A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues

Abstract

Natural products that target lipid II, such as the lantibiotic nisin, are strategically important in the development of new antibacterial agents to combat the rise of antimicrobial resistance. Understanding the structural factors that govern the highly selective molecular recognition of lipid II by the N‐terminal region of nisin, nisin(1–12), is a crucial step in exploiting the potential of such compounds. In order to elucidate the relationships between amino acid sequence and conformation of this bicyclic peptide fragment, we have used solid‐phase peptide synthesis to prepare two novel analogues of nisin(1–12) in which the dehydro residues have been replaced. We have carried out an NMR ensemble analysis of one of these analogues and of the wild‐type nisin(1–12) peptide in order to compare the conformations of these two bicyclic peptides. Our analysis has shown the effects of residue mutation on ring conformation. We have also demonstrated that the individual rings of nisin(1–12) are pre‐organised to an extent for binding to the pyrophosphate group of lipid II, with a high degree of flexibility exhibited in the central amide bond joining the two rings.

Environmental and dynamic effects explain how nisin captures membrane-bound lipid II

“…This provides evidence that the nisin/lipid II recognition mode defined by the latter structure is not unique. Recently published NMR data on the conformational ensemble of nisin 1-12 in an aqueous solution 40 confirmed the existence of the predicted N1 conformation, which to some extent validates the proposed computer models.…”

“…It is important to note that recently published data on NMR ensemble of nisin 1-12 revealed the very similar set of 6 conformations in solution, within which the N1 state described above was observed 40 . Thus, nisin 1-11 represents a good model system of full nisin, since the C-terminal membrane-active module does not participate in lipid II recognition, but instead may contribute to decoy conformations, and, more importantly, recognition module structure and dynamics are preserved in both cases.…”

Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs

“…Conformational analysis by NAMFIS requires experimentally determined proton–proton distances obtained from NOE build‐up measurements, and dihedral angles calculated from vicinal scalar couplings as input; this data was therefore generated for the four selected macrocycles (see the Supporting Information, Sections 1 and 2). NAMFIS has previously been successfully used to determine the solution conformations of Ro5‐ and bRo5‐compounds, including both peptides and macrocycles …”

“…In addition, our initial attempts to determine the solution ensembles of roxithromycin succeeded when a theoretical conformational ensemble for the neutral form was used, but failed for an ensemble of the charged form. Based on these observations, and on several reports on the successful use of the theoretical ensembles of the neutral form of complex and charged compounds, we generated theoretical ensembles for the neutral and non‐ionic form of the four macrocycles studied herein. Unrestrained Monte Carlo conformational searches with different force fields and both water and chloroform solvent models produced comprehensive ensembles within an energy window of 42 kJ mol −1 (see the Supporting Information, Section 3).…”

“…Herein, we address this scientific gap by determining the solution conformational ensembles for a carefully selected set of orally available, non‐peptidic macrocyclic drugs by an NMR spectroscopic technique proven to be successful for flexible compounds . In‐depth analysis of the ensembles obtained in both aqueous and apolar solutions provides broader experimental evidence that drugs in the bRo5 space behave as molecular chameleons.…”