An integrated experimental and computational pipeline for crystallographic fragment screening of membrane protein in the lipid cubic phase.

X-ray crystallographic fragment screening is a powerful strategy in modern drug discovery, enabling the identification of small-molecule starting points for rational hit-to-lead optimization. While highly effective for soluble proteins, its application to membrane proteins remains challenging due to low expression yields, high hydrophobicity, and the complexities of crystallization-particularly when using lipid cubic phase (LCP), which is often essential for high-resolution structural studies of targets like G-protein-coupled receptors (GPCRs). In this study, we present a methodology that integrates high-throughput X-ray crystallography with computational modeling and complementary biophysical validation to overcome these barriers. Using a thermostabilized human adenosine A2A receptor crystallized in LCP as a test system, we screened 568 fragments and identified 23 initial hits. The work represents the first large-scale fragment screening effort targeting crystals of a membrane protein grown in LCP. Structure-guided virtual screening of these hits led to the design of 109 follow-up compounds, of which 56 yielded crystal structures. Of these, 19 were additionally confirmed to bind by grating-coupled interferometry (GCI), providing complementary biophysical validation. Our results demonstrated the feasibility and effectiveness of this integrated approach for fragment-based drug discovery on membrane proteins crystallized in LCP. Moreover, the detection of ligands at a previously uncharacterized intracellular pocket in a GPCR highlights the potential of this strategy to accelerate the discovery of therapeutically relevant compounds for challenging drug targets.