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Sobhi Amjad Z, Shojaeian A, Sadri Nahand J, Bayat M, Taghizadieh M, Rostamian M, Babaei F, Moghoofei M. Oncoviruses: Induction of cancer development and metastasis by increasing anoikis resistance. Heliyon 2023; 9:e22598. [PMID: 38144298 PMCID: PMC10746446 DOI: 10.1016/j.heliyon.2023.e22598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
The phenomenon of cell death is a vital aspect in the regulation of aberrant cells such as cancer cells. Anoikis is a kind of cell death that occurs when cells get separated from the extracellular matrix. Some cancer cells can inhibit anoikis in order to progress metastasis. One of the key variables that might be implicated in anoikis resistance (AR) is viral infections. The most important viruses involved in this process are Epstein-Barr virus, human papillomavirus, hepatitis B virus, human herpes virus 8, human T-cell lymphotropic virus type 1, and hepatitis C virus. A better understanding of how carcinogenic viruses suppress anoikis might be helpful in developing an effective treatment for virus-associated cancers. In the current study, we review the role of the mentioned viruses and their gene products in anoikis inhibition.
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Affiliation(s)
- Zahra Sobhi Amjad
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mobina Bayat
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mosayeb Rostamian
- Nosocomial Infections Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farhad Babaei
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Infectious Diseases Research Center, Health Research Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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2
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Pauli TM, Julius A, Costa F, Eschrig S, Moosmüller J, Fischer L, Schanzenbach C, Schmidt FC, Ortner M, Langosch D. Interaction of Substrates with γ-Secretase at the Level of Individual Transmembrane Helices-A Methodological Approach. Int J Mol Sci 2023; 24:14396. [PMID: 37762696 PMCID: PMC10531681 DOI: 10.3390/ijms241814396] [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: 07/27/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Intramembrane proteases, such as γ secretase, typically recruit multiple substrates from an excess of single-span membrane proteins. It is currently unclear to which extent substrate recognition depends on specific interactions of their transmembrane domains (TMDs) with TMDs of a protease. Here, we investigated a large number of potential pairwise interactions between TMDs of γ secretase and a diverse set of its substrates using two different configurations of BLaTM, a genetic reporter system. Our results reveal significant interactions between TMD2 of presenilin, the enzymatic subunit of γ secretase, and the TMD of the amyloid precursor protein, as well as of several other substrates. Presenilin TMD2 is a prime candidate for substrate recruitment, as has been shown from previous studies. In addition, the amyloid precursor protein TMD enters interactions with presenilin TMD 4 as well as with the TMD of nicastrin. Interestingly, the Gly-rich interfaces between the amyloid precursor protein TMD and presenilin TMDs 2 and 4 are highly similar to its homodimerization interface. In terms of methodology, the economics of the newly developed library-based method could prove to be a useful feature in related future work for identifying heterotypic TMD-TMD interactions within other biological contexts.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Martin Ortner
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany; (T.M.P.); (A.J.); (F.C.); (S.E.); (J.M.); (L.F.); (C.S.); (F.C.S.)
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany; (T.M.P.); (A.J.); (F.C.); (S.E.); (J.M.); (L.F.); (C.S.); (F.C.S.)
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3
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García-Murria MJ, Gadea-Salom L, Moreno S, Rius-Salvador M, Zaragoza O, Brun A, Mingarro I, Martínez-Gil L. Identification of small molecules capable of enhancing viral membrane fusion. Virol J 2023; 20:99. [PMID: 37226231 DOI: 10.1186/s12985-023-02068-1] [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: 02/07/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Several approaches have been developed to analyze the entry of highly pathogenic viruses. In this study, we report the implementation of a Bimolecular Multicellular Complementation (BiMuC) assay to safely and efficiently monitor SARS-CoV-2 S-mediated membrane fusion without the need for microscopy-based equipment. Using BiMuC, we screened a library of approved drugs and identified compounds that enhance S protein-mediated cell-cell membrane fusion. Among them, ethynylestradiol promotes the growth of SARS-CoV-2 and Influenza A virus in vitro. Our findings demonstrate the potential of BiMuC for identifying small molecules that modulate the life cycle of enveloped viruses, including SARS-CoV-2.
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Affiliation(s)
- Mª Jesús García-Murria
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, E-46100, Spain
| | - Laura Gadea-Salom
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, E-46100, Spain
| | - Sandra Moreno
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
| | - Marina Rius-Salvador
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, E-46100, Spain
| | - Oscar Zaragoza
- Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases (CIBERINFEC, Health Institute Carlos III, CB21/13/00105), Madrid, Spain
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal, CISA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (INIA/CSIC)), Madrid, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, E-46100, Spain
| | - Luis Martínez-Gil
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, E-46100, Spain.
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4
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Duart G, Elazar A, Weinstein JY, Gadea-Salom L, Ortiz-Mateu J, Fleishman SJ, Mingarro I, Martinez-Gil L. Computational design of BclxL inhibitors that target transmembrane domain interactions. Proc Natl Acad Sci U S A 2023; 120:e2219648120. [PMID: 36881618 PMCID: PMC10089226 DOI: 10.1073/pnas.2219648120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/03/2023] [Indexed: 03/08/2023] Open
Abstract
Several methods have been developed to explore interactions among water-soluble proteins or regions of proteins. However, techniques to target transmembrane domains (TMDs) have not been examined thoroughly despite their importance. Here, we developed a computational approach to design sequences that specifically modulate protein-protein interactions in the membrane. To illustrate this method, we demonstrated that BclxL can interact with other members of the B cell lymphoma 2 (Bcl2) family through the TMD and that these interactions are required for BclxL control of cell death. Next, we designed sequences that specifically recognize and sequester the TMD of BclxL. Hence, we were able to prevent BclxL intramembrane interactions and cancel its antiapoptotic effect. These results advance our understanding of protein-protein interactions in membranes and provide a means to modulate them. Moreover, the success of our approach may trigger the development of a generation of inhibitors targeting interactions between TMDs.
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Affiliation(s)
- Gerard Duart
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot46100, Spain
| | - Assaf Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot76100, Israel
| | - Jonathan Y. Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot76100, Israel
| | - Laura Gadea-Salom
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot46100, Spain
| | - Juan Ortiz-Mateu
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot46100, Spain
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot76100, Israel
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot46100, Spain
| | - Luis Martinez-Gil
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot46100, Spain
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5
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Berber E, Sumbria D, Kokkaya S. A metabolic blueprint of COVID-19 and long-term vaccine efficacy. Drug Metab Pers Ther 2023; 38:15-29. [PMID: 36166711 DOI: 10.1515/dmpt-2022-0148] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Viruses are obligatory protein-coated units and often utilize the metabolic functions of the cells they infect. Viruses hijack cellular metabolic functions and cause consequences that can range from minor to devastating, as we have all witnessed during the COVID-19 pandemic. For understanding the virus-driven pathogenesis and its implications on the host, the cellular metabolism needs to be elucidated. How SARS-CoV-2 triggers metabolic functions and rewires the metabolism remains unidentified but the implications of the metabolic patterns are under investigation by several researchers. In this review, we have described the SARS-CoV-2-mediated metabolic alterations from in vitro studies to metabolic changes reported in victims of COVID-19. We have also discussed potential therapeutic targets to diminish the viral infection and suppress the inflammatory response, with respect to evidenced studies based on COVID-19 research. Finally, we aimed to explain how we could extend vaccine-induced immunity in people by targeting the immunometabolism.
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Affiliation(s)
- Engin Berber
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN, USA
| | - Deepak Sumbria
- College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Rampura Phul, Bathinda, India
| | - Serkan Kokkaya
- Faculty of Veterinary Medicine, Bozok University, Yozgat, Turkey
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6
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Irnaten M, O’Brien CJ. Calcium-Signalling in Human Glaucoma Lamina Cribrosa Myofibroblasts. Int J Mol Sci 2023; 24:ijms24021287. [PMID: 36674805 PMCID: PMC9862249 DOI: 10.3390/ijms24021287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/20/2022] [Accepted: 01/01/2023] [Indexed: 01/11/2023] Open
Abstract
Glaucoma is one of the most common causes of treatable visual impairment in the developed world, affecting approximately 64 million people worldwide, some of whom will be bilaterally blind from irreversible optic nerve damage. The optic nerve head is a key site of damage in glaucoma where there is fibrosis of the connective tissue in the lamina cribrosa (LC) extracellular matrix. As a ubiquitous second messenger, calcium (Ca2+) can interact with various cellular proteins to regulate multiple physiological processes and contribute to a wide range of diseases, including cancer, fibrosis, and glaucoma. Our research has shown evidence of oxidative stress, mitochondrial dysfunction, an elevated expression of Ca2+ entry channels, Ca2+-dependent pumps and exchangers, and an abnormal rise in cytosolic Ca2+ in human glaucomatous LC fibroblast cells. We have evidence that this increase is dependent on Ca2+ entry channels located in the plasma membrane, and its release is from internal stores in the endoplasmic reticulum (ER), as well as from the mitochondria. Here, we summarize some of the molecular Ca2+-dependent mechanisms related to this abnormal Ca2+-signalling in human glaucoma LC cells, with a view toward identifying potential therapeutic targets for ongoing optic neuropathy.
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7
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Nainu F, Ophinni Y, Shiratsuchi A, Nakanishi Y. Apoptosis and Phagocytosis as Antiviral Mechanisms. Subcell Biochem 2023; 106:77-112. [PMID: 38159224 DOI: 10.1007/978-3-031-40086-5_3] [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] [Indexed: 01/03/2024]
Abstract
Viruses are infectious entities that make use of the replication machinery of their hosts to produce more progenies, causing disease and sometimes death. To counter viral infection, metazoan hosts are equipped with various defense mechanisms, from the rapid-evoking innate immune responses to the most advanced adaptive immune responses. Previous research demonstrated that cells in fruit flies and mice infected with Drosophila C virus and influenza, respectively, undergo apoptosis, which triggers the engulfment of apoptotic virus-infected cells by phagocytes. This process involves the recognition of eat-me signals on the surface of virus-infected cells by receptors of specialized phagocytes, such as macrophages and neutrophils in mice and hemocytes in fruit flies, to facilitate the phagocytic elimination of virus-infected cells. Inhibition of phagocytosis led to severe pathologies and death in both species, indicating that apoptosis-dependent phagocytosis of virus-infected cells is a conserved antiviral mechanism in multicellular organisms. Indeed, our understanding of the mechanisms underlying apoptosis-dependent phagocytosis of virus-infected cells has shed a new perspective on how hosts defend themselves against viral infection. This chapter explores the mechanisms of this process and its potential for developing new treatments for viral diseases.
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Affiliation(s)
- Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia.
| | - Youdiil Ophinni
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
- Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Akiko Shiratsuchi
- Center for Medical Education, Sapporo Medical University, Sapporo, Japan
- Division of Biological Function and Regulation, Graduate School of Medicine, Sapporo Medical University, Sapporo, Japan
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8
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Wolf P, Schoeniger A, Edlich F. Pro-apoptotic complexes of BAX and BAK on the outer mitochondrial membrane. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119317. [PMID: 35752202 DOI: 10.1016/j.bbamcr.2022.119317] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/02/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
In multicellular organisms the regulated cell death apoptosis is critically important for both ontogeny and homeostasis. Mitochondria are indispensable for stress-induced apoptosis. The BCL-2 protein family controls mitochondrial apoptosis and initiates cell death through the pro-apoptotic activities of BAX and BAK at the outer mitochondrial membrane (OMM). Cellular survival is ensured by the retrotranslocation of mitochondrial BAX and BAK into the cytosol by anti-apoptotic BCL-2 proteins. BAX/BAK-dependent OMM permeabilization releases the mitochondrial cytochrome c (cyt c), which initiates activation of caspase-9. The caspase cascade leads to cell shrinkage, plasma membrane blebbing, chromatin condensation, and apoptotic body formation. Although it is clear that ultimately complexes of active BAX and BAK commit the cell to apoptosis, the nature of these complexes is still enigmatic. Excessive research has described a range of complexes, varying from a few molecules to several 10,000, in different systems. BAX/BAK complexes potentially form ring-like structures that could expose the inner mitochondrial membrane. It has been suggested that these pores allow the efflux of small proteins and even mitochondrial DNA. Here we summarize the current state of knowledge for mitochondrial BAX/BAK complexes and the interactions between these proteins and the membrane.
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Affiliation(s)
- Philipp Wolf
- Institute of Biochemistry, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Axel Schoeniger
- Institute of Biochemistry, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Frank Edlich
- Institute of Biochemistry, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany.
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9
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How Do Hexokinases Inhibit Receptor-Mediated Apoptosis? BIOLOGY 2022; 11:biology11030412. [PMID: 35336786 PMCID: PMC8945020 DOI: 10.3390/biology11030412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary In multicellular animals, cells autonomously respond to lethal stress by inducing cell death programs. The most common regulated cell death is apoptosis. Cells protect their neighbors from damage by their cell contents or infection through this process. Apoptosis can occur as a result of intrinsic stress or induced by surface receptors, for example, by immune cells. In most cases, receptor-mediated apoptosis also requires the intrinsic signaling pathway. Intrinsic apoptosis is controlled by proteins of the B-cell lymphoma 2 (BCL-2) family. Pro-apoptotic BCL-2 proteins are inhibited by retrotranslocation from the mitochondria into the cytosol until the cell commits to apoptosis. Increasingly, discoveries show that BCL-2 proteins are regulated by proteins that are not themselves members of the BCL-2 family. Here, we discuss the selective inhibition of the link between death receptors activation and intrinsic apoptosis by hexokinases. These enzymes funnel glucose into the cellular metabolism. Independently, hexokinases retrotranslocate BCL-2 proteins and thereby protect cells from receptor-mediated apoptosis. Abstract The regulated cell death apoptosis enables redundant or compromised cells in ontogeny and homeostasis to remove themselves receptor-dependent after extrinsic signaling or after internal stress by BCL-2 proteins on the outer mitochondrial membrane (OMM). Mitochondrial BCL-2 proteins are also often needed for receptor-mediated signaling in apoptosis. Then, the truncated BH3-only protein BID (tBID) blocks retrotranslocation of the pro-apoptotic BCL-2 proteins BAX and BAK from the mitochondria into the cytosol. BAX and BAK in turn permeabilize the OMM. Although the BCL-2 proteins are controlled by a complex regulatory network, a specific mechanism for the inhibition of tBID remained unknown. Curiously, it was suggested that hexokinases, which channel glucose into the metabolism, have an intriguing function in the regulation of apoptosis. Recent analysis of transient hexokinase interactions with BAX revealed its participation in the inhibition of BAX and also BAK by retrotranslocation from mitochondria to the cytosol. In contrast to general apoptosis inhibition by anti-apoptotic BCL-2 proteins, hexokinase I and hexokinase 2 specifically inhibit tBID and thus the mitochondrial apoptosis pathway in response to death receptor signaling. Mitochondrial hexokinase localization and BH3 binding of cytosolic hexokinase domains are prerequisites for protection against receptor-mediated cell death, whereas glucose metabolism is not. This mechanism protects cells from apoptosis induced by cytotoxic T cells.
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10
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Tummers B, Green DR. The evolution of regulated cell death pathways in animals and their evasion by pathogens. Physiol Rev 2022; 102:411-454. [PMID: 34898294 PMCID: PMC8676434 DOI: 10.1152/physrev.00002.2021] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 09/01/2021] [Accepted: 09/01/2022] [Indexed: 12/21/2022] Open
Abstract
The coevolution of host-pathogen interactions underlies many human physiological traits associated with protection from or susceptibility to infections. Among the mechanisms that animals utilize to control infections are the regulated cell death pathways of pyroptosis, apoptosis, and necroptosis. Over the course of evolution these pathways have become intricate and complex, coevolving with microbes that infect animal hosts. Microbes, in turn, have evolved strategies to interfere with the pathways of regulated cell death to avoid eradication by the host. Here, we present an overview of the mechanisms of regulated cell death in Animalia and the strategies devised by pathogens to interfere with these processes. We review the molecular pathways of regulated cell death, their roles in infection, and how they are perturbed by viruses and bacteria, providing insights into the coevolution of host-pathogen interactions and cell death pathways.
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Affiliation(s)
- Bart Tummers
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
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11
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Zhang L, Xiao Y, Yang R, Wang S, Ma S, Liu J, Xiao W, Wang Y. Systems pharmacology to reveal multi-scale mechanisms of traditional Chinese medicine for gastric cancer. Sci Rep 2021; 11:22149. [PMID: 34773055 PMCID: PMC8589993 DOI: 10.1038/s41598-021-01535-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Because of the complex etiology, the treatment of gastric cancer is a formidable challenge for contemporary medical. The current treatment method focuses on traditional surgical procedures, supplemented by other treatments. Among these other treatments, Traditional Chinese Medicine (TCM) plays an important role. Here, we used the systems pharmacology approach to reveal the potential molecular mechanism of PRGRC on gastric cancer which composes of Pinellia ternata(Thunb.) Breit., Rheum palmatumL., Gentiana scabraBunge, Radix Aucklandiae and Citrus aurantium L. This approach combines pharmacokinetics analysis with pharmacodynamics evaluation for the active compounds screening, targets prediction and pathways assessing. Firstly, through pharmacokinetic evaluation and target prediction models, 83 potential compounds and 184 gastric cancer-related targets were screened out. Then, the results of network analysis suggested that the targets of PRGRC were mainly involved two aspects: apoptosis and inflammation. Finally, we verified the reliability of the above analysis at the cellular level by using naringenin and luteolin with good pharmacokinetic activity as representative compounds. Overall, we found that PRGRC could influence the development of gastric cancer from a multi-scale perspective. This study provided a new direction for analyzing the mechanism of TCM.
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Affiliation(s)
- Lulu Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Yue Xiao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Ruijie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Siyi Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - ShuangXin Ma
- Lab of Systems Pharmacology, Center of Bioinformatics, College of Life Science, Northwest A&F University, Yangling, China
| | - Jianling Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.
| | - Wei Xiao
- State Key Laboratory of New-Tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang, 222002, China.
| | - Yonghua Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.
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12
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Methodological approaches for the analysis of transmembrane domain interactions: A systematic review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183712. [PMID: 34331948 DOI: 10.1016/j.bbamem.2021.183712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/28/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022]
Abstract
The study of protein-protein interactions (PPI) has proven fundamental for the understanding of the most relevant cell processes. Any protein domain can participate in PPI, including transmembrane (TM) segments that can establish interactions with other TM domains (TMDs). However, the hydrophobic nature of TMDs and the environment they occupy complicates the study of intramembrane PPI, which demands the use of specific approaches and techniques. In this review, we will explore some of the strategies available to study intramembrane PPI in vitro, in vivo, and, in silico, focusing on those techniques that could be carried out in a standard molecular biology laboratory regarding its previous experience with membrane proteins.
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13
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Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol 2021; 433:167144. [PMID: 34229012 DOI: 10.1016/j.jmb.2021.167144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Jennifer A Schuster
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, F-69367 Lyon, France
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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Duart G, Mingarro I, Martinez-Gil L. The importance of transmembrane domain interactions in the viral control of apoptosis. Mol Cell Oncol 2021; 8:1911290. [PMID: 34027047 DOI: 10.1080/23723556.2021.1911290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Viral control of apoptosis occurs through the expression of viral encoded anti-apoptotic B-cell lymphoma 2 (BCL2) analogs. These proteins are thought to restrain apoptosis by interacting with cellular BCL2 family members. We identified that protein-protein interactions between cellular and viral BCL2 transmembrane domains are crucial for the viral protein's function.
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Affiliation(s)
- Gerard Duart
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot, Spain
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot, Spain
| | - Luis Martinez-Gil
- Department of Biochemistry and Molecular Biology, Institut de Biotecnologia i Biomedicina, Universitat de València, Burjassot, Spain
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