Preliminary Exploration of Antimicrobial Peptide Simulations
Title: Preliminary Exploration of Antimicrobial Peptide Simulations
SNIC Project: SNIC 2021/22-650
Project Type: SNIC Small Compute
Principal Investigator: Sanjiv Kumar <sanjiv.kumar@oru.se>
Affiliation: Örebro universitet
Duration: 2021-08-30 – 2022-09-01
Classification: 30109
Keywords:

Abstract

The present project aims to perform a preliminary exploration of the mechanism of action of Antimicrobial Peptides (AMPs) using simulation studies. This would help in determining the possible mechanism of action of the novel AMPs identified and optimized in our lab. AMPs, are small peptides produced by numerous bacterial species for survival and dominance in a complex environment. AMPs have been shown to have high potency and have broad-spectrum antimicrobial activity. There is also a very low risk of development of resistance against AMPs and limited effect on normal gut flora along with beneficial effects on host tissue healing. Our lab has previously identified, optimized, and characterized a few highly efficient AMPs with activity against numerous human pathogens. In order to better understand the mechanism of actions and the effect of these peptides and their interactions with proteins and various cell membranes (bacterial, host etc.), we are implementing molecular dynamics (MD) simulation studies. This would require a rather large amount of computational and storage resources. Successful completion of the project would not only indicate the possible mechanism of action of these AMPs and their interactions with various proteins and membranes but would also complement our experimental data. The project would also lead to the development, optimization and implementation of model system (lipid bilayer membrane models) which will help with understanding the mechanism of action/interaction for other ongoing studies on human pathogens in our lab.