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:: Volume 29, Issue 1 (3-2021) ::
Journal of Ilam University of Medical Sciences 2021, 29(1): 50-64 Back to browse issues page
In Silico Analysis of the Effect of Scrophularia striata Linalool on VacA Protein of Helicobacter Pylori
Bahman Fazeli-Nasab *
1Research Department of Agronomy and Plant Breeding, Agricultural Research Institute, University of Zabol, Zabol, Iran, ZIP; 9861335856, TellFax; +98-5432240696 , bfazelinasab@gmail.com
Abstract:   (2150 Views)
Introduction: Some plants, such as Scrophularia striata, has been traditionally used for the treatment of infection and ulcer among people living in Zagros District. Previous studies revealed the beneficial effect of hydroalcoholic and water extract of Scrophularia striata on ethanolic induced oxidative stress and stomach ulcer in rats. This study aimed to conduct a bioinformatics analysis to investigate the effect of linalool on the prevention of Helicobacter Pylori VacA protein activity.
Materials & Methods: DNA and protein sequences of linalool of Arabidopsis thaliana and VacA gene sequence of Helicobacter pylori were obtained from the NCBI. The alignment of DNA and protein sequence of VacA and linalool was achieved by Clustalw 2 software. Furthermore, all conserved motif and domains were searched using the MEME online software. The phylogenetic tree was drawn by Mega 5 software. The ExpasyPred3D Swiss-Model, and Galaxy Web software were used to predict the third structure and molecular docking based on homology.
Ethics code: IR.UOZ.REC.1399.002
Findings: Linalool protein sequences in all plants have three motifs (100-300 amino acids) based on the NCBI. The VacA protein has three types of the second cytoplasm, membrane, and kinase domain. The best molecular docking model was obtained based on the highest level of interaction (21.0) and accuracy (0.133) between linalool and VacA protein. The results showed that some molecular groups, such as aliphatic, polar, and hydrophilic, were found in both VacA and linalool protein structure. The presence of aliphatic and hydrophilic groups in VacA protein could give it the ability to pass through the cells by lymphocyte cells and caused pathogenesis if they could escape from degradation. On the other hand, the presence of these groups in linalool could block the VacA protein effect.
Discussions & Conclusions: Bioinformatics analysis showed that linalool eliminated the effects of Helicobacter pylori. Furthermore, the results of this study could be used as a scientific basis for future studies to evaluate the effect of each ingredient of Scrophularia striata, especially linalool, on Helicobacter pylori.
Keywords: Gastric cancer, Molecular docking, Scrophularia striata, VacA protein
Full-Text [PDF 1159 kb]   (834 Downloads)    
Type of Study: Research | Subject: biotechnolohgy
Received: 2020/10/13 | Accepted: 2021/01/24 | Published: 2021/03/30
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Fazeli-Nasab B. In Silico Analysis of the Effect of Scrophularia striata Linalool on VacA Protein of Helicobacter Pylori. J. Ilam Uni. Med. Sci. 2021; 29 (1) :50-64
URL: http://sjimu.medilam.ac.ir/article-1-6801-en.html

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Volume 29, Issue 1 (3-2021) Back to browse issues page
مجله دانشگاه علوم پزشکی ایلام Journal of Ilam University of Medical Sciences
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