Mass spectrometry-based methods for characterizing transient protein–protein interactions

The dynamic associations of transient protein–protein interactions (PPIs) are critical mediators of myriad biochemical processes. These specific, low-affinity interactions are often mediated by conserved amino acid sequences or short linear motifs (SLiMs) that interact with corresponding binding domains. The short-lived and dynamic nature of these interactions make their biophysical characterization a significant challenge. This review focuses on the development and future directions of mass spectrometry (MS)-based techniques for elucidating and characterizing SLiM-mediated PPIs. This includes the application of protein footprinting techniques to infer the location of SLiM binding sites and the growing role of native MS for direct observation of protein–SLiM interactions, highlighting their potential for the assessment of small molecule modulation of transient PPIs and the identification of interfacial SLiMs.</p

Native Mass Spectrometry-Guided Screening Identifies Hit Fragments for HOP-HSP90 PPI Inhibition

Contemporary medicinal chemistry considers fragment‐based drug discovery (FBDD) and inhibition of protein‐protein interactions (PPI) as important means of expanding the volume of druggable chemical space. However, the ability to robustly identify valid fragments and PPI inhibitors is an enormous challenge, requiring the application of sensitive biophysical methodology. Accordingly, in this study, we exploited the speed and sensitivity of nanoelectrospray (nano‐ESI) native mass spectrometry to identify a small collection of fragments which bind to the TPR2AB domain of HOP. Follow‐up biophysical assessment of a small selection of binding fragments confirmed binding to the single TPR2A domain, and that this binding translated into PPI inhibitory activity between TPR2A and the HSP90 C‐terminal domain. An in‐silico assessment of binding fragments at the PPI interfacial region, provided valuable structural insight for future fragment elaboration strategies, including the identification of losartan as a weak, albeit dose‐dependent inhibitor of the target PPI