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Nagaraj A, Srinivasa Raghavan S, Niraikulam A, Gautham N, Gunasekaran K. Sanggenol B, a plant bioactive, as a safer alternative to tackle cancer by antagonising human FGFR. J Biomol Struct Dyn 2024; 42:8331-8342. [PMID: 37551114 DOI: 10.1080/07391102.2023.2245047] [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: 04/26/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Fibroblast Growth Receptor Factor (FGFR) are a family of proteins which are, in addition to their biological role, are involved in various pathological functions, such as cancer cellular proliferation, and metastasis. Deregulation of FGFRs at various points could result in malignancy. A conformational transition of the DFG (Asp-Phe-Gly) motif can switch the enzyme from a catalytically active (DFG-in) to an inactive (DFG-out) state. There are a few FDFR inhibitors which have received approval from the FDA, but these have adverse side effects. Hence, there is a demand for safer alternatives. With this aim, Ligand and Structure based virtual screening was carried to identify suitable lead molecule. In this process, Four Featured atom-based 3D Pharmacophore with quantitative structure-activity relationship analysis (3D-QSAR) was developed. The External validation of the hypothesis was carried invoking criteria such as Area under the ROC curve. Natural plant compound databases such as the Traditional Chinese medicine, NPACT and the ZINC Natural databases were chosen for pharmacophore filtering, which was followed by virtual screening against FGFR isoforms. The compound Sanggenol B was identified as the most suitable lead molecule. Structural stability of the protein-ligand complex and interactions of the ligand (Sanggenol B & the reference compound Ponatinib) with FGFR were analysed for 1000 ns (triplicate) by means of molecular simulation and the binding free energy was calculated using MMGBSA. Sanggenol B (PubChem CID: 15233694) binds effectively at the active site with favourable energies and is proposed as a safe alternative from a natural source.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Achyuta Nagaraj
- Department of Crystallography and Biophysics, University of Madras, Chennai, India
| | - Sriram Srinivasa Raghavan
- Department of Crystallography and Biophysics, University of Madras, Chennai, India
- RIKEN Centre for Computational Science, Kobe, Japan
| | - Ayyadurai Niraikulam
- Division of Biotechnology, Council of Scientific and Industrial Research-Central Leather Research Institute (CSIR-CLRI), Chennai, India
| | - Namasivayam Gautham
- Department of Crystallography and Biophysics, University of Madras, Chennai, India
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2
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Striedner Y, Arbeithuber B, Moura S, Nowak E, Reinhardt R, Muresan L, Salazar R, Ebner T, Tiemann-Boege I. Exploring the Micro-Mosaic Landscape of FGFR3 Mutations in the Ageing Male Germline and Their Potential Implications in Meiotic Differentiation. Genes (Basel) 2024; 15:191. [PMID: 38397181 PMCID: PMC10888257 DOI: 10.3390/genes15020191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Advanced paternal age increases the risk of transmitting de novo germline mutations, particularly missense mutations activating the receptor tyrosine kinase (RTK) signalling pathway, as exemplified by the FGFR3 mutation, which is linked to achondroplasia (ACH). This risk is attributed to the expansion of spermatogonial stem cells carrying the mutation, forming sub-clonal clusters in the ageing testis, thereby increasing the frequency of mutant sperm and the number of affected offspring from older fathers. While prior studies proposed a correlation between sub-clonal cluster expansion in the testis and elevated mutant sperm production in older donors, limited data exist on the universality of this phenomenon. Our study addresses this gap by examining the testis-expansion patterns, as well as the increases in mutations in sperm for two FGFR3 variants-c.1138G>A (p.G380R) and c.1948A>G (p.K650E)-which are associated with ACH or thanatophoric dysplasia (TDII), respectively. Unlike the ACH mutation, which showed sub-clonal expansion events in an aged testis and a significant increase in mutant sperm with the donor's age, as also reported in other studies, the TDII mutation showed focal mutation pockets in the testis but exhibited reduced transmission into sperm and no significant age-related increase. The mechanism behind this divergence remains unclear, suggesting potential pleiotropic effects of aberrant RTK signalling in the male germline, possibly hindering differentiation requiring meiosis. This study provides further insights into the transmission risks of micro-mosaics associated with advanced paternal age in the male germline.
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Affiliation(s)
- Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Sofia Moura
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Elisabeth Nowak
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Ronja Reinhardt
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 2EL, UK;
- Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
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3
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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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4
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Hartl I, Brumovska V, Striedner Y, Yasari A, Schütz GJ, Sevcsik E, Tiemann-Boege I. Measurement of FGFR3 signaling at the cell membrane via total internal reflection fluorescence microscopy to compare the activation of FGFR3 mutants. J Biol Chem 2023; 299:102832. [PMID: 36581204 PMCID: PMC9900515 DOI: 10.1016/j.jbc.2022.102832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) initiate signal transduction via the RAS/mitogen-activated protein kinase pathway by their tyrosine kinase activation known to determine cell growth, tissue differentiation, and apoptosis. Recently, many missense mutations have been reported for FGFR3, but we only know the functional effect for a handful of them. Some mutations result in aberrant FGFR3 signaling and are associated with various genetic disorders and oncogenic conditions. Here, we employed micropatterned surfaces to specifically enrich fluorophore-tagged FGFR3 (monomeric GFP [mGFP]-FGFR3) in certain areas of the plasma membrane of living cells. We quantified receptor activation via total internal reflection fluorescence microscopy of FGFR3 signaling at the cell membrane that captured the recruitment of the downstream signal transducer growth factor receptor-bound 2 (GRB2) tagged with mScarlet (GRB2-mScarlet) to FGFR3 micropatterns. With this system, we tested the activation of FGFR3 upon ligand addition (fgf1 and fgf2) for WT and four FGFR3 mutants associated with congenital disorders (G380R, Y373C, K650Q, and K650E). Our data showed that ligand addition increased GRB2 recruitment to WT FGFR3, with fgf1 having a stronger effect than fgf2. For all mutants, we found an increased basal receptor activity, and only for two of the four mutants (G380R and K650Q), activity was further increased upon ligand addition. Compared with previous reports, two mutant receptors (K650Q and K650E) had either an unexpectedly high or low activation state, respectively. This can be attributed to the different methodology, since micropatterning specifically captures signaling events at the plasma membrane. Collectively, our results provide further insight into the functional effects of mutations to FGFR3.
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Affiliation(s)
- Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Atena Yasari
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Eva Sevcsik
- Insitute of Applied Physics, TU Wien, Vienna, Austria.
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5
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Shvartsbart A, Roach JJ, Witten MR, Koblish H, Harris JJ, Covington M, Hess R, Lin L, Frascella M, Truong L, Leffet L, Conlen P, Beshad E, Klabe R, Katiyar K, Kaldon L, Young-Sciame R, He X, Petusky S, Chen KJ, Horsey A, Lei HT, Epling LB, Deller MC, Vechorkin O, Yao W. Discovery of Potent and Selective Inhibitors of Wild-Type and Gatekeeper Mutant Fibroblast Growth Factor Receptor (FGFR) 2/3. J Med Chem 2022; 65:15433-15442. [DOI: 10.1021/acs.jmedchem.2c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Jeremy J. Roach
- Proteovant Therapeutics, King of Prussia, Pennsylvania 19406, United States
| | | | - Holly Koblish
- Ikena Oncology, Boston, Massachusetts 02210, United States
| | | | | | - Rodrigo Hess
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Luping Lin
- WuXi AppTec, Philadelphia, Pennsylvania 19112, United States
| | | | - Lisa Truong
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Lynn Leffet
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Patricia Conlen
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Elham Beshad
- Proteovant Therapeutics, King of Prussia, Pennsylvania 19406, United States
| | - Ron Klabe
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Kamna Katiyar
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Laura Kaldon
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | | | - Xin He
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Susan Petusky
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Kwang-Jong Chen
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - April Horsey
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Hsiang-Ting Lei
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | | | - Marc C. Deller
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Oleg Vechorkin
- Incyte Corporation, Wilmington, Delaware 19803, United States
| | - Wenqing Yao
- Synnovation Therapeutics, Wilmington, Delaware 19803, United States
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6
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Ryu S, Nam Y, Kim N, Shin I, Jeon E, Kim Y, Kim ND, Sim T. Identification of Pyridinyltriazine Derivatives as Potent panFGFR Inhibitors against Gatekeeper Mutants for Overcoming Drug Resistance. J Med Chem 2022; 65:6017-6038. [PMID: 35436119 DOI: 10.1021/acs.jmedchem.1c01776] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although FGFR inhibitors hold promise in treating various cancers, resistance to the FGFR inhibitors caused by acquired secondary mutations has emerged. To discover novel FGFR inhibitors capable of inhibiting FGFR mutations, including gatekeeper mutations, we designed and synthesized several new pyridinyltriazine derivatives. A structure-activity relationship (SAR) study led to the identification of 17a as a highly potent panFGFR inhibitor against wild-type and mutant FGFRs. Notably, 17a is superior to infigratinib in terms of kinase-inhibitory and cellular activities, especially against V555M-FGFR3. Molecular dynamics simulations provide a clear understanding of why pyridinyltraizine derivative 17a possesses activity against V555M-FGFR3. Moreover, 17a significantly suppresses proliferation of cancer cells harboring FGFR mutations via FGFR signaling blockade, cell cycle arrest, and apoptosis. Furthermore, 17a and 17b exhibited remarkable efficacies in TEL-V555M-FGFR3 Ba/F3 xenograft mouse model and 17a is more efficacious than infigratinib. This study provides new insight into the design of novel FGFR inhibitors that are active against FGFR mutants.
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Affiliation(s)
- SeongShick Ryu
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yunju Nam
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Namkyoung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Injae Shin
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Eunhye Jeon
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Younghoon Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Nam Doo Kim
- Voronoibio Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.,Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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7
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Clay MC, Saleh T, Kamatham S, Rossi P, Kalodimos CG. Progress toward automated methyl assignments for methyl-TROSY applications. Structure 2022; 30:69-79.e2. [PMID: 34914892 PMCID: PMC8741727 DOI: 10.1016/j.str.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023]
Abstract
Methyl-TROSY spectroscopy has extended the reach of solution-state NMR to supra-molecular machineries over 100 kDa in size. Methyl groups are ideal probes for studying structure, dynamics, and protein-protein interactions in quasi-physiological conditions with atomic resolution. Successful implementation of the methodology requires accurate methyl chemical shift assignment, and the task still poses a significant challenge in the field. In this work, we outline the current state of technology for methyl labeling, data collection, data analysis, and nuclear Overhauser effect (NOE)-based automated methyl assignment approaches. We present MAGIC-Act and MAGIC-View, two Python extensions developed as part of the popular NMRFAM-Sparky package, and MAGIC-Net a standalone structure-based network analysis program. MAGIC-Act conducts statistically driven amino acid typing, Leu/Val pairing guided by 3D HMBC-HMQC, and NOESY cross-peak symmetry checking. MAGIC-Net provides model-based NOE statistics to aid in selection of a methyl labeling scheme. The programs provide a versatile, semi-automated framework for rapid methyl assignment.
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Affiliation(s)
- Mary C. Clay
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tamjeed Saleh
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Samuel Kamatham
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Paolo Rossi
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Corresponding authors: ,
| | - Charalampos G. Kalodimos
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Lead Contact,Corresponding authors: ,
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8
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Aitcheson G, Mahipal A, John BV. Targeting FGFR in intrahepatic cholangiocarcinoma [iCCA]: leading the way for precision medicine in biliary tract cancer [BTC]? Expert Opin Investig Drugs 2021; 30:463-477. [PMID: 33678096 DOI: 10.1080/13543784.2021.1900821] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: The increasing availability of next-generation DNA sequencing (NGS) opens the opportunity to tailor therapies to potential targets. Intrahepatic cholangiocarcinoma (iCCA) has the most actionable genomic targets of the hepatobiliary malignancies, including mutations in Isocitrate Dehydrogenase (IDH) and Fibroblast Growth Factor Receptor (FGFR), particularly FGFR2. With the recent accelerated approval of pemigatinib and several trials currently underway, FGFR2 inhibition will set the mold for tailored therapies in hepatobiliary cancer.Areas covered: We review the current standard of therapy for iCCA, the genomic targets, and the role of FGFR inhibitors in developing the treatment landscape. The FGFR mechanism of actionand use of IDH1/2 inhibition and immunotherapy in iCCA are also discussed. We queried the PubMed and ClinicalTrials.gov databases, along with conference proceedings for relevant data.Expert opinion: While more mature data are needed from the trials in progress, currently published analyses show survival benefit with FGFR2 inhibitors in patients positive for FGFR2 fusion who have failed the standard of care. Infigratinib, futibatinib, pemigatinib and derazantinib have all demonstrated promising activity iCCA patients harboring FGFR2 fusion. Eventually, head-to-head trials will be needed to fully understand the benefits of each agent and the role of reversible versus irreversible FGFR2 inhibitors.
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Affiliation(s)
| | - Amit Mahipal
- Division of Hematology and Oncology, Mayo Clinic, Rochester, MN, USA
| | - Binu V John
- Division of Hepatology, Bruce W Carter VA Medical Center, Miami, FL, USA.,Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
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9
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Abstract
The identification of mutations in FGFR3 in bladder tumors in 1999 led to major interest in this receptor and during the subsequent 20 years much has been learnt about the mutational profiles found in bladder cancer, the phenotypes associated with these and the potential of this mutated protein as a target for therapy. Based on mutational and expression data, it is estimated that >80% of non-muscle-invasive bladder cancers (NMIBC) and ∼40% of muscle-invasive bladder cancers (MIBC) have upregulated FGFR3 signalling, and these frequencies are likely to be even higher if alternative splicing of the receptor, expression of ligands and changes in regulatory mechanisms are taken into account. Major efforts by the pharmaceutical industry have led to development of a range of agents targeting FGFR3 and other FGF receptors. Several of these have entered clinical trials, and some have presented very encouraging early results in advanced bladder cancer. Recent reviews have summarised the drugs and related clinical trials in this area. This review will summarise what is known about the effects of FGFR3 and its mutant forms in normal urothelium and bladder tumors, will suggest when and how this protein contributes to urothelial cancer pathogenesis and will highlight areas that may benefit from further study.
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Affiliation(s)
- Margaret A. Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Leeds LS9 7TF, UK
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10
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Silverman IM, Hollebecque A, Friboulet L, Owens S, Newton RC, Zhen H, Féliz L, Zecchetto C, Melisi D, Burn TC. Clinicogenomic Analysis of FGFR2-Rearranged Cholangiocarcinoma Identifies Correlates of Response and Mechanisms of Resistance to Pemigatinib. Cancer Discov 2020; 11:326-339. [PMID: 33218975 DOI: 10.1158/2159-8290.cd-20-0766] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/16/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
Pemigatinib, a selective FGFR1-3 inhibitor, has demonstrated antitumor activity in FIGHT-202, a phase II study in patients with cholangiocarcinoma harboring FGFR2 fusions/rearrangements, and has gained regulatory approval in the United States. Eligibility for FIGHT-202 was assessed using genomic profiling; here, these data were utilized to characterize the genomic landscape of cholangiocarcinoma and to uncover unique molecular features of patients harboring FGFR2 rearrangements. The results highlight the high percentage of patients with cholangiocarcinoma harboring potentially actionable genomic alterations and the diversity in gene partners that rearrange with FGFR2. Clinicogenomic analysis of pemigatinib-treated patients identified mechanisms of primary and acquired resistance. Genomic subsets of patients with other potentially actionable FGF/FGFR alterations were also identified. Our study provides a framework for molecularly guided clinical trials and underscores the importance of genomic profiling to enable a deeper understanding of the molecular basis for response and nonresponse to targeted therapy. SIGNIFICANCE: We utilized genomic profiling data from FIGHT-202 to gain insights into the genomic landscape of cholangiocarcinoma, to understand the molecular diversity of patients with FGFR2 fusions or rearrangements, and to interrogate the clinicogenomics of patients treated with pemigatinib. Our study highlights the utility of genomic profiling in clinical trials.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
| | | | | | | | | | | | - Luis Féliz
- Incyte Biosciences International Sàrl, Morges, Switzerland
| | - Camilla Zecchetto
- Digestive Molecular Clinical Oncology Research Unit, Section of Medical Oncology, Università degli Studi di Verona, Verona, Italy
| | - Davide Melisi
- Digestive Molecular Clinical Oncology Research Unit, Section of Medical Oncology, Università degli Studi di Verona, Verona, Italy
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11
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Schittenhelm J, Ziegler L, Sperveslage J, Mittelbronn M, Capper D, Burghardt I, Poso A, Biskup S, Skardelly M, Tabatabai G. FGFR3 overexpression is a useful detection tool for FGFR3 fusions and sequence variations in glioma. Neurooncol Pract 2020; 8:209-221. [PMID: 33898054 DOI: 10.1093/nop/npaa075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Fibroblast growth factor receptor (FGFR) inhibitors are currently used in clinical development. A subset of glioblastomas carries gene fusion of FGFR3 and transforming acidic coiled-coil protein 3. The prevalence of other FGFR3 alterations in glioma is currently unclear. Methods We performed RT-PCR in 101 glioblastoma samples to detect FGFR3-TACC3 fusions ("RT-PCR cohort") and correlated results with FGFR3 immunohistochemistry (IHC). Further, we applied FGFR3 IHC in 552 tissue microarray glioma samples ("TMA cohort") and validated these results in two external cohorts with 319 patients. Gene panel sequencing was carried out in 88 samples ("NGS cohort") to identify other possible FGFR3 alterations. Molecular modeling was performed on newly detected mutations. Results In the "RT-PCR cohort," we identified FGFR3-TACC3 fusions in 2/101 glioblastomas. Positive IHC staining was observed in 73/1024 tumor samples of which 10 were strongly positive. In the "NGS cohort," we identified FGFR3 fusions in 9/88 cases, FGFR3 amplification in 2/88 cases, and FGFR3 gene mutations in 7/88 cases in targeted sequencing. All FGFR3 fusions and amplifications and a novel FGFR3 K649R missense mutation were associated with FGFR3 overexpression (sensitivity and specificity of 93% and 95%, respectively, at cutoff IHC score > 7). Modeling of these data indicated that Tyr647, a residue phosphorylated as a part of FGFR3 activation, is affected by the K649R mutation. Conclusions FGFR3 IHC is a useful screening tool for the detection of FGFR3 alterations and could be included in the workflow for isocitrate dehydrogenase (IDH) wild-type glioma diagnostics. Samples with positive FGFR3 staining could then be selected for NGS-based diagnostic tools.
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Affiliation(s)
- Jens Schittenhelm
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,Department of Neuropathology, Institute of Pathology and Neuropathology, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Lukas Ziegler
- Department of Neuropathology, Institute of Pathology and Neuropathology, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Jan Sperveslage
- Department of Pathology, Institute of Pathology and Neuropathology, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Michel Mittelbronn
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg.,Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.,National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg.,Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Edinger Institute (Neurological Institute), University of Frankfurt, Frankfurt, Germany
| | - David Capper
- Institute of Neuropathology, Berlin Institute of Health, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Isabel Burghardt
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,Department of Neurology & Interdisciplinary Neurooncology, University Hospital Tübingen, Hertie-Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tuebingen, Germany
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, Germany
| | - Marco Skardelly
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,Department of Neurosurgery, University Hospital of Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ghazaleh Tabatabai
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,Department of Neurology & Interdisciplinary Neurooncology, University Hospital Tübingen, Hertie-Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tuebingen, Germany.,Center for Personalized Medicine, Eberhard Karls University of Tuebingen, Tuebingen, Germany.,German Consortium for Translational Cancer Research (DKTK), DKFZ partner site Tuebingen, Tuebingen, Germany
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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: 6.5] [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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Wang Y, Dai Y, Wu X, Li F, Liu B, Li C, Liu Q, Zhou Y, Wang B, Zhu M, Cui R, Tan X, Xiong Z, Liu J, Tan M, Xu Y, Geng M, Jiang H, Liu H, Ai J, Zheng M. Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design. J Med Chem 2019; 62:7473-7488. [DOI: 10.1021/acs.jmedchem.9b00510] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | - Fei Li
- School of Chemistry, Shanghai University, 99 ShangDa Road, Shanghai 200444, China
| | | | | | | | - Yuanyang Zhou
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bao Wang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 200031, China
| | | | | | - Xiaoqin Tan
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhaoping Xiong
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 200031, China
| | | | | | | | | | - Hualiang Jiang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 200031, China
| | | | - Jing Ai
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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14
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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: 13] [Impact Index Per Article: 2.6] [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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15
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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: 74] [Impact Index Per Article: 12.3] [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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16
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Sanfelice D, Koss H, Bunney TD, Thompson GS, Farrell B, Katan M, Breeze AL. NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 3 in apo state and in complex with inhibitor PD173074. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:231-235. [PMID: 29582384 PMCID: PMC6132846 DOI: 10.1007/s12104-018-9814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/20/2018] [Indexed: 05/03/2023]
Abstract
Fibroblast growth factors receptors (FGFR) are transmembrane protein tyrosine kinases involved in many cellular process, including growth, differentiation and angiogenesis. Dysregulation of FGFR enzymatic activity is associated with developmental disorders and cancers; therefore FGFRs have become attractive targets for drug discovery, with a number of agents in late-stage clinical trials. Here, we present the backbone resonance assignments of FGFR3 tyrosine kinase domain in the ligand-free form and in complex with the canonical FGFR kinase inhibitor PD173074. Analysis of chemical shift changes upon inhibitor binding highlights a characteristic pattern of allosteric network perturbations that is of relevance for future drug discovery activities aimed at development of conformationally-selective FGFR inhibitors.
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Affiliation(s)
- Domenico Sanfelice
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London, WC1E 6BT, UK.
| | - Hans Koss
- 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
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Wellcome Trust Biomolecular NMR Facility, School of Biosciences, University of Kent, Canterbury, CT2 7NZ, UK
| | - Brendan Farrell
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London, WC1E 6BT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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17
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Zinkle A, Mohammadi M. A threshold model for receptor tyrosine kinase signaling specificity and cell fate determination. F1000Res 2018; 7:F1000 Faculty Rev-872. [PMID: 29983915 PMCID: PMC6013765 DOI: 10.12688/f1000research.14143.1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 11/20/2022] Open
Abstract
Upon ligand engagement, the single-pass transmembrane receptor tyrosine kinases (RTKs) dimerize to transmit qualitatively and quantitatively different intracellular signals that alter the transcriptional landscape and thereby determine the cellular response. The molecular mechanisms underlying these fundamental events are not well understood. Considering recent insights into the structural biology of fibroblast growth factor signaling, we propose a threshold model for RTK signaling specificity in which quantitative differences in the strength/longevity of ligand-induced receptor dimers on the cell surface lead to quantitative differences in the phosphorylation of activation loop (A-loop) tyrosines as well as qualitative differences in the phosphorylation of tyrosines mediating substrate recruitment. In this model, quantitative differences on A-loop tyrosine phosphorylation result in gradations in kinase activation, leading to the generation of intracellular signals of varying amplitude/duration. In contrast, qualitative differences in the pattern of tyrosine phosphorylation on the receptor result in the recruitment/activation of distinct substrates/intracellular pathways. Commensurate with both the dynamics of the intracellular signal and the types of intracellular pathways activated, unique transcriptional signatures are established. Our model provides a framework for engineering clinically useful ligands that can tune receptor dimerization stability so as to bias the cellular transcriptome to achieve a desired cellular output.
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Affiliation(s)
- Allen Zinkle
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Moosa Mohammadi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
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18
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Bunney TD, Inglis AJ, Sanfelice D, Farrell B, Kerr CJ, Thompson GS, Masson GR, Thiyagarajan N, Svergun DI, Williams RL, Breeze AL, Katan M. Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System. Structure 2018; 26:446-458.e8. [PMID: 29478821 PMCID: PMC5846801 DOI: 10.1016/j.str.2018.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/06/2017] [Accepted: 01/26/2018] [Indexed: 11/21/2022]
Abstract
Receptor tyrosine kinase FGFR3 is involved in many signaling networks and is frequently mutated in developmental disorders and cancer. The Hsp90/Cdc37 chaperone system is essential for function of normal and neoplastic cells. Here we uncover the mechanistic inter-relationships between these proteins by combining approaches including NMR, HDX-MS, and SAXS. We show that several disease-linked mutations convert FGFR3 to a stronger client, where the determinant underpinning client strength involves an allosteric network through the N-lobe and at the lobe interface. We determine the architecture of the client kinase/Cdc37 complex and demonstrate, together with site-specific information, that binding of Cdc37 to unrelated kinases induces a common, extensive conformational remodeling of the kinase N-lobe, beyond localized changes and interactions within the binary complex. As further shown for FGFR3, this processing by Cdc37 deactivates the kinase and presents it, in a specific orientation established in the complex, for direct recognition by Hsp90.
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Affiliation(s)
- Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK.
| | - Alison J Inglis
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Domenico Sanfelice
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Brendan Farrell
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, UK
| | - Christopher J Kerr
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, UK
| | - Glenn R Masson
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany
| | - Roger L Williams
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, 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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19
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Montone R, Romanelli MG, Baruzzi A, Ferrarini F, Liboi E, Lievens PMJ. Mutant FGFR3 associated with SADDAN disease causes cytoskeleton disorganization through PLCγ1/Src-mediated paxillin hyperphosphorylation. Int J Biochem Cell Biol 2017; 95:17-26. [PMID: 29242050 DOI: 10.1016/j.biocel.2017.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/15/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
K650M/E substitutions in the Fibroblast growth factor receptor 3 (FGFR3) are associated with Severe Achondroplasia with Developmental Delay and Acanthosis Nigricans (SADDAN) and Thanatophoric Dysplasia type II (TDII), respectively. Both SADDAN and TDII present with affected endochondral ossification marked by impaired chondrocyte functions and growth plate disorganization. In vitro, K650M/E substitutions confer FGFR3 constitutive kinase activity leading to impaired biosynthesis and accumulation of immature receptors in endoplasmic reticulum (ER)/Golgi. From those compartments, both SADDAN-FGFR3 and TDII-FGFR3 receptors engender uncontrolled signalling, activating PLCγ1, signal transducer and activator of transcription 1, 3 and 5 (STAT1/3/5) and ERK1/2 effectors. Here, we investigated the impact of SADDAN-FGFR3 and TDII-FGFR3 signalling on cytoskeletal organization. We report that SADDAN-FGFR3, but not TDII-FGFR3, affects F-actin organization by inducing tyrosine hyperphosphorylation of paxillin, a key regulator of focal adhesions and actin dynamics. Paxillin phosphorylation was upregulated at tyrosine 118, a functional target of Src and FAK kinases. By using Src-deficient cells and a Src kinase inhibitor, we established a role played by Src activation in paxillin hyperphosphorylation. Moreover, we found that SADDAN-FGFR3 induced FAK phosphorylation at tyrosines 576/577, suggesting its involvement as a Src co-activator in paxillin phosphorylation. Interestingly, paxillin hyperphosphorylation by SADDAN-FGFR3 caused paxillin mislocalization and partial co-localization with the mutant receptor. Finally, the SADDAN-FGFR3 double mutant unable to bind PLCγ1 failed to promote paxillin hyperphosphorylation, pointing to PLCγ1 as an early player in mediating paxillin alterations. Overall, our findings contribute to elucidate the molecular mechanism leading to cell dysfunctions caused by SADDAN-FGFR3 signalling.
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Affiliation(s)
- R Montone
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona Medical School, Verona, Italy
| | - M G Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona Medical School, Verona, Italy
| | - A Baruzzi
- Department of Pathology and Diagnostics, University of Verona Medical School, Verona, Italy
| | - F Ferrarini
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona Medical School, Verona, Italy
| | - E Liboi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona Medical School, Verona, Italy
| | - P M-J Lievens
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona Medical School, Verona, Italy.
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20
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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: 1.1] [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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21
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Goyal L, Saha SK, Liu LY, Siravegna G, Leshchiner I, Ahronian LG, Lennerz JK, Vu P, Deshpande V, Kambadakone A, Mussolin B, Reyes S, Henderson L, Sun JE, Van Seventer EE, Gurski JM, Baltschukat S, Schacher-Engstler B, Barys L, Stamm C, Furet P, Ryan DP, Stone JR, Iafrate AJ, Getz G, Porta DG, Tiedt R, Bardelli A, Juric D, Corcoran RB, Bardeesy N, Zhu AX. Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2017; 7:252-263. [PMID: 28034880 PMCID: PMC5433349 DOI: 10.1158/2159-8290.cd-16-1000] [Citation(s) in RCA: 377] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 12/16/2022]
Abstract
Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter- and intralesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies.Significance: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target. Cancer Discov; 7(3); 252-63. ©2016 AACR.See related commentary by Smyth et al., p. 248This article is highlighted in the In This Issue feature, p. 235.
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MESH Headings
- Adult
- Antineoplastic Agents/therapeutic use
- Bile Duct Neoplasms/drug therapy
- Bile Duct Neoplasms/genetics
- Bile Duct Neoplasms/pathology
- Cell Cycle Proteins
- Cholangiocarcinoma/drug therapy
- Cholangiocarcinoma/genetics
- Cholangiocarcinoma/pathology
- Circulating Tumor DNA/genetics
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Fusion
- Humans
- Male
- Membrane Transport Proteins
- Middle Aged
- Mutation
- Phenylurea Compounds/therapeutic use
- Pyrimidines/therapeutic use
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/chemistry
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 3/chemistry
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factor TFIIIA/genetics
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Affiliation(s)
- Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Leah Y Liu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Leanne G Ahronian
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Avinash Kambadakone
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Stephanie Reyes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Laura Henderson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jiaoyuan Elisabeth Sun
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Joseph M Gurski
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | | | - Louise Barys
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - David P Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Translational Research, Basel, Switzerland
| | - Alberto Bardelli
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Torino, Italy
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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22
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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: 5.6] [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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23
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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: 4] [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: 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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24
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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: 4.4] [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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25
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di Martino E, Tomlinson DC, Williams SV, Knowles MA. A place for precision medicine in bladder cancer: targeting the FGFRs. Future Oncol 2016; 12:2243-63. [PMID: 27381494 DOI: 10.2217/fon-2016-0042] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bladder tumors show diverse molecular features and clinical outcome. Muscle-invasive bladder cancer has poor prognosis and novel approaches to systemic therapy are urgently required. Non-muscle-invasive bladder cancer has good prognosis, but high recurrence rate and the requirement for life-long disease monitoring places a major burden on patients and healthcare providers. Studies of tumor tissues from both disease groups have identified frequent alterations of FGFRs, including mutations of FGFR3 and dysregulated expression of FGFR1 and FGFR3 that suggest that these may be valid therapeutic targets. We summarize current understanding of the molecular alterations affecting these receptors in bladder tumors, preclinical studies validating them as therapeutic targets, available FGFR-targeted agents and results from early clinical trials in bladder cancer patients.
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Affiliation(s)
- Erica di Martino
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural & Molecular Biology, School of Molecular & Cellular Biology, Astbury Building, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah V Williams
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Margaret A Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
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26
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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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27
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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: 0.4] [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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28
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Ichiyama S, Funasaka Y, Otsuka Y, Takayama R, Kawana S, Saeki H, Kubo A. Effective treatment by glycolic acid peeling for cutaneous manifestation of familial generalized acanthosis nigricans caused by FGFR3 mutation. J Eur Acad Dermatol Venereol 2016; 30:442-5. [PMID: 26818779 DOI: 10.1111/jdv.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/27/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Acanthosis nigricans (AN) can occur as a cutaneous manifestation of genetic diseases, one of which is associated with activating mutations of the fibroblast growth factor receptor 3 gene (FGFR3). OBJECTIVE We explored familial AN patients with FGFR3 mutations and examined the effectiveness of glycolic acid (GA) peeling in improving their skin manifestations. METHODS Sanger sequencing was performed for the genomic DNA extracted from leucocytes of the family members involving familial AN. GA peeling was carried out for the two patients of familial AN once every 2 weeks. RESULTS Heterozygous c.1949A>C (p.K650T) mutation in FGFR3 was identified for the affected family members examined, whereas the wild-type sequence was found for two unaffected individuals. Hyperpigmentation and coarseness of the skin were improved by GA peeling at regular intervals with few adverse effects. CONCLUSION We diagnosed our cases as familial generalized AN caused by heterozygous c.1949A>C (p.K650T) mutation of FGFR3. We propose that GA peeling is a useful and safe therapeutic option to treat familial AN.
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Affiliation(s)
- S Ichiyama
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - Y Funasaka
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - Y Otsuka
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - R Takayama
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - S Kawana
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - H Saeki
- Department of Dermatology, Nippon Medical School Hospital, Tokyo, Japan
| | - A Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
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29
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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: 3.2] [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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30
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Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Sci Signal 2015; 8:rs13. [PMID: 26628682 DOI: 10.1126/scisignal.aaa6711] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kimberly L Malecka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lauren Fink
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - E Joseph Jordan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Duffy
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Samuel Kolander
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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31
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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: 41] [Impact Index Per Article: 4.6] [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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32
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St-Germain JR, Taylor P, Zhang W, Li Z, Ketela T, Moffat J, Neel BG, Trudel S, Moran MF. Differential regulation of FGFR3 by PTPN1 and PTPN2. Proteomics 2014; 15:419-33. [PMID: 25311528 DOI: 10.1002/pmic.201400259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/04/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
Aberrant expression and activation of FGFR3 is associated with disease states including bone dysplasia and malignancies of bladder, cervix, and bone marrow. MS analysis of protein-phosphotyrosine in multiple myeloma cells revealed a prevalent phosphorylated motif, D/EYYR/K, derived from the kinase domain activation loops of tyrosine kinases including FGFR3 corresponding to a recognition sequence of protein-tyrosine phosphatase PTPN1. Knockdown of PTPN1 or the related enzyme PTPN2 by RNAi resulted in ligand-independent activation of FGFR3. Modulation of FGFR3 activation loop phosphorylation by both PTPN1 and PTPN2 was a function of receptor trafficking and phosphotyrosine phosphatase (PTP) compartmentalization. The FGFR3 activation loop motif DYYKK(650) is altered to DYYKE(650) in the oncogenic variant FGFR3(K650E) , and consequently it is constitutively fully activated and unaffected by activation loop phosphorylation. FGFR3(K650E) was nevertheless remarkably sensitive to negative regulation by PTPN1 and PTPN2. This suggests that in addition to modulating FGFR3 phosphorylation, PTPN1 and PTPN2 constrain the kinase domain by fostering an inactive-state. Loss of this constraint in response to ligand or impaired PTPN1/N2 may initiate FGFR3 activation. These results suggest a model wherein PTP expression levels may define conditions that select for ectopic FGFR3 expression and activation during tumorigenesis.
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Affiliation(s)
- Jonathan R St-Germain
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Canada
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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: 81] [Impact Index Per Article: 8.1] [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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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: 3.5] [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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Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors. Proc Natl Acad Sci U S A 2014; 111:E4869-77. [PMID: 25349422 DOI: 10.1073/pnas.1403438111] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The human FGF receptors (FGFRs) play critical roles in various human cancers, and several FGFR inhibitors are currently under clinical investigation. Resistance usually results from selection for mutant kinases that are impervious to the action of the drug or from up-regulation of compensatory signaling pathways. Preclinical studies have demonstrated that resistance to FGFR inhibitors can be acquired through mutations in the FGFR gatekeeper residue, as clinically observed for FGFR4 in embryonal rhabdomyosarcoma and neuroendocrine breast carcinomas. Here we report on the use of a structure-based drug design to develop two selective, next-generation covalent FGFR inhibitors, the FGFR irreversible inhibitors 2 (FIIN-2) and 3 (FIIN-3). To our knowledge, FIIN-2 and FIIN-3 are the first inhibitors that can potently inhibit the proliferation of cells dependent upon the gatekeeper mutants of FGFR1 or FGFR2, which confer resistance to first-generation clinical FGFR inhibitors such as NVP-BGJ398 and AZD4547. Because of the conformational flexibility of the reactive acrylamide substituent, FIIN-3 has the unprecedented ability to inhibit both the EGF receptor (EGFR) and FGFR covalently by targeting two distinct cysteine residues. We report the cocrystal structure of FGFR4 with FIIN-2, which unexpectedly exhibits a "DFG-out" covalent binding mode. The structural basis for dual FGFR and EGFR targeting by FIIN3 also is illustrated by crystal structures of FIIN-3 bound with FGFR4 V550L and EGFR L858R. These results have important implications for the design of covalent FGFR inhibitors that can overcome clinical resistance and provide the first example, to our knowledge, of a kinase inhibitor that covalently targets cysteines located in different positions within the ATP-binding pocket.
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Structure-functional prediction and analysis of cancer mutation effects in protein kinases. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:653487. [PMID: 24817905 PMCID: PMC4000980 DOI: 10.1155/2014/653487] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 12/31/2013] [Accepted: 02/28/2014] [Indexed: 12/17/2022]
Abstract
A central goal of cancer research is to discover and characterize the functional effects of mutated genes that contribute to tumorigenesis. In this study, we provide a detailed structural classification and analysis of functional dynamics for members of protein kinase families that are known to harbor cancer mutations. We also present a systematic computational analysis that combines sequence and structure-based prediction models to characterize the effect of cancer mutations in protein kinases. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinase-inactivating mutations that decrease activity. Mapping of cancer mutations onto the conformational mobility profiles of known crystal structures demonstrated that activating mutations could reduce a steric barrier for the movement from the basal “low” activity state to the “active” state. According to our analysis, the mechanism of activating mutations reflects a combined effect of partial destabilization of the kinase in its inactive state and a concomitant stabilization of its active-like form, which is likely to drive tumorigenesis at some level. Ultimately, the analysis of the evolutionary and structural features of the major cancer-causing mutational hotspot in kinases can also aid in the correlation of kinase mutation effects with clinical outcomes.
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