Probing protein–small molecule interactions using native mass spectrometry

Abstract

The in-depth characterisation of protein–small molecule complexes is of paramount importance to both drug discovery and fundamental molecular biology. Understanding the structural and thermodynamic properties of such biomolecular assemblies can enable the rational development of new therapeutics, assist in the elucidation of protein function, or provide insights into the molecular mechanisms through which biological activity is regulated.

Native mass spectrometry (MS) has emerged as a powerful tool for the investigation of protein–small molecule interactions within heterogenous biomolecular systems. Using native MS, numerous protein–small molecule complexes can be resolved in a single mass spectrum, allowing for the quantitative characterisation of multiple ligand binding events. This is in stark contrast to most established biophysical techniques, which are typically unable to characterise multiple protein–ligand interactions simultaneously.

This thesis aims to explore proven applications of native MS in the study of protein–small molecule interactions, and to identify novel methods that facilitate the investigation of complex biochemical systems using such approaches. Chapter 1 provides a comprehensive review of the relevant literature, exploring the critical developments in MS instrumentation and methodologies that have enabled the high-resolution characterisation of protein–ligand complexes. Through a critical analysis of past investigations, the review outlines major challenges facing the field and suggests potential approaches for addressing many of these issues.

The second chapter of this thesis outlines a novel native MS-based method for the direct identification of protein–ligand complexes formed from natural extracts containing more than 5,000 potential small-molecule binders. Using this approach, several novel ligands of a key human drug target are identified. Improvements in method efficiency are subsequently made to ensure that the approach could be employed for large-scale pharmaceutical screening campaigns or used for the elucidation of novel interactions between protein complexes and endogenous metabolites.

Finally, chapter three aims to identify novel chemical additives that can reduce the charge of protein–ligand complexes in native MS. Charge-reducing agents for positive-mode native MS have been previously shown to facilitate accurate quantitative analysis of protein–small molecule interactions, by increasing the kinetic stability of the gas-phase ions. In this chapter the author explores the properties of several chemical agents that reduce the charge of anionic protein complexes. The effect of these agents on the charge state of various model proteins is characterised to critically evaluate their analytical utility. Furthermore, their effect on the gas-phase stability of a labile protein–ligand complex is also explored. Such agents may prove useful in the quantification of weak interactions that cannot be accurately characterised using standard native MS-based approaches.