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

How to Cite

Akram, A., Ahmad, W., Arif, M. M., Saqib, K. A., Pirzada, R. H., & Naqvi, S. Z. H. (2023). In silico docking studies of Ag nanoparticles and its derivatives against NS5B protein (HCV): Integrating nanobiotechnology and nanoinformatics. Journal of the Pakistan Institute of Chemical Engineers, 51(2). https://doi.org/10.54693/piche.05124

Issue

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

Section

Articles

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