Structure and Working of Viral Fusion Machinery

: Infectious diseases caused by viruses have become a serious public health issue in the recent past, including the current pandemic situation of COVID-19. Enveloped viruses are most commonly known to cause emerging and recurring infectious diseases. Viral and cell membrane fusion is the major key event in the case of enveloped viruses that is required for their entry into the cell. Viral fusion proteins play an important role in the fusion process and in infection establishment. Because of this, the fusion process targeting antivirals become an interest to fight against viral diseases caused by the enveloped virus. Lower respiratory tract infections casing viruses like influenza, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus (SARS-CoV) are examples of such enveloped viruses that are at the top in public health issues. Here, we summarized the viral fusion protein targeted antiviral peptides along with their mechanism and specific design to combat the viral fusion process. The pandemic COVID-19, severe respiratory syndrome disease is an outbreak worldwide. There are no definitive drugs yet, but few are in on-going trials. Here, an approach of fragmentbased drug design (FBDD) methodology is used to identify the broad spectrum agent target to the conserved region of fusion protein of SARS CoV-2. Three dipeptides (DL, LQ and ID) were chosen from the library and designed by the systematic combination along with their possible modifications of amino acids to the target sites. Designed peptides were docked with targeted fusion protein after energy minimization. Results show strong and significant binding affinity (DL = -60.1 kcal/mol; LQ = - 62.8 kcal/mol; ID= -71.5 kcal/mol) during interaction. Anyone of the active peptides from the developed libraries may help to block the target sites competitively to successfully control COVID-19.

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Targeting Viral Surface Proteins through Structure-Based Design

Viruses ◽

10.3390/v13071320 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1320

Author(s):

Yogesh B Narkhede ◽

Karen J Gonzalez ◽

Eva-Maria Strauch

Keyword(s):

Public Health ◽

Viral Infections ◽

Respiratory Viruses ◽

Surface Proteins ◽

Host Cells ◽

Viral Fusion ◽

Health It ◽

Viral Particles ◽

Pathogenic Viruses ◽

Viral Surface

The emergence of novel viral infections of zoonotic origin and mutations of existing human pathogenic viruses represent a serious concern for public health. It warrants the establishment of better interventions and protective therapies to combat the virus and prevent its spread. Surface glycoproteins catalyzing the fusion of viral particles and host cells have proven to be an excellent target for antivirals as well as vaccines. This review focuses on recent advances for computational structure-based design of antivirals and vaccines targeting viral fusion machinery to control seasonal and emerging respiratory viruses.

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Lysophosphatidylcholine reversibly arrests exocytosis and viral fusion at a stage between triggering and membrane merger.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)74455-x ◽

1993 ◽

Vol 268 (34) ◽

pp. 25764-25768

Author(s):

S S Vogel ◽

E A Leikina ◽

L V Chernomordik

Keyword(s):

Viral Fusion

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Structural comparison of three viral “fusion” proteins

Biochemical Society Transactions ◽

10.1042/bst019312s ◽

1991 ◽

Vol 19 (3) ◽

pp. 312S-312S

Author(s):

BRUCE H NICHOLSON ◽

MAHMOUD NAASE

Keyword(s):

Fusion Proteins ◽

Viral Fusion ◽

Structural Comparison ◽

Viral Fusion Proteins

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HIV-1 requires Arf6-mediated membrane dynamics to efficiently enter and infect T lymphocytes

Molecular Biology of the Cell ◽

10.1091/mbc.e10-08-0722 ◽

2011 ◽

Vol 22 (8) ◽

pp. 1148-1166 ◽

Cited By ~ 22

Author(s):

Laura García-Expósito ◽

Jonathan Barroso-González ◽

Isabel Puigdomènech ◽

José-David Machado ◽

Julià Blanco ◽

...

Keyword(s):

Plasma Membrane ◽

T Lymphocytes ◽

Viral Entry ◽

Membrane Trafficking ◽

Membrane Dynamics ◽

Viral Fusion ◽

Viral Attachment ◽

Immunodeficiency Virus ◽

Vesicular Stomatitis ◽

Hiv 1

As the initial barrier to viral entry, the plasma membrane along with the membrane trafficking machinery and cytoskeleton are of fundamental importance in the viral cycle. However, little is known about the contribution of plasma membrane dynamics during early human immunodeficiency virus type 1 (HIV-1) infection. Considering that ADP ribosylation factor 6 (Arf6) regulates cellular invasion via several microorganisms by coordinating membrane trafficking, our aim was to study the function of Arf6-mediated membrane dynamics on HIV-1 entry and infection of T lymphocytes. We observed that an alteration of the Arf6–guanosine 5′-diphosphate/guanosine 5′-triphosphate (GTP/GDP) cycle, by GDP-bound or GTP-bound inactive mutants or by specific Arf6 silencing, inhibited HIV-1 envelope–induced membrane fusion, entry, and infection of T lymphocytes and permissive cells, regardless of viral tropism. Furthermore, cell-to-cell HIV-1 transmission of primary human CD4+T lymphocytes was inhibited by Arf6 knockdown. Total internal reflection fluorescence microscopy showed that Arf6 mutants provoked the accumulation of phosphatidylinositol-(4,5)-biphosphate–associated structures on the plasma membrane of permissive cells, without affecting CD4-viral attachment but impeding CD4-dependent HIV-1 entry. Arf6 silencing or its mutants did not affect fusion, entry, and infection of vesicular stomatitis virus G–pseudotyped viruses or ligand-induced CXCR4 or CCR5 endocytosis, both clathrin-dependent processes. Therefore we propose that efficient early HIV-1 infection of CD4+T lymphocytes requires Arf6-coordinated plasma membrane dynamics that promote viral fusion and entry.

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Membrane Interactions of the Tick-Borne Encephalitis Virus Fusion Protein E at Low pH

Journal of Virology ◽

10.1128/jvi.76.8.3784-3790.2002 ◽

2002 ◽

Vol 76 (8) ◽

pp. 3784-3790 ◽

Cited By ~ 89

Author(s):

Karin Stiasny ◽

Steven L. Allison ◽

Juliane Schalich ◽

Franz X. Heinz

Keyword(s):

Fusion Protein ◽

Membrane Binding ◽

Low Ph ◽

Encephalitis Virus ◽

Soluble Form ◽

Viral Fusion ◽

Sequence Element ◽

Viral Fusion Protein ◽

Tick Borne Encephalitis ◽

Tick Borne Encephalitis Virus

ABSTRACT Membrane fusion of the flavivirus tick-borne encephalitis virus is triggered by the mildly acidic pH of the endosome and is mediated by envelope protein E, a class II viral fusion protein. The low-pH trigger induces an oligomeric rearrangement in which the subunits of the native E homodimers dissociate and the monomeric subunits then reassociate into homotrimers. Here we provide evidence that membrane binding is mediated by the intermediate monomeric form of E, generated by low-pH-induced dissociation of the dimer. Liposome coflotation experiments revealed that association with target membranes occurred only when liposomes were present at the time of acidification, whereas pretreating virions at low pH in the absence of membranes resulted in the loss of their ability to stably attach to liposomes. With the cleavable cross-linker ethylene glycolbis(succinimidylsuccinate), it was shown that a truncated soluble form of the E protein (sE) could bind to membranes only when the dimers were free to dissociate at low pH, and binding could be blocked by a monoclonal antibody that recognizes the fusion peptide, which is at the distal tip of the E monomer but is buried in the native dimer. Surprisingly, analysis of the membrane-associated sE proteins revealed that they had formed trimers. This was unexpected because this protein lacks a sequence element in the C-terminal stem-anchor region, which was shown to be essential for trimerization in the absence of a target membrane. It can therefore be concluded that the formation of a trimeric form of sE is facilitated by membrane binding. Its stability is apparently maintained by contacts between the ectodomains only and is not dependent on sequence elements in the stem-anchor region as previously assumed.

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Inhibition of Measles Viral Fusion Is Enhanced by Targeting Multiple Domains of the Fusion Protein

ACS Nano ◽

10.1021/acsnano.1c02057 ◽

2021 ◽

Author(s):

Francesca T. Bovier ◽

Ksenia Rybkina ◽

Sudipta Biswas ◽

Olivia Harder ◽

Tara C. Marcink ◽

...

Keyword(s):

Fusion Protein ◽

Viral Fusion ◽

Multiple Domains

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The Use of Lectins as Tools to Combat SARS-CoV-2

Current Pharmaceutical Design ◽

10.2174/1381612827666210830094743 ◽

2021 ◽

Vol 27 ◽

Author(s):

Daniela Martinez ◽

Diego Amaral ◽

David Markovitz ◽

Luciano Pinto

Keyword(s):

Viral Infection ◽

Host Cells ◽

Viral Fusion ◽

Cell Receptors ◽

First Case ◽

Mannose Binding ◽

New Treatments ◽

Viral Surface

Background: in december 2019, china announced the first case of an infection caused by an, until then, unknown virus: sars-cov-2. since then, researchers have been looking for viable alternatives for the treatment and/or cure of viral infection. among the possible complementary solutions are lectins, and proteins that are reversibly bound to different carbohydrates. the spike protein, present on the viral surface, can interact with different cell receptors: ace2, cd147, and dc-signr. since lectins have an affinity for different carbohydrates, the binding with the glycosylated cell receptors represents a possibility of preventing the virus from binding to the receptors of host cells. Objective: in this review we discuss the main lectins that are possible candidates for use in the treatment of covid-19, highlighting those that have already demonstrated antiviral activity in vivo and in vitro, including mannose-binding lectin, griffithsin, banlec, and others. we also aim to discuss the possible mechanism of action of lectins, which appears to occur through the mediation of viral fusion in host cells, by binding of lectins to glycosylated receptors found in human cells and/or binding of these proteins with the spike glycoprotein, present in virus surface.moreover, we also discuss the use of lectins in clinical practice. Conclusion: Even with the development of effective vaccines, new cases of viral infection with the same virus, or new outbreaks with different viruses can occur; so, the development of new treatments should not be discarded. moreover, the discussions made in this work are relevant regarding the anti-viral properties of lectins.

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Structural Basis for the Understanding of Entry Inhibitors Against SARS Viruses

Current Medicinal Chemistry ◽

10.2174/0929867328666210514122418 ◽

2021 ◽

Vol 28 ◽

Author(s):

Prem Kumar Kushwaha ◽

Neha Kumari ◽

Sneha Nayak ◽

Keshav Kishor ◽

Ashoke Sharon

Keyword(s):

Viral Entry ◽

Molecular Level ◽

Virus Entry ◽

Holistic Approach ◽

Symptomatic Treatment ◽

Host Cells ◽

Structural Basis ◽

Viral Fusion ◽

Structural Studies ◽

Entry Inhibitors

: Outbreaks due to Severe Acute Respiratory Syndrome-Corona virus 2 (SARS-CoV-2) initiated in Wuhan city, China, in December 2019 which continued to spread internationally, posing a pandemic threat as declared by WHO and as of March 10, 2021, confirmed cases reached 118 million along with 2.6 million deaths worldwide. In the absence of specific antiviral medication, symptomatic treatment and physical isolation remain the options to control the contagion. The recent clinical trials on antiviral drugs highlighted some promising compounds such as umifenovir (haemagglutinin-mediated fusion inhibitor), remdesivir (RdRp nucleoside inhibitor), and favipiravir (RdRp Inhibitor). WHO launched a multinational clinical trial on several promising analogs as a potential treatment to combat SARS infection. This situation urges a holistic approach to invent safe and specific drugs as a prophylactic and therapeutic cure for SARS-related-viral diseases, including COVID-19. : It is significant to note that researchers worldwide have been doing their best to handle the crisis and have produced an extensive and promising literature body. It opens a scope and allows understanding the viral entry at the molecular level. A structure-based approach can reveal the molecular-level understanding of viral entry interaction. The ligand profiling and non-covalent interactions among participating amino-acid residues are critical information to delineate a structural interpretation. The structural investigation of SARS virus entry into host cells will reveal the possible strategy for designing drugs like entry inhibitors. : The structure-based approach demonstrates details at the 3D molecular level. It shows specificity about SARS-CoV-2 spike interaction, which uses human angiotensin-converting enzyme 2 (ACE2) as a receptor for entry, and the human protease completes the process of viral fusion and infection. : The 3D structural studies reveal the existence of two units, namely S1 and S2. S1 is called a receptor-binding domain (RBD) and responsible for interacting with the host (ACE2), and the S2 unit participates in the fusion of viral and cellular membranes. TMPRSS2 mediates the cleavage at S1/S2 subunit interface in S-protein of SARS CoV-2, leading to viral fusion. Conformational difference associated with S1 binding alters ACE2 interaction and inhibits viral fusion. Overall, the detailed 3D structural studies help understand the 3D structural basis of interaction between viruses with host factors and available scope for the new drug discovery process targeting SARS-related virus entry into the host cell.

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Herpes simplex virus glycoprotein B (gB) mutations define structural sites in domain I, the membrane proximal region, and the cytodomain that regulate entry.

Journal of Virology ◽

10.1128/jvi.01050-21 ◽

2021 ◽

Author(s):

Qing Fan ◽

Richard Longnecker ◽

Sarah A. Connolly

Keyword(s):

Cell Fusion ◽

Virus Entry ◽

Proximal Region ◽

Glycoprotein B ◽

Viral Fusion ◽

Viral Fusion Protein ◽

Membrane Proximal Region ◽

Domain V ◽

Domain I ◽

Cell Cell

The viral fusion protein glycoprotein B (gB) is conserved in all herpesviruses and is essential for virus entry. During entry, gB fuses viral and host cell membranes by refolding from a prefusion to a postfusion form. We previously introduced three structure-based mutations (gB-I671A/H681A/F683A) into the domain V arm of the gB ectodomain that resulted in reduced cell-cell fusion. A virus carrying these three mutations (called gB3A) displayed a small plaque phenotype and remarkably delayed entry into cells. To identify mutations that could counteract this phenotype, we serially passaged the gB3A virus and selected for revertant viruses with increased plaque size. Genomic sequencing revealed that the revertant viruses had second-site mutations in gB, including E187A, M742T, and S383F/G645R/V705I/V880G. Using expression constructs encoding these mutations, only gB-V880G was shown to enhance cell-cell fusion. In contrast, all of the revertant viruses showed enhanced entry kinetics, underscoring the fact that cell-cell fusion and virus-cell fusion are different. The results indicate that mutations in three different regions of gB (domain I, the membrane proximal region, and the cytoplasmic tail domain) can counteract the slow entry phenotype of gB3A virus. Mapping these compensatory mutations to prefusion and postfusion structural models suggests sites of intramolecular functional interactions with the gB domain V arm that may contribute to the gB fusion function. Importance The nine human herpesviruses are ubiquitous and cause a range of disease in humans. Glycoprotein B (gB) is an essential viral fusion protein that is conserved in all herpesviruses. During host cell entry, gB mediates virus-cell membrane fusion by undergoing a conformational change. Structural models for the prefusion and postfusion form of gB exist, but the details of how the protein converts from one to the other are unclear. We previously introduced structure-based mutations into gB that inhibited virus entry and fusion. By passaging this entry-deficient virus over time, we selected second-site mutations that partially restore virus entry. The location of these mutations suggest regulatory sites that contribute to fusion and gB refolding during entry. gB is a target of neutralizing antibodies and defining how gB refolds during entry could provide a basis for the development of fusion inhibitors for future research or clinical use.

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