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Kinnun JJ, Carrillo JMY, Collier CP, Smith MD, Katsaras J. Amantadine interactions with phase separated lipid membranes. Chem Phys Lipids 2024; 262:105397. [PMID: 38740276 DOI: 10.1016/j.chemphyslip.2024.105397] [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: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Amantadine, a small amphilphic organic compound that consists of an adamantane backbone and an amino group, was first recognized as an antiviral in 1963 and received approval for prophylaxis against the type A influenza virus in 1976. Since then, it has also been used to treat Parkinson's disease-related dyskinesia and is being considered as a treatment for corona viruses. Since amantadine usually targets membrane-bound proteins, its interactions with the membrane are also thought to be important. Biological membranes are now widely understood to be laterally heterogeneous and certain proteins are known to preferentially co-localize within specific lipid domains. Does amantadine, therefore, preferentially localize in certain lipid composition domains? To address this question, we studied amantadine's interactions with phase separating membranes composed of cholesterol, DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine), POPC (1-palmitoyl-2-oleoyl-glycero-3-phosphocholine), and DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), as well as single-phase DPhPC (1,2-diphytanoyl-sn-glycero-3-phos-phocholine) membranes. From Langmuir trough and differential scanning calorimetry (DSC) measurements, we determined, respectively, that amantadine preferentially binds to disordered lipids, such as POPC, and lowers the phase transition temperature of POPC/DSPC/cholesterol mixtures, implying that amantadine increases membrane disorder. Further, using droplet interface bilayers (DIBs), we observed that amantadine disrupts DPhPC membranes, consistent with its disordering properties. Finally, we carried out molecular dynamics (MD) simulations on POPC/DSPC/cholesterol membranes with varying amounts of amantadine. Consistent with experiment, MD simulations showed that amantadine prefers to associate with disordered POPC-rich domains, domain boundaries, and lipid glycerol backbones. Since different proteins co-localize with different lipid domains, our results have possible implications as to which classes of proteins may be better targets for amantadine.
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Affiliation(s)
- Jacob J Kinnun
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States.
| | - Jan Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Micholas Dean Smith
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, United States
| | - John Katsaras
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
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2
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Wang J, Mim C, Dahll G, Barro-Soria R. A metastasis-associated Pannexin1 mutant (Panx1 1-89 ) forms a minimalist ATP release channel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584732. [PMID: 38559162 PMCID: PMC10980048 DOI: 10.1101/2024.03.12.584732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A truncated form of the ATP release channel pannexin 1 (Panx1), Panx1 1-89 , is enriched in metastatic breast cancer cells and has been proposed to mediate metastatic cell survival by increasing ATP release through mechanosensitive Panx1 channels. However, whether Panx1 1-89 on its own (without the presence of wtPanx1) mediates ATP release has not been tested. Here, we show that Panx1 1-89 by itself can form a constitutively active membrane channel, capable of releasing ATP even in the absence of wild type Panx1. Our biophysical characterization reveals that most basic structure-function features of the channel pore are conserved in the truncated Panx1 1-89 peptide. Thus, augmenting extracellular potassium ion concentrations enhances Panx1 1-89 -mediated conductance. Moreover, despite the severe truncation, Panx1 1-89 retains the sensitivity to most of wtPanx1 channel inhibitors and can thus be targeted. Therefore, Panx1 blockers have the potential to be of therapeutic value to combat metastatic cell survival. Our study not only elucidates a mechanism for ATP release from cancer cells, but it also supports that the Panx1 1-89 mutant should facilitate structure-function analysis of Panx1 channels.
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [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: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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Santos IA, Pereira AKDS, Guevara-Vega M, de Paiva REF, Sabino-Silva R, Bergamini FRG, Corbi PP, Jardim ACG. Repurposing potential of rimantadine hydrochloride and development of a promising platinum(II)-rimantadine metallodrug for the treatment of Chikungunya virus infection. Acta Trop 2022; 227:106300. [PMID: 34979144 DOI: 10.1016/j.actatropica.2021.106300] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/15/2022]
Abstract
Most of the patients infected with Chikungunya virus (CHIKV) develop chronic manifestations characterized by pain and deformity in joints, impacting their quality of life. The aminoadamantanes, in their turn, have been exploited due to their biological activities, with amantadine and memantine recently described with anti-CHIKV activities. Here we evaluated the antiviral activity of rimantadine hydrochloride (rtdH), a well-known antiviral agent against influenza A, its platinum complex (Pt-rtd), and the precursor cis-[PtCl2(dmso)2], against CHIKV infection in vitro. The rtdH demonstrated significant antiviral activity in all stages of CHIKV replication (29% in pre-treatment; 57% in early stages of infection; 60% in post-entry stages). The Pt-rtd complex protected the cells against infection in 92%, inhibited 100% of viral entry, mainly by a virucidal effect, and impaired 60% of post-entry stages. Alternatively, cis-[PtCl2(dmso)2] impaired viral entry in 100% and post-entry steps in 60%, but had no effect in protecting cells when administered prior to CHIKV infection. Collectively, the obtained data demonstrated that rtdH and Pt-rtd significantly interfered in the early stages of CHIKV life cycle, with the strongest effect observed to Pt-rtd complex, which reduced up to 100% of CHIKV infection. Moreover, molecular docking analysis and infrared spectroscopy data (ATR-FTIR) suggest an interaction of Pt-rtd with CHIKV glycoproteins, potentially related to the mechanism of inhibition of viral entry by Pt-rtd. Through a migration retardation assay, it was also shown that Pt-rtd and cis-[PtCl2(dmso)2] interacted with the dsRNA in 87% and 100%, respectively. The obtained results highlight the repurposing potential of rtdH as an anti-CHIKV drug, as well as the synthesis of promising platinum(II) metallodrugs with potential application for the treatment of CHIKV infections. Importance Chikungunya fever is a disease that can result in persistent symptoms due to the chronic infection process. Infected patients can develop physical disability, resulting and high costs to the health system and significant impacts on the quality of life of affected individuals. Additionally, there are no licensed vaccines or antivirals against the Chikungunya virus (CHIKV) and the virus is easily transmitted due to the abundance of viable vectors in epidemic regions. In this context, our study highlights the repurposing potential of the commercial drug rimantadine hydrochloride (rtdH) as an antiviral agent for the treatment of CHIKV infections. Moreover, our data demonstrated that a platinum(II)-rimantadine metallodrug (Pt-rtd) poses as a potent anti-CHIKV molecule with potential application for the treatment of Chikungunya fever. Altogether, rtdH and Pt-rtd significantly interfered in the early stages of CHIKV life cycle, reducing up to 100% of CHIKV infection in vitro.
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Affiliation(s)
- Igor Andrade Santos
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia-MG 38405-302, Brazil
| | | | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Brazil
| | | | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Fernando R G Bergamini
- Laboratory of Synthesis of Bioinspired Molecules, Institute of Chemistry, Federal University of Uberlândia, Uberlândia-MG 34000-902, Brazil.
| | - Pedro P Corbi
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas-SP 13083-871, Brazil.
| | - Ana Carolina G Jardim
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia-MG 38405-302, Brazil; Institute of Biosciences, Humanities and Exact Sciences (Ibilce), São Paulo State University (Unesp), Campus São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.
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5
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Wei S, Liu C, Du L, Wu B, Zhong J, Tong Y, Wang S, OuYang B. Identification of a novel class of cyclic penta-peptides against hepatitis C virus as p7 channel blockers. Comput Struct Biotechnol J 2022; 20:5902-5910. [PMID: 36382186 PMCID: PMC9636413 DOI: 10.1016/j.csbj.2022.10.035] [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: 06/23/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/29/2022] Open
Abstract
The hepatitis C virus (HCV) p7 viroporin protein is essential for viral assembly and release, suggesting its unrealised potential as a target for HCV interventions. Several classes of small molecules that can inhibit p7 through allosteric mechanisms have shown low efficacy. Here, we used a high throughput virtual screen to design a panel of eight novel cyclic penta-peptides (CPs) that target the p7 channel with high binding affinity. Further examination of the effects of these CPs in viral production assays indicated that CP7 exhibits the highest potency against HCV among them. Moreover, the IC50 efficacy of CP7 in tests of strain Jc1-S282T suggested that this cyclopeptide could also effectively inhibit a drug-resistant HCV strain. A combination of nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations revealed that CP7 blocking activity relies on direct binding to the p7 channel lumen at the N-terminal bottleneck region. These findings thus present a promising anti-HCV cyclic penta-peptide targeting p7 viroporin, while also describing an alternative strategy for designing a new class of p7 channel blockers for strains resistant to direct-acting antiviral agents (DAA).
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Affiliation(s)
- Shukun Wei
- State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaolun Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- ShanghaiTech University, Shanghai 201210, China
| | - Lingyu Du
- State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jin Zhong
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- ShanghaiTech University, Shanghai 201210, China
| | - Yimin Tong
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- Corresponding authors at: University of Chinese Academy of Sciences, Beijing 100049, China (Y. Tong); State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China (B. OuYang).
| | - Shuqing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
- Corresponding authors at: University of Chinese Academy of Sciences, Beijing 100049, China (Y. Tong); State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China (B. OuYang).
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding authors at: University of Chinese Academy of Sciences, Beijing 100049, China (Y. Tong); State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China (B. OuYang).
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Tan TH, Patton E, Munro CA, Corzo-Leon DE, Porter AJ, Palliyil S. Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein. Viruses 2021; 13:2201. [PMID: 34835009 PMCID: PMC8624585 DOI: 10.3390/v13112201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/15/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
ORF3a has been identified as a viroporin of SARS-CoV-2 and is known to be involved in various pathophysiological activities including disturbance of cellular calcium homeostasis, inflammasome activation, apoptosis induction and disruption of autophagy. ORF3a-targeting antibodies may specifically and favorably modulate these viroporin-dependent pathological activities. However, suitable viroporin-targeting antibodies are difficult to generate because of the well-recognized technical challenge associated with isolating antibodies to complex transmembrane proteins. Here we exploited a naïve human single chain antibody phage display library, to isolate binders against carefully chosen ORF3a recombinant epitopes located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide antigens. These binders were subjected to further characterization using enzyme-linked immunosorbent assays and surface plasmon resonance analysis to assess their binding affinities to the target epitopes. Binding to full-length ORF3a protein was evaluated by western blot and fluorescent microscopy using ORF3a transfected cells and SARS-CoV-2 infected cells. Co-localization analysis was also performed to evaluate the "pairing potential" of the selected binders as possible alternative diagnostic or prognostic biomarkers for COVID-19 infections. Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified in our study. Whilst the linear nature of peptides might not always represent their native conformations in the context of full protein, with carefully designed selection protocols, we have been successful in isolating anti-ORF3a binders capable of recognising regions of the transmembrane protein that are exposed either on the "inside" or "outside" of the infected cell. Their therapeutic potential will be discussed.
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Affiliation(s)
- Tyng Hwey Tan
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Elizabeth Patton
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
| | - Carol A. Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Dora E. Corzo-Leon
- Aberdeen Fungal Group, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; (C.A.M.); (D.E.C.-L.)
| | - Andrew J. Porter
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
| | - Soumya Palliyil
- Scottish Biologics Facility, Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZP, UK; (T.H.T.); (E.P.)
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Sikdar S, Banerjee M, Vemparala S. Effect of cholesterol on the membrane partitioning dynamics of hepatitis A virus-2B peptide. SOFT MATTER 2021; 17:7963-7977. [PMID: 34378608 DOI: 10.1039/d1sm01019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding viral peptide detection and partitioning and the subsequent host membrane composition-based response is essential for gaining insights into the viral mechanism. Here, we probe the crucial role of the presence of membrane lipid packing defects, depending on the membrane composition, in allowing the viral peptide belonging to C-terminal Hepatitis A Virus-2B (HAV-2B) to detect, attach and subsequently partition into host cell membrane mimics. Using molecular dynamics simulations, we conclusively show that the hydrophobic residues in the viral peptide detect transiently present lipid packing defects, insert themselves into such defects, form anchor points and facilitate the partitioning of the peptide, thereby inducing membrane disruption. We also show that the presence of cholesterol significantly alters such lipid packing defects, both in size and in number, thus mitigating the partitioning of the membrane active viral peptide into cholesterol-rich membranes. Our results are in excellent agreement with previously published experimental data and further explain the role of lipid defects in understanding such data. These results show differential ways in which the presence and absence of cholesterol can alter the permeability of the host membranes to the membrane active peptide component of HAV-2B virus, via lipid packing defects, and can possibly be a part of the general membrane detection mechanism for viroporins.
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Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
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8
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Barrantes FJ. Structural biology of coronavirus ion channels. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:391-402. [PMID: 33825700 DOI: 10.1107/s2059798321001431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
Viral infection compromises specific organelles of the cell and readdresses its functional resources to satisfy the needs of the invading body. Around 70% of the coronavirus positive-sense single-stranded RNA encodes proteins involved in replication, and these viruses essentially take over the biosynthetic and transport mechanisms to ensure the efficient replication of their genome and trafficking of their virions. Some coronaviruses encode genes for ion-channel proteins - the envelope protein E (orf4a), orf3a and orf8 - which they successfully employ to take control of the endoplasmic reticulum-Golgi complex intermediate compartment or ERGIC. The E protein, which is one of the four structural proteins of SARS-CoV-2 and other coronaviruses, assembles its transmembrane protomers into homopentameric channels with mild cationic selectivity. Orf3a forms homodimers and homotetramers. Both carry a PDZ-binding domain, lending them the versatility to interact with more than 400 target proteins in infected host cells. Orf8 is a very short 29-amino-acid single-passage transmembrane peptide that forms cation-selective channels when assembled in lipid bilayers. This review addresses the contribution of biophysical and structural biology approaches that unravel different facets of coronavirus ion channels, their effects on the cellular machinery of infected cells and some structure-functional correlations with ion channels of higher organisms.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA) - National Scientific and Technical Research Council (CONICET), C1107AFF Buenos Aires, Argentina
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9
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Stavropoulou E, Bezirtzoglou E. Probiotics as a Weapon in the Fight Against COVID-19. Front Nutr 2020; 7:614986. [PMID: 33385008 PMCID: PMC7769760 DOI: 10.3389/fnut.2020.614986] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Affiliation(s)
- Elisavet Stavropoulou
- Department of Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.,Service of Infectious Diseases, Central Institute of Valais Hospitals, Sion, Switzerland.,Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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10
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Schoeman D, Fielding BC. Is There a Link Between the Pathogenic Human Coronavirus Envelope Protein and Immunopathology? A Review of the Literature. Front Microbiol 2020; 11:2086. [PMID: 33013759 PMCID: PMC7496634 DOI: 10.3389/fmicb.2020.02086] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Since the severe acute respiratory syndrome (SARS) outbreak in 2003, human coronaviruses (hCoVs) have been identified as causative agents of severe acute respiratory tract infections. Two more hCoV outbreaks have since occurred, the most recent being SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The clinical presentation of SARS and MERS is remarkably similar to COVID-19, with hyperinflammation causing a severe form of the disease in some patients. Previous studies show that the expression of the SARS-CoV E protein is associated with the hyperinflammatory response that could culminate in acute respiratory distress syndrome (ARDS), a potentially fatal complication. This immune-mediated damage is largely caused by a cytokine storm, which is induced by significantly elevated levels of inflammatory cytokines interleukin (IL)-1β and IL-6, which are partly mediated by the expression of the SARS-CoV E protein. The interaction between the SARS-CoV E protein and the host protein, syntenin, as well as the viroporin function of SARS-CoV E, are linked to this cytokine dysregulation. This review aims to compare the clinical presentation of virulent hCoVs with a specific focus on the cause of the immunopathology. The review also proposes that inhibition of IL-1β and IL-6 in severe cases can improve patient outcome.
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Affiliation(s)
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
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11
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Jalily PH, Duncan MC, Fedida D, Wang J, Tietjen I. Put a cork in it: Plugging the M2 viral ion channel to sink influenza. Antiviral Res 2020; 178:104780. [PMID: 32229237 PMCID: PMC7102647 DOI: 10.1016/j.antiviral.2020.104780] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022]
Abstract
The ongoing threat of seasonal and pandemic influenza to human health requires antivirals that can effectively supplement existing vaccination strategies. The M2 protein of influenza A virus (IAV) is a proton-gated, proton-selective ion channel that is required for virus replication and is an established antiviral target. While licensed adamantane-based M2 antivirals have been historically used, M2 mutations that confer major adamantane resistance are now so prevalent in circulating virus strains that these drugs are no longer recommended. Here we review the current understanding of IAV M2 structure and function, mechanisms of inhibition, the rise of drug resistance mutations, and ongoing efforts to develop new antivirals that target resistant forms of M2.
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Affiliation(s)
- Pouria H Jalily
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - David Fedida
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tuscon, AZ, USA
| | - Ian Tietjen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; The Wistar Institute, Philadelphia, PA, USA.
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12
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Pokhrel R, Pavadai E, Gerstman BS, Chapagain PP. Membrane pore formation and ion selectivity of the Ebola virus delta peptide. Phys Chem Chem Phys 2019; 21:5578-5585. [DOI: 10.1039/c8cp07323f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Ebola virus delta peptide homo-oligomerizes in the host cell membrane to form amphipathic pores that alter the membrane properties.
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Affiliation(s)
| | | | - Bernard S. Gerstman
- Department of Physics
- Miami
- USA
- Biomolecular Sciences Institute Florida International University
- Miami
| | - Prem P. Chapagain
- Department of Physics
- Miami
- USA
- Biomolecular Sciences Institute Florida International University
- Miami
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13
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Shiryaev VA, Radchenko EV, Palyulin VA, Zefirov NS, Bormotov NI, Serova OA, Shishkina LN, Baimuratov MR, Bormasheva KM, Gruzd YA, Ivleva EA, Leonova MV, Lukashenko AV, Osipov DV, Osyanin VA, Reznikov AN, Shadrikova VA, Sibiryakova AE, Tkachenko IM, Klimochkin YN. Molecular design, synthesis and biological evaluation of cage compound-based inhibitors of hepatitis C virus p7 ion channels. Eur J Med Chem 2018; 158:214-235. [PMID: 30218908 DOI: 10.1016/j.ejmech.2018.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/04/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022]
Abstract
The hepatitis C caused by the hepatitis C virus (HCV) is an acute and/or chronic liver disease ranging in severity from a mild brief ailment to a serious lifelong illness that affects up to 3% of the world population and imposes significant and increasing social, economic, and humanistic burden. Over the past decade, its treatment was revolutionized by the development and introduction into clinical practice of the direct acting antiviral (DAA) agents targeting the non-structural viral proteins NS3/4A, NS5A, and NS5B. However, the current treatment options still have important limitations, thus, the development of new classes of DAAs acting on different viral targets and having better pharmacological profile is highly desirable. The hepatitis C virus p7 viroporin is a relatively small hydrophobic oligomeric viral ion channel that plays a critical role during virus assembly and maturation, making it an attractive and validated target for the development of the cage compound-based inhibitors. Using the homology modeling, molecular dynamics, and molecular docking techniques, we have built a representative set of models of the hepatitis C virus p7 ion channels (Gt1a, Gt1b, Gt1b_L20F, Gt2a, and Gt2b), analyzed the inhibitor binding sites, and identified a number of potential broad-spectrum inhibitor structures targeting them. For one promising compound, the binding to these targets was additionally confirmed and the binding modes and probable mechanisms of action were clarified by the molecular dynamics simulations. A number of compounds were synthesized, and the tests of their antiviral activity (using the BVDV model) and cytotoxicity demonstrate their potential therapeutic usefulness and encourage further more detailed studies. The proposed approach is also suitable for the design of broad-spectrum ligands interacting with other multiple labile targets including various viroporins.
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Affiliation(s)
- Vadim A Shiryaev
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia.
| | - Eugene V Radchenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Nikolay S Zefirov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Nikolay I Bormotov
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Olga A Serova
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Larisa N Shishkina
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Marat R Baimuratov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Kseniya M Bormasheva
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Yulia A Gruzd
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Elena A Ivleva
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Marina V Leonova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Anton V Lukashenko
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Dmitry V Osipov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Vitaliy A Osyanin
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Alexander N Reznikov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Vera A Shadrikova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Anastasia E Sibiryakova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Ilya M Tkachenko
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Yuri N Klimochkin
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
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14
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Mandour YM, Breitinger U, Ma C, Wang J, Boeckler FM, Breitinger HG, Zlotos DP. Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:1019-1031. [PMID: 29750015 PMCID: PMC5933338 DOI: 10.2147/dddt.s157104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background Adamantane-based compounds have been identified to interfere with the ion-channel activity of viroporins and thereby inhibit viral infection. To better understand the difference in the inhibition mechanism of viroporins, we synthesized symmetric dimeric adamantane analogs of various alkyl-spacer lengths. Methods Symmetric dimeric adamantane derivatives were synthesized where two amantadine or rimantadine molecules were linked by various alkyl-spacers. The inhibitory activity of the compounds was studied on two viroporins: the influenza virus M2 protein, expressed in Xenopus oocytes, using the two-electrode voltage-clamp technique, and the hepatitis C virus (HCV) p7 channels for five different genotypes (1a, 1b, 2a, 3a, and 4a) expressed in HEK293 cells using whole-cell patch-clamp recording techniques. Results Upon testing on M2 protein, dimeric compounds showed significantly lower inhibitory activity relative to the monomeric amantadine. The lack of channel blockage of the dimeric amantadine and rimantadine analogs against M2 wild type and M2-S31N mutant was consistent with previously proposed drug-binding mechanisms and further confirmed that the pore-binding model is the pharmacologically relevant drug-binding model. On the other hand, these dimers showed similar potency to their respective monomeric analogs when tested on p7 protein in HCV genotypes 1a, 1b, and 4a while being 700-fold and 150-fold more potent than amantadine in genotypes 2a and 3a, respectively. An amino group appears to be important for inhibiting the ion-channel activity of p7 protein in genotype 2a, while its importance was minimal in all other genotypes. Conclusion Symmetric dimeric adamantanes can be considered a prospective class of p7 inhibitors that are able to address the differences in adamantane sensitivity among the various genotypes of HCV.
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Affiliation(s)
| | - Ulrike Breitinger
- Department of Biochemistry, The German University in Cairo, Cairo, Egypt
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Frank M Boeckler
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, German University in Cairo
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15
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Chen W, Dev J, Mezhyrova J, Pan L, Piai A, Chou JJ. The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure 2018; 26:627-634.e4. [PMID: 29551287 PMCID: PMC5884736 DOI: 10.1016/j.str.2018.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/24/2018] [Accepted: 02/09/2018] [Indexed: 01/14/2023]
Abstract
The p7 protein of the hepatitis C virus (HCV) can oligomerize in membrane to form cation channels. Previous studies showed that the channel assembly in detergent micelles adopts a unique flower-shaped oligomer, but the unusual architecture also presented problems for understanding how this viroporin resides in the membrane. Moreover, the oligomeric state of p7 remains controversial, as both hexamer and heptamer have been proposed. Here we address the above issues using p7 reconstituted in bicelles that mimic a lipid bilayer. We found, using a recently developed oligomer-labeling method, that p7 forms hexamers in the bicelles. Solvent paramagnetic relaxation enhancement analyses showed that the bilayer thickness around the HCV ion channel is substantially smaller than expected, and thus a significant portion of the previously assigned membrane-embedded region is solvent exposed. Our study provides an effective approach for characterizing the transmembrane partition of small ion channels in near lipid bilayer environment.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jyoti Dev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Liqiang Pan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, China.
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16
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Carrara G, Parsons M, Saraiva N, Smith GL. Golgi anti-apoptotic protein: a tale of camels, calcium, channels and cancer. Open Biol 2018; 7:rsob.170045. [PMID: 28469007 PMCID: PMC5451544 DOI: 10.1098/rsob.170045] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
Golgi anti-apoptotic protein (GAAP), also known as transmembrane Bax inhibitor-1 motif-containing 4 (TMBIM4) or Lifeguard 4 (Lfg4), shares remarkable amino acid conservation with orthologues throughout eukaryotes, prokaryotes and some orthopoxviruses, suggesting a highly conserved function. GAAPs regulate Ca2+ levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store-operated Ca2+ entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that are resident in Golgi membranes and form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers, a feature that distinguishes them from other virus-encoded ion channels that must oligomerize for function. This review summarizes the known functions of GAAPs and discusses their potential importance in disease.
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Affiliation(s)
- Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Nuno Saraiva
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK .,CBIOS, Universidade Lusófona Research Centre for Biosciences and Health Technologies, Campo Grande 376, Lisbon 1749-024, Portugal
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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17
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Dey D, Banerjee M. Inhibitor-Based Therapeutics for Treatment of Viral Hepatitis. J Clin Transl Hepatol 2016; 4:248-257. [PMID: 27777893 PMCID: PMC5075008 DOI: 10.14218/jcth.2016.00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 12/12/2022] Open
Abstract
Viral hepatitis remains a significant worldwide threat, in spite of the availability of several successful therapeutic and vaccination strategies. Complications associated with acute and chronic infections, such as liver failure, cirrhosis and hepatocellular carcinoma, are the cause of considerable morbidity and mortality. Given the significant burden on the healthcare system caused by viral hepatitis, it is essential that novel, more effective therapeutics be developed. The present review attempts to summarize the current treatments against viral hepatitis, and provides an outline for upcoming, promising new therapeutics. Development of novel therapeutics requires an understanding of the viral life cycles and viral effectors in molecular detail. As such, this review also discusses virally-encoded effectors, found to be essential for virus survival and replication in the host milieu, which may be utilized as potential candidates for development of alternative therapies in the future.
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Affiliation(s)
- Debajit Dey
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
- *Correspondence to: Dr. Manidipa Banerjee, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Block 1A, Hauz Khas, New Delhi 110016, India. Tel: +91-11-26597538, Fax: +91-11-26597530, E-mail:
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18
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19
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Membrane protein assembly: two cytoplasmic phosphorylated serine sites of Vpu from HIV-1 affect oligomerization. Sci Rep 2016; 6:28866. [PMID: 27353136 PMCID: PMC4926278 DOI: 10.1038/srep28866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/06/2016] [Indexed: 11/08/2022] Open
Abstract
Viral protein U (Vpu) encoded by human immunodeficiency virus type 1 (HIV-1) is a short integral membrane protein which is known to self-assemble within the lipid membrane and associate with host factors during the HIV-1 infectivity cycle. In this study, full-length Vpu (M group) from clone NL4-3 was over-expressed in human cells and purified in an oligomeric state. Various single and double mutations were constructed on its phosphorylation sites to mimic different degrees of phosphorylation. Size exclusion chromatography of wild-type Vpu and mutants indicated that the smallest assembly unit of Vpu was a dimer and over time Vpu formed higher oligomers. The rate of oligomerization increased when (i) the degree of phosphorylation at serines 52 and 56 was decreased and (ii) when the ionic strength was increased indicating that the cytoplasmic domain of Vpu affects oligomerization. Coarse-grained molecular dynamic simulations with models of wild-type and mutant Vpu in a hydrated lipid bilayer supported the experimental data in demonstrating that, in addition to a previously known role in downregulation of host factors, the phosphorylation sites of Vpu also modulate oligomerization.
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20
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Laasch N, Kalita MM, Griffin S, Fischer WB. Small molecule ligand docking to genotype specific bundle structures of hepatitis C virus (HCV) p7 protein. Comput Biol Chem 2016; 64:56-63. [PMID: 27258799 DOI: 10.1016/j.compbiolchem.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 04/28/2016] [Indexed: 01/26/2023]
Abstract
The genome of hepatitis C virus encodes for an essential 63 amino acid polytopic protein p7 of most likely two transmembrane domains (TMDs). The protein is identified to self-assemble thereby rendering lipid membranes permeable to ions. A series of small molecules such as adamantanes, imino sugars and guanidinium compounds are known to interact with p7. A set of 9 of these small molecules is docked against hexameric bundles of genotypes 5a (bundle-5a) and 1b (bundle-1b) using LeadIT. Putative sites for bundle-5a are identified within the pore and at pockets on the outside of the bundle. For bundle-1b preferred sites are found at the site of the loops. Binding energies are in favour of the guanidinium compounds. Rescoring of the identified poses with HYDE reveals a dehydration penalty for the guanidinium compounds, leaving the adamantanes and imino sugar in a better position. Binding energies calculated by HYDE and those by LeadIT indicate that all compounds are moderate binders.
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Affiliation(s)
- Niklas Laasch
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Stephen Griffin
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, and Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
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21
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Jalily PH, Eldstrom J, Miller SC, Kwan DC, Tai SSH, Chou D, Niikura M, Tietjen I, Fedida D. Mechanisms of Action of Novel Influenza A/M2 Viroporin Inhibitors Derived from Hexamethylene Amiloride. Mol Pharmacol 2016; 90:80-95. [PMID: 27193582 DOI: 10.1124/mol.115.102731] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/12/2016] [Indexed: 01/09/2023] Open
Abstract
The increasing prevalence of influenza viruses with resistance to approved antivirals highlights the need for new anti-influenza therapeutics. Here we describe the functional properties of hexamethylene amiloride (HMA)-derived compounds that inhibit the wild-type and adamantane-resistant forms of the influenza A M2 ion channel. For example, 6-(azepan-1-yl)-N-carbamimidoylnicotinamide ( 9: ) inhibits amantadine-sensitive M2 currents with 3- to 6-fold greater potency than amantadine or HMA (IC50 = 0.2 vs. 0.6 and 1.3 µM, respectively). Compound 9: competes with amantadine for M2 inhibition, and molecular docking simulations suggest that 9: binds at site(s) that overlap with amantadine binding. In addition, tert-butyl 4'-(carbamimidoylcarbamoyl)-2',3-dinitro-[1,1'-biphenyl]-4-carboxylate ( 27: ) acts both on adamantane-sensitive and a resistant M2 variant encoding a serine to asparagine 31 mutation (S31N) with improved efficacy over amantadine and HMA (IC50 = 0.6 µM and 4.4 µM, respectively). Whereas 9: inhibited in vitro replication of influenza virus encoding wild-type M2 (EC50 = 2.3 µM), both 27: and tert-butyl 4'-(carbamimidoylcarbamoyl)-2',3-dinitro-[1,1'-biphenyl]-4-carboxylate ( 26: ) preferentially inhibited viruses encoding M2(S31N) (respective EC50 = 18.0 and 1.5 µM). This finding indicates that HMA derivatives can be designed to inhibit viruses with resistance to amantadine. Our study highlights the potential of HMA derivatives as inhibitors of drug-resistant influenza M2 ion channels.
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Affiliation(s)
- Pouria H Jalily
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Jodene Eldstrom
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Scott C Miller
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Daniel C Kwan
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Sheldon S-H Tai
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Doug Chou
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Masahiro Niikura
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - Ian Tietjen
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
| | - David Fedida
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver (P.H.J., J.E., S.C.M., D.C.K., D.C., I.T., D.F.), and Faculty of Health Sciences, Simon Fraser University, Burnaby (S.S.-H.T., M.N., I.T.), British Columbia, Canada
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22
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Kalita MM, Fischer WB. Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1462-70. [PMID: 27079148 DOI: 10.1016/j.bbamem.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/01/2023]
Abstract
Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
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23
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Fischer WB, Kalita MM, Heermann D. Viral channel forming proteins--How to assemble and depolarize lipid membranes in silico. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1710-21. [PMID: 26806161 PMCID: PMC7094687 DOI: 10.1016/j.bbamem.2016.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/23/2023]
Abstract
Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug–protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Early references about the discovery of viral channel forming proteins. Latest structural information about the class of proteins. Identification of structural motifs, assembly mechanism of function and drug action using computational methods. Outlook for the use of coarse grained techniques to address assembly and integration into cellular processes.
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Affiliation(s)
- Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Dieter Heermann
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
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24
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Lin MH, Chen CP, Fischer WB. Patch formation of a viral channel forming protein within a lipid membrane – Vpu of HIV-1. MOLECULAR BIOSYSTEMS 2016; 12:1118-27. [DOI: 10.1039/c5mb00798d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dimer-first formation leads to larger assemblies with potentially relevant structures.
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Affiliation(s)
- Meng-Han Lin
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Chin-Pei Chen
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Wolfgang B. Fischer
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
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Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? Viruses 2015; 7:5375-87. [PMID: 26501313 PMCID: PMC4632388 DOI: 10.3390/v7102880] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/02/2015] [Accepted: 10/12/2015] [Indexed: 12/20/2022] Open
Abstract
Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. These viroporins mediate the flow of ions and a range of solutes across cellular membranes and are necessary for manipulating a myriad of host processes. As such they contribute to all stages of the virus life cycle. Recent discoveries have identified proteins encoded by the small DNA tumor viruses that display a number of viroporin like properties. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention.
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A coiled-coil motif in non-structural protein 3 (NS3) of bluetongue virus forms an oligomer. Virus Genes 2015; 51:244-51. [PMID: 26318174 DOI: 10.1007/s11262-015-1230-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Bluetongue, an arthropod-borne non-contagious hemorrhagic disease of small ruminants, is caused by bluetongue virus (BTV). Several structural and non-structural proteins encoded by BTV have been associated with virulence mechanisms. In the present study, the NS3 protein sequences of bluetongue viral serotypes were analyzed for the presence of heptad regions and oligomer formation. Bioinformatic analysis of NS3 sequences of all 26 BTV serotypes revealed the presence of at least three coiled-coil motifs (CCMs). A conserved α-helical heptad sequence was identified at 14-26 aa (CCM-I), 185-198aa (CCM-II), and 94-116 aa (CCM-III). Among these, CCM-I occurs close to the N-terminus of NS3 and was presumed to be involved in oligomerization. Furthermore, the N-terminus of NS3 (1M-R117 aa) was over-expressed as a recombinant fusion protein in a prokaryotic expression system. Biochemical characterization of recombinant NS3Nt protein revealed that it forms SDS-resistant dimers and high-order oligomers (hexamer and/or octamer) under reducing or non-reducing conditions. Coiled-coil motifs are believed to be critical for NS protein oligomerization and have potential roles in the formation of viroporin ring/pore either with six/eight subunits and this is the first study toward characterization of CCMs in NS3 of bluetongue virus.
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"Too little, too late?" Will inhibitors of the hepatitis C virus p7 ion channel ever be used in the clinic? Future Med Chem 2015; 6:1893-907. [PMID: 25495983 DOI: 10.4155/fmc.14.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is a virus-coded ion channel, or 'viroporin'. p7 is an essential HCV protein, promoting infectious virion production, and this process can be blocked by prototypic p7 inhibitors. However, prototype potency is weak and effects in clinical trials are unsatisfactory. Nevertheless, recent structural studies render p7 amenable to modern drug discovery, with studies supporting that effective drug-like molecules should be achievable. However, burgeoning HCV therapies clear infection in the majority of treated patients. This perspective summarizes current understanding of p7 channel function and structure, pertaining to the development of improved p7 inhibitors. We ask, 'is this too little, too late', or could p7 inhibitors play a role in the long-term management of HCV disease?
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Martinez-Gil L, Mingarro I. Viroporins, Examples of the Two-Stage Membrane Protein Folding Model. Viruses 2015; 7:3462-82. [PMID: 26131957 PMCID: PMC4517110 DOI: 10.3390/v7072781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/21/2022] Open
Abstract
Viroporins are small, α-helical, hydrophobic virus encoded proteins, engineered to form homo-oligomeric hydrophilic pores in the host membrane. Viroporins participate in multiple steps of the viral life cycle, from entry to budding. As any other membrane protein, viroporins have to find the way to bury their hydrophobic regions into the lipid bilayer. Once within the membrane, the hydrophobic helices of viroporins interact with each other to form higher ordered structures required to correctly perform their porating activities. This two-step process resembles the two-stage model proposed for membrane protein folding by Engelman and Poppot. In this review we use the membrane protein folding model as a leading thread to analyze the mechanism and forces behind the membrane insertion and folding of viroporins. We start by describing the transmembrane segment architecture of viroporins, including the number and sequence characteristics of their membrane-spanning domains. Next, we connect the differences found among viroporin families to their viral genome organization, and finalize focusing on the pathways used by viroporins in their way to the membrane and on the transmembrane helix-helix interactions required to achieve proper folding and assembly.
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Affiliation(s)
- Luis Martinez-Gil
- Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain.
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain.
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Viral Membrane Channels: Role and Function in the Virus Life Cycle. Viruses 2015; 7:3261-84. [PMID: 26110585 PMCID: PMC4488738 DOI: 10.3390/v7062771] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 05/20/2015] [Accepted: 06/12/2015] [Indexed: 12/23/2022] Open
Abstract
Viroporins are small, hydrophobic trans-membrane viral proteins that oligomerize to form hydrophilic pores in the host cell membranes. These proteins are crucial for the pathogenicity and replication of viruses as they aid in various stages of the viral life cycle, from genome uncoating to viral release. In addition, the ion channel activity of viroporin causes disruption in the cellular ion homeostasis, in particular the calcium ion. Fluctuation in the calcium level triggers the activation of the host defensive programmed cell death pathways as well as the inflammasome, which in turn are being subverted for the viruses’ replication benefits. This review article summarizes recent developments in the functional investigation of viroporins from various viruses and their contributions to viral replication and virulence.
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30
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Opella SJ. Relating structure and function of viral membrane-spanning miniproteins. Curr Opin Virol 2015; 12:121-5. [PMID: 26057606 DOI: 10.1016/j.coviro.2015.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/25/2022]
Abstract
Many viruses express small hydrophobic membrane proteins. These proteins are often referred to as viroporins because they exhibit ion channel activity. However, the channel activity has not been definitively associated with a biological function in all cases. More generally, protein-protein and protein-phospholipid interactions have been associated with specific biological activities of these proteins. As research has progressed there is a decreased emphasis on potential roles of the channel activity, and increased research on multiple other biological functions. This being the case, it may be more appropriate to refer to them as 'viral membrane-spanning miniproteins'. Structural studies are illustrated with Vpu from HIV-1 and p7 from HCV.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA.
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31
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Kalita MM, Griffin S, Chou JJ, Fischer WB. Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1383-92. [PMID: 25772504 PMCID: PMC7094707 DOI: 10.1016/j.bbamem.2015.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/12/2015] [Accepted: 03/06/2015] [Indexed: 12/12/2022]
Abstract
The 63 amino acid polytopic membrane protein, p7, encoded by hepatitis C virus (HCV) is involved in the modulation of electrochemical gradients across membranes within infected cells. Structural information relating to p7 from multiple genotypes has been generated in silico (e.g. genotype (GT) 1a), as well as obtained from experiments in form of monomeric and hexameric structures (GTs 1b and 5a, respectively). However, sequence diversity and structural differences mean that comparison of their channel gating behaviour has not thus far been simulated. Here, a molecular model of the monomeric GT 1a protein is optimized and assembled into a hexameric bundle for comparison with both the 5a hexamer structure and another hexameric bundle generated using the GT 1b monomer structure. All bundles tend to turn into a compact structure during molecular dynamics (MD) simulations (Gromos96 (ffG45a3)) in hydrated lipid bilayers, as well as when simulated at 'low pH', which may trigger channel opening according to some functional studies. Both GT 1a and 1b channel models are gated via movement of the parallel aligned helices, yet the scenario for the GT 5a protein is more complex, with a short N-terminal helix being involved. However, all bundles display pulsatile dynamics identified by monitoring water dynamics within the pore.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, TW
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology, Faculty of Medicine and Health, St James' University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, UK
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, TW.
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Carrara G, Saraiva N, Parsons M, Byrne B, Prole DL, Taylor CW, Smith GL. Golgi anti-apoptotic proteins are highly conserved ion channels that affect apoptosis and cell migration. J Biol Chem 2015; 290:11785-801. [PMID: 25713081 PMCID: PMC4416878 DOI: 10.1074/jbc.m115.637306] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 12/03/2022] Open
Abstract
Golgi anti-apoptotic proteins (GAAPs) are multitransmembrane proteins that are expressed in the Golgi apparatus and are able to homo-oligomerize. They are highly conserved throughout eukaryotes and are present in some prokaryotes and orthopoxviruses. Within eukaryotes, GAAPs regulate the Ca2+ content of intracellular stores, inhibit apoptosis, and promote cell adhesion and migration. Data presented here demonstrate that purified viral GAAPs (vGAAPs) and human Bax inhibitor 1 form ion channels and that vGAAP from camelpox virus is selective for cations. Mutagenesis of vGAAP, including some residues conserved in the recently solved structure of a related bacterial protein, BsYetJ, altered the conductance (E207Q and D219N) and ion selectivity (E207Q) of the channel. Mutation of residue Glu-207 or -178 reduced the effects of GAAP on cell migration and adhesion without affecting protection from apoptosis. In contrast, mutation of Asp-219 abrogated the anti-apoptotic activity of GAAP but not its effects on cell migration and adhesion. These results demonstrate that GAAPs are ion channels and define residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion, and migration independently.
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Affiliation(s)
- Guia Carrara
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nuno Saraiva
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Maddy Parsons
- the Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Bernadette Byrne
- the Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom, and
| | - David L Prole
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Colin W Taylor
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Geoffrey L Smith
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
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Xiao X, Min JL, Lin WZ, Liu Z, Cheng X, Chou KC. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach. J Biomol Struct Dyn 2015; 33:2221-33. [DOI: 10.1080/07391102.2014.998710] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Xuan Xiao
- Computer Department, Jing-De-Zhen Ceramic Institute , Jing-De-Zhen 333046, China
- Information School, ZheJiang Textile & Fashion College , NingBo 315211, China
- Gordon Life Science Institute , 53 South Cottage Road, Boston 02478, MA, USA
| | - Jian-Liang Min
- Computer Department, Jing-De-Zhen Ceramic Institute , Jing-De-Zhen 333046, China
| | - Wei-Zhong Lin
- Computer Department, Jing-De-Zhen Ceramic Institute , Jing-De-Zhen 333046, China
| | - Zi Liu
- Computer Department, Jing-De-Zhen Ceramic Institute , Jing-De-Zhen 333046, China
| | - Xiang Cheng
- Computer Department, Jing-De-Zhen Ceramic Institute , Jing-De-Zhen 333046, China
| | - Kuo-Chen Chou
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University , JeddaH 21589, Saudi Arabia
- Gordon Life Science Institute , 53 South Cottage Road, Boston 02478, MA, USA
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Bichmann L, Wang YT, Fischer WB. Docking assay of small molecule antivirals to p7 of HCV. Comput Biol Chem 2014; 53PB:308-317. [PMID: 25462337 DOI: 10.1016/j.compbiolchem.2014.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 10/31/2014] [Accepted: 11/08/2014] [Indexed: 01/14/2023]
Abstract
Protein p7 of HCV is a 63 amino acid channel forming membrane protein essential for the progression of viral infection. With this momentousness, p7 emerges as an important target for antiviral therapy. A series of small molecule drugs, such as amantadine, rimantadine, amiloride, hexamethylene amiloride, NN-DNJ and BIT225 have been found to affect the channel activity. These compounds are docked against monomeric and hexameric structures of p7 taken at various time steps from a molecular dynamics simulation of the protein embedded in a hydrated lipid bilayer. The energetics of binding identifies the guanidine based ligands as the most potent ligands. The adamantanes and NN-DNJ show weaker binding energies. The lowest energy poses are those at the site of the loop region for the monomer and hexamer. For the latter, the poses show a tendency of the ligand to face the lumen of the pore. The mode of binding is that of a balance between hydrophobic interactions and hydrogen bond formation with backbone atoms of the protein.
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Affiliation(s)
- Leon Bichmann
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan, ROC
| | - Yi-Ting Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan, ROC
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan, ROC.
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Stepwise priming by acidic pH and a high K+ concentration is required for efficient uncoating of influenza A virus cores after penetration. J Virol 2014; 88:13029-46. [PMID: 25165113 DOI: 10.1128/jvi.01430-14] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED Influenza A virus (IAV) uses the low pH in late endocytic vacuoles as a cue for penetration by membrane fusion. Here, we analyzed the prefusion reactions that prepare the core for uncoating after it has been delivered to the cytosol. We found that this priming process occurs in two steps that are mediated by the envelope-embedded M2 ion channel. The first weakens the interactions between the matrix protein, M1, and the viral ribonucleoprotein bundle. It involves a conformational change in a linker sequence and the C-terminal domain of M1 after exposure to a pH below 6.5. The second step is triggered by a pH of <6.0 and by the influx of K(+) ions. It causes additional changes in M1 as well as a loss of stability in the viral ribonucleoprotein bundle. Our results indicate that both the switch from Na(+) to K(+) in maturing endosomes and the decreasing pH are needed to prime IAV cores for efficient uncoating and infection of the host cell. IMPORTANCE The entry of IAV involves several steps, including endocytosis and fusion at late endosomes. Entry also includes disassembly of the viral core, which is composed of the viral ribonucleoproteins and the RNA genome. We have found that the uncoating process of IAV is initiated long before the core is delivered into the cytosol. M2, an ion channel in the viral membrane, is activated when the virus passes through early endosomes. Here, we show that protons entering the virus through M2 cause a conformational change in the matrix protein, M1. This weakens interactions between M1 and the viral ribonucleoproteins. A second change was found to occur when the virus enters late endosomes. The preacidified core is then exposed to a high concentration of K(+), which affects the interactions between the ribonucleoproteins. Thus, when cores are finally delivered to the cytosol, they are already partially destabilized and, therefore, uncoating competent and infectious.
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