Molecular dynamics for antimicrobial peptide discovery.

Palmer, Nicholas; Maasch, Jacqueline R M A; Torres, Marcelo D T; de la Fuente-Nunez, Cesar

Although antimicrobial resistance is an increasingly significant public health concern, there have only been two new classes of antibiotics approved for human use since the 1960s. Understanding the mechanisms of action of antibiotics is critical for novel antibiotic discovery, though novel approaches are needed that do not exclusively rely on experiments. Molecular dynamics simulation is a computational tool that uses simple models of the atoms in a system to discover nanoscale insights into the dynamic relationship between mechanism and biological function. Such insights can lay the framework for elucidating mechanism of action and optimizing antibiotic templates. Antimicrobial peptides represent a promising solution to escalating antimicrobial resistance given their lesser tendency to induce resistance than small molecule antibiotics. Simulations of these agents have already revealed how they interact with bacterial membranes and the underlying physiochemical features directing their structure and function. In this Minireview, we discuss how traditional molecular dynamics simulation works, and its role and potential for the development of new antibiotic candidates with an emphasis on antimicrobial peptides.