scholarly journals Erratum: Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Muhammad Usman Mirza ◽  
Shazia Rafique ◽  
Amjad Ali ◽  
Mobeen Munir ◽  
Nazia Ikram ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Zika Virus ◽  
Viral Proteins ◽  
Peptide Vaccines ◽  
Dynamics Simulations ◽  
Antigenic Epitopes

scholarly journals Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Muhammad Usman Mirza ◽  
Shazia Rafique ◽  
Amjad Ali ◽  
Mobeen Munir ◽  
Nazia Ikram ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Zika Virus ◽  
Peptide Vaccine ◽  
Viral Proteins ◽  
Health Concern ◽  
Mhc I ◽  
Ctl Epitopes ◽  
Dynamics Simulations ◽  
Antigenic Epitopes

Abstract The recent outbreak of Zika virus (ZIKV) infection in Brazil has developed to a global health concern due to its likely association with birth defects (primary microcephaly) and neurological complications. Consequently, there is an urgent need to develop a vaccine to prevent or a medicine to treat the infection. In this study, immunoinformatics approach was employed to predict antigenic epitopes of Zika viral proteins to aid in development of a peptide vaccine against ZIKV. Both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted for ZIKV Envelope (E), NS3 and NS5 proteins. We further investigated the binding interactions of altogether 15 antigenic CTL epitopes with three class I major histocompatibility complex (MHC I) proteins after docking the peptides to the binding groove of the MHC I proteins. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlight the limits of rigid-body docking methods. Some of the antigenic epitopes predicted and analyzed in this work might present a preliminary set of peptides for future vaccine development against ZIKV.

Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity

2017 ◽  
Vol 492 (4) ◽  
pp. 643-651 ◽  
Author(s):  
Melina Mottin ◽  
Rodolpho C. Braga ◽  
Roosevelt A. da Silva ◽  
Joao H. Martins da Silva ◽  
Alexander L. Perryman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Zika Virus ◽  
Rna Binding ◽  
Dynamics Simulations

scholarly journals Breaking the “unbreakable” ZIKA virus envelope

2018 ◽  
Author(s):  
Chinmai Pindi ◽  
Venkat R Chirasani ◽  
Mohd. Homaidur Rahman ◽  
Mohd. Ahsan ◽  
Prasanna D Revanasiddappa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Temperatures ◽  
Zika Virus ◽  
Atomic Level ◽  
High Fever ◽  
Coarse Grained ◽  
Rapid Spread ◽  
Dynamics Simulations ◽  
Harsh Conditions

ABSTRACTThe rapid spread of zika virus (ZIKV) and its association with microcephaly and Guillain-Barre syndrome have raised major concerns worldwide. Studies have shown that ZIKV can survive in harsh conditions, e.g. high fever; in sharp contrast to the dengue virus (DENV) of same Flaviviridae family. In spite of recent cryo-EM structures that showed similar architecture of the ZIKV and DENV envelopes, little is known of what makes ZIKV envelope so robust and unique. Here, we present a detailed analysis of the constituent raft-raft and protein-protein interactions on ZIKV and DENV envelopes to undermine their differential stability at near-atomic to atomic level using coarse-grained (CG) and all-atom (AA) molecular dynamics simulations. Our results from CG simulations show that, at high temperatures, ZIKV envelope retains its structural integrity, while DENV2 disintegrate through the formation of holes at 5- and 3-fold vertices. Protein structural network from AA simulations shows a stronger inter-raft communications in ZIKV through multiple electrostatic and H-bond interactions. Particularly, the intricate network of interlocking DE-loop and FG-loop among five DIII domains in ZIKA vertices was exceedingly robust that makes this envelope stable, even at high temperatures. Our results are validated by alanine mutations to the CD-loop residues Gln350 and Thr351 that showed no effect on ZIKA stability, in close accordance with a recent mutagenesis study. These detailed information, which were difficult to extract experimentally, broadened our understanding of the flaviviruses and can accelerate the structure-based drug designing processes aiming ZIKA and DENV therapeutics.IMPORTANCEThe rapid spread of zika virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV can survive in harsh conditions, e.g. high fever, unlike dengue (DENV) and other flaviviruses. Here, we unravel the molecular basis of ZIKV unprecedented stability over DENV at high temperatures, mimicking fever. Our study, based on coarse-grained and all-atom molecular dynamics simulations, could not only explore the mechanism of DENV envelope breaking at high temperatures, but also captured atomic-level contacts and interactions at raft-raft and protein-protein interfaces that keep ZIKV envelope intact in similar conditions. The obtained results are validated by in-silico and reported in-vitro mutagenesis studies by showing the presence of specific H-bonding and electrostatic interactions among ZIKV E protein residues. At the end, our study was successful to define potential ZIKV epitopes and provide residue-level insights for designing specific ZIKV antibodies and small molecule inhibitors.

Identification of a Potential Zika Virus Inhibitor Targeting NS5 Methyltransferase Using Virtual Screening and Molecular Dynamics Simulations

2020 ◽  
Vol 60 (2) ◽  
pp. 562-568 ◽  
Author(s):  
Felipe R. S. Santos ◽  
William G. Lima ◽  
Eduardo H. B. Maia ◽  
Letícia C. Assis ◽  
Danilo Davyt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Zika Virus ◽  
Virus Inhibitor ◽  
Dynamics Simulations
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