Molecular docking and simulation of Zika virus NS3 helicase

• Published in: BMC 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
• Language: English
• 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
• ISSN: 2661-801X; 2661-801X
• DOI: 10.1186/s13065-019-0582-y

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.