PMC3743502 DOI: 10.1074/jbc.m113.462101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/31/2013] [Indexed: 01/04/2023] Open
Abstract
The MAP kinase cascades, composed of a MAP3K, a MAP2K, and a MAPK, control switch responses to extracellular stimuli and stress in eukaryotes. The most important feature of these modules is thought to be the two double phosphorylation reactions catalyzed by MAP3Ks and MAP2Ks. We addressed whether the reactions are sequential or random in the p38 MAP kinase module. Mass spectrometry was used to track the phosphorylation of the MAP2K MEK6 by two MAP3Ks, TAO2 and ASK1, and the subsequent phosphorylation of p38α by MEK6/S*T* (where S (Ser) and T (Thr) are the two phosphorylation sites and * denotes phosphorylation). Both double phosphorylation reactions are precisely ordered. MEK6 is phosphorylated first on Thr-211 and then on Ser-207 by both MAP3Ks. This is the first demonstration of a precise reaction order for a MAP2K. p38α is phosphorylated first on Tyr-182 and then on Thr-180, the same reaction order observed previously in ERK2. Thus, intermediates were MEK6/ST* and p38α/TY*. Similarly, the phosphorylation of the p38α transcription factor substrate ATF2 occurs in a precise sequence. Progress curves for the appearance of intermediates were fit to kinetic models. The models confirmed the reaction order, revealed processivity in the phosphorylation of MEK6 by ASK1, and suggested that the order of phosphorylation is dictated by both binding and catalysis rates.
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Affiliation(s)
- John M. Humphreys
- From the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Alexander T. Piala
- From the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Radha Akella
- From the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Haixia He
- From the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Elizabeth J. Goldsmith
- From the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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16
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Martz KE, Dorn A, Baur B, Schattel V, Goettert MI, Mayer-Wrangowski SC, Rauh D, Laufer SA. Targeting the Hinge Glycine Flip and the Activation Loop: Novel Approach to Potent p38α Inhibitors. J Med Chem 2012; 55:7862-74. [DOI: 10.1021/jm300951u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kathrin E. Martz
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Angelika Dorn
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Benjamin Baur
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Verena Schattel
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Márcia I. Goettert
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Svenja C. Mayer-Wrangowski
- Faculty of Chemistry−Chemical
Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry−Chemical
Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Department
of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
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17
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Azevedo R, van Zeeland M, Raaijmakers H, Kazemier B, de Vlieg J, Oubrie A. X-ray structure of p38α bound to TAK-715: comparison with three classic inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1041-50. [PMID: 22868770 DOI: 10.1107/s090744491201997x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/03/2012] [Indexed: 11/11/2022]
Abstract
The p38α mitogen-activated protein kinase regulates the synthesis of pro-inflammatory cytokines in response to stimulation by a diverse set of stress signals. Various different chemotypes and clinical candidates that inhibit p38α function have been reported over the years. In this publication, the novel structure of p38α cocrystallized with the clinical candidate TAK-715 is reported. Owing to the impact of crystallization conditions on the conformation of protein kinases (and in particular p38α), the structures of complexes of p38α with SB-203580, SCIO-469 and VX-745 have also been determined to enable in-depth comparison of ligand-induced protein conformations. The impact of experimental conditions on p38α-inhibitor complex structures, most importantly soaking versus cocrystallization, is discussed. Analysis of the structures and quantification of the protein-ligand interactions couples ligand-induced protein conformations to the number of interactions and to inhibitor selectivity against the human kinome. This shows that for the design of novel kinase inhibitors, selectivity is best obtained through maximization of the number of interactions throughout the ATP pocket and the exploitation of specific features in the active site.
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Affiliation(s)
- Rita Azevedo
- Merck Research Laboratories, MSD, PO Box 20, 5340 BH Oss, The Netherlands
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18
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C, Habeck M. Inferential NMR/X-ray-based structure determination of a dibenzo[a,d]cycloheptenone inhibitor-p38α MAP kinase complex in solution. Angew Chem Int Ed Engl 2012; 51:2359-62. [PMID: 22275118 DOI: 10.1002/anie.201105241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/23/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Valerie S Honndorf
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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19
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C, Habeck M. Inferential NMR/X-ray-Based Structure Determination of a Dibenzo[a,d]cycloheptenone Inhibitor-p38α MAP Kinase Complex in Solution. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Wongtrakul J, Sukittikul S, Saisawang C, Ketterman AJ. Mitogen-activated protein kinase p38b interaction with delta class glutathione transferases from the fruit fly, Drosophila melanogaster. JOURNAL OF INSECT SCIENCE (ONLINE) 2012; 12:107. [PMID: 23438069 PMCID: PMC3605031 DOI: 10.1673/031.012.10701] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/17/2012] [Indexed: 05/29/2023]
Abstract
Glutathione transferases (GSTs) are a family of multifunctional enzymes involved in xenobiotic biotransformation, drug metabolism, and protection against oxidative damage. The p38b mitogen-activated protein kinase is involved in cellular stress response. This study screened interactions between Drosophila melanogaster Meigen (Diptera: Drosophilidae) Delta class glutathione transferases (DmGSTs) and the D. melanogaster p38b MAPK. Therefore, 12 DmGSTs and p38b kinase were obtained as recombinant proteins. The study showed that DmGSTD8 and DmGSTD11b significantly increased p38b activity toward ATF2 and jun, which are transcription factor substrates. DmGSTD3 and DmGSTD5 moderately increased p38b activity for jun. In addition, GST activity in the presence of p38b was also measured. It was found that p38b affected substrate specificity toward CDNB (1-chloro-2,4-dinitrobenzene) and DCNB (1,2-dichloro-4-nitrobenzene) of several GST isoforms, i.e., DmGSTD2, DmGSTD5, DmGSTD8, and DmGSTD11b. The interaction of a GST and p38b can affect the substrate specificity of either enzyme, which suggests induced conformational changes affecting catalysis. Similar interactions do not occur for all the Delta enzymes and p38b, which suggests that these interactions could be specific.
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Affiliation(s)
- Jeerang Wongtrakul
- Research Institute for Health Sciences (RIHES), Chiang Mai University, P.O.BOX 80 CMU, Chiang Mai, Thailand
50200
| | - Suchada Sukittikul
- Research Institute for Health Sciences (RIHES), Chiang Mai University, P.O.BOX 80 CMU, Chiang Mai, Thailand
50200
| | - Chonticha Saisawang
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand 73170
| | - Albert J. Ketterman
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand 73170
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21
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22
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Simard JR, Grütter C, Pawar V, Aust B, Wolf A, Rabiller M, Wulfert S, Robubi A, Klüter S, Ottmann C, Rauh D. High-throughput screening to identify inhibitors which stabilize inactive kinase conformations in p38alpha. J Am Chem Soc 2010; 131:18478-88. [PMID: 19950957 DOI: 10.1021/ja907795q] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule kinase inhibitors are an attractive means to modulate kinase activities in medicinal chemistry and chemical biology research. In the physiological setting of a cell, kinase function is orchestrated by a plethora of regulatory processes involving the structural transition of kinases between inactive and enzymatically competent conformations and vice versa. The development of novel kinase inhibitors is mainly fostered by high-throughput screening initiatives where the small molecule perturbation of the phosphorylation reaction is measured to identify inhibitors. Such setups require enzymatically active kinase preparations and present a risk of solely identifying classical ATP-competitive Type I inhibitors. Here we report the high-throughput screening of a library of approximately 35000 small organic molecules with an assay system that utilizes enzymatically inactive human p38alpha MAP kinase to detect stabilizers of the pharmacologically more desirable DFG-out conformation. We used protein X-ray crystallography to characterize the binding mode of hit compounds and reveal structural features which explain how these ligands stabilize and/or induce the DFG-out conformation. Lastly, we show that although some of the hit compounds were confirmed by protein X-ray crystallography, they were not detected in classic phosphorylation assays, thus validating the unique sensitivity of the assay system used in this study and highlighting the potential of screening with inactive kinase preparations.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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23
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Simard JR, Getlik M, Grütter C, Pawar V, Wulfert S, Rabiller M, Rauh D. Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors. J Am Chem Soc 2010; 131:13286-96. [PMID: 19572644 DOI: 10.1021/ja902010p] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kinase disregulation disrupts the intricate network of intracellular signaling pathways and contributes to the onset of diseases such as cancer. Although several kinase inhibitors are on the market, inhibitor selectivity and drug resistance mutations persist as fundamental challenges in the development of effective long-term treatments. Chemical entities binding to less conserved allosteric sites would be expected to offer new opportunities for scaffold development. Because no high-throughput method was previously available, we developed a fluorescence-based kinase binding assay for identifying and characterizing ligands which stabilize the inactive kinase conformation. Here, we present a description of the development and validation of this assay using the serine/threonine kinase p38alpha. By covalently attaching fluorophores to the activation loop of the kinase, we were able to detect conformational changes and measure the K(d), k(on), and k(off) associated with the binding and dissociation of ligands to the allosteric pocket. We report the SAR of a synthesized focused library of pyrazolourea derivatives, a scaffold known to bind with high affinity to the allosteric pocket of p38alpha. Additionally, we used protein X-ray crystallography together with our assay to examine the binding and dissociation kinetics to characterize potent quinazoline- and quinoline-based type II inhibitors, which also utilize this binding pocket in p38alpha. Last, we identified the b-Raf inhibitor sorafenib as a potent low nanomolar inhibitor of p38alpha and used protein X-ray crystallography to confirm a unique binding mode to the inactive kinase conformation.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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24
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Abstract
MAPK cascade components have been the subject of structural analysis, advancing our understanding of how these enzymes are activated and how they interact. A surprising finding has been that unique inactive conformers are adopted by many of these kinases. These inactive conformers are interesting and often require experimental phases to determine their crystal structures because molecular replacement techniques are not successful. Here, we describe the preparation of MAP2K MEK6 and MAP3K TAO2 substituted with selenomethionine (SeMet) for de novo phasing. TAO2 and SeMet TAO2 were expressed in insect cells.
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Affiliation(s)
- Elizabeth J Goldsmith
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
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25
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Klüter S, Grütter C, Naqvi T, Rabiller M, Simard JR, Pawar V, Getlik M, Rauh D. Displacement Assay for the Detection of Stabilizers of Inactive Kinase Conformations. J Med Chem 2009; 53:357-67. [DOI: 10.1021/jm901297e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sabine Klüter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Tabassum Naqvi
- DiscoveRx Corporation, 42501 Albrae Street, Fremont, California 94538
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Vijaykumar Pawar
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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26
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Honndorf VS, Coudevylle N, Laufer S, Becker S, Griesinger C. Dynamics in the p38alpha MAP kinase-SB203580 complex observed by liquid-state NMR spectroscopy. Angew Chem Int Ed Engl 2008; 47:3548-51. [PMID: 18389508 DOI: 10.1002/anie.200705614] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Valerie S Honndorf
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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27
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Honndorf V, Coudevylle N, Laufer S, Becker S, Griesinger C. Dynamics in the p38α MAP Kinase–SB203580 Complex Observed by Liquid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Cazzola M, Ciaprini C, Page CP, Matera MG. Targeting systemic inflammation: novel therapies for the treatment of chronic obstructive pulmonary disease. Expert Opin Ther Targets 2007; 11:1273-86. [PMID: 17907958 DOI: 10.1517/14728222.11.10.1273] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The increasing evidence that inflammation in the lungs leads to the structural changes observed in chronic obstructive pulmonary disease, whereas extrapulmonary symptoms and comorbidities may be systemic manifestations of these inflammatory processes, highlights an urgent need to discover novel, effective anti-inflammatory treatments for this disease. Some studies are suggesting that, by decreasing dynamic hyperinflation, bronchodilators might reduce systemic inflammation; inhaled corticosteroids and their combination with long-acting beta2-agonists might contribute to this goal. Even so, the opinion that suppression of the inflammatory response might improve systemic complications is stimulating a search for novel anti-inflammatory therapies. Many drugs include those that inhibit the recruitment and activation of inflammatory cells and/or antagonise their products. However, many of these therapeutic strategies are not specific for neutrophilic inflammation because they affect other cell types, thus, it is difficult to interpret whether any clinical benefit observed is a result of a reduction in airway neutrophils. In any case, there is some evidence that drugs used to treat a co-morbid condition, such as statins, angiotensin converting enzyme (ACE) inhibitors and angiontensin II type 1 (AT1) receptor blockers as well as glycosaminoglycans and peroxisome proliferator-activated receptor (PPAR) agonists, might benefit chronic obstructive pulmonary disease patients because they deal with the extrapulmonary, systemic component of chronic obstructive pulmonary disease.
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Affiliation(s)
- Mario Cazzola
- Associate Professor of Respiratory Medicine, Universitá di Roma Tor Vergata, Dipartimento di Medicina Interna, Via Montpellier 1, 00133 Roma, Italy.
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29
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Kulis MD, Shuker SB. Expression, purification, and refolding of mouse islet neogenesis associated protein-related protein for NMR studies. Protein Expr Purif 2006; 48:224-31. [PMID: 16545961 DOI: 10.1016/j.pep.2006.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 01/31/2006] [Accepted: 02/02/2006] [Indexed: 11/20/2022]
Abstract
Islet neogenesis associated protein-related protein (INGAPrP) is thought to be involved in the differentiation of non-insulin-producing cells to insulin-secreting cells. INGAPrP is a mouse gene product that has a 72% identical amino acid sequence to a known islet-generating factor, hamster islet-neogenesis-associated protein (INGAP), which acts by differentiating pancreatic ductal cells into beta-cells. The three-dimensional structure of these proteins is unknown. The structure would provide information about the conformation of the active portion of INGAP, the so-called INGAP pentadecapeptide, leading to a well-defined target for rational drug design. An efficient procedure for the production of INGAPrP would facilitate the process of structure determination. We have successfully produced and isolated (15)N-labeled INGAPrP by expression in Escherichia coli Rosetta (DE3) cells in Spectra-9 media followed by a two-step purification and refolding protocol. The hexahistidine tag engineered at the N-terminus of the protein is used in the first step for standard immobilized-metal affinity chromatography purification under denaturing conditions. The secondary purification step utilizes a gel permeation chromatography column, producing homogeneous INGAPrP as well as refolding the protein. To verify that the protein was folded, we performed a (1)H-(15)N HSQC NMR experiment that showed excellent dispersion of signals, indicative of a folded protein. We also performed circular dichroism experiments, which demonstrated the presence of secondary structure. In summary, we report the first expression and isolation of INGAPrP, as well as demonstrate that our method produces a folded protein, which is necessary for structure determination.
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Affiliation(s)
- Michael D Kulis
- School of Chemistry and Biochemistry, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, 30332, USA
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30
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Michelotti EL, Moffett KK, Nguyen D, Kelly MJ, Shetty R, Chai X, Northrop K, Namboodiri V, Campbell B, Flynn GA, Fujimoto T, Hollinger FP, Bukhtiyarova M, Springman EB, Karpusas M. Two classes of p38α MAP kinase inhibitors having a common diphenylether core but exhibiting divergent binding modes. Bioorg Med Chem Lett 2005; 15:5274-9. [PMID: 16169718 DOI: 10.1016/j.bmcl.2005.08.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/12/2005] [Accepted: 08/15/2005] [Indexed: 10/25/2022]
Abstract
Two new classes of diphenylether inhibitors of p38alpha MAP kinase are described. Both chemical classes are based on a common diphenylether core that is identified by simulated fragment annealing as one of the most favored chemotypes within a prominent hydrophobic pocket of the p38alpha ATP-binding site. In the fully elaborated molecules, the diphenylether moiety acts as an anchor occupying the deep pocket, while polar extensions make specific interactions with either the adenine binding site or the phosphate binding site of ATP. The synthesis, crystallographic analysis, and biological activity of these p38alpha inhibitors are discussed.
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Affiliation(s)
- Enrique L Michelotti
- Department of Chemistry, Locus Pharmaceuticals, Inc., Four Valley Square, 512 Township Line Rd, Blue Bell, PA 19422, USA
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31
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Goodell V, Disis ML. Human tumor cell lysates as a protein source for the detection of cancer antigen-specific humoral immunity. J Immunol Methods 2005; 299:129-38. [PMID: 15914197 DOI: 10.1016/j.jim.2005.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 01/24/2005] [Accepted: 02/07/2005] [Indexed: 10/25/2022]
Abstract
Measurement of humoral tumor-specific immunity can predict what proteins are specific tumor antigens, be used to evaluate patient diagnosis or prognosis, and function as a method by which one can measure the effects of an immune intervention, such as a vaccine. Antibody assays can easily be adapted to high throughput formats; however, specific reagents needed for assay development often are not available. Developing methods to produce large quantities of purified recombinant tumor antigen proteins for indirect ELISA is both laborious and expensive. In addition, using proteins derived from E. coli might preclude the detection of certain antibody epitopes. We questioned whether a human tumor cell-based ELISA could be developed to assess antibody immunity to common tumor-associated antigens and whether such an ELISA could be optimized to the clinical standards needed for evaluation of large scale trials. Assays were based on the detection of HER-2/neu and p53 antibodies by capture ELISA, using human tumor cell lysate as a protein source. After optimization, the HER-2/neu and p53 ELISA intra-assay coefficients of variation (CV) of positive control sera were consistently 9% and 12%, respectively, at a 1:100 dilution. The HER-2/neu and p53 inter-assay CV of positive control sera over a 5-month time period were 20% and 15%, respectively. The sensitivity and specificity of the ELISAs were evaluated based on comparison to immunoblot. Analysis demonstrated the HER-2/neu ELISA had a specificity of 77% and sensitivity of 89%, and the p53 ELISA had a specificity of 100% and sensitivity of 93%. Cell-based ELISA can be developed to be Clinical Laboratory Improvement Act (CLIA)-compliant and the flexibility of the approach will allow adaptation of the assay to multiple tumor antigen systems.
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Affiliation(s)
- Vivian Goodell
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, Seattle, WA 98195-8050, United States.
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Huber W. A new strategy for improved secondary screening and lead optimization using high-resolution SPR characterization of compound-target interactions. J Mol Recognit 2005; 18:273-81. [PMID: 15997470 DOI: 10.1002/jmr.744] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biophysical label-free assays such as those based on SPR are essential tools in generating high-quality data on affinity, kinetic, mechanistic and thermodynamic aspects of interactions between target proteins and potential drug candidates. Here we show examples of the integration of SPR with bioinformatic approaches and mutation studies in the early drug discovery process. We call this combination 'structure-based biophysical analysis'. Binding sites are identified on target proteins using information that is either extracted from three-dimensional structural analysis (X-ray crystallography or NMR), or derived from a pharmacore model based on known binders. The binding site information is used for in silico screening of a large substance library (e.g. available chemical directory), providing virtual hits. The three-dimensional structure is also used for the design of mutants where the binding site has been impaired. The wild-type target and the impaired mutant are then immobilized on different spots of the sensor chip and the interactions of compounds with the wild-type and mutant are compared in order to identify selective binders for the binding site of the target protein. This method can be used as a cost-effective alternative to high-throughput screening methods in cases when detailed binding site information is available. Here, we present three examples of how this technique can be applied to provide invaluable data during different phases of the drug discovery process.
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Affiliation(s)
- Walter Huber
- F. Hoffman-La Roche Ltd, Pharmaceutical Research, Discovery Chemistry, Basel, Switzerland.
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