Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques

Abstract

The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.

Ion Mobility-Mass Spectrometry Coupled to Droplet Microfluidics for Rapid Protein Structure Analysis and Drug Discovery

“…8 MS technologies can evaluate low volume samples, are compatible with a relatively wide range of solution conditions, provide universal detection of ligand biding events, and provide the ability to make measurements within complex mixtures. 9 In particular, native MS has become an important addition to the biophysical characterization toolbox. Under native MS conditions, noncovalent interactions within and between biomolecules can be preserved for direct interrogation by MS, thus providing ligand binding stoichiometry and dissociation constant (K D ) information.…”

Deciphering the mechanism of action of antitubercular compounds with metabolomics

“…Mass spectrometry imaging (MSI) has recently been employed to understand the mode of action of drugs in vivo and in situ by spatially characterizing metabolic changes in tissue samples [44] , [45] . The MSI protocol consists of (1) sample preparation, (2) analyte desorption and ionization, (3) mass analysis, and (4) image registration ( Fig.…”

Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses

“…Currently, MS ligand affinity and specificity screening methods are available to evaluate both covalent and noncovalent interactions, which is the result of decades of advances in “soft ionization techniques”. 55 , 56 Such methods have direct applications for testing proposed target proteins for the control of infectious diseases, establishing ligand binding, and providing information regarding binding affinities and the nature of the binding site interactions. Importantly, these analyses can be used both for established ligands before or after bioassay evaluation and for screening of compound libraries and NP extracts.…”

“…Analytical methods for evaluating the interactions between small molecules and biologically relevant proteins are critical for discerning a potential therapeutic compound’s utility and has been made easier by the wide commercial availability of major drug targets. Currently, MS ligand affinity and specificity screening methods are available to evaluate both covalent and noncovalent interactions, which is the result of decades of advances in “soft ionization techniques”. , Such methods have direct applications for testing proposed target proteins for the control of infectious diseases, establishing ligand binding, and providing information regarding binding affinities and the nature of the binding site interactions. Importantly, these analyses can be used both for established ligands before or after bioassay evaluation and for screening of compound libraries and NP extracts. , This advantage facilitates the validation of in silico binding affinities of known NPs without having to isolate the compound from the source material when the pure compound is not commercially available, but the source organism, or a closely related species, is obtainable.…”