1
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Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551866. [PMID: 37577651 PMCID: PMC10418267 DOI: 10.1101/2023.08.03.551866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MET is a receptor tyrosine kinase (RTK) responsible for initiating signaling pathways involved in development and wound repair. MET activation relies on ligand binding to the extracellular receptor, which prompts dimerization, intracellular phosphorylation, and recruitment of associated signaling proteins. Mutations, which are predominantly observed clinically in the intracellular juxtamembrane and kinase domains, can disrupt typical MET regulatory mechanisms. Understanding how juxtamembrane variants, such as exon 14 skipping (METΔEx14), and rare kinase domain mutations can increase signaling, often leading to cancer, remains a challenge. Here, we perform a parallel deep mutational scan (DMS) of the MET intracellular kinase domain in two fusion protein backgrounds: wild type and METΔEx14. Our comparative approach has revealed a critical hydrophobic interaction between a juxtamembrane segment and the kinase αC-helix, pointing to potential differences in regulatory mechanisms between MET and other RTKs. Additionally, we have uncovered a β5 motif that acts as a structural pivot for the kinase domain in MET and other TAM family of kinases. We also describe a number of previously unknown activating mutations, aiding the effort to annotate driver, passenger, and drug resistance mutations in the MET kinase domain.
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Affiliation(s)
- Gabriella O. Estevam
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco,United States
- Tetrad Graduate Program, University of California San Francisco, San Francisco, United States
| | - Edmond M. Linossi
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, United States
| | - Christian B. Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco,United States
| | - Carla A. Espinoza
- Tetrad Graduate Program, University of California San Francisco, San Francisco, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, United States
| | - Jennifer M. Michaud
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco,United States
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco,United States
- Quantitative Biosciences Institute, University of California, San Francisco, United States, United States
| | - Eric A. Collisson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
- Department of Medicine/Hematology and Oncology, University of California, San Francisco, United States
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, United States
- Quantitative Biosciences Institute, University of California, San Francisco, United States, United States
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco,United States
- Quantitative Biosciences Institute, University of California, San Francisco, United States, United States
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2
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Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
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Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
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3
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Grädler U, Schwarz D, Wegener A, Eichhorn T, Bandeiras TM, Freitas MC, Lammens A, Ganichkin O, Augustin M, Minguzzi S, Becker F, Bomke J. Biophysical and structural characterization of the impacts of MET phosphorylation on tepotinib binding. J Biol Chem 2023; 299:105328. [PMID: 37806493 PMCID: PMC10654029 DOI: 10.1016/j.jbc.2023.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/16/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
The receptor tyrosine kinase MET is activated by hepatocyte growth factor binding, followed by phosphorylation of the intracellular kinase domain (KD) mainly within the activation loop (A-loop) on Y1234 and Y1235. Dysregulation of MET can lead to both tumor growth and metastatic progression of cancer cells. Tepotinib is a highly selective, potent type Ib MET inhibitor and approved for treatment of non-small cell lung cancer harboring METex14 skipping alterations. Tepotinib binds to the ATP site of unphosphorylated MET with critical π-stacking contacts to Y1230 of the A-loop, resulting in a high residence time. In our study, we combined protein crystallography, biophysical methods (surface plasmon resonance, differential scanning fluorimetry), and mass spectrometry to clarify the impacts of A-loop conformation on tepotinib binding using different recombinant MET KD protein variants. We solved the first crystal structures of MET mutants Y1235D, Y1234E/1235E, and F1200I in complex with tepotinib. Our biophysical and structural data indicated a linkage between reduced residence times for tepotinib and modulation of A-loop conformation either by mutation (Y1235D), by affecting the overall Y1234/Y1235 phosphorylation status (L1195V and F1200I) or by disturbing critical π-stacking interactions with tepotinib (Y1230C). We corroborated these data with target engagement studies by fluorescence cross-correlation spectroscopy using KD constructs in cell lysates or full-length receptors from solubilized cellular membranes as WT or activated mutants (Y1235D and Y1234E/1235E). Collectively, our results provide further insight into the MET A-loop structural determinants that affect the binding of the selective inhibitor tepotinib.
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Affiliation(s)
- Ulrich Grädler
- The Healthcare Business of Merck KGaA, Darmstadt, Germany.
| | - Daniel Schwarz
- The Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Ansgar Wegener
- The Healthcare Business of Merck KGaA, Darmstadt, Germany
| | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Micael C Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | | | | | | | | | - Jörg Bomke
- The Healthcare Business of Merck KGaA, Darmstadt, Germany
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4
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Wang C, Lu X. Targeting MET: Discovery of Small Molecule Inhibitors as Non-Small Cell Lung Cancer Therapy. J Med Chem 2023. [PMID: 37262349 DOI: 10.1021/acs.jmedchem.3c00028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
MET has been considered as a promising drug target for the treatment of MET-dependent diseases, particularly non-small cell lung cancer (NSCLC). Small molecule MET inhibitors with mainly three types of binding modes (Ia/Ib, II, and III) have been developed. In this Review, we provide an overview of the structural features, activation mechanism, and dysregulation pathway of MET and summarize progress on the development and discovery strategies utilized for MET inhibitors as well as mechanisms of acquired resistance to current approved inhibitors. The insights will accelerate discovery of new generation MET inhibitors to overcome clinical acquired resistance.
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Affiliation(s)
- Chaofan Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou, 510632, China
| | - Xiaoyun Lu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450001, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou, 510632, China
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5
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Marcos Santos L, da Silveira NJF. Current Fragment-to-lead Approaches Starting from the 7-azaindole: The Pharmacological Versatility of a Privileged Molecular Fragment. Curr Top Med Chem 2023; 23:2116-2130. [PMID: 37461366 DOI: 10.2174/1568026623666230718100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
Fragment-based drug discovery is one of the most powerful paradigms in the recent context of medicinal chemistry and is being widely practiced by academic and industrial researchers. Currently, azaindoles are among the most exploited molecular fragments in pharmaceutical innovation projects inspired by fragment-to-lead strategies. The 7-azaindole is the most prominent representative within this remarkable family of pyrrolopyridine fragments, as it is present in the chemical structure of several approved antitumor drugs and also of numerous therapeutic candidates. In this paper, a brief overview on existing proofs of concept in the literature will be presented, as well as some recent works that corroborate 7-azaindole as a privileged and pharmacologically versatile molecular fragment.
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Affiliation(s)
- Leandro Marcos Santos
- Laboratory of Molecular Modeling and Computer Simulation / MolMod-CS (D311-F), Institute of Chemistry, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
- Pharmaceutical Chemistry Research Laboratory / LQFar (D202A), Department of Food and Medicines, Faculty of Pharmaceutical Sciences, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
| | - Nelson José Freitas da Silveira
- Laboratory of Molecular Modeling and Computer Simulation / MolMod-CS (D311-F), Institute of Chemistry, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
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6
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Huggins DJ. Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations. J Chem Theory Comput 2022; 18:2616-2630. [PMID: 35266690 DOI: 10.1021/acs.jctc.1c01208] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying chemical starting points is a vital first step in small molecule drug discovery and can take significant time and money. For this reason, computational approaches to virtual screening are of great interest as they can lower the cost and shorten timeframes. However, simple approaches such as molecular docking and pharmacophore screening are of limited accuracy and provide a low probability of success. Alchemical binding free energies represent a promising approach for virtual screening as they naturally incorporate the key effects of water molecules, protein flexibility, and binding entropy. However, the calculations are technically very challenging, with performance depending on the specific forcefield used. For this reason, it is important that the community has access to benchmark test sets to assess prediction accuracy. In this paper, we present an approach to alchemical binding free energies using OpenMM. We identify effective simulation parameters using an existing BRD4(1) test set and present two new benchmark sets (cMET and PDE2A) that can be used in the community for validation purposes. Our findings also highlight the effectiveness of some AMBER forcefields, in particular, AMBER ff15ipq.
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Affiliation(s)
- David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10021, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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7
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State of the structure address on MET receptor activation by HGF. Biochem Soc Trans 2021; 49:645-661. [PMID: 33860789 DOI: 10.1042/bst20200394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
The MET receptor tyrosine kinase (RTK) and its cognate ligand hepatocyte growth factor (HGF) comprise a signaling axis essential for development, wound healing and tissue homeostasis. Aberrant HGF/MET signaling is a driver of many cancers and contributes to drug resistance to several approved therapeutics targeting other RTKs, making MET itself an important drug target. In RTKs, homeostatic receptor signaling is dependent on autoinhibition in the absence of ligand binding and orchestrated set of conformational changes induced by ligand-mediated receptor dimerization that result in activation of the intracellular kinase domains. A fundamental understanding of these mechanisms in the MET receptor remains incomplete, despite decades of research. This is due in part to the complex structure of the HGF ligand, which remains unknown in its full-length form, and a lack of high-resolution structures of the complete MET extracellular portion in an apo or ligand-bound state. A current view of HGF-dependent MET activation has evolved from biochemical and structural studies of HGF and MET fragments and here we review what these findings have thus far revealed.
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8
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Collie GW, Michaelides IN, Embrey K, Stubbs CJ, Börjesson U, Dale IL, Snijder A, Barlind L, Song K, Khurana P, Phillips C, Storer RI. Structural Basis for Targeting the Folded P-Loop Conformation of c-MET. ACS Med Chem Lett 2021; 12:162-167. [PMID: 33488978 PMCID: PMC7812667 DOI: 10.1021/acsmedchemlett.0c00392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
![]()
We report here a
fragment screen directed toward the c-MET kinase
from which we discovered a series of inhibitors able to bind to a
rare conformation of the protein in which the P-loop adopts a collapsed,
or folded, arrangement. Preliminary SAR exploration led to an inhibitor
(7) with nanomolar biochemical activity against c-MET
and promising cell activity and kinase selectivity. These findings
increase our structural understanding of the folded P-loop conformation
of c-MET and provide a sound structural and chemical basis for further
investigation of this underexplored yet potentially therapeutically
exploitable conformational state.
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Affiliation(s)
- Gavin W. Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Kevin Embrey
- Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Ulf Börjesson
- Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Ian L. Dale
- Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Arjan Snijder
- Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Louise Barlind
- Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Kun Song
- Oncology, R&D, AstraZeneca, Boston, United States
| | - Puneet Khurana
- Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - R. Ian Storer
- Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
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9
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Dekel N, Eisenberg-Domovich Y, Karlas A, Meyer TF, Bracher F, Lebendiker M, Danieli T, Livnah O. Expression, purification and crystallization of CLK1 kinase - A potential target for antiviral therapy. Protein Expr Purif 2020; 176:105742. [PMID: 32866611 DOI: 10.1016/j.pep.2020.105742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Cdc-like kinase 1 (CLK1) is a dual-specificity kinase capable of autophosphorylation on tyrosine residues and Ser/Thr phosphorylation of its substrates. CLK1 belongs to the CLK kinase family that regulates alternative splicing through phosphorylation of serine-arginine rich (SR) proteins. Recent studies have demonstrated that CLK1 has an important role in the replication of influenza A and chikungunya viruses. Furthermore, CLK1 was found to be relevant for the replication of HIV-1 and the West Nile virus, making CLK1 an interesting cellular candidate for the development of a host-directed antiviral therapy that might be efficient for treatment of newly emerging viruses. We describe here our attempts and detailed procedures to obtain the recombinant kinase domain of CLK1 in suitable amounts for crystallization in complex with specific inhibitors. The key solution for the reproducibility of crystals resides in devising and refining expression and purification protocols leading to homogeneous protein. Co-expression of CLK1 with λ-phosphatase and careful purification has yielded crystals of CLK1 complexed with the KH-CB19 inhibitor that diffracted to 1.65 Å. These results paved the path to the screening of more structures of CLK1 complexed compounds, leading to further optimization of their inhibitory activity. Moreover, since kinases are desired targets in numerous pathologies, the approach we report here, the co-expression of kinases with λ-phosphatase, previously used in other kinases, can be adopted as a general protocol in numerous kinase targets for obtaining reproducible and homogenic non-phosphorylated (inactive) forms suitable for biochemical and structural studies thus facilitating the development of novel inhibitors.
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Affiliation(s)
- Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Franz Bracher
- Ludwig-Maximilians University, Department of Pharmacy-Center for Drug Research, Butenandstrasse 5-13, 81377, Munich, Germany
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel.
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10
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Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Cui Y, Sun G. Structural versatility that serves the function of the HRD motif in the catalytic loop of protein tyrosine kinase, Src. Protein Sci 2018; 28:533-542. [PMID: 30461096 DOI: 10.1002/pro.3554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
Site-directed mutagenesis is a traditional approach for structure-function analysis of protein tyrosine kinases, and it requires the generation, expression, purification, and analysis of each mutant enzyme. In this study, we report a versatile high throughput bacterial screening system that can identify functional kinase mutants by immunological detection of tyrosine phosphorylation. Two key features of this screening system are noteworthy. First, instead of blotting bacterial colonies directly from Agar plates to nitrocellulose membrane, the colonies were cultured in 96-well plates, and then spotted in duplicate onto the membrane with appropriate controls. This made the screening much more reliable compared with direct colony blotting transfer. A second feature is the parallel use of a protein tyrosine phosphatase (PTP)-expressing host and a non-PTP-expressing host. Because high activity Src mutants are toxic to the host, the PTP system allowed the identification of Src mutants with high activity, while the non-PTP system identified Src mutants with low activity. This approach was applied to Src mutant libraries randomized in the highly conserved HRD motif in the catalytic loop, and revealed that structurally diverse residues can replace the His and Arg residues, while the Asp residue is irreplaceable for catalytic activity.
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Affiliation(s)
- Yixin Cui
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
| | - Gongqin Sun
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
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12
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Du J, Wu X, Tong X, Wang X, Wei J, Yang Y, Chang Z, Mao Y, Shao YW, Liu B. Circulating tumor DNA profiling by next generation sequencing reveals heterogeneity of crizotinib resistance mechanisms in a gastric cancer patient with MET amplification. Oncotarget 2018; 8:26281-26287. [PMID: 28460431 PMCID: PMC5432256 DOI: 10.18632/oncotarget.15457] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 02/04/2017] [Indexed: 12/18/2022] Open
Abstract
Crizotinib has been used to counter MET gene amplification in a number of different human malignancies. Transient response to crizotinib in MET-amplified gastric cancer has been reported, but the mechanisms of resistance are not well studied. Here, we reported a stage IV gastric cancer patient with high levels of MET amplification. The implementation of crizotinib treatment led to significant symptomatic improvement in the first 2 months, but was followed by rapid disease progression. Periodic mutation profiling of patient's circulating tumor DNA (ctDNA) by next generation sequencing (NGS) revealed a number of genetic alterations including re-occurrence of MET amplification, multiple secondary MET mutations, a dramatic increase of FGFR2 gene relative copy number as well as mutations in other downstream and bypassing elements, which may collectively related to the patient's cancer progression. Our results illustrate the complex and heterogeneous molecular mechanisms for crizotinib resistance in this patient, and demonstrate the great potential of ctDNA profiling for treatment decision-making and prognosis in clinical practice.
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Affiliation(s)
- Juan Du
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Xue Wu
- Geneseeq Technology Inc., Toronto, Ontario, M5G1L7, Canada
| | - Xiaoling Tong
- Geneseeq Technology Inc., Toronto, Ontario, M5G1L7, Canada
| | - Xiaonan Wang
- Nanjing Geneseeq Technology Inc., Sino-Danish Life Science Park, Nanjing, Jiangsu, 210032, China
| | - Jia Wei
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Yang Yang
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Zhili Chang
- Nanjing Geneseeq Technology Inc., Sino-Danish Life Science Park, Nanjing, Jiangsu, 210032, China
| | - Yu Mao
- Nanjing Geneseeq Technology Inc., Sino-Danish Life Science Park, Nanjing, Jiangsu, 210032, China
| | - Yang W Shao
- Geneseeq Technology Inc., Toronto, Ontario, M5G1L7, Canada
| | - Baorui Liu
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, 210008, China
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13
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Yuan H, Liu Q, Zhang L, Hu S, Chen T, Li H, Chen Y, Xu Y, Lu T. Discovery, optimization and biological evaluation for novel c-Met kinase inhibitors. Eur J Med Chem 2018; 143:491-502. [DOI: 10.1016/j.ejmech.2017.11.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 11/23/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
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14
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Pal K, Bandyopadhyay A, Zhou XE, Xu Q, Marciano DP, Brunzelle JS, Yerrum S, Griffin PR, Vande Woude G, Melcher K, Xu HE. Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases. Structure 2017; 25:867-877.e3. [PMID: 28528776 DOI: 10.1016/j.str.2017.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/22/2017] [Accepted: 04/28/2017] [Indexed: 01/01/2023]
Abstract
The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature. We further show that fusion of TPR(2-142) to the MET intracellular domain strongly and selectively stabilizes the αG helix of the MET kinase domain, and mutations of only the TPR leucine zipper residues at the junction to MET, but not other leucine zipper residues, abolish kinase activation. Together, these results provide critical insight into the TPR structure and its ability to induce dimerization and activation of fusion kinases.
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Affiliation(s)
- Kuntal Pal
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Abhishek Bandyopadhyay
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Qingping Xu
- GMCA at Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - David P Marciano
- Department of Molecular Medicine, Translational Research Institute, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology & Biological Chemistry, Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL 60439, USA
| | - Smitha Yerrum
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Translational Research Institute, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - George Vande Woude
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
| | - H Eric Xu
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; VARI-SIMM Center for Structure and Function of Drug Targets and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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15
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Meshram RJ, Baladhye VB, Gacche RN, Karale BK, Gaikar RB. Pharmacophore Mapping Approach for Drug Target Identification: A Chemical Synthesis and in Silico Study on Novel Thiadiazole Compounds. J Clin Diagn Res 2017; 11:KF01-KF08. [PMID: 28658808 DOI: 10.7860/jcdr/2017/22761.9925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/23/2016] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Compounds containing thiadiazole moiety are cognized to possess with variety of clinical and therapeutic activity. Finding a suitable drug target for newly synthesized compounds remain a major bottle neck in current high throughout medicinal chemistry era. AIM To effectively synthesize di substituted thiadiazole compounds and demonstrate drug target identification using an in silico pharmacophore probing approach. Moreover, we also aim to validate the suitability of identified drug target. MATERIALS AND METHODS A cost-effective and environmental friendly chemical synthesis scheme for production of di substituted thiadiazole compounds was employed. Target identification was conducted by Pharmmapper software. Validation was accomplished by performing molecular docking and further Molecular Hydrophobic Potential (MHP) analysis. RESULTS Pharmacophore probing base approach identified hepatocyte growth factor receptor (c-Met) as a suitable biological target for newly synthesized compounds. Binding free energy values indicate that compound 4b, 4e, 4g and 4h has tremendous potential to be further used as lead compound to design selective inhibitors of c-Met receptor. MHP data from current study supports the possibility that hydrophobic contacts might act as major factor stabilizing thiadiazole- c-Met complex. Moreover, in silico observations of current study are in absolute accordance with previously described in vitro and crystallographic analysis. CONCLUSION We demonstrate that thiadiazole compounds synthesized in current investigation has high potential to act in modulation of hepatocyte growth factor receptor (c-Met) activity and thereby act as putative therapeutic agent in cancer therapy.
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Affiliation(s)
- Rohan J Meshram
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Vijay B Baladhye
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N Gacche
- Professor, Department of Botany, School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Bhausaheb K Karale
- Professor, Department of Chemistry, Radhabai Kale Mahila Mahavidayalaya, Ahmednagar, Maharashtra, India
| | - Rajendra B Gaikar
- Assistant Professor, Department of Chemistry, Padmashri Vikhe Patil College, Loni, Maharashtra, India
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16
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Abstract
Recombinant protein expression is widely used to generate milligram quantities of protein kinases for crystallographic, enzymatic, or other biophysical assays in vitro. Expression in E. coli is fast, cheap, and reliable. Here I present a detailed protocol for the production of human Aurora-A kinase. I begin with transformation of a suitable plasmid into an expression strain of E. coli, followed by growth and harvesting of bacterial cell cultures. Finally, I describe the purification of Aurora-A to homogeneity using immobilized metal affinity and size exclusion chromatographies.
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Affiliation(s)
- Charlotte A Dodson
- Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, Room 364, South Kensington Campus, London, SW7 2AZ, UK.
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17
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Papillary renal cell carcinoma with a somatic mutation in MET in a patient with autosomal dominant polycystic kidney disease. Cancer Genet 2015; 209:11-20. [PMID: 26718059 DOI: 10.1016/j.cancergen.2015.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/16/2022]
Abstract
Autosomal-dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1 and PKD2 and is characterized by proliferation of renal tubular epithelium and progressive chronic kidney disease. Derangements in similar cellular signaling pathways occur in ADPKD and renal malignancies, although an association of these disorders has not been established. Herein, we present a case of papillary RCC (pRCC) incidentally discovered in a patient with ADPKD following bilateral native nephrectomy during renal transplantation. Whole exome sequencing of the pRCC found a somatic missense mutation in MET proto-oncogene, p.Val1110Ile, not present in kidney cyst epithelium or non-cystic tissue. RNA sequencing demonstrated increased mRNA expression of MET and pathway-related genes, but no significant copy number variation of MET was detected. Genetic analysis of PKD genes from peripheral blood lymphocytes and renal cyst epithelium identified a constitutional PKD1 germline mutation, p.Trp1582Ser, predicted to be pathogenic. Unique somatic mutations in PKD1 were also detected in 80% of the renal cysts analyzed, but not in the pRCC. These results suggest that, in this patient, the pRCC utilized a signaling pathway involving MET that was distinct from the pathogenesis of ADPKD. This is the first report of PKD1 mutations and a somatic mutation of the MET oncogene in a pRCC in ADPKD.
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18
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The indole alkaloid meleagrin, from the olive tree endophytic fungus Penicillium chrysogenum, as a novel lead for the control of c-Met-dependent breast cancer proliferation, migration and invasion. Bioorg Med Chem 2015; 24:113-22. [PMID: 26692349 DOI: 10.1016/j.bmc.2015.11.038] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/16/2015] [Accepted: 11/27/2015] [Indexed: 12/15/2022]
Abstract
Fungi of the genus Penicillium produce unique and chemically diverse biologically active secondary metabolites, including indole alkaloids. The role of dysregulated hepatocyte growth factor (HGF) and its receptor, c-Met, in the development and progression of breast carcinoma is documented. The goal of this work is to explore the chemistry and bioactivity of the secondary metabolites of the endophytic Penicillium chrysogenum cultured from the leaf of the olive tree Olea europea, collected in its natural habitat in Egypt. This fungal extract showed good inhibitory activities against the proliferation and migration of several human breast cancer lines. The CH2Cl2 extract of P. chrysogenum mycelia was subjected to bioguided chromatographic separation to afford three known indole alkaloids; meleagrin (1), roquefortine C (2) and DHTD (3). Meleagrin inhibited the growth of the human breast cancer cell lines MDA-MB-231, MDA-468, BT-474, SK BR-3, MCF7 and MCF7-dox, while similar treatment doses were found to have no effect on the growth and viability of the non-tumorigenic human mammary epithelial cells MCF10A. Meleagrin also showed excellent ATP competitive c-Met inhibitory activity in Z-Lyte assay, which was further confirmed via molecular docking studies and Western blot analysis. In addition, meleagrin treatment caused a dose-dependent inhibition of HGF-induced cell migration, and invasion of breast cancer cell lines. Meleagrin treatment potently suppressed the invasive triple negative breast tumor cell growth in an orthotopic athymic nude mice model, promoting this unique natural product from hit to a lead rank. The indole alkaloid meleagrin is a novel lead c-Met inhibitory entity useful for the control of c-Met-dependent metastatic and invasive breast malignancies.
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19
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Liu X, Kung A, Malinoski B, Prakash GKS, Zhang C. Development of Alkyne-Containing Pyrazolopyrimidines To Overcome Drug Resistance of Bcr-Abl Kinase. J Med Chem 2015; 58:9228-37. [PMID: 26562217 DOI: 10.1021/acs.jmedchem.5b01125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Despite the success of imatinib at inhibiting Bcr-Abl and treating chronic myelogenous leukemia (CML), resistance to the therapy occurs over time in patients. In particular, the resistance to imatinib caused by the gatekeeper mutation T315I in Bcr-Abl remains a challenge in the clinic. Inspired by the successful development of ponatinib to curb drug resistance, we hypothesize that the incorporation of an alkyne linker in other heterocyclic scaffolds can also achieve potent inhibition of Bcr-Abl(T315I) by allowing for simultaneous occupancy of both the active site and the allosteric pocket in the Abl kinase domain. Herein, we describe the design, synthesis, and characterization of a series of alkyne-containing pyrazolopyrimidines as Bcr-Abl inhibitors. Our results demonstrate that some alkyne-containing pyrazolopyrimidines potently inhibit not only Abl(T315I) in vitro but also Bcr-Abl(T315I) in cells. These pyrazolopyrimidines can serve as lead compounds for future development of novel targeted therapy to overcome drug resistance of CML.
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Affiliation(s)
- Xu Liu
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Alvin Kung
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Brock Malinoski
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - G K Surya Prakash
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Chao Zhang
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,USC Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, California 90089, United States
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20
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Sakai K, Aoki S, Matsumoto K. Hepatocyte growth factor and Met in drug discovery. J Biochem 2015; 157:271-84. [PMID: 25770121 DOI: 10.1093/jb/mvv027] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/13/2015] [Indexed: 12/14/2022] Open
Abstract
Activation of the hepatocyte growth factor (HGF)-Met pathway evokes dynamic biological responses that support the morphogenesis, regeneration and survival of cells and tissues. A characterization of conditional Met knockout mice indicates that the HGF-Met pathway plays important roles in the regeneration, protection and homeostasis of cells such as hepatocytes, renal tubular cells and neurons. Preclinical studies in disease models have indicated that recombinant HGF protein and expression plasmid for HGF are biological drug candidates for the treatment of patients with diseases or injuries that involve impaired tissue function. The phase-I and phase-I/II clinical trials of the intrathecal administration of HGF protein for the treatment of patients with amyotrophic lateral sclerosis and spinal cord injury, respectively, are ongoing. Biological actions of HGF that promote the dynamic movement, morphogenesis and survival of cells also closely participate in invasion-metastasis and resistance to the molecular-targeted drugs in tumour cells. Different types of HGF-Met pathway inhibitors are now in clinical trials for treatment of malignant tumours. Basic research on HGF and Met has lead to drug discoveries in regenerative medicine and tumour biology.
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Affiliation(s)
- Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; and Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
| | - Shunsuke Aoki
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; and Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; and Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
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21
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Durinck S, Stawiski EW, Pavía-Jiménez A, Modrusan Z, Kapur P, Jaiswal BS, Zhang N, Toffessi-Tcheuyap V, Nguyen TT, Pahuja KB, Chen YJ, Saleem S, Chaudhuri S, Heldens S, Jackson M, Peña-Llopis S, Guillory J, Toy K, Ha C, Harris CJ, Holloman E, Hill HM, Stinson J, Rivers CS, Janakiraman V, Wang W, Kinch LN, Grishin NV, Haverty PM, Chow B, Gehring JS, Reeder J, Pau G, Wu TD, Margulis V, Lotan Y, Sagalowsky A, Pedrosa I, de Sauvage FJ, Brugarolas J, Seshagiri S. Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. Nat Genet 2014; 47:13-21. [PMID: 25401301 DOI: 10.1038/ng.3146] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/24/2014] [Indexed: 12/17/2022]
Abstract
To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non-clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors.
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Affiliation(s)
- Steffen Durinck
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA.,Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA.,Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Andrea Pavía-Jiménez
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Payal Kapur
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Vanina Toffessi-Tcheuyap
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Sadia Saleem
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Sherry Heldens
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Marlena Jackson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Samuel Peña-Llopis
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Corissa J Harris
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Eboni Holloman
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Haley M Hill
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | | | | | - Weiru Wang
- Structural Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lisa N Kinch
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Nick V Grishin
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Peter M Haverty
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bernard Chow
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Julian S Gehring
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jens Reeder
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Gregoire Pau
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Vitaly Margulis
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yair Lotan
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Arthur Sagalowsky
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ivan Pedrosa
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - James Brugarolas
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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22
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Structural Analysis of the Human Fibroblast Growth Factor Receptor 4 Kinase. J Mol Biol 2014; 426:3744-3756. [DOI: 10.1016/j.jmb.2014.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 11/20/2022]
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23
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Stachel SJ, Sanders JM, Henze DA, Rudd MT, Su HP, Li Y, Nanda KK, Egbertson MS, Manley PJ, Jones KLG, Brnardic EJ, Green A, Grobler JA, Hanney B, Leitl M, Lai MT, Munshi V, Murphy D, Rickert K, Riley D, Krasowska-Zoladek A, Daley C, Zuck P, Kane SA, Bilodeau MT. Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain. J Med Chem 2014; 57:5800-16. [PMID: 24914455 DOI: 10.1021/jm5006429] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have identified several series of small molecule inhibitors of TrkA with unique binding modes. The starting leads were chosen to maximize the structural and binding mode diversity derived from a high throughput screen of our internal compound collection. These leads were optimized for potency and selectivity employing a structure based drug design approach adhering to the principles of ligand efficiency to maximize binding affinity without overly relying on lipophilic interactions. This endeavor resulted in the identification of several small molecule pan-Trk inhibitor series that exhibit high selectivity for TrkA/B/C versus a diverse panel of kinases. We have also demonstrated efficacy in both inflammatory and neuropathic pain models upon oral dosing. Herein we describe the identification process, hit-to-lead progression, and binding profiles of these selective pan-Trk kinase inhibitors.
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Affiliation(s)
- Shawn J Stachel
- Departments of Medicinal Chemistry, Biological Chemistry, Pain & Migraine, Molecular Systems, and Structural Biology, Merck Research Laboratories , P.O. Box 4, West Point, Pennsylvania 19486, United States
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24
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Cui JJ. Targeting receptor tyrosine kinase MET in cancer: small molecule inhibitors and clinical progress. J Med Chem 2013; 57:4427-53. [PMID: 24320965 DOI: 10.1021/jm401427c] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The HGF/MET signaling pathway is critical in mediating a wide range of normal physiological functions including embryological development, wound healing, and tissue regeneration. Aberrant activation of the pathway has frequently been found in human cancers via protein overexpression, mutation, gene amplification, and also paracrine or autocrine up-regulation. In addition, the activation of HGF/MET signaling confers resistance to the effects of cancer treatments. Therefore, inhibition of the HGF/MET signaling pathway has great potential for therapeutic intervention in cancer. Currently, there are three approaches toward modulating HGF/MET signaling in human clinical studies of cancer: anti-HGF monoclonal antibodies, MET monoclonal antibodies, and small molecule MET inhibitors. Preliminary clinical benefit from inhibition of HGF or MET has been reported. This Perspective will provide an overview of the HGF/MET signaling pathway in cancer and then will review the development of small molecule MET inhibitors and their progress in clinical applications.
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Affiliation(s)
- J Jean Cui
- TP Therapeutics, Inc. , 6150 Lusk Boulevard, Suite B100, San Diego, California 92121, United States
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25
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Xue Y, Wan PT, Hillertz P, Schweikart F, Zhao Y, Wissler L, Dekker N. X-ray Structural Analysis of Tau-Tubulin Kinase 1 and Its Interactions with Small Molecular Inhibitors. ChemMedChem 2013; 8:1846-54. [DOI: 10.1002/cmdc.201300274] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Indexed: 11/11/2022]
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26
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Biochemical and biophysical characterization of four EphB kinase domains reveals contrasting thermodynamic, kinetic and inhibition profiles. Biosci Rep 2013; 33:BSR20130028. [PMID: 23627399 PMCID: PMC3673036 DOI: 10.1042/bsr20130028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Eph (erythropoietin-producing hepatocellular carcinoma) B receptors are important in a variety of cellular processes through their roles in cell-to-cell contact and signalling; their up-regulation and down-regulation has been shown to have implications in a variety of cancers. A greater understanding of the similarities and differences within this small, highly conserved family of tyrosine kinases will be essential to the identification of effective therapeutic opportunities for disease intervention. In this study, we have developed a route to production of multi-milligram quantities of highly purified, homogeneous, recombinant protein for the kinase domain of these human receptors in Escherichia coli. Analyses of these isolated catalytic fragments have revealed stark contrasts in their amenability to recombinant expression and their physical properties: e.g., a >16°C variance in thermal stability, a 3-fold difference in catalytic activity and disparities in their inhibitor binding profiles. We find EphB3 to be an outlier in terms of both its intrinsic stability, and more importantly its ligand-binding properties. Our findings have led us to speculate about both their biological significance and potential routes for generating EphB isozyme-selective small-molecule inhibitors. Our comprehensive methodologies provide a template for similar in-depth studies of other kinase superfamily members.
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27
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Alton GR, Lunney EA. Targeting the unactivated conformations of protein kinases for small molecule drug discovery. Expert Opin Drug Discov 2013; 3:595-605. [PMID: 23506143 DOI: 10.1517/17460441.3.6.595] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The number of drugs in active clinical development or on the market that target the unactivated conformational states of protein kinases is growing and represents a significant portion of kinase research at biopharmaceutical companies. These non-classical kinase inhibitors have a mode of action which may overcome some of the liabilities of classical ATP-site inhibitors that substantially overlap the space that ATP occupies in the activated kinase. OBJECTIVE This review will discuss state-of-the-art methods of inhibiting protein kinases by targeting the unactivated conformations of the enzyme with small molecules directed to the ATP binding region. METHODS Biochemical and structural biology publications and public domain crystal structures were evaluated to identify key concepts in drug discovery for unactivated protein kinase inhibitors that target the ATP binding region. CONCLUSION The potential for enhanced selectivity, potency and duration of pharmacological action may allow non-classical kinase therapeutics to be used for chronic dosing in non-life-threatening indications. Moreover, by targeting additional conformational space on the kinase protein it is possible that new chemical matter will be discovered such that current intellectual property limitations on traditional ATP-site chemical scaffolds may be circumvented.
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Affiliation(s)
- Gordon R Alton
- Senior Principal Scientist Pfizer Global Research and Development, Department of Biochemical Pharmacology, 10628 Science Center Drive, San Diego, CA 92121, USA +1 858 526 4926 ; 858 526 4236 ;
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28
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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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29
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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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Busnena BA, Foudah AI, Melancon T, El Sayed KA. Olive secoiridoids and semisynthetic bioisostere analogues for the control of metastatic breast cancer. Bioorg Med Chem 2013; 21:2117-27. [PMID: 23403296 DOI: 10.1016/j.bmc.2012.12.050] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/19/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
(-)-Oleocanthal (1) and ligstroside aglycone (2) are common bioactive olive oil secoiridoids. Secoiridoid 1 has been previously reported as a c-MET inhibitor. Chemically, (-)-oleocanthal is the elenolic acid ester of the common olive phenolic alcohol tyrosol. Therefore, several analogues (4-13) were synthesized by esterification and carbamoylation of tyrosol using diverse phenolic naturally occurring in olive and heterocyclic acids as elenolic acid bioisosteres to assess the effect of replacing the acid moiety of (-)-oleocanthal. Their c-MET inhibitory activity as well as their antiproliferative, antimigratory, and anti-invasive activities against the highly metastatic human breast cancer cell line MDA-MB231 has been assessed. Ligstroside aglycone (2) showed the best antimigratory activity. Generally, tyrosol esters showed better activities versus carbamate analogues. Tyrosol sinapate (5) showed the best c-MET phosphorylation inhibitory activity in Z'-LYTE kinase assay. Both 1 and 5 competitively inhibited the ATP binding into its pocket in the c-MET catalytic domain. Compound 5 showed selective activities against tumor cells without toxicity to the non-tumorigenic human breast MCF10A epithelial cell line. Tyrosol esters with a phenolic acid containing hydrogen bond donor and/or acceptor groups at the para-position have better anticancer and c-MET inhibitory activities. Olive oil secoiridoids are excellent scaffolds for the design of novel c-MET inhibitors.
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Affiliation(s)
- Belnaser A Busnena
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, United States
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31
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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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32
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Wu K, Ai J, Liu Q, Chen T, Zhao A, Peng X, Wang Y, Ji Y, Yao Q, Xu Y, Geng M, Zhang A. Multisubstituted quinoxalines and pyrido[2,3-d]pyrimidines: Synthesis and SAR study as tyrosine kinase c-Met inhibitors. Bioorg Med Chem Lett 2012; 22:6368-72. [DOI: 10.1016/j.bmcl.2012.08.075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/07/2012] [Accepted: 08/20/2012] [Indexed: 12/22/2022]
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Xu R, Liu D, Cowburn D. Abl kinase constructs expressed in bacteria: facilitation of structural and functional studies including segmental labeling by expressed protein ligation. MOLECULAR BIOSYSTEMS 2012; 8:1878-85. [PMID: 22592215 PMCID: PMC3586340 DOI: 10.1039/c2mb25051a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A great portion of tyrosine kinases are involved in cell development and their structural alteration is intimately involved in associated pathologies of development and oncology. These kinases are one of the major groups of targets under investigation for molecular therapeutics. To carry out biochemical and structural biological studies on these kinases, economical production of their purified forms is highly desirable. However over-expressing tyrosine kinases as recombinant forms in bacterial systems and their purification is a significant challenge. Abelson kinase (Abl) has previously been expressed on a large scale to facilitate X-ray crystallography and NMR structure studies mainly in baculovirus infected insect cells. Even though success has been achieved in expression of soluble tyrosine kinases in E. coli with chaperones to improve correct folding, low expression levels of kinases are intrinsic in such systems because of diversion of resources to produce chaperones. Here we present a straightforward method to express and purify isolated Abl kinase domain and SH3-SH2-kinase multi-domain structures. The expressed Abl protein retains its correct folding and biological function. The yield of soluble protein is in a several mg L(-1) range in minimal media. Furthermore we demonstrate that segmental isotopic labelling using expressed protein ligation can be achieved using bacterial expressed Abl kinase domain constructs, which is especially useful in NMR structure-activity studies.
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Affiliation(s)
- Rong Xu
- Dept. of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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34
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Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface 2012; 9:1409-37. [PMID: 22552919 DOI: 10.1098/rsif.2011.0843] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of patients experience adverse effects more severe than anticipated. The unacceptable risk-benefit profile for many drugs mandates a paradigm shift towards personalized medicine. However, prior to adoption of patient-specific approaches, it is useful to understand the molecular details underlying variable drug response among diverse patient populations. Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms correlated with differential therapeutic outcomes. Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein-drug interactions and, ultimately, drug response. In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions. Next, we describe the impact of coding mutations on protein structures and drug response. Finally, we highlight tools for analysing protein structures and protein-drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants.
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Affiliation(s)
- Jennifer L Lahti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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35
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Levinson NM, Boxer SG. Structural and spectroscopic analysis of the kinase inhibitor bosutinib and an isomer of bosutinib binding to the Abl tyrosine kinase domain. PLoS One 2012; 7:e29828. [PMID: 22493660 PMCID: PMC3320885 DOI: 10.1371/journal.pone.0029828] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/22/2012] [Indexed: 01/02/2023] Open
Abstract
Chronic myeloid leukemia (CML) is caused by the kinase activity of the BCR-Abl fusion protein. The Abl inhibitors imatinib, nilotinib and dasatinib are currently used to treat CML, but resistance to these inhibitors is a significant clinical problem. The kinase inhibitor bosutinib has shown efficacy in clinical trials for imatinib-resistant CML, but its binding mode is unknown. We present the 2.4 Å structure of bosutinib bound to the kinase domain of Abl, which explains the inhibitor's activity against several imatinib-resistant mutants, and reveals that similar inhibitors that lack a nitrile moiety could be effective against the common T315I mutant. We also report that two distinct chemical compounds are currently being sold under the name "bosutinib", and report spectroscopic and structural characterizations of both. We show that the fluorescence properties of these compounds allow inhibitor binding to be measured quantitatively, and that the infrared absorption of the nitrile group reveals a different electrostatic environment in the conserved ATP-binding sites of Abl and Src kinases. Exploiting such differences could lead to inhibitors with improved selectivity.
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MESH Headings
- Aniline Compounds/chemistry
- Aniline Compounds/pharmacology
- Benzamides
- Binding Sites
- Dasatinib
- Drug Resistance, Neoplasm
- Escherichia coli
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate
- Isomerism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Models, Molecular
- Mutation
- Nitriles/chemistry
- Nitriles/pharmacology
- Piperazines/chemistry
- Piperazines/pharmacology
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Structure, Tertiary
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/chemistry
- Protein-Tyrosine Kinases/metabolism
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
- Quinolines/chemistry
- Quinolines/pharmacology
- Recombinant Proteins/antagonists & inhibitors
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Spectrophotometry, Infrared
- Static Electricity
- Thiazoles/chemistry
- Thiazoles/pharmacology
- X-Ray Diffraction
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Affiliation(s)
- Nicholas M Levinson
- Department of Chemistry, Stanford University, Stanford, California, United States of America.
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36
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Abstract
Uncontrolled cell survival, growth, angiogenesis and metastasis are essential hallmarks of cancer. Genetic and biochemical data have demonstrated that the growth and motility factor hepatocyte growth factor/scatter factor (HGF/SF) and its receptor, the tyrosine kinase MET, have a causal role in all of these processes, thus providing a strong rationale for targeting these molecules in cancer. Parallel progress in understanding the structure and function of HGF/SF, MET and associated signalling components has led to the successful development of blocking antibodies and a large number of small-molecule MET kinase inhibitors. In this Review, we discuss these advances, as well as results from recent clinical studies that demonstrate that inhibiting MET signalling in several types of solid human tumours has major therapeutic value.
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Affiliation(s)
- Ermanno Gherardi
- Medical Research Council (MRC) Centre, Hills Road, Cambridge CB2 2QH, UK.
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37
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Allen JV, Bardelle C, Blades K, Buttar D, Chapman L, Colclough N, Dossetter AG, Garner AP, Girdwood A, Lambert C, Leach AG, Law B, Major J, Plant H, Slater AM. The discovery of benzanilides as c-Met receptor tyrosine kinase inhibitors by a directed screening approach. Bioorg Med Chem Lett 2011; 21:5224-9. [DOI: 10.1016/j.bmcl.2011.07.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/26/2022]
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38
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Tiedt R, Degenkolbe E, Furet P, Appleton BA, Wagner S, Schoepfer J, Buck E, Ruddy DA, Monahan JE, Jones MD, Blank J, Haasen D, Drueckes P, Wartmann M, McCarthy C, Sellers WR, Hofmann F. A drug resistance screen using a selective MET inhibitor reveals a spectrum of mutations that partially overlap with activating mutations found in cancer patients. Cancer Res 2011; 71:5255-64. [PMID: 21697284 DOI: 10.1158/0008-5472.can-10-4433] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The emergence of drug resistance is a primary concern in any cancer treatment, including with targeted kinase inhibitors as exemplified by the appearance of Bcr-Abl point mutations in chronic myeloid leukemia (CML) patients treated with imatinib. In vitro approaches to identify resistance mutations in Bcr-Abl have yielded mutation spectra that faithfully recapitulated clinical observations. To predict resistance mutations in the receptor tyrosine kinase MET that could emerge during inhibitor treatment in patients, we conducted a resistance screen in BaF3 TPR-MET cells using the novel selective MET inhibitor NVP-BVU972. The observed spectrum of mutations in resistant cells was dominated by substitutions of tyrosine 1230 but also included other missense mutations and partially overlapped with activating MET mutations that were previously described in cancer patients. Cocrystallization of the MET kinase domain in complex with NVP-BVU972 revealed a key role for Y1230 in binding of NVP-BVU972, as previously reported for multiple other selective MET inhibitors. A second resistance screen in the same format with the MET inhibitor AMG 458 yielded a distinct spectrum of mutations rich in F1200 alterations, which is consistent with a different predicted binding mode. Our findings suggest that amino acid substitutions in the MET kinase domain of cancer patients need to be carefully monitored before and during treatment with MET inhibitors, as resistance may preexist or emerge. Compounds binding in the same manner as NVP-BVU972 might be particularly susceptible to the development of resistance through mutations in Y1230, a condition that may be addressed by MET inhibitors with alternative binding modes.
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MESH Headings
- Amino Acid Substitution
- Aminopyridines/metabolism
- Aminopyridines/pharmacology
- Animals
- Antineoplastic Agents/metabolism
- Antineoplastic Agents/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/metabolism
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Line, Transformed
- Cell Line, Tumor
- Crystallography, X-Ray
- DNA Mutational Analysis
- DNA, Neoplasm/genetics
- Drug Resistance, Neoplasm/genetics
- Enzyme Activation/genetics
- Humans
- Mice
- Models, Molecular
- Mutagenesis
- Mutation, Missense
- Neoplasms/drug therapy
- Neoplasms/genetics
- Point Mutation
- Protein Binding
- Protein Conformation
- Protein Kinase Inhibitors/metabolism
- Protein Kinase Inhibitors/pharmacology
- Protein Structure, Tertiary
- Proto-Oncogene Proteins c-met/antagonists & inhibitors
- Proto-Oncogene Proteins c-met/chemistry
- Proto-Oncogene Proteins c-met/genetics
- Pyrazoles/metabolism
- Pyrazoles/pharmacology
- Quinolines/metabolism
- Quinolines/pharmacology
- Receptors, Growth Factor/antagonists & inhibitors
- Receptors, Growth Factor/chemistry
- Receptors, Growth Factor/genetics
- Tyrosine/metabolism
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Affiliation(s)
- Ralph Tiedt
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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39
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Eathiraj S, Palma R, Volckova E, Hirschi M, France DS, Ashwell MA, Chan TCK. Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197. J Biol Chem 2011; 286:20666-76. [PMID: 21454604 PMCID: PMC3121448 DOI: 10.1074/jbc.m110.213801] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/15/2011] [Indexed: 11/06/2022] Open
Abstract
A number of human malignancies exhibit sustained stimulation, mutation, or gene amplification of the receptor tyrosine kinase human mesenchymal-epithelial transition factor (c-Met). ARQ 197 is a clinically advanced, selective, orally bioavailable, and well tolerated c-Met inhibitor, currently in Phase 3 clinical testing in non-small cell lung cancer patients. Herein, we describe the molecular and structural basis by which ARQ 197 selectively targets c-Met. Through our analysis we reveal a previously undisclosed, novel inhibitory mechanism that utilizes distinct regulatory elements of the c-Met kinase. The structure of ARQ 197 in complex with the c-Met kinase domain shows that the inhibitor binds a conformation that is distinct from published kinase structures. ARQ 197 inhibits c-Met autophosphorylation and is highly selective for the inactive or unphosphorylated form of c-Met. Through our analysis of the interplay between the regulatory and catalytic residues of c-Met, and by comparison between the autoinhibited canonical conformation of c-Met bound by ARQ 197 to previously described kinase domains of type III receptor tyrosine kinases, we believe this to be the basis of a powerful new in silico approach for the design of similar inhibitors for other protein kinases of therapeutic interest.
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Affiliation(s)
| | - Rocio Palma
- From ArQule, Inc., Woburn, Massachusetts 01801
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40
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Jura N, Zhang X, Endres NF, Seeliger MA, Schindler T, Kuriyan J. Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. Mol Cell 2011; 42:9-22. [PMID: 21474065 DOI: 10.1016/j.molcel.2011.03.004] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 12/23/2022]
Abstract
In contrast to the active conformations of protein kinases, which are essentially the same for all kinases, inactive kinase conformations are structurally diverse. Some inactive conformations are, however, observed repeatedly in different kinases, perhaps reflecting an important role in catalysis. In this review, we analyze one of these recurring conformations, first identified in CDK and Src kinases, which turned out to be central to understanding of how kinase domain of the EGF receptor is activated. This mechanism, which involves the stabilization of the active conformation of an α helix, has features in common with mechanisms operative in several other kinases.
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Affiliation(s)
- Natalia Jura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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41
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Rickert KW, Patel SB, Allison TJ, Byrne NJ, Darke PL, Ford RE, Guerin DJ, Hall DL, Kornienko M, Lu J, Munshi SK, Reid JC, Shipman JM, Stanton EF, Wilson KJ, Young JR, Soisson SM, Lumb KJ. Structural basis for selective small molecule kinase inhibition of activated c-Met. J Biol Chem 2011; 286:11218-25. [PMID: 21247903 DOI: 10.1074/jbc.m110.204404] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The receptor tyrosine kinase c-Met is implicated in oncogenesis and is the target for several small molecule and biologic agents in clinical trials for the treatment of cancer. Binding of the hepatocyte growth factor to the cell surface receptor of c-Met induces activation via autophosphorylation of the kinase domain. Here we describe the structural basis of c-Met activation upon autophosphorylation and the selective small molecule inhibiton of autophosphorylated c-Met. MK-2461 is a potent c-Met inhibitor that is selective for the phosphorylated state of the enzyme. Compound 1 is an MK-2461 analog with a 20-fold enthalpy-driven preference for the autophosphorylated over unphosphorylated c-Met kinase domain. The crystal structure of the unbound kinase domain phosphorylated at Tyr-1234 and Tyr-1235 shows that activation loop phosphorylation leads to the ejection and disorder of the activation loop and rearrangement of helix αC and the G loop to generate a viable active site. Helix αC adopts a orientation different from that seen in activation loop mutants. The crystal structure of the complex formed by the autophosphorylated c-Met kinase domain and compound 1 reveals a significant induced fit conformational change of the G loop and ordering of the activation loop, explaining the selectivity of compound 1 for the autophosphorylated state. The results highlight the role of structural plasticity within the kinase domain in imparting the specificity of ligand binding and provide the framework for structure-guided design of activated c-Met inhibitors.
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Affiliation(s)
- Keith W Rickert
- Global Structural Biology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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42
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Nakamura T, Sakai K, Nakamura T, Matsumoto K. Hepatocyte growth factor twenty years on: Much more than a growth factor. J Gastroenterol Hepatol 2011; 26 Suppl 1:188-202. [PMID: 21199531 DOI: 10.1111/j.1440-1746.2010.06549.x] [Citation(s) in RCA: 343] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liver regeneration depends on the proliferation of mature hepatocytes. In the 1980s, the method for the cultivation of mature hepatocytes provided an opportunity for the discovery of hepatocyte growth factor (HGF) as a protein that is structurally and functionally different from other growth factors. In 1991, the scatter factor, tumor cytotoxic factor, and 3-D epithelial morphogen were identified as HGF, and Met tyrosine kinase was identified as the receptor for HGF. Thus, the connection of apparently unrelated research projects rapidly enriched the research on HGF in different fields. The HGF-Met pathway plays important roles in the embryonic development of the liver and the placenta, in the migration of myogenic precursor cells, and in epithelial morphogenesis. The use of tissue-specific knockout mice demonstrated that in mature tissues the HGF-Met pathway plays a critical role in tissue protection and regeneration, and in providing less susceptibility to chronic inflammation and fibrosis. In various injury and disease models, HGF promotes cell survival, regeneration of tissues, and suppresses and improves chronic inflammation and fibrosis. Drug development using HGF has been challenging, but extensive preclinical studies to address its therapeutic effects have provided significant results sufficient for the development of HGF as a biological drug in the regeneration-based therapy of diseases. Clinical trials using recombinant human HGF protein, or HGF genes, are in progress for the treatment of diseases.
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43
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Francis DM, Page R. Strategies to optimize protein expression in E. coli. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2010; Chapter 5:5.24.1-5.24.29. [PMID: 20814932 PMCID: PMC7162232 DOI: 10.1002/0471140864.ps0524s61] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recombinant protein expression in Escherichia coli (E. coli) is simple, fast, inexpensive, and robust, with the expressed protein comprising up to 50 percent of the total cellular protein. However, it also has disadvantages. For example, the rapidity of bacterial protein expression often results in unfolded/misfolded proteins, especially for heterologous proteins that require longer times and/or molecular chaperones to fold correctly. In addition, the highly reductive environment of the bacterial cytosol and the inability of E. coli to perform several eukaryotic post-translational modifications results in the insoluble expression of proteins that require these modifications for folding and activity. Fortunately, multiple, novel reagents and techniques have been developed that allow for the efficient, soluble production of a diverse range of heterologous proteins in E. coli. This overview describes variables at each stage of a protein expression experiment that can influence solubility and offers a summary of strategies used to optimize soluble expression in E. coli.
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44
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Behshad E, Klabe RM, Margulis A, Becker-Pasha M, Rupar MJ, Collier P, Liu PC, Hollis GF, Burn TC, Wynn R. Phosphorylation State-Dependent High Throughput Screening of the c-Met Kinase. CURRENT CHEMICAL GENOMICS 2010; 4:27-33. [PMID: 20556206 PMCID: PMC2885599 DOI: 10.2174/1875397301004010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/02/2010] [Accepted: 03/03/2010] [Indexed: 11/22/2022]
Abstract
High-throughput screening (HTS) of ~50,000 chemical compounds against phosphorylated and unphosphorylated c-Met, a tyrosine kinase receptor for hepatocyte growth factor (HGF), was carried out in order to compare hit rates, hit potencies and also to explore scaffolds that might serve as potential leads targeting only the unphosphorylated form of the enzyme. The hit rate and potency for the confirmed hit molecules were higher for the unphosphoryalted form of c-Met. While the target of small molecule inhibitor discovery efforts has traditionally been the phosphorylated form, there are now examples of small molecules that target unphosphorylated kinases. Screening for inhibitors of unphosphorylated kinases may represent a complementary approach for prioritizing chemical scaffolds for hit-to-lead follow ups.
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Affiliation(s)
- Elham Behshad
- Incyte Corporation, Applied Technology Group, Experimental Station, Route 141 & Henry Clay Road, Wilmington, DE 19880, USA
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45
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Fabbro D, Manley PW, Jahnke W, Liebetanz J, Szyttenholm A, Fendrich G, Strauss A, Zhang J, Gray NS, Adrian F, Warmuth M, Pelle X, Grotzfeld R, Berst F, Marzinzik A, Cowan-Jacob SW, Furet P, Mestan J. Inhibitors of the Abl kinase directed at either the ATP- or myristate-binding site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:454-62. [PMID: 20152788 DOI: 10.1016/j.bbapap.2009.12.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 11/20/2022]
Abstract
The ATP-competitive inhibitors dasatinib and nilotinib, which bind to catalytically different conformations of the Abl kinase domain, have recently been approved for the treatment of imatinib-resistant CML. These two new drugs, albeit very efficient against most of the imatinib-resistant mutants of Bcr-Abl, fail to effectively suppress the Bcr-Abl activity of the T315I (or gatekeeper) mutation. Generating new ATP site-binding drugs that target the T315I in Abl has been hampered, amongst others, by target selectivity, which is frequently an issue when developing ATP-competitive inhibitors. Recently, using an unbiased cellular screening approach, GNF-2, a non-ATP-competitive inhibitor, has been identified that demonstrates cellular activity against Bcr-Abl transformed cells. The exquisite selectivity of GNF-2 is due to the finding that it targets the myristate binding site located near the C-terminus of the Abl kinase domain, as demonstrated by genetic approaches, solution NMR and X-ray crystallography. GNF-2, like myristate, is able to induce and/or stabilize the clamped inactive conformation of Abl analogous to the SH2-Y527 interaction of Src. The molecular mechanism for allosteric inhibition by the GNF-2 inhibitor class, and the combined effects with ATP-competitive inhibitors such as nilotinib and imatinib on wild-type Abl and imatinib-resistant mutants, in particular the T315I gatekeeper mutant, are reviewed.
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Affiliation(s)
- Doriano Fabbro
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland.
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46
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Pan BS, Chan GKY, Chenard M, Chi A, Davis LJ, Deshmukh SV, Gibbs JB, Gil S, Hang G, Hatch H, Jewell JP, Kariv I, Katz JD, Kunii K, Lu W, Lutterbach BA, Paweletz CP, Qu X, Reilly JF, Szewczak AA, Zeng Q, Kohl NE, Dinsmore CJ. MK-2461, a novel multitargeted kinase inhibitor, preferentially inhibits the activated c-Met receptor. Cancer Res 2010; 70:1524-33. [PMID: 20145145 DOI: 10.1158/0008-5472.can-09-2541] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The receptor tyrosine kinase c-Met is an attractive target for therapeutic blockade in cancer. Here, we describe MK-2461, a novel ATP-competitive multitargeted inhibitor of activated c-Met. MK-2461 inhibited in vitro phosphorylation of a peptide substrate recognized by wild-type or oncogenic c-Met kinases (N1100Y, Y1230C, Y1230H, Y1235D, and M1250T) with IC(50) values of 0.4 to 2.5 nmol/L. In contrast, MK-2461 was several hundredfold less potent as an inhibitor of c-Met autophosphorylation at the kinase activation loop. In tumor cells, MK-2461 effectively suppressed constitutive or ligand-induced phosphorylation of the juxtamembrane domain and COOH-terminal docking site of c-Met, and its downstream signaling to the phosphoinositide 3-kinase-AKT and Ras-extracellular signal-regulated kinase pathways, without inhibiting autophosphorylation of the c-Met activation loop. BIAcore studies indicated 6-fold tighter binding to c-Met when it was phosphorylated, suggesting that MK-2461 binds preferentially to activated c-Met. MK-2461 displayed significant inhibitory activities against fibroblast growth factor receptor (FGFR), platelet-derived growth factor receptor, and other receptor tyrosine kinases. In cell culture, MK-2461 inhibited hepatocyte growth factor/c-Met-dependent mitogenesis, migration, cell scatter, and tubulogenesis. Seven of 10 MK-2461-sensitive tumor cell lines identified from a large panel harbored genomic amplification of MET or FGFR2. In a murine xenograft model of c-Met-dependent gastric cancer, a well-tolerated oral regimen of MK-2461 administered at 100 mg/kg twice daily effectively suppressed c-Met signaling and tumor growth. Similarly, MK-2461 inhibited the growth of tumors formed by s.c. injection of mouse NIH-3T3 cells expressing oncogenic c-Met mutants. Taken together, our findings support further preclinical development of MK-2461 for cancer therapy.
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Affiliation(s)
- Bo-Sheng Pan
- Department of In Vitro Sciences, Merck Research Laboratories, BMB-11, 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
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47
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Manley PW, Drueckes P, Fendrich G, Furet P, Liebetanz J, Martiny-Baron G, Mestan J, Trappe J, Wartmann M, Fabbro D. Extended kinase profile and properties of the protein kinase inhibitor nilotinib. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:445-53. [PMID: 19922818 DOI: 10.1016/j.bbapap.2009.11.008] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 10/30/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
As a drug used to treat imatinib-resistant and -intolerant, chronic and advanced phase chronic myelogenous leukaemia, nilotinib is well characterised as a potent inhibitor of the Abl tyrosine kinase activity of wild-type and imatinib-resistant mutant forms of BCR-Abl. Here we review the profile of nilotinib as a protein kinase inhibitor. Although an ATP-competitive inhibitor of Abl, nilotinib binds to a catalytically inactive conformation (DFG-out) of the activation loop. As a consequence of this, nilotinib exhibits time-dependent inhibition of Abl kinase in enzymatic assays, which can be extrapolated to other targets to explain differences between biochemical activity and cellular assays. Although these differences confound assessment of kinase selectivity, as assessed using a combination of protein binding and transphosphorylation assays, together with cellular autophosporylation and proliferation assays, well established kinase targets of nilotinib in rank order of inhibitory potency are DDR-1>DDR-2>BCR-Abl (Abl)>PDGFRalpha/beta>KIT>CSF-1R. In addition nilotinib has now been found to bind to both MAPK11 (p38beta) and MAPK12 (p38alpha), as well as with very high affinity to ZAK kinase. Although neither enzymatic nor cellular data are yet available to substantiate the drug as an inhibitor of ZAK phosphorylation, modeling predicts that it binds in an ATP-competitive fashion.
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Affiliation(s)
- Paul W Manley
- Novartis Institutes for Biomedical Research, Basel, Switzerland.
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48
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Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, Verkhivker GM. Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One 2009; 4:e7485. [PMID: 19834613 PMCID: PMC2759519 DOI: 10.1371/journal.pone.0007485] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 09/25/2009] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are the most common protein domains implicated in cancer, where somatically acquired mutations are known to be functionally linked to a variety of cancers. Resequencing studies of protein kinase coding regions have emphasized the importance of sequence and structure determinants of cancer-causing kinase mutations in understanding of the mutation-dependent activation process. We have developed an integrated bioinformatics resource, which consolidated and mapped all currently available information on genetic modifications in protein kinase genes with sequence, structure and functional data. The integration of diverse data types provided a convenient framework for kinome-wide study of sequence-based and structure-based signatures of cancer mutations. The database-driven analysis has revealed a differential enrichment of SNPs categories in functional regions of the kinase domain, demonstrating that a significant number of cancer mutations could fall at structurally equivalent positions (mutational hotspots) within the catalytic core. We have also found that structurally conserved mutational hotspots can be shared by multiple kinase genes and are often enriched by cancer driver mutations with high oncogenic activity. Structural modeling and energetic analysis of the mutational hotspots have suggested a common molecular mechanism of kinase activation by cancer mutations, and have allowed to reconcile the experimental data. According to a proposed mechanism, structural effect of kinase mutations with a high oncogenic potential may manifest in a significant destabilization of the autoinhibited kinase form, which is likely to drive tumorigenesis at some level. Structure-based functional annotation and prediction of cancer mutation effects in protein kinases can facilitate an understanding of the mutation-dependent activation process and inform experimental studies exploring molecular pathology of tumorigenesis.
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Affiliation(s)
- Anshuman Dixit
- Graduate Program for Bioinformatics, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, Kansas, United States of America
| | - Lin Yi
- Graduate Program for Bioinformatics, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
| | - Ragul Gowthaman
- Graduate Program for Bioinformatics, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
| | - Ali Torkamani
- Scripps Genomic Medicine, Department of Molecular and Experimental Medicine, Scripps Health and The Scripps Research Institute, La Jolla, California, United States of America
| | - Nicholas J. Schork
- Scripps Genomic Medicine, Department of Molecular and Experimental Medicine, Scripps Health and The Scripps Research Institute, La Jolla, California, United States of America
| | - Gennady M. Verkhivker
- Graduate Program for Bioinformatics, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, Kansas, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Qian F, Engst S, Yamaguchi K, Yu P, Won KA, Mock L, Lou T, Tan J, Li C, Tam D, Lougheed J, Yakes FM, Bentzien F, Xu W, Zaks T, Wooster R, Greshock J, Joly AH. Inhibition of tumor cell growth, invasion, and metastasis by EXEL-2880 (XL880, GSK1363089), a novel inhibitor of HGF and VEGF receptor tyrosine kinases. Cancer Res 2009; 69:8009-16. [PMID: 19808973 DOI: 10.1158/0008-5472.can-08-4889] [Citation(s) in RCA: 271] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Met receptor tyrosine kinase and its ligand, hepatocyte growth factor (HGF), are overexpressed and/or activated in a wide variety of human malignancies. Vascular endothelial growth factor (VEGF) receptors are expressed on the surface of vascular endothelial cells and cooperate with Met to induce tumor invasion and vascularization. EXEL-2880 (XL880, GSK1363089) is a small-molecule kinase inhibitor that targets members of the HGF and VEGF receptor tyrosine kinase families, with additional inhibitory activity toward KIT, Flt-3, platelet-derived growth factor receptor beta, and Tie-2. Binding of EXEL-2880 to Met and VEGF receptor 2 (KDR) is characterized by a very slow off-rate, consistent with X-ray crystallographic data showing that the inhibitor is deeply bound in the Met kinase active site cleft. EXEL-2880 inhibits cellular HGF-induced Met phosphorylation and VEGF-induced extracellular signal-regulated kinase phosphorylation and prevents both HGF-induced responses of tumor cells and HGF/VEGF-induced responses of endothelial cells. In addition, EXEL-2880 prevents anchorage-independent proliferation of tumor cells under both normoxic and hypoxic conditions. In vivo, these effects produce significant dose-dependent inhibition of tumor burden in an experimental model of lung metastasis. Collectively, these data indicate that EXEL-2880 may prevent tumor growth through a direct effect on tumor cell proliferation and by inhibition of invasion and angiogenesis mediated by HGF and VEGF receptors.
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Affiliation(s)
- Fawn Qian
- Exelixis, Inc, South San Francisco, California 94083, USA
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Chaperone over-expression in Escherichia coli: Apparent increased yields of soluble recombinant protein kinases are due mainly to soluble aggregates. Protein Expr Purif 2009; 64:185-93. [DOI: 10.1016/j.pep.2008.10.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 10/30/2008] [Accepted: 10/30/2008] [Indexed: 11/18/2022]
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