Membrane proteins are without a doubt an important drug target: about 60% of all confirmed drug targets are located on the cell surface. However, studying these proteins in vitro has long been challenging due to their complex interactions with cellular membranes. To overcome this, protein-lipid nanodiscs were developed to make membrane proteins more amenable to biophysical studies. Nanodiscs consist of a protein belt surrounding a lipid bilayer, with one or more copies of the membrane protein embedded within the structure. These nanodiscs mimic the natural environment of cellular membranes, enabling the observation of small molecules partitioning into the lipid bilayer. As a result, nanodiscs provide an excellent tool for studying small molecule binding to reconstitute membrane proteins.
Scientists from Professor Ubbink’s lab at Leiden University have teamed up with the Assay Development and Screening (ADS) team at ZoBio (part of the Oncodesign-ZoBio Group) to explore how the lipid composition of nanodiscs impacts fragment-based drug discovery. This innovative project, funded by an Applied and Engineering Sciences (AES) grant from the Dutch Research Council (NWO), has yielded interesting results, which were recently published in Chemical Biology and Drug Design.
Using Surface Plasmon Resonance (SPR) experiments, the team investigated how different lipid compositions in nanodiscs affect the results of fragment screening, a vital method in identifying potential drug candidates. Their research revealed that many small molecule fragments bound to the lipids themselves rather than to the membrane-anchored enzyme cytochrome P450 3A4 (CYP3A4), causing a high level of non-specific interactions. Importantly, altering the lipid composition in nanodiscs was found to significantly influence the level of off-target binding, with the lipid type playing a crucial role in refining the results.
The collaboration’s findings provide new insights into how the choice of lipid composition can impact drug discovery screening, especially for complex membrane proteins. Notably, the study also demonstrated that fewer potential binders were rejected due to atypical binding kinetics when using the native membrane protein in nanodiscs, compared to testing a non-native version of CYP3A4.
This partnership represents a significant step forward in making membrane proteins more accessible for fragment-based drug discovery campaigns, offering an improved method for studying these challenging targets.