Structure and Activity of Antimicrobial
Peptoids

Abstract

This thesis concerns complementary experimental and computational investigations into
the relationship between the primary sequence and secondary structure of peptoids. Peptoids
are a class of peptide mimetic molecules with applications as novel antimicrobial
agents. The antimicrobial properties of peptoids are linked to their interactions with lipid
bilayers in cell membranes, which in turn are linked to their helical secondary structure,
making understanding sequence to structure relationships crucial to the design of functional
sequences. Here we investigate a library of linear, cationic peptoid sequences with
structural variations in the proportion and positioning of helix inducing residues and the
chemical nature of the cationic side chains. We use circular dichroism spectroscopy to
characterise the peptoids in aqueous and organic solvent and also to investigate structural
changes upon binding to lipid bilayers designed to mimic mammalian and bacterial membranes.
We present a new set of force field parameters, derived from GAFF and quantum
mechanical calculations, that accurately capture the backbone torsional preferences of
peptoids. Subsequently we use the modified force field to perform atomistic MD simulations
of our library of peptoid sequences, using Hamiltonian replica exchange to improve
sampling at less computational expense than traditional replica exchange methods.

The CD spectra reveal that the peptoids adopt characteristically helical secondary
structures with variations depending on primary sequence. The intensity of helical features
increases upon increasing the proportion of helix inducing residues, switching from an
aqueous to an organic environment and as extra methylene groups are added to the cationic
side chains, increasing their length. The length and proportion of cationic side chains also
influences the folded hydrophobicity of the peptoids, though this does not correlate to
their antimicrobial activity. Modelling the binding of the peptoids to lipids as a two state
system enables us to estimate, in some cases, the free energy of transfer into the bilayer,
where the length of the cationic side chain is also influential. MD simulations do not
reveal a clear distinction in peptoid backbone conformation depending on cationic side
chain length however it is clear that the peptoid backbone is more flexible and deviates
more from a perfect helical conformation in aqueous than organic solvent. Ultimately
these findings may aid in the rational design of new sequences.