1
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Breitinger U, Sedky CA, Sticht H, Breitinger HG. Patch-clamp studies and cell viability assays suggest a distinct site for viroporin inhibitors on the E protein of SARS-CoV-2. Virol J 2023; 20:142. [PMID: 37422646 PMCID: PMC10329798 DOI: 10.1186/s12985-023-02095-y] [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: 07/30/2022] [Accepted: 06/08/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND SARS-CoV-2 has caused a worldwide pandemic since December 2019 and the search for pharmaceutical targets against COVID-19 remains an important challenge. Here, we studied the envelope protein E of SARS-CoV and SARS-CoV-2, a highly conserved 75-76 amino acid viroporin that is crucial for virus assembly and release. E protein channels were recombinantly expressed in HEK293 cells, a membrane-directing signal peptide ensured transfer to the plasma membrane. METHODS Viroporin channel activity of both E proteins was investigated using patch-clamp electrophysiology in combination with a cell viability assay. We verified inhibition by classical viroporin inhibitors amantadine, rimantadine and 5-(N,N-hexamethylene)-amiloride, and tested four ivermectin derivatives. RESULTS Classical inhibitors showed potent activity in patch-clamp recordings and viability assays. In contrast, ivermectin and milbemycin inhibited the E channel in patch-clamp recordings but displayed only moderate activity on the E protein in the cell viability assay, which is also sensitive to general cytotoxic activity of the tested compounds. Nemadectin and ivermectin aglycon were inactive. All ivermectin derivatives were cytotoxic at concentrations > 5 µM, i.e. below the level required for E protein inhibition. CONCLUSIONS This study demonstrates direct inhibition of the SARS-CoV-2 E protein by classical viroporin inhibitors. Ivermectin and milbemycin inhibit the E protein channel but their cytotoxicity argues against clinical application.
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Affiliation(s)
- Ulrike Breitinger
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt.
| | - Christine Adel Sedky
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt
| | - Heinrich Sticht
- Division of Bioinformatics, Institute for Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Georg Breitinger
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt
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2
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Somberg NH, Wu WW, Medeiros-Silva J, Dregni AJ, Jo H, DeGrado WF, Hong M. SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers. Biochemistry 2022; 61:2280-2294. [PMID: 36219675 PMCID: PMC9583936 DOI: 10.1021/acs.biochem.2c00464] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/26/2022] [Indexed: 11/30/2022]
Abstract
The SARS-CoV-2 envelope (E) protein is a viroporin associated with the acute respiratory symptoms of COVID-19. E forms cation-selective ion channels that assemble in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment. The channel activity of E is linked to the inflammatory response of the host cell to the virus. Like many viroporins, E is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the E stoichiometry have led to inconclusive results and suggested mixtures of oligomers whose exact nature might vary with the detergent used. Here, we employ 19F solid-state nuclear magnetic resonance and the centerband-only detection of exchange (CODEX) technique to determine the oligomeric number of E's transmembrane domain (ETM) in lipid bilayers. The CODEX equilibrium value, which corresponds to the inverse of the oligomeric number, indicates that ETM assembles into pentamers in lipid bilayers, without any detectable fraction of low-molecular-weight oligomers. Unexpectedly, at high peptide concentrations and in the presence of the lipid phosphatidylinositol, the CODEX data indicate that more than five 19F spins are within a detectable distance of about 2 nm, suggesting that the ETM pentamers cluster in the lipid bilayer. Monte Carlo simulations that take into account peptide-peptide and peptide-lipid interactions yielded pentamer clusters that reproduced the CODEX data. This supramolecular organization is likely important for E-mediated virus assembly and budding and for the channel function of the protein.
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Affiliation(s)
- Noah H. Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Westley W. Wu
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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3
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Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES 2022; 1864:183994. [PMID: 35724739 PMCID: PMC9212275 DOI: 10.1016/j.bbamem.2022.183994] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 01/20/2023]
Abstract
SARS-CoV-2 contains four structural proteins in its genome. These proteins aid in the assembly and budding of new virions at the ER-Golgi intermediate compartment (ERGIC). Current fundamental research efforts largely focus on one of these proteins – the spike (S) protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other structural proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length envelope (E) protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.
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4
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Breitinger U, Farag NS, Sticht H, Breitinger HG. Viroporins: Structure, function, and their role in the life cycle of SARS-CoV-2. Int J Biochem Cell Biol 2022; 145:106185. [PMID: 35219876 PMCID: PMC8868010 DOI: 10.1016/j.biocel.2022.106185] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Viroporins are indispensable for viral replication. As intracellular ion channels they disturb pH gradients of organelles and allow Ca2+ flux across ER membranes. Viroporins interact with numerous intracellular proteins and pathways and can trigger inflammatory responses. Thus, they are relevant targets in the search for antiviral drugs. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underlies the world-wide pandemic of COVID-19, where an effective therapy is still lacking despite impressive progress in the development of vaccines and vaccination campaigns. Among the 29 proteins of SARS-CoV-2, the E- and ORF3a proteins have been identified as viroporins that contribute to the massive release of inflammatory cytokines observed in COVID-19. Here, we describe structure and function of viroporins and their role in inflammasome activation and cellular processes during the virus replication cycle. Techniques to study viroporin function are presented, with a focus on cellular and electrophysiological assays. Contributions of SARS-CoV-2 viroporins to the viral life cycle are discussed with respect to their structure, channel function, binding partners, and their role in viral infection and virus replication. Viroporin sequences of new variants of concern (α–ο) of SARS-CoV-2 are briefly reviewed as they harbour changes in E and 3a proteins that may affect their function.
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Affiliation(s)
- Ulrike Breitinger
- Department of Biochemistry, German University in Cairo, New Cairo, Egypt
| | - Noha S Farag
- Department of Microbiology and Immunology, German University in Cairo, New Cairo, Egypt
| | - Heinrich Sticht
- Division of Bioinformatics, Institute for Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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5
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Dwivedi V, Gupta RK, Gupta A, Chaudhary VK, Gupta S, Gupta V. Repurposing Novel Antagonists to p7 Viroporin of HCV Using in silico Approach. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220124112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Background: P7 viroporin in HCV is a cation-selective ion channel-forming protein, functional in the oligomeric form. It is considered to be a potential target for anti-HCV compounds due to its crucial role in viral entry, assembly and release.
Method:
Conserved crucial residues present in HCV p7 protein were delineated with a specific focus on the genotypes 3a &1b prevalent in India from the available literature. Using the Flex-X docking tool, a library of FDA-approved drugs was docked on the receptor sites prepared around crucial residues. In the present study, we propose drug repurposing to target viroporin p7, which may help in the rapid development of effective anti-HCV therapies.
Results:
With our approach of poly-pharmacology, a variety of drugs currently identified classified as antibiotics, anti-parasitic, antiemetic, anti-retroviral, and anti-neoplastic were found to dock successfully with the p7 viroporin. Noteworthy among these are general-purpose cephalosporin antibiotics, leucal, phthalylsulfathiazole, and granisetron, which may be useful in acute HCV infection and anti-neoplastic sorafenib and nilotinib, which may be valuable in advanced HCV-HCC cases.
Conclusion:
This study could pave the way for quick repurposing of these compounds as anti-HCV therapeutics.
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Affiliation(s)
- Varsha Dwivedi
- Department of Microbiology, Ram Lal Anand College, Delhi University, Benito Juarez Road, New Delhi, India
| | - Rakesh Kumar Gupta
- Department of Microbiology, Ram Lal Anand College, Delhi University, Benito Juarez Road, New Delhi, India
| | - Amita Gupta
- Department of Biochemistry and Centre for Innovation in Infectious Disease Research, Education and Training, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
| | - Vijay K Chaudhary
- Department of Biochemistry and Centre for Innovation in Infectious Disease Research, Education and Training, University of Delhi South Campus, Benito Juarez Marg, New Delhi, India
| | - Sanjay Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, Delhi University, Benito Juarez Road, New Delhi, India
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6
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Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
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Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
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7
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Inhibitor Development against p7 Channel in Hepatitis C Virus. Molecules 2021; 26:molecules26051350. [PMID: 33802584 PMCID: PMC7961618 DOI: 10.3390/molecules26051350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022] Open
Abstract
Hepatitis C Virus (HCV) is the key cause of chronic and severe liver diseases. The recent direct-acting antiviral agents have shown the clinical success on HCV-related diseases, but the rapid HCV mutations of the virus highlight the sustaining necessity to develop new drugs. p7, the viroporin protein from HCV, has been sought after as a potential anti-HCV drug target. Several classes of compounds, such as amantadine and rimantadine have been testified for p7 inhibition. However, the efficacies of these compounds are not high. Here, we screened some novel p7 inhibitors with amantadine scaffold for the inhibitor development. The dissociation constant (Kd) of 42 ARD-series compounds were determined by nuclear magnetic resonance (NMR) titrations. The efficacies of the two best inhibitors, ARD87 and ARD112, were further confirmed using viral production assay. The binding mode analysis and binding stability for the strongest inhibitor were deciphered by molecular dynamics (MD) simulation. These ARD-series compounds together with 49 previously published compounds were further analyzed by molecular docking. Key pharmacophores were identified among the structure-similar compounds. Our studies suggest that different functional groups are highly correlated with the efficacy for inhibiting p7 of HCV, in which hydrophobic interactions are the dominant forces for the inhibition potency. Our findings provide guiding principles for designing higher affinity inhibitors of p7 as potential anti-HCV drug candidates.
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8
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Shaw J, Gosain R, Kalita MM, Foster TL, Kankanala J, Mahato DR, Abas S, King BJ, Scott C, Brown E, Bentham MJ, Wetherill L, Bloy A, Samson A, Harris M, Mankouri J, Rowlands DJ, Macdonald A, Tarr AW, Fischer WB, Foster R, Griffin S. Rationally derived inhibitors of hepatitis C virus (HCV) p7 channel activity reveal prospect for bimodal antiviral therapy. eLife 2020; 9:e52555. [PMID: 33169665 PMCID: PMC7714397 DOI: 10.7554/elife.52555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
Since the 1960s, a single class of agent has been licensed targeting virus-encoded ion channels, or 'viroporins', contrasting the success of channel blocking drugs in other areas of medicine. Although resistance arose to these prototypic adamantane inhibitors of the influenza A virus (IAV) M2 proton channel, a growing number of clinically and economically important viruses are now recognised to encode essential viroporins providing potential targets for modern drug discovery. We describe the first rationally designed viroporin inhibitor with a comprehensive structure-activity relationship (SAR). This step-change in understanding not only revealed a second biological function for the p7 viroporin from hepatitis C virus (HCV) during virus entry, but also enabled the synthesis of a labelled tool compound that retained biological activity. Hence, p7 inhibitors (p7i) represent a unique class of HCV antiviral targeting both the spread and establishment of infection, as well as a precedent for future viroporin-targeted drug discovery.
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Affiliation(s)
- Joseph Shaw
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Rajendra Gosain
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Monoj Mon Kalita
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Toshana L Foster
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jayakanth Kankanala
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - D Ram Mahato
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Sonia Abas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Barnabas J King
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | - Claire Scott
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Emma Brown
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Matthew J Bentham
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Laura Wetherill
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Abigail Bloy
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Adel Samson
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
| | - Mark Harris
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jamel Mankouri
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Andrew Macdonald
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Alexander W Tarr
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | | | - Richard Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Stephen Griffin
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
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9
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Alzahrani N, Wu MJ, Shanmugam S, Yi M. Delayed by Design: Role of Suboptimal Signal Peptidase Processing of Viral Structural Protein Precursors in Flaviviridae Virus Assembly. Viruses 2020; 12:v12101090. [PMID: 32993149 PMCID: PMC7601889 DOI: 10.3390/v12101090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The Flaviviridae virus family is classified into four different genera, including flavivirus, hepacivirus, pegivirus, and pestivirus, which cause significant morbidity and mortality in humans and other mammals, including ruminants and pigs. These are enveloped, single-stranded RNA viruses sharing a similar genome organization and replication scheme with certain unique features that differentiate them. All viruses in this family express a single polyprotein that encodes structural and nonstructural proteins at the N- and C-terminal regions, respectively. In general, the host signal peptidase cleaves the structural protein junction sites, while virus-encoded proteases process the nonstructural polyprotein region. It is known that signal peptidase processing is a rapid, co-translational event. Interestingly, certain signal peptidase processing site(s) in different Flaviviridae viral structural protein precursors display suboptimal cleavage kinetics. This review focuses on the recent progress regarding the Flaviviridae virus genus-specific mechanisms to downregulate signal peptidase-mediated processing at particular viral polyprotein junction sites and the role of delayed processing at these sites in infectious virus particle assembly.
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10
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Cao Y, Yang R, Wang W, Lee I, Zhang R, Zhang W, Sun J, Xu B, Meng X. Computational Study of the Ion and Water Permeation and Transport Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel. Front Mol Biosci 2020; 7:565797. [PMID: 33173781 PMCID: PMC7538787 DOI: 10.3389/fmolb.2020.565797] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/04/2020] [Indexed: 12/28/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is a public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 shares a high level of homology with severe acute respiratory syndrome coronavirus (SARS-CoV). In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms using a combination of in silico methods. Based on our results, the pentameric E protein promotes the penetration of cation ions through the channel. An analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore exhibits a clear wetting/dewetting transition with cation selectivity under transmembrane voltage, indicating that it is a hydrophobic voltage-dependent channel. Overall, these results provide structure-based insights and molecular dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin, China
| | - Ruiping Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Bo Xu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Center for Intelligent Oncology, Chongqing University School of Medicine and Chongqing University Cancer Hospital, Chongqing, China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
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11
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Farag NS, Breitinger U, Breitinger HG, El Azizi MA. Viroporins and inflammasomes: A key to understand virus-induced inflammation. Int J Biochem Cell Biol 2020; 122:105738. [PMID: 32156572 PMCID: PMC7102644 DOI: 10.1016/j.biocel.2020.105738] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
The article provides a summary on cellular receptors involved in virus immunity. It summarizes key findings on viroporins, a novel class of viral proteins and their role in the virus life cycle and host cell interactions. It presents an overview of the current understanding of inflammasomes complex activation, with special focus on NLRP3. It discusses the correlation between viroporins and inflammasomes activation and aggravated inflammatory cytokines production.
Viroporins are virus encoded proteins that alter membrane permeability and can trigger subsequent cellular signals. Oligomerization of viroporin subunits results in formation of a hydrophilic pore which facilitates ion transport across host cell membranes. These viral channel proteins may be involved in different stages of the virus infection cycle. Inflammasomes are large multimolecular complexes best recognized for their ability to control activation of caspase-1, which in turn regulates the maturation of interleukin-1 β (IL-1β) and interleukin 18 (IL-18). IL-1β was originally identified as a pro-inflammatory cytokine able to induce both local and systemic inflammation and a febrile reaction in response to infection or injury. Excessive production of IL-1β is associated with autoimmune and inflammatory diseases. Microbial derivatives, bacterial pore-forming toxins, extracellular ATP and other pathogen-associated molecular patterns trigger activation of NLRP3 inflammasomes. Recent studies have reported that viroporin activity is capable of inducing inflammasome activity and production of IL-1β, where NLRP3 is shown to be regulated by fluxes of K+, H+ and Ca2+ in addition to reactive oxygen species, autophagy and endoplasmic reticulum stress. The aim of this review is to present an overview of the key findings on viroporin activity with special emphasis on their role in virus immunity and as possible activators of inflammasomes.
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Affiliation(s)
- N S Farag
- Department of Microbiology and Immunology, German University inCairo, New Cairo, Egypt.
| | - U Breitinger
- Department of Biochemistry, German University in Cairo, New Cairo, Egypt
| | - H G Breitinger
- Department of Biochemistry, German University in Cairo, New Cairo, Egypt
| | - M A El Azizi
- Department of Microbiology and Immunology, German University inCairo, New Cairo, Egypt
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12
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Oestringer BP, Bolivar JH, Claridge JK, Almanea L, Chipot C, Dehez F, Holzmann N, Schnell JR, Zitzmann N. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features. Sci Rep 2019; 9:8383. [PMID: 31182749 PMCID: PMC6557816 DOI: 10.1038/s41598-019-44413-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
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Affiliation(s)
- Benjamin P Oestringer
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RY, United Kingdom
| | - Juan H Bolivar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Jolyon K Claridge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Latifah Almanea
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Chris Chipot
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois, 61801, United States
| | - François Dehez
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Nicole Holzmann
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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13
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Glasner DR, Puerta-Guardo H, Beatty PR, Harris E. The Good, the Bad, and the Shocking: The Multiple Roles of Dengue Virus Nonstructural Protein 1 in Protection and Pathogenesis. Annu Rev Virol 2018; 5:227-253. [PMID: 30044715 DOI: 10.1146/annurev-virology-101416-041848] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dengue virus (DENV) is the most prevalent medically important mosquito-borne virus in the world. Upon DENV infection of a host cell, DENV nonstructural protein 1 (NS1) can be found intracellularly as a monomer, associated with the cell surface as a dimer, and secreted as a hexamer into the bloodstream. NS1 plays a variety of roles in the viral life cycle, particularly in RNA replication and immune evasion of the complement pathway. Over the past several years, key roles for NS1 in the pathogenesis of severe dengue disease have emerged, including direct action of the protein on the vascular endothelium and triggering release of vasoactive cytokines from immune cells, both of which result in endothelial hyperpermeability and vascular leak. Importantly, the adaptive immune response generates a robust response against NS1, and its potential contribution to dengue vaccines is also discussed.
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Affiliation(s)
- Dustin R Glasner
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California 94720-3370, USA; , , ,
| | - Henry Puerta-Guardo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California 94720-3370, USA; , , ,
| | - P Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California 94720-3370, USA; , , ,
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California 94720-3370, USA; , , ,
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14
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Cao Y, Dong Y, Chou JJ. Structural and Functional Properties of Viral Membrane Proteins. ADVANCES IN MEMBRANE PROTEINS 2018. [PMCID: PMC7122571 DOI: 10.1007/978-981-13-0532-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Viruses have developed a large variety of transmembrane proteins to carry out their infectious cycles. Some of these proteins are simply anchored to membrane via transmembrane helices. Others, however, adopt more interesting structures to perform tasks such as mediating membrane fusion and forming ion-permeating channels. Due to the dynamic or plastic nature shown by many of the viral membrane proteins, structural and mechanistic understanding of these proteins has lagged behind their counterparts in prokaryotes and eukaryotes. This chapter provides an overview of the use of NMR spectroscopy to unveil the transmembrane and membrane-proximal regions of viral membrane proteins, as well as their interactions with potential therapeutics.
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Affiliation(s)
- Yu Cao
- Institute of Precision Medicine, The Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Scrima R, Piccoli C, Moradpour D, Capitanio N. Targeting Endoplasmic Reticulum and/or Mitochondrial Ca 2+ Fluxes as Therapeutic Strategy for HCV Infection. Front Chem 2018; 6:73. [PMID: 29619366 PMCID: PMC5871704 DOI: 10.3389/fchem.2018.00073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/06/2018] [Indexed: 01/16/2023] Open
Abstract
Chronic hepatitis C is characterized by metabolic disorders and by a microenvironment in the liver dominated by oxidative stress, inflammation and regeneration processes that can in the long term lead to liver cirrhosis and hepatocellular carcinoma. Several lines of evidence suggest that mitochondrial dysfunctions play a central role in these processes. However, how these dysfunctions are induced by the virus and whether they play a role in disease progression and neoplastic transformation remains to be determined. Most in vitro studies performed so far have shown that several of the hepatitis C virus (HCV) proteins also localize to mitochondria, but the consequences of these interactions on mitochondrial functions remain contradictory and need to be confirmed in the context of productively replicating virus and physiologically relevant in vitro and in vivo model systems. In the past decade we have been proposing a temporal sequence of events in the HCV-infected cell whereby the primary alteration is localized at the mitochondria-associated ER membranes and causes release of Ca2+ from the ER, followed by uptake into mitochondria. This ensues successive mitochondrial dysfunction leading to the generation of reactive oxygen and nitrogen species and a progressive metabolic adaptive response consisting in decreased oxidative phosphorylation and enhanced aerobic glycolysis and lipogenesis. Here we resume the major results provided by our group in the context of HCV-mediated alterations of the cellular inter-compartmental calcium flux homeostasis and present new evidence suggesting targeting of ER and/or mitochondrial calcium transporters as a novel therapeutic strategy.
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Affiliation(s)
- Rosella Scrima
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Darius Moradpour
- Service of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
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16
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Dahl SL, Kalita MM, Fischer WB. Interaction of antivirals with a heptameric bundle model of the p7 protein of hepatitis C virus. Chem Biol Drug Des 2018; 91:942-950. [DOI: 10.1111/cbdd.13162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/01/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Sophie L. Dahl
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Heidelberg Germany
| | - 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
| | - 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
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17
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Patch-Clamp Study of Hepatitis C p7 Channels Reveals Genotype-Specific Sensitivity to Inhibitors. Biophys J 2017; 110:2419-2429. [PMID: 27276260 DOI: 10.1016/j.bpj.2016.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/14/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C is a major worldwide disease and health hazard, affecting ∼3% of the world population. The p7 protein of hepatitis C virus (HCV) is an intracellular ion channel and pH regulator that is involved in the viral replication cycle. It is targeted by various classical ion channel blockers. Here, we generated p7 constructs corresponding to HCV genotypes 1a, 2a, 3a, and 4a for recombinant expression in HEK293 cells, and studied p7 channels using patch-clamp recording techniques. The pH50 values for recombinant p7 channels were between 6.0 and 6.5, as expected for proton-activated channels, and current-voltage dependence did not show any differences between genotypes. Inhibition of p7-mediated currents by amantadine, however, exhibited significant, genotype-specific variation. The IC50 values of p7-1a and p7-4a were 0.7 ± 0.1 nM and 3.2 ± 1.2 nM, whereas p7-2a and p7-3a had 50- to 1000-fold lower sensitivity, with IC50 values of 2402 ± 334 nM and 344 ± 64 nM, respectively. The IC50 values for rimantadine were low across all genotypes, ranging from 0.7 ± 0.1 nM, 1.6 ± 0.6 nM, and 3.0 ± 0.8 nM for p7-1a, p7-3a, and p7-4a, respectively, to 24 ± 4 nM for p7-2a. Results from patch-clamp recordings agreed well with cellular assays of p7 activity, namely, measurements of intracellular pH and hemadsorption assays, which confirmed the much reduced amantadine sensitivity of genotypes 2a and 3a. Thus, our results establish patch-clamp studies of recombinant viroporins as a valid analytical tool that can provide quantitative information about viroporin channel properties, complementing established techniques.
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18
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Holzmann N, Chipot C, Penin F, Dehez F. Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments. Bioorg Med Chem 2016; 24:4920-4927. [PMID: 27501910 DOI: 10.1016/j.bmc.2016.07.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
The viroporin p7 of the hepatitis C virus forms multimeric channels eligible for ion transport across the endoplasmic reticulum membrane. Currently the subject of many studies and discussion, the molecular assembly of the ion channel and the structural characteristics of the p7 monomer are not yet fully understood. Structural investigation of p7 has been carried out only in detergent environments, making the interpretation of the experimental results somewhat questionable. Here, we analyze by means of molecular dynamics simulations the structure of the p7 monomer as a function of its sequence, initial conformation and environment. We investigate the conductance properties of three models of a hexameric p7 ion channel by examining ion translocation in a pure lipid bilayer. It is noteworthy that although none of the models reflects the experimentally observed trend to conduct preferentially cations, we were able to identify the position and orientation of titratable acidic or basic residues playing a crucial role in ion selectivity and in the overall conductance of the channel. In addition, too compact a packing of the monomers leads to channel collapse rather than formation of a reasonable pore, amenable to ion translocation. The present findings are envisioned to help assess the physiological relevance of p7 ion channel models consisting of multimeric structures obtained in non-native environments.
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Affiliation(s)
- Nicole Holzmann
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Christophe Chipot
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Penin
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, UMR 5086, Université de Lyon, 69367 Lyon, France; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, UMR 5086, CNRS, 69367 Lyon, France
| | - François Dehez
- Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France; Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, CNRS, B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France.
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19
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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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20
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Ion Channel Function and Cross-Species Determinants in Viral Assembly of Nonprimate Hepacivirus p7. J Virol 2016; 90:5075-5089. [PMID: 26962224 DOI: 10.1128/jvi.00132-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/03/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Nonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to date, has recently been discovered in horses. Even though the two viruses share a similar genomic organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for the production of infectious particles. In this study, we analyzed the structural and functional features of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models for NPHV p7 using various nuclear magnetic resonance spectroscopy (NMR) structures were generated, highlighting the conserved residues important for ion channel function. By applying a liposome permeability assay, we observed that NPHV p7 exhibited liposome permeability features similar to those of HCV p7, indicative of similar ion channel activity. Next, we characterized the viral protein using a p7-based trans-complementation approach. A similar subcellular localization pattern at the ER membrane was observed, although production of infectious particles was likely hindered by genetic incompatibilities with HCV proteins. To further characterize these cross-species constraints, chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. The N terminus and transmembrane domains were nonexchangeable and therefore constitute a cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious trans-complemented viral particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins, including liposome permeability, and broadly acting determinants that modulate hepaciviral virion assembly and contribute to the host-species barrier were identified. IMPORTANCE The recent discovery of new relatives of hepatitis C virus (HCV) enables for the first time the study of cross-species determinants shaping hepaciviral pathogenesis. Nonprimate hepacivirus (NPHV) was described to infect horses and represents so far the closest homolog of HCV. Both viruses encode the same viral proteins; however, NPHV protein functions remain poorly understood. In this study, we aimed to dissect NPHV p7 on a structural and functional level. By using various NMR structures of HCV p7 as templates, three-dimensional homology models for NPHV p7 were generated, highlighting conserved residues that are important for ion channel function. A p7-based trans-complementation approach and the construction of NPHV/HCV p7 chimeric viruses showed that the N terminus and transmembrane domains were nonexchangeable. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious viral particles. These results identify species-specific constraints as well as exchangeable determinants in hepaciviral assembly.
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21
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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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22
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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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Abstract
Since the discovery that certain small viral membrane proteins, collectively termed as viroporins, can permeabilize host cellular membranes and also behave as ion channels, attempts have been made to link this feature to specific biological roles. In parallel, most viroporins identified so far are virulence factors, and interest has focused toward the discovery of channel inhibitors that would have a therapeutic effect, or be used as research tools to understand the biological roles of viroporin ion channel activity. However, this paradigm is being shifted by the difficulties inherent to small viral membrane proteins, and by the realization that protein-protein interactions and other diverse roles in the virus life cycle may represent an equal, if not, more important target. Therefore, although targeting the channel activity of viroporins can probably be therapeutically useful in some cases, the focus may shift to their other functions in following years. Small-molecule inhibitors have been mostly developed against the influenza A M2 (IAV M2 or AM2). This is not surprising since AM2 is the best characterized viroporin to date, with a well-established biological role in viral pathogenesis combined the most extensive structural investigations conducted, and has emerged as a validated drug target. For other viroporins, these studies are still mostly in their infancy, and together with those for AM2, are the subject of the present review.
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The N-terminal Helical Region of the Hepatitis C Virus p7 Ion Channel Protein Is Critical for Infectious Virus Production. PLoS Pathog 2015; 11:e1005297. [PMID: 26588073 PMCID: PMC4654572 DOI: 10.1371/journal.ppat.1005297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 11/01/2015] [Indexed: 12/16/2022] Open
Abstract
The hepatitis C virus (HCV) p7 protein is required for infectious virus production via its role in assembly and ion channel activity. Although NMR structures of p7 have been reported, the location of secondary structural elements and orientation of the p7 transmembrane domains differ among models. Furthermore, the p7 structure-function relationship remains unclear. Here, extensive mutagenesis, coupled with infectious virus production phenotyping and molecular modeling, demonstrates that the N-terminal helical region plays a previously underappreciated yet critical functional role, especially with respect to E2/p7 cleavage efficiency. Interrogation of specific N-terminal helix residues identified as having p7-specific defects and predicted to point toward the channel pore, in a context of independent E2/p7 cleavage, further supports p7 as a structurally plastic, minimalist ion channel. Together, our findings indicate that the p7 N-terminal helical region is critical for E2/p7 processing, protein-protein interactions, ion channel activity, and infectious HCV production. Hepatitis C virus (HCV) infection can lead to significant liver disease and, without a vaccine, continues to pose a significant public health threat. The viral p7 protein is a multifunctional protein that is required for infectious virus production via its role in orchestrating virion assembly and its activity as an ion channel. However, while there is accumulating structural information on p7, there is no consensus on which conformation(s) exist during a natural infection or how structural elements relate to p7 functions. By comparing two prominent, yet highly divergent models of p7, we identified one region of structural similarity–the N-terminal helical region. While mutagenesis screening of other regions of the protein are in keeping with p7 conformational flexibility, mutations within the N-terminal helical region had a significant impact on infectious virus production, due in part to a loss of efficient E2/p7 cleavage. We further postulated the precise functional impact of mutations throughout p7 by homology modeling and demonstrated tolerance for diverse amino acid substitutions for specific N-terminal helix residues with putative ion channel defects. Together, these data not only support p7 as a structurally plastic, minimalistic ion channel, but also provide extensive insight into the p7 structure-function relationship and highlight the importance of the N-terminal helical region in E2/p7 processing, protein-protein interactions, ion channel activity, and infectious HCV production.
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Soranzo T, Cortès S, Gilde F, Kreir M, Picart C, Lenormand JL. Functional characterization of p7 viroporin from hepatitis C virus produced in a cell-free expression system. Protein Expr Purif 2015; 118:83-91. [PMID: 26477501 DOI: 10.1016/j.pep.2015.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/21/2015] [Accepted: 10/09/2015] [Indexed: 01/05/2023]
Abstract
Using a cell-free expression system we produced the p7 viroporin embedded into a lipid bilayer in a single-step manner. The protein quality was assessed using different methods. We examined the channel forming activity of p7 and verified its inhibition by 5-(N,N-Hexamethylene) amiloride (HMA). Fourier transformed infrared spectroscopy (FTIR) experiments further showed that when p7 was inserted into synthetic liposomes, the protein displayed a native-like conformation similar to p7 obtained from other sources. Photoactivable amino acid analogs used for p7 protein synthesis enabled oligomerization state analysis in liposomes by cross-linking. Therefore, these findings emphasize the quality of the cell-free produced p7 proteoliposomes which can benefit the field of the hepatitis C virus (HCV) protein production and characterization and also provide tools for the development of new inhibitors to reinforce our therapeutic arsenal against HCV.
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Affiliation(s)
- Thomas Soranzo
- Synthelis SAS, 5 avenue du Grand Sablon, 38700, La Tronche, France; TheREx Laboratory, TIMC-IMAG, UMR 5525, CNRS /UJF, University Joseph Fourier, UFR de Médecine, 38706, La Tronche, France
| | - Sandra Cortès
- Synthelis SAS, 5 avenue du Grand Sablon, 38700, La Tronche, France
| | - Flora Gilde
- CNRS, UMR 5628 (LMGP), 3 parvis Louis Néel, 38016, Grenoble, France; University of Grenoble Alpes, Grenoble Institute of Technology, 38016, Grenoble, France
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraβe 9, 80636, Munich, Germany
| | - Catherine Picart
- CNRS, UMR 5628 (LMGP), 3 parvis Louis Néel, 38016, Grenoble, France; University of Grenoble Alpes, Grenoble Institute of Technology, 38016, Grenoble, France
| | - Jean-Luc Lenormand
- TheREx Laboratory, TIMC-IMAG, UMR 5525, CNRS /UJF, University Joseph Fourier, UFR de Médecine, 38706, La Tronche, France.
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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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Structural and Functional Properties of the Hepatitis C Virus p7 Viroporin. Viruses 2015; 7:4461-81. [PMID: 26258788 PMCID: PMC4576187 DOI: 10.3390/v7082826] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
The high prevalence of hepatitis C virus (HCV) infection in the human population has triggered intensive research efforts that have led to the development of curative antiviral therapy. Moreover, HCV has become a role model to study fundamental principles that govern the replication cycle of a positive strand RNA virus. In fact, for most HCV proteins high-resolution X-ray and NMR (Nuclear Magnetic Resonance)-based structures have been established and profound insights into their biochemical and biological properties have been gained. One example is p7, a small hydrophobic protein that is dispensable for RNA replication, but crucial for the production and release of infectious HCV particles from infected cells. Owing to its ability to insert into membranes and assemble into homo-oligomeric complexes that function as minimalistic ion channels, HCV p7 is a member of the viroporin family. This review compiles the most recent findings related to the structure and dual pore/ion channel activity of p7 of different HCV genotypes. The alternative conformations and topologies proposed for HCV p7 in its monomeric and oligomeric state are described and discussed in detail. We also summarize the different roles p7 might play in the HCV replication cycle and highlight both the ion channel/pore-like function and the additional roles of p7 unrelated to its channel activity. Finally, we discuss possibilities to utilize viroporin inhibitors for antagonizing p7 ion channel/pore-like activity.
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28
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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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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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Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
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Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
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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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Abstract
Hepatocytes express an array of plasma membrane and intracellular ion channels, yet their role during the hepatitis C virus (HCV) life cycle remains largely undefined. Here, we show that HCV increases intracellular hepatic chloride (Cl(-)) influx that can be inhibited by selective Cl(-) channel blockers. Through pharmacological and small interfering RNA (siRNA)-mediated silencing, we demonstrate that Cl(-) channel inhibition is detrimental to HCV replication. This represents the first observation of the involvement of Cl(-) channels during the HCV life cycle.
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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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Panjwani A, Strauss M, Gold S, Wenham H, Jackson T, Chou JJ, Rowlands DJ, Stonehouse NJ, Hogle JM, Tuthill TJ. Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore. PLoS Pathog 2014; 10:e1004294. [PMID: 25102288 PMCID: PMC4125281 DOI: 10.1371/journal.ppat.1004294] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 06/24/2014] [Indexed: 01/18/2023] Open
Abstract
Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family. Human rhinovirus (HRV) is a non-enveloped virus of the picornavirus family and is responsible for respiratory infections (common colds) costing billions of dollars ($) annually. There remains no vaccine or licensed drug to prevent or reduce infection. Related members of the picornavirus family include significant pathogens such as poliovirus, enterovirus 71 and foot-and-mouth disease virus, for which improved control measures are also required. A fundamental step in virus infection is the delivery of the viral genetic material through the barrier of the cellular membrane. Viruses such as HIV and influenza are enveloped in an outer membrane which can fuse with the host cell membrane to allow the viral genome to penetrate into the cytoplasm. However, non-enveloped viruses such as picornaviruses lack a membrane and the mechanisms for penetration of the membrane by these viruses remain poorly understood. The capsid protein VP4 has previously been implicated in the delivery of the picornavirus genome. In this study we demonstrate that HRV VP4 interacts with membranes to make them permeable by the formation of multimeric, size-selective membrane pores with properties consistent with the transport of viral genome through the membrane. This function of VP4 provides a novel antiviral target for this family of viruses.
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Affiliation(s)
- Anusha Panjwani
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, West Yorkshire, United Kingdom
| | - Mike Strauss
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sarah Gold
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Hannah Wenham
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Terry Jackson
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - James J. Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Rowlands
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, West Yorkshire, United Kingdom
| | - Nicola J. Stonehouse
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, West Yorkshire, United Kingdom
| | - James M. Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
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35
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Ion-dynamics in hepatitis C virus p7 helical transmembrane domains — a molecular dynamics simulation study. Biophys Chem 2014; 192:33-40. [DOI: 10.1016/j.bpc.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/31/2022]
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36
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Atoom AM, Taylor NGA, Russell RS. The elusive function of the hepatitis C virus p7 protein. Virology 2014; 462-463:377-87. [PMID: 25001174 PMCID: PMC7112009 DOI: 10.1016/j.virol.2014.04.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) is a major global health burden with 2–3% of the world׳s population being chronically infected. Persistent infection can lead to cirrhosis and hepatocellular carcinoma. Recently available treatment options show enhanced efficacy of virus clearance, but are associated with resistance and significant side effects. This warrants further research into the basic understanding of viral proteins and their pathophysiology. The p7 protein of HCV is an integral membrane protein that forms an ion-channel. The role of p7 in the HCV life cycle is presently uncertain, but most of the research performed to date highlights its role in the virus assembly process. The aim of this review is to provide an overview of the literature investigating p7, its structural and functional details, and to summarize the developments to date regarding potential anti-p7 compounds. A better understanding of this protein may lead to development of a new and effective therapy. This review paper provides an overview of the literature investigating HCV. The content focuses on p7 structural and functional details. We summarize the developments to date regarding potential anti-p7 compounds.
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Affiliation(s)
- Ali M Atoom
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada
| | - Nathan G A Taylor
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada
| | - Rodney S Russell
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada.
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37
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Hagen N, Bayer K, Rösch K, Schindler M. The intraviral protein interaction network of hepatitis C virus. Mol Cell Proteomics 2014; 13:1676-89. [PMID: 24797426 DOI: 10.1074/mcp.m113.036301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) is a global health problem and one of the main reasons for chronic liver diseases such as cirrhosis and hepatocellular carcinoma. The HCV genome is translated into a polyprotein which is proteolytically processed into 10 viral proteins. The interactome of the HCV proteins with the host cell has been worked out; however, it remains unclear how viral proteins interact with each other. We aimed to generate the interaction network of these 10 HCV proteins using a flow-cytometry-based FRET assay established in our laboratory (Banning, C., Votteler, J., Hoffmann, D., Koppensteiner, H., Warmer, M., Reimer, R., Kirchhoff, F., Schubert, U., Hauber, J., and Schindler, M. (2010) A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells. PLoS One 5, e9344). HCV proteins were constructed as fusions with the chromophores CFP and YFP. All HCV fusions were expressed and localized to specific subcellular compartments, indicating that they were functional. FACS-FRET measurements identified a total of 20 interactions; 13 of these were previously described and have now been confirmed in living cells via our method. Among the seven novel protein binding pairs, HCV p7 plays a pivotal role. It binds to the HCV capsid protein Core and the two glycoproteins E1 and E2. These interplays were further demonstrated in the relevant context of Huh7.5 liver cells expressing infectious HCV. Our work demonstrates the feasibility of rapidly generating small interaction networks via FACS-FRET and defines the network of intra-HCV protein interactions. Furthermore, our data support an important role of p7 in HCV assembly.
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Affiliation(s)
- Nicole Hagen
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Karen Bayer
- ¶Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Kathrin Rösch
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Michael Schindler
- From the ‡Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; ¶Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany; ‖Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, 72076 Tübingen, Germany
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38
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Foster TL, Thompson GS, Kalverda AP, Kankanala J, Bentham M, Wetherill LF, Thompson J, Barker AM, Clarke D, Noerenberg M, Pearson AR, Rowlands DJ, Homans SW, Harris M, Foster R, Griffin S. Structure-guided design affirms inhibitors of hepatitis C virus p7 as a viable class of antivirals targeting virion release. Hepatology 2014; 59:408-22. [PMID: 24022996 PMCID: PMC4298801 DOI: 10.1002/hep.26685] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 08/07/2013] [Indexed: 01/02/2023]
Abstract
UNLABELLED Current interferon-based therapy for hepatitis C virus (HCV) infection is inadequate, prompting a shift toward combinations of direct-acting antivirals (DAA) with the first protease-targeted drugs licensed in 2012. Many compounds are in the pipeline yet primarily target only three viral proteins, namely, NS3/4A protease, NS5B polymerase, and NS5A. With concerns growing over resistance, broadening the repertoire for DAA targets is a major priority. Here we describe the complete structure of the HCV p7 protein as a monomeric hairpin, solved using a novel combination of chemical shift and nuclear Overhauser effect (NOE)-based methods. This represents atomic resolution information for a full-length virus-coded ion channel, or "viroporin," whose essential functions represent a clinically proven class of antiviral target exploited previously for influenza A virus therapy. Specific drug-protein interactions validate an allosteric site on the channel periphery and its relevance is demonstrated by the selection of novel, structurally diverse inhibitory small molecules with nanomolar potency in culture. Hit compounds represent a 10,000-fold improvement over prototypes, suppress rimantadine resistance polymorphisms at submicromolar concentrations, and show activity against other HCV genotypes. CONCLUSION This proof-of-principle that structure-guided design can lead to drug-like molecules affirms p7 as a much-needed new target in the burgeoning era of HCV DAA.
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Affiliation(s)
- Toshana L Foster
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK,School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Gary S Thompson
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Arnout P Kalverda
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Jayakanth Kankanala
- School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Matthew Bentham
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK
| | - Laura F Wetherill
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK
| | - Joseph Thompson
- School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Amy M Barker
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Dean Clarke
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Marko Noerenberg
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Arwen R Pearson
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - David J Rowlands
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Steven W Homans
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Mark Harris
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
| | - Richard Foster
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK,School of Chemistry, Faculty of Mathematics and Physical Sciences, University of LeedsLeeds, West Yorkshire, UK,Address reprint requests to: Stephen Griffin, Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St. James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire, LS9 7TF, UK. E-mail: ; fax: (+44)113 3438501
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology & CRUK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of LeedsLeeds, West Yorkshire, UK,School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, West Yorkshire, UK
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39
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Two different conformations in hepatitis C virus p7 protein account for proton transport and dye release. PLoS One 2014; 9:e78494. [PMID: 24409277 PMCID: PMC3883635 DOI: 10.1371/journal.pone.0078494] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 10/18/2013] [Indexed: 12/28/2022] Open
Abstract
The p7 protein from the hepatitis C virus (HCV) is a 63 amino acid long polypeptide that is essential for replication, and is involved in protein trafficking and proton transport. Therefore, p7 is a possible target for antivirals. The consensus model for the channel formed by p7 protein is a hexameric or heptameric oligomer of α-helical hairpin monomers, each having two transmembrane domains, TM1 and TM2, where the N-terminal TM1 would face the lumen of this channel. A reported high-throughput functional assay to search for p7 channel inhibitors is based on carboxyfluorescein (CF) release from liposomes after p7 addition. However, the rationale for the dual ability of p7 to serve as an ion or proton channel in the infected cell, and to permeabilize membranes to large molecules like CF is not clear. We have recreated both activities in vitro, examining the conformation present in these assays using infrared spectroscopy. Our results indicate that an α-helical form of p7, which can transport protons, is not able to elicit CF release. In contrast, membrane permeabilization to CF is observed when p7 contains a high percentage of β-structure, or when using a C-terminal fragment of p7, encompassing TM2. We propose that the reported inhibitory effect of some small compounds, e.g., rimantadine, on both CF release and proton transport can be explained via binding to the membrane-inserted C-terminal half of p7, increasing its rigidity, in a similar way to the influenza A M2-rimantadine interaction.
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Atkins E, Tatineni R, Li H, Gretch D, Harris M, Griffin S. The stability of secreted, acid-labile H77/JFH-1 hepatitis C virus (HCV) particles is altered by patient isolate genotype 1a p7 sequences. Virology 2014; 448:117-24. [PMID: 24314642 PMCID: PMC7615703 DOI: 10.1016/j.virol.2013.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/05/2013] [Accepted: 10/03/2013] [Indexed: 12/17/2022]
Abstract
Secreted infectious particles generated by the genotype 2a JFH-1 hepatitis C virus infectious clone are resistant to acidic pH, whereas intracellular virions remain acid-labile. Thus, JFH-1 particles are thought to undergo pH maturation as they are secreted from the cell. Here, we demonstrate that both infectious intracellular and secreted genotype 1a (H77)/JFH-1 chimaeric particles display enhanced acid sensitivity compared with JFH-1, although pH maturation still occurs upon release. Introduction of p7 sequences from genotype 1a infected HCV patients into the H77/JFH-1 background yielded variable effects on infectious particle production and sensitivity to small molecule inhibitors. However, two selected patient p7 sequences increased the acid stability of secreted, but not intracellular H77/JFH-1 particles, suggesting that p7 directly influences particle pH maturation via an as yet undefined mechanism. We propose that HCV particles vary in acid stability, and that this may be dictated by variations in both canonical structural proteins and p7.
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Affiliation(s)
- Elizabeth Atkins
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
| | - Ranjitha Tatineni
- Leeds Institute of Cancer & Pathology (LICAP) and Leeds Cancer Research UK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, United Kingdom
| | - Hui Li
- Department of Laboratory Medicine, University of Washington School of Medicine, Harborview Medical Centre, Ninth & Jefferson Building, 908 Jefferson Street, Seattle, WA 98104, USA
| | - David Gretch
- Department of Laboratory Medicine, University of Washington School of Medicine, Harborview Medical Centre, Ninth & Jefferson Building, 908 Jefferson Street, Seattle, WA 98104, USA
| | - Mark Harris
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
| | - Stephen Griffin
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
- Leeds Institute of Cancer & Pathology (LICAP) and Leeds Cancer Research UK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, United Kingdom
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Shrivastava S, Mukherjee A, Ray R, Ray RB. Hepatitis C virus induces interleukin-1β (IL-1β)/IL-18 in circulatory and resident liver macrophages. J Virol 2013; 87:12284-90. [PMID: 24006444 PMCID: PMC3807883 DOI: 10.1128/jvi.01962-13] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV)-mediated chronic liver disease is a global health problem, and inflammation is believed to be an important player in disease pathogenesis. HCV infection often leads to severe fibrosis/cirrhosis and hepatocellular carcinoma, although the mechanisms for advancement of disease are not fully understood. The proinflammatory cytokines interleukin-1β (IL-1β) and IL-18 have critical roles in establishment of inflammation. In this study, we examined induction of IL-1β/IL-18 secretion following HCV infection. Our results demonstrated that monocyte-derived human macrophages (THP-1) incubated with cell culture-grown HCV enhance the secretion of IL-1β/IL-18 into culture supernatants. A similar cytokine release was also observed for peripheral blood mononuclear cell (PBMC)-derived primary human macrophages and Kupffer cells (liver-resident macrophages) upon incubation with HCV. THP-1 cells incubated with HCV led to caspase-1 activation and release of proinflammatory cytokines. Subsequent studies demonstrated that HCV induces pro-IL-1β and pro-IL-18 synthesis via the NF-κB signaling pathway in macrophages. Furthermore, introduction of HCV viroporin p7 RNA into THP-1 cells was sufficient to cause IL-1β secretion. Together, our results suggested that human macrophages exposed to HCV induce IL-1β and IL-18 secretion, which may play a role in hepatic inflammation.
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Affiliation(s)
| | | | - Ranjit Ray
- Internal Medicine, Saint Louis University, St. Louis, Missouri, USA
| | - Ratna B. Ray
- Departments of Pathology
- Internal Medicine, Saint Louis University, St. Louis, Missouri, USA
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Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain. J Virol 2013; 88:628-42. [PMID: 24173222 DOI: 10.1128/jvi.02052-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) NS4A is a single-pass transmembrane (TM) protein essential for viral replication and particle assembly. The sequence of the NS4A TM domain is highly conserved, suggesting that it may be important for protein-protein interactions. To test this hypothesis, we measured the potential dimerization of the NS4A TM domain in a well-characterized two-hybrid TM protein interaction system. The NS4A TM domain exhibited a strong homotypic interaction that was comparable in affinity to glycophorin A, a well-studied human blood group antigen that forms TM homodimers. Several mutations predicted to cluster on a common surface of the NS4A TM helix caused significant reductions in dimerization, suggesting that these residues form an interface for NS4A dimerization. Mutations in the NS4A TM domain were further examined in the JFH-1 genotype 2a replicon system; importantly, all mutations that destabilized NS4A dimers also caused defects in RNA replication and/or virus assembly. Computational modeling of NS4A TM interactions suggests a right-handed dimeric interaction of helices with an interface that is consistent with the mutational effects. Furthermore, defects in NS4A oligomerization and virus particle assembly of two mutants were rescued by NS4A A15S, a TM mutation recently identified through forward genetics as a cell culture-adaptive mutation. Together, these data provide the first example of a functionally important TM dimer interface within an HCV nonstructural protein and reveal a fundamental role of the NS4A TM domain in coordinating HCV RNA replication and virus particle assembly.
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Viral channel proteins in intracellular protein-protein communication: Vpu of HIV-1, E5 of HPV16 and p7 of HCV. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1113-21. [PMID: 24035804 DOI: 10.1016/j.bbamem.2013.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/06/2013] [Accepted: 08/09/2013] [Indexed: 01/20/2023]
Abstract
Viral channel forming proteins are known for their capability to make the lipid membrane of the host cell and its subcellular compartments permeable to ions and small compounds. There is increasing evidence that some of the representatives of this class of proteins are also strongly interacting with host proteins and the effectiveness of this interaction seems to be high. Interaction of viral channel proteins with host factors has been proposed by bioinformatics approaches and has also been identified experimentally. An overview of the interactions with host proteins is given for Vpu from HIV-1, E5 from HPV-16 and p7 from HCV. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking.
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Lindenbach BD, Rice CM. The ins and outs of hepatitis C virus entry and assembly. Nat Rev Microbiol 2013; 11:688-700. [PMID: 24018384 DOI: 10.1038/nrmicro3098] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus, a major human pathogen, produces infectious virus particles with several unique features, such as an ability to interact with serum lipoproteins, a dizzyingly complicated process of virus entry, and a pathway of virus assembly and release that is closely linked to lipoprotein secretion. Here, we review these unique features, with an emphasis on recent discoveries concerning virus particle structure, virus entry and virus particle assembly and release.
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Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06536, USA
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Efficiency of E2-p7 processing modulates production of infectious hepatitis C virus. J Virol 2013; 87:11255-66. [PMID: 23946462 DOI: 10.1128/jvi.01807-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Previous studies indicate that the processing of hepatitis C virus (HCV) E2-p7-NS2 precursor mediated by host signal peptidase is relatively inefficient, resulting in the accumulation of E2-p7-NS2 and E2-p7 precursors in addition to E2 in mammalian cells. In this study, we discovered that a significant inhibition of the processing at an E2-p7 junction site is detrimental for HCV production, whether it was caused by the mutations in p7 or by the strategic introduction of a mutation at a terminal residue of E2 to block the signal peptidase-mediated cleavage of this junction site. However, complete separation of E2 and p7 by inserting an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) between these two proteins also moderately inhibited virus production. These results indicate that optimal processing of the E2-p7 junction site is critical for efficient HCV production. We further demonstrated that disrupting E2-p7 processing inhibits both NS2 localization to the putative virus assembly sites near lipid droplets (LD) and NS2 interaction with NS3 and E2. However, the impact, if any, of the p7-NS2 processing efficiency on HCV production seems relatively minor. In conclusion, these results imply that effective release of E2 and p7 from the precursor E2-p7 promotes HCV production by enhancing NS2-associated virus assembly complex formation near LD.
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Abstract
Hepatitis C Virus (HCV) particles exhibit several unusual properties that are not found in other enveloped RNA viruses, most notably their low buoyant density and interaction with serum lipoproteins. With the advent of systems to grow HCV in cell culture, the molecular basis of HCV particle assembly and release can now be addressed. The process of virus assembly involves protein-protein interactions between viral structural and nonstructural proteins and the coordinated action of host factors. This chapter reviews our current understanding of these interactions and factors.
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Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
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Moradpour D, Penin F. Hepatitis C virus proteins: from structure to function. Curr Top Microbiol Immunol 2013; 369:113-42. [PMID: 23463199 DOI: 10.1007/978-3-642-27340-7_5] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Great progress has been made over the past years in elucidating the structure and function of the hepatitis C virus (HCV) proteins, most of which are now actively being pursued as antiviral targets. The structural proteins, which form the viral particle, include the core protein and the envelope glycoproteins E1 and E2. The nonstructural proteins include the p7 viroporin, the NS2 protease, the NS3-4A complex harboring protease and NTPase/RNA helicase activities, the NS4B and NS5A proteins, and the NS5B RNA-dependent RNA polymerase. NS4B is a master organizer of replication complex formation while NS5A is a zinc-containing phosphoprotein involved in the regulation of HCV RNA replication versus particle production. Core to NS2 make up the assembly module while NS3 to NS5B represent the replication module (replicase). However, HCV proteins exert multiple functions during the viral life cycle, and these may be governed by different structural conformations and/or interactions with viral and/or cellular partners. Remarkably, each viral protein is anchored to intracellular membranes via specific determinants that are essential to protein function in the cell. This review summarizes current knowledge of the structure and function of the HCV proteins and highlights recent advances in the field.
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Affiliation(s)
- Darius Moradpour
- Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.
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Cook GA, Dawson LA, Tian Y, Opella SJ. Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance. Biochemistry 2013; 52:5295-303. [PMID: 23841474 DOI: 10.1021/bi4006623] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hepatitis C virus (HCV) protein p7 plays an important role in the assembly and release of mature virus particles. This small 63-residue membrane protein has been shown to induce channel activity, which may contribute to its functions. p7 is highly conserved throughout the entire range of HCV genotypes, which contributes to making p7 a potential target for antiviral drugs. The secondary structure of p7 from the J4 genotype and the tilt angles of the helices within bilayers have been previously characterized by nuclear magnetic resonance (NMR). Here we describe the three-dimensional structure of p7 in short chain phospholipid (1,2-dihexanoyl-sn-glycero-3-phosphocholine) micelles, which provide a reasonably effective membrane-mimicking environment that is compatible with solution NMR experiments. Using a combination of chemical shifts, residual dipolar couplings, and PREs, we determined the structure of p7 using an implicit membrane potential combining both CS-Rosetta decoys and Xplor-NIH refinement. The final set of structures has a backbone root-mean-square deviation of 2.18 Å. Molecular dynamics simulations in NAMD indicate that several side chain interactions might be taking place and that these could affect the dynamics of the protein. In addition to probing the dynamics of p7, we evaluated several drug-protein and protein-protein interactions. Established channel-blocking compounds such as amantadine, hexamethylene amiloride, and long alkyl chain iminosugar derivatives inhibit the ion channel activity of p7. It has also been shown that the protein interacts with HCV nonstructural protein 2 at the endoplasmic reticulum and that this interaction may be important for the infectivity of the virus. Changes in the chemical shift frequencies of solution NMR spectra identify the residues taking part in these interactions.
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Affiliation(s)
- Gabriel A Cook
- Department of Chemistry and Biochemistry, University of California at San Diego , La Jolla, California 92093, United States
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Wang YT, Hsu HJ, Fischer WB. Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs. SPRINGERPLUS 2013; 2:324. [PMID: 23961398 PMCID: PMC3724979 DOI: 10.1186/2193-1801-2-324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/11/2013] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus p7 protein is a 63 amino acid polytopic protein with two transmembrane domains (TMDs) and one of the prime targets for anti HCV drug development. A bio-inspired modeling pathway is used to generate plausible computational models of the two TMDs forming the monomeric protein model. A flexible region between Leu-13 and Gly-15 is identified for TMD11-32 and a region around Gly-46 to Trp-48 for TMD236-58. Mutations of the tyrosine residues in TMD236-58 into phenylalanine and serine are simulated to identify their role in shaping TMD2. Lowest energy structures of the two TMDs connected with the loop residues are used for a posing study in which small molecule drugs BIT225, amantadine, rimantadine and NN-DNJ, are identified to bind to the loop region. BIT225 is identified to interact with the backbone of the functionally important residues Arg-35 and Trp-36.
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Affiliation(s)
- Yi-Ting Wang
- Department of Life Science, Tzu Chi University, Hualien, 970 Taiwan
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Li LH, Hsu HJ, Fischer WB. Assembling viral channel forming proteins: Vpu from HIV-1. Biopolymers 2013; 99:517-29. [DOI: 10.1002/bip.22210] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 10/17/2012] [Accepted: 12/22/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Li-Hua Li
- Institute of Biophotonics, School of Biomedical Science and Engineering and Biophotonics and Molecular Imaging Research Center (BMIRC); National Yang-Ming University; Taipei 112; Taiwan
| | - Hao-Jen Hsu
- Institute of Biophotonics, School of Biomedical Science and Engineering and Biophotonics and 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 and Molecular Imaging Research Center (BMIRC); National Yang-Ming University; Taipei 112; Taiwan
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