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Salaria P, Subrahmanyeswara Rao NN, Dhameliya TM, Amarendar Reddy M. In silico investigation of potential phytoconstituents against ligand- and voltage-gated ion channels as antiepileptic agents. 3 Biotech 2024; 14:99. [PMID: 38456083 PMCID: PMC10914661 DOI: 10.1007/s13205-024-03948-1] [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: 10/18/2023] [Accepted: 01/28/2024] [Indexed: 03/09/2024] Open
Abstract
The most promising anticonvulsant phytocompounds were explored in this work using docking, molecular dynamic (MD) simulation, and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) approaches. A total of 70 phytochemicals were screened against α-amino-3-hydroxyl-5-methyl-4-isoxazole propionic acid (AMPA), N-methyl-d-aspartate (NMDA), voltage-gated sodium ion channels (VGSC), and carbonic anhydrase enzyme II (CA II) receptors, and the docking results were compared to the reference drug phenytoin. Amentoflavone displayed the highest affinity for AMPA and VGSC receptors, with docking scores of - 10.4 and - 10.1 kcal/mol, respectively. Oliganthin H-NMDA and epigallocatechin-3-gallate-CA II complexes showed docking scores of - 10.9 and - 6.9 kcal/mol, respectively. All four complexes depicted a high dock score compared to the phenytoin complex at the binding site of the corresponding proteins. The MD simulation investigated the stabilities and favorable conformation of apoproteins and ligand/reference-bound complexes. The results revealed that proteins AMPA, VGSC, and CA II were more efficiently stabilized by lead phytochemicals than phenytoin binding. Additionally, principal component analysis and MM-PBSA results suggested that these lead phytocompounds have good compactness and strong binding free energy. Further, physicochemical and pharmacokinetic studies revealed that these final lead phytochemicals would be suitable for oral intake, have sufficient intestinal permeability, and have the ability to cross the blood-brain barrier (BBB). Comprehensively, this study predicted amentoflavone as the best lead phytochemical out of the 70 anticonvulsant phytocompounds that can be used to treat epilepsy. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03948-1.
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Affiliation(s)
- Punam Salaria
- Department of Chemistry, School of Sciences, National Institute of Technology Andhra Pradesh, Tadepalligudem, Andhra Pradesh 534101 India
| | - N N Subrahmanyeswara Rao
- Department of Chemical Engineering, Gayatri Vidya Parishad College of Engineering (Autonomous), Visakhapatnam, Andhra Pradesh India
| | - Tejas M Dhameliya
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - M Amarendar Reddy
- Department of Chemistry, School of Sciences, National Institute of Technology Andhra Pradesh, Tadepalligudem, Andhra Pradesh 534101 India
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2
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Kim J, Chun Y, Ramirez CB, Hoffner LA, Jung S, Jang KH, Rubtsova VI, Jang C, Lee G. MAPK13 stabilization via m 6A mRNA modification limits anticancer efficacy of rapamycin. J Biol Chem 2023; 299:105175. [PMID: 37599001 PMCID: PMC10511813 DOI: 10.1016/j.jbc.2023.105175] [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: 01/31/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023] Open
Abstract
N6-adenosine methylation (m6A) is the most abundant mRNA modification that controls gene expression through diverse mechanisms. Accordingly, m6A-dependent regulation of oncogenes and tumor suppressors contributes to tumor development. However, the role of m6A-mediated gene regulation upon drug treatment or resistance is poorly understood. Here, we report that m6A modification of mitogen-activated protein kinase 13 (MAPK13) mRNA determines the sensitivity of cancer cells to the mechanistic target of rapamycin complex 1 (mTORC1)-targeting agent rapamycin. mTORC1 induces m6A modification of MAPK13 mRNA at its 3' untranslated region through the methyltransferase-like 3 (METTL3)-METTL14-Wilms' tumor 1-associating protein(WTAP) methyltransferase complex, facilitating its mRNA degradation via an m6A reader protein YTH domain family protein 2. Rapamycin blunts this process and stabilizes MAPK13. On the other hand, genetic or pharmacological inhibition of MAPK13 enhances rapamycin's anticancer effects, which suggests that MAPK13 confers a progrowth signal upon rapamycin treatment, thereby limiting rapamycin efficacy. Together, our data indicate that rapamycin-mediated MAPK13 mRNA stabilization underlies drug resistance, and it should be considered as a promising therapeutic target to sensitize cancer cells to rapamycin.
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Affiliation(s)
- Joohwan Kim
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Yujin Chun
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Cuauhtemoc B Ramirez
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Lauren A Hoffner
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Sunhee Jung
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Ki-Hong Jang
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Varvara I Rubtsova
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; School of Biological Sciences, University of California Irvine, Irvine, California, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA.
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Wydra VR, Ditzinger RB, Seidler NJ, Hacker FW, Laufer SA. A patent review of MAPK inhibitors (2018 - present). Expert Opin Ther Pat 2023; 33:421-444. [PMID: 37501497 DOI: 10.1080/13543776.2023.2242584] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION The mitogen-activated protein kinase (MAPK) family consist of p38 MAP kinases, c-Jun N-terminal kinases (JNKs) and extracellular signal-regulated kinases (ERKs). They are involved in a multitude of diseases, including inflammatory, autoimmune, neurodegenerative, and metabolic diseases as well as cancer. In recent years, further developments in the field of MAPK-inhibitors have been reported, including an isoform or downstream target selective inhibition of MAPKs as well as target protein degradation approaches. AREAS COVERED This review summarizes newly patented MAPK-inhibitors that were claimed between 2018 and early 2023. Presented are the patents as well as their corresponding publications, the storyline of development, and clinical trials involving these compounds. This article elaborates a total of 27 patents, which were identified using established search engines. EXPERT OPINION Although industrial research on MAPK-inhibitors has been ongoing for more than 20 years, novel clinical trials of MAPK-inhibitors as potential drug candidates are still being conducted in the period under review. Recently reported inhibitors show an excellent selectivity profile and are even achieving selectivity between closely related isoforms. This progression offers the possibility to eliminate unwanted side effects and may finally lead to the approval of the first MAPK-inhibitor.
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Affiliation(s)
- Valentin R Wydra
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universit't Tübingen, Tübingen, Germany
| | - Raphael B Ditzinger
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universit't Tübingen, Tübingen, Germany
| | - Nico J Seidler
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universit't Tübingen, Tübingen, Germany
| | - Frederik W Hacker
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universit't Tübingen, Tübingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universit't Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided & Functionally Instructed Tumor Therapies", Eberhard Karls Universität Tübingen, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (Tücad2), Tübingen, Germany
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Malekinejad Z, Baghbanzadeh A, Nakhlband A, Baradaran B, Jafari S, Bagheri Y, Raei F, Montazersaheb S, Farahzadi R. Recent clinical findings on the role of kinase inhibitors in COVID-19 management. Life Sci 2022; 306:120809. [PMID: 35841979 PMCID: PMC9278000 DOI: 10.1016/j.lfs.2022.120809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
The highly pathogenic, novel coronavirus disease (COVID-19) outbreak has emerged as a once-in-a-century pandemic with poor consequences, urgently calling for new therapeutics, cures, and supportive interventions. It has already affected over 250 million people worldwide; thereby, there is a need for novel therapies to alleviate the related complications. There is a paradigm shift in developing drugs and clinical practices to combat COVID-19. Several clinical trials have been performed or are testing diverse pharmacological interventions to alleviate viral load and complications such as cytokine release storm (CRS). Kinase-inhibitors have appeared as potential antiviral agents for COVID-19 patients due to their efficacy against CRS. Combination of kinase inhibitors with other therapies can achieve more efficacy against COVID-19. Based on the pre-clinical trials, kinase inhibitors such as Janus kinase-signal transducer and activator of transcription (JAK/STAT) inhibitors, Brutton's tyrosin kinase (BTK) inhibitors, p38 mitogen-activated protein kinases (p38 MAPK) inhibitors, Glycogen synthase kinase 3 (GSK-3) inhibitors can be a promising strategy against COVID-19. Kinase inhibitors possess crucial pharmacological properties for a successful re-purposing in terms of dual anti-inflammatory and anti-viral effects. This review will address the current clinical evidence and the newest discovery regarding the application of kinase inhibitors in COVID-19. An outlook on ongoing clinical trials (clinicaltrials.gov) and unpublished data is also presented here. Besides, Kinase inhibitors' function on COVID-19-mediated CRS is discussed.
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Affiliation(s)
- Zahra Malekinejad
- Faculty of Veterinary Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ailar Nakhlband
- Research Center of Psychiatry and Behavioral Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sevda Jafari
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasin Bagheri
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faezeh Raei
- Departement of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Raheleh Farahzadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Recent Advances in PROTACs for Drug Targeted Protein Research. Int J Mol Sci 2022; 23:ijms231810328. [PMID: 36142231 PMCID: PMC9499226 DOI: 10.3390/ijms231810328] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 01/30/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is a heterobifunctional molecule. Typically, PROTAC consists of two terminals which are the ligand of the protein of interest (POI) and the specific ligand of E3 ubiquitin ligase, respectively, via a suitable linker. PROTAC degradation of the target protein is performed through the ubiquitin–proteasome system (UPS). The general process is that PROTAC binds to the target protein and E3 ligase to form a ternary complex and label the target protein with ubiquitination. The ubiquitinated protein is recognized and degraded by the proteasome in the cell. At present, PROTAC, as a new type of drug, has been developed to degrade a variety of cancer target proteins and other disease target proteins, and has shown good curative effects on a variety of diseases. For example, PROTACs targeting AR, BR, BTK, Tau, IRAK4, and other proteins have shown unprecedented clinical efficacy in cancers, neurodegenerative diseases, inflammations, and other fields. Recently, PROTAC has entered a phase of rapid development, opening a new field for biomedical research and development. This paper reviews the various fields of targeted protein degradation by PROTAC in recent years and summarizes and prospects the hot targets and indications of PROTAC.
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Liu R, Verma N, Henderson JA, Zhan S, Shen J. Profiling MAP kinase cysteines for targeted covalent inhibitor design. RSC Med Chem 2022; 13:54-63. [PMID: 35224496 PMCID: PMC8792824 DOI: 10.1039/d1md00277e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/28/2021] [Indexed: 07/20/2023] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important therapeutic targets, and yet no inhibitors have advanced to the market. Here we applied the GPU-accelerated continuous constant pH molecular dynamics (CpHMD) to calculate the pK a's and profile the cysteine reactivities of all 14 MAPKs for assisting the targeted covalent inhibitor design. The simulations not only recapitulated but also rationalized the reactive cysteines in the front pocket of JNK1/2/3 and the extended front pocket of p38α. Interestingly, the DFG - 1 cysteine in the DFG-in conformation of ERK1/ERK2 was found somewhat reactive or unreactive; however, simulations of MKK7 showed that switching to the DFG-out conformation makes the DFG - 1 cysteine reactive, suggesting the advantage of type II covalent inhibitors. Additionally, the simulations prospectively predicted several druggable cysteine and lysine sites, including the αH head cysteine in JNK1/3 and DFG + 6 cysteine in JNK2, corroborating the chemical proteomic screening data. Given the low cost and the ability to offer physics-based rationales, we envision CpHMD simulations to complement the chemo-proteomic platform for systematic profiling cysteine reactivities for targeted covalent drug discovery.
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Affiliation(s)
- Ruibin Liu
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Neha Verma
- University of Maryland School of Pharmacy Baltimore MD USA
| | | | - Shaoqi Zhan
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Jana Shen
- University of Maryland School of Pharmacy Baltimore MD USA
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The p38 MAPK Components and Modulators as Biomarkers and Molecular Targets in Cancer. Int J Mol Sci 2021; 23:ijms23010370. [PMID: 35008796 PMCID: PMC8745478 DOI: 10.3390/ijms23010370] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) family is an important bridge in the transduction of extracellular and intracellular signals in different responses at the cellular level. Within this MAPK family, the p38 kinases can be found altered in various diseases, including cancer, where these kinases play a fundamental role, sometimes with antagonistic mechanisms of action, depending on several factors. In fact, this family has an immense number of functionalities, many of them yet to be discovered in terms of regulation and action in different types of cancer, being directly involved in the response to cancer therapies. To date, three main groups of MAPKs have been identified in mammals: the extracellular signal-regulated kinases (ERK), Jun N-terminal kinase (JNK), and the different isoforms of p38 (α, β, γ, δ). In this review, we highlight the mechanism of action of these kinases, taking into account their extensive regulation at the cellular level through various modifications and modulations, including a wide variety of microRNAs. We also analyze the importance of the different isoforms expressed in the different tissues and their possible role as biomarkers and molecular targets. In addition, we include the latest preclinical and clinical trials with different p38-related drugs that are ongoing with hopeful expectations in the present/future of developing precision medicine in cancer.
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8
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Chen J, Wang W, Sun H, Pang L, Bao H. Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies. Comput Biol Med 2021; 134:104485. [PMID: 33993013 DOI: 10.1016/j.compbiomed.2021.104485] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
The p38α MAP Kinase has been an important target of drug design for treatment of inflammatory diseases and cancers. This work applies multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics generalized Born surface area (MM-GBSA) method to probe the binding mechanism of inhibitors L51, R24 and 1AU to p38α. Dynamics analyses show that inhibitor bindings exert significant effect on conformational changes of the active helix α2 and the conserved DFG loop. The rank of binding free energies calculated with MM-GBSA not only agrees well with that determined by the experimental IC50 values but also suggests that mutual compensation between the enthalpy and entropy changes can improve binding of inhibitors to p38α. The analyses of free energy landscapes indicate that the L51, R24 and 1AU bound p38α display a DFG-out conformation. The residue-based free energy decomposition method is used to evaluate contributions of separate residues to the inhibitor-p38α binding and the results imply that residues V30, V38, L74, L75, I84, T106, H107, L108, M109, L167, F169 and D168 can be utilized as efficient targets of potent inhibitors toward p38α.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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9
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Anton DB, Ducati RG, Timmers LFSM, Laufer S, Goettert MI. A Special View of What Was Almost Forgotten: p38δ MAPK. Cancers (Basel) 2021; 13:2077. [PMID: 33923030 PMCID: PMC8123357 DOI: 10.3390/cancers13092077] [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: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
The p38δ mitogen-activated protein kinase is an important signal transduction enzyme. p38δ has recently emerged as a drug target due to its tissue-specific expression patterns and its critical roles in regulation of cellular processes related to cancer and inflammatory diseases, such as cell proliferation, cell migration, apoptosis, and inflammatory responses. However, potent and specific p38δ inhibitors have not been defined so far. Moreover, in cancer disease, p38δ appears to act as a tumor suppressor or tumor promoter according to cancer and cell type studied. In this review, we outline the current understanding of p38δ roles in each cancer type, to define whether it is possible to delineate new cancer therapies based on small-molecule p38δ inhibitors. We also highlight recent advances made in the design of molecules with potential to inhibit p38 isoforms and discuss structural approaches to guide the search for p38δ inhibitors.
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Affiliation(s)
- Débora Bublitz Anton
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil; (D.B.A.); (R.G.D.); (L.F.S.M.T.)
| | - Rodrigo Gay Ducati
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil; (D.B.A.); (R.G.D.); (L.F.S.M.T.)
| | - Luís Fernando Saraiva Macedo Timmers
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil; (D.B.A.); (R.G.D.); (L.F.S.M.T.)
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Faculty of Sciences, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Márcia Inês Goettert
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil; (D.B.A.); (R.G.D.); (L.F.S.M.T.)
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul CEP 95914-014, Brazil
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Liu Y, Chang Y, Cai Y. circTNFRSF21, a newly identified circular RNA promotes endometrial carcinoma pathogenesis through regulating miR-1227-MAPK13/ATF2 axis. Aging (Albany NY) 2020; 12:6774-6792. [PMID: 32299063 PMCID: PMC7202486 DOI: 10.18632/aging.103037] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/20/2020] [Indexed: 12/22/2022]
Abstract
Background: Circular RNA is a type of non-coding RNA with great potential in regulating gene expression and associated with disease progression. However, the role of circular RNA in endometrial carcinoma (EC) remains largely unknown. Results: In this study, we found that circTNFRSF21 was highly expressed in EC cells and tumor tissues. In vitro and in vivo results showed that circTNFRSF21 was linked to increased EC cell growth and EC xenografts formation in nude mice. Mechanically, we showed that circTNFRSF21 acts as a sponge of miR-1227 in EC cells to rescue MAPK13/ATF2 signaling pathway activity. Conclusions: Our studies suggested that in the EC, circTNFRSF21 promotes EC formation through downregulating miR-1227 expression and activating MAPK13/ATF2 signaling pathway. These findings provide strong evidence that circTNFRSF21-miR-1227-MAPK13/ATF2 axis is a promising target for EC treatment. Methods: qRT-PCR was used to detect circTNFRSF21expression in EC patients and EC cell lines. Cell growth, cell colony formation, cell apoptosis, cell cycle progression, and in vivo tumor formation assays were used to evaluate the roles of circTNFRSF21 in EC. Western blot, luciferase assay, RNA pull-down, siRNA knockdown, and CRISPR gene knock out assays were applied to study the mechanisms through which circTNFRSF21 regulates EC formation.
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Affiliation(s)
- Yun Liu
- Department of Obstetrics and Gynecology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yue Chang
- Department of Obstetrics and Gynecology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yixuan Cai
- Department of Obstetrics and Gynecology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
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11
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Smith BE, Wang SL, Jaime-Figueroa S, Harbin A, Wang J, Hamman BD, Crews CM. Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase. Nat Commun 2019; 10:131. [PMID: 30631068 PMCID: PMC6328587 DOI: 10.1038/s41467-018-08027-7] [Citation(s) in RCA: 298] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/07/2018] [Indexed: 01/10/2023] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) are hetero-bifunctional molecules that recruit an E3 ubiquitin ligase to a given substrate protein resulting in its targeted degradation. Many potent PROTACs with specificity for dissimilar targets have been developed; however, the factors governing degradation selectivity within closely-related protein families remain elusive. Here, we generate isoform-selective PROTACs for the p38 MAPK family using a single warhead (foretinib) and recruited E3 ligase (von Hippel-Lindau). Based on their distinct linker attachments and lengths, these two PROTACs differentially recruit VHL, resulting in degradation of p38α or p38δ. We characterize the role of ternary complex formation in driving selectivity, showing that it is necessary, but insufficient, for PROTAC-induced substrate ubiquitination. Lastly, we explore the p38δ:PROTAC:VHL complex to explain the different selectivity profiles of these PROTACs. Our work attributes the selective degradation of two closely-related proteins using the same warhead and E3 ligase to heretofore underappreciated aspects of the ternary complex model.
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Affiliation(s)
- Blake E Smith
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Stephen L Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Alicia Harbin
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Jing Wang
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Brian D Hamman
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, New Haven, CT, 06511, USA. .,Department of Pharmacology, Yale University, New Haven, CT, 06511, USA.
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12
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Wang C, Steiner U, Sepe A. Synchrotron Big Data Science. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802291. [PMID: 30222245 DOI: 10.1002/smll.201802291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/27/2018] [Indexed: 06/08/2023]
Abstract
The rapid development of synchrotrons has massively increased the speed at which experiments can be performed, while new techniques have increased the amount of raw data collected during each experiment. While this has created enormous new opportunities, it has also created tremendous challenges for national facilities and users. With the huge increase in data volume, the manual analysis of data is no longer possible. As a result, only a fraction of the data collected during the time- and money-expensive synchrotron beam-time is analyzed and used to deliver new science. Additionally, the lack of an appropriate data analysis environment limits the realization of experiments that generate a large amount of data in a very short period of time. The current lack of automated data analysis pipelines prevents the fine-tuning of beam-time experiments, further reducing their potential usage. These effects, collectively known as the "data deluge," affect synchrotrons in several different ways including fast data collection, available local storage, data management systems, and curation of the data. This review highlights the Big Data strategies adopted nowadays at synchrotrons, documenting this novel and promising hybridization between science and technology, which promise a dramatic increase in the number of scientific discoveries.
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Affiliation(s)
- Chunpeng Wang
- Big Data Science Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Ullrich Steiner
- Adolphe Merkle Institute, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Alessandro Sepe
- Big Data Science Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201204, Shanghai, China
- Adolphe Merkle Institute, University of Fribourg, CH-1700, Fribourg, Switzerland
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13
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Cuenda A, Sanz-Ezquerro JJ. p38γ and p38δ: From Spectators to Key Physiological Players. Trends Biochem Sci 2017; 42:431-442. [PMID: 28473179 DOI: 10.1016/j.tibs.2017.02.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/14/2017] [Accepted: 02/22/2017] [Indexed: 12/20/2022]
Abstract
Although the physiological roles of p38γ and p38δ signalling pathways are largely unknown, new genetic and pharmacological tools are providing groundbreaking information on the function of these two stress-activated protein kinases. Recent studies show the importance of p38γ and p38δ in the regulation of processes as diverse as cytokine production, protein synthesis, exocytosis, cell migration, gene expression, and neuron activity, which have an acute impact on the development of pathologies related to inflammation, diabetes, neurodegeneration, and cancer. These recent breakthroughs are resolving some of the questions that have long been asked regarding the function of p38γ and p38δ in biology and pathology.
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Affiliation(s)
- Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Juan José Sanz-Ezquerro
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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14
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Abbott JA, Livingston NM, Egri SB, Guth E, Francklyn CS. Characterization of aminoacyl-tRNA synthetase stability and substrate interaction by differential scanning fluorimetry. Methods 2016; 113:64-71. [PMID: 27794454 DOI: 10.1016/j.ymeth.2016.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 11/30/2022] Open
Abstract
Differential scanning fluorimetry (DSF) is a fluorescence-based assay to evaluate protein stability by determining protein melting temperatures. Here, we describe the application of DSF to investigate aminoacyl-tRNA synthetase (AARS) stability and interaction with ligands. Employing three bacterial AARS enzymes as model systems, methods are presented here for the use of DSF to measure the apparent temperatures at which AARSs undergo melting transitions, and the effect of AARS substrates and inhibitors. One important observation is that the extent of temperature stability realized by an AARS in response to a particular bound ligand cannot be predicted a priori. The DSF method thus serves as a rapid and highly quantitative approach to measure AARS stability, and the ability of ligands to influence the temperature at which unfolding transitions occur.
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Affiliation(s)
- Jamie A Abbott
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA.
| | - Nathan M Livingston
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
| | - Shawn B Egri
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
| | - Ethan Guth
- Chemistry & Biochemistry Department, Norwich University, Northfield, VT 05663, USA
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