Bioinformatical study of nigella sativa extract on nonstructural protein 5b of hepatitis c virus

Zahra Latif,1,* Alireza jalalvand,2

1. Research Centre for Biosciences and Biotechnology, Malek-Ashtar University of Technology, Tehran, Iran
2. Department of Influenza and other respiratory viruses, Pasteur Institute of Iran, Tehran, Iran.

Abstract

Introduction

Hepatitis c virus (hcv) infection is one of the major causes of chronic liver disease worldwide. hcv infects an estimated 170 million people worldwide. about 60-80 % of patients develop chronic infection, whereby the infection may progress to cirrhosis and hepatocellular carcinoma (hcc). nonstructural protein 5b (ns5b) is an important protein in replication of viral rna with polymerization property. the aim of present research is the pharmacodynamics study of nigella sativa extract including nigellicin, nigellimine, kaempferol, quercitin, thymoquinone, and thymohydroquinon on ns5b for inhibition of the replication process with docking technique.

Methods

The structure of mentioned compounds were drawn by chemsketch software. crystallography structure of ns5b was prepared from protein data bank (pdb id 3phe resolution 2.2 angstrom). after energy minimization with spdbv software, gridding parameter file and docking parameter file was acquired from autodocktools 4 software. gpf file and dpf file was ruined with cygwin software. according to output of present research, dlg files were analyzed for finding best affinity between compounds and proteins. conformational analysis was performed by chimera software.

Results

According to acquired rmsd tables from dlg file, nigellicin, nigellimine, kaempferol, quercitin, thymoquinone, and thymohydroquinon binds to receptor with energy binding -5.63 kcal/mol, -6.75 kcal/mol, -8.01 kcal/mol, -7.77 kcal/mol, -6.81 kcal/mol, and -6.15 kcal/mol, respectively. kaempferol and nigellicin have highest and lowest affinity with ns5b.

Conclusion

Present research demonstrates nigella sativa is an herbal source that can inhibit replication of hepatitis c virus. among mentioned 6 compounds, kaempferol is better than other compounds for inhibition of ns5b. conformational analysis indicates kaempferol covers binding site of ns5b appropriately. we suggest to perform molecular dynamics and pharmacokinetics studies on kaempferol.

Keywords

Nigella sativa, hepatitis c virus, ns5b, kaempferol, bioinformatics