scholarly journals Peptide Ligands Selected with CD4-Induced Epitopes on Native Dualtropic HIV-1 Envelope Proteins Mimic Extracellular Coreceptor Domains and Bind to HIV-1 gp120 Independently of Coreceptor Usage

2010 ◽  
Vol 84 (19) ◽  
pp. 10131-10138 ◽  
Author(s):  
Xavier Dervillez ◽  
Volker Klaukien ◽  
Ralf Dürr ◽  
Joachim Koch ◽  
Alexandra Kreutz ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Peptide Ligands ◽  
Viral Envelope ◽  
Peptide Ligand ◽  
Pseudotyped Virus ◽  
Coreceptor Usage ◽  
Peptide Arrays ◽  
Functional Conservation ◽  
Random Peptide ◽  
Hiv 1

ABSTRACT During HIV-1 entry, binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor triggers conformational changes resulting in exposure of new epitopes, the highly conserved CD4-induced (CD4i) epitopes that are essential for subsequent binding to chemokine receptor CCR5 or CXCR4. Due to their functional conservation, CD4i epitopes represent attractive viral targets for HIV-1 entry inhibition. The aim of the present study was to select peptide ligands for CD4i epitopes on native dualtropic (R5X4) HIV-1 envelope (Env) glycoproteins by phage display. Using CD4-activated retroviral particles carrying Env from the R5X4 HIV-1 89.6 strain as the target, we performed screenings of random peptide phage libraries under stringent selection conditions. Selected peptides showed partial identity with amino acids in the extracellular domains of CCR5/CXCR4, including motifs rich in tyrosines and aspartates at the N terminus known to be important for gp120 binding. A synthetic peptide derivative (XD3) corresponding to the most frequently selected phages was optimized for Env binding on peptide arrays. Interestingly, the optimized peptide could bind specifically to gp120 derived from HIV-1 strains with different coreceptor usage, competed with binding of CD4i-specific monoclonal antibody (MAb) 17b, and interfered with entry of both a CCR5 (R5)-tropic and a CXCR4 (X4)-tropic Env pseudotyped virus. This peptide ligand therefore points at unique properties of CD4i epitopes shared by gp120 with different coreceptor usage and could thus serve to provide new insight into the conserved structural details essential for coreceptor binding for further drug development.

scholarly journals Time-resolved Imaging of HIV-1 Env-mediated Lipid and Content Mixing between a Single Virion and Cell Membrane

2005 ◽  
Vol 16 (12) ◽  
pp. 5502-5513 ◽  
Author(s):  
Ruben M. Markosyan ◽  
Fredric S. Cohen ◽  
Grigory B. Melikyan
Keyword(s):  
Temperature Jump ◽  
Viral Envelope ◽  
Pseudotyped Virus ◽  
Target Cells ◽  
Time Resolved ◽  
Virus Content ◽  
Long Time ◽  
Viral Envelopes ◽  
Time Resolved Imaging ◽  
Hiv 1

A method has been developed to follow fusion of individual pseudotyped virus expressing HIV-1 Env to cells by time-resolved fluorescence microscopy. Viral envelopes were labeled with a fluorescent lipid dye (DiD) and virus content was rendered visible by incorporating a Gag-GFP chimera. The Gag-GFP is naturally cleaved to the much smaller NC-GFP fragment in the mature virions. NC-GFP was readily released upon permeabilization of the viral envelope, whereas the capsid was retained. The NC-GFP thus provides a relatively small and mobile aqueous marker to follow viral content transfer. In fusion experiments, virions were bound to cells at low temperature, and fusion was synchronously triggered by a temperature jump. DiD transferred from virions to cells without a significant lag after the temperature jump. Some virions released DiD but retained NC-GFP. Surprisingly, the fraction of lipid mixing events yielding NC-GFP transfer was dependent on the type of target cell: of three infectable cell lines, only one permitted NC-GFP transfer within minutes of raising temperature. NC-GFP release did not correlate with the level of CD4 or coreceptor expression in the target cells. The data indicate that fusion pores formed by HIV-1 Env can remain small for a relatively long time before they enlarge.

scholarly journals Mutations in gp120 Contribute to the Resistance of Human Immunodeficiency Virus Type 1 to Membrane-Anchored C-Peptide maC46

2009 ◽  
Vol 83 (10) ◽  
pp. 4844-4853 ◽  
Author(s):  
Felix G. Hermann ◽  
Lisa Egerer ◽  
Frances Brauer ◽  
Christian Gerum ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Conformational Changes ◽  
Viral Envelope ◽  
Heptad Repeat ◽  
Systematic Analysis ◽  
C Peptide ◽  
Helix Bundle ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Binding of the human immunodeficiency virus (HIV) envelope glycoprotein (Env) to the cellular CD4 receptor and a chemokine coreceptor initiates a series of conformational changes in the Env subunits gp120 and gp41. Eventually, the trimeric gp41 folds into a six-helix bundle, thereby inducing fusion of the viral and cellular membranes. C peptides derived from the C-terminal heptad repeat (CHR) of gp41 are efficient entry inhibitors as they block the six-helix bundle formation. Previously, we developed a membrane-anchored C peptide (maC46) expressed from a retroviral vector that also shows high activity against virus strains resistant to enfuvirtide (T-20), an antiviral C peptide approved for clinical use. Here, we present a systematic analysis of mutations in Env that confer resistance of HIV type 1 (HIV-1) to maC46. We selected an HIV-1 BaL strain with 10-fold reduced sensitivity to maC46 (BaL_C46) by passaging virus for nearly 200 days in the presence of gradually increasing concentrations of maC46. In comparison to wild-type BaL, BaL_C46 had five mutations at highly conserved positions in Env, three in gp120, one in the N-terminal heptad-repeat (NHR), and one in the CHR of gp41. No mutations were found in the NHR domain around the GIV motif that are known to cause resistance to enfuvirtide. Instead, maC46 resistance was found to depend on complementary mutations in the NHR and CHR that considerably favor binding of the mutated NHR to the mutated CHR over binding to maC46. In addition, resistance was highly dependent on mutations in gp120 that accelerated entry. Taken together, resistance to maC46 did not develop readily and required multiple cooperating mutations at conserved positions of the viral envelope glycoproteins gp120 and gp41.

DESIGNING DISULFIDE CYCLIC PEPTIDE AS FUSION INHIBITOR THAT TARGETS DENV ENVELOPE PROTEIN

2016 ◽  
Vol 78 (4-3) ◽  
Author(s):  
Usman Sumo Friend Tambunan ◽  
William Chua ◽  
Arli Aditya Parikesit ◽  
Djati Kerami
Keyword(s):  
Conformational Changes ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Peptide Ligands ◽  
Viral Envelope ◽  
Fusion Process ◽  
Dynamics Simulation ◽  
Health Concern ◽  
Fusion Inhibitor ◽  
Host Cell Membrane

Dengue has been a major health concern and currently there is no available option to treat the infection. It is an arboviral disease caused by dengue virus (DENV), an enveloped flavivirus. DENV initiates fusion process between viral envelope and host cell membrane, transfers its viral genome into target cell and infects host. Our research is focused on designing disulfide cyclic peptides that can fit into fusion cavity and interact with fusion peptide, interrupt conformational changes and therefore inhibit the fusion process. Computational approaches were conducted to calculate the binding affinity and stability of disulfide cyclic peptide ligands with target DENV E glycoprotein. Molecular docking and molecular dynamics simulation were performed using Molecular Operating Environment 2008.10 software (MOE 2008.10). Screening of 1320 designed ligands resulted in 3 best ligands, CLREC, CYREC and CYREC that can form interaction with target cavity and peptide fusion. These ligands showed good affinity with target DENV E glycoprotein based on free binding energy and interactions. To evaluate protein-ligand stability, we performed molecular dynamic simulation. Only CLREC showed protein-ligand stability and maintained interaction between ligand and target cavity. Therefore we propose CLREC as potential DENV fusion inhibitor candidates.  

scholarly journals Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1599
Author(s):  
Nejat Düzgüneş ◽  
Narcis Fernandez-Fuentes ◽  
Krystyna Konopka
Keyword(s):  
Membrane Fusion ◽  
Conformational Changes ◽  
Surface Protein ◽  
Peptide Inhibitors ◽  
Viral Envelope ◽  
Hepatitis Viruses ◽  
Protein Interfaces ◽  
Protein Gp41 ◽  
Viral Membrane Fusion ◽  
Hiv 1

Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a “six-helix bundle” after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.

scholarly journals Quaternary Interaction of the HIV-1 Envelope Trimer with CD4 and Neutralizing Antibodies

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1405
Author(s):  
Qingbo Liu ◽  
Peng Zhang ◽  
Paolo Lusso
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Neutralizing Antibodies ◽  
Current Knowledge ◽  
Viral Envelope ◽  
Host Cells ◽  
Initial Contact ◽  
Cd4 Receptor ◽  
Cd4 Binding Site ◽  
Hiv 1

The entry of HIV-1 into host cells is initiated by the interaction of the viral envelope (Env) spike with the CD4 receptor. During this process, the spike undergoes a series of conformational changes that eventually lead to the exposure of the fusion peptide located at the N-terminus of the transmembrane glycoprotein, gp41. Recent structural and functional studies have provided important insights into the interaction of Env with CD4 at various stages. However, a fine elucidation of the earliest events of CD4 contact and its immediate effect on the Env conformation remains a challenge for investigation. Here, we summarize the discovery of the quaternary nature of the CD4-binding site in the HIV-1 Env and the role of quaternary contact in the functional interaction with the CD4 receptor. We propose two models for this initial contact based on the current knowledge and discuss how a better understanding of the quaternary interaction may lead to improved immunogens and antibodies targeting the CD4-binding site.

scholarly journals Identification of gp120 Binding Sites on CXCR4 by Using CD4-Independent Human Immunodeficiency Virus Type 2 Env Proteins

2003 ◽  
Vol 77 (2) ◽  
pp. 931-942 ◽  
Author(s):  
George Lin ◽  
Frédéric Baribaud ◽  
Josephine Romano ◽  
Robert W. Doms ◽  
James A. Hoxie
Keyword(s):  
Human Immunodeficiency Virus ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Chemokine Receptor ◽  
Binding Sites ◽  
Viral Envelope ◽  
Alanine Scanning Mutagenesis ◽  
Immunodeficiency Virus ◽  
N Terminus ◽  
Hiv 1

ABSTRACT Human immunodeficiency virus (HIV) and simian (SIV) immunodeficiency virus entry is mediated by binding of the viral envelope glycoprotein (Env) to CD4 and chemokine receptors, CCR5 and/or CXCR4. CD4 induces extensive conformational changes that expose and/or induce formation of a chemokine receptor binding site on gp120. CD4-independent Env's of HIV type 1 (HIV-1), HIV-2, and SIV have been identified that exhibit exposed chemokine receptor binding sites and can bind directly to CCR5 or CXCR4 in the absence of CD4. While many studies have examined determinants for gp120-CCR5 binding, analysis of gp120-CXCR4 binding has been hindered by the apparently lower affinity of this interaction for X4-tropic HIV-1 isolates. We show here that gp120 proteins from two CD4-independent HIV-2 Env's, VCP and ROD/B, bind directly to CXCR4 with an apparently high affinity. By use of CXCR4 N-terminal deletion constructs, CXCR4-CXCR2 chimeras, and human-rat CXCR4 chimeras, binding determinants were shown to reside in the amino (N) terminus, extracellular loop 2 (ECL2), and ECL3. Alanine-scanning mutagenesis of charged residues, tyrosines, and phenylalanines in extracellular CXCR4 domains implicated multiple amino acids in the N terminus (E14/E15, D20, Y21, and D22), ECL2 (D187, R188, F189, Y190, and D193), and ECL3 (D262, E268, E277, and E282) in binding, although minor differences were noted between VCP and ROD/B. However, mutations in CXCR4 that markedly reduced binding did not necessarily hinder cell-cell fusion by VCP or ROD/B, especially in the presence of CD4. These gp120 proteins will be useful in dissecting determinants for CXCR4 binding and Env triggering and in evaluating pharmacologic inhibitors of the gp120-CXCR4 interaction.

scholarly journals Neutralization Profiles of Primary Human Immunodeficiency Virus Type 1 Isolates in the Context of Coreceptor Usage

1998 ◽  
Vol 72 (9) ◽  
pp. 6988-6996 ◽  
Author(s):  
D. Cecilia ◽  
Vineet N. KewalRamani ◽  
Jeanne O’Leary ◽  
Barbara Volsky ◽  
Phillipe Nyambi ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Cell Lines ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Viral Envelope ◽  
Coreceptor Usage ◽  
Neutralization Sensitivity ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Most strains of human immunodeficiency virus type 1 (HIV-1) which have only been carried in vitro in peripheral blood mononuclear cells (primary isolates) can be neutralized by antibodies, but their sensitivity to neutralization varies considerably. To study the parameters that contribute to the differential neutralization sensitivity of primary HIV-1 isolates, we developed a neutralization assay with a panel of genetically engineered cell lines (GHOST cells) that express CD4, one of eight chemokine receptors which function as HIV-1 coreceptors, and a Tat-dependent green fluorescent protein reporter cassette which permits the evaluation and quantitation of HIV-1 infection by flow cytometry. All 21 primary isolates from several clades could grow in the various GHOST cell lines, and their use of one or more coreceptors could easily be defined by flow cytometric analysis. Ten of these primary isolates, three that were CXCR4 (X4)-tropic, three that were CCR5 (R5)-tropic, and four that were dual- or polytropic were chosen for study of their sensitivity to neutralization by human monoclonal and polyclonal antibodies. Viruses from the X4-tropic category of viruses were first tested since they have generally been considered to be particularly neutralization sensitive. It was found that the X4-tropic virus group contained both neutralization-sensitive and neutralization-resistant viruses. Similar results were obtained with R5-tropic viruses and with dual- or polytropic viruses. Within each category of viruses, neutralization sensitivity and resistance could be observed. Therefore, sensitivity to neutralization appears to be the consequence of factors that influence the antibody-virus interaction and its sequelae rather than coreceptor usage. Neutralization of various viruses by the V3-specific monoclonal antibody, 447-52D, was shown to be dependent not only on the presence of the relevant epitope but also on its presentation. An epitope within the envelope of a particular virus is not sufficient to render a virus sensitive to neutralization by an antibody that recognizes that epitope. Moreover, conformation-dependent factors may overcome the need for absolute fidelity in the match between an antibody and its core epitope, permitting sufficient affinity between the viral envelope protein and the antibody to neutralize the virus. The studies indicate that the neutralization sensitivity of HIV-1 primary isolates is a consequence of the complex interaction between virus, antibody, and target cell.

scholarly journals HIV-1 Envelope Conformation, Allostery, and Dynamics

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 852
Author(s):  
Ashley Lauren Bennett ◽  
Rory Henderson
Keyword(s):  
Host Cell ◽  
Conformational Changes ◽  
Neutralizing Antibodies ◽  
Critical Role ◽  
Cell Receptor ◽  
Broadly Neutralizing Antibodies ◽  
Structural Mapping ◽  
Host Cell Receptor ◽  
Immunogen Design ◽  
Hiv 1

The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.

scholarly journals Functional conservation and coherence of HIV-1 subtype A Vpu alleles

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Bizhan Romani ◽  
Amirarsalan Kavyanifard ◽  
Elham Allahbakhshi
Keyword(s):  
Functional Conservation ◽  
Subtype A ◽  
Hiv 1
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