1
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Abouelenein MG, Mohamed MBI, Elsenety MM, El-Rashedy AA, Ghalib SH, Mohamed FAE, El-Ebiary NMA, Ageeli AA. Facile and Novel Synthetic Approach, Molecular Docking, Molecular Dynamics, and Drug-Likeness Evaluation of 9-Substituted Acridine Derivatives as Dual Anticancer and Antimicrobial Agents. Chem Biodivers 2024; 21:e202301986. [PMID: 38478727 DOI: 10.1002/cbdv.202301986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024]
Abstract
In the present study, numerous acridine derivatives A1-A20 were synthesized via aromatic nucleophilic substitution (SNAr) reaction of 9-chloroacridine with carbonyl hydrazides, amines, or phenolic derivatives depending upon facile, novel, and eco-friendly approaches (Microwave and ultrasonication assisted synthesis). The structures of the new compounds were elucidated using spectroscopic methods. The title products were assessed for their antimicrobial, antioxidant, and antiproliferative activities using numerous assays. Promisingly, the investigated compounds mainstream revealed promising antibacterial and anticancer activities. Thereafter, the investigated compounds' expected mode of action was debated by using an array of in silico studies. Compounds A2 and A3 were the most promising antimicrobial agents, while compounds A2, A5, and A7 revealed the most cytotoxic activities. Accordingly, RMSD, RMSF, Rg, and SASA analyses of compounds A2 and A3 were performed, and MMPBSA was calculated. Lastly, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) analyses of the novel acridine derivatives were investigated. The tested compounds' existing screening results afford an inspiring basis leading to developing new compelling antimicrobial and anticancer agents based on the acridine scaffold.
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Affiliation(s)
- Mohamed G Abouelenein
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Koam, Menofia, Egypt
| | | | - Mohamed M Elsenety
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt, P.O., 11884
| | - Ahmed A El-Rashedy
- Natural and Microbial Products Department, National Research Center (NRC), Egypt
| | - Samirah H Ghalib
- Chemistry Department, Faculty of Science, Jazan University, Jazan, P.O. Box, 82817, Saudi Arabia
| | | | - Nora M A El-Ebiary
- Chemistry Department, Faculty of Science, Jazan University, Jazan, P.O. Box, 82817, Saudi Arabia
| | - Abeer A Ageeli
- Chemistry Department, Faculty of Science, Jazan University, Jazan, P.O. Box, 82817, Saudi Arabia
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2
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Lian Y, Bodian D, Shehu A. Elucidating the Role of Wildtype and Variant FGFR2 Structural Dynamics in (Dys)Function and Disorder. Int J Mol Sci 2024; 25:4523. [PMID: 38674107 PMCID: PMC11050683 DOI: 10.3390/ijms25084523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The fibroblast growth factor receptor 2 (FGFR2) gene is one of the most extensively studied genes with many known mutations implicated in several human disorders, including oncogenic ones. Most FGFR2 disease-associated gene mutations are missense mutations that result in constitutive activation of the FGFR2 protein and downstream molecular pathways. Many tertiary structures of the FGFR2 kinase domain are publicly available in the wildtype and mutated forms and in the inactive and activated state of the receptor. The current literature suggests a molecular brake inhibiting the ATP-binding A loop from adopting the activated state. Mutations relieve this brake, triggering allosteric changes between active and inactive states. However, the existing analysis relies on static structures and fails to account for the intrinsic structural dynamics. In this study, we utilize experimentally resolved structures of the FGFR2 tyrosine kinase domain and machine learning to capture the intrinsic structural dynamics, correlate it with functional regions and disease types, and enrich it with predicted structures of variants with currently no experimentally resolved structures. Our findings demonstrate the value of machine learning-enabled characterizations of structure dynamics in revealing the impact of mutations on (dys)function and disorder in FGFR2.
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Affiliation(s)
- Yiyang Lian
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA;
| | - Dale Bodian
- Diamond Age Data Science, Boston, MA 02143, USA;
| | - Amarda Shehu
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA;
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
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3
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Mahapatra S, Jonniya NA, Koirala S, Kar P. Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase. J Biomol Struct Dyn 2024; 42:2929-2941. [PMID: 37160693 DOI: 10.1080/07391102.2023.2209189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
The Fibroblast Growth Factor Receptor1 (FGFR1) kinase wields exquisite control on cell fate, proliferation, differentiation, and homeostasis. An imbalance of FGFR1 signaling leads to several pathogeneses of diseases ranging from multiple cancers to allergic and neurodegenerative disorders. In this study, we investigated the phosphorylation-induced conformational dynamics of FGFR1 in apo and ATP-bound states via all-atom molecular dynamics simulations. All simulations were performed for 2 × 2 µs. We have also investigated the energetics of the binding of ATP to FGFR1 using the molecular mechanics Poisson-Boltzmann scheme. Our study reveals that the FGFR1 kinase can reach a fully active configuration through phosphorylation and ATP binding. A 3-10 helix formation in the activation loop signifies its rearrangement leading to stability upon ATP binding. The interaction of phosphorylated tyrosine (pTyr654) with positively charged residues forms strong salt-bridge interactions, driving the compactness of the structure. The dynamic cross-correlation map reveals phosphorylation enhances correlated motions and reduces anti-correlated motions between different domains. We believe that the mechanistic understanding of large-conformational changes upon the activation of the FGFR1 kinase will aid the development of novel targeted therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subhasmita Mahapatra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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4
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Zhang Y, Yin XL, Ji M, Chen Y, Chai Z. Decoupling the dynamic mechanism revealed by FGFR2 mutation-induced population shift. J Biomol Struct Dyn 2024; 42:1940-1951. [PMID: 37254996 DOI: 10.1080/07391102.2023.2217924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
The fibroblast growth factor receptor 2 (FGFR2) is a key component in cellular signaling networks, and its dysfunctional activation has been implicated in various diseases including cancer and developmental disorders. Mutations at the activation loop (A-loop) have been suggested to trigger an increased basal kinase activity. However, the molecular mechanism underlying this highly dynamic process has not been fully understood due to the limitation of static structural information. Here, we conducted multiple, large-scale Gaussian accelerated molecular dynamics simulations of five (K659E, K659N, K659M, K659Q, and K659T) FGFR2 mutants at the A-loop, and comprehensively analyzed the dynamic molecular basis of FGFR2 activation. The results quantified the population shift of each system, revealing that all mutants had a higher proportion of active-like states. Using Markov state models, we extracted the representative structure of different conformational states and identified key residues related to the increased kinase activity. Furthermore, community network analysis showed enhanced information connections in the mutants, highlighting the long-range allosteric communication between the A-loop and the hinge region. Our findings may provide insights into the dynamic mechanism for FGFR2 dysfunctional activation and allosteric drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuxiang Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Lan Yin
- Department of Radiotherapy, Shanghai 411 Hospital, China RongTong Medical Healthcare Group Co. Ltd, Shanghai, China
| | - Mingfei Ji
- Department of Urology, The Second Affiliated Hospital of Navy Medical University, Shanghai, China
| | - Yi Chen
- Department of Ultrasound interventional, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Zongtao Chai
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hepatic Surgery, Shanghai Geriatric Medical Center, Shanghai, China
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5
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Vishnu T, Veerabhadraiah M, Krishna Chaitanya V, Nagamani M, Raghavender M, Jalapathi P. Design, synthesis and anticancer activity of 5-((2-(4-bromo/chloro benzoyl) benzofuran-5-yl) methyl)-2-((1-(substituted)-1H-1,2,3-triazol-4-yl)methoxy)benzaldehyde analogues. Mol Divers 2023; 27:2695-2713. [PMID: 36436134 DOI: 10.1007/s11030-022-10575-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/20/2022] [Indexed: 11/28/2022]
Abstract
Novel 5-((2-(4-bromo/chloro benzoyl) benzofuran-5-yl) methyl)-2-((1-(substituted)-1H-1,2,3-triazol-4-yl)methoxy)benzaldehyde analogues about twenty-one were synthesized all through standard chemical procedures. The structure of the compounds were confirmed by 1H NMR, 13C NMR and Mass spectral analysis after purification. All the compounds were screened for In Vitro lung and cervical cancer activity against A-549 and HeLa cell lines, respectively, by MTT assay protocol using various nanomolar (nM) concentrations. IC50 value were calculated from cell viability data. 2-(trifluoromethyl)benzyl substituted derivative presented outstanding activity against both the cell lines compared to standard drug doxorubicin. The methoxy, chloro, fluoro and formyl substituted analogues showed a moderate activity and whereas methyl substituted analogues activity was poor. The morphological deformation of both cell lines by best IC50 value analogues proved as potent inhibitors of cancer cells growth. Molecular docking studies were performed against extracellular signal-regulated kinase 2 and fibroblast growth factor receptor 2 these results are incredibly in agreement with the investigational data.
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Affiliation(s)
- T Vishnu
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India
- Department of Sciences and Humanities, Matrusri Engineering College, Hyderabad, 500059, India
| | - M Veerabhadraiah
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India
| | - V Krishna Chaitanya
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India
| | - M Nagamani
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India
| | - M Raghavender
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India
| | - P Jalapathi
- Department of Chemistry, Osmania University, Hyderabad, Telangana, 500007, India.
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6
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Lin CC, Wieteska L, Poncet-Montange G, Suen KM, Arold ST, Ahmed Z, Ladbury JE. The combined action of the intracellular regions regulates FGFR2 kinase activity. Commun Biol 2023; 6:728. [PMID: 37452126 PMCID: PMC10349056 DOI: 10.1038/s42003-023-05112-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) are typically activated through a precise sequence of intracellular phosphorylation events starting with a tyrosine residue on the activation loop (A-loop) of the kinase domain (KD). From this point the mono-phosphorylated enzyme is active, but subject to stringent regulatory mechanisms which can vary dramatically across the different RTKs. In the absence of extracellular stimulation, fibroblast growth factor receptor 2 (FGFR2) exists in the mono-phosphorylated state in which catalytic activity is regulated to allow rapid response upon ligand binding, whilst restricting ligand-independent activation. Failure of this regulation is responsible for pathologic outcomes including cancer. Here we reveal the molecular mechanistic detail of KD control based on combinatorial interactions of the juxtamembrane (JM) and the C-terminal tail (CT) regions of the receptor. JM stabilizes the asymmetric dimeric KD required for substrate phosphorylation, whilst CT binding opposes dimerization, and down-regulates activity. Direct binding between JM and CT delays the recruitment of downstream effector proteins adding a further control step as the receptor proceeds to full activation. Our findings underscore the diversity in mechanisms of RTK oligomerisation and activation.
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Affiliation(s)
- Chi-Chuan Lin
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Lukasz Wieteska
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Guillaume Poncet-Montange
- Center for the Development of Therapeutics, Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Kin Man Suen
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090, Montpellier, France
| | - Zamal Ahmed
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John E Ladbury
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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7
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Arauzo-Aguilera K, Buscajoni L, Koch K, Thompson G, Robinson C, Berkemeyer M. Yields and product comparison between Escherichia coli BL21 and W3110 in industrially relevant conditions: anti-c-Met scFv as a case study. Microb Cell Fact 2023; 22:104. [PMID: 37208750 PMCID: PMC10197847 DOI: 10.1186/s12934-023-02111-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION In the biopharmaceutical industry, Escherichia coli is one of the preferred expression hosts for large-scale production of therapeutic proteins. Although increasing the product yield is important, product quality is a major factor in this industry because greatest productivity does not always correspond with the highest quality of the produced protein. While some post-translational modifications, such as disulphide bonds, are required to achieve the biologically active conformation, others may have a negative impact on the product's activity, effectiveness, and/or safety. Therefore, they are classified as product associated impurities, and they represent a crucial quality parameter for regulatory authorities. RESULTS In this study, fermentation conditions of two widely employed industrial E. coli strains, BL21 and W3110 are compared for recombinant protein production of a single-chain variable fragment (scFv) in an industrial setting. We found that the BL21 strain produces more soluble scFv than the W3110 strain, even though W3110 produces more recombinant protein in total. A quality assessment on the scFv recovered from the supernatant was then performed. Unexpectedly, even when our scFv is correctly disulphide bonded and cleaved from its signal peptide in both strains, the protein shows charge heterogeneity with up to seven distinguishable variants on cation exchange chromatography. Biophysical characterization confirmed the presence of altered conformations of the two main charged variants. CONCLUSIONS The findings indicated that BL21 is more productive for this specific scFv than W3110. When assessing product quality, a distinctive profile of the protein was found which was independent of the E. coli strain. This suggests that alterations are present in the recovered product although the exact nature of them could not be determined. This similarity between the two strains' generated products also serves as a sign of their interchangeability. This study encourages the development of innovative, fast, and inexpensive techniques for the detection of heterogeneity while also provoking a debate about whether intact mass spectrometry-based analysis of the protein of interest is sufficient to detect heterogeneity in a product.
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Affiliation(s)
| | - Luisa Buscajoni
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Karin Koch
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Gary Thompson
- Wellcome Trust Biological NMR Facility, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Matthias Berkemeyer
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
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8
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Besch A, Marsiglia WM, Mohammadi M, Zhang Y, Traaseth NJ. Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proc Natl Acad Sci U S A 2023; 120:e2213090120. [PMID: 36791110 PMCID: PMC9974468 DOI: 10.1073/pnas.2213090120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/10/2023] [Indexed: 02/16/2023] Open
Abstract
Many types of human cancers are being treated with small molecule ATP-competitive inhibitors targeting the kinase domain of receptor tyrosine kinases. Despite initial successful remission, long-term treatment almost inevitably leads to the emergence of drug resistance mutations at the gatekeeper residue hindering the access of the inhibitor to a hydrophobic pocket at the back of the ATP-binding cleft. In addition to reducing drug efficacy, gatekeeper mutations elevate the intrinsic activity of the tyrosine kinase domain leading to more aggressive types of cancer. However, the mechanism of gain-of-function by gatekeeper mutations is poorly understood. Here, we characterized fibroblast growth factor receptor (FGFR) tyrosine kinases harboring two distinct gatekeeper mutations using kinase activity assays, NMR spectroscopy, bioinformatic analyses, and MD simulations. Our data show that gatekeeper mutations destabilize the autoinhibitory conformation of the DFG motif locally and of the kinase globally, suggesting they impart gain-of-function by facilitating the kinase's ability to populate the active state.
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Affiliation(s)
- Alida Besch
- Department of Chemistry, New York University, New York, NY10003
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY10016
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY10003
- Simons Center for Computational Physical Chemistry, New York University, New York, NY10003
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9
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Modh DH, Modi SJ, Deokar H, Yadav S, Kulkarni VM. Fibroblast growth factor receptor (FGFR) inhibitors as anticancer agents: 3D-QSAR, molecular docking and dynamics simulation studies of 1, 6-naphthyridines and pyridopyrimidines. J Biomol Struct Dyn 2022; 41:3591-3606. [PMID: 35318898 DOI: 10.1080/07391102.2022.2053206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fibroblast growth factor receptor (FGFR) plays a vital role in tissue regeneration, angiogenesis, and embryogenesis. 3D-QSAR and molecular modeling methods are widely used for designing novel compounds for the determination of inhibitory activity against the biological target. In the present study, 3D-QSAR (CoMFA and CoMSIA) analysis was performed on 1, 6-naphthyridines, and pyridopyrimidines as potential FGFR inhibitors as anticancer agents. The best CoMFA and CoMSIA models were generated from test and training set derivatives with leave-one-out correlation coefficients (q2) 0.591 and 0.667, cross-validated correlation coefficients (r2cv) 0.584 and 0.652, conventional coefficients (r2ncv) 0.978 and 0.975 respectively. The developed models were validated by a test set of 12 compounds providing acceptable predictive correlation coefficient (r2pred) 0.61 and 0.68 for both models. The generated CoMFA and CoMSIA contour maps could be used to design novel 1, 6-naphthyridine analogs. Molecular docking studies indicated that compound 75 occupied the active site of the FGFR kinase interacting with Glu520 in the catalytic region, Asp630 in the DFG motif, and Met524 in the hinge region which compared with standard drug Ponatinib. The molecular dynamics simulation analysis revealed that the inhibitor 75 displayed binding stability in the active site of the FGFR4 by making two hydrogen bonds and one π-cation interaction. Collectively the outcome of the study suggested that the applications of ligand-based and structure-based approaches could be applied for the design of new FGFR4 inhibitors as anticancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharti H Modh
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | - Siddharth J Modi
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | - Hemant Deokar
- Department of Pharmaceutical Sciences, College of Pharmacy, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Savita Yadav
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | - Vithal M Kulkarni
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
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10
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Kyhoiesh HAK, Al-Adilee KJ. Synthesis, spectral characterization and biological activities of Ag(I), Pt(IV) and Au(III) complexes with novel azo dye ligand (N, N, O) derived from 2-amino-6-methoxy benzothiazole. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02072-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Das R, Choithramani A, Shard A. A molecular perspective for the use of type IV tyrosine kinase inhibitors as anticancer therapeutics. Drug Discov Today 2021; 27:808-821. [PMID: 34920095 DOI: 10.1016/j.drudis.2021.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/21/2021] [Accepted: 12/10/2021] [Indexed: 11/03/2022]
Abstract
Tyrosine kinases are enzymes that can transfer a phosphate group from ATP to a specific protein tyrosine, serine or threonine residue within a cell, operating as a switch that can turn 'on' and 'off' causing different physiological alterations in the body. Mutated kinases have been shown to display an equilibrium shift toward the activated state. Types I-III have been studied intensively leading to drugs like imatinib (type II), cobimetinib (type III), among others. It is the same scenario for types V-VII; however, there is a lacuna in information regarding type IV inhibitors, although recently some advances have surfaced. This review aims to accumulate the knowledge gained so far about type IV inhibitors.
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Affiliation(s)
- Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Asmita Choithramani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India.
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12
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Chen L, Marsiglia WM, Chen H, Katigbak J, Erdjument-Bromage H, Kemble DJ, Fu L, Ma J, Sun G, Zhang Y, Liang G, Neubert TA, Li X, Traaseth NJ, Mohammadi M. Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation. Nat Chem Biol 2020; 16:267-277. [PMID: 31959966 PMCID: PMC7040854 DOI: 10.1038/s41589-019-0455-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022]
Abstract
A long-standing mystery shrouds the mechanism by which catalytically repressed receptor tyrosine kinase domains accomplish transphosphorylation of activation loop (A-loop) tyrosines. Here we show that this reaction proceeds via an asymmetric complex that is thermodynamically disadvantaged because of an electrostatic repulsion between enzyme and substrate kinases. Under physiological conditions, the energetic gain resulting from ligand-induced dimerization of extracellular domains overcomes this opposing clash, stabilizing the A-loop-transphosphorylating dimer. A unique pathogenic fibroblast growth factor receptor gain-of-function mutation promotes formation of the complex responsible for phosphorylation of A-loop tyrosines by eliminating this repulsive force. We show that asymmetric complex formation induces a more phosphorylatable A-loop conformation in the substrate kinase, which in turn promotes the active state of the enzyme kinase. This explains how quantitative differences in the stability of ligand-induced extracellular dimerization promotes formation of the intracellular A-loop-transphosphorylating asymmetric complex to varying extents, thereby modulating intracellular kinase activity and signaling intensity.
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MESH Headings
- AAA Domain/genetics
- AAA Domain/physiology
- Catalytic Domain
- Dimerization
- Enzyme Activation
- Humans
- Ligands
- Phosphorylation
- Protein Binding
- Protein Conformation
- Protein-Tyrosine Kinases/metabolism
- Protein-Tyrosine Kinases/physiology
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor Protein-Tyrosine Kinases/physiology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Signal Transduction
- Structure-Activity Relationship
- Tyrosine/chemistry
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Affiliation(s)
- Lingfeng Chen
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Huaibin Chen
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Joseph Katigbak
- Department of Chemistry, New York University, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - David J Kemble
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Lili Fu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinghong Ma
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Gongqin Sun
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
| | - Guang Liang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Thomas A Neubert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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13
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Ndagi U, Abdullahi M, Hamza AN, Soliman ME. An analogue of a kinase inhibitor exhibits subjective characteristics that contribute to its inhibitory activities as a potential anti-cancer candidate: insights through computational biomolecular modelling of UM-164 binding with lyn protein. RSC Adv 2020; 10:145-161. [PMID: 35492550 PMCID: PMC9047091 DOI: 10.1039/c9ra07204g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The recent emergence of lyn kinase as a driver of aggressive behaviour in triple-negative breast cancer (TNBC) remains a major concern posing a burden for people living with breast cancer and drug development. The binding of UM-164 to lyn protein has been noted to impact the conformational dynamics required for drug fitness. Herein, we provide the first account of the molecular impact of an experimental drug, UM-164 binding on lyn protein using various computational approaches including molecular docking and molecular dynamics simulation. These computational modelling methods enabled us to analyse parameters, for example principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, hydrogen bond occupancy, thermodynamics calculation and ligand–residue interaction. Findings from these analyses revealed that UM-164 exhibited a higher binding affinity of −9.9 kcal mol−1 with lyn protein than Dasatinib, with a binding affinity of −8.3 kcal mol−1 on docking. It was observed that the binding of UM-164 to lyn protein decreases the capacity of its loop to fluctuate, influences the ligand optimum orientation on the conformational space of lyn protein, and increases the hydrogen bond formation in the lyn-UM-164 system. Also, an increase in drug binding energy of UM-164 was recorded with increasing residue correlation in the lyn-UM-164 system. It is quite informative to note that Met85 was a key stabilising factor in the binding of UM-164 to lyn protein. These findings can provide important insights that will potentially serve as a baseline in the design of novel lyn inhibitors. It could also stimulate further research into multidimensional approaches required to curb the influence of lyn protein in TNBC. This study provides the first account of the molecular impact of UM-164 binding on lyn protein using various computational approaches.![]()
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Affiliation(s)
- Umar Ndagi
- Faculty of Natural Sciences
- Ibrahim Badamasi Babangida University
- Nigeria
| | - Maryam Abdullahi
- Molecular Bio-Computation and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4000
- South Africa
| | - Asmau N. Hamza
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University
- Zaria
- Nigeria
| | - Mahmoud E. Soliman
- Molecular Bio-Computation and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4000
- South Africa
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14
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Wu C, Chen X, Chen D, Xia Q, Liu Z, Li F, Yan Y, Cai Y. Insight into ponatinib resistance mechanisms in rhabdomyosarcoma caused by the mutations in FGFR4 tyrosine kinase using molecular modeling strategies. Int J Biol Macromol 2019; 135:294-302. [DOI: 10.1016/j.ijbiomac.2019.05.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 01/03/2023]
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15
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A Conserved Allosteric Pathway in Tyrosine Kinase Regulation. Structure 2019; 27:1308-1315.e3. [PMID: 31204250 DOI: 10.1016/j.str.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 05/08/2019] [Indexed: 01/01/2023]
Abstract
An autoinhibitory network of hydrogen bonds located at the kinase hinge (referred to as the "molecular brake") regulates the activity of several receptor tyrosine kinases. The mechanism whereby mutational disengagement of the brake allosterically activates the kinase in human disease is incompletely understood. We used a combination of NMR, bioinformatics, and molecular dynamics simulation to show that mutational disruption of the molecular brake triggers localized conformational perturbations that propagate to the active site. This entails changes in interactions of an isoleucine, one of three hydrophobic residues that lock the phenylalanine of the DFG motif in an inactive conformation. Structural analysis of tyrosine kinases provides evidence that this allosteric control mechanism is shared across the tyrosine kinase family. We also show that highly activating mutations at the brake diminish the enzyme's thermostability, thereby explaining why these mutations cause milder skeletal syndromes compared with less-activating mutations in the activation loop.
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16
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Farrell B, Breeze AL. Structure, activation and dysregulation of fibroblast growth factor receptor kinases: perspectives for clinical targeting. Biochem Soc Trans 2018; 46:1753-1770. [PMID: 30545934 PMCID: PMC6299260 DOI: 10.1042/bst20180004] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 01/22/2023]
Abstract
The receptor tyrosine kinase family of fibroblast growth factor receptors (FGFRs) play crucial roles in embryonic development, metabolism, tissue homeostasis and wound repair via stimulation of intracellular signalling cascades. As a consequence of FGFRs' influence on cell growth, proliferation and differentiation, FGFR signalling is frequently dysregulated in a host of human cancers, variously by means of overexpression, somatic point mutations and gene fusion events. Dysregulation of FGFRs is also the underlying cause of many developmental dysplasias such as hypochondroplasia and achondroplasia. Accordingly, FGFRs are attractive pharmaceutical targets, and multiple clinical trials are in progress for the treatment of various FGFR aberrations. To effectively target dysregulated receptors, a structural and mechanistic understanding of FGFR activation and regulation is required. Here, we review some of the key research findings from the last couple of decades and summarise the strategies being explored for therapeutic intervention.
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Affiliation(s)
- Brendan Farrell
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
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17
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Tan Q, Chen B, Wang Q, Xu W, Wang Y, Lin Z, Luo F, Huang S, Zhu Y, Su N, Jin M, Li C, Kuang L, Qi H, Ni Z, Wang Z, Luo X, Jiang W, Chen H, Chen S, Li F, Zhang B, Huang J, Zhang R, Jin K, Xu X, Deng C, Du X, Xie Y, Chen L. A novel FGFR1-binding peptide attenuates the degeneration of articular cartilage in adult mice. Osteoarthritis Cartilage 2018; 26:1733-1743. [PMID: 30201491 DOI: 10.1016/j.joca.2018.08.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVE We previously reported that genetic ablation of (Fibroblast Growth Factors Receptors) FGFR1 in knee cartilage attenuates the degeneration of articular cartilage in adult mice, which suggests that FGFR1 is a potential targeting molecule for osteoarthritis (OA). Here, we identified R1-P1, an inhibitory peptide for FGFR1 and investigated its effect on the pathogenesis of OA in mice induced by destabilization of medial meniscus (DMM). DESIGN Binding ability between R1-P1 and FGFR1 protein was evaluated by enzyme-linked immuno sorbent assay (ELISA) and molecular docking. Alterations in cartilage were evaluated histologically. The expression levels of molecules associated with articular cartilage homeostasis and FGFR1 signaling were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting and immunohistochemistry (IHC). The chondrocyte apoptosis was detected by terminal-deoxynucleoitidyl transferase mediated nick end labeling (TUNEL) assay. RESULTS R1-P1 had highly binding affinities to human FGFR1 protein, and efficiently inhibited extracellular signal-regulated kinase (ERK)1/2 pathway in mouse primary chondrocytes. In addition, R1-P1 attenuated the IL-1β induced significant loss of proteoglycan in full-thickness cartilage tissue from human femur head. Moreover, this peptide can significantly restore the IL-1β mediated loss of proteoglycan and type II collagen (Col II) and attenuate the expression of matrix metalloproteinase-13 (MMP13) in mouse primary chondrocytes. Finally, intra-articular injection of R1-P1 remarkably attenuated the loss of proteoglycan and the destruction of articular cartilage and decreased the expressions of extracellular matrix (ECM) degrading enzymes and apoptosis in articular chondrocytes of mice underwent DMM surgery. CONCLUSIONS R1-P1, a novel inhibitory peptide for FGFR1, attenuates the degeneration of articular cartilage in adult mice, which is a potential leading molecule for the treatment of OA.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Arthritis, Experimental/metabolism
- Arthritis, Experimental/pathology
- Arthritis, Experimental/prevention & control
- Cartilage, Articular/drug effects
- Cartilage, Articular/metabolism
- Cartilage, Articular/pathology
- Cells, Cultured
- Chondrocytes/drug effects
- Chondrocytes/pathology
- Drug Evaluation, Preclinical/methods
- Extracellular Matrix/drug effects
- Extracellular Matrix/pathology
- Humans
- MAP Kinase Signaling System/drug effects
- Male
- Mice, Inbred C57BL
- Oligopeptides/pharmacology
- Oligopeptides/therapeutic use
- Osteoarthritis/metabolism
- Osteoarthritis/pathology
- Osteoarthritis/prevention & control
- Proteoglycans/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Tissue Culture Techniques
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Affiliation(s)
- Q Tan
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - B Chen
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Q Wang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - W Xu
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Y Wang
- College of Bioengineering, Chongqing Institute of Technology, Chongqing 400050, China
| | - Z Lin
- College of Bioengineering, Chongqing Institute of Technology, Chongqing 400050, China
| | - F Luo
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - S Huang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Y Zhu
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - N Su
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - M Jin
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - C Li
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - L Kuang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - H Qi
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Z Ni
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Z Wang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - X Luo
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - W Jiang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - H Chen
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - S Chen
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - F Li
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - B Zhang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - J Huang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - R Zhang
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - K Jin
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - X Xu
- Faculty of Health Sciences, University of Macau, Macau SAR 00853, China
| | - C Deng
- Faculty of Health Sciences, University of Macau, Macau SAR 00853, China
| | - X Du
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
| | - Y Xie
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
| | - L Chen
- Department of Rehabilitation Medicine, Laboratory for the Rehabilitation of Traumatic Injuries, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
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18
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Sarabipour S. Parallels and Distinctions in FGFR, VEGFR, and EGFR Mechanisms of Transmembrane Signaling. Biochemistry 2017. [DOI: 10.1021/acs.biochem.7b00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sarvenaz Sarabipour
- Institute for Computational
Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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19
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Jeske YW, Ali S, Byron SA, Gao F, Mannel RS, Ghebre RG, DiSilvestro PA, Lele SB, Pearl ML, Schmidt AP, Lankes HA, Ramirez NC, Rasty G, Powell M, Goodfellow PJ, Pollock PM. FGFR2 mutations are associated with poor outcomes in endometrioid endometrial cancer: An NRG Oncology/Gynecologic Oncology Group study. Gynecol Oncol 2017; 145:366-373. [PMID: 28314589 PMCID: PMC5433848 DOI: 10.1016/j.ygyno.2017.02.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 11/19/2022]
Abstract
PURPOSE Activating FGFR2 mutations have been identified in ~10% of endometrioid endometrial cancers (ECs). We have previously reported that mutations in FGFR2 are associated with shorter disease free survival (DFS) in stage I/II EC patients. Here we sought to validate the prognostic importance of FGFR2 mutations in a large, multi-institutional patient cohort. METHODS Tumors were collected as part of the GOG 210 clinical trial "Molecular Staging of Endometrial Cancer" where samples underwent rigorous pathological review and had more than three years of detailed clinical follow-up. DNA was extracted and four exons encompassing the FGFR2 mutation hotspots were amplified and sequenced. RESULTS Mutations were identified in 144 of the 973 endometrioid ECs, of which 125 were classified as known activating mutations and were included in the statistical analyses. Consistent with FGFR2 having an association with more aggressive disease, FGFR2 mutations were more common in patients initially diagnosed with stage III/IV EC (29/170;17%) versus stage I/II EC (96/803; 12%; p=0.07, Chi-square test). Additionally, incidence of progression (progressed, recurred or died from disease) was significantly more prevalent (32/125, 26%) among patients with FGFR2 mutation versus wild type (120/848, 14%; p<0.001, Chi-square test). Using Cox regression analysis adjusting for known prognostic factors, patients with FGFR2 mutation had significantly (p<0.025) shorter progression-free survival (PFS; HR 1.903; 95% CI 1.177-3.076) and endometrial cancer specific survival (ECS; HR 2.013; 95% CI 1.096-3.696). CONCLUSION In summary, our findings suggest that clinical trials testing the efficacy of FGFR inhibitors in the adjuvant setting to prevent recurrence and death are warranted.
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Affiliation(s)
- Yvette W Jeske
- Queensland University of Technology (QUT) at the Translational Research Institute, Brisbane, Australia
| | - Shamshad Ali
- NRG Oncology Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sara A Byron
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Feng Gao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Robert S Mannel
- Gynecologic Oncology, The Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rahel G Ghebre
- University of Minnesota Medical Center - Fairview, Minneapolis, MN, USA
| | | | - Shashikant B Lele
- Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Michael L Pearl
- Obstetrics and Gynecology, Stony Brook University Hospital, Stony Brook, NY, USA
| | - Amy P Schmidt
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St Louis, MO, USA
| | - Heather A Lankes
- NRG Oncology Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Nilsa C Ramirez
- GOG Tissue Bank/NRG Oncology Biospecimen Bank - Columbus, Biopathology Center, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Golnar Rasty
- Department of Laboratory Medicine, University of Toronto, ON, M5G2C, CANADA
| | - Matthew Powell
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St Louis, MO, USA
| | - Paul J Goodfellow
- Department of Obstetrics and Gynecology, The Ohio State University and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Pamela M Pollock
- Queensland University of Technology (QUT) at the Translational Research Institute, Brisbane, Australia; Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
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20
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Chen H, Marsiglia WM, Cho MK, Huang Z, Deng J, Blais SP, Gai W, Bhattacharya S, Neubert TA, Traaseth NJ, Mohammadi M. Elucidation of a four-site allosteric network in fibroblast growth factor receptor tyrosine kinases. eLife 2017; 6:e21137. [PMID: 28166054 PMCID: PMC5293489 DOI: 10.7554/elife.21137] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/02/2017] [Indexed: 01/07/2023] Open
Abstract
Receptor tyrosine kinase (RTK) signaling is tightly regulated by protein allostery within the intracellular tyrosine kinase domains. Yet the molecular determinants of allosteric connectivity in tyrosine kinase domain are incompletely understood. By means of structural (X-ray and NMR) and functional characterization of pathogenic gain-of-function mutations affecting the FGF receptor (FGFR) tyrosine kinase domain, we elucidated a long-distance allosteric network composed of four interconnected sites termed the 'molecular brake', 'DFG latch', 'A-loop plug', and 'αC tether'. The first three sites repress the kinase from adopting an active conformation, whereas the αC tether promotes the active conformation. The skewed design of this four-site allosteric network imposes tight autoinhibition and accounts for the incomplete mimicry of the activated conformation by pathogenic mutations targeting a single site. Based on the structural similarity shared among RTKs, we propose that this allosteric model for FGFR kinases is applicable to other RTKs.
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Affiliation(s)
- Huaibin Chen
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | | | - Min-Kyu Cho
- Department of Chemistry, New York University, New York, United States
| | | | - Jingjing Deng
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Steven P Blais
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Weiming Gai
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | | | - Thomas A Neubert
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
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21
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Karp JM, Sparks S, Cowburn D. Effects of FGFR2 kinase activation loop dynamics on catalytic activity. PLoS Comput Biol 2017; 13:e1005360. [PMID: 28151998 PMCID: PMC5313233 DOI: 10.1371/journal.pcbi.1005360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/16/2017] [Accepted: 01/12/2017] [Indexed: 12/17/2022] Open
Abstract
The structural mechanisms by which receptor tyrosine kinases (RTKs) regulate catalytic activity are diverse and often based on subtle changes in conformational dynamics. The regulatory mechanism of one such RTK, fibroblast growth factor receptor 2 (FGFR2) kinase, is still unknown, as the numerous crystal structures of the unphosphorylated and phosphorylated forms of the kinase domains show no apparent structural change that could explain how phosphorylation could enable catalytic activity. In this study, we use several enhanced sampling molecular dynamics (MD) methods to elucidate the structural changes to the kinase's activation loop that occur upon phosphorylation. We show that phosphorylation favors inward motion of Arg664, while simultaneously favoring outward motion of Leu665 and Pro666. The latter structural change enables the substrate to bind leading to its resultant phosphorylation. Inward motion of Arg664 allows it to interact with the γ-phosphate of ATP as well as the substrate tyrosine. We show that this stabilizes the tyrosine and primes it for the catalytic phosphotransfer, and it may lower the activation barrier of the phosphotransfer reaction. Our work demonstrates the value of including dynamic information gleaned from computer simulation in deciphering RTK regulatory function.
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Affiliation(s)
- Jerome M. Karp
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Samuel Sparks
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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22
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Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PMW, Chin JW, Gervasio FL, Tate EW, Katan M. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Alan R. Lowe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- London Centre for Nanotechnology, 17-19 Gower St, London, WC1H 0AH, UK
- Division of Biosciences, Birkbeck College, Malet St, London, WC1E 7HX, UK
| | - Giorgio Saladino
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jason W. Chin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Luigi Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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23
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McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N. KinView: a visual comparative sequence analysis tool for integrated kinome research. MOLECULAR BIOSYSTEMS 2016; 12:3651-3665. [PMID: 27731453 PMCID: PMC5508867 DOI: 10.1039/c6mb00466k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats.
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Affiliation(s)
| | - Shima Dastgheib
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Steven Thomas Scott
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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24
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Taiwo BJ, Taiwo GO, Olubiyi OO, Fatokun AA. Polyphenolic compounds with anti-tumour potential from Corchorus olitorius (L.) Tiliaceae, a Nigerian leaf vegetable. Bioorg Med Chem Lett 2016; 26:3404-10. [DOI: 10.1016/j.bmcl.2016.06.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 06/19/2016] [Accepted: 06/22/2016] [Indexed: 12/16/2022]
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25
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Patani H, Bunney TD, Thiyagarajan N, Norman RA, Ogg D, Breed J, Ashford P, Potterton A, Edwards M, Williams SV, Thomson GS, Pang CS, Knowles MA, Breeze AL, Orengo C, Phillips C, Katan M. Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use. Oncotarget 2016; 7:24252-68. [PMID: 26992226 PMCID: PMC5029699 DOI: 10.18632/oncotarget.8132] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/28/2016] [Indexed: 01/09/2023] Open
Abstract
Frequent genetic alterations discovered in FGFRs and evidence implicating some as drivers in diverse tumors has been accompanied by rapid progress in targeting FGFRs for anticancer treatments. Wider assessment of the impact of genetic changes on the activation state and drug responses is needed to better link the genomic data and treatment options. We here apply a direct comparative and comprehensive analysis of FGFR3 kinase domain variants representing the diversity of point-mutations reported in this domain. We reinforce the importance of N540K and K650E and establish that not all highly activating mutations (for example R669G) occur at high-frequency and conversely, that some "hotspots" may not be linked to activation. Further structural characterization consolidates a mechanistic view of FGFR kinase activation and extends insights into drug binding. Importantly, using several inhibitors of particular clinical interest (AZD4547, BGJ-398, TKI258, JNJ42756493 and AP24534), we find that some activating mutations (including different replacements of the same residue) result in distinct changes in their efficacy. Considering that there is no approved inhibitor for anticancer treatments based on FGFR-targeting, this information will be immediately translatable to ongoing clinical trials.
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Affiliation(s)
- Harshnira Patani
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Richard A. Norman
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Derek Ogg
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Jason Breed
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Andrew Potterton
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Mina Edwards
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Sarah V. Williams
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds LS9 7TF, UK
| | - Gary S. Thomson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Camilla S.M. Pang
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Margaret A. Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds LS9 7TF, UK
| | - Alexander L. Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Christine Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Chris Phillips
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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26
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Kobashigawa Y, Amano S, Yoza K, Himeno R, Amemiya S, Morioka H, Yokogawa M, Kumeta H, Schlessinger J, Inagaki F. Nuclear magnetic resonance analysis of the conformational state of cancer mutant of fibroblast growth factor receptor 1 tyrosine kinase domain. Genes Cells 2016; 21:350-7. [DOI: 10.1111/gtc.12345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/28/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Shinjiro Amano
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Kaito Yoza
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Rika Himeno
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Shun Amemiya
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Mariko Yokogawa
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Hiroyuki Kumeta
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Joseph Schlessinger
- Department of Pharmacology; Yale University School of Medicine; New Haven CT 06520 USA
| | - Fuyuhiko Inagaki
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
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27
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Moosa S, Wollnik B. Altered FGF signalling in congenital craniofacial and skeletal disorders. Semin Cell Dev Biol 2015; 53:115-25. [PMID: 26686047 DOI: 10.1016/j.semcdb.2015.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023]
Abstract
The fibroblast growth factor (FGF) signalling pathway has been the focus of intense genetic and functional research for several decades. The emerging data implicate FGF signalling in diverse regulatory processes, both in the developing embryo as well as in the adult organism. Alterations in this tightly regulated pathway can lead to a number of pathological conditions, ranging from well-recognized congenital disorders to cancer. In order to mediate their cellular processes, FGFs signal through a subfamily of tyrosine kinase receptors, called FGF receptors (FGFRs). In humans, four FGFRs are described, and, to date, mutations in FGFR1, FGFR2, and FGFR3 have been shown to underlie human developmental disorders. FGFs/FGFRs are known to be key players in both endochondral and intramembranous bone development. In this review, we focus on the major developmental craniofacial and skeletal disorders which result from altered FGF signalling.
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Affiliation(s)
- Shahida Moosa
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany; Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany; Institute of Human Genetics, University of Cologne, Cologne, Germany.
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28
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Huang Z, Marsiglia WM, Basu Roy U, Rahimi N, Ilghari D, Wang H, Chen H, Gai W, Blais S, Neubert TA, Mansukhani A, Traaseth NJ, Li X, Mohammadi M. Two FGF Receptor Kinase Molecules Act in Concert to Recruit and Transphosphorylate Phospholipase Cγ. Mol Cell 2015; 61:98-110. [PMID: 26687682 DOI: 10.1016/j.molcel.2015.11.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
The molecular basis by which receptor tyrosine kinases (RTKs) recruit and phosphorylate Src Homology 2 (SH2) domain-containing substrates has remained elusive. We used X-ray crystallography, NMR spectroscopy, and cell-based assays to demonstrate that recruitment and phosphorylation of Phospholipase Cγ (PLCγ), a prototypical SH2 containing substrate, by FGF receptors (FGFR) entails formation of an allosteric 2:1 FGFR-PLCγ complex. We show that the engagement of pTyr-binding pocket of the cSH2 domain of PLCγ by the phosphorylated tail of an FGFR kinase induces a conformational change at the region past the cSH2 core domain encompassing Tyr-771 and Tyr-783 to facilitate the binding/phosphorylation of these tyrosines by another FGFR kinase in trans. Our data overturn the current paradigm that recruitment and phosphorylation of substrates are carried out by the same RTK monomer in cis and disclose an obligatory role for receptor dimerization in substrate phosphorylation in addition to its canonical role in kinase activation.
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Affiliation(s)
- Zhifeng Huang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Upal Basu Roy
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Nader Rahimi
- Department of Pathology and Laboratory of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Dariush Ilghari
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Huiyan Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Huaibin Chen
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Weiming Gai
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Steven Blais
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Alka Mansukhani
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Moosa Mohammadi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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29
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Ubiquitination switches EphA2 vesicular traffic from a continuous safeguard to a finite signalling mode. Nat Commun 2015; 6:8047. [PMID: 26292967 PMCID: PMC4560775 DOI: 10.1038/ncomms9047] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/11/2015] [Indexed: 01/15/2023] Open
Abstract
Autocatalytic phosphorylation of receptor tyrosine kinases (RTKs) enables diverse, context-dependent responses to extracellular signals but comes at the price of autonomous, ligand-independent activation. Using a conformational biosensor that reports on the kinase activity of the cell guidance ephrin receptor type-A (EphA2) in living cells, we observe that autonomous EphA2 activation is suppressed by vesicular recycling and dephosphorylation by protein tyrosine phosphatases 1B (PTP1B) near the pericentriolar recycling endosome. This spatial segregation of catalytically superior PTPs from RTKs at the plasma membrane is essential to preserve ligand responsiveness. Ligand-induced clustering, on the other hand, promotes phosphorylation of a c-Cbl docking site and ubiquitination of the receptor, thereby redirecting it to the late endosome/lysosome. We show that this switch from cyclic to unidirectional receptor trafficking converts a continuous suppressive safeguard mechanism into a transient ligand-responsive signalling mode.
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30
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Huang Z, Tan L, Wang H, Liu Y, Blais S, Deng J, Neubert TA, Gray NS, Li X, Mohammadi M. DFG-out mode of inhibition by an irreversible type-1 inhibitor capable of overcoming gate-keeper mutations in FGF receptors. ACS Chem Biol 2015; 10:299-309. [PMID: 25317566 PMCID: PMC4301177 DOI: 10.1021/cb500674s] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Drug-resistance
acquisition through kinase gate-keeper mutations is a major hurdle
in the clinic. Here, we determined the first crystal structures of
the human FGFR4 kinase domain (FGFR4K) alone and complexed with ponatinib,
a promiscuous type-2 (DFG-out) kinase inhibitor, and an oncogenic
FGFR4K harboring the V550L gate-keeper mutation bound to FIIN-2, a
new type-1 irreversible inhibitor. Remarkably, like ponatinib, FIIN-2
also binds in the DFG-out mode despite lacking a functional group
necessary to occupy the pocket vacated upon the DFG-out flip. Structural
analysis reveals that the covalent bond between FIIN-2 and a cysteine,
uniquely present in the glycine-rich loop of FGFR kinases, facilitates
the DFG-out conformation, which together with the internal flexibility
of FIIN-2 enables FIIN-2 to avoid the steric clash with the gate-keeper
mutation that causes the ponatinib resistance. The structural data
provide a blueprint for the development of next generation anticancer
inhibitors through combining the salient inhibitory mechanisms of
ponatinib and FIIN-2.
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Affiliation(s)
- Zhifeng Huang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Li Tan
- Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Huiyan Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | | | | | | | | | - Nathanael S. Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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31
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Abstract
The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases.
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Affiliation(s)
- Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
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32
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Karp JM, Erylimaz E, Cowburn D. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 61:35-45. [PMID: 25416617 PMCID: PMC4715900 DOI: 10.1007/s10858-014-9879-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.
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Affiliation(s)
- Jerome M. Karp
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Ertan Erylimaz
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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33
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Tucker JA, Klein T, Breed J, Breeze AL, Overman R, Phillips C, Norman RA. Structural insights into FGFR kinase isoform selectivity: diverse binding modes of AZD4547 and ponatinib in complex with FGFR1 and FGFR4. Structure 2014; 22:1764-1774. [PMID: 25465127 DOI: 10.1016/j.str.2014.09.019] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 09/19/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023]
Abstract
The fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases has been implicated in a wide variety of cancers. Despite a high level of sequence homology in the ATP-binding site, the majority of reported inhibitors are selective for the FGFR1-3 isoforms and display much reduced potency toward FGFR4, an exception being the Bcr-Abl inhibitor ponatinib. Here we present the crystal structure of the FGFR4 kinase domain and show that both FGFR1 and FGFR4 kinase domains in complex with ponatinib adopt a DFG-out activation loop conformation. Comparison with the structure of FGFR1 in complex with the candidate drug AZD4547, combined with kinetic characterization of the binding of ponatinib and AZD4547 to FGFR1 and FGFR4, sheds light on the observed differences in selectivity profiles and provides a rationale for developing FGFR4-selective inhibitors.
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Affiliation(s)
- Julie A Tucker
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Tobias Klein
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Jason Breed
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Alexander L Breeze
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Ross Overman
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Chris Phillips
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Richard A Norman
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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34
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Structural Analysis of the Human Fibroblast Growth Factor Receptor 4 Kinase. J Mol Biol 2014; 426:3744-3756. [DOI: 10.1016/j.jmb.2014.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 11/20/2022]
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35
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Emerging concepts in the regulation of the EGF receptor and other receptor tyrosine kinases. Trends Biochem Sci 2014; 39:437-46. [DOI: 10.1016/j.tibs.2014.08.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 11/21/2022]
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36
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Kushner EJ, Ferro LS, Liu JY, Durrant JR, Rogers SL, Dudley AC, Bautch VL. Excess centrosomes disrupt endothelial cell migration via centrosome scattering. ACTA ACUST UNITED AC 2014; 206:257-72. [PMID: 25049273 PMCID: PMC4107782 DOI: 10.1083/jcb.201311013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Centrosome–microtubule interactions during interphase are important for centrosome clustering and cell polarity. Supernumerary centrosomes contribute to spindle defects and aneuploidy at mitosis, but the effects of excess centrosomes during interphase are poorly understood. In this paper, we show that interphase endothelial cells with even one extra centrosome exhibit a cascade of defects, resulting in disrupted cell migration and abnormal blood vessel sprouting. Endothelial cells with supernumerary centrosomes had increased centrosome scattering and reduced microtubule (MT) nucleation capacity that correlated with decreased Golgi integrity and randomized vesicle trafficking, and ablation of excess centrosomes partially rescued these parameters. Mechanistically, tumor endothelial cells with supernumerary centrosomes had less centrosome-localized γ-tubulin, and Plk1 blockade prevented MT growth, whereas overexpression rescued centrosome γ-tubulin levels and centrosome dynamics. These data support a model whereby centrosome–MT interactions during interphase are important for centrosome clustering and cell polarity and further suggest that disruption of interphase cell behavior by supernumerary centrosomes contributes to pathology independent of mitotic effects.
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Affiliation(s)
- Erich J Kushner
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Luke S Ferro
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jie-Yu Liu
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jessica R Durrant
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephen L Rogers
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew C Dudley
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Victoria L Bautch
- Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599Department of Biology, McAllister Heart Institute, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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Plaza-Menacho I, Barnouin K, Goodman K, Martínez-Torres RJ, Borg A, Murray-Rust J, Mouilleron S, Knowles P, McDonald NQ. Oncogenic RET kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans. Mol Cell 2014; 53:738-51. [PMID: 24560924 PMCID: PMC3988870 DOI: 10.1016/j.molcel.2014.01.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 01/17/2014] [Indexed: 01/09/2023]
Abstract
To decipher the molecular basis for RET kinase activation and oncogenic deregulation, we defined the temporal sequence of RET autophosphorylation by label-free quantitative mass spectrometry. Early autophosphorylation sites map to regions flanking the kinase domain core, while sites within the activation loop only form at later time points. Comparison with oncogenic RET kinase revealed that late autophosphorylation sites become phosphorylated much earlier than wild-type RET, which is due to a combination of an enhanced enzymatic activity, increased ATP affinity, and surprisingly, by providing a better intermolecular substrate. Structural analysis of oncogenic M918T and wild-type RET kinase domains reveal a cis-inhibitory mechanism involving tethering contacts between the glycine-rich loop, activation loop, and αC-helix. Tether mutations only affected substrate presentation but perturbed the autophosphorylation trajectory similar to oncogenic mutations. This study reveals an unappreciated role for oncogenic RET kinase mutations in promoting intermolecular autophosphorylation by enhancing substrate presentation. Kinetics of RET autophosphorylation identify early and late autophosphorylation sites Evidence for a RET kinase domain cis-inhibitory tether is presented Oncogenic RET subverts cis-inhibition and perturbs the autophosphorylation trajectory Oncogenic RET kinase is overactive and a better trans-autophosphorylation substrate
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Affiliation(s)
- Iván Plaza-Menacho
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK.
| | - Karin Barnouin
- Protein Analysis and Proteomics, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Kerry Goodman
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Rubén J Martínez-Torres
- Protein Structure Function Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Annabel Borg
- Protein Production Facility, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Judith Murray-Rust
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Stephane Mouilleron
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Phillip Knowles
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK
| | - Neil Q McDonald
- Structural Biology Laboratory, London Research Institute, Cancer Research UK, WC2A 3LY London, UK; Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, WC1E 7HX London, UK.
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Molina-Vila MA, Nabau-Moretó N, Tornador C, Sabnis AJ, Rosell R, Estivill X, Bivona TG, Marino-Buslje C. Activating mutations cluster in the "molecular brake" regions of protein kinases and do not associate with conserved or catalytic residues. Hum Mutat 2014; 35:318-28. [PMID: 24323975 DOI: 10.1002/humu.22493] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/03/2013] [Indexed: 01/08/2023]
Abstract
Mutations leading to activation of proto-oncogenic protein kinases (PKs) are a type of drivers crucial for understanding tumorogenesis and as targets for antitumor drugs. However, bioinformatics tools so far developed to differentiate driver mutations, typically based on conservation considerations, systematically fail to recognize activating mutations in PKs. Here, we present the first comprehensive analysis of the 407 activating mutations described in the literature, which affect 41 PKs. Unexpectedly, we found that these mutations do not associate with conserved positions and do not directly affect ATP binding or catalytic residues. Instead, they cluster around three segments that have been demonstrated to act, in some PKs, as "molecular brakes" of the kinase activity. This finding led us to hypothesize that an auto inhibitory mechanism mediated by such "brakes" is present in all PKs and that the majority of activating mutations act by releasing it. Our results also demonstrate that activating mutations of PKs constitute a distinct group of drivers and that specific bioinformatics tools are needed to identify them in the numerous cancer sequencing projects currently underway. The clustering in three segments should represent the starting point of such tools, a hypothesis that we tested by identifying two somatic mutations in EPHA7 that might be functionally relevant.
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Structural mimicry of a-loop tyrosine phosphorylation by a pathogenic FGF receptor 3 mutation. Structure 2013; 21:1889-96. [PMID: 23972473 PMCID: PMC3839590 DOI: 10.1016/j.str.2013.07.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/26/2013] [Accepted: 07/16/2013] [Indexed: 01/07/2023]
Abstract
The K650E gain-of-function mutation in the tyrosine kinase domain of FGF receptor 3 (FGFR3) causes Thanatophoric Dysplasia type II, a neonatal lethal congenital dwarfism syndrome, and when acquired somatically, it contributes to carcinogenesis. In this report, we determine the crystal structure of the FGFR3 kinase domain harboring this pathogenic mutation and show that the mutation introduces a network of intramolecular hydrogen bonds to stabilize the active-state conformation. In the crystal, the mutant FGFR3 kinases are caught in the act of trans-phosphorylation on a kinase insert autophosphorylation site, emphasizing the fact that the K650E mutation circumvents the requirement for A-loop tyrosine phosphorylation in kinase activation. Analysis of this trans-phosphorylation complex sheds light onto the determinants of tyrosine trans-phosphorylation specificity. We propose that the targeted inhibition of this pathogenic FGFR3 kinase may be achievable by small molecule kinase inhibitors that selectively bind the active-state conformation of FGFR3 kinase.
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