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Faruqui T, Akhtar A, Showket F, Dar MJ, Akhter Y. Identification and Evaluation of IGF1R and Its Associated Proteins as Targets and Design of Novel Inhibitors for Cancer Therapy. J Cell Biochem 2025; 126:e70008. [PMID: 40023828 DOI: 10.1002/jcb.70008] [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: 09/04/2024] [Revised: 01/29/2025] [Accepted: 02/06/2025] [Indexed: 03/04/2025]
Abstract
The insulin-like growth factor 1 receptor (IGF1R) is a crucial receptor tyrosine kinase involved in cellular growth, survival, and metabolism. Abnormal overexpression and activation are common in various cancers and contribute to tumor development and resistance to treatment. The STRING database was used to analyze the protein-protein interaction network of IGF1R and was visualized using Cytoscape to identify the key associated proteins. We assessed IGF1R and its associated protein expression levels across pan-cancer types and compared them to healthy controls using a TNMplot and cBioPortal. The objective of this study was to identify novel, low-toxicity inhibitors targeting the IGF1R and its associated proteins (e.g., AKT1 and EGFR) with better pharmacokinetic profiles for effective cancer treatment, including brain cancer. We screened 693 million drug-like compounds and selected the top 400 for toxicity analysis using ProTox-II, which identified 83 nontoxic candidates. These were categorized as either blood-brain barrier (BBB) permeant or impermeant. Molecular docking studies with AutoDock Vina 4.1 were performed on 17 target proteins, including IGF1R, with the top three compounds. Subsequently, molecular dynamics simulations using Desmond were conducted on the two most promising candidates: two BBB permeants and two impermeants. Our study identified six nontoxic IGF1R inhibitors and 16 other target protein inhibitors. Docking and MD simulations confirmed the potential of these compounds in targeted therapies. Notably, both BBB-permeant and -impermeant compounds in complex with the target proteins showed stability over 50 and 400 ns molecular simulation experiments, highlighting their potential in cancer therapy and suggesting the need for further in vitro and in vivo validation.
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Affiliation(s)
- Tabrez Faruqui
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Aubaidah Akhtar
- Cancer Pharmacology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research(AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Farheen Showket
- Cancer Pharmacology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research(AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Mohd Jamal Dar
- Cancer Pharmacology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
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2
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Dsouza NR, Haque N, Tripathi S, Zimmermann MT. Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants. Int J Mol Sci 2024; 25:12018. [PMID: 39596086 PMCID: PMC11594063 DOI: 10.3390/ijms252212018] [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: 09/24/2024] [Revised: 10/31/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024] Open
Abstract
Clinical genomics sequencing is rapidly expanding the number of variants that need to be functionally elucidated. Interpreting genetic variants (i.e., mutations) usually begins by identifying how they affect protein-coding sequences. Still, the three-dimensional (3D) protein molecule is rarely considered for large-scale variant analysis, nor in analyses of how proteins interact with each other and their environment. We propose a standardized approach to scoring protein surface property changes as a new dimension for functionally and mechanistically interpreting genomic variants. Further, it directs hypothesis generation for functional genomics research to learn more about the encoded protein's function. We developed a novel method leveraging 3D structures and time-dependent simulations to score and statistically evaluate protein surface property changes. We evaluated positive controls composed of eight thermophilic versus mesophilic orthologs and variants that experimentally change the protein's solubility, which all showed large and statistically significant differences in charge distribution (p < 0.01). We scored static 3D structures and dynamic ensembles for 43 independent variants (23 pathogenic and 20 uninterpreted) across four proteins. Focusing on the potassium ion channel, KCNK9, the average local surface potential shifts were 0.41 kBT/ec with an average p-value of 1 × 10-2. In contrast, dynamic ensemble shifts averaged 1.15 kBT/ec with an average p-value of 1 × 10-5, enabling the identification of changes far from mutated sites. This study demonstrates that an objective assessment of how mutations affect electrostatic distributions of protein surfaces can aid in interpreting genomic variants discovered through clinical genomic sequencing.
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Affiliation(s)
- Nikita R. Dsouza
- Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (N.R.D.); (N.H.); (S.T.)
| | - Neshatul Haque
- Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (N.R.D.); (N.H.); (S.T.)
| | - Swarnendu Tripathi
- Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (N.R.D.); (N.H.); (S.T.)
| | - Michael T. Zimmermann
- Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (N.R.D.); (N.H.); (S.T.)
- Data Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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3
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [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: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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4
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Khanal P, Patil VS, Bhandare VV, Patil PP, Patil BM, Dwivedi PSR, Bhattacharya K, Harish DR, Roy S. Systems and in vitro pharmacology profiling of diosgenin against breast cancer. Front Pharmacol 2023; 13:1052849. [PMID: 36686654 PMCID: PMC9846155 DOI: 10.3389/fphar.2022.1052849] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Aim: The purpose of this study was to establish a mode of action for diosgenin against breast cancer employing a range of system biology tools and to corroborate its results with experimental facts. Methodology: The diosgenin-regulated domains implicated in breast cancer were enriched in the Kyoto Encyclopedia of Genes and Genomes database to establish diosgenin-protein(s)-pathway(s) associations. Later, molecular docking and the lead complexes were considered for molecular dynamics simulations, MMPBSA, principal component, and dynamics cross-correlation matrix analysis using GROMACS v2021. Furthermore, survival analysis was carried out for the diosgenin-regulated proteins that were anticipated to be involved in breast cancer. For gene expression analyses, the top three targets with the highest binding affinity for diosgenin and tumor expression were examined. Furthermore, the effect of diosgenin on cell proliferation, cytotoxicity, and the partial Warburg effect was tested to validate the computational findings using functional outputs of the lead targets. Results: The protein-protein interaction had 57 edges, an average node degree of 5.43, and a p-value of 3.83e-14. Furthermore, enrichment analysis showed 36 KEGG pathways, 12 cellular components, 27 molecular functions, and 307 biological processes. In network analysis, three hub proteins were notably modulated: IGF1R, MDM2, and SRC, diosgenin with the highest binding affinity with IGF1R (binding energy -8.6 kcal/mol). Furthermore, during the 150 ns molecular dynamics (MD) projection run, diosgenin exhibited robust intermolecular interactions and had the least free binding energy with IGF1R (-35.143 kcal/mol) compared to MDM2 (-34.619 kcal/mol), and SRC (-17.944 kcal/mol). Diosgenin exhibited the highest cytotoxicity against MCF7 cell lines (IC50 12.05 ± 1.33) µg/ml. Furthermore, in H2O2-induced oxidative stress, the inhibitory constant (IC50 7.68 ± 0.51) µg/ml of diosgenin was lowest in MCF7 cell lines. However, the reversal of the Warburg effect by diosgenin seemed to be maximum in non-cancer Vero cell lines (EC50 15.27 ± 0.95) µg/ml compared to the rest. Furthermore, diosgenin inhibited cell proliferation in SKBR3 cell lines more though. Conclusion: The current study demonstrated that diosgenin impacts a series of signaling pathways, involved in the advancement of breast cancer, including FoxO, PI3K-Akt, p53, Ras, and MAPK signaling. Additionally, diosgenin established a persistent diosgenin-protein complex and had a significant binding affinity towards IGF1R, MDM2, and SRC. It is possible that this slowed down cell growth, countered the Warburg phenomenon, and showed the cytotoxicity towards breast cancer cells.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India,*Correspondence: Pukar Khanal, ; Darasaguppe R. Harish,
| | - Vishal S. Patil
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | | | - Priyanka P. Patil
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | - B. M. Patil
- PRES’s Pravara Rural College of Pharmacy Pravaranagar, Loni, Maharashtra, India
| | - Prarambh S. R. Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India,Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, India
| | - Darasaguppe R. Harish
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India,*Correspondence: Pukar Khanal, ; Darasaguppe R. Harish,
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
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5
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Turvey SJ, McPhillie MJ, Kearney MT, Muench SP, Simmons KJ, Fishwick CWG. Recent developments in the structural characterisation of the IR and IGF1R: implications for the design of IR-IGF1R hybrid receptor modulators. RSC Med Chem 2022; 13:360-374. [PMID: 35647546 PMCID: PMC9020618 DOI: 10.1039/d1md00300c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/12/2022] [Indexed: 12/16/2022] Open
Abstract
The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are dimeric disulfide-linked receptor tyrosine kinases, whose actions regulate metabolic and mitogenic signalling pathways inside the cell. It is well documented that in tissues co-expressing the IR and IGF1R, their respective monomers can heterodimerise to form IR-IGF1R hybrid receptors. Increased populations of the IR-IGF1R hybrid receptors are associated with several disease states, including type 2 diabetes and cancer. Recently, progress in the structural biology of IR and IGF1R has given insights into their structure-function relationships and mechanism of action. However, challenges in isolating IR-IGF1R hybrid receptors mean that their structural properties remain relatively unexplored. This review discusses the advances in the structural understanding of the IR and IGF1R, and how these discoveries can inform the design of small-molecule modulators of the IR-IGF1R hybrid receptors to understand their role in cell biology.
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Affiliation(s)
- Samuel J Turvey
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
| | | | - Mark T Kearney
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre, University of Leeds UK
| | - Katie J Simmons
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
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Bano N, Hossain MM, Bhat AQ, Ayaz MO, Kumari M, Sandhu P, Akhter Y, Dar MJ. Analyzing structural differences between insulin receptor (IR) and IGF1R for designing small molecule allosteric inhibitors of IGF1R as novel anti-cancer agents. Growth Horm IGF Res 2020; 55:101343. [PMID: 32877816 DOI: 10.1016/j.ghir.2020.101343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
IR and insulin-like growth factor-1 receptor (IGF-1R) share high degree of sequence and structural similarity that hinders the development of anticancer drugs targeting IGF1R, which is dysregulated in many cancers. Although IR and IGF1R mediate their activities through similar signalling pathways, yet they show different physiological effects. The exact molecular mechanism(s) how IR and IGF1R exert their distinct functions remain largely unknown. Here, we performed in silico analysis and generated GFP-fusion proteins of wild type IR and its K1079R mutant to analyze their subcellular localization, cytoplasmic and nuclear activities in comparison to IGF1R and its K1055R mutant. We showed that, like K1055R mutation in IGF1R, K1079R mutation does not impede the subcellular localization and nuclear activities of IR. Although K1079R mutation significantly decreases the kinase activity of IR but not as much as K1055R mutation, which was seen to drastically reduce the kinase activity of IGF1R. Moreover, K1079 residue in IR is seen to be sitting in a pocket which is different than the allosteric inhibitor binding pocket present in its homologue (IGF1R). This is for the first time such a study has been conducted to identify structural differences between these receptors that could be exploited for designing small molecule allosteric inhibitor(s) of IGF1R as novel anti-cancer drugs.
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Affiliation(s)
- Nasima Bano
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Md Mehedi Hossain
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Aadil Qadir Bhat
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Mir Owais Ayaz
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Monika Kumari
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Himachal Pradesh 176206, India
| | - Padmani Sandhu
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India
| | - Mohd Jamal Dar
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India.
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7
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Delle Bovi RJ, Miller WT. Expression and purification of functional insulin and insulin-like growth factor 1 holoreceptors from mammalian cells. Anal Biochem 2017; 536:69-77. [PMID: 28830678 PMCID: PMC5701837 DOI: 10.1016/j.ab.2017.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/25/2022]
Abstract
The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are receptor tyrosine kinases (RTKs) involved in the regulation of many important cellular processes. The current proposed models of activation are derived from structural studies using soluble extracellular domains and cytoplasmic tyrosine kinase domains. Preparations of full length IR and IGF1R have been hampered by the need for unconventional affinity chromatography resins and/or harsh eluting conditions. Here, we present a purification protocol to obtain full-length, detergent solubilized IR and IGF1R at quantities suitable for biochemical and structural characterization. We screened a panel of 24 structurally diverse detergents for optimal ligand activation. The receptors purified in n-dodecyl-β-D-maltoside showed ligand-stimulated autophosphorylation and kinase activity, suggesting an intact transmembrane signaling mechanism. This convenient purification protocol can be used to produce high quantities of IR, IGF1R, or other RTKs, and can be adapted for other challenging membrane proteins.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/isolation & purification
- Antigens, CD/metabolism
- Chromatography, Affinity
- HEK293 Cells
- Humans
- Receptor, IGF Type 1
- Receptor, Insulin/genetics
- Receptor, Insulin/isolation & purification
- Receptor, Insulin/metabolism
- Receptors, Somatomedin/genetics
- Receptors, Somatomedin/isolation & purification
- Receptors, Somatomedin/metabolism
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Affiliation(s)
- Richard J Delle Bovi
- Department of Physiology and Biophysics, Stony Brook University, NY, United States.
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, NY, United States; Department of Veterans Affairs Medical Center, Northport, NY, United States.
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8
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He H, Weir RL, Toutounchian JJ, Pagadala J, Steinle JJ, Baudry J, Miller DD, Yates CR. The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism. PLoS One 2017; 12:e0180808. [PMID: 28796787 PMCID: PMC5552119 DOI: 10.1371/journal.pone.0180808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/21/2017] [Indexed: 12/03/2022] Open
Abstract
Retinal microaneurysms, an early disease manifestation of diabetic retinopathy, are associated with retinal endothelial cell (REC) death and macular edema. We previously demonstrated that a quinic acid (QA) analog, KZ-41, promoted REC survival by blunting stress-induced p38 MAPK activation. Herein, we sought to expand our understanding of the pro-survival signal transduction pathways actuated by KZ-41. Using human RECs exposed to high glucose (25 mM, 72 hours), we demonstrated that KZ-41 blocks caspase-3 activation by triggering phosphorylation of the PI3K regulatory subunit (p85; Tyr458) and its downstream target Akt (Ser473). Akt signal transduction was accompanied by autophosphorylation of the receptor tyrosine kinase, insulin growth factor-1 receptor (IGF-1R). IGF-1R knockdown using either the tyrosine kinase inhibitor AG1024 or silencing RNA abolished KZ-41’s pro-survival effect. Under high glucose stress, caspase-3 activation correlated with elevated ERK1/2 phosphorylation and decreased insulin receptor substrate-1 (IRS-1) levels. KZ-41 decreased ERK1/2 phosphorylation and reversed the glucose-dependent reduction in IRS-1. To gain insight into the mechanistic basis for IGF-1R activation by KZ-41, we used molecular modeling and docking simulations to explore a possible protein:ligand interaction between the IGF-1R kinase domain and KZ-41. Computational investigations suggest two possible KZ-41 binding sites within the kinase domain: a region with high homology to the insulin receptor contains one potential allosteric binding site, and another potential site on the other side of the kinase domain, near the hinge domain. These data, together with previous proof-of-concept efficacy studies demonstrating KZ-41 mitigates pathologic retinal neovascularization in the murine oxygen-induced retinopathy model, suggests that QA derivatives may offer therapeutic benefit in ischemic retinopathies.
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Affiliation(s)
- Hui He
- Department of Pharmaceutical Sciences, UTHSC College of Pharmacy, Memphis, Tennessee, United States of America
| | - Rebecca L. Weir
- Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jordan J. Toutounchian
- Department of Pharmaceutical Sciences, UTHSC College of Pharmacy, Memphis, Tennessee, United States of America
| | - Jayaprakash Pagadala
- Department of Pharmaceutical Sciences, UTHSC College of Pharmacy, Memphis, Tennessee, United States of America
| | - Jena J. Steinle
- Department of Anatomy, Wayne State University, Detroit, Michigan, United States of America
| | - Jerome Baudry
- Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Duane D. Miller
- Department of Pharmaceutical Sciences, UTHSC College of Pharmacy, Memphis, Tennessee, United States of America
| | - Charles R. Yates
- Department of Pharmaceutical Sciences, UTHSC College of Pharmacy, Memphis, Tennessee, United States of America
- Department of Ophthalmology, UTHSC College of Medicine, Memphis, Tennessee, United States of America
- * E-mail:
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9
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Mohammadiarani H, Vashisth H. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors. Front Endocrinol (Lausanne) 2016; 7:68. [PMID: 27379020 PMCID: PMC4913204 DOI: 10.3389/fendo.2016.00068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor.
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Affiliation(s)
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
- *Correspondence: Harish Vashisth,
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10
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Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Sci Signal 2015; 8:rs13. [PMID: 26628682 DOI: 10.1126/scisignal.aaa6711] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kimberly L Malecka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lauren Fink
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - E Joseph Jordan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Duffy
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Samuel Kolander
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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11
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Tatulian SA. Structural Dynamics of Insulin Receptor and Transmembrane Signaling. Biochemistry 2015; 54:5523-32. [PMID: 26322622 DOI: 10.1021/acs.biochem.5b00805] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The insulin receptor (IR) is a (αβ)2-type transmembrane tyrosine kinase that plays a central role in cell metabolism. Each αβ heterodimer consists of an extracellular ligand-binding α-subunit and a membrane-spanning β-subunit that comprises the cytoplasmic tyrosine kinase (TK) domain and the phosphorylation sites. The α- and β-subunits are linked via a single disulfide bridge, and the (αβ)2 tetramer is formed by disulfide bonds between the α-chains. Insulin binding induces conformational changes in IR that reach the intracellular β-subunit followed by a protein phosphorylation and activation cascade. Defects in this signaling process, including IR dysfunction caused by mutations, result in type 2 diabetes. Rational drug design aimed at treatment of diabetes relies on knowledge of the detailed structure of IR and the dynamic structural transformations during transmembrane signaling. Recent X-ray crystallographic studies have provided important clues about the mode of binding of insulin to IR, the resulting structural changes and their transmission to the TK domain, but a complete understanding of the structural basis underlying insulin signaling has not been achieved. This review presents a critical analysis of the current status of the structure-function relationship of IR, with a comparative assessment of the other IR family receptors, and discusses potential advancements that may provide insight into the molecular mechanism of insulin signaling.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida , 4111 Libra Drive, Orlando, Florida 32816, United States
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12
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Maruyama IN. Activation of transmembrane cell-surface receptors via a common mechanism? The "rotation model". Bioessays 2015; 37:959-67. [PMID: 26241732 PMCID: PMC5054922 DOI: 10.1002/bies.201500041] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has long been thought that transmembrane cell-surface receptors, such as receptor tyrosine kinases and cytokine receptors, among others, are activated by ligand binding through ligand-induced dimerization of the receptors. However, there is growing evidence that prior to ligand binding, various transmembrane receptors have a preformed, yet inactive, dimeric structure on the cell surface. Various studies also demonstrate that during transmembrane signaling, ligand binding to the extracellular domain of receptor dimers induces a rotation of transmembrane domains, followed by rearrangement and/or activation of intracellular domains. The paper here describes transmembrane cell-surface receptors that are known or proposed to exist in dimeric form prior to ligand binding, and discusses how these preformed dimers are activated by ligand binding.
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Affiliation(s)
- Ichiro N Maruyama
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Cabail MZ, Li S, Lemmon E, Bowen ME, Hubbard SR, Miller WT. The insulin and IGF1 receptor kinase domains are functional dimers in the activated state. Nat Commun 2015; 6:6406. [PMID: 25758790 DOI: 10.1038/ncomms7406] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
The insulin receptor (IR) and insulin-like growth factor-1 receptor (IGF1R) are highly related receptor tyrosine kinases with a disulfide-linked homodimeric architecture. Ligand binding to the receptor ectodomain triggers tyrosine autophosphorylation of the cytoplasmic domains, which stimulates catalytic activity and creates recruitment sites for downstream signalling proteins. Whether the two phosphorylated tyrosine kinase domains within the receptor dimer function independently or cooperatively to phosphorylate protein substrates is not known. Here we provide crystallographic, biophysical and biochemical evidence demonstrating that the phosphorylated kinase domains of IR and IGF1R form a specific dimeric arrangement involving an exchange of the juxtamembrane region proximal to the kinase domain. In this dimer, the active position of α-helix C in the kinase N lobe is stabilized, which promotes downstream substrate phosphorylation. These studies afford a novel strategy for the design of small-molecule IR agonists as potential therapeutic agents for type 2 diabetes.
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Affiliation(s)
- M Zulema Cabail
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shiqing Li
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Eric Lemmon
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
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Vashisth H. Theoretical and computational studies of peptides and receptors of the insulin family. MEMBRANES 2015; 5:48-83. [PMID: 25680077 PMCID: PMC4384091 DOI: 10.3390/membranes5010048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Synergistic interactions among peptides and receptors of the insulin family are required for glucose homeostasis, normal cellular growth and development, proliferation, differentiation and other metabolic processes. The peptides of the insulin family are disulfide-linked single or dual-chain proteins, while receptors are ligand-activated transmembrane glycoproteins of the receptor tyrosine kinase (RTK) superfamily. Binding of ligands to the extracellular domains of receptors is known to initiate signaling via activation of intracellular kinase domains. While the structure of insulin has been known since 1969, recent decades have seen remarkable progress on the structural biology of apo and liganded receptor fragments. Here, we review how this useful structural information (on ligands and receptors) has enabled large-scale atomically-resolved simulations to elucidate the conformational dynamics of these biomolecules. Particularly, applications of molecular dynamics (MD) and Monte Carlo (MC) simulation methods are discussed in various contexts, including studies of isolated ligands, apo-receptors, ligand/receptor complexes and intracellular kinase domains. The review concludes with a brief overview and future outlook for modeling and computational studies in this family of proteins.
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Affiliation(s)
- Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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Kavran JM, McCabe JM, Byrne PO, Connacher MK, Wang Z, Ramek A, Sarabipour S, Shan Y, Shaw DE, Hristova K, Cole PA, Leahy DJ. How IGF-1 activates its receptor. eLife 2014; 3:03772. [PMID: 25255214 PMCID: PMC4381924 DOI: 10.7554/elife.03772] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/23/2014] [Indexed: 12/20/2022] Open
Abstract
The type I insulin-like growth factor receptor (IGF1R) is involved in growth and survival of normal and neoplastic cells. A ligand-dependent conformational change is thought to regulate IGF1R activity, but the nature of this change is unclear. We point out an underappreciated dimer in the crystal structure of the related Insulin Receptor (IR) with Insulin bound that allows direct comparison with unliganded IR and suggests a mechanism by which ligand regulates IR/IGF1R activity. We test this mechanism in a series of biochemical and biophysical assays and find the IGF1R ectodomain maintains an autoinhibited state in which the TMs are held apart. Ligand binding releases this constraint, allowing TM association and unleashing an intrinsic propensity of the intracellular regions to autophosphorylate. Enzymatic studies of full-length and kinase-containing fragments show phosphorylated IGF1R is fully active independent of ligand and the extracellular-TM regions. The key step triggered by ligand binding is thus autophosphorylation.
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Affiliation(s)
- Jennifer M Kavran
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jacqueline M McCabe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Patrick O Byrne
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Mary Katherine Connacher
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Zhihong Wang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, United States
| | | | - Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
| | | | - David E Shaw
- DE Shaw Research, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Daniel J Leahy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
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16
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Maruyama IN. Mechanisms of activation of receptor tyrosine kinases: monomers or dimers. Cells 2014; 3:304-30. [PMID: 24758840 PMCID: PMC4092861 DOI: 10.3390/cells3020304] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) play essential roles in cellular processes, including metabolism, cell-cycle control, survival, proliferation, motility and differentiation. RTKs are all synthesized as single-pass transmembrane proteins and bind polypeptide ligands, mainly growth factors. It has long been thought that all RTKs, except for the insulin receptor (IR) family, are activated by ligand-induced dimerization of the receptors. An increasing number of diverse studies, however, indicate that RTKs, previously thought to exist as monomers, are present as pre-formed, yet inactive, dimers prior to ligand binding. The non-covalently associated dimeric structures are reminiscent of those of the IR family, which has a disulfide-linked dimeric structure. Furthermore, recent progress in structural studies has provided insight into the underpinnings of conformational changes during the activation of RTKs. In this review, I discuss two mutually exclusive models for the mechanisms of activation of the epidermal growth factor receptor, the neurotrophin receptor and IR families, based on these new insights.
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Affiliation(s)
- Ichiro N Maruyama
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495, Japan.
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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: 105] [Impact Index Per Article: 8.8] [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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18
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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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Epstein LF, Chen H, Emkey R, Whittington DA. The R1275Q neuroblastoma mutant and certain ATP-competitive inhibitors stabilize alternative activation loop conformations of anaplastic lymphoma kinase. J Biol Chem 2012; 287:37447-57. [PMID: 22932897 DOI: 10.1074/jbc.m112.391425] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that, when genetically altered by mutation, amplification, chromosomal translocation or inversion, has been shown to play an oncogenic role in certain cancers. Small molecule inhibitors targeting the kinase activity of ALK have proven to be effective therapies in certain ALK-driven malignancies and one such inhibitor, crizotinib, is now approved for the treatment of EML4-ALK-driven, non-small cell lung cancer. In neuroblastoma, activating point mutations in the ALK kinase domain can drive disease progression, with the two most common mutations being F1174L and R1275Q. We report here crystal structures of the ALK kinase domain containing the F1174L and R1275Q mutations. Also included are crystal structures of ALK in complex with novel small molecule ALK inhibitors, including a classic type II inhibitor, that stabilize previously unobserved conformations of the ALK activation loop. Collectively, these structures illustrate a different series of activation loop conformations than has been observed in previous ALK crystal structures and provide insight into the activating nature of the R1275Q mutation. The novel active site topologies presented here may also aid the structure-based drug design of a new generation of ALK inhibitors.
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Affiliation(s)
- Linda F Epstein
- Department of Molecular Structure and Characterization, Amgen Inc., Cambridge, Massachusetts 02142, USA
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20
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Effects of somatic mutations in the C-terminus of insulin-like growth factor 1 receptor on activity and signaling. JOURNAL OF SIGNAL TRANSDUCTION 2012; 2012:804801. [PMID: 22778948 PMCID: PMC3384887 DOI: 10.1155/2012/804801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/28/2012] [Indexed: 02/03/2023]
Abstract
The insulin-like growth factor I receptor (IGF1R) is overexpressed in several forms of human cancer, and it has emerged as an important target for anticancer drug design. Cancer genome sequencing efforts have recently identified three somatic mutations in IGF1R: A1374V, a deletion of S1278 in the C-terminal tail region of the receptor, and M1255I in the C-terminal lobe of the kinase catalytic domain. The possible effects of these mutations on IGF1R activity and biological function have not previously been tested. Here, we tested the effects of the mutations on the in vitro biochemical activity of IGF1R and on major IGF1R signaling pathways in mammalian cells. While the mutations do not affect the intrinsic tyrosine kinase activity of the receptor, we demonstrate that the basal (unstimulated) levels of MAP kinase and Akt activation are increased in the mutants (relative to wild-type IGF1R). We hypothesize that the enhanced signaling potential of these mutants is due to changes in protein-protein interactions between the IGF1R C-terminus and cellular substrates or modulators.
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21
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Kelly GM, Buckley DA, Kiely PA, Adams DR, O'Connor R. Serine phosphorylation of the insulin-like growth factor I (IGF-1) receptor C-terminal tail restrains kinase activity and cell growth. J Biol Chem 2012; 287:28180-94. [PMID: 22685298 DOI: 10.1074/jbc.m112.385757] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Insulin-like growth factor I receptor (IGF-1R) signaling is essential for cell, organ, and animal growth. The C-terminal tail of the IGF-1R exhibits regulatory function, but the mechanism is unknown. Here, we show that mutation of Ser-1248 (S1248A) enhances IGF-1R in vitro kinase activity, autophosphorylation, Akt/mammalian target of rapamycin activity, and cell growth. Ser-1248 phosphorylation is mediated by GSK-3β in a mechanism that involves a priming phosphorylation on Ser-1252. GSK-3β knock-out cells exhibit reduced IGF-1R cell surface expression, enhanced IGF-1R kinase activity, and signaling. Examination of crystallographic structures of the IGF-1R kinase domain revealed that the (1248)SFYYS(1252) motif adopts a conformation tightly packed against the kinase C-lobe when Ser-1248 is in the unphosphorylated state that favors kinase activity. S1248A mutation is predicted to lock the motif in this position. In contrast, phosphorylation of Ser-1248 will drive profound structural transition of the sequence, critically affecting connection of the C terminus as well as exposing potential protein docking sites. Decreased kinase activity of a phosphomimetic S1248E mutant and enhanced kinase activity in mutants of its predicted target residue Lys-1081 support this auto-inhibitory model. Thus, the SFYYS motif controls the organization of the IGF-1R C terminus relative to the kinase domain. Its phosphorylation by GSK-3β restrains kinase activity and regulates receptor trafficking and signaling.
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Affiliation(s)
- Geraldine M Kelly
- Cell Biology Laboratory, Department of Biochemistry, BioSciences Institute, University College Cork, Cork, Ireland
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22
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Article withdrawal: Disruption of the protein interaction between FAK and IGF-1R inhibits melanoma tumor growth. Carcinogenesis 2012; 33:473. [DOI: 10.1093/carcin/bgr115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Iacaruso MF, Galli S, Martí M, Villalta JI, Estrin DA, Jares-Erijman EA, Pietrasanta LI. Structural Model for p75NTR–TrkA Intracellular Domain Interaction: A Combined FRET and Bioinformatics Study. J Mol Biol 2011; 414:681-98. [DOI: 10.1016/j.jmb.2011.09.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/09/2011] [Accepted: 09/14/2011] [Indexed: 11/16/2022]
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24
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Azarova AM, Gautam G, George RE. Emerging importance of ALK in neuroblastoma. Semin Cancer Biol 2011; 21:267-75. [PMID: 21945349 DOI: 10.1016/j.semcancer.2011.09.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/08/2011] [Indexed: 02/04/2023]
Abstract
Since the original descriptions of gain-of function mutations in anaplastic lymphoma kinase (ALK), interest in the role of this receptor tyrosine kinase in neuroblastoma development and as a potential therapeutic target has escalated. As a group, the activating point mutations in full-length ALK, found in approximately 8% of all neuroblastoma tumors, are distributed evenly across different clinical stages. However, the most frequent somatic mutation, F1174L, is associated with amplification of the MYCN oncogene. This combination of features appears to confer a worse prognosis than MYCN amplification alone, suggesting a cooperative effect on neuroblastoma formation by these two proteins. Indeed, F1174L has shown more potent transforming activity in vivo than the second most common activating mutation, R1275Q, and is responsible for innate and acquired resistance to crizotinib, a clinically relevant ALK inhibitor that will soon be commercially available. These advances cast ALK as a bona fide oncoprotein in neuroblastoma and emphasize the need to understand ALK-mediated signaling in this tumor. This review addresses many of the current issues surrounding the role of ALK in normal development and neuroblastoma pathogenesis, and discusses the prospects for clinically effective targeted treatments based on ALK inhibition.
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Affiliation(s)
- Anna M Azarova
- Department of Pediatric Hematology and Oncology, Dana Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School, 450 Brookline Ave, Boston, MA 02115, USA
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Annenkov A, Rigby A, Amor S, Zhou D, Yousaf N, Hemmer B, Chernajovsky Y. A chimeric receptor of the insulin-like growth factor receptor type 1 (IGFR1) and a single chain antibody specific to myelin oligodendrocyte glycoprotein activates the IGF1R signalling cascade in CG4 oligodendrocyte progenitors. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1813:1428-37. [PMID: 21600935 DOI: 10.1016/j.bbamcr.2011.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 11/24/2022]
Abstract
In order to generate neural stem cells with increased ability to survive after transplantation in brain parenchyma we developed a chimeric receptor (ChR) that binds to myelin oligodendrocyte glycoprotein (MOG) via its ectodomain and activates the insulin-like growth factor receptor type 1 (IGF1R) signalling cascade. Activation of this pro-survival pathway in response to ligand broadly available in the brain might increase neuroregenerative potential of transplanted precursors. The ChR was produced by fusing a MOG-specific single chain antibody with the extracellular boundary of the IGF1R transmembrane segment. The ChR is expressed on the cellular surface, predominantly as a monomer, and is not N-glycosylated. To show MOG-dependent functionality of the ChR, neuroblastoma cells B104 expressing this ChR were stimulated with monolayers of cells expressing recombinant MOG. The ChR undergoes MOG-dependent tyrosine phosphorylation and homodimerisation. It promotes insulin and IGF-independent growth of the oligodendrocyte progenitor cell line CG4. The proposed mode of the ChR activation is by MOG-induced dimerisation which promotes kinase domain transphosphorylation, by-passing the requirement of conformation changes known to be important for IGF1R activation. Another ChR, which contains a segment of the β-chain ectodomain, was produced in an attempt to recapitulate some of these conformational changes, but proved non-functional.
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Affiliation(s)
- Alexander Annenkov
- Bone and Joint Research Unit, William Harvey Research Institute, Bart's and the London School of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
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Bossi RT, Saccardo MB, Ardini E, Menichincheri M, Rusconi L, Magnaghi P, Orsini P, Avanzi N, Borgia AL, Nesi M, Bandiera T, Fogliatto G, Bertrand JA. Crystal structures of anaplastic lymphoma kinase in complex with ATP competitive inhibitors. Biochemistry 2010; 49:6813-25. [PMID: 20695522 DOI: 10.1021/bi1005514] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase involved in the development of several human cancers and, as a result, is a recognized target for the development of small-molecule inhibitors for the treatment of ALK-positive malignancies. Here, we present the crystal structures of the unphosphorylated human ALK kinase domain in complex with the ATP competitive ligands PHA-E429 and NVP-TAE684. Analysis of these structures provides valuable information concerning the specific characteristics of the ALK active site as well as giving indications about how to obtain selective ALK inhibitors. In addition, the ALK-KD-PHA-E429 structure led to the identification of a potential regulatory mechanism involving a link made between a short helical segment immediately following the DFG motif and an N-terminal two-stranded beta-sheet. Finally, mapping of the activating mutations associated with neuroblastoma onto our structures may explain the roles these residues have in the activation process.
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Affiliation(s)
- Roberto T Bossi
- Nerviano Medical Sciences S.r.l., Viale Pasteur 10, 20014 Nerviano (MI), Italy
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Heinrich T, Grädler U, Böttcher H, Blaukat A, Shutes A. Allosteric IGF-1R Inhibitors. ACS Med Chem Lett 2010; 1:199-203. [PMID: 24900194 DOI: 10.1021/ml100044h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 05/10/2010] [Indexed: 11/29/2022] Open
Abstract
Targeting allosteric protein sites is a promising approach to interfere selectively with cellular signaling cascades. We have discovered a novel class of allosteric insulin-like growth factor-I receptor (IGF-1R) inhibitors. 3-Cyano-1H-indole-7-carboxylic acid {1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}amide (10) was found with nanomolar biochemical, micromolar, cellular IGF-1R activity and no relevant interference with cellular insulin receptor signaling up to 30 μM. The allosteric binding site was characterized by X-ray crystallographic studies, and the structural information was used to explain the unique mode of action of this new class of inhibitors.
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Affiliation(s)
- Timo Heinrich
- Merck Serono, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Ulrich Grädler
- Merck Serono, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Andree Blaukat
- Merck Serono, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Adam Shutes
- EMD Serono Research Institute, One Technology Place, Rockland, Massachusetts 02370
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28
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Nemecek C, Metz WA, Wentzler S, Ding FX, Venot C, Souaille C, Dagallier A, Maignan S, Guilloteau JP, Bernard F, Henry A, Grapinet S, Lesuisse D. Design of Potent IGF1-R Inhibitors Related to Bis-azaindoles. Chem Biol Drug Des 2010; 76:100-6. [DOI: 10.1111/j.1747-0285.2010.00991.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Zheng D, Kurenova E, Ucar D, Golubovskaya V, Magis A, Ostrov D, Cance WG, Hochwald SN. Targeting of the protein interaction site between FAK and IGF-1R. Biochem Biophys Res Commun 2009; 388:301-5. [PMID: 19664602 PMCID: PMC2742998 DOI: 10.1016/j.bbrc.2009.07.156] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
Abstract
The interaction of focal adhesion kinase (FAK) and insulin-like growth factor-1 receptor (IGF-1R) plays an important role in cancer cell survival. Targeting this interaction with small molecule drugs could be a novel strategy in cancer therapy. By a series of pull-down assays using GST-tagged FAK fragments and His-tagged IGF-1R intracellular fragments, we showed that the FAK-NT2 (a.a. 127-243) domain directly interacts with the N-terminal part of the IGF-1R intracellular domain. Overexpressed FAK-NT2 domain was also shown to co-localize with IGF-1R in pancreatic cells. Computational modeling was used to predict the binding configuration of these two domains and to screen for small molecules binding to the interaction site. This strategy successfully identified a lead compound that disrupts FAK/IGF-1R interaction.
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Affiliation(s)
- Donghang Zheng
- Department of Surgery, University of Florida, Gainesville, FL
- UF Shands Cancer Center, University of Florida, Gainesville, FL
| | - Elena Kurenova
- Department of Surgery, Roswell Park Cancer Institute, Buffalo, NY
| | - Deniz Ucar
- Department of Surgery, University of Florida, Gainesville, FL
| | | | - Andrew Magis
- UF Shands Cancer Center, University of Florida, Gainesville, FL
| | - David Ostrov
- UF Shands Cancer Center, University of Florida, Gainesville, FL
- Pathology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - William G. Cance
- Department of Surgery, Roswell Park Cancer Institute, Buffalo, NY
| | - Steven N. Hochwald
- Department of Surgery, University of Florida, Gainesville, FL
- Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- UF Shands Cancer Center, University of Florida, Gainesville, FL
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30
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Wood ER, Shewchuk L, Hassel A, Nichols J, Truesdale AT, Smith D, Carter HL, Weaver K, Barrett G, Leesnitzer T, Alvarez E, Bardera AI, Alamillo A, Cantizani J, Martin J, Smith GK, Jensen DE, Xie H, Mook R, Kumar R, Kuntz K. Discovery of an inhibitor of insulin-like growth factor 1 receptor activation: implications for cellular potency and selectivity over insulin receptor. Biochem Pharmacol 2009; 78:1438-47. [PMID: 19665448 DOI: 10.1016/j.bcp.2009.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/23/2009] [Accepted: 07/29/2009] [Indexed: 01/10/2023]
Abstract
Insulin-like growth factor 1 receptor (IGF-1R) is an attractive target for anti-cancer therapy due to its anti-apoptotic effect on tumor cells, but inhibition of insulin receptor (IR) may have undesired metabolic consequences. The primary sequences of the ATP substrate-binding sites of these receptors are identical and the crystal structures of the activated kinase domains are correspondingly similar. Thus, most small-molecule inhibitors described to date are equally potent against the activated kinase domains of IGF-1R and IR. In contrast, the non-phosphorylated kinase domains of these receptors have several structural features that may accommodate differences in binding affinity for kinase inhibitors. We used a cell-based assay measuring IGF-1R autophosphorylation as an inhibitor screen, and identified a potent purine derivative that is selective compared to IR. Surprisingly, the compound is a weak inhibitor of the activated IGF-1R tyrosine kinase domain. Biochemical and structural studies are presented that indicate the compound preferentially binds to the ATP site of non-phosphorylated IGF-1R compared to phosphorylated IGF-1R. The potential selectivity and potency advantages of this binding mode are discussed.
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Affiliation(s)
- Edgar R Wood
- Department of Biological Reagents and Assay Development, Research Triangle Park, GlaxoSmithKline, Inc., NC 27709, United States.
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31
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Discovery of 4,6-bis-anilino-1H-pyrrolo[2,3-d]pyrimidines: potent inhibitors of the IGF-1R receptor tyrosine kinase. Bioorg Med Chem Lett 2008; 19:469-73. [PMID: 19056263 DOI: 10.1016/j.bmcl.2008.11.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 11/08/2008] [Accepted: 11/12/2008] [Indexed: 11/23/2022]
Abstract
The evaluation of a series of 4,6-bis-anilino-1H-pyrrolo[2,3-d]pyrimidines as inhibitors of the IGF-1R (IGF-IR) receptor tyrosine kinase is reported. Examples demonstrate nanomolar potencies in in vitro enzyme and mechanistic cellular assays as well as promising in vivo pharmacokinetics in rat.
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32
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Wu J, Li W, Craddock BP, Foreman KW, Mulvihill MJ, Ji QS, Miller WT, Hubbard SR. Small-molecule inhibition and activation-loop trans-phosphorylation of the IGF1 receptor. EMBO J 2008; 27:1985-94. [PMID: 18566589 PMCID: PMC2486273 DOI: 10.1038/emboj.2008.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 05/20/2008] [Indexed: 11/09/2022] Open
Abstract
The insulin-like growth factor-1 receptor (IGF1R) is a receptor tyrosine kinase (RTK) that has a critical role in mitogenic signalling during embryogenesis and an antiapoptotic role in the survival and progression of many human tumours. Here, we present the crystal structure of the tyrosine kinase domain of IGF1R (IGF1RK), in its unphosphorylated state, in complex with a novel compound, cis-3-[3-(4-methyl-piperazin-l-yl)-cyclobutyl]-1-(2-phenyl-quinolin-7-yl)-imidazo[1,5-a]pyrazin-8-ylamine (PQIP), which we show is a potent inhibitor of both the unphosphorylated (basal) and phosphorylated (activated) states of the kinase. PQIP interacts with residues in the ATP-binding pocket and in the activation loop, which confers specificity for IGF1RK and the highly related insulin receptor (IR) kinase. In this crystal structure, the IGF1RK active site is occupied by Tyr1135 from the activation loop of an symmetry (two-fold)-related molecule. This dimeric arrangement affords, for the first time, a visualization of the initial trans-phosphorylation event in the activation loop of an RTK, and provides a molecular rationale for a naturally occurring mutation in the activation loop of the IR that causes type II diabetes mellitus.
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Affiliation(s)
- Jinhua Wu
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, and Department of Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Wanqing Li
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | | | - Qun-sheng Ji
- (OSI) Oncology, OSI Pharmaceuticals Inc., Farmingdale, NY, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stevan R Hubbard
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, and Department of Pharmacology, New York University School of Medicine, New York, NY, USA
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Hubbard RD, Wilsbacher JL. Advances towards the development of ATP-competitive small-molecule inhibitors of the insulin-like growth factor receptor (IGF-IR). ChemMedChem 2008; 2:41-6. [PMID: 17089440 DOI: 10.1002/cmdc.200600174] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Robert D Hubbard
- Cancer Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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34
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Craddock BP, Cotter C, Miller WT. Autoinhibition of the insulin-like growth factor I receptor by the juxtamembrane region. FEBS Lett 2007; 581:3235-40. [PMID: 17586502 PMCID: PMC1986766 DOI: 10.1016/j.febslet.2007.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/23/2007] [Accepted: 06/07/2007] [Indexed: 11/20/2022]
Abstract
The juxtamembrane (JM) regions of several receptor tyrosine kinases are involved in autoinhibitory interactions that maintain the low basal activity of the receptors; mutations can give rise to constitutive kinase activity and signaling. In this report, we show that the JM region of the human insulin-like growth factor I receptor (IGF1R) plays a role in kinase regulation. We mutated JM residues that were conserved in this subfamily of receptor tyrosine kinases, and expressed and purified the cytoplasmic domains using the Sf9/baculovirus system. We show that a kinase-proximal mutation (Y957F) and (to a lesser extent) a mutation in the central part of the JM region (N947A) increase the autophosphorylation activity of the kinase. Steady-state kinetic measurements show the mutations cause an increase in V(max) for phosphorylation of peptide substrates. When the holoreceptors were expressed in fibroblasts derived from IGF1R-deficient mice, the Y957F mutation led to a large increase in basal and in IGF1-stimulated receptor autophosphorylation. Together, these data demonstrate that the JM region of IGF1R plays an important role in limiting the basal activity of the receptor.
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Affiliation(s)
- Barbara P. Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794
| | - Christopher Cotter
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794
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35
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Structural basis for a high affinity inhibitor bound to protein kinase MK2. J Mol Biol 2007; 369:735-45. [PMID: 17449059 DOI: 10.1016/j.jmb.2007.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/05/2007] [Accepted: 03/06/2007] [Indexed: 11/21/2022]
Abstract
The Ser/Thr protein kinase MAPKAP kinase 2 (MK2) plays a crucial role in inflammation. We determined the structure of the kinase domain of MK2 in complex with a low molecular mass inhibitor in two different crystal forms, obtained from soaking and co-crystallization. To our knowledge, these are the first structures of MK2 showing the binding mode of an inhibitor with high binding affinity (IC50 8.5 nM). The two crystal forms revealed conformational flexibility in the binding site and extend the experimental basis for rational drug design. Crystal form-1 contained one MK2 molecule per asymmetric unit. Form-2 contained 12 molecules, which arrange into two different types of MK2 trimers. One of them may serve as a model for an intermediate state during substrate phosphorylation, as each MK2 monomer places its activation segment into the substrate peptide binding groove of the trimer neighbor.
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36
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Jin HX, Wu TX, Jiang YJ, Zou JW, Zhuang SL, Mao X, Yu QS. Role of phosphorylated Thr-197 in the catalytic subunit of cAMP-dependent protein kinase. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Schalk-Hihi C, Ma HC, Struble GT, Bayoumy S, Williams R, Devine E, Petrounia IP, Mezzasalma T, Zeng L, Schubert C, Grasberger B, Springer BA, Deckman IC. Protein Engineering of the Colony-stimulating Factor-1 Receptor Kinase Domain for Structural Studies. J Biol Chem 2007; 282:4085-93. [PMID: 17132625 DOI: 10.1074/jbc.m608182200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A parallel approach to designing crystallization constructs for the c-FMS kinase domain was implemented, resulting in proteins suitable for structural studies. Sequence alignment and limited proteolysis were used to identify and eliminate unstructured and surface-exposed domains. A small library of chimeras was prepared in which the kinase insert domain of FMS was replaced with the kinase insert domain of previously crystallized receptor-tyrosine kinases. Characterization of the newly generated FMS constructs by enzymology and thermoshift assays demonstrated similar activities and compound binding to the FMS full-length cytoplasmic domain. Two chimeras were evaluated for crystallization in the presence and absence of a variety of ligands resulting in crystal structures, and leading to a successful structure-based drug design project for this important inflammation target.
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Affiliation(s)
- Céline Schalk-Hihi
- Structural Biology, Johnson & Johnson Pharmaceuticals Research and Development, LLC, Exton, Pennsylvania 19341, USA.
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38
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Kornienko M, Montalvo A, Carpenter BE, Lenard M, Abeywickrema P, Hall DL, Darke PL, Kuo LC. Protein expression plasmids produced rapidly: streamlining cloning protocols and robotic handling. Assay Drug Dev Technol 2006; 3:661-74. [PMID: 16438661 DOI: 10.1089/adt.2005.3.661] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As many processes in the preclinical drug discovery process become highly parallel, the need to also produce a large number of different proteins in parallel has become acute, such as for protein crystallization and activity screening. In turn, the requisite DNA constructions to produce these proteins must now be done at a rate that requires automated cloning procedures, each with an intrinsic low failure probability per sample. The high-throughput cloning solutions presented here achieve production of 192 different expression plasmids at a success rate of greater than 95% of the targeted open reading frames. Time for completion of the set by one person is reduced to approximately 11 working days, starting with polymerase chain reactions for a number of source clones and ending with purified expression plasmids. Achievement of this throughput utilizes the following: (1) the Beckman Coulter (Fullerton, CA) Biomek FX liquid handler for most manipulations, (2) Gateway cloning technology (Invitrogen Corp., Carlsbad, CA), and (3) computer programs designed for parallel processing of all sample information, including primer design and the resulting DNA and protein sequence assembly. Exemplary data are presented for discovery of a form of the Rho-kinase that crystallizes (ROCK2).
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Affiliation(s)
- Maria Kornienko
- Department of Structural Biology, Merck Research Laboratories, West Point, PA 19486, USA.
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39
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Kwon MJ, Nam TJ. Porphyran induces apoptosis related signal pathway in AGS gastric cancer cell lines. Life Sci 2006; 79:1956-62. [PMID: 16876203 DOI: 10.1016/j.lfs.2006.06.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 10/24/2022]
Abstract
Porphyrans, the sulfated polysaccharides, are the main components of Porphyra. The potential apoptotic activities of porphyran were evaluated using AGS human gastric cancer cells. Porphyran did not affect the growth of normal cells, but did induce cancer cell death in a dose-dependent manner. The addition of 0.1% porphyran also reduced DNA synthesis after 24 h of exposure, suggesting that porphyran inhibits cancer cell growth by both decreasing cell proliferation and inducing apoptosis. AGS cells treated with porphyran displayed a marked increase in poly(ADP-ribose) polymerase (PARP) cleavage, as well as caspase-3 activation. The ability of porphyran to promote apoptosis may contribute to its usefulness as an agent capable of significantly inhibiting cell growth in AGS human gastric cancer cells. Insulin-like growth factor-I receptor (IGF-IR) phosphorylation was decreased in porphyran-treated AGS cells compared to control cells, which correlated with Akt activation. Thus, porphyran appears to negatively regulate IGF-IR phosphorylation by causing a decrease in the expression levels in AGS gastric cancer cells, and then inducing caspase-3 activation.
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Affiliation(s)
- Mi-Jin Kwon
- Faculty of Food Science and Biotechnology, Pukyong National University, Busan 608-737, Republic of Korea
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40
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Li W, Miller WT. Role of the activation loop tyrosines in regulation of the insulin-like growth factor I receptor-tyrosine kinase. J Biol Chem 2006; 281:23785-91. [PMID: 16793764 DOI: 10.1074/jbc.m605269200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tyrosine kinase activity of insulin-like growth factor I receptor (IGF1R) is under tight control. Ligand binding to the extracellular portion of IGF1R stimulates autophosphorylation at three sites (Tyr1131, Tyr1135, and Tyr1136) in the activation loop within the tyrosine kinase catalytic domain. Autophosphorylation at all three sites is required for maximum enzyme activity, and for IGF1-stimulated cellular activity of the receptor. Previous studies have not clarified the contributions of the individual tyrosines to enzymatic activation. Here, we produced single Tyr-to-Phe mutations at these positions, and compared activities of the purified kinase domains (unphosphorylated and phosphorylated) with wild-type IGF1R. Rates of autophosphorylation of the three mutants were more rapid than for wild-type IGF1R; this was most apparent for the Y1135F mutant. Substrate phosphorylation studies on the unphosphorylated forms of IGF1R confirmed that the value of Vmax for Y1135F was elevated relative to wild-type IGF1R, consistent with a disruption of an autoinhibitory interaction. In contrast, activity measurements on the fully phosphorylated enzymes indicated that kcat/Km values were lowered relative to wild-type IGF1R; this effect was most dramatic for Y1136F. We confirmed these findings using limited proteolysis and tryptophan fluorescence experiments. The results demonstrate that Tyr1135 plays a particularly important role in stabilizing the autoinhibited conformation of the activation loop, while Tyr1136 plays the key role in stabilizing the open, activated conformation of IGF1R.
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Affiliation(s)
- Wanqing Li
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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41
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Blanquart C, Boute N, Lacasa D, Issad T. Monitoring the activation state of the insulin-like growth factor-1 receptor and its interaction with protein tyrosine phosphatase 1B using bioluminescence resonance energy transfer. Mol Pharmacol 2005; 68:885-94. [PMID: 15976035 DOI: 10.1124/mol.105.013151] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have developed two bioluminescence resonance energy transfer (BRET)-based approaches to monitor 1) ligand-induced conformational changes within partially purified insulin-like growth factor-1 (IGF-1) receptors (IGF1R) and 2) IGF1R interaction with a substrate-trapping mutant of protein tyrosine phosphatase 1B (PTP1B-D181A) in living cells. In the first assay, human IGF1R fused to Renilla reniformis luciferase (Rluc) or yellow fluorescent protein (YFP) were cotransfected in human embryonic kidney (HEK)-293 cells. The chimeric receptors were then partially purified by wheat germ lectin chromatography, and BRET measurements were performed in vitro. In the second assay, BRET measurements were performed on living HEK-293 cells cotransfected with IGF1R-Rluc and YFP-PTP1B-D181A. Ligand-induced conformational changes within the IGF1R and interaction of the IGF1R with PTP1B could be detected as an energy transfer between Rluc and YFP. Dose-response experiments with IGF-1, IGF-2, and insulin demonstrated that the effects of these ligands on BRET correlate well with their known pharmacological properties toward the IGF1R. Inhibition of IGF1R autophosphorylation by the tyrphostin AG1024 (3-bromo-5-t-butyl-4-hydroxy-benzylidenemalonitrile) resulted in the inhibition of IGF1-induced BRET signal between the IGF1R and PTP1B. In addition, an anti-IGF1R antibody known to inhibit the biological effects of IGF-1 inhibited ligand-induced BRET signal within the IGF1R, as well as between IGF1R and PTP1B. This inhibition of BRET signal paralleled the inhibition of the ligand-induced autophosphorylation of the IGF1R by this antibody. In conclusion, these BRET-based assays permit 1) the rapid evaluation of the effects of agonists or inhibitory molecules on IGF1R activation and 2) the analysis of the regulation of IGF1R-PTP1B interaction in living cells.
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Affiliation(s)
- Christophe Blanquart
- Department of Cell Biology, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
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42
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Hofmann F, García-Echeverría C. Blocking the insulin-like growth factor-I receptor as a strategy for targeting cancer. Drug Discov Today 2005; 10:1041-7. [PMID: 16055020 DOI: 10.1016/s1359-6446(05)03512-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clear links between cancer and cellular signaling triggered by the insulin-like growth factor-I (IGF-I) receptor (IGF-IR) and its cognate ligands (IGF-I and IGF-II) have been reported throughout the past two decades. Experimental results suggest that the pharmaceutical targeting of this signaling pathway could be beneficial for the treatment of cancer. Here, more recent advances towards potentially clinically viable strategies to interfere with the function of IGF-IR will be discussed.
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Affiliation(s)
- Francesco Hofmann
- Oncology Research, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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43
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Abstract
This review examines the rationale for targeting the insulin-like growth factor (IGF)-I receptor in the therapy of human tumours and their metastases. The rationale is based on two crucial findings: 1) in experimental animals, normal cells are only partially affected by the deletion of the IGF-I receptor, whereas tumour cells undergo apoptosis when the IGF-I receptor is downregulated; and 2) cells with a deleted IGF-I receptor are refractory to transformation by viral and cellular oncogenes. This review focuses on the mechanisms underlying the experimental findings, and discusses the possibility of extrapolating the results obtained in animals to the cure of human tumours.
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Affiliation(s)
- Renato Baserga
- Thomas Jefferson University, Kimmel Cancer Center, 233 S. 10th Street, 624 BLSB, Philadelphia, PA 19107, USA.
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44
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Klammt J, Garten A, Barnikol-Oettler A, Beck-Sickinger AG, Kiess W. Comparative analysis of the signaling capabilities of the insulin receptor-related receptor. Biochem Biophys Res Commun 2005; 327:557-64. [DOI: 10.1016/j.bbrc.2004.12.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2004] [Indexed: 10/26/2022]
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45
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Rubin R, Harrison R, Chen XF, Corzitotto J, Hoek JB, Hallak H. Inhibition of insulin-like growth factor I receptor tyrosine kinase by ethanol. Biochem Pharmacol 2004; 68:2009-17. [PMID: 15476672 DOI: 10.1016/j.bcp.2004.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 06/28/2004] [Indexed: 11/17/2022]
Abstract
Ethanol inhibits insulin and insulin-like growth factor-I (IGF-I) signaling in a variety of cell types leading to reduced mitogenesis and impaired survival. This effect is associated with inhibition of insulin receptor (IR) and insulin-like growth factor-I receptor (IGF-IR) autophosphorylation, which implicates these receptors as direct targets for ethanol. It was demonstrated previously that ethanol inhibits the autophosphorylation and kinase activity of the purified cytoplasmic tyrosine kinase domain of the IR. We performed computer modeling of the ethanol interaction with the IR and IGF-IR kinases (IRK and IGF-IRK). The analysis predicted binding of alcohols within the hydrophobic pocket of the kinase activation cleft, with stabilization at specific polar residues. Using IGF-IRK purified from baculovirus-infected insect cells, ethanol inhibited peptide substrate phosphorylation by non-phosphorylated IGF-IRK, but had no effect on the autophosphorylated enzyme. In common with the IRK, ethanol inhibited IGF-IRK autophosphorylation. In cerebellar granule neurons, ethanol inhibited autophosphorylation of the apo-IGF-IR, but did not reverse IGF-IR phosphorylation after IGF-I stimulation. In summary, the findings demonstrate direct inhibition of IGF-IR tyrosine kinase by ethanol. The data are consistent with a model wherein ethanol prevents the initial phase of IRK and IGF-IRK activation, by inhibiting the engagement of the kinase activation loop.
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Affiliation(s)
- Raphael Rubin
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, 226 Alumni Hall, Philadelphia, PA 19107, USA.
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46
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Abstract
The cytoplasmic serine/threonine kinase BRAF and receptor tyrosine kinases of the platelet-derived growth factor receptor (PDGFR) family are frequently activated in cancer by mutations of an equivalent amino acid. Structural studies have provided important insights into why these very different kinases share similar oncogenic hot spots and why the PDGFR juxtamembrane region is also a frequent oncogenic target. This research has implications for other kinases that are mutated in human tumours and for the treatment of cancer using kinase inhibitors.
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Affiliation(s)
- Nick J Dibb
- Institute of Reproductive and Developmental Biology, Imperial College, Hammersmith Campus, London W12 ONN, UK.
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47
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Li W, Favelyukis S, Yang J, Zeng Y, Yu J, Gangjee A, Miller WT. Inhibition of insulin-like growth factor I receptor autophosphorylation by novel 6-5 ring-fused compounds. Biochem Pharmacol 2004; 68:145-54. [PMID: 15183126 DOI: 10.1016/j.bcp.2004.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 03/19/2004] [Indexed: 10/26/2022]
Abstract
The insulin-like growth factor 1 receptor (IGF1R) plays an important role in cell transformation, and it has emerged as a target for anti-cancer drug design. IGF1R is activated by autophosphorylation at three sites in the enzyme activation loop. We describe here a group of 6-5 ring-fused compounds that are the first reported inhibitors selective for the unphosphorylated (0P) form of IGF1R. These compounds do not significantly inhibit the fully activated, triply phosphorylated (3P) form. IGF1R was produced from baculovirus-infected Spodoptera frugiperda (Sf9) cells, and the 0P and 3P forms were purified to homogeneity. We used a continuous spectrophotometric assay to measure inhibition of the 0P and 3P forms. Analysis by native gel electrophoresis confirmed that the step inhibited in the autoactivation process was the transition between the 0P and IP forms of IGF1R. The compounds were also active against IGF1R autophosphorylation in intact Chinese hamster ovary (CHO) cells. Most of the compounds also inhibited the closely related insulin receptor to varying degrees, although some compounds showed selectivity for IGF1R or insulin receptor. This class of compounds could form the basis of design efforts to selectively block the autoinhibited conformation of IGF1R.
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Affiliation(s)
- Wanqing Li
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Basic Science Tower T-6, Stony Brook, NY 11794-8661, USA
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48
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Griffith J, Black J, Faerman C, Swenson L, Wynn M, Lu F, Lippke J, Saxena K. The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. Mol Cell 2004; 13:169-78. [PMID: 14759363 DOI: 10.1016/s1097-2765(03)00505-7] [Citation(s) in RCA: 368] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Revised: 11/20/2003] [Accepted: 11/24/2003] [Indexed: 10/26/2022]
Abstract
FLT3 is a type III receptor tyrosine kinase that is thought to play a key role in hematopoiesis. Certain classes of FLT3 mutations cause constitutively activated forms of the receptor that are found in significant numbers of patients with acute myelogenous leukemia (AML). The mutations occur either in the activation loop, for example, as point mutations of Asp835 or as internal tandem duplication (ITD) sequences in the juxtamembrane (JM) domain. To further understand the nature of FLT3 autoinhibition and regulation, we have determined the crystal structure of the autoinhibited form of FLT3. This structure shows the autoinhibitory conformation of a complete JM domain in this class of receptor tyrosine kinases. The detailed inhibitory mechanism of the JM domain is revealed, which is likely utilized by other members of type III receptor tyrosine kinases.
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Affiliation(s)
- James Griffith
- Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA.
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Li S, Covino ND, Stein EG, Till JH, Hubbard SR. Structural and biochemical evidence for an autoinhibitory role for tyrosine 984 in the juxtamembrane region of the insulin receptor. J Biol Chem 2003; 278:26007-14. [PMID: 12707268 DOI: 10.1074/jbc.m302425200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tyrosine 984 in the juxtamembrane region of the insulin receptor, between the transmembrane helix and the cytoplasmic tyrosine kinase domain, is conserved among all insulin receptor-like proteins from hydra to humans. Crystallographic studies of the tyrosine kinase domain and proximal juxtamembrane region reveal that Tyr-984 interacts with several other conserved residues in the N-terminal lobe of the kinase domain, stabilizing a catalytically nonproductive position of alpha-helix C. Steady-state kinetics measurements on the soluble kinase domain demonstrate that replacement of Tyr-984 with phenylalanine results in a 4-fold increase in kcat in the unphosphorylated (basal state) enzyme. Moreover, mutation of Tyr-984 in the full-length insulin receptor results in significantly elevated receptor phosphorylation levels in cells, both in the absence of insulin and following insulin stimulation. These data demonstrate that Tyr-984 plays an important structural role in maintaining the quiescent, basal state of the insulin receptor. In addition, the structural studies suggest a possible target site for small molecule activators of the insulin receptor, with potential use in the treatment of noninsulin-dependent diabetes mellitus.
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Affiliation(s)
- Shiqing Li
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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Abstract
The insulin-like growth factor (IGF) family of ligands, binding proteins and receptors is an important growth factor system involved in both the development of the organism and the maintenance of normal function of many cells of the body. The system also has powerful anti-apoptotic effects. More recently, evidence has accrued to demonstrate that the IGFs play an important role in cancer. Individuals with serum IGF-II levels in the upper quartile of the normal range (and IGF binding protein-3 levels in the lower quartiles) have a relative risk for developing breast, prostate, colon and lung cancer. IGF-II is commonly expressed by tumor cells and may act as an autocrine growth factor; occasionally even reaching target tissues and causing tumor-induced hypoglycemia. The IGF-I receptor is commonly (though not always) overexpressed in many cancers, and many recent studies have identified new signaling pathways emanating from the IGF-I receptor that affect cancer cell proliferation, adhesion, migration and cell death; functions that are critical for cancer cell survival and metastases. In this review, many aspects of the IGF system and its relationship to cancer will be discussed.
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Affiliation(s)
- Derek LeRoith
- Diabetes Branch, Room 8D12, Building 10, National Institutes of Health MSC 1758, Bethesda, MD 20892-1758, USA.
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