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Shankar S, Chew TW, Chichili VPR, Low BC, Sivaraman J. Structural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP. Cell Mol Life Sci 2024; 81:216. [PMID: 38740643 PMCID: PMC11090974 DOI: 10.1007/s00018-024-05238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
p50RhoGAP is a key protein that interacts with and downregulates the small GTPase RhoA. p50RhoGAP is a multifunctional protein containing the BNIP-2 and Cdc42GAP Homology (BCH) domain that facilitates protein-protein interactions and lipid binding and the GAP domain that regulates active RhoA population. We recently solved the structure of the BCH domain from yeast p50RhoGAP (YBCH) and showed that it maintains the adjacent GAP domain in an auto-inhibited state through the β5 strand. Our previous WT YBCH structure shows that a unique kink at position 116 thought to be made by a proline residue between alpha helices α6 and α7 is essential for the formation of intertwined dimer from asymmetric monomers. Here we sought to establish the role and impact of this Pro116. However, the kink persists in the structure of P116A mutant YBCH domain, suggesting that the scaffold is not dictated by the proline residue at this position. We further identified Tyr124 (or Tyr188 in HBCH) as a conserved residue in the crucial β5 strand. Extending to the human ortholog, when substituted to acidic residues, Tyr188D or Tyr188E, we observed an increase in RhoA binding and self-dimerization, indicative of a loss of inhibition of the GAP domain by the BCH domain. These results point to distinct roles and impact of the non-conserved and conserved amino acid positions in regulating the structural and functional complexity of the BCH domain.
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Affiliation(s)
- Srihari Shankar
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Ti Weng Chew
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | | | - Boon Chuan Low
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- NUS College, National University of Singapore, Singapore, 138593, Singapore.
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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2
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Gizzio J, Thakur A, Haldane A, Post CB, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584161. [PMID: 38559238 PMCID: PMC10979876 DOI: 10.1101/2024.03.08.584161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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3
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Kohlmayr JM, Grabner GF, Nusser A, Höll A, Manojlović V, Halwachs B, Masser S, Jany-Luig E, Engelke H, Zimmermann R, Stelzl U. Mutational scanning pinpoints distinct binding sites of key ATGL regulators in lipolysis. Nat Commun 2024; 15:2516. [PMID: 38514628 PMCID: PMC10958042 DOI: 10.1038/s41467-024-46937-x] [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: 05/26/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
ATGL is a key enzyme in intracellular lipolysis and plays an important role in metabolic and cardiovascular diseases. ATGL is tightly regulated by a known set of protein-protein interaction partners with activating or inhibiting functions in the control of lipolysis. Here, we use deep mutational protein interaction perturbation scanning and generate comprehensive profiles of single amino acid variants that affect the interactions of ATGL with its regulatory partners: CGI-58, G0S2, PLIN1, PLIN5 and CIDEC. Twenty-three ATGL amino acid variants yield a specific interaction perturbation pattern when validated in co-immunoprecipitation experiments in mammalian cells. We identify and characterize eleven highly selective ATGL switch mutations which affect the interaction of one of the five partners without affecting the others. Switch mutations thus provide distinct interaction determinants for ATGL's key regulatory proteins at an amino acid resolution. When we test triglyceride hydrolase activity in vitro and lipolysis in cells, the activity patterns of the ATGL switch variants trace to their protein interaction profile. In the context of structural data, the integration of variant binding and activity profiles provides insights into the regulation of lipolysis and the impact of mutations in human disease.
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Affiliation(s)
- Johanna M Kohlmayr
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Gernot F Grabner
- Institute of Molecular Biosciences, Biochemistry, University of Graz, Graz, Austria
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Anna Nusser
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Anna Höll
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Verina Manojlović
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Bettina Halwachs
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Sarah Masser
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Evelyne Jany-Luig
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Hanna Engelke
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Robert Zimmermann
- Institute of Molecular Biosciences, Biochemistry, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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4
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Chakraborty MP, Das D, Mondal P, Kaul P, Bhattacharyya S, Kumar Das P, Das R. Molecular basis of VEGFR1 autoinhibition at the plasma membrane. Nat Commun 2024; 15:1346. [PMID: 38355851 PMCID: PMC10866885 DOI: 10.1038/s41467-024-45499-2] [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: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Ligand-independent activation of VEGFRs is a hallmark of diabetes and several cancers. Like EGFR, VEGFR2 is activated spontaneously at high receptor concentrations. VEGFR1, on the other hand, remains constitutively inactive in the unligated state, making it an exception among VEGFRs. Ligand stimulation transiently phosphorylates VEGFR1 and induces weak kinase activation in endothelial cells. Recent studies, however, suggest that VEGFR1 signaling is indispensable in regulating various physiological or pathological events. The reason why VEGFR1 is regulated differently from other VEGFRs remains unknown. Here, we elucidate a mechanism of juxtamembrane inhibition that shifts the equilibrium of VEGFR1 towards the inactive state, rendering it an inefficient kinase. The juxtamembrane inhibition of VEGFR1 suppresses its basal phosphorylation even at high receptor concentrations and transiently stabilizes tyrosine phosphorylation after ligand stimulation. We conclude that a subtle imbalance in phosphatase activation or removing juxtamembrane inhibition is sufficient to induce ligand-independent activation of VEGFR1 and sustain tyrosine phosphorylation.
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Affiliation(s)
- Manas Pratim Chakraborty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Diptatanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Purav Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Pragya Kaul
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Soumi Bhattacharyya
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Prosad Kumar Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India.
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5
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Fadaly WAA, Nemr MTM, Zidan TH, Mohamed FEA, Abdelhakeem MM, Abu Jayab NN, Omar HA, Abdellatif KRA. New 1,2,3-triazole/1,2,4-triazole hybrids linked to oxime moiety as nitric oxide donor selective COX-2, aromatase, B-RAF V600E and EGFR inhibitors celecoxib analogs: design, synthesis, anti-inflammatory/anti-proliferative activities, apoptosis and molecular modeling study. J Enzyme Inhib Med Chem 2023; 38:2290461. [PMID: 38061801 PMCID: PMC11003496 DOI: 10.1080/14756366.2023.2290461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
A new series of bis-triazole 19a-l was synthesised for the purpose of being hybrid molecules with both anti-inflammatory and anti-cancer activities and assessed for cell cycle arrest, NO release. Compounds 19c, 19f, 19h, 19 l exhibited COX-2 selectivity indexes in the range of 18.48 to 49.38 compared to celecoxib S.I. = 21.10), inhibit MCF-7 with IC50 = 9-16 μM compared to tamoxifen (IC50 = 27.9 μM). and showed good inhibitory activity against HEP-3B with IC50 = 4.5-14 μM compared to sorafenib (IC50 = 3.5 μM) (HEP-3B). Moreover, derivatives 19e, 19j, 19k, 19 l inhibit HCT-116 with IC50 = 5.3-13.7 μM compared to 5-FU with IC50 = 4.8 μM (HCT-116). Compounds 19c, 19f, 19h, 19 l showed excellent inhibitory activity against A549 with IC50 = 3-4.5 μM compared to 5-FU with IC50 = 6 μM (A549). Compounds 19c, 19f, 19h, 19 l inhibit aromatase (IC50 of 22.40, 23.20, 22.70, 30.30 μM), EGFR (IC50 of 0.112, 0.205, 0.169 and 0.066 μM) and B-RAFV600E (IC50 of 0.09, 0.06, 0.07 and 0.05 μM).
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Affiliation(s)
- Wael A A Fadaly
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed T M Nemr
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Taha H Zidan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Fatma E A Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Marwa M Abdelhakeem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Nour N Abu Jayab
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Pharmacology Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Khaled R A Abdellatif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
- Pharmaceutical Sciences Department, Ibn Sina National College for Medical Studies, Jeddah, Saudi Arabia
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6
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Fadaly WAA, Zidan TH, Kahk NM, Mohamed FEA, Abdelhakeem MM, Khalil RG, Nemr MTM. New pyrazolyl-thiazolidinone/thiazole derivatives as celecoxib/dasatinib analogues with selective COX-2, HER-2 and EGFR inhibitory effects: design, synthesis, anti-inflammatory/anti-proliferative activities, apoptosis, molecular modelling and ADME studies. J Enzyme Inhib Med Chem 2023; 38:2281262. [PMID: 38010912 PMCID: PMC11003491 DOI: 10.1080/14756366.2023.2281262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/05/2023] [Indexed: 11/29/2023] Open
Abstract
Two new series of pyrazolyl-thiazolidinone/thiazole derivatives 16a-b and 18a-j were synthesised, merging the scaffolds of celecoxib and dasatinib. Compounds 16a, 16b and 18f inhibit COX-2 with S.I. 134.6, 26.08 and 42.13 respectively (celecoxib S.I. = 24.09). Compounds 16a, 16b, 18c, 18d and 18f inhibit MCF-7 with IC50 = 0.73-6.25 μM (dasatinib IC50 = 7.99 μM) and (doxorubicin IC50 = 3.1 μM) and inhibit A549 with IC50 = 1.64-14.3 μM (dasatinib IC50 = 11.8 μM and doxorubicin IC50 = 2.42 μM) with S.I. (F180/MCF7) of 33.15, 7.13, 18.72, 13.25 and 8.28 respectively higher than dasatinib (4.03) and doxorubicin (3.02) and S.I. (F180/A549) of 14.75, 12.96, 4.16, 7.07 and 18.88 respectively higher than that of dasatinib (S.I. = 2.72) and doxorubicin (S.I = 3.88). Derivatives 16a, 18c, 18d, 18f inhibit EGFR and HER-2 IC50 for EGFR of 0.043, 0.226, 0.388, 0.19 μM respectively and for HER-2 of 0.032, 0.144, 0.195, 0.201 μM respectively.
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Affiliation(s)
- Wael A. A. Fadaly
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Taha H. Zidan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Nesma M. Kahk
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Fatma E. A. Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Marwa M. Abdelhakeem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Rehab G. Khalil
- Immunology Division, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed T. M. Nemr
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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7
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He M, Cao C, Ni Z, Liu Y, Song P, Hao S, He Y, Sun X, Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct Target Ther 2022; 7:181. [PMID: 35680848 PMCID: PMC9178337 DOI: 10.1038/s41392-022-00999-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) technology is a new protein-degradation strategy that has emerged in recent years. It uses bifunctional small molecules to induce the ubiquitination and degradation of target proteins through the ubiquitin–proteasome system. PROTACs can not only be used as potential clinical treatments for diseases such as cancer, immune disorders, viral infections, and neurodegenerative diseases, but also provide unique chemical knockdown tools for biological research in a catalytic, reversible, and rapid manner. In 2019, our group published a review article “PROTACs: great opportunities for academia and industry” in the journal, summarizing the representative compounds of PROTACs reported before the end of 2019. In the past 2 years, the entire field of protein degradation has experienced rapid development, including not only a large increase in the number of research papers on protein-degradation technology but also a rapid increase in the number of small-molecule degraders that have entered the clinical and will enter the clinical stage. In addition to PROTAC and molecular glue technology, other new degradation technologies are also developing rapidly. In this article, we mainly summarize and review the representative PROTACs of related targets published in 2020–2021 to present to researchers the exciting developments in the field of protein degradation. The problems that need to be solved in this field will also be briefly introduced.
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Affiliation(s)
- Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.,Tsinghua-Peking Center for Life Sciences, 100084, Beijing, P. R. China
| | - Zhihao Ni
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongbo Liu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Peilu Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Shuang Hao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China. .,School of Pharmaceutical Sciences, Zhengzhou University, 450001, Zhengzhou, China.
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8
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Carlin CR. Role of EGF Receptor Regulatory Networks in the Host Response to Viral Infections. Front Cell Infect Microbiol 2022; 11:820355. [PMID: 35083168 PMCID: PMC8785968 DOI: 10.3389/fcimb.2021.820355] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
In this review article, we will first provide a brief overview of EGF receptor (EGFR) structure and function, and its importance as a therapeutic target in epithelial carcinomas. We will then compare what is currently known about canonical EGFR trafficking pathways that are triggered by ligand binding, versus ligand-independent pathways activated by a variety of intrinsic and environmentally induced cellular stresses. Next, we will review the literature regarding the role of EGFR as a host factor with critical roles facilitating viral cell entry and replication. Here we will focus on pathogens exploiting virus-encoded and endogenous EGFR ligands, as well as EGFR-mediated trafficking and signaling pathways that have been co-opted by wild-type viruses and recombinant gene therapy vectors. We will also provide an overview of a recently discovered pathway regulating non-canonical EGFR trafficking and signaling that may be a common feature of viruses like human adenoviruses which signal through p38-mitogen activated protein kinase. We will conclude by discussing the emerging role of EGFR signaling in innate immunity to viral infections, and how viral evasion mechanisms are contributing to our understanding of fundamental EGFR biology.
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Affiliation(s)
- Cathleen R. Carlin
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States,Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, United States,*Correspondence: Cathleen R. Carlin,
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9
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Class I PI3K Biology. Curr Top Microbiol Immunol 2022; 436:3-49. [DOI: 10.1007/978-3-031-06566-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Rajpurohit YS, Sharma DK, Misra HS. Involvement of Serine / Threonine protein kinases in DNA damage response and cell division in bacteria. Res Microbiol 2021; 173:103883. [PMID: 34624492 DOI: 10.1016/j.resmic.2021.103883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022]
Abstract
The roles of Serine/Threonine protein kinases (STPKs) in bacterial physiology, including bacterial responses to nutritional stresses and under pathogenesis have been well documented. STPKs roles in bacterial cell cycle regulation and DNA damage response have not been much emphasized, possibly because the LexA/RecA type SOS response became the synonym to DNA damage response and cell cycle regulation in bacteria. This review summarizes current knowledge of STPKs genetics, domain organization, and their roles in DNA damage response and cell division regulation in bacteria.
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Affiliation(s)
- Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
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11
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Identification of a cross-talk between EGFR and Wnt/beta-catenin signaling pathways in HepG2 liver cancer cells. Cell Signal 2020; 79:109885. [PMID: 33340661 DOI: 10.1016/j.cellsig.2020.109885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
Abstract
EGFRis a transmembrane receptor tyrosine kinase involved in regulating cell proliferation, differentiation and survival. EGFR is actively pursued as a therapeutic target because its aberrant expression or activity has been reported in several cancers. Several studies have reported the nuclear localization of the EGFR in various cell types, however, its exact nuclear functions are not clear yet. In this study, we have generated GFP fusion constructs of EGFR and its mutants to analyze their subcellular localizationin normal and cancer cells and impact of its sub-cellular location on its various activities using immunoblotting, confocal microscopy, reporter assays, loss-of-function EGFR mutants, and EGFR specific small molecule inhibitors. We show that EGFR is involved in modulating TCF dependent β-catenin transcriptional activity in HepG2 cells in a similar fashion as IGF1R tyrosine kinase. Moreover, we show that cytoplasmic and nuclear functions are two independent activities of EGFR.
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12
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Keretsu S, Ghosh S, Cho SJ. Molecular Modeling Study of c-KIT/PDGFRα Dual Inhibitors for the Treatment of Gastrointestinal Stromal Tumors. Int J Mol Sci 2020; 21:ijms21218232. [PMID: 33153146 PMCID: PMC7662224 DOI: 10.3390/ijms21218232] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common Mesenchymal Neoplasm of the gastrointestinal tract. The tumorigenesis of GISTs has been associated with the gain-of-function mutation and abnormal activation of the stem cell factor receptor (c-KIT) and platelet-derived growth factor receptor alpha (PDGFRα) kinases. Hence, inhibitors that target c-KIT and PDGFRα could be a therapeutic option for the treatment of GISTs. The available approved c-KIT/PDGFRα inhibitors possessed low efficacy with off-target effects, which necessitated the development of potent inhibitors. We performed computational studies of 48 pyrazolopyridine derivatives that showed inhibitory activity against c-KIT and PDGFRα to study the structural properties important for inhibition of both the kinases. The derivative of phenylurea, which has high activities for both c-KIT (pIC50 = 8.6) and PDGFRα (pIC50 = 8.1), was used as the representative compound for the dataset. Molecular docking and molecular dynamics simulation (100 ns) of compound 14 was performed. Compound 14 showed the formation of hydrogen bonding with Cys673, Glu640, and Asp810 in c-KIT, and Cys677, Glu644, and Asp836 in PDGFRα. The results also suggested that Thr670/T674 substitution in c-KIT/PDGFRα induced conformational changes at the binding site of the receptors. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed based on the inhibitors. Contour map analysis showed that electropositive and bulky substituents at the para-position and the meta-position of the benzyl ring of compound 14 was favorable and may increase the inhibitory activity against both c-KIT and PDGFRα. Analysis of the results suggested that having bulky and hydrophobic substituents that extend into the hydrophobic pocket of the binding site increases the activity for both c-KIT and PDGFRα. Based on the contour map analysis, 50 compounds were designed, and the activities were predicted. An evaluation of binding free energy showed that eight of the designed compounds have potential binding affinity with c-KIT/PDGFRα. Absorption, distribution, metabolism, excretion and toxicity (ADMET) and synthetic feasibility tests showed that the designed compounds have reasonable pharmaceutical properties and synthetic feasibility. Further experimental study of the designed compounds is recommended. The structural information from this study could provide useful insight into the future development of c-KIT and PDGFRα inhibitors.
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Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea; (S.K.); (S.G.)
| | - Suparna Ghosh
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea; (S.K.); (S.G.)
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea; (S.K.); (S.G.)
- Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju 501-759, Korea
- Correspondence: ; Tel.: +82-62-230-7482 or +82-11-479-1010
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Li L, Liu D, Liu A, Li J, Wang H, Zhou J. Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification. Evol Bioinform Online 2020; 16:1176934320922519. [PMID: 32546936 PMCID: PMC7249569 DOI: 10.1177/1176934320922519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/05/2022] Open
Abstract
Tyrosine kinases (TKs) play key roles in the regulation of multicellularity in
organisms and involved primarily in cell growth, differentiation, and
cell-to-cell communication. Genome-wide characterization of TKs has been
conducted in many metazoans; however, systematic information regarding this
superfamily in Electrophorus electricus (electric eel) is still
lacking. In this study, we identified 114 TK genes in the E
electricus genome and investigated their evolution, molecular
features, and domain architecture using phylogenetic profiling to gain a better
understanding of their similarities and specificity. Our results suggested that
the electric eel TK (EeTK) repertoire was shaped by whole-genome duplications
(WGDs) and tandem duplication events. Compared with other vertebrate TKs, gene
members in Jak, Src, and EGFR subfamily duplicated specifically, but with
members lost in Eph, Axl, and Ack subfamily in electric eel. We also conducted
an exhaustive survey of TK genes in genomic databases, identifying 1674 TK
proteins in 31 representative species covering all the main metazoan lineages.
Extensive evolutionary analysis indicated that TK repertoire in vertebrates
tended to be remarkably conserved, but the gene members in each subfamily were
very variable. Comparative expression profile analysis showed that electric
organ tissues and muscle shared a similar pattern with specific highly expressed
TKs (ie, epha7, musk, jak1, and pdgfra), suggesting that regulation of TKs might
play an important role in specifying an electric organ identity from its muscle
precursor. We further identified TK genes exhibiting tissue-specific expression
patterns, indicating that members in TKs participated in subfunctionalization
representing an evolutionary divergence required for the performance of
different tissues. This work generates valuable information for further gene
function analysis and identifying candidate TK genes reflecting their unique
tissue-function specializations in electric eel.
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Affiliation(s)
- Ling Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Dangyun Liu
- Department of Central Laboratory, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, P.R. China
| | - Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, P.R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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14
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Das S, Bhattacharya B, Das B, Sinha B, Jamatia T, Paul K. Etiologic Role of Kinases in the Progression of Human Cancers and Its Targeting Strategies. Indian J Surg Oncol 2019; 12:34-45. [PMID: 33994726 DOI: 10.1007/s13193-019-00972-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/07/2019] [Indexed: 11/30/2022] Open
Abstract
Cancer is one of the dominant causes of death worldwide while lifelong prognosis is still inauspicious. The maturation of the cancer is seen as a process of transformation of a healthy cell into a tumor-sensitive cell, which is held entirely at the cellular, molecular, and genetic levels of the organism. Tyrosine kinases can play a major, etiologic role in the inception of malignancy and devote to the uncontrolled proliferation of cancerous cells and the progression of a tumor as well as the development of metastatic disease. Angiogenesis and oncogene activation are the major event in cell proliferation. The growth of a tumor and metastasis are fully depending on angiogenesis and lymphangiogenesis triggered by chemical signals from tumor cells in a phase of rapid growth. Tyrosine kinase inhibitors are compounds that inhibit tyrosine kinases and effective in targeting angiogenesis and blocking the signaling pathways of oncogenes. Small molecule tyrosine kinase inhibitors like afatinib, erlotinib, crizotinib, gefitinib, and cetuximab are shown to a selective cut off tactic toward the constitutive activation of an oncogene in tumor cells, and thus contemplated as promising therapeutic approaches for the diagnosis of cancer and malignancies.
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Affiliation(s)
- Sanjoy Das
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | - Bireswar Bhattacharya
- Regional Institute of Pharmaceutical Science and Technology, Agartala, Tripura 799005 India
| | - Biplajit Das
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | - Bibek Sinha
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | - Taison Jamatia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | - Kishan Paul
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
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15
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Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism. Biochem J 2018; 475:2209-2224. [DOI: 10.1042/bcj20180077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022]
Abstract
The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6 Å resolution as well as in complex with ATP to a 1.41 Å resolution and with an ATP analogue AMP-PCP to a 1.45 Å resolution. The residues in the activation loop of PpkA-294 were fully determined, and the N-terminus of the loop was folded into an unprecedented inhibitory helix, revealing that the PpkA kinase domain was in an auto-inhibitory state. The ternary MgATP–PpkA-294 complex was also inactive with nucleotide ribose and phosphates in unexpected and unproductive conformations. The αC-helix in the inactive PpkA-294 adopted a conformation towards the active site but with the conserved glutamate in the helix rotated away, which we suggest to be a general conformation for all STPK kinases in the inactive form. Structural comparison of PpkA with its eukaryotic homologues reinforced the universal regulation mechanism of protein kinases.
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16
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Yunn NO, Kim J, Kim Y, Leibiger I, Berggren PO, Ryu SH. Mechanistic understanding of insulin receptor modulation: Implications for the development of anti-diabetic drugs. Pharmacol Ther 2018; 185:86-98. [DOI: 10.1016/j.pharmthera.2017.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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El Sayed MT, Hussein HAR, Elebiary NM, Hassan GS, Elmessery SM, Elsheakh AR, Nayel M, Abdel-Aziz HA. Tyrosine kinase inhibition effects of novel Pyrazolo[1,5-a]pyrimidines and Pyrido[2,3-d]pyrimidines ligand: Synthesis, biological screening and molecular modeling studies. Bioorg Chem 2018; 78:312-323. [PMID: 29625271 DOI: 10.1016/j.bioorg.2018.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 01/04/2023]
Abstract
Tyrosine kinases are one of the most critical mediators in the signaling path way. Late studies have proved the part of tyrosine kinases in the pathophysiology of cancer diseases. This current research paper has focused on investigating the novel Pyrazolo[1,5-a]pyrimidines and Pyrido[2,3-d]pyrimidines as a small molecules that can inhibit tyrosine kinase in cancer cells. NCI protocol was applied to test the antitumor activity of such compounds. Leukemia and renal cancer cell lines proved to be sensitive to some derivatives such as 6b-d, 9a and 11 with GI% values ranging from 30.4 to 41.3%. In addition, compound 11 proved to be the most active against MCF-7 with GI% 62.5. The synthesized compounds were also evaluated for their inhibitory effects against EGFR kinase enzyme. Compound 9b proved to be the most active one among the synthesized series with inhibition % value of 81.72 at 25 nM concentration and IC50 8.4 nM which is very close to the reference drug Sorafenib. In vitro cytotoxicity test was also performed using the MCF-7 breast cell line. Computer modeling using the active site of tyrosine kinase as a template and the most active tyrosine kinase inhibitors were calculated. Docking studies of the synthesized compounds into the active site of EGFR kinase domain showed good agreement with the obtained biological results.
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Affiliation(s)
- Mardia T El Sayed
- Deparment of Applied Organic Chemistry, National Research Centre, 12622 Dokki, Egypt
| | - Hoda A R Hussein
- Department of Photochemistry, National Research Centre, 12622 Dokki, Egypt
| | - Nora M Elebiary
- Department of Green Chemistry, National Research Centre, 12622 Dokki, Egypt
| | - Ghada S Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt.
| | - Shahenda M Elmessery
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Ahmed R Elsheakh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Mohamed Nayel
- National Cancer Institute, Chemotherapeutic Agents Repository, Fisher BioServices, Germantown, MD 20874, USA
| | - Hatem A Abdel-Aziz
- Deparment of Applied Organic Chemistry, National Research Centre, 12622 Dokki, Egypt
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19
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Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE. Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src- related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS). Mol Cell Proteomics 2018; 17:925-947. [PMID: 29496907 DOI: 10.1074/mcp.ra118.000643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 01/23/2023] Open
Abstract
SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites), also known as PTK 70 (Protein tyrosine kinase 70), is a non-receptor tyrosine kinase that belongs to the BRK family of kinases (BFKs). To date less is known about the cellular role of SRMS primarily because of the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS. Our analyses led to the identification of 1258 tyrosine-phosphorylated peptides which mapped to 663 phosphoproteins, exclusively from SRMS-expressing cells. DOK1, a previously characterized SRMS substrate, was also identified in our analyses. Functional enrichment analyses revealed that the candidate SRMS substrates were enriched in various biological processes including protein ubiquitination, mitotic cell cycle, energy metabolism and RNA processing, as well as Wnt and TNF signaling. Analyses of the sequence surrounding the phospho-sites in these proteins revealed novel candidate SRMS consensus substrate motifs. We utilized customized high-throughput peptide arrays to validate a subset of the candidate SRMS substrates identified in our MS-based analyses. Finally, we independently validated Vimentin and Sam68, as bona fide SRMS substrates through in vitro and in vivo assays. Overall, our study identified a number of novel and biologically relevant SRMS candidate substrates, which suggests the involvement of the kinase in a vast array of unexplored cellular functions.
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Affiliation(s)
- Raghuveera Kumar Goel
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada
| | - Marta Paczkowska
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada
| | - Jüri Reimand
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada.,¶Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto M5G 1L7, Ontario, Canada
| | - Scott Napper
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada.,‖Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), 120 Veterinary Road, University of Saskatchewan, Saskatoon S7N 5E3, Saskatchewan, Canada
| | - Kiven Erique Lukong
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada;
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20
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Ma TKW, McAdoo SP, Tam FWK. Targeting the tyrosine kinase signalling pathways for treatment of immune-mediated glomerulonephritis: from bench to bedside and beyond. Nephrol Dial Transplant 2017; 32:i129-i138. [PMID: 28391340 PMCID: PMC5410974 DOI: 10.1093/ndt/gfw336] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/18/2016] [Indexed: 12/25/2022] Open
Abstract
Glomerulonephritis (GN) affects patients of all ages and is an important cause of morbidity and mortality. Non-selective immunosuppressive drugs have been used in immune-mediated GN but often result in systemic side effects and occasionally fatal infective complications. There is increasing evidence from both preclinical and clinical studies that abnormal activation of receptor and non-receptor tyrosine kinase signalling pathways are implicated in the pathogenesis of immune-mediated GN. Activation of spleen tyrosine kinase (SYK), Bruton's tyrosine kinase (BTK), platelet-derived growth factor receptor (PDGFR), epidermal growth factor receptor (EGFR) and discoidin domain receptor 1 (DDR1) have been demonstrated in anti-GBM disease. SYK is implicated in the pathogenesis of ANCA-associated GN. SYK, BTK, PDGFR, EFGR, DDR1 and Janus kinase are implicated in the pathogenesis of lupus nephritis. A representative animal model of IgA nephropathy (IgAN) is lacking. Based on the results from in vitro and human renal biopsy study results, a phase II clinical trial is ongoing to evaluate the efficacy and safety of fostamatinib (an oral SYK inhibitor) in high-risk IgAN patient. Various tyrosine kinase inhibitors (TKIs) have been approved for cancer treatment. Clinical trials of TKIs in GN may be justified given their long-term safety data. In this review we will discuss the current unmet medical needs in GN treatment and research as well as the current stage of development of TKIs in GN treatment and propose an accelerated translational research approach to investigate whether selective inhibition of tyrosine kinase provides a safer and more efficacious option for GN treatment.
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Affiliation(s)
- Terry King-Wing Ma
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK.,Carol and Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Stephen P McAdoo
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK
| | - Frederick Wai Keung Tam
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK
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21
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Fischer T, Krüger T, Najjar A, Totzke F, Schächtele C, Sippl W, Ritter C, Hilgeroth A. Discovery of novel substituted benzo-anellated 4-benzylamino pyrrolopyrimidines as dual EGFR and VEGFR2 inhibitors. Bioorg Med Chem Lett 2017; 27:2708-2712. [DOI: 10.1016/j.bmcl.2017.04.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 12/24/2022]
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22
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Pal K, Bandyopadhyay A, Zhou XE, Xu Q, Marciano DP, Brunzelle JS, Yerrum S, Griffin PR, Vande Woude G, Melcher K, Xu HE. Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases. Structure 2017; 25:867-877.e3. [PMID: 28528776 DOI: 10.1016/j.str.2017.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/22/2017] [Accepted: 04/28/2017] [Indexed: 01/01/2023]
Abstract
The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature. We further show that fusion of TPR(2-142) to the MET intracellular domain strongly and selectively stabilizes the αG helix of the MET kinase domain, and mutations of only the TPR leucine zipper residues at the junction to MET, but not other leucine zipper residues, abolish kinase activation. Together, these results provide critical insight into the TPR structure and its ability to induce dimerization and activation of fusion kinases.
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Affiliation(s)
- Kuntal Pal
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Abhishek Bandyopadhyay
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Qingping Xu
- GMCA at Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - David P Marciano
- Department of Molecular Medicine, Translational Research Institute, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology & Biological Chemistry, Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL 60439, USA
| | - Smitha Yerrum
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Translational Research Institute, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - George Vande Woude
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
| | - H Eric Xu
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; VARI-SIMM Center for Structure and Function of Drug Targets and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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23
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Fajer M, Meng Y, Roux B. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. J Phys Chem B 2017; 121:3352-3363. [PMID: 27715044 PMCID: PMC5398919 DOI: 10.1021/acs.jpcb.6b08409] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.
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Affiliation(s)
| | | | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, USA
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24
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Opening the door to the development of novel Abl kinase inhibitors. Future Med Chem 2016; 8:2143-2165. [PMID: 27774798 DOI: 10.4155/fmc-2016-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The discovery of the importance of kinase activity and its relationship to the emergence and proliferation of cancer cells, due to changes in normal physiology, opened a remarkable pathway for the treatment of chronic myelogenous leukemia through intense search of drug candidates. Six Abl kinase inhibitors have received the US FDA approval as chronic myelogenous leukemia treatment, and continuous efforts in obtaining new, more effective and selective molecules are being carried out. Herein we discuss the mechanisms of Abl inhibition, structural features and ligand/protein interactions that are important for the design of new Abl kinase inhibitors. This review provides a broad overview of binding mode predictions, through molecular docking, which can be an approach to discover novel Abl kinase inhibitors.
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25
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Wu K, Tan XY, Xu YH, Shi X, Fan YF, Li DD, Liu X. JAK family members: Molecular cloning, expression profiles and their roles in leptin influencing lipid metabolism in Synechogobius hasta. Comp Biochem Physiol B Biochem Mol Biol 2016; 203:122-131. [PMID: 27789245 DOI: 10.1016/j.cbpb.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 01/09/2023]
Abstract
Janus kinase (JAK) is a family of non-receptor tyrosine kinases that participate in transducing cytokine signals from the external environment to the nucleus in various biological processes. Currently, information about their genes structure and evolutionary history has been extensively studied in mammals as well as in several fish species. By contrast, limited reports have addressed potential role of diverse JAK in signaling responses to leptin in fish. In this study, we identified and characterized five JAK members of Synechogobius hasta. Compared to mammals, more members of the JAK family were found in S. hasta, which provided evidence that the JAK family members had arisen by the whole genome duplications during vertebrate evolution. For protein structure, all of these members possessed similar domains compared with those of mammals. Their mRNAs were expressed in a wide range of tissues, but at the different levels. Incubation in vitro of freshly isolated hepatocytes of S. hasta with different concentrations of recombinant human leptin decreased the intracellular triglyceride content and lipogenic genes expression, and increased mRNA expression of several JAK and lipolytic genes. AG490, a specific inhibitor of JAK, reversed leptin-induced effects on TG content and JAK2a, JAK2b, hormone-sensitive lipase (HSL2) and acetyl-CoA carboxylase (ACCa), indicating that the JAK2a/b may have mediated the actions of leptin on lipid metabolism at transcriptional level.
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Affiliation(s)
- Kun Wu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Ying Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Collaborative Innovative Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
| | - Yi-Huan Xu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Shi
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao-Fang Fan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Dan Li
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Liu
- Panjin Guanghe Crab Co., Ltd., Panjin 124200, China
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26
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Bian Y, Li L, Dong M, Liu X, Kaneko T, Cheng K, Liu H, Voss C, Cao X, Wang Y, Litchfield D, Ye M, Li SSC, Zou H. Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat Chem Biol 2016; 12:959-966. [DOI: 10.1038/nchembio.2178] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 07/11/2016] [Indexed: 12/26/2022]
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Ma TKW, McAdoo SP, Tam FWK. Spleen Tyrosine Kinase: A Crucial Player and Potential Therapeutic Target in Renal Disease. Nephron Clin Pract 2016; 133:261-9. [PMID: 27476075 DOI: 10.1159/000446879] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/24/2016] [Indexed: 02/06/2023] Open
Abstract
Spleen tyrosine kinase (Syk), a 72 kDa cytoplasmic non-receptor protein-tyrosine kinase, plays an important role in signal transduction in a variety of cell types. Ever since its discovery in the early 1990s, there has been accumulating evidence to suggest a pathogenic role of Syk in various allergic disorders, autoimmune diseases and malignancies. Additionally, there is emerging data from both pre-clinical and clinical studies that Syk is implicated in the pathogenesis of proliferative glomerulonephritis (GN), including anti-glomerular basement membrane disease, anti-neutrophil cytoplasmic antibody-associated GN, lupus nephritis and immunoglobulin A nephropathy (IgAN). Moreover, recent animal studies have shed light on the importance of Syk in mediating acute renal allograft rejection, Epstein Barr virus-associated post-transplant lymphoproliferative disease and kidney fibrosis. Fostamatinib, an oral Syk inhibitor, has undergone clinical testing in rheumatoid arthritis, refractory immune thrombocytopenic purpura, leukemia and lymphoma. The recent STOP-IgAN trial showed that the addition of non-selective immunosuppressive therapy to intensive supportive care did not improve clinical outcomes in high-risk IgAN patients. A Syk-targeted approach may be beneficial and is currently being evaluated in a phase II randomized controlled trial. In this review, we will discuss the pathogenic role of Syk and potential use of Syk inhibitor in a variety of renal diseases.
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Affiliation(s)
- Terry King-Wing Ma
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, Hammersmith Hospital, London, UK
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28
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Akçakaya P, Lui WO. MicroRNAs and Gastrointestinal Stromal Tumor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 889:51-70. [PMID: 26658996 DOI: 10.1007/978-3-319-23730-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is the most commonly diagnosed mesenchymal tumor in the gastrointestinal tract. This tumor type is driven by gain-of-function mutations in receptor tyrosine kinases (such as KIT, PDGFRA, and BRAF) or loss-of-function mutations in succinate dehydrogenase complex subunit genes (SDHx). Molecular studies on GIST have improved our understanding of the biology of the disease and have led to the use of targeted therapy approach, such as imatinib for KIT/PDGFRA-mutated GIST. Recently, microRNAs have emerged as important regulators of KIT expression, cancer cell behavior, and imatinib response in GIST. This chapter aims to provide an overview on current understanding of the biological roles of microRNAs in GIST and possible implications in prognosis and therapeutic response.
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Affiliation(s)
- Pinar Akçakaya
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, SE-17176, Sweden. .,Cancer Center Karolinska, Karolinska University Hospital, Stockholm, SE-17176, Sweden.
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, SE-17176, Sweden. .,Cancer Center Karolinska, Karolinska University Hospital, Stockholm, SE-17176, Sweden.
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29
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Wu K, Tan XY, Xu YH, Chen QL, Pan YX. JAK and STAT members of yellow catfish Pelteobagrus fulvidraco and their roles in leptin affecting lipid metabolism. Gen Comp Endocrinol 2016; 226:14-26. [PMID: 26704851 DOI: 10.1016/j.ygcen.2015.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 01/01/2023]
Abstract
The present study clones and characterizes the full-length cDNA sequences of members in JAK-STAT pathway, explores their mRNA tissue expression and the biological role in leptin influencing lipid metabolism in yellow catfish Pelteobagrus fulvidraco. Full-length cDNA sequences of five JAKs and seven STAT members, including some splicing variants, were obtained from yellow catfish. Compared to mammals, more members of the JAKs and STATs family were found in yellow catfish, which provided evidence that the JAK and STAT family members had arisen by the whole genome duplications during vertebrate evolution. All of these members were widely expressed across the eleven tissues (liver, white muscle, spleen, brain, gill, mesenteric fat, anterior intestine, heart, mid-kidney, testis and ovary) but at the variable levels. Intraperitoneal injection in vivo and incubation in vitro of recombinant human leptin changed triglyceride content and mRNA expression of several JAKs and STATs members, and genes involved in lipid metabolism. AG490, a specific inhibitor of JAK2-STAT pathway, partially reversed leptin-induced effects, indicating that the JAK2a/b-STAT3 pathway exerts main regulating actions of leptin on lipid metabolism at transcriptional level. Meanwhile, the different splicing variants were differentially regulated by leptin incubation. Thus, our data suggest that leptin activated the JAK/STAT pathway and increases the expression of target genes, which partially accounts for the leptin-induced changes in lipid metabolism in yellow catfish.
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Affiliation(s)
- Kun Wu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan 430070, China
| | - Xiao-Ying Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan 430070, China.
| | - Yi-Huan Xu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan 430070, China
| | - Qi-Liang Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan 430070, China
| | - Ya-Xiong Pan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of P.R.C., Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan 430070, China
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30
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Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Sci Signal 2015; 8:rs13. [PMID: 26628682 DOI: 10.1126/scisignal.aaa6711] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kimberly L Malecka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lauren Fink
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - E Joseph Jordan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Duffy
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Samuel Kolander
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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31
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Investigation of new 2-aryl substituted Benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors targeting vascular endothelial growth factor receptor 2. Eur J Med Chem 2015; 103:29-43. [PMID: 26318056 DOI: 10.1016/j.ejmech.2015.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 02/06/2023]
Abstract
Vascular Endothelial Growth Factor (VEGF) pathway has emerged as one of the most important positive modulators of Angiogenesis, a central process implicated in tumour growth and metastatic dissemination. This led to the design and development of anti-VEGF monoclonal antibodies and small-molecule ATP-competitive VEGFR-inhibitors. In this study, we describe the synthesis and the biological evaluation of novel 2-aryl substituted benzothiopyrano-fused pyrimidines 1a-i, 2a-i and 3a-i. The ability of the compounds to target the VEGF pathway was determined in vitro exploiting the compounds' antiproliferative efficacy against HUVEC cells. The VEGFR-2 inhibition was confirmed by enzymatic assays on recombinant human kinase insert domain receptor (KDR), by cell-based phospho-VEGFR-2 inhibition assays, and by ex vivo rat aortic ring tests. The selectivity profile of the best performing derivatives belonging to series 2 was further explored combining modeling studies and additional assays in a panel of human cell lines and other kinases.
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32
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Yunn NO, Koh A, Han S, Lim JH, Park S, Lee J, Kim E, Jang SK, Berggren PO, Ryu SH. Agonistic aptamer to the insulin receptor leads to biased signaling and functional selectivity through allosteric modulation. Nucleic Acids Res 2015; 43:7688-701. [PMID: 26245346 PMCID: PMC4652772 DOI: 10.1093/nar/gkv767] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/16/2015] [Indexed: 12/13/2022] Open
Abstract
Due to their high affinity and specificity, aptamers have been widely used as effective inhibitors in clinical applications. However, the ability to activate protein function through aptamer-protein interaction has not been well-elucidated. To investigate their potential as target-specific agonists, we used SELEX to generate aptamers to the insulin receptor (IR) and identified an agonistic aptamer named IR-A48 that specifically binds to IR, but not to IGF-1 receptor. Despite its capacity to stimulate IR autophosphorylation, similar to insulin, we found that IR-A48 not only binds to an allosteric site distinct from the insulin binding site, but also preferentially induces Y1150 phosphorylation in the IR kinase domain. Moreover, Y1150-biased phosphorylation induced by IR-A48 selectively activates specific signaling pathways downstream of IR. In contrast to insulin-mediated activation of IR, IR-A48 binding has little effect on the MAPK pathway and proliferation of cancer cells. Instead, AKT S473 phosphorylation is highly stimulated by IR-A48, resulting in increased glucose uptake both in vitro and in vivo. Here, we present IR-A48 as a biased agonist able to selectively induce the metabolic activity of IR through allosteric binding. Furthermore, our study also suggests that aptamers can be a promising tool for developing artificial biased agonists to targeted receptors.
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Affiliation(s)
- Na-Oh Yunn
- The School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Ara Koh
- The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Seungmin Han
- The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Jong Hun Lim
- The POSTECH Aptamer Initiative Program, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Sehoon Park
- The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Jiyoun Lee
- The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Eui Kim
- The Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Sung Key Jang
- The School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, South Korea The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea The Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Per-Olof Berggren
- The Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Sung Ho Ryu
- The School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, South Korea The Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea The Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea
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33
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Abstract
Protein tyrosine kinases differ widely in their propensity to undergo rearrangements
of the N-terminal Asp–Phe–Gly (DFG) motif of the activation
loop, with some, including FGFR1 kinase, appearing refractory to this so-called
‘DFG flip'. Recent inhibitor-bound structures have unexpectedly
revealed FGFR1 for the first time in a ‘DFG-out' state. Here we
use conformationally selective inhibitors as chemical probes for interrogation of
the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our
detailed structural and biophysical insights identify contributions from altered
dynamics in distal elements, including the αH helix, towards the
outstanding stability of the DFG-out complex with the inhibitor ponatinib. We
conclude that the αC-β4 loop and ‘molecular
brake' regions together impose a high energy barrier for this
conformational rearrangement, and that this may have significance for maintaining
autoinhibition in the non-phosphorylated basal state of FGFR1. Receptor tyrosine kinases are key mediators of cell proliferation
that have been implicated in several disease states for which they represent promising
drug targets. Here the authors determine the thermodynamic basis for the low propensity
of FGFR1 to access the DFG-Phe-out conformation required to bind type-II
inhibitors.
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34
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Wang Q, Zorn JA, Kuriyan J. A structural atlas of kinases inhibited by clinically approved drugs. Methods Enzymol 2015; 548:23-67. [PMID: 25399641 DOI: 10.1016/b978-0-12-397918-6.00002-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aberrant activation of protein kinases is associated with many human diseases, most notably cancer. Due to this link between kinase deregulation and disease progression, kinases are one of the most targeted protein families for small-molecule inhibition. Within the last 15 years, the U.S. Food and Drug Administration has approved over 20 small-molecule inhibitors of protein kinases for use in the clinic. These inhibitors target the kinase active site and represent the successful hurdling by medicinal chemists of the formidable challenge posed by the high similarity among the active sites of the approximately 500 human kinases. We review the conserved structural features of kinases that are important for inhibitor binding as well as for catalysis. Many clinically approved drugs elicit selectivity by exploiting subtle variation within the kinase active site. We highlight some of the crystallographic studies on the kinase-inhibitor complexes that have provided valuable guidance for the development of these drugs as well as for future drug design efforts.
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Affiliation(s)
- Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - Julie A Zorn
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Department of Chemistry, University of California, Berkeley, California, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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35
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Shabani M, Naseri J, Shokri F. Receptor tyrosine kinase-like orphan receptor 1: a novel target for cancer immunotherapy. Expert Opin Ther Targets 2015; 19:941-55. [DOI: 10.1517/14728222.2015.1025753] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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36
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Alfieri C, Kavvadas P, Simonini P, Ikehata M, Dussaule JC, Chadjichristos CE, Rastaldi MP, Messa P, Chatziantoniou C. Discoidin domain receptor-1 and periostin: new players in chronic kidney disease. Nephrol Dial Transplant 2015; 30:1965-71. [PMID: 25829327 DOI: 10.1093/ndt/gfv074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/05/2015] [Indexed: 11/14/2022] Open
Abstract
The incidence and prevalence of chronic kidney disease represents an important problem for public health. In renal diseases, the main histologic alterations derive from the development of renal fibrosis which results from the loss of the balance between pro- and anti-fibrotic factors. Tyrosine kinase receptors (RTKs) and matricellular proteins (MPs) are nowadays studied as potential modulators of renal injury. RTKs regulate cell cycle, migration, metabolism and cellular differentiation. Discoidin domain receptor-1 (DDR-1) is an RTK that has been extensively studied in cancer, and lung and renal diseases. It modulates inflammatory recruitment, extracellular matrix deposition and fibrosis; in renal diseases, it appears to act independently of the underlying disease. MPs regulate cell-matrix interactions and matrix accumulation, cellular adhesion and migration, and expression of inflammatory cells. Periostin is an MP, mainly studied in bone, heart, lung and cancer. Several studies demonstrated that it mediates cell-matrix interactions, migration of inflammatory cells and development of fibrosis. Recently, it has been reported in several nephropathies. In this review, we discuss the potential pathological roles of DDR-1 and periostin focussing on the kidney in both experimental models and human diseases.
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Affiliation(s)
- Carlo Alfieri
- Institut National de la Santé et de la Recherche Médicale Research Unit S_1155, Bâtiment Recherche, Tenon Hospital, Paris, France Department of Medicine and Medical Specialties, Unit of Nephrology, Dialysis, and Renal Transplant, Fondazione Istituto di Ricerca e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Panagiotis Kavvadas
- Institut National de la Santé et de la Recherche Médicale Research Unit S_1155, Bâtiment Recherche, Tenon Hospital, Paris, France
| | - Paola Simonini
- Department of Medicine and Medical Specialties, Unit of Nephrology, Dialysis, and Renal Transplant, Fondazione Istituto di Ricerca e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Masami Ikehata
- Research Laboratory of Nephrology, Fondazione Istituto di Ricerca e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Jean Claude Dussaule
- Institut National de la Santé et de la Recherche Médicale Research Unit S_1155, Bâtiment Recherche, Tenon Hospital, Paris, France
| | - Christos E Chadjichristos
- Institut National de la Santé et de la Recherche Médicale Research Unit S_1155, Bâtiment Recherche, Tenon Hospital, Paris, France
| | - Maria Pia Rastaldi
- Research Laboratory of Nephrology, Fondazione Istituto di Ricerca e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Piergiorgio Messa
- Department of Medicine and Medical Specialties, Unit of Nephrology, Dialysis, and Renal Transplant, Fondazione Istituto di Ricerca e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Christos Chatziantoniou
- Institut National de la Santé et de la Recherche Médicale Research Unit S_1155, Bâtiment Recherche, Tenon Hospital, Paris, France
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37
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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: 0.7] [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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38
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Kamstra RL, Freywald A, Floriano WB. N-(2,4)-dinitrophenyl-L-arginine Interacts with EphB4 and Functions as an EphB4 Kinase Modulator. Chem Biol Drug Des 2015; 86:476-86. [DOI: 10.1111/cbdd.12510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/10/2014] [Accepted: 12/15/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Rhiannon L. Kamstra
- Department of Chemistry; Lakehead University; Thunder Bay ON P7B 5E1 Canada
- Thunder Bay Regional Research Institute; Thunder Bay ON P7A 7T1 Canada
| | - Andrew Freywald
- Department of Pathology; University of Saskatchewan; Saskatoon SK S7N 0W0 Canada
| | - Wely B. Floriano
- Department of Chemistry; Lakehead University; Thunder Bay ON P7B 5E1 Canada
- Thunder Bay Regional Research Institute; Thunder Bay ON P7A 7T1 Canada
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39
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Structural dynamic analysis of apo and ATP-bound IRAK4 kinase. Sci Rep 2014; 4:5748. [PMID: 25034608 PMCID: PMC4103033 DOI: 10.1038/srep05748] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022] Open
Abstract
Interleukin-1 receptor-associated kinases (IRAKs) are Ser/Thr protein kinases that play an important role as signaling mediators in the signal transduction facilitated by the Toll-like receptor (TLR) and interleukin-1 receptor families. Among IRAK family members, IRAK4 is one of the drug targets for diseases related to the TLR and IL-1R signaling pathways. Experimental evidence suggests that the IRAK4 kinase domain is phosphorylated in its activation loop at T342, T345, and S346 in the fully activated state. However, the molecular interactions of subdomains within the active and inactive IRAK4 kinase domain are poorly understood. Hence, we employed a long-range molecular dynamics (MD) simulation to compare apo IRAK4 kinase domains (phosphorylated and unphosphorylated) and ATP-bound phosphorylated IRAK4 kinase domains. The MD results strongly suggested that lobe uncoupling occurs in apo unphosphorylated IRAK4 kinase via the disruption of the R334/T345 and R310/T345 interaction. In addition, apo unphosphorylated trajectory result in high mobility, particularly in the N lobe, activation segment, helix αG, and its adjoining loops. The Asp-Phe-Gly (DFG) and His-Arg-Asp (HRD) conserved kinase motif analysis showed the importance of these motifs in IRAK4 kinase activation. This study provides important information on the structural dynamics of IRAK4 kinase, which will aid in inhibitor development.
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40
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Bainbridge TW, DeAlmeida VI, Izrael-Tomasevic A, Chalouni C, Pan B, Goldsmith J, Schoen AP, Quiñones GA, Kelly R, Lill JR, Sandoval W, Costa M, Polakis P, Arnott D, Rubinfeld B, Ernst JA. Evolutionary divergence in the catalytic activity of the CAM-1, ROR1 and ROR2 kinase domains. PLoS One 2014; 9:e102695. [PMID: 25029443 PMCID: PMC4100928 DOI: 10.1371/journal.pone.0102695] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/23/2014] [Indexed: 12/15/2022] Open
Abstract
Receptor tyrosine kinase-like orphan receptors (ROR) 1 and 2 are atypical members of the receptor tyrosine kinase (RTK) family and have been associated with several human diseases. The vertebrate RORs contain an ATP binding domain that deviates from the consensus amino acid sequence, although the impact of this deviation on catalytic activity is not known and the kinase function of these receptors remains controversial. Recently, ROR2 was shown to signal through a Wnt responsive, β-catenin independent pathway and suppress a canonical Wnt/β-catenin signal. In this work we demonstrate that both ROR1 and ROR2 kinase domains are catalytically deficient while CAM-1, the C. elegans homolog of ROR, has an active tyrosine kinase domain, suggesting a divergence in the signaling processes of the ROR family during evolution. In addition, we show that substitution of the non-consensus residues from ROR1 or ROR2 into CAM-1 and MuSK markedly reduce kinase activity, while restoration of the consensus residues in ROR does not restore robust kinase function. We further demonstrate that the membrane-bound extracellular domain alone of either ROR1 or ROR2 is sufficient for suppression of canonical Wnt3a signaling, and that this domain can also enhance Wnt5a suppression of Wnt3a signaling. Based on these data, we conclude that human ROR1 and ROR2 are RTK-like pseudokinases.
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Affiliation(s)
- Travis W. Bainbridge
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Venita I. DeAlmeida
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Anita Izrael-Tomasevic
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Cécile Chalouni
- Center for Advanced Light Microscopy, Genentech, Inc., South San Francisco, California, United States of America
| | - Borlan Pan
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Joshua Goldsmith
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Alia P. Schoen
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Gabriel A. Quiñones
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Ryan Kelly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Jennie R. Lill
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Mike Costa
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Paul Polakis
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - David Arnott
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Bonnee Rubinfeld
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - James A. Ernst
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
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Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine. Isr J Chem 2014. [DOI: 10.1002/ijch.201400009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Griffin BA, Ramchand R, Almirall D, Slaughter ME, Burgette LF, McCaffery DF. Estimating the causal effects of cumulative treatment episodes for adolescents using marginal structural models and inverse probability of treatment weighting. Drug Alcohol Depend 2014; 136:69-78. [PMID: 24440050 PMCID: PMC3969884 DOI: 10.1016/j.drugalcdep.2013.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 12/10/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Substance use treatment is rarely a one-time event for individuals with substance use disorders. Sustained reductions in substance use and its related symptoms may result from multiple treatment episodes. METHODS We use a marginal structural model with inverse-probability-of-treatment weighting to estimate the causal effects of cumulative treatment experiences over a period of 9 months on drug use at the end of 1-year among 2870 adolescents receiving care in community-based treatment settings. During the 9 months, adolescents move in and out of outpatient and residential treatment with periods where they only receive biological drug screening (BDS) or no treatment at all. The use of inverse-probability-of-treatment weighting reduces confounding bias due to observed baseline and time-varying measures over the course of follow-up; weights were estimated using generalized boosted models. RESULTS Each additional period of treatment (representing at least one day, 1 session, or 1 BDS during the 90 day period between follow-up visits) yielded reductions in average substance use frequency at 1-year relative to no treatment during the 90-day period. For residential treatment it was a 16% decrease (95% CI=-27%, -7%), for outpatient treatment it was a 9% decrease (95% CI=-18%, -0%), and for BDS (with no additional outpatient or residential treatment) it was an 11% decrease (95% CI=-20%, -3%). CONCLUSIONS Using robust statistical methods, we find promising (albeit preliminary) evidence that additional periods of outpatient and residential treatment, as well as biological drug screening, lead to reductions in substance use outcomes at one year.
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Demir E, Akça H, Kaya B, Burgucu D, Tokgün O, Turna F, Aksakal S, Vales G, Creus A, Marcos R. Zinc oxide nanoparticles: genotoxicity, interactions with UV-light and cell-transforming potential. JOURNAL OF HAZARDOUS MATERIALS 2014; 264:420-429. [PMID: 24316814 DOI: 10.1016/j.jhazmat.2013.11.043] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 11/12/2013] [Accepted: 11/14/2013] [Indexed: 06/02/2023]
Abstract
The in vitro genotoxic and the soft agar anchorage independent cell transformation ability of zinc oxide nanoparticles (NPs) and its bulky forms have been evaluated in human embryonic kidney (HEK293) and in mouse embryonic fibroblast (NIH/3T3) cells, either alone or in combination with UVB-light. The comet assay, with and without the use of FPG and Endo III enzymes, the micronucleus assay and the soft-agar colony assay were used. For the comet assay a statistically significant induction of DNA damage, with and without the enzymes, were observed up of 100μg/mL. ZnO NPs were able to increase significantly the frequency of micronuclei, and similar results were observed in the cell transformation assay where such NPs were able to induce cell-anchorage independent growth. These effects were observed at doses up 100μg/mL. Although UVB-light was able to induce genotoxic damage and cell-anchorage growth, a significant antagonist interaction effect was observed in combination with ZnO NPs. These in vitro results, obtained with the selected cell lines, contribute to increase our genotoxicity database on the ZnO NPs effects as well as to open the discussion about their risk in photo-protection sun screens.
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Affiliation(s)
- Eşref Demir
- Akdeniz University, Faculty of Sciences, Department of Biology, 07058 Antalya, Turkey
| | - Hakan Akça
- Medical Biology Department, School of Medicine, Pamukkale University, Kinikli, Denizli, Turkey
| | - Bülent Kaya
- Akdeniz University, Faculty of Sciences, Department of Biology, 07058 Antalya, Turkey
| | - Durmuş Burgucu
- Akdeniz University, Faculty of Medicine, Department of Physiology, 07058 Antalya, Turkey
| | - Onur Tokgün
- Medical Biology Department, School of Medicine, Pamukkale University, Kinikli, Denizli, Turkey
| | - Fatma Turna
- Akdeniz University, Faculty of Sciences, Department of Biology, 07058 Antalya, Turkey
| | - Sezgin Aksakal
- Akdeniz University, Faculty of Sciences, Department of Biology, 07058 Antalya, Turkey
| | - Gerard Vales
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Spain
| | - Amadeu Creus
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Spain; CIBER Epidemiología y Salud Pública, ISCIII, Spain
| | - Ricard Marcos
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Spain; CIBER Epidemiología y Salud Pública, ISCIII, Spain.
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Intra-cellular tyrosine kinase. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kocieniewski P, Lipniacki T. MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response. Phys Biol 2013; 10:035006. [PMID: 23735655 DOI: 10.1088/1478-3975/10/3/035006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Raf/MEK/ERK cascade is one of the most studied and important signal transduction pathways. However, existing models largely ignore the existence of isoforms of the constituent kinases and their interactions. Here, we propose a model of the ERK cascade that includes heretofore neglected differences between isoforms of MEK. In particular, MEK1 is subject to a negative feedback from activated ERK, which is further conferred to MEK2 via hetero-dimerization. Specifically, ERK phosphorylates MEK1 at the residue Thr292, hypothetically creating an additional phosphatase binding site, accelerating MEK1 and MEK2 dephosphorylation. We incorporated these recently discovered interactions into a mathematical model of the ERK cascade that reproduces the experimental results of Catalanotti et al (2009 Nature Struct. Mol. Biol. 16 294-303) and Kamioka et al (2010 J. Biol. Chem. 285 33540-8). Furthermore, the model allows for predictions regarding the differences in the catalytic activity and function of the MEK isoforms. We propose that the MEK1/MEK2 ratio regulates the duration of the response, which increases with the level of MEK2 and decreases with the level of MEK1. In turn, the amplitude of the response is controlled by the total amount of the two isoforms. We confirm the proposed model structure performing a random parameter sampling, which led us to the conclusion that the sampled parameters, selected to properly reproduce wild-type (WT) cell behavior, to allow for qualitative reproduction of differences in behavior WT cells and cell mutants studied experimentally.
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Affiliation(s)
- Pawel Kocieniewski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland
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Abstract
Receptor tyrosine kinases (RTKs) exhibit basal tyrosine phosphorylation and activity in the absence of ligand stimulation, which has been attributed to the "leaky" nature of tyrosine kinase autoinhibition and stochastic collisions of receptors in the membrane bilayer. This basal phosphorylation does not produce a signal of sufficient amplitude and intensity to manifest in a biological response and hence is considered to be a passive, futile process that does not have any biological function. This paradigm has now been challenged by a study showing that the basal phosphorylation of RTKs is a physiologically relevant process that is actively inhibited by the intracellular adaptor protein growth factor receptor-bound 2 (Grb2) and serves to "prime" receptors for a rapid response to ligand stimulation. Grb2 is conventionally known for playing positive roles in RTK signaling. The discovery of a negative regulatory role for Grb2 reveals that this adaptor acts as a double-edged sword in the regulation of RTK signaling.
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Affiliation(s)
- Artur A Belov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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Ogawa N, Yuki H, Tanaka A. Insights from Pim1 structure for anti-cancer drug design. Expert Opin Drug Discov 2012; 7:1177-92. [DOI: 10.1517/17460441.2012.727394] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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48
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Mohebiany AN, Nikolaienko RM, Bouyain S, Harroch S. Receptor-type tyrosine phosphatase ligands: looking for the needle in the haystack. FEBS J 2012; 280:388-400. [PMID: 22682003 DOI: 10.1111/j.1742-4658.2012.08653.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reversible protein phosphorylation plays a pivotal role in intercellular communication. Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) are involved in the regulation of key cellular processes by controlling the phosphorylation levels of diverse effectors. Among PTPs, receptor-like protein tyrosine phosphatases (RPTPs) are involved in important developmental processes, particularly in the formation of the nervous system. Until recently, few ligands had been identified for RPTPs, making it difficult to grasp the effects these receptors have on cellular processes, as well as the mechanisms through which their functions are mediated. However, several potential RPTP ligands have now been identified to provide us with unparalleled insights into RPTP function. In this review, we focus on the nature and biological outcomes of these extracellular interactions between RPTPs and their associated ligands.
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Affiliation(s)
- Alma N Mohebiany
- Department of Neuroscience, Institut Pasteur de Paris, Paris, France
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Iwata H, Oki H, Okada K, Takagi T, Tawada M, Miyazaki Y, Imamura S, Hori A, Lawson JD, Hixon MS, Kimura H, Miki H. A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases. ACS Med Chem Lett 2012; 3:342-6. [PMID: 24900475 DOI: 10.1021/ml3000403] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Abstract
We present a straightforward process for the discovery of novel back pocket-binding fragment molecules against protein tyrosine kinases. The approach begins by screening against the nonphosphorylated target kinase with subsequent counterscreening of hits against the phosphorylated enzyme. Back pocket-binding fragments are inactive against the phosphorylated kinase. Fragment molecules are of insufficient size to span both regions of the ATP binding pocket; thus, the outcome is binary (back pocket-binding or hinge-binding). Next, fragments with the appropriate binding profile are assayed in combination with a known hinge-binding fragment and subsequently with a known back pocket-binding fragment. Confirmation of back pocket-binding by Yonetani-Theorell plot analysis progresses candidate fragments to crystallization trials. The method is exemplified by a fragment screening campaign against vascular endothelial growth factor receptor 2, and a novel back pocket-binding fragment is presented.
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Affiliation(s)
| | | | | | | | | | | | | | | | - J. David Lawson
- Takeda California Inc., 10410 Science Center Drive, San Diego, California
92121, United States
| | - Mark S. Hixon
- Takeda California Inc., 10410 Science Center Drive, San Diego, California
92121, United States
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50
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Balla P, Moskovszky L, Sapi Z, Forsyth R, Knowles H, Athanasou NA, Szendroi M, Kopper L, Rajnai H, Pinter F, Petak I, Benassi MS, Picci P, Conti A, Krenacs T. Epidermal growth factor receptor signalling contributes to osteoblastic stromal cell proliferation, osteoclastogenesis and disease progression in giant cell tumour of bone. Histopathology 2012; 59:376-89. [PMID: 22034878 DOI: 10.1111/j.1365-2559.2011.03948.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIMS Epidermal growth factor receptor (EGFR) is implicated in bone remodelling. The aim was to determine whether EGFR protein expression contributes to the aggressiveness and recurrence potential of giant cell tumour of bone (GCTB), an osteolytic primary bone tumour that can exhibit markedly variable clinical behaviour. METHODS AND RESULTS Immunohistochemical analysis on tissue microarrays (TMA) of 231 primary, 97 recurrent, 17 metastatic and 26 malignant GCTBs was performed using TMA analysis software and whole digital slides allowing validated scoring. EGFR expression was restricted to neoplastic stromal cells and was significantly more frequent in recurrent (71 of 92; 77%) than in non-recurrent GCTBs (86 of 162; 53%) (P = 0.002); and in clinicoradiologically aggressive (31 of 43; 72%) than latent (27 of 54; 50%) cases (P = 0.034). Detecting phosphotyrosine epitopes pY1068 and -pY1173 indicated active EGFR signalling, and finding EGFR ligands EGF and transforming growth factor-α restricted to cells of the monocytic lineage suggested paracrine EGFR activation in stromal cells. In functional studies EGF supported proliferation of GCTB stromal cells, and the addition of EGF and macrophage-colony stimulating factor promoted osteoclastogenesis. CONCLUSION In GCTB, EGFR signalling in neoplastic stromal cells may contribute to disease progression through promoting stromal cell proliferation and osteoclastogenesis.
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Affiliation(s)
- Peter Balla
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
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