1
|
Gędaj A, Gregorczyk P, Żukowska D, Chorążewska A, Ciura K, Kalka M, Porębska N, Opaliński Ł. Glycosylation of FGF/FGFR: An underrated sweet code regulating cellular signaling programs. Cytokine Growth Factor Rev 2024; 77:39-55. [PMID: 38719671 DOI: 10.1016/j.cytogfr.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 06/22/2024]
Abstract
Fibroblast growth factors (FGFs) and their receptors (FGFRs) constitute plasma-membrane localized signaling hubs that transmit signals from the extracellular environment to the cell interior, governing pivotal cellular processes like motility, metabolism, differentiation, division and death. FGF/FGFR signaling is critical for human body development and homeostasis; dysregulation of FGF/FGFR units is observed in numerous developmental diseases and in about 10% of human cancers. Glycosylation is a highly abundant posttranslational modification that is critical for physiological and pathological functions of the cell. Glycosylation is also very common within FGF/FGFR signaling hubs. Vast majority of FGFs (15 out of 22 members) are N-glycosylated and few FGFs are O-glycosylated. Glycosylation is even more abundant within FGFRs; all FGFRs are heavily N-glycosylated in numerous positions within their extracellular domains. A growing number of studies points on the multiple roles of glycosylation in fine-tuning FGF/FGFR signaling. Glycosylation modifies secretion of FGFs, determines their stability and affects interaction with FGFRs and co-receptors. Glycosylation of FGFRs determines their intracellular sorting, constitutes autoinhibitory mechanism within FGFRs and adjusts FGF and co-receptor recognition. Sugar chains attached to FGFs and FGFRs constitute also a form of code that is differentially decrypted by extracellular lectins, galectins, which transform FGF/FGFR signaling at multiple levels. This review focuses on the identified functions of glycosylation within FGFs and FGFRs and discusses their relevance for the cell physiology in health and disease.
Collapse
Affiliation(s)
- Aleksandra Gędaj
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Paulina Gregorczyk
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Dominika Żukowska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Aleksandra Chorążewska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Krzysztof Ciura
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Marta Kalka
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Natalia Porębska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Łukasz Opaliński
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland.
| |
Collapse
|
2
|
Lian Y, Bodian D, Shehu A. Elucidating the Role of Wildtype and Variant FGFR2 Structural Dynamics in (Dys)Function and Disorder. Int J Mol Sci 2024; 25:4523. [PMID: 38674107 PMCID: PMC11050683 DOI: 10.3390/ijms25084523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The fibroblast growth factor receptor 2 (FGFR2) gene is one of the most extensively studied genes with many known mutations implicated in several human disorders, including oncogenic ones. Most FGFR2 disease-associated gene mutations are missense mutations that result in constitutive activation of the FGFR2 protein and downstream molecular pathways. Many tertiary structures of the FGFR2 kinase domain are publicly available in the wildtype and mutated forms and in the inactive and activated state of the receptor. The current literature suggests a molecular brake inhibiting the ATP-binding A loop from adopting the activated state. Mutations relieve this brake, triggering allosteric changes between active and inactive states. However, the existing analysis relies on static structures and fails to account for the intrinsic structural dynamics. In this study, we utilize experimentally resolved structures of the FGFR2 tyrosine kinase domain and machine learning to capture the intrinsic structural dynamics, correlate it with functional regions and disease types, and enrich it with predicted structures of variants with currently no experimentally resolved structures. Our findings demonstrate the value of machine learning-enabled characterizations of structure dynamics in revealing the impact of mutations on (dys)function and disorder in FGFR2.
Collapse
Affiliation(s)
- Yiyang Lian
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA;
| | - Dale Bodian
- Diamond Age Data Science, Boston, MA 02143, USA;
| | - Amarda Shehu
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA;
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
| |
Collapse
|
3
|
Katoh M, Loriot Y, Brandi G, Tavolari S, Wainberg ZA, Katoh M. FGFR-targeted therapeutics: clinical activity, mechanisms of resistance and new directions. Nat Rev Clin Oncol 2024; 21:312-329. [PMID: 38424198 DOI: 10.1038/s41571-024-00869-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Fibroblast growth factor (FGF) signalling via FGF receptors (FGFR1-4) orchestrates fetal development and contributes to tissue and whole-body homeostasis, but can also promote tumorigenesis. Various agents, including pan-FGFR inhibitors (erdafitinib and futibatinib), FGFR1/2/3 inhibitors (infigratinib and pemigatinib), as well as a range of more-specific agents, have been developed and several have entered clinical use. Erdafitinib is approved for patients with urothelial carcinoma harbouring FGFR2/3 alterations, and futibatinib and pemigatinib are approved for patients with cholangiocarcinoma harbouring FGFR2 fusions and/or rearrangements. Clinical benefit from these agents is in part limited by hyperphosphataemia owing to off-target inhibition of FGFR1 as well as the emergence of resistance mutations in FGFR genes, activation of bypass signalling pathways, concurrent TP53 alterations and possibly epithelial-mesenchymal transition-related isoform switching. The next generation of small-molecule inhibitors, such as lirafugratinib and LOXO-435, and the FGFR2-specific antibody bemarituzumab are expected to have a reduced risk of hyperphosphataemia and the ability to overcome certain resistance mutations. In this Review, we describe the development and current clinical role of FGFR inhibitors and provide perspective on future research directions including expansion of the therapeutic indications for use of FGFR inhibitors, combination of these agents with immune-checkpoint inhibitors and the application of novel technologies, such as artificial intelligence.
Collapse
Affiliation(s)
| | - Yohann Loriot
- Drug Development Department (DITEP), Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U981, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Giovanni Brandi
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Simona Tavolari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Zev A Wainberg
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Masaru Katoh
- M & M Precision Medicine, Tokyo, Japan.
- Department of Omics Network, National Cancer Center, Tokyo, Japan.
| |
Collapse
|
4
|
Spahn S, Kleinhenz F, Shevchenko E, Stahl A, Rasen Y, Geisler C, Ruhm K, Klaumuenzer M, Kronenberger T, Laufer SA, Sundberg-Malek H, Bui KC, Horger M, Biskup S, Schulze-Osthoff K, Templin M, Malek NP, Poso A, Bitzer M. The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma. Nat Commun 2024; 15:1287. [PMID: 38346946 PMCID: PMC10861557 DOI: 10.1038/s41467-024-45247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Fibroblast growth factor receptor (FGFR)-2 can be inhibited by FGFR-selective or non-selective tyrosine kinase inhibitors (TKIs). Selective TKIs are approved for cholangiocarcinoma (CCA) with FGFR2 fusions; however, their application is limited by a characteristic pattern of adverse events or evocation of kinase domain mutations. A comprehensive characterization of a patient cohort treated with the non-selective TKI lenvatinib reveals promising efficacy in FGFR2-driven CCA. In a bed-to-bench approach, we investigate FGFR2 fusion proteins bearing critical tumor-relevant point mutations. These mutations confer growth advantage of tumor cells and increased resistance to selective TKIs but remain intriguingly sensitive to lenvatinib. In line with clinical observations, in-silico analyses reveal a more favorable interaction pattern of lenvatinib with FGFR2, including an increased flexibility and ligand efficacy, compared to FGFR-selective TKIs. Finally, the treatment of a patient with progressive disease and a newly developed kinase mutation during therapy with a selective inhibitor results in a striking response to lenvatinib. Our in vitro, in silico, and clinical data suggest that lenvatinib is a promising treatment option for FGFR2-driven CCA, especially when insurmountable adverse reactions of selective TKIs or acquired kinase mutations occur.
Collapse
Affiliation(s)
- Stephan Spahn
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
| | - Fabian Kleinhenz
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Aaron Stahl
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Yvonne Rasen
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Christine Geisler
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | | | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Holly Sundberg-Malek
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Khac Cuong Bui
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Marius Horger
- Department of Diagnostic and Interventional Radiology, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik, 72076, Tuebingen, Germany
| | - Klaus Schulze-Osthoff
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Nisar P Malek
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany.
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany.
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany.
| |
Collapse
|
5
|
Zhang Y, Yin XL, Ji M, Chen Y, Chai Z. Decoupling the dynamic mechanism revealed by FGFR2 mutation-induced population shift. J Biomol Struct Dyn 2024; 42:1940-1951. [PMID: 37254996 DOI: 10.1080/07391102.2023.2217924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
The fibroblast growth factor receptor 2 (FGFR2) is a key component in cellular signaling networks, and its dysfunctional activation has been implicated in various diseases including cancer and developmental disorders. Mutations at the activation loop (A-loop) have been suggested to trigger an increased basal kinase activity. However, the molecular mechanism underlying this highly dynamic process has not been fully understood due to the limitation of static structural information. Here, we conducted multiple, large-scale Gaussian accelerated molecular dynamics simulations of five (K659E, K659N, K659M, K659Q, and K659T) FGFR2 mutants at the A-loop, and comprehensively analyzed the dynamic molecular basis of FGFR2 activation. The results quantified the population shift of each system, revealing that all mutants had a higher proportion of active-like states. Using Markov state models, we extracted the representative structure of different conformational states and identified key residues related to the increased kinase activity. Furthermore, community network analysis showed enhanced information connections in the mutants, highlighting the long-range allosteric communication between the A-loop and the hinge region. Our findings may provide insights into the dynamic mechanism for FGFR2 dysfunctional activation and allosteric drug discovery.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Yuxiang Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Lan Yin
- Department of Radiotherapy, Shanghai 411 Hospital, China RongTong Medical Healthcare Group Co. Ltd, Shanghai, China
| | - Mingfei Ji
- Department of Urology, The Second Affiliated Hospital of Navy Medical University, Shanghai, China
| | - Yi Chen
- Department of Ultrasound interventional, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Zongtao Chai
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hepatic Surgery, Shanghai Geriatric Medical Center, Shanghai, China
| |
Collapse
|
6
|
Lemos LMS, Ọlọ Ba-Whẹ Nù OA, Olasupo IA, Balogun SO, Macho A, Pavan E, de Oliveira Martins DT. Brasiliensic acid: in vitro cytotoxic and genotoxic, in vivo acute toxicity and in silico pharmacological prediction of a new promising molecule. J Biomol Struct Dyn 2023:1-14. [PMID: 38054294 DOI: 10.1080/07391102.2023.2280713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
Brasiliensic acid (Bras) is a chromanone isolated from Calophyllum brasiliense Cambèss. bark extracts with confirmed potential activity on gastric ulcer and Helicobacter pylori infection. This study aimed to investigate the in vitro and in vivo toxicity of Bras and molecular docking studies on its interactions with the H. pylori virulence factors and selected gastric cancer-related proteins. Cytotoxicity was evaluated by alamarBlue© assay, genotoxicity by micronucleus and comet assays, and on cell cycle by flow cytometry, using Chinese hamster epithelial ovary cells. Bras was not cytotoxic to CHO-K1 cells, and caused no chromosomal aberrations, nor altered DNA integrity. Furthermore, Bras inhibited damages to DNA by H2O2 at 1.16 µM. No cell cycle arrest was observed, but apoptosis accounted for 31.2% of the cell death observed in the CHO-K1 at 24 h incubation of the IC50. Oral acute toxicity by Hippocratic screening test in mice showed no relevant behavioral change/mortality seen up to 1,000 mg/kg. The molecular docking approach indicated potential interactions between Bras and the various targets for peptic ulcer and gastric cancer, notably CagA virulence factor of H. pylori and VEGFR-2. In conclusion, Bras is apparently safe and an optimization for Bras can be considered for gastric ulcer and cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Larissa Maria Scalon Lemos
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
- Área de Farmacologia, Faculdade de Ciências da Saúde, Universidade do Estado de Mato Grosso (Unemat), Cáceres, MT, Brazil
| | | | | | - Sikiru Olaitan Balogun
- Programa de Pós-Graduação em Ciências da Saúde (PPGCS), Universidade Federal da Grande Dourados (UFGD), Dourados, MS, Brazil
| | - Antonio Macho
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada (NuPMIA). Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Eduarda Pavan
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
| | - Domingos Tabajara de Oliveira Martins
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
| |
Collapse
|
7
|
Liu B, Ding J, Liu Y, Wu J, Wu X, Chen Q, Li W. Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis. J Comput Aided Mol Des 2023; 37:325-338. [PMID: 37269435 DOI: 10.1007/s10822-023-00510-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
FGFR3 kinase mutations are associated with a variety of malignancies, but FGFR3 mutant inhibitors have rarely been studied. Furthermore, the mechanism of pan-FGFR inhibitors resistance caused by kinase domain mutations is still unclear. In this study, we try to explain the mechanism of drug resistance to FGFR3 mutation through global analysis and local analysis based on molecular dynamics simulation, binding free energy analysis, umbrella sampling and community network analysis. The results showed that FGFR3 mutations caused a decrease in the affinity between drugs and FGFR3 kinase, which was consistent with the reported experimental results. Possible mechanisms are that mutations affect drug-protein affinity by altering the environment of residues near the hinge region where the protein binds to the drug, or by affecting the A-loop and interfering with the allosteric communication networks. In conclusion, we systematically elucidated the underlying mechanism of pan-FGFR inhibitor resistance caused by FGFR3 mutation based on molecular dynamics simulation strategy, which provided theoretical guidance for the development of FGFR3 mutant kinase inhibitors.
Collapse
Affiliation(s)
- Bo Liu
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Juntao Ding
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yugang Liu
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jianzhang Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaoping Wu
- Institute of Tissue Transplantation and Immunology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, 510632, China
| | - Qian Chen
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China.
| | - Wulan Li
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China.
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| |
Collapse
|
8
|
Li W, Zhou J, Lan Q, Ding XL, Pan XT, Ahmed SA, Ji LN, Wang K, Xia XH. Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore. NANO LETTERS 2023; 23:2586-2592. [PMID: 36942994 DOI: 10.1021/acs.nanolett.2c04848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.
Collapse
Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Tong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
9
|
Besch A, Marsiglia WM, Mohammadi M, Zhang Y, Traaseth NJ. Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proc Natl Acad Sci U S A 2023; 120:e2213090120. [PMID: 36791110 PMCID: PMC9974468 DOI: 10.1073/pnas.2213090120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/10/2023] [Indexed: 02/16/2023] Open
Abstract
Many types of human cancers are being treated with small molecule ATP-competitive inhibitors targeting the kinase domain of receptor tyrosine kinases. Despite initial successful remission, long-term treatment almost inevitably leads to the emergence of drug resistance mutations at the gatekeeper residue hindering the access of the inhibitor to a hydrophobic pocket at the back of the ATP-binding cleft. In addition to reducing drug efficacy, gatekeeper mutations elevate the intrinsic activity of the tyrosine kinase domain leading to more aggressive types of cancer. However, the mechanism of gain-of-function by gatekeeper mutations is poorly understood. Here, we characterized fibroblast growth factor receptor (FGFR) tyrosine kinases harboring two distinct gatekeeper mutations using kinase activity assays, NMR spectroscopy, bioinformatic analyses, and MD simulations. Our data show that gatekeeper mutations destabilize the autoinhibitory conformation of the DFG motif locally and of the kinase globally, suggesting they impart gain-of-function by facilitating the kinase's ability to populate the active state.
Collapse
Affiliation(s)
- Alida Besch
- Department of Chemistry, New York University, New York, NY10003
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY10016
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY10003
- Simons Center for Computational Physical Chemistry, New York University, New York, NY10003
| | | |
Collapse
|
10
|
Skeens E, Lisi GP. Analysis of coordinated NMR chemical shifts to map allosteric regulatory networks in proteins. Methods 2023; 209:40-47. [PMID: 36535575 PMCID: PMC10173519 DOI: 10.1016/j.ymeth.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The exquisite sensitivity of the NMR chemical shift to local environment makes it an ideal probe to assess atomic level perturbations in proteins of all sizes and structural compositions. Recent advances in solution and solid-state NMR spectroscopy of biomolecules have leveraged the chemical shift to report on short- and long-range couplings between individual amino acids to establish "networks" of residues that form the basis of allosteric pathways that transmit chemical signals through the protein matrix to induce functional responses. The simple premise that thermodynamically and functionally coupled regions of a protein (i.e. active and allosteric sites) should be reciprocally sensitive to structural or dynamic perturbations has enabled NMR spectroscopy, the premier method for molecular resolution of protein structural fluctuations, to occupy a place at the forefront of investigations into protein allostery. Here, we detail several key methods of NMR chemical shift analysis to extract mechanistic information about long-range chemical signaling in a protein, focusing on practical methodological aspects and the circumstances under which a given approach would be relevant. We also detail some of the experimental considerations that should be made when applying these methods to specific protein systems.
Collapse
Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, United States
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, United States.
| |
Collapse
|
11
|
Signaling pathways and targeted therapies in lung squamous cell carcinoma: mechanisms and clinical trials. Signal Transduct Target Ther 2022; 7:353. [PMID: 36198685 PMCID: PMC9535022 DOI: 10.1038/s41392-022-01200-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/03/2022] [Accepted: 09/18/2022] [Indexed: 11/08/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death across the world. Unlike lung adenocarcinoma, patients with lung squamous cell carcinoma (LSCC) have not benefitted from targeted therapies. Although immunotherapy has significantly improved cancer patients' outcomes, the relatively low response rate and severe adverse events hinder the clinical application of this promising treatment in LSCC. Therefore, it is of vital importance to have a better understanding of the mechanisms underlying the pathogenesis of LSCC as well as the inner connection among different signaling pathways, which will surely provide opportunities for more effective therapeutic interventions for LSCC. In this review, new insights were given about classical signaling pathways which have been proved in other cancer types but not in LSCC, including PI3K signaling pathway, VEGF/VEGFR signaling, and CDK4/6 pathway. Other signaling pathways which may have therapeutic potentials in LSCC were also discussed, including the FGFR1 pathway, EGFR pathway, and KEAP1/NRF2 pathway. Next, chromosome 3q, which harbors two key squamous differentiation markers SOX2 and TP63 is discussed as well as its related potential therapeutic targets. We also provided some progress of LSCC in epigenetic therapies and immune checkpoints blockade (ICB) therapies. Subsequently, we outlined some combination strategies of ICB therapies and other targeted therapies. Finally, prospects and challenges were given related to the exploration and application of novel therapeutic strategies for LSCC.
Collapse
|
12
|
Identification of Core Allosteric Sites through Temperature- and Nucleus-Invariant Chemical Shift Covariance. Biophys J 2022; 121:2035-2045. [PMID: 35538664 DOI: 10.1016/j.bpj.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/11/2022] [Accepted: 05/04/2022] [Indexed: 11/22/2022] Open
Abstract
Allosteric regulation is essential to control biological function. In addition, allosteric sites offer a promising venue for selective drug targeting. However, accurate mapping of allosteric sites remains challenging since allostery relies on often subtle, yet functionally relevant, structural and dynamical changes. A viable approach proposed to overcome such challenge is the chemical shift covariance analysis (CHESCA). Although CHESCA offers an exhaustive map of allosteric networks, it is critical to define the core allosteric sites to be prioritized in subsequent functional studies or the design of allosteric drugs. Here we propose two new CHESCA-based methodologies, called temperature CHESCA (T-CHESCA) and CLASS-CHESCA, aimed at narrowing down allosteric maps to the core allosteric residues. Both T- and CLASS-CHESCAs rely on the invariance of core inter-residue correlations to changes in the chemical shifts of the active and inactive conformations interconverting in fast exchange. In the T-CHESCA the chemical shifts of such states are modulated through temperature changes, while in the CLASS-CHESCA through variations in the spin-active nuclei involved in pairwise correlations. The T- and CLASS-CHESCAs as well as complete-linkage CHESCA were applied to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC), which serves as a prototypical allosteric switch. Residues consistently identified by the three CHESCA methods were found in previously identified EPAC allosteric core sites. Hence, the T-, CLASS- and CL-CHESCA provide a toolset to establish allosteric site hierarchy and triage allosteric sites to be further analyzed by mutations and functional assays. Furthermore, the core allosteric networks selectively revealed through T- and CLASS-CHESCA are expected to facilitate the mechanistic understanding of disease-related mutations and the design of selective allosteric modulators.
Collapse
|
13
|
Bou Zerdan M, Ghorayeb T, Saliba F, Allam S, Bou Zerdan M, Yaghi M, Bilani N, Jaafar R, Nahleh Z. Triple Negative Breast Cancer: Updates on Classification and Treatment in 2021. Cancers (Basel) 2022; 14:cancers14051253. [PMID: 35267561 PMCID: PMC8909187 DOI: 10.3390/cancers14051253] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Triple negative breast cancer (TNBC) represents 15 to 20% of all breast cancers in the United States. The main treatment option remains chemotherapy, despite limited efficacy. New biologic and targeted agents are increasingly emerging for the treatment of TNBC. Given the continuous advances in the field of TNBC, this review assesses the latest developments in basic characterization, subtyping, and treatment of TNBC, including novel drug developments with antibody-drug conjugates, immune checkpoint inhibitors, PARP inhibitors, and androgen receptor targeted agents. Abstract Breast cancer (BC) is the most common malignancy affecting women. It is a highly heterogeneous disease broadly defined by the differential expression of cell surface receptors. In the United States, triple negative breast cancer (TNBC) represents 15 to 20% of all BC. When compared with other subtypes of BC, TNBC tends to present in younger women, and has a higher mortality rate of 40% in advanced stages within the first 5 years after diagnosis. TNBC has historically had limited treatment options when compared to other types of BC. The mainstay of treatment for TNBC remains cytotoxic chemotherapy despite the emergence of new biologic and targeted agents. Defining the specific tumor molecular profile including PDL-1 and androgen receptor testing is expanding treatment options in the clinical setting. Identifying more targetable, novel biomarkers that may better define therapeutic targets or prognostic markers is currently underway. TNBC nomenclature is expected to be updated in favor of other nomenclature which would help direct therapy, and further redefine TNBC’s heterogeneity. Given the continuous advances in the field of TNBC, this review assesses the latest developments in basic characterization, subtyping, and treatment of TNBC, including novel drug developments with antibody-drug conjugates, immune checkpoint inhibitors, PARP inhibitors and androgen receptor targeted agents. Future trials are necessary in the face of these innovations to further support the use of new therapies in TNBC and the detection of the appropriate biomarkers.
Collapse
Affiliation(s)
- Maroun Bou Zerdan
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL 33331, USA; (M.B.Z.); (M.Y.)
- Department of Internal Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Tala Ghorayeb
- Department of Obstetrics and Gynecology, McGovern Medical School, UTHealth Texas, Houston, TX 77030, USA;
| | - Fares Saliba
- Faculty of Medicine and Medical Sciences, Holy Spirit University of Kaslik (USEK), Jounieh 1200, Lebanon;
| | - Sabine Allam
- Faculty of Medicine, University of Balamand, Beirut 11 00 2807, Lebanon;
| | - Morgan Bou Zerdan
- Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon;
| | - Marita Yaghi
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL 33331, USA; (M.B.Z.); (M.Y.)
| | - Nadeem Bilani
- Department of Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Rola Jaafar
- Department of Surgery, Faculty of Medicine, American University of Beirut Medical Center, Beirut 11097 2020, Lebanon;
| | - Zeina Nahleh
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL 33331, USA; (M.B.Z.); (M.Y.)
- Correspondence:
| |
Collapse
|
14
|
Novel potential oncogenic and druggable mutations of FGFRs recur in the kinase domain across cancer types. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166313. [PMID: 34826586 DOI: 10.1016/j.bbadis.2021.166313] [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: 06/23/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are recurrently altered by single nucleotide variants (SNVs) in many human cancers. The prevalence of SNVs in FGFRs depends on the cancer type. In some tumors, such as the urothelial carcinoma, mutations of FGFRs occur at very high frequency (up to 60%). Many characterized mutations occur in the extracellular or transmembrane domains, while fewer known mutations are found in the kinase domain. In this study, we performed a bioinformatics analysis to identify novel putative cancer driver or therapeutically actionable mutations of the kinase domain of FGFRs. To pinpoint those mutations that may be clinically relevant, we exploited the recurrence of alterations on analogous amino acid residues within the kinase domain (PK_Tyr_Ser-Thr) of different kinases as a predictor of functional impact. By exploiting MutationAligner and LowMACA bioinformatics resources, we highlighted novel uncharacterized mutations of FGFRs which recur in other protein kinases. By revealing unanticipated correspondence with known variants, we were able to infer their functional effects, as alterations clustering on similar residues in analogous proteins have a high probability to elicit similar effects. As FGFRs represent an important class of oncogenes and drug targets, our study opens the way for further studies to validate their driver and/or actionable nature and, in the long term, for a more efficacious application of precision oncology.
Collapse
|
15
|
Modi V, Dunbrack RL. Kincore: a web resource for structural classification of protein kinases and their inhibitors. Nucleic Acids Res 2022; 50:D654-D664. [PMID: 34643709 PMCID: PMC8728253 DOI: 10.1093/nar/gkab920] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
The active form of kinases is shared across different family members, as are several commonly observed inactive forms. We previously performed a clustering of the conformation of the activation loop of all protein kinase structures in the Protein Data Bank (PDB) into eight classes based on the dihedral angles that place the Phe side chain of the DFG motif at the N-terminus of the activation loop. Our clusters are strongly associated with the placement of the activation loop, the C-helix, and other structural elements of kinases. We present Kincore, a web resource providing access to our conformational assignments for kinase structures in the PDB. While other available databases provide conformational states or drug type but not both, KinCore includes the conformational state and the inhibitor type (Type 1, 1.5, 2, 3, allosteric) for each kinase chain. The user can query and browse the database using these attributes or determine the conformational labels of a kinase structure using the web server or a standalone program. The database and labeled structure files can be downloaded from the server. Kincore will help in understanding the conformational dynamics of these proteins and guide development of inhibitors targeting specific states. Kincore is available at http://dunbrack.fccc.edu/kincore.
Collapse
Affiliation(s)
- Vivek Modi
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19148, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19148, USA
| |
Collapse
|
16
|
Chen L, Zhang Y, Yin L, Cai B, Huang P, Li X, Liang G. Fibroblast growth factor receptor fusions in cancer: opportunities and challenges. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:345. [PMID: 34732230 PMCID: PMC8564965 DOI: 10.1186/s13046-021-02156-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/25/2021] [Indexed: 12/27/2022]
Abstract
Fibroblast growth factors (FGFs) and their receptors (FGFRs) play critical roles in many biological processes and developmental functions. Chromosomal translocation of FGFRs result in the formation of chimeric FGFR fusion proteins, which often cause aberrant signaling leading to the development and progression of human cancer. Due to the high recurrence rate and carcinogenicity, oncogenic FGFR gene fusions have been identified as promising therapeutic targets. Erdafitinib and pemigatinib, two FGFR selective inhibitors targeting FGFR fusions, have been approved by the U.S. Food and Drug Administration (FDA) to treat patients with urothelial cancer and cholangiocarcinoma, respectively. Futibatinib, a third-generation FGFR inhibitor, is under phase III clinical trials in patients with FGFR gene rearrangements. Herein, we review the current understanding of the FGF/FGFRs system and the oncogenic effect of FGFR fusions, summarize promising inhibitors under clinical development for patients with FGFR fusions, and highlight the challenges in this field.
Collapse
Affiliation(s)
- Lingfeng Chen
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China. .,School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, 310012, Zhejiang, China.
| | - Yanmei Zhang
- School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, 310012, Zhejiang, China
| | - Lina Yin
- School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, 310012, Zhejiang, China
| | - Binhao Cai
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ping Huang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Guang Liang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China. .,School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, 310012, Zhejiang, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| |
Collapse
|
17
|
Comprehensive functional evaluation of variants of fibroblast growth factor receptor genes in cancer. NPJ Precis Oncol 2021; 5:66. [PMID: 34272467 PMCID: PMC8285406 DOI: 10.1038/s41698-021-00204-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 06/08/2021] [Indexed: 01/16/2023] Open
Abstract
Various genetic alterations of the fibroblast growth factor receptor (FGFR) family have been detected across a wide range of cancers. However, inhibition of FGFR signaling by kinase inhibitors demonstrated limited clinical effectiveness. Herein, we evaluated the transforming activity and sensitivity of 160 nonsynonymous FGFR mutations and ten fusion genes to seven FGFR tyrosine kinase inhibitors (TKI) using the mixed-all-nominated-in-one (MANO) method, a high-throughput functional assay. The oncogenicity of 71 mutants was newly discovered in this study. The FGFR TKIs showed anti-proliferative activities against the wild-type FGFRs and their fusions, while several hotspot mutants were relatively resistant to those TKIs. The drug sensitivities assessed with the MANO method were well concordant with those evaluated using in vitro and in vivo assays. Comprehensive analysis of published FGFR structures revealed a possible mechanism through which oncogenic FGFR mutations reduce sensitivity to TKIs. It was further revealed that recurrent compound mutations within FGFRs affect the transforming potential and TKI-sensitivity of corresponding kinases. In conclusion, our study suggests the importance of selecting suitable inhibitors against individual FGFR variants. Moreover, it reveals the necessity to develop next-generation FGFR inhibitors, which are effective against all oncogenic FGFR variants.
Collapse
|
18
|
Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Veglia G, Markley JL, Melacini G, Lee W. CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinformatics 2021; 37:1176-1177. [PMID: 32926121 DOI: 10.1093/bioinformatics/btaa781] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Correlated Nuclear Magnetic Resonance (NMR) chemical shift changes identified through the CHEmical Shift Projection Analysis (CHESPA) and CHEmical Shift Covariance Analysis (CHESCA) reveal pathways of allosteric transitions in biological macromolecules. To address the need for an automated platform that implements CHESPA and CHESCA and integrates them with other NMR analysis software packages, we introduce here integrated plugins for NMRFAM-SPARKY that implement the seamless detection and visualization of allosteric networks. AVAILABILITY AND IMPLEMENTATION CHESCA-SPARKY and CHESPA-SPARKY are available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). The assigned spectra involved in this study and tutorial videos using this dataset are available at https://sites.google.com/view/chescachespa-sparky. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Online.
Collapse
Affiliation(s)
- Hongzhao Shao
- Department of Chemistry and Chemical Biology, Hamilton, ON L8S 4L8, Canada
| | - Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, MN 55455, USA
| | - Hebatallah Mohamed
- Department of Chemistry and Chemical Biology, Hamilton, ON L8S 4L8, Canada
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, Hamilton, ON L8S 4L8, Canada
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, MN 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - John L Markley
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53717, USA
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, Hamilton, ON L8S 4L8, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Woonghee Lee
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53717, USA.,Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Bredrup C, Cristea I, Safieh LA, Di Maria E, Gjertsen BT, Tveit KS, Thu F, Bull N, Edward DP, Hennekam RCM, Høvding G, Haugen OH, Houge G, Rødahl E, Bruland O. Temperature-dependent autoactivation associated with clinical variability of PDGFRB Asn666 substitutions. Hum Mol Genet 2021; 30:72-77. [PMID: 33450762 PMCID: PMC8033145 DOI: 10.1093/hmg/ddab014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Ocular pterygium-digital keloid dysplasia (OPDKD) presents in childhood with ingrowth of vascularized connective tissue on the cornea leading to severely reduced vision. Later the patients develop keloids on digits but are otherwise healthy. The overgrowth in OPDKD affects body parts that typically have lower temperature than 37°C. We present evidence that OPDKD is associated with a temperature sensitive, activating substitution, p.(Asn666Tyr), in PDGFRB. Phosphorylation levels of PDGFRB and downstream targets were higher in OPDKD fibroblasts at 37°C but were further greatly increased at the average corneal temperature of 32°C. This suggests that the substitution cause significant constitutive autoactivation mainly at lower temperature. In contrast, a different substitution in the same codon, p.(Asn666Ser), is associated with Penttinen type of premature aging syndrome. This devastating condition is characterized by widespread tissue degeneration, including pronounced chronic ulcers and osteolytic resorption in distal limbs. In Penttinen syndrome fibroblasts, equal and high levels of phosphorylated PDGFRB was present at both 32°C and 37°C. This indicates that this substitution causes severe constitutive autoactivation of PDGFRB regardless of temperature. In line with this, most downstream targets were not affected by lower temperature. However, STAT1, important for tissue wasting, did show further increased phosphorylation at 32°C. Temperature-dependent autoactivation offers an explanation to the strikingly different clinical outcomes of substitutions in the Asn666 codon of PDGFRB.
Collapse
Affiliation(s)
- Cecilie Bredrup
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway.,Department of Clinical Medicine, University of Bergen, Bergen 5020, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Ileana Cristea
- Department of Clinical Medicine, University of Bergen, Bergen 5020, Norway
| | - Leen Abu Safieh
- Research Department, King Khaled Eye Specialist Hospital, Riyadh 11462, Kingdom of Saudi Arabia.,Genomics Research Department, Research Center, King Fahad Medical City, Riyadh 11564, Kingdom of Saudi Arabia
| | - Emilio Di Maria
- Department of Health Sciences, University of Genova, Genova 16132, Italy.,Unit of Medical Genetics, Galliera Hospital, Genova 16128, Italy
| | - Bjørn Tore Gjertsen
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen 5021, Norway
| | - Kåre Steinar Tveit
- Department of Dermatology, Haukeland University Hospital, Bergen 5021, Norway
| | - Frode Thu
- Department of Orthopaedic Surgery, Oslo University Hospital, Oslo 4956, Norway
| | - Nils Bull
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway
| | - Deepak P Edward
- Research Department, King Khaled Eye Specialist Hospital, Riyadh 11462, Kingdom of Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Raoul C M Hennekam
- Department of Pediatrics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam 1105AZ, the Netherlands
| | - Gunnar Høvding
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway.,Department of Clinical Medicine, University of Bergen, Bergen 5020, Norway
| | - Olav H Haugen
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway.,Department of Clinical Medicine, University of Bergen, Bergen 5020, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Eyvind Rødahl
- Department of Ophthalmology, Haukeland University Hospital, Bergen 5021, Norway.,Department of Clinical Medicine, University of Bergen, Bergen 5020, Norway
| | - Ove Bruland
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| |
Collapse
|
21
|
Xie T, Saleh T, Rossi P, Kalodimos CG. Conformational states dynamically populated by a kinase determine its function. Science 2020; 370:science.abc2754. [PMID: 33004676 DOI: 10.1126/science.abc2754] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Protein kinases intrinsically sample a number of conformational states with distinct catalytic and binding activities. We used nuclear magnetic resonance spectroscopy to describe in atomic-level detail how Abl kinase interconverts between an active and two discrete inactive structures. Extensive differences in key structural elements between the conformational states give rise to multiple intrinsic regulatory mechanisms. The findings explain how oncogenic mutants can counteract inhibitory mechanisms to constitutively activate the kinase. Energetic dissection revealed the contributions of the activation loop, the Asp-Phe-Gly (DFG) motif, the regulatory spine, and the gatekeeper residue to kinase regulation. Characterization of the transient conformation to which the drug imatinib binds enabled the elucidation of drug-resistance mechanisms. Structural insight into inactive states highlights how they can be leveraged for the design of selective inhibitors.
Collapse
Affiliation(s)
- Tao Xie
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | |
Collapse
|
22
|
Boulton S, Van K, VanSchouwen B, Augustine J, Akimoto M, Melacini G. Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding. Biophys J 2020; 119:1135-1146. [PMID: 32882185 DOI: 10.1016/j.bpj.2020.07.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Quantifying chemical substituent contributions to ligand-binding free energies is challenging due to nonadditive effects. Protein allostery is a frequent cause of nonadditivity, but the underlying allosteric mechanisms often remain elusive. Here, we propose a general NMR-based approach to elucidate such mechanisms and we apply it to the HCN4 ion channel, whose cAMP-binding domain is an archetypal conformational switch. Using NMR, we show that nonadditivity arises not only from concerted conformational transitions, but also from conformer-specific effects, such as steric frustration. Our results explain how affinity-reducing functional groups may lead to affinity gains if combined. Surprisingly, our approach also reveals that nonadditivity depends markedly on the receptor conformation. It is negligible for the inhibited state but highly significant for the active state, opening new opportunities to tune potency and agonism of allosteric effectors.
Collapse
Affiliation(s)
- Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Jerry Augustine
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada.
| |
Collapse
|
23
|
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.
Collapse
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
Collapse
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.
| |
Collapse
|
24
|
Casadei C, Dizman N, Schepisi G, Cursano MC, Basso U, Santini D, Pal SK, De Giorgi U. Targeted therapies for advanced bladder cancer: new strategies with FGFR inhibitors. Ther Adv Med Oncol 2019; 11:1758835919890285. [PMID: 31803255 PMCID: PMC6878604 DOI: 10.1177/1758835919890285] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
Inhibitors of fibroblast growth factor receptor (FGFR) represent an outstanding treatment approach for selected patients with urothelial cancer (UC). These agents are changing the clinical approach to a subgroup of UC, the luminal-papillary subtype, characterized by FGFR mutations, fusions, or amplification. In this review, we provide an overview of the results of recent clinical trials on FGFR tyrosine kinase inhibitors (TKIs) currently in clinical development for the treatment of UC: erdafitinib, rogaratinib, infigratinib, and the monoclonal antibody vofatamab. The Food and Drug Administration recently granted accelerated approval to erdafitinib for patients with advanced UC with alterations of FGFR2 or FGFR3 after progression on platinum-based chemotherapy. We also look at future therapeutic options of combination regimens with immune-checkpoint inhibitors as strategies for improving the antitumor effects of this class of drug, and for preventing or delaying the development of resistance.
Collapse
Affiliation(s)
- Chiara Casadei
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Nazli Dizman
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Giuseppe Schepisi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Umberto Basso
- Medical Oncology Unit, Istituto Oncologico Veneto, IOV-IRCCS, Padova, Italy
| | - Daniele Santini
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Rome, Italy
| | - Sumanta K. Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ugo De Giorgi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Maroncelli 40, Meldola, 47014, Italy
| |
Collapse
|
25
|
Nussinov R, Tsai C, Jang H. Autoinhibition can identify rare driver mutations and advise pharmacology. FASEB J 2019; 34:16-29. [DOI: 10.1096/fj.201901341r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section Basic Science Program Frederick National Laboratory for Cancer Research Frederick MD USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| | - Chung‐Jung Tsai
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| | - Hyunbum Jang
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| |
Collapse
|
26
|
Nussinov R, Tsai CJ, Jang H. Why Are Some Driver Mutations Rare? Trends Pharmacol Sci 2019; 40:919-929. [PMID: 31699406 DOI: 10.1016/j.tips.2019.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
Understanding why driver mutations that promote cancer are sometimes rare is important for precision medicine since it would help in their identification. Driver mutations are largely discovered through their frequencies. Thus, rare mutations often escape detection. Unlike high-frequency drivers, low-frequency drivers can be tissue specific; rare drivers have extremely low frequencies. Here, we discuss rare drivers and strategies to discover them. We suggest that allosteric driver mutations shift the protein ensemble from the inactive to the active state. Rare allosteric drivers are statistically rare since, to switch the protein functional state, they cooperate with additional mutations, and these are not considered in the patient cancer-specific protein sequence analysis. A complete landscape of mutations that drive cancer will reveal tumor-specific therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| |
Collapse
|
27
|
Futami T, Kawase T, Mori K, Asaumi M, Kihara R, Shindoh N, Kuromitsu S. Identification of a novel oncogenic mutation of FGFR4 in gastric cancer. Sci Rep 2019; 9:14627. [PMID: 31601997 PMCID: PMC6787178 DOI: 10.1038/s41598-019-51217-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/27/2019] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer remains one of the leading causes of cancer death worldwide. Despite intensive investigations of treatments over the past three decades, the poor prognosis of patients with unresectable advanced or recurrent gastric cancer has not significantly changed, and improved therapies are required. Here, we report the identification of an oncogenic mutation in FGFR4 in a human gastric tumour that leads to constitutive activation of its product, FGFR4. The G636C-FGFR4 tyrosine kinase domain mutation was found in 1 of 83 primary human gastric tumours. The G636C mutation increased FGFR4 autophosphorylation, and activated FGFR4 downstream signalling molecules and enhanced anchorage-independent cell growth when expressed in NIH/3T3 cells. 3D-structural analysis and modelling of FGFR4 suggest that G636C destabilizes an auto-inhibitory conformation and stabilizes an active conformation, leading to increased kinase activation. Ba/F3 cell lines expressing the G636C-FGFR4 mutant were significantly more sensitive to ASP5878, a selective FGFR inhibitor, than the control. Oral administration of ASP5878 significantly inhibited the growth of tumours in mice engrafted with G636C-FGFR4/3T3 cells. Together, our results demonstrate that mutationally activated FGFR4 acts as an oncoprotein. These findings support the therapeutic targeting of FGFR4 in gastric cancer.
Collapse
Affiliation(s)
- Takashi Futami
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan.
| | - Tatsuya Kawase
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| | - Kenichi Mori
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| | - Makoto Asaumi
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| | - Rumi Kihara
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| | - Nobuaki Shindoh
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| | - Sadao Kuromitsu
- Drug Discovery Research, Astellas Pharma Inc., Ibaraki, Japan
| |
Collapse
|
28
|
Wu C, Chen X, Chen D, Xia Q, Liu Z, Li F, Yan Y, Cai Y. Insight into ponatinib resistance mechanisms in rhabdomyosarcoma caused by the mutations in FGFR4 tyrosine kinase using molecular modeling strategies. Int J Biol Macromol 2019; 135:294-302. [DOI: 10.1016/j.ijbiomac.2019.05.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 01/03/2023]
|
29
|
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.
Collapse
|
30
|
Sundaresan L, Kumar P, Manivannan J, Balaguru UM, Kasiviswanathan D, Veeriah V, Anishetty S, Chatterjee S. Thalidomide and Its Analogs Differentially Target Fibroblast Growth Factor Receptors: Thalidomide Suppresses FGFR Gene Expression while Pomalidomide Dampens FGFR2 Activity. Chem Res Toxicol 2019; 32:589-602. [PMID: 30834740 DOI: 10.1021/acs.chemrestox.8b00286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Thalidomide is an infamous teratogen and it is continuously being explored for its anticancer properties. Fibroblast growth factor receptors (FGFRs) are implicated in embryo development and cancer pathophysiology. With striking similarities observed between FGFR implicated conditions and thalidomide embryopathy, we hypothesized thalidomide targets FGFRs. We utilized three different cell lines and chicken embryo model to investigate the effects of thalidomide and analogs on FGFR expression. We performed molecular docking, KINOMEscan analysis, and kinase activity assays to study the drug-protein interactions. The expression of FGFR1 and FGFR2 was differentially regulated by all the three drugs in cells as well as in developing organs. Transcriptome analysis of thalidomide-treated chick embryo strongly suggests the modulation of FGFR signaling and key transcription factors. Corroboration with previous studies suggests that thalidomide might affect FGFR expression through the transcription factor, E2F1. At the protein level, molecular docking predicted all three analogs to interact with lysine residue at 517th and 508th positions of FGFR2 and FGFR3, respectively. This lysine coordinates the ATP binding site of FGFR, thus hinting at the possible perturbation of FGFR activity by thalidomide. Kinome analysis revealed that kinase activities of FGFR2 and FGFR3 (G697C) reduced by 31% and 65%, respectively, in the presence of 10 μM thalidomide. Further, we checked and confirmed that the analogs inhibited the FGFR2 kinase activity in a dose-dependent manner. This study suggests that FGFRs could be potential targets of thalidomide and the two analogs, and also endorses the link between the teratogenicity and antitumor activities of the drugs.
Collapse
|
31
|
He X, Ni D, Lu S, Zhang J. Characteristics of Allosteric Proteins, Sites, and Modulators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:107-139. [DOI: 10.1007/978-981-13-8719-7_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
32
|
Lamberti D, Cristinziano G, Porru M, Leonetti C, Egan JB, Shi CX, Buglioni S, Amoreo CA, Castellani L, Borad MJ, Alemà S, Anastasi S, Segatto O. HSP90 Inhibition Drives Degradation of FGFR2 Fusion Proteins: Implications for Treatment of Cholangiocarcinoma. Hepatology 2019; 69:131-142. [PMID: 30067876 DOI: 10.1002/hep.30127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/31/2018] [Indexed: 12/14/2022]
Abstract
About 15% of intrahepatic cholangiocarcinomas (ICCs) express constitutively active fibroblast growth factor receptor 2 (FGFR2) fusion proteins (FFs) generated by chromosomal translocations. FFs have been nominated as oncogenic drivers because administration of FGFR tyrosine kinase inhibitors (F-TKIs) can elicit meaningful objective clinical responses in patients carrying FF-positive ICC. Thus, optimization of FF targeting is a pressing clinical need. Herein, we report that three different FFs, previously isolated from ICC samples, are heat shock protein 90 (HSP90) clients and undergo rapid degradation upon HSP90 pharmacological blockade by the clinically advanced HSP90 inhibitor ganetespib. Combining catalytic suppression by the F-TKI BGJ398 with HSP90 blockade by ganetespib suppressed FGFR2-TACC3 (transforming acidic coiled-coil containing protein 3) signaling in cultured cells more effectively than either BGJ398 or ganetespib in isolation. The BGJ398 + ganetespib combo was also superior to single agents when tested in mice carrying subcutaneous tumors generated by transplantation of FGFR2-TACC3 NIH3T3 transformants. Of note, FF mutants known to enforce clinical resistance to BGJ398 in ICC patients retained full sensitivity to ganetespib in cultured cells. Conclusion: Our data provide a proof of principle that upfront treatment with the BGJ398 + ganetespib combo improves therapeutic targeting of FGFR2 fusions in an experimental setting, which may be relevant to precision medicine approaches to FF-driven ICC.
Collapse
Affiliation(s)
- Dante Lamberti
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Cristinziano
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Manuela Porru
- Animal Facility (SAFU), IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Carlo Leonetti
- Animal Facility (SAFU), IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Jan B Egan
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Chang-Xin Shi
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Simonetta Buglioni
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Carla A Amoreo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Loriana Castellani
- Dipartimento di Scienze Umane, Sociali e della Salute, Università di Cassino, Cassino, Italy.,Institute of Cell Biology and Neurobiology, National Research Council (CNR), Monterotondo, Italy
| | - Mitesh J Borad
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Stefano Alemà
- Institute of Cell Biology and Neurobiology, National Research Council (CNR), Monterotondo, Italy
| | - Sergio Anastasi
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Oreste Segatto
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| |
Collapse
|
33
|
Bredrup C, Stokowy T, McGaughran J, Lee S, Sapkota D, Cristea I, Xu L, Tveit KS, Høvding G, Steen VM, Rødahl E, Bruland O, Houge G. A tyrosine kinase-activating variant Asn666Ser in PDGFRB causes a progeria-like condition in the severe end of Penttinen syndrome. Eur J Hum Genet 2018; 27:574-581. [PMID: 30573803 DOI: 10.1038/s41431-018-0323-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023] Open
Abstract
Missense variants located to the "molecular brake" in the tyrosine kinase hinge region of platelet-derived growth factor receptor-β, encoded by PFGFRB, can cause Penttinen-type (Val665Ala) and Penttinen-like (Asn666His) premature ageing syndromes, as well as infantile myofibromatosis (Asn666Lys and Pro660Thr). We have found the same de novo PDGFRB c.1997A>G p.(Asn666Ser) variants in two patients with lipodystrophy, acro-osteolysis and severely reduced vision due to corneal neovascularisation, reminiscent of a severe form of Penttinen syndrome with more pronounced connective tissue destruction. In line with this phenotype, patient skin fibroblasts were prone to apoptosis. Both in patient fibroblasts and stably transduced HeLa and HEK293 cells, autophosphorylation of PDGFRβ was observed, as well as increased phosphorylation of downstream signalling proteins such as STAT1, PLCγ1, PTPN11/SHP2-Tyr580 and AKT. Phosphorylation of MAPK3 (ERK1) and PTPN11/SHP2-Tyr542 appeared unaffected. This suggests that this missense change not only weakens tyrosine kinase autoinhibition, but also influences substrate binding, as both PTPN11 tyrosines (Tyr542 and Tyr580) usually are phosphorylated upon PDGFR activation. Imatinib was a strong inhibitor of phosphorylation of all these targets, suggesting an option for precision medicine based treatment.
Collapse
Affiliation(s)
- Cecilie Bredrup
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Ophthalmology, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Tomasz Stokowy
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | - Julie McGaughran
- Genetic Health QLD, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Samuel Lee
- Genetic Health QLD, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Dipak Sapkota
- Department of Oncology and Medical Physics, Haukeland University Hospital, 5021, Bergen, Norway.,Institute of Oral Biology, University of Oslo, 0315, Oslo, Norway
| | - Ileana Cristea
- Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Linda Xu
- Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Kåre Steinar Tveit
- Department of Dermatology, Haukeland University Hospital, 5021, Bergen, Norway
| | - Gunnar Høvding
- Department of Ophthalmology, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Vidar Martin Steen
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | - Eyvind Rødahl
- Department of Ophthalmology, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Ove Bruland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway.
| |
Collapse
|
34
|
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: 69] [Impact Index Per Article: 11.5] [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.
Collapse
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.
| |
Collapse
|
35
|
Xu L, Jensen H, Johnston JJ, Di Maria E, Kloth K, Cristea I, Sapp JC, Darling TN, Huryn LA, Tranebjærg L, Cinotti E, Kubisch C, Rødahl E, Bruland O, Biesecker LG, Houge G, Bredrup C. Recurrent, Activating Variants in the Receptor Tyrosine Kinase DDR2 Cause Warburg-Cinotti Syndrome. Am J Hum Genet 2018; 103:976-983. [PMID: 30449416 DOI: 10.1016/j.ajhg.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
We have investigated a distinct disorder with progressive corneal neovascularization, keloid formation, chronic skin ulcers, wasting of subcutaneous tissue, flexion contractures of the fingers, and acro-osteolysis. In six affected individuals from four families, we found one of two recurrent variants in discoidin domain receptor tyrosine kinase 2 (DDR2): c.1829T>C (p.Leu610Pro) or c.2219A>G (p.Tyr740Cys). DDR2 encodes a collagen-responsive receptor tyrosine kinase that regulates connective-tissue formation. In three of the families, affected individuals comprise singleton adult individuals, and parental samples were not available for verification of the de novo occurrence of the DDR2 variants. In the fourth family, a mother and two of her children were affected, and the c.2219A>G missense variant was proven to be de novo in the mother. Phosphorylation of DDR2 was increased in fibroblasts from affected individuals, suggesting reduced receptor autoinhibition and ligand-independent kinase activation. Evidence for activation of other growth-regulatory signaling pathways was not found. Finally, we found that the protein kinase inhibitor dasatinib prevented DDR2 autophosphorylation in fibroblasts, suggesting an approach to treatment. We propose this progressive, fibrotic condition should be designated as Warburg-Cinotti syndrome.
Collapse
|
36
|
Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
Collapse
Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| |
Collapse
|
37
|
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.
Collapse
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.
| |
Collapse
|
38
|
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.
Collapse
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.
| |
Collapse
|
39
|
Opalinski L, Szczepara M, Sokolowska-Wedzina A, Zakrzewska M, Otlewski J. The autoinhibitory function of D1 domain of FGFR1 goes beyond the inhibition of ligand binding. Int J Biochem Cell Biol 2017; 89:193-198. [PMID: 28652212 DOI: 10.1016/j.biocel.2017.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 01/12/2023]
Abstract
Fibroblast growth factors (FGFs) and their plasma membrane-localized receptors (FGFRs) transduce signals that regulate developmental processes and metabolism. In numerous cancer types genetic aberrations of FGFR1 lead to its uncontrolled activation. To circumvent the unrestrained signal transduction, several intramolecular inhibitory mechanisms within FGFR1 have evolved. In vitro experiments with receptor truncation have demonstrated that the N-terminal D1 domain of FGFR1 negatively regulates ligand binding to the receptor. Here, we show that D1-specific monovalent antibody fragments can activate FGFR1 and its downstream signaling cascades in the absence of ligand. These data suggest that the D1 domain of FGFR1 may play autoinhibitory role not only by controlling ligand binding, but also by regulating the overall conformation of FGFR1, keeping it in a state that disfavors autoactivation in the absence of its cognate growth factor.
Collapse
Affiliation(s)
- Lukasz Opalinski
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Martyna Szczepara
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Aleksandra Sokolowska-Wedzina
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Malgorzata Zakrzewska
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| |
Collapse
|