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Della Corte CM, Viscardi G, Di Liello R, Fasano M, Martinelli E, Troiani T, Ciardiello F, Morgillo F. Role and targeting of anaplastic lymphoma kinase in cancer. Mol Cancer 2018; 17:30. [PMID: 29455642 PMCID: PMC5817803 DOI: 10.1186/s12943-018-0776-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/01/2018] [Indexed: 01/05/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) gene activation is involved in the carcinogenesis process of several human cancers such as anaplastic large cell lymphoma, lung cancer, inflammatory myofibroblastic tumors and neuroblastoma, as a consequence of fusion with other oncogenes (NPM, EML4, TIM, etc) or gene amplification, mutation or protein overexpression. ALK is a transmembrane tyrosine kinase receptor that, upon ligand binding to its extracellular domain, undergoes dimerization and subsequent autophosphorylation of the intracellular kinase domain. When activated in cancer it represents a target for specific inhibitors, such as crizotinib, ceritinib, alectinib etc. which use has demonstrated significant effectiveness in ALK-positive patients, in particular ALK-positive non- small cell lung cancer. Several mechanisms of resistance to these inhibitors have been described and new strategies are underway to overcome the limitations of current ALK inhibitors.
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Affiliation(s)
- Carminia Maria Della Corte
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Giuseppe Viscardi
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Raimondo Di Liello
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Morena Fasano
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Erika Martinelli
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi", University of Campania "Luigi Vanvitelli", via S. Pansini 5, 80131, Naples, Italy.
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52
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Vishwamitra D, George SK, Shi P, Kaseb AO, Amin HM. Type I insulin-like growth factor receptor signaling in hematological malignancies. Oncotarget 2018; 8:1814-1844. [PMID: 27661006 PMCID: PMC5352101 DOI: 10.18632/oncotarget.12123] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/12/2016] [Indexed: 12/19/2022] Open
Abstract
The insulin-like growth factor (IGF) signaling system plays key roles in the establishment and progression of different types of cancer. In agreement with this idea, substantial evidence has shown that the type I IGF receptor (IGF-IR) and its primary ligand IGF-I are important for maintaining the survival of malignant cells of hematopoietic origin. In this review, we discuss current understanding of the role of IGF-IR signaling in cancer with a focus on the hematological neoplasms. We also address the emergence of IGF-IR as a potential therapeutic target for the treatment of different types of cancer including plasma cell myeloma, leukemia, and lymphoma.
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Affiliation(s)
- Deeksha Vishwamitra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Suraj Konnath George
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ahmed O Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA
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Drug Design for ALK-Positive NSCLC: an Integrated Pharmacophore-Based 3D QSAR and Virtual Screening Strategy. Appl Biochem Biotechnol 2017; 185:289-315. [DOI: 10.1007/s12010-017-2650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/26/2017] [Indexed: 12/27/2022]
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54
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Abstract
A vast array of oncogenic variants has been identified for anaplastic lymphoma kinase (ALK). Therefore, there is a need to better understand the role of ALK in cancer biology in order to optimise treatment strategies. This review summarises the latest research on the receptor tyrosine kinase ALK, and how this information can guide the management of patients with cancer that is ALK-positive. A variety of ALK gene alterations have been described across a range of tumour types, including point mutations, deletions and rearrangements. A wide variety of ALK fusions, in which the kinase domain of ALK and the amino-terminal portion of various protein partners are fused, occur in cancer, with echinoderm microtubule-associated protein-like 4 (EML4)-ALK being the most prevalent in non-small-cell lung cancer (NSCLC). Different ALK fusion proteins can mediate different signalling outputs, depending on properties such as subcellular localisation and protein stability. The ALK fusions found in tumours lack spatial and temporal regulation, which can also affect dimerisation and substrate specificity. Two ALK tyrosine kinase inhibitors (TKIs), crizotinib and ceritinib, are currently approved in Europe for use in ALK-positive NSCLC and several others are in development. These ALK TKIs bind slightly differently within the ATP-binding pocket of the ALK kinase domain and are associated with the emergence of different resistance mutation patterns during therapy. This emphasises the need to tailor the sequence of ALK TKIs according to the ALK signature of each patient. Research into the oncogenic functions of ALK, and fast paced development of ALK inhibitors, has substantially improved outcomes for patients with ALK-positive NSCLC. Limited data are available surrounding the physiological ligand-stimulated activation of ALK signalling and further research is needed. Understanding the role of ALK in tumour biology is key to further optimising therapeutic strategies for ALK-positive disease.
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Affiliation(s)
- B Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - R H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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55
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Novel Mechanisms of ALK Activation Revealed by Analysis of the Y1278S Neuroblastoma Mutation. Cancers (Basel) 2017; 9:cancers9110149. [PMID: 29084134 PMCID: PMC5704167 DOI: 10.3390/cancers9110149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/09/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Numerous mutations have been observed in the Anaplastic Lymphoma Kinase (ALK) receptor tyrosine kinase (RTK) in both germline and sporadic neuroblastoma. Here, we have investigated the Y1278S mutation, observed in four patient cases, and its potential importance in the activation of the full length ALK receptor. Y1278S is located in the 1278-YRASYY-1283 motif of the ALK activation loop, which has previously been reported to be important in the activation of the ALK kinase domain. In this study, we have characterized activation loop mutations within the context of the full length ALK employing cell culture and Drosophila melanogaster model systems. Our results show that the Y1278S mutant observed in patients with neuroblastoma harbors gain-of-function activity. Secondly, we show that the suggested interaction between Y1278 and other amino acids might be of less importance in the activation process of the ALK kinase than previously proposed. Thirdly, of the three individual tyrosines in the 1278-YRASYY-1283 activation loop, we find that Y1283 is the critical tyrosine in the activation process. Taken together, our observations employing different model systems reveal new mechanistic insights on how the full length ALK receptor is activated and highlight differences with earlier described activation mechanisms observed in the NPM-ALK fusion protein, supporting a mechanism of activation more in line with those observed for the Insulin Receptor (InR).
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56
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Anaplastic lymphoma kinase L1198F and G1201E mutations identified in anaplastic thyroid cancer patients are not ligand-independent. Oncotarget 2017; 8:11566-11578. [PMID: 28030793 PMCID: PMC5355286 DOI: 10.18632/oncotarget.14141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Activating mutations in full length anaplastic lymphoma kinase (ALK) have been reported in neuroblastoma and in anaplastic thyroid cancer. ALK-L1198F and ALK-G1201E mutations were originally identified in anaplastic thyroid cancer (ATC) and characterized as constitutively activating mutations. In this study, we employed in vitro cell culture assays together with biochemical and in vivo Drosophila analyses to characterize their sensitivity to either activation by the FAM150A (AUG-β) and FAM150B (AUG-α) ALK ligands or inhibition by ALK inhibitors. Here we report that neither ALK-L1198F nor ALK-G1201E mutations result in ligand independent gain-of-function (GOF) activity in either in vitro biochemical analysis or the various model systems employed. ALK-L1198F is activated by the FAM150 (AUG) ligands and its ligand-dependant activity is similar to the wild type full length ALK receptor. ALK-G1201E is only very weakly activated by the FAM150 (AUG) ligands, most likely due to impaired protein stability. We conclude that neither ALK-L1198F nor ALK-G1201E displays ligand independent kinase activity, with ALK-L1198F belonging to the class of ligand dependent ALK mutations which are not constitutively active but that responds to ligand activation, while the ALK-G1201E mutation generates an unstable receptor with very low levels of kinase activity.
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57
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Takita J. The role of anaplastic lymphoma kinase in pediatric cancers. Cancer Sci 2017; 108:1913-1920. [PMID: 28756644 PMCID: PMC5623752 DOI: 10.1111/cas.13333] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023] Open
Abstract
The anaplastic lymphoma kinase (ALK) gene was initially identified as a fusion partner of the nucleophosmin gene in anaplastic large-cell lymphoma with t(2;5)(p23;q35) translocation, and then described with different genetic abnormalities in a number of tumors. Although ALK is known to be involved in the pathogenesis of neuroblastoma through activating mutations or gene amplification, its role in the pathogenesis of other pediatric cancers is still elusive. In addition to neuroblastoma, the high-grade amplification of ALK has been described in a subset of rhabdomyosarcoma cases. Normal ALK protein expression is restricted to the nervous systems of adult mammals, but the aberrant expression of ALK has been observed in a variety of pediatric cancers, including glioma and Ewing sarcoma. The discovery of oncogenic activation of ALK in neuroblastoma suggests that this cancer could be potentially treated with an ALK inhibitor, as could other cancers, such as non-small-cell lung cancer and anaplastic large-cell lymphoma. However, cellular responses to mutant ALK are complex when compared to rearranged ALK, and treatment remains a challenge. This review focuses on the biology of ALK in pediatric cancers and possible therapeutic strategies for ALK-associated tumors.
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Affiliation(s)
- Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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58
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F1174V mutation alters the ALK active conformation in response to Crizotinib in NSCLC: Insight from molecular simulations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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59
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TKI-addicted ROS1-rearranged cells are destined to survival or death by the intensity of ROS1 kinase activity. Sci Rep 2017; 7:5519. [PMID: 28717217 PMCID: PMC5514057 DOI: 10.1038/s41598-017-05736-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022] Open
Abstract
ROS1 rearrangement is observed in 1–2% of non-small cell lung cancers (NSCLC). The ROS1 tyrosine kinase inhibitor (TKI) crizotinib has induced marked tumour shrinkage in ROS1-rearranged cancers. However, emergence of acquired resistance to TKI is inevitable within a few years. Previous findings indicate that cabozantinib overcomes secondary mutation–mediated crizotinib-resistance in ROS1-fusion-positive cells. Here we attempted to establish cabozantinib-resistant cells by N-ethyl-N-nitrosourea mutagenesis screening using CD74-ROS1–expressing Ba/F3 cells. Two resistant cell lines with CD74-ROS1 F2004V or F2075C mutations, which are homologous to ALK F1174 or F1245 mutations, survived in the presence of a low dose of ROS1-TKI. Removal of ROS1-TKI from these TKI-addicted cells induced excessive activation of ROS1 tyrosine kinase followed by apoptosis. We succeeded in recapturing the TKI-addicted phenotype using doxycycline-inducible CD74-ROS1 mutant over-expression in Ba/F3 cells, suggesting that excessive ROS1 oncogenic signaling itself induced apoptosis instead of cell growth. Phosphoproteomic analysis and high-throughput inhibitor screening revealed that excessive ROS1 signaling in the TKI-addicted cells phosphorylated or activated apoptosis-related molecules such as FAF1 or p38. Collectively, our findings partly clarify molecular mechanisms of excessive ROS1 oncogenic signaling that mediates paradoxical induction of apoptosis.
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60
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Zhao Z, Xie L, Bourne PE. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS One 2017; 12:e0179936. [PMID: 28628649 PMCID: PMC5476283 DOI: 10.1371/journal.pone.0179936] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/06/2017] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are critical drug targets for treating a large variety of human diseases. Type-III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We hypothesize that the helix-folding activation loop is a hallmark allosteric binding site for type-III inhibitors. Subsequently, we screened and predicted allosteric binding sites across the human kinome, suggesting other kinases as potential targets suitable for type-III inhibitors.
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Affiliation(s)
- Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, United States of America
- The Graduate Center, The City University of New York, New York, United States of America
| | - Philip E. Bourne
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
- Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
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61
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Roskoski R. Anaplastic lymphoma kinase (ALK) inhibitors in the treatment of ALK-driven lung cancers. Pharmacol Res 2017; 117:343-356. [DOI: 10.1016/j.phrs.2017.01.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/24/2022]
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62
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Palmirotta R, Quaresmini D, Lovero D, Silvestris F. ALK gene alterations in cancer: biological aspects and therapeutic implications. Pharmacogenomics 2017; 18:277-292. [PMID: 28112990 DOI: 10.2217/pgs-2016-0166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
ALK was first reported in 1994 as a translocation in anaplastic large cell lymphoma and then described with different abnormalities in a number of tumors. Recently, a shortly accumulated biomedical research clarified the numerous biological processes underlying its ability to support cancer development, growth and progression. Advent of precision medicine has finally provided unexpected advances, leading to the development of ALK-targeting inhibitors with superior efficacy as compared with standard chemotherapy regimens, as well as the identification of resistance mechanisms and the creation of ‘next-generation’ treatments. This review summarizes the current understanding of ALK-driven cancers from the oncogenesis and mutation frequency by The Cancer Genome Atlas database through the diagnostic approach, to an updated portrait of available tyrosine kinase inhibitors, considering their effectiveness in cancer treatment, the molecular reasons of therapeutic failure, and the actual and future ways to overcome resistances.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Davide Quaresmini
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Domenica Lovero
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
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63
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Chen J, Wang J, Zhu W. Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling. Phys Chem Chem Phys 2017; 19:30239-30248. [DOI: 10.1039/c7cp05418a] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the treatment of tumors and the mutation L1196M induces different levels of drug resistance toward the existing inhibitors.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University
- Jinan
- China
| | - Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences
- Shanghai
- China
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences
- Shanghai
- China
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Molecular dynamics simulations reveal the allosteric effect of F1174C resistance mutation to ceritinib in ALK-associated lung cancer. Comput Biol Chem 2016; 65:54-60. [DOI: 10.1016/j.compbiolchem.2016.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/13/2016] [Accepted: 10/05/2016] [Indexed: 01/14/2023]
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65
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Zhao Z, Verma V, Zhang M. Anaplastic lymphoma kinase: Role in cancer and therapy perspective. Cancer Biol Ther 2016; 16:1691-701. [PMID: 26529396 DOI: 10.1080/15384047.2015.1095407] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is correlated with oncogenesis in different types of cancers, such as anaplastic large cell lymphoma, lung cancer, neuroblastoma, and even breast cancer, by abnormal fusion of ALK or non-fusion ALK activation. ALK is a receptor tyrosine kinase, with a single transmembrane domain, that plays an important role in development. Upon ligand binding to the extracellular domain, the receptor undergoes dimerization and subsequent autophosphorylation of the intracellular kinase domain. In recent years, ALK inhibitors have been developed for cancer treatment. These inhibitors target ALK activity and show effectiveness in ALK-positive non-small cell lung cancer. However, acquired treatment resistance makes the future of this therapy unclear; new strategies are underway to overcome the limitations of current ALK inhibitors.
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Affiliation(s)
- Zhihong Zhao
- a Munroe-Meyer Institute; University of Nebraska Medical Center ; Omaha , NE , USA
| | - Vivek Verma
- b Department of Radiation Oncology ; University of Nebraska Medical Center ; Omaha , NE , USA
| | - Mutian Zhang
- b Department of Radiation Oncology ; University of Nebraska Medical Center ; Omaha , NE , USA
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66
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Insight into drug resistance mechanisms and discovery of potential inhibitors against wild-type and L1196M mutant ALK from FDA-approved drugs. J Mol Model 2016; 22:231. [PMID: 27585676 DOI: 10.1007/s00894-016-3099-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/08/2016] [Indexed: 01/10/2023]
Abstract
Anaplastic lymphoma kinase (ALK) plays a crucial role in multiple malignant cancers. It is known as a well-established target for the treatment of ALK-dependent cancers. Even though substantial efforts have been made to develop ALK inhibitors, only crizotinib, ceritinib, and alectinib had been approved by the U.S. Food and Drug Administration for patients with ALK-positive non-small cell lung cancer (NSCLC). The secondary mutations with drug-resistance bring up difficulties to develop effective drugs for ALK-positive cancers. To give a comprehensive understanding of molecular mechanism underlying inhibitor response to ALK tyrosine kinase mutations, we established an accurate assessment for the extensive profile of drug against ALK mutations by means of computational approaches. The molecular mechanics-generalized Born surface area (MM-GBSA) method based on molecular dynamics (MD) simulation was carried out to calculate relative binding free energies for receptor-drug systems. In addition, the structure-based virtual screening was utilized to screen effective inhibitors targeting wild-type ALK and the gatekeeper mutation L1196M from 3180 approved drugs. Finally, the mechanism of drug resistance was discussed, several novel potential wild-type and L1196M mutant ALK inhibitors were successfully identified.
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67
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Sami N, Kumar V, Islam A, Ali S, Ahmad F, Hassan I. Exploring Missense Mutations in Tyrosine Kinases Implicated with Neurodegeneration. Mol Neurobiol 2016; 54:5085-5106. [PMID: 27544236 DOI: 10.1007/s12035-016-0046-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022]
Abstract
Protein kinases are one of the largest families of evolutionarily related proteins and the third most common protein class of human genome. All the protein kinases share the same structural organization. They are made up of an extracellular domain, transmembrane domain and an intra cellular kinase domain. Missense mutations in these kinases have been studied extensively and correlated with various neurological disorders. Individual mutations in the kinase domain affect the functions of protein. The enhanced or reduced expression of protein leads to hyperactivation or inactivation of the signalling pathways, resulting in neurodegeneration. Here, we present extensive analyses of missense mutations in the tyrosine kinase focussing on the neurodegenerative diseases encompassing structure function relationship. This is envisaged to enhance our understanding about the neurodegeneration and possible therapeutic measures.
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Affiliation(s)
- Neha Sami
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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68
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Sun H, Pan P, Tian S, Xu L, Kong X, Li Y, Dan Li, Hou T. Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery. Sci Rep 2016; 6:24817. [PMID: 27102549 PMCID: PMC4840416 DOI: 10.1038/srep24817] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/06/2016] [Indexed: 01/23/2023] Open
Abstract
The MIEC-SVM approach, which combines molecular interaction energy components (MIEC) derived from free energy decomposition and support vector machine (SVM), has been found effective in capturing the energetic patterns of protein-peptide recognition. However, the performance of this approach in identifying small molecule inhibitors of drug targets has not been well assessed and validated by experiments. Thereafter, by combining different model construction protocols, the issues related to developing best MIEC-SVM models were firstly discussed upon three kinase targets (ABL, ALK, and BRAF). As for the investigated targets, the optimized MIEC-SVM models performed much better than the models based on the default SVM parameters and Autodock for the tested datasets. Then, the proposed strategy was utilized to screen the Specs database for discovering potential inhibitors of the ALK kinase. The experimental results showed that the optimized MIEC-SVM model, which identified 7 actives with IC50 < 10 μM from 50 purchased compounds (namely hit rate of 14%, and 4 in nM level) and performed much better than Autodock (3 actives with IC50 < 10 μM from 50 purchased compounds, namely hit rate of 6%, and 2 in nM level), suggesting that the proposed strategy is a powerful tool in structure-based virtual screening.
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Affiliation(s)
- Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Lei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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69
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Mologni L, Ceccon M, Pirola A, Chiriano G, Piazza R, Scapozza L, Gambacorti-Passerini C. NPM/ALK mutants resistant to ASP3026 display variable sensitivity to alternative ALK inhibitors but succumb to the novel compound PF-06463922. Oncotarget 2016; 6:5720-34. [PMID: 25749034 PMCID: PMC4467397 DOI: 10.18632/oncotarget.3122] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/09/2015] [Indexed: 01/12/2023] Open
Abstract
ALK is involved in the onset of several tumors. Crizotinib (XalkoriTM), a potent ALK inhibitor, represents the current front-line treatment for ALK+ NSCLC and shows great clinical efficacy. However, resistant disease often develops after initial response. ASP3026 is a novel second-generation ALK inhibitor with activity on crizotinib-resistant ALK-L1196M gatekeeper mutant. As resistance is likely to be a relevant hurdle for any drug, we sought to determine the resistance profile of ASP3026 in the context of NPM/ALK+ ALCL. We selected six ASP3026-resistant cell lines by culturing human ALCL cells in the presence of increasing concentrations of drug. The established resistant cell lines carry several point mutations in the ALK kinase domain (G1128S, C1156F, I1171N/T, F1174I, N1178H, E1210K and C1156F/D1203N were the most frequent) that are shown to confer resistance to ASP3026 in the Ba/F3 cell model. All mutants were profiled for cross-resistance against a panel of clinically relevant inhibitors including ceritinib, alectinib, crizotinib, AP26113 and PF-06463922. Finally, a genetically heterogeneous ASP3026-resistant cell line was exposed to second-line treatment simulations with all inhibitors. The population evolved according to relative sensitivity of its mutant subclones to the various drugs. Compound PF-06463922 did not allow the outgrowth of any resistant clone, at non-toxic doses.
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Affiliation(s)
- Luca Mologni
- University of Milano-Bicocca, Dept. of Health Sciences, Monza, Italy
| | - Monica Ceccon
- University of Milano-Bicocca, Dept. of Health Sciences, Monza, Italy
| | - Alessandra Pirola
- University of Milano-Bicocca, Dept. of Health Sciences, Monza, Italy
| | - Gianpaolo Chiriano
- University of Geneva, School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Rocco Piazza
- University of Milano-Bicocca, Dept. of Health Sciences, Monza, Italy
| | - Leonardo Scapozza
- University of Geneva, School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Carlo Gambacorti-Passerini
- University of Milano-Bicocca, Dept. of Health Sciences, Monza, Italy.,San Gerardo Hospital, Hematology Unit, Monza, Italy
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70
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Bayliss R, Choi J, Fennell DA, Fry AM, Richards MW. Molecular mechanisms that underpin EML4-ALK driven cancers and their response to targeted drugs. Cell Mol Life Sci 2016; 73:1209-24. [PMID: 26755435 PMCID: PMC4761370 DOI: 10.1007/s00018-015-2117-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/14/2015] [Indexed: 02/05/2023]
Abstract
A fusion between the EML4 (echinoderm microtubule-associated protein-like) and ALK (anaplastic lymphoma kinase) genes was identified in non-small cell lung cancer (NSCLC) in 2007 and there has been rapid progress in applying this knowledge to the benefit of patients. However, we have a poor understanding of EML4 and ALK biology and there are many challenges to devising the optimal strategy for treating EML4-ALK NSCLC patients. In this review, we describe the biology of EML4 and ALK, explain the main features of EML4-ALK fusion proteins and outline the therapies that target EML4-ALK. In particular, we highlight the recent advances in our understanding of the structures of EML proteins, describe the molecular mechanisms of resistance to ALK inhibitors and assess current thinking about combinations of ALK drugs with inhibitors that target other kinases or Hsp90.
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Affiliation(s)
- Richard Bayliss
- Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester, LE2 9HN, UK.
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43 gil, Seoul, Korea
| | - Dean A Fennell
- Cancer Research UK Centre, University of Leicester, Lancaster Road, Leicester, LE3 9SQ, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester, LE2 9HN, UK
| | - Mark W Richards
- Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester, LE2 9HN, UK
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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71
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Tucker ER, Danielson LS, Innocenti P, Chesler L. Tackling Crizotinib Resistance: The Pathway from Drug Discovery to the Pediatric Clinic. Cancer Res 2015; 75:2770-4. [PMID: 26122839 PMCID: PMC4539575 DOI: 10.1158/0008-5472.can-14-3817] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 03/24/2015] [Indexed: 01/23/2023]
Abstract
Neuroblastoma is a childhood malignancy that has not yet benefitted from the rapid progress in the development of small-molecule therapeutics for cancer. An opportunity to take advantage of pharmaceutical innovation in this area arose when the identification of ALK fusion proteins in non-small cell lung cancer (NSCLC) occurred in parallel to the discovery of point mutations of ALK in neuroblastomas. ALK is now known to be a marker of poor outcome in neuroblastoma, and therefore, urgent development of specific ALK inhibitors to treat this devastating disease is a necessity. However, the translation of small molecules from adult directly into pediatric practice has thus far been challenging, due to mutation-specific structural variances in the ALK kinase domain. We discuss how the most recent structural and biological characterizations of ALK are directing preclinical and clinical studies of ALK inhibitors for both NSCLC and neuroblastoma.
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Affiliation(s)
- Elizabeth R Tucker
- Paediatric Solid Tumour Biology and Therapeutics Team, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Laura S Danielson
- Paediatric Solid Tumour Biology and Therapeutics Team, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Paolo Innocenti
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Louis Chesler
- Paediatric Solid Tumour Biology and Therapeutics Team, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
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72
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Ni Z, Zhang TC. Computationally unraveling how ceritinib overcomes drug-resistance mutations in ALK-rearranged lung cancer. J Mol Model 2015; 21:175. [DOI: 10.1007/s00894-015-2716-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023]
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73
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Puig de la Bellacasa R, Karachaliou N, Estrada-Tejedor R, Teixidó J, Costa C, Borrell JI. ALK and ROS1 as a joint target for the treatment of lung cancer: a review. Transl Lung Cancer Res 2015; 2:72-86. [PMID: 25806218 DOI: 10.3978/j.issn.2218-6751.2013.03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/25/2013] [Indexed: 12/14/2022]
Abstract
Rearrangements of the anaplastic lymphoma kinase (ALK) have been described in multiple malignancies, including non-small cell lung cancer (NSCLC). ALK fusions have gain of function properties while activating mutations in wild-type ALK can also occur within the tyrosine kinase domain. ALK rearrangements define a new molecular subtype of NSCLC that is exquisitely sensitive to ALK inhibition. Crizotinib, an orally available small molecule ATP-mimetic compound which was originally designed as a MET inhibitor, was recognized to have "off-target" anti-ALK activity and has been approved in the USA for the treatment of patients with ALK-positive NSCLC. Chromosomal rearrangements involving the ROS1 receptor tyrosine kinase have also been recently described in NSCLC, while crizotinib is currently under clinical trial in this molecular subset of NSCLC patients. The basic approaches of any computer aided drug design work in terms of structure and ligand based drug design. Details of each of these approaches should be covered with an emphasis on utilizing both in order to develop multi-targeted small-molecule kinase inhibitors. Such multi-targeted tyrosine kinase inhibitors can have antiproliferative activity against both ROS1and ALK rearranged NSCLC. Herein, we highlight the importance of targeting these proteins and the advances in optimizing more potent and selective ALK and ROS1 kinase inhibitors.
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Affiliation(s)
- Raimon Puig de la Bellacasa
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Niki Karachaliou
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - Roger Estrada-Tejedor
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Carlota Costa
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - José I Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
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74
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Ai X, Shen S, Shen L, Lu S. An interaction map of small-molecule kinase inhibitors with anaplastic lymphoma kinase (ALK) mutants in ALK-positive non-small cell lung cancer. Biochimie 2015; 112:111-20. [PMID: 25769414 DOI: 10.1016/j.biochi.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Human anaplastic lymphoma kinase (ALK) has become a well-established target for the treatment of ALK-positive non-small cell lung cancer (NSCLC). Here, we have profiled seven small-molecule inhibitors, including 2 that are approved drugs, against a panel of clinically relevant mutations in ALK tyrosine kinase (TK) domain, aiming at a comprehensive understanding of molecular mechanism and biological implication underlying inhibitor response to ALK TK mutation. We find that (i) the gatekeeper mutation L1196M causes crizotinib resistance by simultaneously increasing and decreasing the binding affinities of, respectively, ATP and inhibitor to ALK, whereas the secondary mutation C1156Y, which is located far away from the ATP-binding site of ALK TK domain, causes the resistance by inducing marked allosteric effect on the site, (ii) the 2nd and 3rd generation kinase inhibitors exhibit relatively high sensitivity towards ALK mutants as compared to 1st generation inhibitors, (iii) the pan-kinase inhibitor staurosporine is insensitive for most mutations due to its high structural compatibility, and (iv) ATP affinity to ALK is generally reduced upon most clinically relevant mutations. Furthermore, we also identify six novel mutation-inhibitor pairs that are potentially associated with drug resistance. In addition, the G1202R and C1156Y mutations are expected to generally cause resistance for many existing inhibitors, since they can address significant effect on the geometric shape and physicochemical property of ALK active pocket.
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Affiliation(s)
- Xinghao Ai
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shengping Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lan Shen
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.
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75
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Parker AR, Petluru PN, Nienaber VL, Zhao M, Ayala PY, Badger J, Chie-Leon B, Sridhar V, Logan C, Kochat H, Hausheer FH. Novel covalent modification of human anaplastic lymphoma kinase (ALK) and potentiation of crizotinib-mediated inhibition of ALK activity by BNP7787. Onco Targets Ther 2015; 8:375-83. [PMID: 25678804 PMCID: PMC4324543 DOI: 10.2147/ott.s73690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BNP7787 (Tavocept, disodium 2,2′-dithio-bis-ethanesulfonate) is a novel, investigational, water-soluble disulfide that is well-tolerated and nontoxic. In separate randomized multicenter Phase II and Phase III clinical trials in non-small-cell lung cancer (NSCLC) patients, treatment with BNP7787 in combination with standard chemotherapy resulted in substantial increases in the overall survival of patients with advanced adenocarcinoma of the lung in the first-line treatment setting. We hypothesized that BNP7787 might interact with and modify human anaplastic lymphoma kinase (ALK). At least seven different variants of ALK fusions with the gene encoding the echinoderm microtubule-associated protein-like 4 (EML4) are known to occur in NSCLC. EML4–ALK fusions are thought to account for approximately 3% of NSCLC cases. Herein, we report the covalent modification of the kinase domain of human ALK by a BNP7787-derived mesna moiety and the functional consequences of this modification in ALK assays evaluating kinase activity. The kinase domain of the ALK protein crystallizes as a monomer, and BNP7787-derived mesna-cysteine adducts were observed at Cys 1235 and Cys 1156. The BNP7787-derived mesna adduct at Cys 1156 is located in close proximity to the active site and results in substantial disorder of the P-loop and activation loop (A-loop). Comparison with the P-loop of apo-ALK suggests that the BNP7787-derived mesna adduct at Cys 1156 interferes with the positioning of Phe 1127 into a small pocket now occupied by mesna, resulting in a destabilization of the loop’s binding orientation. Additionally, in vitro kinase activity assays indicate that BNP7787 inhibits ALK catalytic activity and potentiates the activity of the ALK-targeted drug crizotinib.
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Affiliation(s)
| | | | | | - Min Zhao
- BioNumerik Pharmaceuticals, Inc., San Antonio, TX, USA
| | | | - John Badger
- Zenobia Therapeutics, Inc., La Jolla, CA, USA
| | | | | | | | - Harry Kochat
- BioNumerik Pharmaceuticals, Inc., San Antonio, TX, USA
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76
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Cui W, Parker LL. A time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) activity. Chem Commun (Camb) 2014; 51:362-5. [PMID: 25406835 DOI: 10.1039/c4cc07453j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) was developed. We used a straightforward strategy to modify a known ALK substrate into a peptide biosensor that can accommodate terbium luminescence sensitization upon its phosphorylation by ALK. Since this strategy is generalizable, this high-throughput screening compatible assay serves as an example for development of other kinase assays that employ terbium luminescence as a read-out.
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Affiliation(s)
- Wei Cui
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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77
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Bresler SC, Weiser DA, Huwe PJ, Park JH, Krytska K, Ryles H, Laudenslager M, Rappaport EF, Wood AC, McGrady PW, Hogarty MD, London WB, Radhakrishnan R, Lemmon MA, Mossé YP. ALK mutations confer differential oncogenic activation and sensitivity to ALK inhibition therapy in neuroblastoma. Cancer Cell 2014; 26:682-94. [PMID: 25517749 PMCID: PMC4269829 DOI: 10.1016/j.ccell.2014.09.019] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/13/2014] [Accepted: 09/25/2014] [Indexed: 02/01/2023]
Abstract
Genetic studies have established anaplastic lymphoma kinase (ALK), a cell surface receptor tyrosine kinase, as a tractable molecular target in neuroblastoma. We describe comprehensive genomic, biochemical, and computational analyses of ALK mutations across 1,596 diagnostic neuroblastoma samples. ALK tyrosine kinase domain mutations occurred in 8% of samples--at three hot spots and 13 minor sites--and correlated significantly with poorer survival in high- and intermediate-risk neuroblastoma. Biochemical and computational studies distinguished oncogenic (constitutively activating) from nononcogenic mutations and allowed robust computational prediction of their effects. The mutated variants also showed differential in vitro crizotinib sensitivities. Our studies identify ALK genomic status as a clinically important therapeutic stratification tool in neuroblastoma and will allow tailoring of ALK-targeted therapy to specific mutations.
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Affiliation(s)
- Scott C Bresler
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Daniel A Weiser
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter J Huwe
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jin H Park
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hannah Ryles
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marci Laudenslager
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eric F Rappaport
- Nucleic Acid Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andrew C Wood
- Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Patrick W McGrady
- Department of Biostatistics, Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL 32611, USA
| | - Michael D Hogarty
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wendy B London
- Department of Biostatistics, Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL 32611, USA; Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
| | - Ravi Radhakrishnan
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark A Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Yaël P Mossé
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Oncology and Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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78
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Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective. BIOMED RESEARCH INTERNATIONAL 2014; 2014:895831. [PMID: 25054154 PMCID: PMC4098886 DOI: 10.1155/2014/895831] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 01/13/2023]
Abstract
Over the past decade, advancements in next generation sequencing technology have placed personalized genomic medicine upon horizon. Understanding the likelihood of disease causing mutations in complex diseases as pathogenic or neutral remains as a major task and even impossible in the structural context because of its time consuming and expensive experiments. Among the various diseases causing mutations, single nucleotide polymorphisms (SNPs) play a vital role in defining individual's susceptibility to disease and drug response. Understanding the genotype-phenotype relationship through SNPs is the first and most important step in drug research and development. Detailed understanding of the effect of SNPs on patient drug response is a key factor in the establishment of personalized medicine. In this paper, we represent a computational pipeline in anaplastic lymphoma kinase (ALK) for SNP-centred study by the application of in silico prediction methods, molecular docking, and molecular dynamics simulation approaches. Combination of computational methods provides a way in understanding the impact of deleterious mutations in altering the protein drug targets and eventually leading to variable patient's drug response. We hope this rapid and cost effective pipeline will also serve as a bridge to connect the clinicians and in silico resources in tailoring treatments to the patients' specific genotype.
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79
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Tomiyama A, Uekita T, Kamata R, Sasaki K, Takita J, Ohira M, Nakagawara A, Kitanaka C, Mori K, Yamaguchi H, Sakai R. Flotillin-1 regulates oncogenic signaling in neuroblastoma cells by regulating ALK membrane association. Cancer Res 2014; 74:3790-801. [PMID: 24830726 DOI: 10.1158/0008-5472.can-14-0241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neuroblastomas harbor mutations in the nonreceptor anaplastic lymphoma kinase (ALK) in 8% to 9% of cases where they serve as oncogenic drivers. Strategies to reduce ALK activity offer clinical interest based on initial findings with ALK kinase inhibitors. In this study, we characterized phosphotyrosine-containing proteins associated with ALK to gain mechanistic insights in this setting. Flotillin-1 (FLOT1), a plasma membrane protein involved in endocytosis, was identified as a binding partner of ALK. RNAi-mediated attenuation of FLOT1 expression in neuroblastoma cells caused ALK dissociation from endosomes along with membrane accumulation of ALK, thereby triggering activation of ALK and downstream effector signals. These features enhanced the malignant properties of neuroblastoma cells in vitro and in vivo. Conversely, oncogenic ALK mutants showed less binding affinity to FLOT1 than wild-type ALK. Clinically, lower expression levels of FLOT1 were documented in highly malignant subgroups of human neuroblastoma specimens. Taken together, our findings suggest that attenuation of FLOT1-ALK binding drives malignant phenotypes of neuroblastoma by activating ALK signaling.
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Affiliation(s)
- Arata Tomiyama
- Authors' Affiliations: Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute; Department of Neurosurgery, National Defense Medical College, Saitama
| | - Takamasa Uekita
- Authors' Affiliations: Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute; Department of Applied Chemistry, National Defense Academy, Kanagawa
| | - Reiko Kamata
- Authors' Affiliations: Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute
| | - Kazuki Sasaki
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research Institute, Osaka
| | - Junko Takita
- Department of Cell Therapy and Transplantation Medicine, Graduate School of medicine, The University of Tokyo, Tokyo
| | | | - Akira Nakagawara
- Biochemistry and Innovative Cancer, Chiba Cancer Center Research Institute, Chiba; and
| | - Chifumi Kitanaka
- Department of Molecular Cancer Science, Yamagata University School of Medicine, Yamagata, Japan
| | - Kentaro Mori
- Department of Neurosurgery, National Defense Medical College, Saitama
| | - Hideki Yamaguchi
- Authors' Affiliations: Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute
| | - Ryuichi Sakai
- Authors' Affiliations: Division of Metastasis and Invasion Signaling, National Cancer Center Research Institute;
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80
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Karabencheva TG, Lee CC, Black GW, Donev R, Christov CZ. How does conformational flexibility influence key structural features involved in activation of anaplastic lymphoma kinase? MOLECULAR BIOSYSTEMS 2014; 10:1490-5. [PMID: 24675991 DOI: 10.1039/c4mb00141a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Anaplastic Lymphoma Kinase (ALK) plays a major role in developing tumor processes and therefore has emerged as a validated therapeutic target. Applying atomistic molecular dynamics simulations on the wild type enzyme and the nine most frequently occurring and clinically important activation mutants we revealed important conformational effects on key interactions responsible for the activation of the enzyme.
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Affiliation(s)
- Tatyana G Karabencheva
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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81
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Friboulet L, Li N, Katayama R, Lee CC, Gainor JF, Crystal AS, Michellys PY, Awad MM, Yanagitani N, Kim S, Pferdekamper AC, Li J, Kasibhatla S, Sun F, Sun X, Hua S, McNamara P, Mahmood S, Lockerman EL, Fujita N, Nishio M, Harris JL, Shaw AT, Engelman JA. The ALK inhibitor ceritinib overcomes crizotinib resistance in non-small cell lung cancer. Cancer Discov 2014; 4:662-673. [PMID: 24675041 DOI: 10.1158/2159-8290.cd-13-0846] [Citation(s) in RCA: 629] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
UNLABELLED Non-small cell lung cancers (NSCLC) harboring anaplastic lymphoma kinase (ALK) gene rearrangements invariably develop resistance to the ALK tyrosine kinase inhibitor (TKI) crizotinib. Herein, we report the first preclinical evaluation of the next-generation ALK TKI, ceritinib (LDK378), in the setting of crizotinib resistance. An interrogation of in vitro and in vivo models of acquired resistance to crizotinib, including cell lines established from biopsies of patients with crizotinib-resistant NSCLC, revealed that ceritinib potently overcomes crizotinib-resistant mutations. In particular, ceritinib effectively inhibits ALK harboring L1196M, G1269A, I1171T, and S1206Y mutations, and a cocrystal structure of ceritinib bound to ALK provides structural bases for this increased potency. However, we observed that ceritinib did not overcome two crizotinib-resistant ALK mutations, G1202R and F1174C, and one of these mutations was identified in 5 of 11 biopsies from patients with acquired resistance to ceritinib. Altogether, our results demonstrate that ceritinib can overcome crizotinib resistance, consistent with clinical data showing marked efficacy of ceritinib in patients with crizotinib-resistant disease. SIGNIFICANCE The second-generation ALK inhibitor ceritinib can overcome several crizotinib-resistant mutations and is potent against several in vitro and in vivo laboratory models of acquired resistance to crizotinib. These findings provide the molecular basis for the marked clinical activity of ceritinib in patients with ALK-positive NSCLC with crizotinib-resistant disease. Cancer Discov; 4(6); 662-73. ©2014 AACR. See related commentary by Ramalingam and Khuri, p. 634 This article is highlighted in the In This Issue feature, p. 621.
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Affiliation(s)
- Luc Friboulet
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Ryohei Katayama
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, JAPAN
| | - Christian C Lee
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adam S Crystal
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mark M Awad
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Noriko Yanagitani
- Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, JAPAN
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | | | - Jie Li
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | | | - Frank Sun
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Xiuying Sun
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Su Hua
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Peter McNamara
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Sidra Mahmood
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth L Lockerman
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Naoya Fujita
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, JAPAN
| | - Makoto Nishio
- Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, JAPAN
| | - Jennifer L Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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82
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Iqbal MA, Siddiqui FA, Chaman N, Gupta V, Kumar B, Gopinath P, Bamezai RNK. Missense mutations in pyruvate kinase M2 promote cancer metabolism, oxidative endurance, anchorage independence, and tumor growth in a dominant negative manner. J Biol Chem 2014; 289:8098-105. [PMID: 24492614 DOI: 10.1074/jbc.m113.515742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The present study was designed to examine the functional relevance of two heterozygous mutations (H391Y and K422R), observed earlier by us in the Bloom syndrome condition. Cells stably expressing exogenous wild-type or mutant PKM2 (K422R or H391Y) or co-expressing both wild type and mutant (PKM2-K422R or PKM2-H391Y) were assessed for cancer metabolism and tumorigenic potential. Interestingly, cells co-expressing PKM2 and mutant (K422R or H391Y) showed significantly aggressive cancer metabolism as compared with cells expressing either wild-type or mutant PKM2 independently. A similar trend was observed for oxidative endurance, tumorigenic potential, cellular proliferation, and tumor growth. These observations signify the dominant negative nature of mutations. Remarkably, PKM2-H391Y co-expressed cells showed a maximal effect on all the studied parameters. Such a dominant negative impaired function of PKM2 in tumor development is not known; this study demonstrates for the first time the possible predisposition of Bloom syndrome patients with impaired PKM2 activity to cancer and the importance of studying genetic variations in PKM2 in the future to understand their relevance in cancer in general.
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Affiliation(s)
- Mohd Askandar Iqbal
- From the National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067 India
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83
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Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer. Proc Natl Acad Sci U S A 2014; 111:4233-8. [PMID: 24613930 DOI: 10.1073/pnas.1321937111] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thyroid cancer is a common endocrine malignancy that encompasses well-differentiated as well as dedifferentiated cancer types. The latter tumors have high mortality and lack effective therapies. Using a paired-end RNA-sequencing approach, we report the discovery of rearrangements involving the anaplastic lymphoma kinase (ALK) gene in thyroid cancer. The most common of these involves a fusion between ALK and the striatin (STRN) gene, which is the result of a complex rearrangement involving the short arm of chromosome 2. STRN-ALK leads to constitutive activation of ALK kinase via dimerization mediated by the coiled-coil domain of STRN and to a kinase-dependent, thyroid-stimulating hormone-independent proliferation of thyroid cells. Moreover, expression of STRN-ALK transforms cells in vitro and induces tumor formation in nude mice. The kinase activity of STRN-ALK and the ALK-induced cell growth can be blocked by the ALK inhibitors crizotinib and TAE684. In addition to well-differentiated papillary cancer, STRN-ALK was found with a higher prevalence in poorly differentiated and anaplastic thyroid cancers, and it did not overlap with other known driver mutations in these tumors. Our data demonstrate that STRN-ALK fusion occurs in a subset of patients with highly aggressive types of thyroid cancer and provide initial evidence suggesting that it may represent a therapeutic target for these patients.
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84
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Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T. Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Phys Chem Chem Phys 2014; 16:22035-45. [DOI: 10.1039/c4cp03179b] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We have thoroughly investigated the performance of MM/GBSA and MM/PBSA methodologies on virtual screening based on various protocols for kinase targets.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
- College of Pharmaceutical Sciences
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Mingyun Shen
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Lei Xu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou, P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou, P. R. China
| | - Yan Guan
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices and Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou, P. R. China
- College of Pharmaceutical Sciences
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85
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ALK: Anaplastic lymphoma kinase. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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86
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ALK as a paradigm of oncogenic promiscuity: different mechanisms of activation and different fusion partners drive tumors of different lineages. Cancer Genet 2013; 206:357-73. [PMID: 24091028 DOI: 10.1016/j.cancergen.2013.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 12/23/2022]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase protein implicated in a variety of hematological malignancies and solid tumors. Since the identification of the ALK gene in 1994 as the target of the t(2;5) chromosomal translocation in anaplastic large cell lymphoma, ALK has been proven a remarkably promiscuous oncogene. ALK contributes to the development of a notable assortment of tumor types from different lineages, including hematolymphoid, mesenchymal, epithelial and neural tumors, through a variety of genetic mechanisms: gene fusions, activating point mutations, and gene amplification. Recent developments led to significant diagnostic and therapeutic advances, including efficient diagnostic tests and ALK-targeting agents readily available in the clinical setting. This review addresses some therapeutic considerations of ALK-targeted agents and the biologic implications of ALK oncogenic promiscuity, but the main points discussed are: 1) the variety of mechanisms that result in activation of the ALK oncogene, with emphasis on the promiscuous partnerships demonstrated in chromosomal rearrangements; 2) the diversity of tumor types of different lineages in which ALK has been implicated as a pathogenic driver; and 3) the different diagnostic tests available to identify ALK-driven tumors, and their respective indications.
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87
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Abstract
The burgeoning field of anaplastic lymphoma kinase (ALK) in cancer encompasses many cancer types, from very rare cancers to the more prevalent non-small-cell lung cancer (NSCLC). The common activation of ALK has led to the use of the ALK tyrosine kinase inhibitor (TKI) crizotinib in a range of patient populations and to the rapid development of second-generation drugs targeting ALK. In this Review, we discuss our current understanding of ALK function in human cancer and the implications for tumour treatment.
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MESH Headings
- Anaplastic Lymphoma Kinase
- Animals
- Antineoplastic Agents/therapeutic use
- Caenorhabditis elegans Proteins/physiology
- Cell Transformation, Neoplastic/genetics
- Clinical Trials as Topic
- Crizotinib
- Drosophila Proteins/physiology
- Drug Resistance, Neoplasm
- Enzyme Induction
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphoma, Large-Cell, Anaplastic/enzymology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Mice
- Models, Biological
- Models, Molecular
- Mutation
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Neoplasms/drug therapy
- Neoplasms/enzymology
- Neoplasms/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- Protein Conformation
- Protein-Tyrosine Kinases/physiology
- Pyrazoles/therapeutic use
- Pyridines/therapeutic use
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/physiology
- Signal Transduction
- Translocation, Genetic
- Zebrafish Proteins/physiology
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Affiliation(s)
- Bengt Hallberg
- Department of Molecular Biology, Building 6L, Umeå University, Umeå S-90187, Sweden
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88
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Sun H, Li Y, Li D, Hou T. Insight into crizotinib resistance mechanisms caused by three mutations in ALK tyrosine kinase using free energy calculation approaches. J Chem Inf Model 2013; 53:2376-89. [PMID: 23952683 DOI: 10.1021/ci400188q] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a safe and efficacious drug, crizotinib was approved by the U.S. Food and Drug Administration (FDA) in 2011 for the treatment of advanced fusion-type nonsmall-cell lung cancer. Although high response ratio was detected from the patients treated with crizotinib, the cancer has eventually conferred resistance to crizotinib. Several drug resistance mutations have been found in the anaplastic lymphoma kinase (ALK) tyrosine kinase domain as the target for crizotinib, but the drug resistance mechanisms remain unclear. Therefore, in this study, the adaptive biasing force (ABF) method and two-end-state free energy calculation approaches were employed to elucidate the resistance mechanisms of crizotinib induced by the mutations L1152R, G1202R, and S1206Y. The ABF simulation results suggest that the reaction coordinates for the unbinding processes of crizotinib from the binding pockets of the mutated ALKs is different from that of the wild type ALK. The potentials of mean force for the crizotinib unbinding and the binding free energies predicted by the two-end-state free energy calculations are consistent with the experimental data. Our results indicate that the three mutations weaken the binding affinity of crizotinib obviously and lead to drug resistance. The free energy decomposition analysis illustrates the importance of the loss of two important H-bonds in the L1152R and S1206Y mutants on drug resistance. The entropy analysis shows that the entropy term plays a critical role in the substantial change of the conformational entropies of G1202R and L1152R. Our results reveal the mechanisms of drug resistance and provide vital clues for the development of new inhibitors to combat drug resistance.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University , Suzhou, Jiangsu 215123, China
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89
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Wu K, House L, Liu W, Cho WC, 南 娟. [Personalized targeted therapy for lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2013; 16:C21-34. [PMID: 23945250 PMCID: PMC6123569 DOI: 10.3779/j.issn.1009-3419.2013.08.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
由于每一肺癌患者在临床特征、预后、治疗反应和耐受性方面的进展都是独特的,所以肺癌被认为是异质性疾病。个体化用药是指运用标志物来预测哪些患者更易获益于某种治疗。对于肺癌而言,日趋完善的表皮生长因子受体(epidermal growth factor receptor, EGFR)和新发现的棘皮动物微管相关蛋白样4-间变淋巴瘤激酶(echinoderm microtubule associated protein like 4-anaplastic lymphoma kinase, EML4-ALK)是重要的治疗靶标。本综述包括EGFR和EML4-ALK活化的机制、预测性生物标记物、耐药的机理和已有的靶向性酪氨酸激酶抑制剂。本文将通过总结基于生物标记物筛选患者而进行的前瞻性临床试验来探讨EGFR和ALK靶向治疗的疗效。此外,由于革命性的测序和系统生物学技术会为癌症的分子特征提供一个全面的理解,有助于为更适宜靶向治疗的患者提供更精确的区分从而提供更有前景的个体化治疗,本综述也将包括这些技术。同时,非亚裔人群中EGFR和ALK相对较低的突变发生率和突变患者反应的缺乏限制了靶向于EGFR或ALK的治疗的应用。测序和系统生物学策略则可能为这些患者提供新的解决方案。
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Affiliation(s)
- Kehua Wu
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Larry House
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Wanqing Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayete, IN 47907, USA
| | - William C.S. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - 娟 南
- 天津医科大学总医院,天津市肺癌研究所,天津市肺癌转移与肿瘤微环境重点实验室
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90
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Roskoski R. The preclinical profile of crizotinib for the treatment of non-small-cell lung cancer and other neoplastic disorders. Expert Opin Drug Discov 2013; 8:1165-79. [DOI: 10.1517/17460441.2013.813015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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91
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Design of novel anaplastic lymphoma kinase (ALK) inhibitors based on predictive 3D QSAR models using different alignment strategies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0662-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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92
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Zhao B, Tan PH, Li SSC, Pei D. Systematic characterization of the specificity of the SH2 domains of cytoplasmic tyrosine kinases. J Proteomics 2013; 81:56-69. [PMID: 23313216 DOI: 10.1016/j.jprot.2012.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/18/2012] [Accepted: 12/29/2012] [Indexed: 01/26/2023]
Abstract
Cytoplasmic tyrosine kinases (CTK) generally contain a Src-homology 2 (SH2) domain, whose role in the CTK family is not fully understood. Here we report the determination of the specificity of 25 CTK SH2 domains by screening one-bead-one-compound (OBOC) peptide libraries. Based on the peptide sequences selected by the SH2 domains, we built Support Vector Machine (SVM) models for the prediction of binding ligands for the SH2 domains. These models yielded support for the progressive phosphorylation model for CTKs in which the overlapping specificity of the CTK SH2 and kinase domains has been proposed to facilitate targeting of the CTK substrates with at least two potential phosphotyrosine (pTyr) sites. We curated 93 CTK substrates with at least two pTyr sites catalyzed by the same CTK, and showed that 71% of these substrates had at least two pTyr sites predicted to bind a common CTK SH2 domain. More importantly, we found 34 instances where there was at least one pTyr site predicted to be recognized by the SH2 domain of the same CTK, suggesting that the SH2 and kinase domains of the CTKs may cooperate to achieve progressive phosphorylation of a protein substrate. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Bing Zhao
- Department of Biochemistry and Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada N6A 5C1
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93
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Control of ALK (wild type and mutated forms) phosphorylation: specific role of the phosphatase PTP1B. Cell Signal 2013; 25:1505-13. [PMID: 23499906 DOI: 10.1016/j.cellsig.2013.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/14/2013] [Accepted: 02/26/2013] [Indexed: 11/20/2022]
Abstract
Phosphorylation of proteins on tyrosine residues is regulated by the activities of protein tyrosine kinases and protein tyrosine phosphatases. Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase (RTK) essentially and transiently expressed during development of the central and peripheral nervous systems. ALK has been identified as a major neuroblastoma predisposition gene and activating mutations have been identified in a subset of sporadic neuroblastoma tumors. We previously established that the mutated receptors were essentially retained in the endoplasmic reticulum/Golgi compartments due to their constitutive activity. Intriguingly we demonstrated a stronger phosphorylation for the minor pool of receptor addressed to the plasma membrane. We decided to investigate the potential involvement of tyrosine phosphatase in dephosphorylation of this intracellular pool. In this study we first showed that general inhibition of tyrosine phosphatases resulted in a dramatic increase of the tyrosine phosphorylation of the wild type but also of the mutated receptors. This increase not only required the intrinsic kinase activity of the ALK receptor but also involved the Src tyrosine kinase family. Second we provided strong evidences that the endoplasmic reticulum associated phosphatase PTP1B is key player in the control of ALK phosphorylation. Our data shed a new light on the biological significance of the basal phosphorylation levels of both wild type and mutated ALK receptors and could be essential to further understand their roles in malignancies.
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94
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Hubbard SR. The insulin receptor: both a prototypical and atypical receptor tyrosine kinase. Cold Spring Harb Perspect Biol 2013; 5:a008946. [PMID: 23457259 DOI: 10.1101/cshperspect.a008946] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Unlike prototypical receptor tyrosine kinases (RTKs), which are single-chain polypeptides, the insulin receptor (InsR) is a preformed, covalently linked tetramer with two extracellular α subunits and two membrane-spanning, tyrosine kinase-containing β subunits. A single molecule of insulin binds asymmetrically to the ectodomain, triggering a conformational change that is transmitted to the cytoplasmic kinase domains, which facilitates their trans-phosphorylation. As in prototypical RTKs, tyrosine phosphorylation in the juxtamembrane region of InsR creates recruitment sites for downstream signaling proteins (IRS [InsR substrate] proteins, Shc) containing a phosphotyrosine-binding (PTB) domain, and tyrosine phosphorylation in the kinase activation loop stimulates InsR's catalytic activity. For InsR, phosphorylation of the activation loop, which contains three tyrosine residues, also creates docking sites for adaptor proteins (Grb10/14, SH2B2) that possess specialized Src homology-2 (SH2) domains, which are dimeric and engage two phosphotyrosines in the activation loop.
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Affiliation(s)
- Stevan R Hubbard
- Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
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95
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96
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Bose R, Kavuri SM, Searleman AC, Shen W, Shen D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER, Ellis MJ. Activating HER2 mutations in HER2 gene amplification negative breast cancer. Cancer Discov 2013; 3:224-37. [PMID: 23220880 PMCID: PMC3570596 DOI: 10.1158/2159-8290.cd-12-0349] [Citation(s) in RCA: 629] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
UNLABELLED Data from 8 breast cancer genome-sequencing projects identified 25 patients with HER2 somatic mutations in cancers lacking HER2 gene amplification. To determine the phenotype of these mutations, we functionally characterized 13 HER2 mutations using in vitro kinase assays, protein structure analysis, cell culture, and xenograft experiments. Seven of these mutations are activating mutations, including G309A, D769H, D769Y, V777L, P780ins, V842I, and R896C. HER2 in-frame deletion 755-759, which is homologous to EGF receptor (EGFR) exon 19 in-frame deletions, had a neomorphic phenotype with increased phosphorylation of EGFR or HER3. L755S produced lapatinib resistance, but was not an activating mutation in our experimental systems. All of these mutations were sensitive to the irreversible kinase inhibitor, neratinib. These findings show that HER2 somatic mutation is an alternative mechanism to activate HER2 in breast cancer and they validate HER2 somatic mutations as drug targets for breast cancer treatment. SIGNIFICANCE We show that the majority of HER2 somatic mutations in breast cancer patients are activating mutations that likely drive tumorigenesis. Several patients had mutations that are resistant to the reversible HER2 inhibitor lapatinib, but are sensitive to the irreversible HER2 inhibitor, neratinib. Our results suggest that patients with HER2 mutation–positive breast cancers could benefit from existing HER2-targeted drugs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Line
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Amplification
- Gene Expression
- Humans
- Lapatinib
- MCF-7 Cells
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/metabolism
- Mammary Neoplasms, Experimental/pathology
- Mice
- Mice, Nude
- Models, Molecular
- Molecular Sequence Data
- Mutation
- NIH 3T3 Cells
- Protein Structure, Tertiary
- Quinazolines/pharmacology
- Quinolines/pharmacology
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Transplantation, Heterologous
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Affiliation(s)
- Ron Bose
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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97
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Wu D, Yu H, Li J. [Mechanisms of resistance to EML4-ALK inhibitors in non-small cell lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2013; 16:48-53. [PMID: 23327874 PMCID: PMC6000462 DOI: 10.3779/j.issn.1009-3419.2013.01.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Di Wu
- Department of Medical Oncology, Jilin Province Tumor Hospital, Changchun 130012, China;Tumor Center, First Hospital of Jilin University, Changchun 130021, China
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98
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Abstract
To investigate the range of autoinhibitory mechanisms used by TKDs (tyrosine kinase domains) from the insulin receptor family of RTKs (receptor tyrosine kinases), we determined crystal structures of TKDs from TrkA (tropomyosin receptor kinase A, a nerve growth factor receptor) and Ror2 (receptor tyrosine kinase-like orphan receptor 2, an unconventional Wnt receptor). TrkA autoinhibition closely resembles that seen for the insulin receptor, relying on projection of an activation loop tyrosine residue into the substrate-binding site and occlusion of the ATP-binding site by the activation loop. Ror2 employs similar mechanisms, but the unusual replacement of the phenylalanine residue in its Asp-Phe-Gly motif with leucine necessitates occlusion of the ATP-binding site by other means. The unusual Asp-Leu-Gly motif in Ror2 is displaced compared with other inactive kinases, allowing the activation loop to interact directly with the TKD's αC helix, in another mode of autoinhibition that is characteristic of the other extreme of this receptor family: ALK (anaplastic lymphoma kinase) and Met. These findings provide insight into the expected range of activating mutations in these TKDs in cancer. We also describe symmetrical dimers of the inactive TrkA TKD resembling those found in other RTKs, possibly reflecting an arrangement of kinase domains in a pre-formed TrkA dimer.
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99
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LY2801653 is an orally bioavailable multi-kinase inhibitor with potent activity against MET, MST1R, and other oncoproteins, and displays anti-tumor activities in mouse xenograft models. Invest New Drugs 2012; 31:833-44. [PMID: 23275061 PMCID: PMC3717159 DOI: 10.1007/s10637-012-9912-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/03/2012] [Indexed: 01/03/2023]
Abstract
The HGF/MET signaling pathway regulates a wide variety of normal cellular functions that can be subverted to support neoplasia, including cell proliferation, survival, apoptosis, scattering and motility, invasion, and angiogenesis. MET over-expression (with or without gene amplification), aberrant autocrine or paracrine ligand production, and missense MET mutations are mechanisms that lead to activation of the MET pathway in tumors and are associated with poor prognostic outcome. We report here preclinical development of a potent, orally bioavailable, small-molecule inhibitor LY2801653 targeting MET kinase. LY2801653 is a type-II ATP competitive, slow-off inhibitor of MET tyrosine kinase with a dissociation constant (Ki) of 2 nM, a pharmacodynamic residence time (Koff) of 0.00132 min(-1) and t1/2 of 525 min. LY2801653 demonstrated in vitro effects on MET pathway-dependent cell scattering and cell proliferation; in vivo anti-tumor effects in MET amplified (MKN45), MET autocrine (U-87MG, and KP4) and MET over-expressed (H441) xenograft models; and in vivo vessel normalization effects. LY2801653 also maintained potency against 13 MET variants, each bearing a single-point mutation. In subsequent nonclinical characterization, LY2801653 was found to have potent activity against several other receptor tyrosine oncokinases including MST1R, FLT3, AXL, MERTK, TEK, ROS1, DDR1/2 and against the serine/threonine kinases MKNK1/2. The potential value of MET and other inhibited targets within a number of malignancies (such as colon, bile ducts, and lung) is discussed. LY2801653 is currently in phase 1 clinical testing in patients with advanced cancer (trial I3O-MC-JSBA, NCT01285037).
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Chand D, Yamazaki Y, Ruuth K, Schönherr C, Martinsson T, Kogner P, Attiyeh EF, Maris J, Morozova O, Marra MA, Ohira M, Nakagawara A, Sandström PE, Palmer RH, Hallberg B. Cell culture and Drosophila model systems define three classes of anaplastic lymphoma kinase mutations in neuroblastoma. Dis Model Mech 2012; 6:373-82. [PMID: 23104988 PMCID: PMC3597019 DOI: 10.1242/dmm.010348] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Neuroblastoma is a childhood extracranial solid tumour that is associated with a number of genetic changes. Included in these genetic alterations are mutations in the kinase domain of the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (RTK), which have been found in both somatic and familial neuroblastoma. In order to treat patients accordingly requires characterisation of these mutations in terms of their response to ALK tyrosine kinase inhibitors (TKIs). Here, we report the identification and characterisation of two novel neuroblastoma ALK mutations (A1099T and R1464STOP), which we have investigated together with several previously reported but uncharacterised ALK mutations (T1087I, D1091N, T1151M, M1166R, F1174I and A1234T). In order to understand the potential role of these ALK mutations in neuroblastoma progression, we have employed cell culture-based systems together with the model organism Drosophila as a readout for ligand-independent activity. Mutation of ALK at position 1174 (F1174I) generates a gain-of-function receptor capable of activating intracellular targets such as ERK (extracellular signal regulated kinase) and STAT3 (signal transducer and activator of transcription 3) in a ligand-independent manner. Analysis of these previously uncharacterised ALK mutants and comparison with ALKF1174 mutants suggests that ALK mutations observed in neuroblastoma fall into three classes. These classes are: (i) gain-of-function ligand-independent mutations such as ALKF1174l, (ii) kinase-dead ALK mutants, e.g. ALKI1250T (Schönherr et al., 2011a) and (iii) ALK mutations that are ligand-dependent in nature. Irrespective of the nature of the observed ALK mutants, in every case the activity of the mutant ALK receptors could be abrogated by the ALK inhibitor crizotinib (Xalkori/PF-02341066), albeit with differing levels of sensitivity.
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Affiliation(s)
- Damini Chand
- Department of Molecular Biology, Building 6L, Umeå University, Umeå 901 87, Sweden
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