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Using native mass spectrometry to inform drug discovery

Mass spectrometry (MS) performed under native-like conditions (nMS) is a promising approach for studying protein-drug interactions, and has already informed treatments of some of the most intractable diseases including cancer, diabetes and Alzheimer’s.

At the core of nMS is the ability to preserve non-covalent interactions and perform very accurate mass measurements. This ability has enabled advances in structural biology, including the elucidation of protein homogeneity, oligomeric state, sequence variation and the identity of bound ligands. These advances are made possible by preserving proteins in their native state in solution, followed by careful transfer into the gas phase of the mass spectrometer. As a consequence, nMS is finding applications in increasingly diverse research areas such as high-throughput drug screening, the study of amyloid formation and inhibition, the characterisation of antibody-drug conjugates and the elucidation of the interactions of membrane proteins with lipids and therapeutics. This ability to study the influence of small molecule ligand binding on the cascade of protein interactions that underlie many disease states is therefore providing a new paradigm in drug discovery.       

A better understanding of cellular processes is of paramount importance for the development of new therapeutics. These processes are enabled by synchronisation of multiple protein-protein or protein-ligand interactions and, while they dictate how cells interact in tissues, they are guided by molecular rearrangement at the atomic level. Hence, new technologies that are capable of capturing whole protein complexes, yet providing atomic-level details for their structure and function, hold the potential to unravel the complexity of these interactions. Over the last decade nMS in combination with ion mobility (IM) – which measures the overall conformation of an ion – has emerged as a promising method to study protein interactions at equilibrium.

nMS begins with the isolation of protein complexes from their cellular environment and is followed by exchanging the analyte to an MS-compatible medium, while preserving the protein in its folded, native state. Protein complexes are then ionised and transferred into the gas phase via soft ionisation methods such as electrospray ionisation. By optimising the instrumental parameters, ions are desolvated while their folded structure and non-covalent interactions are maintained. This allows the mass of protein and their bound ligands to be determined with high accuracy and resolution, elucidating not only their binding stoichiometry but also the capability to observe each species present in solution. This is a powerful attribute, since most biophysical methods report only the average ensemble present in solution.

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