Designing a Bioinformatics Model to Select Antimicrobial Peptides against Helicobacter pylori Infection

Helicobacter pylori is the most common chronic bacterial infection that colonizes the gastrogenic mucosa ofhalf of the population worldwide. The treatment of H. pylori has been limited to the use of antibiotics, anddue to increase in resistance to antibiotics used in the anti-H. pylori therapy, the development of an alternativetreatment is one of the most common challenges for physicians. Therefore, a strategic, and effectiveantimicrobial peptides (AMPs) design against H. pylori is essential where the use of the most prevalentbioinformatics 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 somecriteria such as hydrophobicity, length, charge, and three-dimensional structure of peptides. In order to createspecific AMPs to target Helicobacter pylori, a designed peptide was added to the end of AMPs. This peptidehas been designed based on the tendency to bind to the predicted binding sites on one of the proteins in theouter membrane of this bacterium (HopB).Twelve AMPs (CPF-St۷, XT-۴, XPF-SE۳, Warnericin RK, Magainin-F۳, Acipensin ۶, Carnobacteriocin B۲,Fallaxin, Dermaseptin-DI۱, Pseudin-۲, Hylin-a۱, Piscidin-۳) were selected considering some importantfactors for gram-negative antibacterial peptides. The designed peptide was added to the N or C-terminal ofAMP considering the AMP properties. Bioinformatics methods can be the first step in achieving new andefficient 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