Combined Molecular Dynamics and Experimental Approach to Understand the Impact of the Oxetane and Azetidine Modification on Peptides

Peptide-based drugs are promising as therapeutics, but they are limited by unfavourable pharmacokinetic properties. Modifying or cyclising the peptide backbone increases their biological activity in many cases. However, cyclic peptides remain challenging to make, and no single backbone modification is universally tolerated. Both oxetanes and azetidines have previously been used in medicinal chemistry, and previous work suggests that oxetane modification of the peptide backbone may bring the termini in close proximity, enhancing efficiency of cyclisation. In order to realise the potential of oxetane and azetidine modification in medicinal chemistry, an investigation into the effects of these modifications on the backbone of peptides is needed. In this work, linear and cyclic oxetane-modified peptides were characterised using CD, NMR spectroscopy and molecular dynamics (MD) simulations. In linear peptides, oxetane modification induces the formation of a turn, as evidenced by the presence of medium-range NOEs observed in NMR experiments. In cyclic peptides, MD simulations reveal that the oxetane-modified peptide is more rigid and the structure is stabilised by the formation of a new hydrogen bond that is absent in the parent peptide. The effect of oxetane modification on _-helicity was also explored. CD spectroscopy revealed that oxetane modification drastically reduces the helical content of a well-characterised sequence. Furthermore, steered MD simulations revealed the molecular determinants of this destabilisation|that oxetane modification introduces a kink in the helical axis, which disrupts the dihedral angles and hydrogen bonding pattern in both directions. NMR experiments showed that, like oxetane, azetidine induces a turn in a short linear peptide. Finally, the impact of azetidine modification on the activity of antimicrobial peptides (AMPs) was assessed using microbiological assays. Following confirmation of activity, a known AMP sequence was modified and/or cyclised, and the activity was measured. It was found that azetidine modification increases the activity of this AMP without increasing its toxicity. Overall, this work may help direct future design of peptide-based drugs.