Application of Fragment-Based Drug Discovery to Membrane Proteins: Identification of Ligands of the Integral Membrane Enzyme DsbB

SummaryMembrane proteins are important pharmaceutical targets, but they pose significant challenges for fragment-based drug discovery approaches. Here, we present the first successful use of biophysical methods to screen for fragment ligands to an integral membrane protein. The Escherichia coli inner membrane protein DsbB was solubilized in detergent micelles and lipid bilayer nanodiscs. The solubilized protein was immobilized with retention of functionality and used to screen 1071 drug fragments for binding using target immobilized NMR Screening. Biochemical and biophysical validation of the eight most potent hits revealed an IC50 range of 7–200 μM. The ability to insert a broad array of membrane proteins into nanodiscs, combined with the efficiency of TINS, demonstrates the feasibility of finding fragments targeting membrane proteins.

Graphical AbstractFigure optionsDownload full-size imageDownload high-quality image (145 K)Download as PowerPoint slideHighlights► Use of NMR to detect weak binding of drug fragments to a membrane protein ► Comparison of different membrane protein solubilization media for ligand discovery ► Biological and biophysical characterization of ligands from library screening