1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Designing a Bioinformatics Model to Select Antimicrobial Peptides against Helicobacter pylori Infection
Paper ID : 1152-ICB10
Authors:
saba Ghasemi1, Karim Heydari2, Maryam Homayoon *3
1Department of Biology, Zarghan Azad University, Zarghan, Iran.
2Department of Computer Science, Zarghan Azad University, Zzarghan, Iran
3Department of Biology - Faculty of Basic Sciences - Zand Institute of Higher Education - Shiraz - Iran
Abstract:
Helicobacter pylori is the most common chronic bacterial infection that colonizes the gastrogenic mucosa of half of the population worldwide. The treatment of H. pylori has been limited to the use of antibiotics, and due to increase in resistance to antibiotics used in the anti-H. pylori therapy, the development of an alternative treatment is one of the most common challenges for physicians. Therefore, a strategic, and effective antimicrobial peptides (AMPs) design against H. pylori is essential where the use of the most prevalent bioinformatics tools could help achieve it.
In this study, biotechnology software and AMP databases were used to design new AMPs against H. pylori. In fact, five AMP databases were used to extract the best AMP for gram-negative bacteria based on some criteria such as hydrophobicity, length, charge, and three-dimensional structure of peptides. In order to create specific AMPs to target Helicobacter pylori, a designed peptide was added to the end of AMPs. This peptide has been designed based on the tendency to bind to the predicted binding sites on one of the proteins in the outer membrane of this bacterium (HopB).
Twelve AMPs (CPF-St7, XT-4, XPF-SE3, Warnericin RK, Magainin-F3, Acipensin 6, Carnobacteriocin B2, Fallaxin, Dermaseptin-DI1, Pseudin-2, Hylin-a1, Piscidin-3) were selected considering some important factors for gram-negative antibacterial peptides. The designed peptide was added to the N or C-terminal of AMP considering the AMP properties. Bioinformatics methods can be the first step in achieving new and efficient AMPs.
The results of this study can be promising to introduce new treatment strategies against H. pylori. However, to validate the therapeutic effects of our AMPs design, in vitro and in vivo studies are required.
Keywords:
Antimicrobial peptide; Bioinformatics; Helicobacter pylori; AMP databases.
Status : Paper Accepted (Poster Presentation)