Structural analysis of human antimicrobial peptides by molecular dynamics simulations

The rapid spread of drug-resistant pathogenic microbial strains has created an urgent need for the development of new anti-infective molecules, having different mechanism of action in comparison to existing drugs.Natural antimicrobial peptides(AMPs) represent a novel class of molecules with a broad spectrum of activity and a low rate in inducing bacterial resistance.Until now, many AMPs have failed in clinical trials because of several production cost.Thus, to overcome the limitations of native peptides, a rational in silico approach to AMPs design becomes a promising strategy that drastically reduce production costs and the time required for evaluation of activity and toxicity.[1]In this project, we will take a step towards the design of new peptides by studying peptides that naturally have antimicrobial properties.Using the APD database human-derived antibacterial peptides that having a length of less than 50 amino acids were selected.[2]Then, using the CAMP server, these candidate peptides were broken into smaller pieces of ten residue.The peptides with high AMP Probability were modeled by using MODELLER software.[3]The Structural analysis were studied by MD Simulation(100ns).The analysis of the simulation results shows that the peptides have a high stability during the simulation and structural changes in them can be investigated during this period.

کلیدواژه ها:

antimicrobial peptide ، antimicrobial peptide database ، molecular dynamics simulation