Cupriavidus necator, an alternative source for isotopic enrichment of proteins expressed in insect cells for NMR investigations

Isotopic enrichment of pharmacologically relevant protein targets is crucial for structural studies by nuclear magnetic resonance (NMR) and plays a key role in advancing structure-guided drug discovery. Many clinically important drug targets require expression in eukaryotic systems-such as mammalian, yeast, or insect cells-rather than prokaryotic hosts. This requirement limits the feasibility of high-throughput isotopic labeling and poses challenges for obtaining uniformly isotope-labeled proteins suitable for NMR analysis. While several enrichment strategies have been developed, no broadly applicable enrichment platform has emerged for eukaryotic expression systems. In this study, we introduce Cupriavidus necator as an alternative biological source for ¹⁵N and ¹³C isotopic enrichment to support protein production in eukaryotic systems. To evaluate this approach, we selected the kinase domain of EPHA2, a receptor tyrosine kinase implicated in colorectal cancer progression and an important target for therapeutic inhibitor development. Isotopic incorporation was quantified using liquid chromatography-mass spectrometry (LC-MS), revealing enrichment levels of 79% for ¹⁵N and 69% for ¹³C. These results demonstrate that Cupriavidus necator can serve as a robust and flexible platform for generating isotopically enriched biomolecules compatible with eukaryotic protein expression, thereby enabling NMR investigations of disease-relevant protein targets.