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 THE COMPUTATION OF CYCLIC PEPTIDE WITH PROLIN-PROLIN BOND AS FUSION INHIBITOR OF DENV ENVELOPE PROTEIN THROUGH MOLECULAR DOCKING AND MOLECULAR DYNAMICS SIMULATION

2015 ◽  
Vol 2 (1) ◽  
pp. 416
Author(s):  
Arli Aditya Parikesit ◽  
Hilyatuzzahroh . ◽  
Andreas S Nugroho ◽  
Amalia Hapsari ◽  
Usman Sumo Friend Tambunan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Dengue Virus ◽  
Envelope Protein ◽  
Cyclic Peptide ◽  
Fusion Process ◽  
Dynamics Simulation ◽  
Fusion Inhibitor ◽  
Dimer Structure

<p>A disease that caused by dengue virus (DENV) has become the major health problem of the world. Nowadays, no effective treatment is available to overcome the disease due to the level of dengue virus pathogeneses. A novel treatment method such as antiviral drug is highly necessary for coping with the dengue disease. Envelope protein is one of the non-structural proteins of DENV, which engaged in the viral fusion process. It penetrates into the host cell to transfer its genetic material into the targeted cell followed by replication and establishment of new virus. Thus, the envelope protein can be utilized as the antiviral inhibitor target. The fusion process is mediated by the conformational change in the protein structure from dimer to trimer state. The previous research showed the existing cavity on the dimer structure of the envelope protein. The existing ligand could get into cavity of the envelope protein, stabilize the dimer structure or hamper the transition of dimer protein into trimer. In this fashion, the fusion process can be prevented. The aim of this research is designing the cyclic peptide with prolin-prolin bond as fusion inhibitor of DENV envelope protein through molecular docking and molecular dynamics simulation. The screening of 3,883 cyclic peptides, each of them connected by prolin-prolin bond, through molecular docking resulted in five best ligands. The result showed that PYRRP was the best ligand. PAWRP was also chosen as the best ligand because it showed good affinity with protein cavity. Stability of ligand-protein complex was analyzed by molecular dynamics simulation. The result showed that PYRRP ligand was able to support the stability of DENV envelope protein dimer structure at 310 K and 312 K. While PAWRP ligand actively formed complex with the DENV envelope protein at 310 K compared to 312 K. Thus the PYRRP ligand has a potential to be developed as DENV fusion inhibitor. </p><p><strong>Keywords</strong>: dengue, envelope protein, fusion process, cavity, cyclic peptide, molecular docking, molecular dynamics</p>

scholarly journals Prefusion structure of human cytomegalovirus glycoprotein B and structural basis for membrane fusion

2021 ◽  
Vol 7 (10) ◽  
pp. eabf3178
Author(s):  
Yuhang Liu ◽  
Kyle P. Heim ◽  
Ye Che ◽  
Xiaoyuan Chi ◽  
Xiayang Qiu ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Human Cytomegalovirus ◽  
Transmembrane Domain ◽  
Proximal Region ◽  
Viral Envelope ◽  
Vaccine Antigen ◽  
Glycoprotein B ◽  
Structural Basis ◽  
Fusion Inhibitor ◽  
Host Cell Membrane

Human cytomegalovirus (HCMV) causes congenital disease with long-term morbidity. HCMV glycoprotein B (gB) transitions irreversibly from a metastable prefusion to a stable postfusion conformation to fuse the viral envelope with a host cell membrane during entry. We stabilized prefusion gB on the virion with a fusion inhibitor and a chemical cross-linker, extracted and purified it, and then determined its structure to 3.6-Å resolution by electron cryomicroscopy. Our results revealed the structural rearrangements that mediate membrane fusion and details of the interactions among the fusion loops, the membrane-proximal region, transmembrane domain, and bound fusion inhibitor that stabilized gB in the prefusion state. The structure rationalizes known gB antigenic sites. By analogy to successful vaccine antigen engineering approaches for other viral pathogens, the high-resolution prefusion gB structure provides a basis to develop stabilized prefusion gB HCMV vaccine antigens.

scholarly journals Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective

2018 ◽  
Vol 47 (1) ◽  
pp. 153-173 ◽  
Author(s):  
Sander Boonstra ◽  
Jelle S. Blijleven ◽  
Wouter H. Roos ◽  
Patrick R. Onck ◽  
Erik van der Giessen ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Host Cell ◽  
Conformational Changes ◽  
Fusion Process ◽  
Host Cell Membrane ◽  
Activation Barriers ◽  
Viral Membrane ◽  
Influenza Hemagglutinin ◽  
Working Together

Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.

scholarly journals Antiviral Efficacy of a Respiratory Syncytial Virus (RSV) Fusion Inhibitor in a Bovine Model of RSV Infection

2015 ◽  
Vol 59 (8) ◽  
pp. 4889-4900 ◽  
Author(s):  
Robert Jordan ◽  
Matt Shao ◽  
Richard L. Mackman ◽  
Michel Perron ◽  
Tomas Cihlar ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Syncytial Virus ◽  
Structural Analog ◽  
Therapeutic Benefit ◽  
Viral Envelope ◽  
Fusion Inhibitor ◽  
Lung Pathology ◽  
Host Cell Membrane ◽  
Rsv Infection ◽  
Syncytial Virus

ABSTRACTRespiratory syncytial virus (RSV) is the leading cause of bronchiolitis and pneumonia in infants. Effective treatment for RSV infection is a significant unmet medical need. While new RSV therapeutics are now in development, there are very few animal models that mimic the pathogenesis of human RSV, making it difficult to evaluate new disease interventions. Experimental infection of Holstein calves with bovine RSV (bRSV) causes a severe respiratory infection that is similar to human RSV infection, providing a relevant model for testing novel therapeutic agents. In this model, viral load is readily detected in nasal secretions by quantitative real-time PCR (qRT-PCR), and cumulative symptom scoring together with histopathology evaluations of infected tissue allow for the assessment of disease severity. The bovine RSV model was used to evaluate the antiviral activity of an RSV fusion inhibitor, GS1, which blocks virus entry by inhibiting the fusion of the viral envelope with the host cell membrane. The efficacy of GS1, a close structural analog of GS-5806 that is being developed to treat RSV infection in humans was evaluated in two randomized, blind, placebo-controlled studies in bRSV-infected calves. Intravenous administration of GS1 at 4 mg/kg of body weight/day for 7 days starting 24 h or 72 h postinoculation provided clear therapeutic benefit by reducing the viral load, disease symptom score, respiration rate, and lung pathology associated with bRSV infection. These data support the use of the bovine RSV model for evaluation of experimental therapeutics for treatment of RSV.

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 GS-5806 Inhibits Pre- to Postfusion Conformational Changes of the Respiratory Syncytial Virus Fusion Protein

2015 ◽  
Vol 59 (11) ◽  
pp. 7109-7112 ◽  
Author(s):  
Dharmaraj Samuel ◽  
Weimei Xing ◽  
Anita Niedziela-Majka ◽  
Jinny S. Wong ◽  
Magdeleine Hung ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Fusion Protein ◽  
Conformational Changes ◽  
Viral Entry ◽  
Viral Envelope ◽  
Host Cell Membrane ◽  
Virus Fusion ◽  
Molecule Inhibitor ◽  
Syncytial Virus

ABSTRACTGS-5806 is a small-molecule inhibitor of human respiratory syncytial virus fusion protein-mediated viral entry. During viral entry, the fusion protein undergoes major conformational changes, resulting in fusion of the viral envelope with the host cell membrane. This process is reproducedin vitrousing a purified, truncated respiratory syncytial virus (RSV) fusion protein. GS-5806 blocked these conformational changes, suggesting a possible mechanism for antiviral activity.

scholarly journals Interplay between the Herpes Simplex Virus 1 gB Cytodomain and the gH Cytotail during Cell-Cell Fusion

2015 ◽  
Vol 89 (24) ◽  
pp. 12262-12272 ◽  
Author(s):  
Henry B. Rogalin ◽  
Ekaterina E. Heldwein
Keyword(s):  
Herpes Simplex ◽  
Cell Fusion ◽  
Conformational Changes ◽  
Vaccine Development ◽  
Viral Envelope ◽  
Herpes Simplex Virus 1 ◽  
Host Cell Membrane ◽  
Herpes Simplex Viruses ◽  
Simplex Virus ◽  
Cell Cell

ABSTRACTHerpesvirus entry into cells is mediated by the viral fusogen gB, which is thought to refold from the prefusion to the postfusion form in a series of large conformational changes that energetically couple refolding to membrane fusion. In contrast to most viral fusogens, gB requires a conserved heterodimer, gH/gL, as well as other nonconserved proteins. In a further mechanistic twist, gB-mediated cell-cell fusion appears restricted by its intraviral or cytoplasmic domain (cytodomain) because mutations within it result in a hyperfusogenic phenotype. Here, we characterized a panel of hyperfusogenic HSV-1 gB cytodomain mutants and show that they are fully functional in cell-cell fusion at shorter coincubation times and at lower temperatures than those for wild-type (WT) gB, which suggests that these mutations reduce the kinetic energy barrier to fusion. Despite this, the mutants require both gH/gL and gD. We confirm previous observations that the gH cytotail is an essential component of the cell-cell fusion mechanism and show that the N-terminal portion of the gH cytotail is critical for this process. Moreover, the fusion levels achieved by all gB constructs, WT and mutant, were proportionate to the length of the gH cytotail. Putting these results together, we propose that the gH cytotail, in addition to the gH/gL ectodomain, plays an essential role in gB activation, potentially acting as a “wedge” to release the gB cytodomain “clamp” and enable gB activation.IMPORTANCEHerpesviruses infect their hosts for life and cause a substantial disease burden. Herpes simplex viruses cause oral and genital sores as well as rare yet severe encephalitis and a panoply of ocular ailments. Infection initiates when the viral envelope fuses with the host cell membrane in a process orchestrated by the viral fusogen gB, assisted by the viral glycoproteins gH, gL, and gD and a cellular gD receptor. This process is more complicated than that of most other viruses and is subject to multiple regulatory inputs. Antiviral and vaccine development would benefit from a detailed mechanistic knowledge of this process and how it is regulated.

scholarly journals Screening of yeast display libraries of enzymatically-cyclized peptides to discover macrocyclic peptide ligands

2020 ◽  
Author(s):  
John Bowen ◽  
John Schneible ◽  
Collin Labar ◽  
Stefano Menegatti ◽  
Balaji M. Rao
Keyword(s):  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Surface Display ◽  
Peptide Ligands ◽  
Yeast Surface Display ◽  
Yeast Display ◽  
Ww Domains ◽  
Tev Protease ◽  
Yeast Surface ◽  
Alternative Routes

AbstractWe present the construction and screening of yeast display libraries of cyclic peptides wherein site-selective enzymatic cyclization of linear peptides is achieved using bacterial transglu-taminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by treatment with recombinant transglutaminase in solution; or (ii) intracellular co-expression of linear peptides and transglutaminase to achieve cyclization in the endoplasmic reticulum prior to yeast surface display. The cyclization yield was evaluated via orthogonal detection of epitope tags integrated in the yeast-displayed peptides by flow cytometry, and via comparative cleavage of cyclic vs. linear peptides by tobacco etch virus (TEV) protease. Subsequently, yeast display libraries of transglutaminase-cyclized peptides were screened to isolate binders to the N-terminal region of the Yes-Associated Protein (YAP) and its WW domains using magnetic selection and fluorescence activated cell sorting (FACS). The identified cyclic peptide cyclo[E-LYLAYPAH-K] featured a KD of 1.67 µM for YAP and 0.84 µM for WW as well as high binding selectivity against albumin and lysozyme. These results demonstrate the usefulness of yeast surface display for screening transglutaminase-cyclized peptide libraries, and efficient identification of cyclic peptide ligands.

A Target-Based Method for Designing Heterochiral Cyclic Peptide Binders: De Novo Inhibitors of the PD-1/PD-L1 Interaction

2020 ◽  
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Jesús Garcia ◽  
Ernest Giralt
Keyword(s):  
Protein Interactions ◽  
Cyclic Peptides ◽  
General Framework ◽  
Large Scale ◽  
Cyclic Peptide ◽  
De Novo ◽  
Inhibitory Effect ◽  
Original Text ◽  
Retraction Notice ◽  
Pharmaceutical Properties

<p>NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above.</p><p><br></p><p>------------------------------------------------------------------------</p><p><br></p><p>Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-<i>i</i>3 and PD-<i>i</i>6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our <i>de novo </i>design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.<i></i></p>

scholarly journals Exaptation of Retroviral Syncytin for Development of Syncytialized Placenta, Its Limited Homology to the SARS-CoV-2 Spike Protein and Arguments against Disturbing Narrative in the Context of COVID-19 Vaccination

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 238
Author(s):  
Malgorzata Kloc ◽  
Ahmed Uosef ◽  
Jacek Z. Kubiak ◽  
Rafik M. Ghobrial
Keyword(s):  
Cell Membrane ◽  
Host Cell ◽  
Envelope Glycoprotein ◽  
Mammalian Species ◽  
Viral Envelope ◽  
Spike Protein ◽  
Mammalian Evolution ◽  
Trophoblast Cells ◽  
Host Cell Membrane ◽  
Uterine Endometrium

Human placenta formation relies on the interaction between fused trophoblast cells of the embryo with uterine endometrium. The fusion between trophoblast cells, first into cytotrophoblast and then into syncytiotrophoblast, is facilitated by the fusogenic protein syncytin. Syncytin derives from an envelope glycoprotein (ENV) of retroviral origin. In exogenous retroviruses, the envelope glycoproteins coded by env genes allow fusion of the viral envelope with the host cell membrane and entry of the virus into a host cell. During mammalian evolution, the env genes have been repeatedly, and independently, captured by various mammalian species to facilitate the formation of the placenta. Such a shift in the function of a gene, or a trait, for a different purpose during evolution is called an exaptation (co-option). We discuss the structure and origin of the placenta, the fusogenic and non-fusogenic functions of syncytin, and the mechanism of cell fusion. We also comment on an alleged danger of the COVID-19 vaccine based on the presupposed similarity between syncytin and the SARS-CoV-2 spike protein.

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