Preliminary Exploration of Antimicrobial Peptide Simulations
Title: Preliminary Exploration of Antimicrobial Peptide Simulations
SNIC Project: SNIC 2022/22-815
Project Type: SNIC Small Compute
Principal Investigator: Sanjiv Kumar <sanjiv.kumar@oru.se>
Affiliation: Örebro universitet
Duration: 2022-09-02 – 2023-10-01
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. Our lab has previously identified, optimized, and characterized a few highly efficient AMPs with activity against numerous human pathogens. 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. Previously, using the resources from SNIC (SNIC_202122-650) we were able to generate membrane models with peptides, perform simulation with two of the peptides and visualize these basic models. We also optimized scripts and analysis for better utilization of allocated resources. Along with that we could also elucidate the possible mechanisms of action of studied antimicrobial peptide against bacterial species with different lipid membrane composition, with an ongoing manuscript in preparation. We further want to explore the role of peptides and their interaction with the membrane components and therefore need further 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.