Molecular docking and simulation of Zika virus NS3 helicase

The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosec...

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Published inBMC chemistry Vol. 13; no. 1; pp. 67 - 8
Main Authors Badshah, Syed Lal, Ahmad, Nasir, Ur Rehman, Ashfaq, Khan, Khalid, Ullah, Asad, Alsayari, Abdulrhman, Muhsinah, Abdullatif Bin, N. Mabkhot, Yahia
Format Journal Article
LanguageEnglish
Published Cham Springer International Publishing 17.05.2019
Springer Nature B.V
BMC
Subjects
Binding
Binding sites
Bonding strength
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Crystal structure
Dengue fever
Derivatives
Enzymes
Genomes
Hydrogen bonding
Ligands
Microcephaly
Molecular docking
Molecular dynamics
Molecular dynamics simulation
Nonstructural protein-3 Helicase
Physical Chemistry
Proteins
Replication
Research Article
Simulation
Software
Stability analysis
Viruses
West Nile virus
Zika virus
ZIKV
ZIKV
Molecular dynamics simulation
Microcephaly
Nonstructural protein-3 Helicase
Molecular docking
Online AccessGet full text
ISSN2661-801X
2661-801X
DOI10.1186/s13065-019-0582-y

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Abstract The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.
AbstractList The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.
Abstract The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.
The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain-Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain-Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.
ArticleNumber 67
Author Badshah, Syed Lal
Muhsinah, Abdullatif Bin
N. Mabkhot, Yahia
Ur Rehman, Ashfaq
Alsayari, Abdulrhman
Khan, Khalid
Ahmad, Nasir
Ullah, Asad
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  email: ygaber@kku.edu.sa
  organization: Department of Pharmaceutical Chemistry, College of Pharamacy, King Khalid University
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31384814$$D View this record in MEDLINE/PubMed
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Issue 1
Keywords ZIKV
Molecular dynamics simulation
Microcephaly
Nonstructural protein-3 Helicase
Molecular docking
Language English
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Snippet The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The...
The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain-Barre Syndrome that resulted in humans. The...
Abstract The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in...
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SourceType Open Website
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Index Database
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Publisher
StartPage 67
SubjectTerms Binding
Binding sites
Bonding strength
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Crystal structure
Dengue fever
Derivatives
Enzymes
Genomes
Hydrogen bonding
Ligands
Microcephaly
Molecular docking
Molecular dynamics
Molecular dynamics simulation
Nonstructural protein-3 Helicase
Physical Chemistry
Proteins
Replication
Research Article
Simulation
Software
Stability analysis
Viruses
West Nile virus
Zika virus
ZIKV
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Title Molecular docking and simulation of Zika virus NS3 helicase
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