In silico docking studies of Ag nanoparticles and its derivatives against NS5B protein (HCV): Integrating nanobiotechnology and nanoinformatics

Authors

  • Arslan Akram University of Lahore, Lahore
  • Waseem Ahmad University of Lahore, Lahore
  • Muhammad Maaz Arif Khawaja Muhammad Safdar Medical College, Sialkot
  • Khaleeq Ahmad Saqib Avicenna International Medical University, Bishkek
  • Rameez Hassan Pirzada Ajou University, Seoul
  • Syed Zeeshan Haider Naqvi University of Lahore, Lahore

DOI:

https://doi.org/10.54693/piche.05124

Keywords:

Silver nanoparticles, Nanoinformatics, Docking, NS5B, HCV replication

Abstract

The present study focused on the prediction of interactions of three ligands, i.e., silver nanoparticles, tyrosine-capped silver nanoparticles, and silver oxide nanoparticles, with the nonstructural protein 5B (NS5B) protein of the hepatitis-C virus (HCV). ΑutoDock 4, Discovery Studio, ChemDraw Ultra, OpenBabel, and Chimera software were used. Computational docking helps to evaluate the conformations of small ligands attached to macromolecular proteins. NS5B plays a crucial role in HCV replication. It is an RNA-dependent RNA membrane-associated polymerase, weighing approximately 66-kDa . The results were obtained from AutoDock 4 and visualized in Discovery Studio and Chimera. Silver nanoparticles showed interactions with  All these three ligands showed promising results to inhibit the NS5B enzyme preventing HCV replication. The most effective ligand was tyrosine-capped silver nanoparticles. Its relative highest binding energy i.e. -5.29 kcal/mol showed its intense binding with the protein molecule causing more damage to the integral residues forming the active site.

Author Biographies

  • Arslan Akram, University of Lahore, Lahore
    Institute of Molecular Biology and Biotechnology
  • Waseem Ahmad, University of Lahore, Lahore
    Institute of Molecular Biology and Biotechnology
  • Muhammad Maaz Arif, Khawaja Muhammad Safdar Medical College, Sialkot
    Demonstrator, Department of Community Medicine
  • Khaleeq Ahmad Saqib, Avicenna International Medical University, Bishkek

    Avicenna International Medical University, Bishkek, Kyrgyzstan

  • Rameez Hassan Pirzada, Ajou University, Seoul
    Molecular Science and Technology Research Center
  • Syed Zeeshan Haider Naqvi, University of Lahore, Lahore

    Assistant Professor,  Institute of Molecular Biology and Biotechnology

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Published

2023-12-23

Issue

Vol. 51 No. 2 (2023): Journal of the Pakistan Institute of Chemical Engineers

Section

Articles

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How to Cite

In silico docking studies of Ag nanoparticles and its derivatives against NS5B protein (HCV): Integrating nanobiotechnology and nanoinformatics. (2023). Journal of the Pakistan Institute of Chemical Engineers, 51(2). https://doi.org/10.54693/piche.05124