Distinguishing Allosteric Effects from Orthosteric Binding in Protein-Ligand Interactions

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A fundamental challenge in deciphering protein-ligand interactions is distinguishing binding changes at orthosteric sites from the associated allosteric changes at distal sites, as structural data does not always reveal allostery. Ligands mediate both orthosteric and allosteric effects on target proteins and hence, in the context of screening low affinity fragments, it is important to describe fragment efficacy in terms of both direct binding and long-range allosteric responses. This presents a significant problem especially for low affinity ligands. Amide Hydrogen Deuterium Exchange Mass Spectrometry (HDXMS) is a robust method that can provide structural insights and information on conformational dynamics for both high affinity and transient protein-ligand interactions. Here, we describe the use of HDXMS on the ATPase domain of Hsp90, to parse orthosteric and allosteric effects mediated by two high affinity ligands and two low affinity fragment compounds. A comparison of deuterium exchange in ligand-bound-Hsp90 versus apo-Hsp90 was used to describe composite changes that combine both orthosteric effects and allosteric changes. Allostery can be discerned by correlating HDXMS results with structural information about orthosteric binding from crystallographic structures of protein-ligand interactions. Results from this approach indicated that fragments and ligands both mediate interactions at overlapping orthosteric sites but elicit distinct allosteric effects. However, orthosteric interactions of Hsp90 with fragments are inherently weaker due to faster dissociation rates (koff). This approach finds important applications in fragment screening, ranking, and lead compound design in fragment-based drug discovery.