51
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Liu Z, Yu S, Chen D, Shen G, Wang Y, Hou L, Lin D, Zhang J, Ye F. Design, synthesis, and biological evaluation of 3-vinyl-quinoxalin-2(1H)-one derivatives as novel antitumor inhibitors of FGFR1. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:1489-500. [PMID: 27217720 PMCID: PMC4861610 DOI: 10.2147/dddt.s88587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
FGFR1 is well known as a molecular target in anticancer drug design. TKI258 plays an important role in RTK inhibitors. Utilizing TKI258 as a lead compound that contains a quinazolinone nucleus, we synthesized four series of 3-vinyl-quinoxalin-2(1H)-one derivatives, a total of 27 compounds. We further evaluated these compounds for FGFR1 inhibition ability as well as cytotoxicity against four cancer cell lines (H460, B16-F10, Hela229, and Hct116) in vitro. Some compounds displayed good-to-excellent potency against the four tested cancer cell lines compared with TKI258. Structure–activity relationship analyses indicated that small substituents at the side chain of the 3-vinyl-quinoxalin-2(1H)-one were more effective than large substituents. Lastly, we used molecular docking to obtain further insight into the interactions between the compounds and FGFR1.
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Affiliation(s)
- Zhiguo Liu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Shufang Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Di Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Guoliang Shen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Yu Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Leping Hou
- Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Dan Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Jinsan Zhang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Faqing Ye
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
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52
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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: 73] [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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53
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Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases. Curr Opin Struct Biol 2016; 37:108-14. [DOI: 10.1016/j.sbi.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/13/2022]
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54
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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55
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Perdios L, Bunney TD, Warren SC, Dunsby C, French PMW, Tate EW, Katan M. Time-resolved FRET reports FGFR1 dimerization and formation of a complex with its effector PLCγ1. Adv Biol Regul 2016; 60:6-13. [PMID: 26482290 PMCID: PMC4739061 DOI: 10.1016/j.jbior.2015.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/22/2015] [Indexed: 11/05/2022]
Abstract
In vitro and in vivo imaging of protein tyrosine kinase activity requires minimally invasive, molecularly precise optical probes to provide spatiotemporal mechanistic information of dimerization and complex formation with downstream effectors. We present here a construct with genetically encoded, site-specifically incorporated, bioorthogonal reporter that can be selectively labelled with exogenous fluorogenic probes to monitor the structure and function of fibroblast growth factor receptor (FGFR). GyrB.FGFR1KD.TC contains a coumermycin-induced artificial dimerizer (GyrB), FGFR1 kinase domain (KD) and a tetracysteine (TC) motif that enables fluorescent labelling with biarsenical dyes FlAsH-EDT2 and ReAsH-EDT2. We generated bimolecular system for time-resolved FRET (TR-FRET) studies, which pairs FlAsH-tagged GyrB.FGFR1KD.TC and N-terminal Src homology 2 (nSH2) domain of phospholipase Cγ (PLCγ), a downstream effector of FGFR1, fused to mTurquoise fluorescent protein (mTFP). We demonstrated phosphorylation-dependent TR-FRET readout of complex formation between mTFP.nSH2 and GyrB.FGFR1KD.TC. By further application of TR-FRET, we also demonstrated formation of the GyrB.FGFR1KD.TC homodimer by coumermycin-induced dimerization. Herein, we present a spectroscopic FRET approach to facilitate and propagate studies that would provide structural and functional insights for FGFR and other tyrosine kinases.
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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
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Sean C Warren
- 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
| | - 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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56
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Lovera S, Morando M, Pucheta-Martinez E, Martinez-Torrecuadrada JL, Saladino G, Gervasio FL. Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. PLoS Comput Biol 2015; 11:e1004578. [PMID: 26606374 PMCID: PMC4659586 DOI: 10.1371/journal.pcbi.1004578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/01/2015] [Indexed: 11/18/2022] Open
Abstract
Due to its inhibition of the Abl kinase domain in the BCR-ABL fusion protein, imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing complete remission. However, as in the case of most targeted anti-cancer therapies, the emergence of drug resistance is a serious concern. Several drug-resistant mutations affecting the catalytic domain of Abl and other tyrosine kinases are now known. But, despite their importance and the adverse effect that they have on the prognosis of the cancer patients harboring them, the molecular mechanism of these mutations is still debated. Here by using long molecular dynamics simulations and large-scale free energy calculations complemented by in vitro mutagenesis and microcalorimetry experiments, we model the effect of several widespread drug-resistant mutations of Abl. By comparing the conformational free energy landscape of the mutants with those of the wild-type tyrosine kinases we clarify their mode of action. It involves significant and complex changes in the inactive-to-active dynamics and entropy/enthalpy balance of two functional elements: the activation-loop and the conserved DFG motif. What is more the T315I gatekeeper mutant has a significant impact on the binding mechanism itself and on the binding kinetics.
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MESH Headings
- Computational Biology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate/chemistry
- Imatinib Mesylate/metabolism
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive
- Molecular Dynamics Simulation
- Mutagenesis, Site-Directed
- Thermodynamics
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Affiliation(s)
- Silvia Lovera
- Department of Chemistry, University College London, London, United Kingdom
| | - Maria Morando
- Center of Technological Development in Health, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | | | | | - Giorgio Saladino
- Department of Chemistry, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- * E-mail: (GS); (FLG)
| | - Francesco L. Gervasio
- Department of Chemistry, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- * E-mail: (GS); (FLG)
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57
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Marino KA, Sutto L, Gervasio FL. The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase. J Am Chem Soc 2015; 137:5280-3. [PMID: 25868080 DOI: 10.1021/jacs.5b01421] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein kinases play a key role in regulating cellular processes. Kinase dysfunction can lead to disease, making them an attractive target for drug design. The B-Raf kinase is a key target for the treatment of melanoma since a single mutation (V600E) is found in more than 50% of all malignant melanomas. Despite the importance of B-Raf in melanoma treatment, the molecular mechanism by which the mutation increases kinase activity remains elusive. Since kinases are tightly regulated by a conformational transition between an active and inactive state, which is difficult to capture experimentally, large-scale enhanced-sampling simulations are performed to examine the mechanism by which the V600E mutation enhances the activity of the B-Raf monomer. The results reveal that the mutation has a twofold effect. First, the mutation increases the barrier of the active to inactive transition trapping B-Raf in the active state. The mutation also increases the flexibility of the activation loop which might speed-up the rate-limiting step of phosphorylation. Both effects can be explained by the formation of salt-bridges with the Glu600 residue.
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Affiliation(s)
| | - Ludovico Sutto
- Department of Chemistry, University College London, London, U.K
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