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Nag S, Stany B, Mishra S, Kumar S, Mohanto S, Ahmed MG, Mathew B, Subramaniyan V. Multireceptor Analysis for Evaluating the Antidiabetic Efficacy of Karanjin: A Computational Approach. Endocrinol Diabetes Metab 2024; 7:e509. [PMID: 38982323 PMCID: PMC11233261 DOI: 10.1002/edm2.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Diabetes mellitus, notably type 2, is a rising global health challenge, prompting the need for effective management strategies. Common medications such as metformin, insulin, repaglinide and sitagliptin can induce side effects like gastrointestinal disturbances, hypoglycemia, weight gain and specific organ risks. Plant-derived therapies like Karanjin from Pongamia pinnata present promising alternatives due to their historical use, holistic health benefits and potentially fewer adverse effects. This study employs in silico analysis to explore Karanjin's interactions with diabetes-associated receptors, aiming to unveil its therapeutic potential while addressing the limitations and side effects associated with conventional medications. METHODOLOGY The research encompassed the selection of proteins from the Protein Data Bank (PDB), followed by structural refinement processes and optimization. Ligands such as Karanjin and standard drugs were retrieved from PubChem, followed by a comprehensive analysis of their ADMET profiling and pharmacokinetic properties. Protein-ligand interactions were evaluated through molecular docking using AutoDockTools 1.5.7, followed by the analysis of structural stability using coarse-grained simulations with CABS Flex 2.0. Molecular dynamics simulations were performed using Desmond 7.2 and the OPLS4 force field to explore how Karanjin interacts with proteins over 100 nanoseconds, focusing on the dynamics and structural stability. RESULTS Karanjin, a phytochemical from Pongamia pinnata, shows superior drug candidate potential compared to common medications, offering advantages in efficacy and reduced side effects. It adheres to drug-likeness criteria and exhibits optimal ADMET properties, including moderate solubility, high gastrointestinal absorption and blood-brain barrier penetration. Molecular docking revealed Karanjin's highest binding energy against receptor 3L2M (Pig pancreatic alpha-amylase) at -9.1 kcal/mol, indicating strong efficacy potential. Molecular dynamics simulations confirmed stable ligand-protein complexes with minor fluctuations in RMSD and RMSF, suggesting robust interactions with receptors 3L2M. CONCLUSION Karanjin demonstrates potential in pharmaceutical expansion for treating metabolic disorders such as diabetes, as supported by computational analysis. Prospects for Karanjin in pharmaceutical development include structural modifications for enhanced efficacy and safety. Nanoencapsulation may improve bioavailability and targeted delivery to pancreatic cells, while combination therapies could optimize treatment outcomes in diabetes management. Clinical trials and experimental studies are crucial to validate its potential as a novel therapeutic agent.
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Affiliation(s)
- Sagnik Nag
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - B Stany
- Department of Biomedical Sciences, School of Bio-Sciences & Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Shatakshi Mishra
- Department of Biomedical Sciences, School of Bio-Sciences & Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, India
| | - Vetriselvan Subramaniyan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J Chem Theory Comput 2024; 20:5337-5351. [PMID: 38856971 PMCID: PMC11209942 DOI: 10.1021/acs.jctc.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.
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Affiliation(s)
- Donghyuk Suh
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Seonghoon Kim
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kwangho Nam
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Wonpil Im
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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Huang W, Zheng N, Niu N, Tan Y, Li Y, Tian H. Potent anti-angiogenic component in Kaempferia galanga L. and its mechanism of action. JOURNAL OF ETHNOPHARMACOLOGY 2024; 324:117811. [PMID: 38286156 DOI: 10.1016/j.jep.2024.117811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/13/2024] [Accepted: 01/20/2024] [Indexed: 01/31/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditionally, the roots of Kaempferia galanga has been used to treat high blood pressure, chest pain, headache, toothache, rheumatism, indigestion, cough, inflammation and cancer in Asia. Nevertheless, most of its pharmacological studies were focused on ethanolic extracts and volatile oils. The exact active chemical constituents and their underlying mechanisms are still poorly understood, especially towards its anti-cancer treatment. Inhibition of angiogenesis is an important atrategy to inhibit tumor growth. It has been reported that the low polar component of the plant possessed anti-angiogenic activity. Yet, the potent compound which is responsible for the effect and its molecular mechanism has not been reported. AIM OF THE STUDY To determine the potent anti-angiogenic component in K.galanga and its mechanism of action. MATERIAL AND METHODS The low polar components of the plant were concentrated using the methods of supercritical fluid extraction (SFE), subcritical extraction (SCE) and steam distillation (SD). The anti-angiogenic activity of the three extracts was evaluated using a zebrafish model. The content of the active compound in those extracts was determined with HPLC analysis. The in-vitro and in-vivo activity of the isolated compound was evaluated using human umbilical vein endothelial cells (HUVECs) model, the aortic ring assay and the matrigel plug assay, respectively. Its molecular mechanism was further studied by the western blotting assay and computer-docking experiments. Besides, its cytotoxicity on cancer and normal cell lines was evaluated using the cell-counting kit. RESULTS HPLC results showed that trans-ethyl p-methoxycinnamate (TEM) was the major component of the extracts. The extract of SFE showed the best effect as it has the highest content of TEM. TEM could inhibit vascular endothelial growth factor (VEGF)-induced viability, migration, invasion and tube formation in human umbilical vein endothelial cells (HUVECs) in vitro. Moreover, it inhibited VEGF-induced sprout formation ex vivo and vessel formation in vivo. Mechanistic study showed that it could suppress tyrosine kinase activity of the receptor of VEGF (VEGFR2) and alter its downstream signaling pathways. In addition, the molecular docking showed that the binding of TEM and VEGFR2 is stable, which mainly attributed to the non-covalent binding interaction. Beside, TEM possessed little toxicity to both cancer and normal cells. CONCLUSION TEM is the major anti-angiogenic component present in K. galanga and its anti-angiogenic property rather than toxicity provides scientific basis for the traditional use of K. galanga in cancer treatment.
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Affiliation(s)
- Weihuan Huang
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China.
| | - Nianjue Zheng
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Naxin Niu
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Ying Tan
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yaolan Li
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Haiyan Tian
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China.
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4
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Woo JR, Bae SH, Wales TE, Engen JR, Lee J, Jang H, Park S. The serine phosphorylations in the IRS-1 PIR domain abrogate IRS-1 and IR interaction. Proc Natl Acad Sci U S A 2024; 121:e2401716121. [PMID: 38625937 PMCID: PMC11046688 DOI: 10.1073/pnas.2401716121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/16/2024] [Indexed: 04/18/2024] Open
Abstract
Serine phosphorylations on insulin receptor substrate 1 (IRS-1) by diverse kinases aoccur widely during obesity-, stress-, and inflammation-induced conditions in models of insulin resistance and type 2 diabetes. In this study, we define a region within the human IRS-1, which is directly C-terminal to the PTB domain encompassing numerous serine phosphorylation sites including Ser307 (mouse Ser302) and Ser312 (mouse 307) creating a phosphorylation insulin resistance (PIR) domain. We demonstrate that the IRS-1 PTB-PIR with its unphosphorylated serine residues interacts with the insulin receptor (IR) but loses the IR-binding when they are phosphorylated. Surface plasmon resonance studies further confirm that the PTB-PIR binds stronger to IR than just the PTB domain, and that phosphorylations at Ser307, Ser312, Ser315, and Ser323 within the PIR domain result in abrogating the binding. Insulin-responsive cells containing the mutant IRS-1 with all these four serines changed into glutamates to mimic phosphorylations show decreased levels of phosphorylations in IR, IRS-1, and AKT compared to the wild-type IRS-1. Hydrogen-deuterium exchange mass spectrometry experiments indicating the PIR domain interacting with the N-terminal lobe and the hinge regions of the IR kinase domain further suggest the possibility that the IRS-1 PIR domain protects the IR from the PTP1B-mediated dephosphorylation.
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Affiliation(s)
- Ju Rang Woo
- Division of Convergence Technology, New Drug Development Center, KBIOHealth, Cheongju28160, Republic of Korea
| | - Seung-Hyun Bae
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center,Goyang10408, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy,Goyang10408, Republic of Korea
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA02115
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA02115
| | - Jongsoon Lee
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan31151, Republic of Korea
| | - Hyonchol Jang
- Division of Rare and Refractory Cancer, Research Institute, National Cancer Center,Goyang10408, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy,Goyang10408, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul06978, Republic of Korea
- Integrative Institute of Basic Sciences, Soongsil University, Seoul06978, Republic of Korea
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5
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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6
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Krishnan H, Ahmed S, Hubbard SR, Miller WT. Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants. FASEB J 2024; 38:e23355. [PMID: 38071609 DOI: 10.1096/fj.202301948r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
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Affiliation(s)
- Harini Krishnan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Department of Veterans Affairs Medical Center, Northport, New York, USA
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7
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Ahmed M, Biswas T, Mondal S. The strategic involvement of IRS in cancer progression. Biochem Biophys Res Commun 2023; 680:141-160. [PMID: 37738904 DOI: 10.1016/j.bbrc.2023.09.036] [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: 07/12/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Insulin Receptor Substrate (IRS), an intracellular molecule devoid of an intrinsic kinase activity, is activated upon binding to IR which thereby works as a scaffold, organizing all signaling complexes and initiating the signaling process downstream. The level of IRS proteins and their stability in the cell is mostly maintained through the phosphorylation status of their tyrosine and serine residues. IRS is positively regulated by phosphorylation of its Tyr residues whereas a Ser residue phosphorylation attenuates it, although there exist some exceptions as well. Other post-translational modifications like O-linked glycosylation, N-linked glycosylation and acetylation also play a prominent role in IRS regulation. Since the discovery of the Warburg effect, people have been curious to find out all possible signaling networks and molecules that could lead to cancer and no doubt, the insulin signaling pathway is identified as one such pathway, which is highly deregulated in cancers. Eminent studies reveal that IRS is a pertinent regulator of cancer and is highly overexpressed in the five most commonly occurring cancers namely- Prostate, Ovarian, Breast, Colon and Lung cancers. IRS1 and IRS2 family members are actively involved in the progression, invasion and metastasis of these cancers. Recently, less studied IRS4 has also emerged as a contributor in ovarian, breast, colorectal and lung cancer, but no such studies related to IRS4 are found in Prostate cancer. The involvement of other IRS family members in cancer is still undiscovered and so paves the way for further exploration. This review is a time-lapse study of IRSs in the context of cancer done over the past two decades and it highlights all the major discoveries made till date, in these cancers from the perspective of IRS.
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Affiliation(s)
- Mehnaz Ahmed
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Tannishtha Biswas
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Susmita Mondal
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
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8
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Yunn NO, Kim J, Ryu SH, Cho Y. A stepwise activation model for the insulin receptor. Exp Mol Med 2023; 55:2147-2161. [PMID: 37779149 PMCID: PMC10618199 DOI: 10.1038/s12276-023-01101-1] [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: 04/28/2023] [Revised: 06/25/2023] [Accepted: 07/24/2023] [Indexed: 10/03/2023] Open
Abstract
The binding of insulin to the insulin receptor (IR) triggers a cascade of receptor conformational changes and autophosphorylation, leading to the activation of metabolic and mitogenic pathways. Recent advances in the structural and functional analyses of IR have revealed the conformations of the extracellular domains of the IR in inactive and fully activated states. However, the early activation mechanisms of this receptor remain poorly understood. The structures of partially activated IR in complex with aptamers provide clues for understanding the initial activation mechanism. In this review, we discuss the structural and functional features of IR complexed with various ligands and propose a model to explain the sequential activation mechanism. Moreover, we discuss the structures of IR complexed with biased agonists that selectively activate metabolic pathways and provide insights into the design of selective agonists and their clinical implications.
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Affiliation(s)
- Na-Oh Yunn
- Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Junhong Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Department of Biomedical Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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9
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Kong F, Wu T, Dai J, Zhai Z, Cai J, Zhu Z, Xu Y, Sun T. Glucagon-like peptide 1 (GLP-1) receptor agonists in experimental Alzheimer's disease models: a systematic review and meta-analysis of preclinical studies. Front Pharmacol 2023; 14:1205207. [PMID: 37771725 PMCID: PMC10525376 DOI: 10.3389/fphar.2023.1205207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/04/2023] [Indexed: 09/30/2023] Open
Abstract
Alzheimer's disease (AD) is a degenerative disease of the nervous system. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs), a drug used to treat type 2 diabetes, have been shown to have neuroprotective effects. This systematic review and meta-analysis evaluated the effects and potential mechanisms of GLP-1 RAs in AD animal models. 26 studies were included by searching relevant studies from seven databases according to a predefined search strategy and inclusion criteria. Methodological quality was assessed using SYRCLE's risk of bias tool, and statistical analysis was performed using ReviewManger 5.3. The results showed that, in terms of behavioral tests, GLP-1 RAs could improve the learning and memory abilities of AD rodents; in terms of pathology, GLP-1 RAs could reduce Aβ deposition and phosphorylated tau levels in the brains of AD rodents. The therapeutic potential of GLP-1 RAs in AD involves a range of mechanisms that work synergistically to enhance the alleviation of various pathological manifestations associated with the condition. A total of five clinical trials were retrieved from ClinicalTrials.gov. More large-scale and high-quality preclinical trials should be conducted to more accurately assess the therapeutic effects of GLP-1 RAs on AD.
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Affiliation(s)
- Fanjing Kong
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tianyu Wu
- School of Acupuncture-Moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jingyi Dai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenwei Zhai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jie Cai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhishan Zhu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying Xu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Sun
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Nam K, Tao Y, Ovchinnikov V. Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway. J Phys Chem B 2023; 127:5789-5798. [PMID: 37363953 PMCID: PMC10332359 DOI: 10.1021/acs.jpcb.3c01804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/22/2023] [Indexed: 06/28/2023]
Abstract
Modulating the transitions between active and inactive conformations of protein kinases is the primary means of regulating their catalytic activity, achieved by phosphorylation of the activation loop (A-loop). To elucidate the mechanism of this conformational activation, we applied the string method to determine the conformational transition path of insulin receptor kinase between the active and inactive conformations and the corresponding free-energy profiles with and without A-loop phosphorylation. The conformational change was found to proceed in three sequential steps: first, the flipping of the DFG motif of the active site; second, rotation of the A-loop; finally, the inward movement of the αC helix. The main energetic bottleneck corresponds to the conformational change in the A-loop, while changes in the DFG motif and αC helix occur before and after A-loop conformational change, respectively. In accordance with this, two intermediate states are identified, the first state just after the DFG flipping and the second state after the A-loop rotation. These intermediates exhibit structural features characteristic of the corresponding inactive and active conformations of other protein kinases. To understand the impact of A-loop phosphorylation on kinase conformation, the free energies of A-loop phosphorylation were determined at several states along the conformational transition path using the free-energy perturbation simulations. The calculated free energies reveal that while the unphosphorylated kinase interconverts between the inactive and active conformations, A-loop phosphorylation restricts access to the inactive conformation, thereby increasing the active conformation population. Overall, this study suggests a consensus mechanism of conformational activation between different protein kinases.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yunwen Tao
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Victor Ovchinnikov
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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11
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Zhang L, Liu Z, Deng Y, He C, Liu W, Li X. The Benefits of Nanosized Magnesium Oxide in Fish Megalobrama amblycephala: Evidence in Growth Performance, Redox Defense, Glucose Metabolism, and Magnesium Homeostasis. Antioxidants (Basel) 2023; 12:1350. [PMID: 37507890 PMCID: PMC10376070 DOI: 10.3390/antiox12071350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
This study evaluated the effects of dietary magnesium oxide nanoparticles (MgO NPs) on the growth, redox defense, glucose metabolism, and magnesium homeostasis in blunt snout bream. Fish (12.42 ± 0.33 g) were fed seven diets containing graded levels of MgO NPs (0, 60, 120, 240, 480, 960, and 1920 mg/kg) for 12 weeks. Whole-body Mg retention decreased significantly as the dietary Mg increased. As dietary MgO NPs levels reached 120 mg/kg, the growth performance and feed utilization remarkably improved. When added at 240 mg/kg, oxidative stress was significantly reduced evidenced by the increased Mn-sod transcription and the decreased CAT and GSH-Px activities and the MDA content. Meanwhile, it enhanced glucose transport, glycolysis, and glycogen synthesis, while inhibiting gluconeogenesis, as was characterized by the increased transcriptions of glut2, gk, and pk, and the decreased transcriptions of fbpase and g6pase. In addition, the supplementation of 120 mg/kg MgO NPs promoted Mg transport marked by a significant increase in the protein expressions of TRMP7, S41A3, and CNNM1. In conclusion, the moderate supplementation of MgO NPs improved the growth performance, reduced hepatic oxidative stress, and promoted glucose transport, glycolysis, glycogen synthesis, and magnesium homeostasis in fish while inhibiting glu.
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Affiliation(s)
- Ling Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Zishang Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Ying Deng
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Chaofan He
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, China
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12
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Bajaj T, Kuriyan J, Gee CL. Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis. PLoS One 2023; 18:e0276413. [PMID: 37310965 DOI: 10.1371/journal.pone.0276413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/28/2023] [Indexed: 06/15/2023] Open
Abstract
Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M. brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.
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Affiliation(s)
- Teena Bajaj
- Graduate Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, California, United States of America
| | - John Kuriyan
- Graduate Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
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13
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Garg R, Katekar R, Parwez S, Agarwal A, Sahu S, Dadge S, Verma S, Goand UK, Siddiqi MI, Gayen JR. Pancreastatin inhibitor PSTi8 ameliorates streptozotocin-induced diabetes by suppressing hepatic glucose production. Eur J Pharmacol 2023; 944:175559. [PMID: 36764353 DOI: 10.1016/j.ejphar.2023.175559] [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: 07/05/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Elevated plasma glucose concentration, as a consequence of excessive hepatic glucose production, plays a pivotal role in the development of diabetes. A chromogranin A-derived diabetogenic peptide Pancreastatin (PST) enhances hepatic glucose output leading to diabetes. Therefore, here we probed the role of PSTi8, a PST inhibitor in ameliorating diabetes by investigating the effect of high glucose (HG) or PST on glucose metabolism. Further, we also explored the action mechanism of the underlying anti-hyperglycemic effect of PSTi8. PSTi8 treatment rescue cultured L6 and HepG2 cells from HG and PST-induced insulin resistance, respectively. It also enhances insulin receptor kinase activity by interacting with the insulin receptor and enhancing GLUT4 translocation and glucose uptake. Thus, our in-silico and in-vitro data support the PST-dependent and independent activity of PSTi8. Additionally, PSTi8 treatment in streptozotocin-induced diabetic rats improved glucose tolerance by lowering blood glucose and plasma PST levels. Concomitantly, the treated animals exhibited reduced hepatic glucose production accompanied by downregulation of hepatic gluconeogenic genes PEPCK and G6Pase. PSTi8-treated rats also exhibited enhanced hepatic glycogen in line with reduced plasma glucagon concentrations. Consistently, improved plasma insulin levels in PSTi8-treated rats enhanced skeletal muscle glucose disposal via enhanced P-Akt expression. In summary, these findings suggest PSTi8 has anti-hyperglycemic properties with enhanced skeletal muscle glucose disposal and reduced hepatic gluconeogenesis both PST dependent as well as independent.
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Affiliation(s)
- Richa Garg
- Pharmaceutics & Pharmacokinetics, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Roshan Katekar
- Pharmaceutics & Pharmacokinetics, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahid Parwez
- Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arun Agarwal
- Pharmaceutics & Pharmacokinetics, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | | | | | - Saurabh Verma
- Pharmaceutics & Pharmacokinetics, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Umesh K Goand
- Pharmaceutics & Pharmacokinetics, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohammad Imran Siddiqi
- Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jiaur R Gayen
- Pharmaceutics & Pharmacokinetics, India; Pharmacology Division, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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14
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Prömer J, Barresi C, Herbst R. From phosphorylation to phenotype - Recent key findings on kinase regulation, downstream signaling and disease surrounding the receptor tyrosine kinase MuSK. Cell Signal 2023; 104:110584. [PMID: 36608736 DOI: 10.1016/j.cellsig.2022.110584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/16/2022] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
Muscle-specific kinase (MuSK) is the key regulator of neuromuscular junction development. MuSK acts via several distinct pathways and is responsible for pre- and postsynaptic differentiation. MuSK is unique among receptor tyrosine kinases as activation and signaling are particularly tightly regulated. Initiation of kinase activity requires Agrin, a heparan sulphate proteoglycan derived from motor neurons, the low-density lipoprotein receptor-related protein-4 (Lrp4) and the intracellular adaptor protein Dok-7. There is a great knowledge gap between MuSK activation and downstream signaling. Recent studies using omics techniques have addressed this knowledge gap, thereby greatly contributing to a better understanding of MuSK signaling. Impaired MuSK signaling causes severe muscle weakness as described in congenital myasthenic syndromes or myasthenia gravis but the underlying pathophysiology is often unclear. This review focuses on recent advances in deciphering MuSK activation and downstream signaling. We further highlight latest break-throughs in understanding and treatment of MuSK-related disorders and discuss the role of MuSK in non-muscle tissue.
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Affiliation(s)
- Jakob Prömer
- Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Cinzia Barresi
- Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ruth Herbst
- Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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15
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Ebrahimi N, Fardi E, Ghaderi H, Palizdar S, Khorram R, Vafadar R, Ghanaatian M, Rezaei-Tazangi F, Baziyar P, Ahmadi A, Hamblin MR, Aref AR. Receptor tyrosine kinase inhibitors in cancer. Cell Mol Life Sci 2023; 80:104. [PMID: 36947256 PMCID: PMC11073124 DOI: 10.1007/s00018-023-04729-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/31/2023] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Targeted therapy is a new cancer treatment approach, involving drugs that particularly target specific proteins in cancer cells, such as receptor tyrosine kinases (RTKs) which are involved in promoting growth and proliferation, Therefore inhibiting these proteins could impede cancer progression. An understanding of RTKs and the relevant signaling cascades, has enabled the development of many targeted drug therapies employing RTK inhibitors (RTKIs) some of which have entered clinical application. Here we discuss RTK structures, activation mechanisms and functions. Moreover, we cover the potential effects of combination drug therapy (including chemotherapy or immunotherapy agents with one RTKI or multiple RTKIs) especially for drug resistant cancers.
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Affiliation(s)
- Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Elmira Fardi
- Medical Branch, Islamic Azad University of Tehran, Tehran, Iran
| | - Hajarossadat Ghaderi
- Laboratory of Regenerative and Medical Innovation, Pasteur Institute of Iran, Tehran, Iran
| | - Sahar Palizdar
- Division of Microbiology, Faculty of Basic Sciences, Islamic Azad University of Tehran East Branch, Tehran, Iran
| | - Roya Khorram
- Bone and Joint Diseases Research Center, Department of Orthopedic Surgery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Vafadar
- Department of Orthopeadic Surgery, Kerman University of Medical Sciences, Kerman, Iran
| | - Masoud Ghanaatian
- Master 1 Bio-Santé-Parcours Toulouse Graduate School of Cancer, Ageing and Rejuvenation (CARe), Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Fatemeh Rezaei-Tazangi
- Department of Anatomy, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, Uinversity of Mazandaran, Babolsar, Iran
| | - Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr, 75169, Iran.
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa.
| | - Amir Reza Aref
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Translational Medicine Group, Xsphera Biosciences, 6 Tide Street, Boston, MA, 02210, USA.
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16
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Maity P, Chatterjee J, Patil KT, Arora S, Katiyar MK, Kumar M, Samarbakhsh A, Joshi G, Bhutani P, Chugh M, Gavande NS, Kumar R. Targeting the Epidermal Growth Factor Receptor with Molecular Degraders: State-of-the-Art and Future Opportunities. J Med Chem 2023; 66:3135-3172. [PMID: 36812395 DOI: 10.1021/acs.jmedchem.2c01242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Epidermal growth factor receptor (EGFR) is an oncogenic drug target and plays a critical role in several cellular functions including cancer cell growth, survival, proliferation, differentiation, and motility. Several small-molecule tyrosine kinase inhibitors (TKIs) and monoclonal antibodies (mAbs) have been approved for targeting intracellular and extracellular domains of EGFR, respectively. However, cancer heterogeneity, mutations in the catalytic domain of EGFR, and persistent drug resistance limited their use. Different novel modalities are gaining a position in the limelight of anti-EGFR therapeutics to overcome such limitations. The current perspective reflects upon newer modalities, importantly the molecular degraders such as PROTACs, LYTACs, AUTECs, and ATTECs, etc., beginning with a snapshot of traditional and existing anti-EGFR therapies including small molecule inhibitors, mAbs, and antibody drug conjugates (ADCs). Further, a special emphasis has been made on the design, synthesis, successful applications, state-of-the-art, and emerging future opportunities of each discussed modality.
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Affiliation(s)
- Pritam Maity
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Joydeep Chatterjee
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Kiran T Patil
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Madhurendra K Katiyar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Manvendra Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Amirreza Samarbakhsh
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Gaurav Joshi
- Department of Pharmaceutical Science, Hemvati Nandan Bahuguna Garhwal (A Central) University, Srinagar 246174, Dist. Garhwal (Uttarakhand), India
| | | | - Manoj Chugh
- In Vitro Diagnostics, Transasia BioMedical Pvt. Ltd. 400072 Mumbai, India
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, United States
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
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17
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GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation. Comput Biol Chem 2023; 104:107835. [PMID: 36893567 DOI: 10.1016/j.compbiolchem.2023.107835] [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: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 03/05/2023]
Abstract
Functional interaction of Ras signaling proteins with upstream, negative regulatory GTPase activating proteins (GAPs) represents a crucial step in cellular decision making related to growth and survival. Key components of the catalytic transition state for Ras deactivation by GAP-accelerated hydrolysis of Ras-bound guanosine triphosphate (GTP) are thought to include an arginine residue from the GAP (the arginine finger), a glutamine residue from Ras (Q61), and a water molecule that is likely coordinated by Q61 to engage in nucleophilic attack on GTP. Here, we use in-vitro fluorescence experiments to show that 0.1-100 mM concentrations of free arginine, imidazole, and other small nitrogenous molecule fail to accelerate GTP hydrolysis, even in the presence of the catalytic domain of a mutant GAP lacking its arginine finger (R1276A NF1). This result is surprising given that imidazole can chemically rescue enzyme activity in arginine-to-alanine mutant protein tyrosine kinases (PTKs) that share many active site components with Ras/GAP complexes. Complementary all-atom molecular dynamics (MD) simulations reveal that an arginine finger GAP mutant still functions to enhance Ras Q61-GTP interaction, though less extensively than wild-type GAP. This increased Q61-GTP proximity may promote more frequent fluctuations into configurations that enable GTP hydrolysis as a component of the mechanism by which GAPs accelerate Ras deactivation in the face of arginine finger mutations. The failure of small molecule analogs of arginine to chemically rescue catalytic deactivation of Ras is consistent with the idea that the influence of the GAP goes beyond the simple provision of its arginine finger. However, the failure of chemical rescue in the presence of R1276A NF1 suggests that the GAPs arginine finger is either unsusceptible to rescue due to exquisite positioning or that it is involved in complex multivalent interactions. Therefore, in the context of oncogenic Ras proteins with mutations at codons 12 or 13 that inhibit arginine finger penetration toward GTP, drug-based chemical rescue of GTP hydrolysis may have bifunctional chemical/geometric requirements that are more difficult to satisfy than those that result from arginine-to-alanine mutations in other enzymes for which chemical rescue has been demonstrated.
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18
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Reinhardt R, Hirzel K, Link G, Eisler SA, Hägele T, Parson MAH, Burke JE, Hausser A, Leonard TA. PKD autoinhibition in trans regulates activation loop autophosphorylation in cis. Proc Natl Acad Sci U S A 2023; 120:e2212909120. [PMID: 36745811 PMCID: PMC9962925 DOI: 10.1073/pnas.2212909120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023] Open
Abstract
Phosphorylation is a ubiquitous mechanism by which signals are transduced in cells. Protein kinases, enzymes that catalyze the phosphotransfer reaction are, themselves, often regulated by phosphorylation. Paradoxically, however, a substantial fraction of more than 500 human protein kinases are capable of catalyzing their own activation loop phosphorylation. Commonly, these kinases perform this autophosphorylation reaction in trans, whereby transient dimerization leads to the mutual phosphorylation of the activation loop of the opposing protomer. In this study, we demonstrate that protein kinase D (PKD) is regulated by the inverse mechanism of dimerization-mediated trans-autoinhibition, followed by activation loop autophosphorylation in cis. We show that PKD forms a stable face-to-face homodimer that is incapable of either autophosphorylation or substrate phosphorylation. Dissociation of this trans-autoinhibited dimer results in activation loop autophosphorylation, which occurs exclusively in cis. Phosphorylation serves to increase PKD activity and prevent trans-autoinhibition, thereby switching PKD on. Our findings not only reveal the mechanism of PKD regulation but also have profound implications for the regulation of many other eukaryotic kinases.
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Affiliation(s)
- Ronja Reinhardt
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter, Vienna1030, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Vienna1090, Austria
| | - Kai Hirzel
- Institute of Cell Biology and Immunology, University of Stuttgart70569, Stuttgart, Germany
| | - Gisela Link
- Institute of Cell Biology and Immunology, University of Stuttgart70569, Stuttgart, Germany
| | - Stephan A. Eisler
- Stuttgart Research Center Systems Biology, University of Stuttgart70569, Stuttgart, Germany
| | - Tanja Hägele
- Institute of Cell Biology and Immunology, University of Stuttgart70569, Stuttgart, Germany
| | - Matthew A. H. Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, CanadaV8W 2Y2
| | - John E. Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, CanadaV8W 2Y2
- Department of Biochemistry and Molecular Biology, The University of British Columbia, VancouverBCV6T 1Z3, Canada
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart70569, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart70569, Stuttgart, Germany
| | - Thomas A. Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter, Vienna1030, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Vienna1090, Austria
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19
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Wang Z, Tan D, Wang F, Guo S, Liu J, Cuthbertson AGS, Qiu B, Sang W. Insulin peptides and their receptors regulate ovarian development and oviposition behavior in Diaphorina citri. INSECT SCIENCE 2023; 30:95-108. [PMID: 35510515 PMCID: PMC10084437 DOI: 10.1111/1744-7917.13048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/19/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Diaphorina citri is an important vector of Citrus Huanglongbing (HLB) disease. After feeding on young host plant shoots, the population of D. citri can increase significantly. Females also only lay eggs on young shoots. However, there are few studies on the mechanism of this phenomenon. Exogenous nutrient signals can affect the insulin signaling system of D. citri after feeding on young shoots. In this study, the expression of upstream factors DcILP1, DcILP2, and DcIR in the insulin signaling system of D. citri was upregulated after feeding on young shoots. After being silenced by RNA interference technology, the results showed that the number of oviposited eggs of D. citri was significantly decreased and the ovarian development was inhibited with severe vacuolation. In addition, detection using quantitative reverse transcription-polymerase chain reaction showed that the upstream regulatory gene DcRheb of the target of rapamycin (TOR) pathway and the downstream reproduction-related DcVg gene were also significantly downregulated. These results suggest that feeding upon young shoots may upregulate the expression levels of upstream factors DcILP1, DcILP2, and DcIR in the insulin signaling system. The signal will be through upregulating the expression of DcRheb, an upstream gene of the TOR signaling pathway. This in turn influences yolk metabolism, which eventually causes the ovaries of female D. citri to mature and therefore initiate oviposition behavior.
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Affiliation(s)
- Ziye Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application of Guangdong ProvinceSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Delong Tan
- Institute of Facility AgricultureGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Feifeng Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application of Guangdong ProvinceSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Shuhao Guo
- Key Laboratory of Bio‐Pesticide Innovation and Application of Guangdong ProvinceSouth China Agricultural UniversityGuangzhouChina
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co.LTDHangzhouChina
| | | | - Baoli Qiu
- Key Laboratory of Bio‐Pesticide Innovation and Application of Guangdong ProvinceSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Wen Sang
- Key Laboratory of Bio‐Pesticide Innovation and Application of Guangdong ProvinceSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
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20
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Sun G, Ayrapetov MK. Dissection of the catalytic and regulatory structure-function relationships of Csk protein tyrosine kinase. Front Cell Dev Biol 2023; 11:1148352. [PMID: 36936693 PMCID: PMC10016382 DOI: 10.3389/fcell.2023.1148352] [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: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Protein tyrosine kinases (PTKs) are a large enzyme family that regulates many cellular processes. The key to their broad role in signaling is their tunable substrate specificity and regulatory mechanisms that allow each to respond to appropriate regulatory signals and phosphorylate the correct physiological protein substrates. Thus, in addition to the general PTK catalytic platform, each PTK acquires unique structural motifs that confer a unique combination of catalytic and regulatory properties. Understanding the structural basis for these properties is essential for understanding and manipulating the PTK-based signaling networks in normal and cancer cells. C-terminal Src kinase (Csk) and its homolog, Csk-homologous kinase (Chk), phosphorylate Src family kinases on a C-terminal Tyr residue and negatively regulate their kinase activity. While this regulatory function is biologically essential, Csk and Chk have also been excellent model PTKs for dissecting the structural basis of PTK catalysis and regulation. In this article, we review the structure-function studies of Csk and Chk that shed light on the regulatory and catalytic mechanisms of protein tyrosine kinases in general.
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21
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Sridaran D, Chouhan S, Mahajan K, Renganathan A, Weimholt C, Bhagwat S, Reimers M, Kim EH, Thakur MK, Saeed MA, Pachynski RK, Seeliger MA, Miller WT, Feng FY, Mahajan NP. Inhibiting ACK1-mediated phosphorylation of C-terminal Src kinase counteracts prostate cancer immune checkpoint blockade resistance. Nat Commun 2022; 13:6929. [PMID: 36376335 PMCID: PMC9663509 DOI: 10.1038/s41467-022-34724-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Solid tumours are highly refractory to immune checkpoint blockade (ICB) therapies due to the functional impairment of effector T cells and their inefficient trafficking to tumours. T-cell activation is negatively regulated by C-terminal Src kinase (CSK); however, the exact mechanism remains unknown. Here we show that the conserved oncogenic tyrosine kinase Activated CDC42 kinase 1 (ACK1) is able to phosphorylate CSK at Tyrosine 18 (pY18), which enhances CSK function, constraining T-cell activation. Mice deficient in the Tnk2 gene encoding Ack1, are characterized by diminished CSK Y18-phosphorylation and spontaneous activation of CD8+ and CD4+ T cells, resulting in inhibited growth of transplanted ICB-resistant tumours. Furthermore, ICB treatment of castration-resistant prostate cancer (CRPC) patients results in re-activation of ACK1/pY18-CSK signalling, confirming the involvement of this pathway in ICB insensitivity. An ACK1 small-molecule inhibitor, (R)-9b, recapitulates inhibition of ICB-resistant tumours, which provides evidence for ACK1 enzymatic activity playing a pivotal role in generating ICB resistance. Overall, our study identifies an important mechanism of ICB resistance and holds potential for expanding the scope of ICB therapy to tumours that are currently unresponsive.
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Affiliation(s)
- Dhivya Sridaran
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Surbhi Chouhan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Arun Renganathan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
- Anatomic and Clinical Pathology, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Shambhavi Bhagwat
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Melissa Reimers
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Eric H Kim
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Muhammad A Saeed
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Russell K Pachynski
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY, 11768, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA.
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA.
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22
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Oost LJ, Tack CJ, de Baaij JHF. Hypomagnesemia and Cardiovascular Risk in Type 2 Diabetes. Endocr Rev 2022; 44:357-378. [PMID: 36346820 PMCID: PMC10166267 DOI: 10.1210/endrev/bnac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/22/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Hypomagnesemia is tenfold more common in individuals with type 2 diabetes (T2D), compared to the healthy population. Factors that are involved in this high prevalence are low Mg2+ intake, gut microbiome composition, medication use and presumably genetics. Hypomagnesemia is associated with insulin resistance, which subsequently increases the risk to develop T2D or deteriorates glycaemic control in existing diabetes. Mg2+ supplementation decreases T2D associated features like dyslipidaemia and inflammation; which are important risk factors for cardiovascular disease (CVD). Epidemiological studies have shown an inverse association between serum Mg2+ and the risk to develop heart failure (HF), atrial fibrillation (AF) and microvascular disease in T2D. The potential protective effect of Mg2+ on HF and AF may be explained by reduced oxidative stress, fibrosis and electrical remodeling in the heart. In microvascular disease, Mg2+ reduces the detrimental effects of hyperglycemia and improves endothelial dysfunction. Though, clinical studies assessing the effect of long-term Mg2+ supplementation on CVD incidents are lacking and gaps remain on how Mg2+ may reduce CVD risk in T2D. Despite the high prevalence of hypomagnesemia in people with T2D, routine screening of Mg2+ deficiency to provide Mg2+ supplementation when needed is not implemented in clinical care as sufficient clinical evidence is lacking. In conclusion, hypomagnesemia is common in people with T2D and is both involved as cause, probably through molecular mechanisms leading to insulin resistance, and consequence and is prospectively associated with development of HF, AF and microvascular complications. Whether long-term supplementation of Mg2+ is beneficial, however, remains to be determined.
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Affiliation(s)
- Lynette J Oost
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cees J Tack
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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23
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Kim J, Yunn NO, Park M, Kim J, Park S, Kim Y, Noh J, Ryu SH, Cho Y. Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures. Nat Commun 2022; 13:6500. [PMID: 36310231 PMCID: PMC9618554 DOI: 10.1038/s41467-022-34292-8] [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: 05/06/2022] [Accepted: 10/20/2022] [Indexed: 12/25/2022] Open
Abstract
Activation of insulin receptor (IR) initiates a cascade of conformational changes and autophosphorylation events. Herein, we determined three structures of IR trapped by aptamers using cryo-electron microscopy. The A62 agonist aptamer selectively activates metabolic signaling. In the absence of insulin, the two A62 aptamer agonists of IR adopt an insulin-accessible arrowhead conformation by mimicking site-1/site-2' insulin coordination. Insulin binding at one site triggers conformational changes in one protomer, but this movement is blocked in the other protomer by A62 at the opposite site. A62 binding captures two unique conformations of IR with a similar stalk arrangement, which underlie Tyr1150 mono-phosphorylation (m-pY1150) and selective activation for metabolic signaling. The A43 aptamer, a positive allosteric modulator, binds at the opposite side of the insulin-binding module, and stabilizes the single insulin-bound IR structure that brings two FnIII-3 regions into closer proximity for full activation. Our results suggest that spatial proximity of the two FnIII-3 ends is important for m-pY1150, but multi-phosphorylation of IR requires additional conformational rearrangement of intracellular domains mediated by coordination between extracellular and transmembrane domains.
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Affiliation(s)
- Junhong Kim
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Na-Oh Yunn
- grid.49100.3c0000 0001 0742 4007Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Mangeun Park
- grid.49100.3c0000 0001 0742 4007Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Jihan Kim
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Seongeun Park
- grid.49100.3c0000 0001 0742 4007Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Yoojoong Kim
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Jeongeun Noh
- grid.49100.3c0000 0001 0742 4007Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Sung Ho Ryu
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
| | - Yunje Cho
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Republic of Korea
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24
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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25
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Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Sci 2022; 31:e4411. [PMID: 36173161 PMCID: PMC9601881 DOI: 10.1002/pro.4411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/27/2022] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
Many tyrosine kinases cannot be expressed readily in Escherichia coli, limiting facile production of these proteins for biochemical experiments. We used ancestral sequence reconstruction to generate a spleen tyrosine kinase (Syk) variant that can be expressed in bacteria and purified in soluble form, unlike the human members of this family (Syk and zeta-chain-associated protein kinase of 70 kDa [ZAP-70]). The catalytic activity, substrate specificity, and regulation by phosphorylation of this Syk variant are similar to the corresponding properties of human Syk and ZAP-70. Taking advantage of the ability to express this novel Syk-family kinase in bacteria, we developed a two-hybrid assay that couples the growth of E. coli in the presence of an antibiotic to successful phosphorylation of a bait peptide by the kinase. Using this assay, we screened a site-saturation mutagenesis library of the kinase domain of this reconstructed Syk-family kinase. Sites of loss-of-function mutations identified in the screen correlate well with residues established previously as critical to function and/or structure in protein kinases. We also identified activating mutations in the regulatory hydrophobic spine and activation loop, which are within key motifs involved in kinase regulation. Strikingly, one mutation in an ancestral Syk-family variant increases the soluble expression of the protein by 75-fold. Thus, through ancestral sequence reconstruction followed by deep mutational scanning, we have generated Syk-family kinase variants that can be expressed in bacteria with very high yield.
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Affiliation(s)
- Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCaliforniaUSA
| | - Neel H. Shah
- Department of ChemistryColumbia UniversityNew YorkNew YorkUSA
| | - Sophie R. Shoemaker
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Susan Marqusee
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Kuriyan
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
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26
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Dewangan PS, Beraki TG, Paiz EA, Appiah Mensah D, Chen Z, Reese ML. Divergent kinase WNG1 is regulated by phosphorylation of an atypical activation sub-domain. Biochem J 2022; 479:1877-1889. [PMID: 35938919 PMCID: PMC9555795 DOI: 10.1042/bcj20220076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Apicomplexan parasites like Toxoplasma gondii grow and replicate within a specialized organelle called the parasitophorous vacuole. The vacuole is decorated with parasite proteins that integrate into the membrane after trafficking through the parasite secretory system as soluble, chaperoned complexes. A regulator of this process is an atypical protein kinase called WNG1. Phosphorylation by WNG1 appears to serve as a switch for membrane integration. However, like its substrates, WNG1 is secreted from the parasite dense granules, and its activity must, therefore, be tightly regulated until the correct membrane is encountered. Here, we demonstrate that, while another member of the WNG family can adopt multiple multimeric states, WNG1 is monomeric and therefore not regulated by multimerization. Instead, we identify two phosphosites on WNG1 that are required for its kinase activity. Using a combination of in vitro biochemistry and structural modeling, we identify basic residues that are also required for WNG1 activity and appear to recognize the activating phosphosites. Among these coordinating residues are the 'HRD' Arg, which recognizes activation loop phosphorylation in canonical kinases. WNG1, however, is not phosphorylated on its activation loop, but rather on atypical phosphosites on its C-lobe. We propose a simple model in which WNG1 is activated by increasing ATP concentration above a critical threshold once the kinase traffics to the parasitophorous vacuole.
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Affiliation(s)
- Pravin S. Dewangan
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
| | - Tsebaot G. Beraki
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
| | - E. Ariana Paiz
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
| | - Delia Appiah Mensah
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
- Honors College, University of Texas at Dallas, Richardson, TX, U.S.A
| | - Zhe Chen
- Department of Biophysics, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
| | - Michael L. Reese
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
- Department of Biochemistry, University of Texas, Southwestern Medical Center, Dallas, TX, U.S.A
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27
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Aulakh SS, Bozelli JC, Epand RM. Exploring the AlphaFold Predicted Conformational Properties of Human Diacylglycerol Kinases. J Phys Chem B 2022; 126:7172-7183. [PMID: 36041230 DOI: 10.1021/acs.jpcb.2c04533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Diacylglycerol kinases (DGKs) are important enzymes in molecular membrane biology, as they can lower the concentration of diacylglycerol through phosphorylation while at the same time producing phosphatidic acid. Dysfunction of DGK is linked with multiple diseases including cancer and autoimmune disorders. Currently, the high-resolution structures have not been determined for any of the 10 human DGK paralogs, which has made it difficult to gain a more complete understanding of the enzyme's mechanism of action and regulation. In the present study, we have taken advantage of the significant developments in protein structural prediction technology by artificial intelligence (i.e., Alphafold 2.0), to conduct a comprehensive investigation on the properties of all 10 human DGK paralogs. Structural alignment of the predictions reveals that the C1, catalytic, and accessory domains are conserved in their spatial arrangement relative to each other, across all paralogs. This suggests a critical role played by this domain architecture in DGK function. Moreover, docking studies corroborate the existence of a conserved ATP-binding site between the catalytic and accessory domains. Interestingly, the ATP bound to the interdomain cleft was also found to be in proximity of the conserved glycine-rich motif, which in protein kinases has been suggested to function in ATP binding. Lastly, the spatial arrangement of DGK, with respect to the membrane, reveals that most paralogs possess a more energetically favorable interaction with curved membranes. In conclusion, AlphaFold predictions of human DGKs provide novel insights into the enzyme's structural and functional properties while also paving the way for future experimentation.
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Affiliation(s)
- Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
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28
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Macrophages, Low-Grade Inflammation, Insulin Resistance and Hyperinsulinemia: A Mutual Ambiguous Relationship in the Development of Metabolic Diseases. J Clin Med 2022; 11:jcm11154358. [PMID: 35955975 PMCID: PMC9369133 DOI: 10.3390/jcm11154358] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Metabolic derangement with poor glycemic control accompanying overweight and obesity is associated with chronic low-grade inflammation and hyperinsulinemia. Macrophages, which present a very heterogeneous population of cells, play a key role in the maintenance of normal tissue homeostasis, but functional alterations in the resident macrophage pool as well as newly recruited monocyte-derived macrophages are important drivers in the development of low-grade inflammation. While metabolic dysfunction, insulin resistance and tissue damage may trigger or advance pro-inflammatory responses in macrophages, the inflammation itself contributes to the development of insulin resistance and the resulting hyperinsulinemia. Macrophages express insulin receptors whose downstream signaling networks share a number of knots with the signaling pathways of pattern recognition and cytokine receptors, which shape macrophage polarity. The shared knots allow insulin to enhance or attenuate both pro-inflammatory and anti-inflammatory macrophage responses. This supposedly physiological function may be impaired by hyperinsulinemia or insulin resistance in macrophages. This review discusses the mutual ambiguous relationship of low-grade inflammation, insulin resistance, hyperinsulinemia and the insulin-dependent modulation of macrophage activity with a focus on adipose tissue and liver.
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29
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De Meyts P. [The insulin receptor discovery is 50 years old - A review of achieved progress]. Biol Aujourdhui 2022; 216:7-28. [PMID: 35876517 DOI: 10.1051/jbio/2022007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Indexed: 06/15/2023]
Abstract
The isolation of insulin from the pancreas and its purification to a degree permitting its safe administration to type 1 diabetic patients were accomplished 100 years ago at the University of Toronto by Banting, Best, Collip and McLeod and constitute undeniably one of the major medical therapeutic revolutions, recognized by the attribution of the 1923 Nobel Prize in Physiology or Medicine to Banting and McLeod. The clinical spin off was immediate as well as the internationalization of insulin's commercial production. The outcomes regarding basic research were much slower, in particular regarding the molecular mechanisms of insulin action on its target cells. It took almost a half-century before the determination of the tri-dimensional structure of insulin in 1969 and the characterization of its cell receptor in 1970-1971. The demonstration that the insulin receptor is in fact an enzyme named tyrosine kinase came in the years 1982-1985, and the crystal structure of the intracellular kinase domain 10 years later. The crystal structure of the first intracellular kinase substrate (IRS-1) in 1991 paved the way for the elucidation of the intracellular signalling pathways but it took 15 more years to obtain the complete crystal structure of the extracellular receptor domain (without insulin) in 2006. Since then, the determination of the structure of the whole insulin-receptor complex in both the inactive and activated states has made considerable progress, not least due to recent improvement in the resolution power of cryo-electron microscopy. I will here review the steps in the development of the concept of hormone receptor, and of our knowledge of the structure and molecular mechanism of activation of the insulin receptor.
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Affiliation(s)
- Pierre De Meyts
- de Duve Institute, Department of Cell Signalling, Avenue Hippocrate 74, B-1200 Bruxelles, Belgique - Novo Nordisk A/S, Department of Stem Cell Research, Novo Nordisk Park 1, DK-2760 Maaloev, Danemark
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30
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le Goff S, Godin JP, Albalat E, Nieves JMR, Balter V. Magnesium stable isotope composition, but not concentration, responds to obesity and early insulin-resistant conditions in minipig. Sci Rep 2022; 12:10941. [PMID: 35768618 PMCID: PMC9243132 DOI: 10.1038/s41598-022-14825-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Hypomagnesemia is frequently associated with type 2 diabetes and generally correlates with unfavorable disease progression, but the magnesium status in pre-diabetic conditions remains unclear. Here, the magnesium metabolism is scrutinized in a minipig model of obesity and insulin resistance by measuring variations of the metallome—the set of inorganic elements—and the magnesium stable isotope composition in six organs of lean and obese minipigs raised on normal and Western-type diet, respectively. We found that metallomic variations are most generally insensitive to lean or obese phenotypes. The magnesium stable isotope composition of plasma, liver, kidney, and heart in lean minipigs are significantly heavier than in obese minipigs. For both lean and obese minipigs, the magnesium isotope composition of plasma and liver were negatively correlated to clinical phenotypes and plasma lipoproteins concentration as well as positively correlated to hyperinsulinemic-euglycemic clamp output. Because the magnesium isotope composition was not associated to insulin secretion, our results suggest that it is rather sensitive to whole body insulin sensitivity, opening perspectives to better comprehend the onset of insulin-resistant diabetic conditions.
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Affiliation(s)
- Samuel le Goff
- Laboratoire de Géologie de Lyon, ENS de Lyon, Université de Lyon, CNRS, Lyon, France
| | - Jean-Philippe Godin
- Nestlé Research, Institute of Food Safety and Analytical Sciences, Lausanne, Switzerland
| | - Emmanuelle Albalat
- Laboratoire de Géologie de Lyon, ENS de Lyon, Université de Lyon, CNRS, Lyon, France
| | | | - Vincent Balter
- Laboratoire de Géologie de Lyon, ENS de Lyon, Université de Lyon, CNRS, Lyon, France.
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31
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Sheetz JB, Lemmon MA, Tsutsui Y. Dynamics of protein kinases and pseudokinases by HDX-MS. Methods Enzymol 2022; 667:303-338. [PMID: 35525545 PMCID: PMC9148214 DOI: 10.1016/bs.mie.2022.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dynamics of the protein kinase fold are deeply intertwined with its structure. The past three decades of kinase biophysical studies revealed key dynamic features of the kinase domain and, more recently, how these features may endow catalytically impaired kinases-or pseudokinases-with signaling properties. Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is proving to be a valuable approach for studies of kinase and pseudokinase domain dynamics. Here, we briefly discuss the methods that have provided insights into protein kinase dynamics, describe how HDX-MS is being used to answer questions in the kinase/pseudokinase field, and provide a detailed protocol for collecting an HDX-MS dataset to study the impacts of small molecule binding to a pseudokinase domain. As more small molecules are discovered that can disrupt pseudokinase conformations, HDX-MS is likely to be a powerful approach for exploring drug-induced changes in pseudokinase dynamics and structure.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States
| | - Mark A Lemmon
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
| | - Yuko Tsutsui
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
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32
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Turvey SJ, McPhillie MJ, Kearney MT, Muench SP, Simmons KJ, Fishwick CWG. Recent developments in the structural characterisation of the IR and IGF1R: implications for the design of IR-IGF1R hybrid receptor modulators. RSC Med Chem 2022; 13:360-374. [PMID: 35647546 PMCID: PMC9020618 DOI: 10.1039/d1md00300c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/12/2022] [Indexed: 12/16/2022] Open
Abstract
The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are dimeric disulfide-linked receptor tyrosine kinases, whose actions regulate metabolic and mitogenic signalling pathways inside the cell. It is well documented that in tissues co-expressing the IR and IGF1R, their respective monomers can heterodimerise to form IR-IGF1R hybrid receptors. Increased populations of the IR-IGF1R hybrid receptors are associated with several disease states, including type 2 diabetes and cancer. Recently, progress in the structural biology of IR and IGF1R has given insights into their structure-function relationships and mechanism of action. However, challenges in isolating IR-IGF1R hybrid receptors mean that their structural properties remain relatively unexplored. This review discusses the advances in the structural understanding of the IR and IGF1R, and how these discoveries can inform the design of small-molecule modulators of the IR-IGF1R hybrid receptors to understand their role in cell biology.
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Affiliation(s)
- Samuel J Turvey
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
| | | | - Mark T Kearney
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre, University of Leeds UK
| | - Katie J Simmons
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds UK
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33
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Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2832889. [PMID: 35356248 PMCID: PMC8958086 DOI: 10.1155/2022/2832889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/16/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.
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34
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Ledoux J, Trouvé A, Tchertanov L. The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT. Int J Mol Sci 2022; 23:ijms23031589. [PMID: 35163518 PMCID: PMC8835827 DOI: 10.3390/ijms23031589] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events.
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35
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Structural Insight and Development of EGFR Tyrosine Kinase Inhibitors. Molecules 2022; 27:molecules27030819. [PMID: 35164092 PMCID: PMC8838133 DOI: 10.3390/molecules27030819] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer has a high prevalence, with a growing number of new cases and mortality every year. Furthermore, the survival rate of patients with non-small-cell lung carcinoma (NSCLC) is still quite low in the majority of cases. Despite the use of conventional therapy such as tyrosine kinase inhibitor for Epidermal Growth Factor Receptor (EGFR), which is highly expressed in most NSCLC cases, there was still no substantial improvement in patient survival. This is due to the drug’s ineffectiveness and high rate of resistance among individuals with mutant EGFR. Therefore, the development of new inhibitors is urgently needed. Understanding the EGFR structure, including its kinase domain and other parts of the protein, and its activation mechanism can accelerate the discovery of novel compounds targeting this protein. This study described the structure of the extracellular, transmembrane, and intracellular domains of EGFR. This was carried out along with identifying the binding pose of commercially available inhibitors in the ATP-binding and allosteric sites, thereby clarifying the research gaps that can be filled. The binding mechanism of inhibitors that have been used clinically was also explained, thereby aiding the structure-based development of new drugs.
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Zhang W, Zhao S, Lu L, Fan Z, Ye S. Activation of neurotrophin signalling with light‑inducible receptor tyrosine kinases. Mol Med Rep 2022; 25:70. [PMID: 35014690 PMCID: PMC8767455 DOI: 10.3892/mmr.2022.12586] [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: 05/06/2020] [Accepted: 12/17/2020] [Indexed: 11/05/2022] Open
Abstract
Optogenetics combined with protein engineering based on natural light-sensitive dimerizing proteins has evolved as a powerful strategy to study cellular functions. The present study focused on tropomyosin kinase receptors (Trks) that have been engineered to be light-sensitive. Trk belongs to the superfamily of receptor tyrosine kinases (RTKs), which are single-pass transmembrane receptors that are activated by natural ligands and serve crucial roles in cellular growth, differentiation, metabolism and motility. However, functional variations exist among receptors fused with light-sensitive proteins. The present study proposed a signal transduction model for light-induced receptor activation. This model is based on analysis of previous light-induced Trk receptors reported to date and comparisons to the activation mechanism of natural receptors. In this model, quantitative differences on the dimerization induced from either top-to-bottom or bottom-to-up may lead to the varying amplitude of intracellular signals. We hypothesize that the top-to-bottom propagation is more favourable for activation and yields better results compared with the bottom-to-top direction. The careful delineation of the dimerization mechanisms fine-tuning activation will guide future design for an optimum cellular output with the precision of light.
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Affiliation(s)
- Wei Zhang
- Anesthesiology Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Shu Zhao
- School of Life Science, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Linjie Lu
- Institute of Genetics, Molecular and Cellular Biology, University of Strasbourg, Illkirch 67400, France
| | - Zhimin Fan
- Anesthesiology Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Shixin Ye
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1195, Bicetre Hospital, Paris‑Saclay University, Le Kremlin-Bicêtre 94276, France
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Modi V, Dunbrack RL. Kincore: a web resource for structural classification of protein kinases and their inhibitors. Nucleic Acids Res 2022; 50:D654-D664. [PMID: 34643709 PMCID: PMC8728253 DOI: 10.1093/nar/gkab920] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
The active form of kinases is shared across different family members, as are several commonly observed inactive forms. We previously performed a clustering of the conformation of the activation loop of all protein kinase structures in the Protein Data Bank (PDB) into eight classes based on the dihedral angles that place the Phe side chain of the DFG motif at the N-terminus of the activation loop. Our clusters are strongly associated with the placement of the activation loop, the C-helix, and other structural elements of kinases. We present Kincore, a web resource providing access to our conformational assignments for kinase structures in the PDB. While other available databases provide conformational states or drug type but not both, KinCore includes the conformational state and the inhibitor type (Type 1, 1.5, 2, 3, allosteric) for each kinase chain. The user can query and browse the database using these attributes or determine the conformational labels of a kinase structure using the web server or a standalone program. The database and labeled structure files can be downloaded from the server. Kincore will help in understanding the conformational dynamics of these proteins and guide development of inhibitors targeting specific states. Kincore is available at http://dunbrack.fccc.edu/kincore.
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Affiliation(s)
- Vivek Modi
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19148, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19148, USA
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Kumar L, Vizgaudis W, Klein-Seetharaman J. Structure-based survey of ligand binding in the human insulin receptor. Br J Pharmacol 2021; 179:3512-3528. [PMID: 34907529 DOI: 10.1111/bph.15777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 11/27/2022] Open
Abstract
The insulin receptor is a membrane protein responsible for regulation of nutrient balance and therefore an attractive target in the treatment of diabetes and metabolic syndrome. Pharmacology of the insulin receptor involves two distinct mechanisms, (1) activation of the receptor by insulin mimetics that bind in the extracellular domain and (2) inhibition of the receptor tyrosine kinase enzymatic activity in the cytoplasmic domain. While a complete structural picture of the full-length receptor comprising the entire sequence covering extracellular, transmembrane, juxtamembrane and cytoplasmic domains is still elusive, recent progress through cryoelectron microscopy has made it possible to describe the initial insulin ligand binding events at atomistic detail. We utilize this opportunity to obtain structural insights into the pharmacology of the insulin receptor. To this end, we conducted a comprehensive docking study of known ligands to the new structures of the receptor. Through this approach, we provide an in-depth, structure-based review of human insulin receptor pharmacology in light of the new structures.
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Affiliation(s)
- Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, CO
| | | | - Judith Klein-Seetharaman
- Department of Chemistry, Colorado School of Mines, Golden, CO.,School of Molecular Sciences & College of Health Solutions, Arizona State University, Phoenix, AZ
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Bombyxin II Regulates Glucose Absorption and Glycogen Synthesis through the PI3K Signaling Pathway in HepG2 Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6639232. [PMID: 34708127 PMCID: PMC8545529 DOI: 10.1155/2021/6639232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 08/08/2021] [Accepted: 08/30/2021] [Indexed: 11/18/2022]
Abstract
Bombyxin, as an insulin-like insect hormone, was discovered in the silkmoth Bombyx mori. It can regulate the metabolism of trehalose and glycogen in Bombyx mori, but whether it has glucose absorption and glycogen synthesis effect on mammalian cells was not clear. BombyxinII (BbxII) and mutant BbxII (mBbxII) genes were cloned into pcDNA3.1(+) vector, respectively; then, gene vectors were transfected into 293FT cells using Lipofectamine 2000. Levels of mRNA and protein expression of BbxII and mBbxII were detected by PCR and Western blot in 293FT cells, respectively. Glucose consumption and glycogenesis were determined by glucose oxidase-peroxidase (GOD-POD) and periodic acid-Schiff (PAS) staining in HepG2 cells; the PI3K signaling pathway was inhibited with wortmannin S1952 in HepG2 cells. Result showed that BbxII and mBbxII genes were being successfully expressed in 293FT cells, respectively. The expression protein of BbxII gene is 10kd pre-bombyxinII, and yet, the expression protein of mBbxII gene is 4kd mature bombyxinII. Only the 4kd bombyxinII showed increased glucose uptake and glycogenesis in HepG2 cells, and the ability of increasing glucose uptake was equal to the human insulin (10 nM). PI3K-wortmannin S1952 inhibitor can decrease the glycogen synthesis induced by bombyxin II protein in HepG2 cells. In conclusion, mature bombyxin II may adjust glucose absorption and glycogen synthesis in HepG2 cells through the PI3K signaling pathway.
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González Wusener AE, González Á, Perez Collado ME, Maza MR, General IJ, Arregui CO. Protein tyrosine phosphatase 1B targets focal adhesion kinase and paxillin in cell-matrix adhesions. J Cell Sci 2021; 134:272564. [PMID: 34553765 DOI: 10.1242/jcs.258769] [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: 04/12/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B, also known as PTPN1) is an established regulator of cell-matrix adhesion and motility. However, the nature of substrate targets at adhesion sites remains to be validated. Here, we used bimolecular fluorescence complementation assays, in combination with a substrate trapping mutant of PTP1B, to directly examine whether relevant phosphotyrosines on paxillin and focal adhesion kinase (FAK, also known as PTK2) are substrates of the phosphatase in the context of cell-matrix adhesion sites. We found that the formation of catalytic complexes at cell-matrix adhesions requires intact tyrosine residues Y31 and Y118 on paxillin, and the localization of FAK at adhesion sites. Additionally, we found that PTP1B specifically targets Y925 on the focal adhesion targeting (FAT) domain of FAK at adhesion sites. Electrostatic analysis indicated that dephosphorylation of this residue promotes the closed conformation of the FAT 4-helix bundle and its interaction with paxillin at adhesion sites.
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Affiliation(s)
- Ana E González Wusener
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Ángela González
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - María E Perez Collado
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Melina R Maza
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Ignacio J General
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Carlos O Arregui
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
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Arif R, Ahmad S, Mustafa G, Mahrosh HS, Ali M, Tahir ul Qamar M, Dar HR. Molecular Docking and Simulation Studies of Antidiabetic Agents Devised from Hypoglycemic Polypeptide-P of Momordica charantia. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5561129. [PMID: 34589547 PMCID: PMC8476269 DOI: 10.1155/2021/5561129] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 12/15/2022]
Abstract
Diabetes mellitus termed as metabolic disorder is a collection of interlinked diseases and mainly body's inability to manage glucose level which leads to cardiovascular diseases, renal failure, neurological disorders, and many others. The drugs contemporarily used for diabetes have many inevitable side effects, and many of them have become less responsive to this multifactorial disorder. Momordica charantia commonly known as bitter gourd has many bioactive compounds with antidiabetic properties. The current study was designed to use computational methods to discover the best antidiabetic peptides devised from hypoglycemic polypeptide-P of M. charantia. The binding affinity and interaction patterns of peptides were evaluated against four receptor proteins (i.e., as agonists of insulin receptor and inhibitors of sodium-glucose cotransporter 1, dipeptidyl peptidase-IV, and glucose transporter 2) using molecular docking approach. A total of thirty-seven peptides were docked against these receptors. Out of which, top five peptides against each receptor were shortlisted based on their S-scores and binding affinities. Finally, the eight best ligands (i.e., LIVA, TSEP, EKAI, LKHA, EALF, VAEK, DFGAS, and EPGGGG) were selected as these ligands strictly followed Lipinski's rule of five and exhibited good ADMET profiling. One peptide EPGGGG showed activity towards insulin and SGLT1 receptor proteins. The top complex for both these targets was subjected to 50 ns of molecular dynamics simulations and MM-GBSA binding energy test that concluded both complexes as highly stable, and the intermolecular interactions were dominated by van der Waals and electrostatic energies. Overall, the selected ligands strongly fulfilled the drug-like evaluation criterion and proved to have good antidiabetic properties.
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Affiliation(s)
- Rawaba Arif
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Hafiza Salaha Mahrosh
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Akhuwat Faisalabad Institute of Research Science and Technology, Faisalabad 38000, Pakistan
| | | | - Hafiza Rabia Dar
- Department of Biochemistry, University of Agriculture, Faisalabad 38040, Pakistan
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Abstract
The molecular mechanisms of cellular insulin action have been the focus of much investigation since the discovery of the hormone 100 years ago. Insulin action is impaired in metabolic syndrome, a condition known as insulin resistance. The actions of the hormone are initiated by binding to its receptor on the surface of target cells. The receptor is an α2β2 heterodimer that binds to insulin with high affinity, resulting in the activation of its tyrosine kinase activity. Once activated, the receptor can phosphorylate a number of intracellular substrates that initiate discrete signaling pathways. The tyrosine phosphorylation of some substrates activates phosphatidylinositol-3-kinase (PI3K), which produces polyphosphoinositides that interact with protein kinases, leading to activation of the kinase Akt. Phosphorylation of Shc leads to activation of the Ras/MAP kinase pathway. Phosphorylation of SH2B2 and of Cbl initiates activation of G proteins such as TC10. Activation of Akt and other protein kinases produces phosphorylation of a variety of substrates, including transcription factors, GTPase-activating proteins, and other kinases that control key metabolic events. Among the cellular processes controlled by insulin are vesicle trafficking, activities of metabolic enzymes, transcriptional factors, and degradation of insulin itself. Together these complex processes are coordinated to ensure glucose homeostasis.
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Yamamoto R, Palmer M, Koski H, Curtis-Joseph N, Tatar M. Aging modulated by the Drosophila insulin receptor through distinct structure-defined mechanisms. Genetics 2021; 217:6064149. [PMID: 33724413 PMCID: PMC8045697 DOI: 10.1093/genetics/iyaa037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations of the Drosophila melanogaster insulin/IGF signaling system slow aging, while also affecting growth and reproduction. To understand this pleiotropy, we produced an allelic series of single codon substitutions in the Drosophila insulin receptor, InR. We generated InR substitutions using homologous recombination and related each to emerging models of receptor tyrosine kinase structure and function. Three mutations when combined as trans-heterozygotes extended lifespan while retarding growth and fecundity. These genotypes reduced insulin-stimulated Akt phosphorylation, suggesting they impede kinase catalytic domain function. Among these genotypes, longevity was negatively correlated with egg production, consistent with life-history trade-off theory. In contrast, one mutation (InR353) was located in the kinase insert domain, a poorly characterized element found in all receptor tyrosine kinases. Remarkably, wild-type heterozygotes with InR353 robustly extended lifespan without affecting growth or reproduction and retained capacity to fully phosphorylate Akt. The Drosophila insulin receptor kinase insert domain contains a previously unrecognized SH2 binding motif. We propose the kinase insert domain interacts with SH2-associated adapter proteins to affect aging through mechanisms that retain insulin sensitivity and are independent of reproduction.
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Affiliation(s)
- Rochele Yamamoto
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Michael Palmer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Helen Koski
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Noelle Curtis-Joseph
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Marc Tatar
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
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Expression of glucose and magnesium transport-associated genes in whole blood RNA of lactating ewes supplemented with magnesium. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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45
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Multiple endocrine neoplasia type 2: A reveiw. Semin Cancer Biol 2021; 79:163-179. [PMID: 33812987 DOI: 10.1016/j.semcancer.2021.03.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 03/13/2021] [Accepted: 03/27/2021] [Indexed: 12/16/2022]
Abstract
Multiple endocrine neoplasias are rare hereditary syndromes some of them with malignant potential. Multiple endocrine neoplasia type 2 (MEN 2) is an autosomal dominant hereditary cancer syndrome due to germline variants in the REarranged during Transfection (RET) proto-oncogene. There are two distinct clinical entities: MEN 2A and MEN 2B. MEN 2A is associated with medullary thyroid carcinoma (MTC), phaeochromocytoma, primary hyperparathyroidism, cutaneous lichen amyloidosis and Hirschprung's disease and MEN 2B with MTC, phaeochromocytoma, ganglioneuromatosis of the aerodigestive tract, musculoskeletal and ophthalmologic abnormalities. Germline RET variants causing MEN 2 result in gain-of-function; since the discovery of the genetic variants a thorough search for genotype-phenotype associations began in order to understand the high variability both between families and within family members. These studies have successfully led to improved risk classification of prognosis in relation to the genotype, thus improving the management of the patients by thorough genetic counseling. The present review summarizes the recent developments in the knowledge of these hereditary syndromes as well as the impact on clinical management, including genetic counseling, of both individual patients and families. It furthermore points to future directions of research for better clarification of timing of treatments of the various manifestations of the syndromes in order to improve survival and morbidity in these patients.
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Brain Insulin Resistance: Focus on Insulin Receptor-Mitochondria Interactions. Life (Basel) 2021; 11:life11030262. [PMID: 33810179 PMCID: PMC8005009 DOI: 10.3390/life11030262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Current hypotheses implicate insulin resistance of the brain as a pathogenic factor in the development of Alzheimer’s disease and other dementias, Parkinson’s disease, type 2 diabetes, obesity, major depression, and traumatic brain injury. A variety of genetic, developmental, and metabolic abnormalities that lead to disturbances in the insulin receptor signal transduction may underlie insulin resistance. Insulin receptor substrate proteins are generally considered to be the node in the insulin signaling system that is critically involved in the development of insulin insensitivity during metabolic stress, hyperinsulinemia, and inflammation. Emerging evidence suggests that lower activation of the insulin receptor (IR) is another common, while less discussed, mechanism of insulin resistance in the brain. This review aims to discuss causes behind the diminished activation of IR in neurons, with a focus on the functional relationship between mitochondria and IR during early insulin signaling and the related roles of oxidative stress, mitochondrial hypometabolism, and glutamate excitotoxicity in the development of IR insensitivity to insulin.
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Verdecchia F, Akcan N, Dastamani A, Morgan K, Semple RK, Shah P. Unusual Glycemic Presentations in a Child with a Novel Heterozygous Intragenic INSR Deletion. Horm Res Paediatr 2021; 93:396-401. [PMID: 33040071 PMCID: PMC7949216 DOI: 10.1159/000510462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Mutations of the insulin receptor (INSR) gene lead to a wide spectrum of inherited insulin resistance (IR) syndromes. Among these, type A-IR, usually caused by dominant negative INSR mutations, generally presents peri-pubertally in girls. CASE A 2.8-year-old girl was referred due to recurrent postprandial and fasting hypoglycemia. She had been born at full-term with birth weight 1.89 kg, and had developed transient neonatal diabetes. Examination showed satisfactory growth, reduced adipose tissue, acanthosis nigricans, and isolated thelarche. After 12 h of fasting, she developed hypoglycemia (glucose 2.8 mmol/L), with inappropriately raised plasma insulin concentration of 5.4 mU/L and suppressed fatty acids and ketone bodies. Oral glucose tolerance testing showed severely increased plasma insulin concentration (>300 mU/L) with hypoglycemia (glucose 1.6 mmol/L) at 2.5 h. She was initially managed on dietary modifications, cornstarch, and then trialed on acarbose for postprandial hyperinsulinemic hypoglycemia (PPHH) with some response. However, she was noted to have increased frequency of hyperglycemia after a couple of years of treatment. She was then switched to metformin and continued to have dietary carbohydrate modification including cornstarch that improved fasting tolerance, hyperglycemia, and postprandial hypoglycemia. Genetic testing identified heterozygous deletion of the last exon of the INSR gene, exon 22. CONCLUSION We present a case of type A-IR, caused by a novel INSR deletion, presenting unusually early with transient neonatal diabetes, followed by episodes of hypoglycemia and hyperglycemia during later childhood. Early life presentations, including neonatal diabetes and PPHH, should lead to consideration of type A-IR.
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Affiliation(s)
- Federica Verdecchia
- Endocrinology Department, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Nese Akcan
- Endocrinology Department, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Antonia Dastamani
- Endocrinology Department, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Kate Morgan
- Endocrinology Department, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Robert K. Semple
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom,**Robert Semple, Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, 47 Little France Crescent, Edinburgh EH16 4TJ (UK),
| | - Pratik Shah
- Endocrinology Department, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom, .,Genetics and Epigenetics in Health and Disease Section, Genetics and Genomics Medicine Program, UCL GOS Institute of Child Health, London, United Kingdom,
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Sabbah DA, Hajjo R, Sweidan K. Review on Epidermal Growth Factor Receptor (EGFR) Structure, Signaling Pathways, Interactions, and Recent Updates of EGFR Inhibitors. Curr Top Med Chem 2021; 20:815-834. [PMID: 32124699 DOI: 10.2174/1568026620666200303123102] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
Abstract
The epidermal growth factor receptor (EGFR) belongs to the ERBB family of tyrosine kinase receptors. EGFR signaling cascade is a key regulator in cell proliferation, differentiation, division, survival, and cancer development. In this review, the EGFR structure and its mutations, signaling pathway, ligand binding and EGFR dimerization, EGF/EGFR interaction, and the progress in the development of EGFR inhibitors have been explored.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Kamal Sweidan
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan
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49
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Ditsiou A, Cilibrasi C, Simigdala N, Papakyriakou A, Milton-Harris L, Vella V, Nettleship JE, Lo JH, Soni S, Smbatyan G, Ntavelou P, Gagliano T, Iachini MC, Khurshid S, Simon T, Zhou L, Hassell-Hart S, Carter P, Pearl LH, Owen RL, Owens RJ, Roe SM, Chayen NE, Lenz HJ, Spencer J, Prodromou C, Klinakis A, Stebbing J, Giamas G. The structure-function relationship of oncogenic LMTK3. SCIENCE ADVANCES 2020; 6:6/46/eabc3099. [PMID: 33188023 PMCID: PMC7673765 DOI: 10.1126/sciadv.abc3099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/30/2020] [Indexed: 05/10/2023]
Abstract
Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therapy.
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Affiliation(s)
- Angeliki Ditsiou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Chiara Cilibrasi
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Nikiana Simigdala
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos," 15341 Athens, Greece
| | - Leanne Milton-Harris
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Viviana Vella
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Joanne E Nettleship
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Jae Ho Lo
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goar Smbatyan
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Panagiota Ntavelou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Teresa Gagliano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Maria Chiara Iachini
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Sahir Khurshid
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Thomas Simon
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Storm Hassell-Hart
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Philip Carter
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Raymond J Owens
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, UK
| | - S Mark Roe
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Naomi E Chayen
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Chrisostomos Prodromou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Apostolos Klinakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Justin Stebbing
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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Acebrón I, Righetto RD, Schoenherr C, de Buhr S, Redondo P, Culley J, Rodríguez CF, Daday C, Biyani N, Llorca O, Byron A, Chami M, Gräter F, Boskovic J, Frame MC, Stahlberg H, Lietha D. Structural basis of Focal Adhesion Kinase activation on lipid membranes. EMBO J 2020; 39:e104743. [PMID: 32779739 PMCID: PMC7527928 DOI: 10.15252/embj.2020104743] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Focal adhesion kinase (FAK) is a key component of the membrane proximal signaling layer in focal adhesion complexes, regulating important cellular processes, including cell migration, proliferation, and survival. In the cytosol, FAK adopts an autoinhibited state but is activated upon recruitment into focal adhesions, yet how this occurs or what induces structural changes is unknown. Here, we employ cryo-electron microscopy to reveal how FAK associates with lipid membranes and how membrane interactions unlock FAK autoinhibition to promote activation. Intriguingly, initial binding of FAK to the membrane causes steric clashes that release the kinase domain from autoinhibition, allowing it to undergo a large conformational change and interact itself with the membrane in an orientation that places the active site toward the membrane. In this conformation, the autophosphorylation site is exposed and multiple interfaces align to promote FAK oligomerization on the membrane. We show that interfaces responsible for initial dimerization and membrane attachment are essential for FAK autophosphorylation and resulting cellular activity including cancer cell invasion, while stable FAK oligomerization appears to be needed for optimal cancer cell proliferation in an anchorage-independent manner. Together, our data provide structural details of a key membrane bound state of FAK that is primed for efficient autophosphorylation and activation, hence revealing the critical event in integrin mediated FAK activation and signaling at focal adhesions.
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Affiliation(s)
- Iván Acebrón
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Christina Schoenherr
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Svenja de Buhr
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Pilar Redondo
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Jayne Culley
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Carlos F Rodríguez
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Csaba Daday
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Nikhil Biyani
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Oscar Llorca
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Adam Byron
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Frauke Gräter
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Jasminka Boskovic
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Margaret C Frame
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Daniel Lietha
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
- Centro de Investigaciones Biológicas Margarita SalasSpanish National Research Council (CSIC)MadridSpain
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