Integrated strategies for producing functional recombinant proteins to advance autoimmune disease therapeutics

Autoimmune diseases result from immune dysregulation, characterized by loss of self-tolerance, chronic inflammation, and multiorgan pathology. However, the immune signaling pathway is a host of complex protein architectures, including polymeric cytokines, transmembrane receptors, and intracellular pathway mediators. Each are essential but challenging due to structural intricacies such as oligomerization, domain organization, and transmembrane regions. Herein, we present an integrated strategy to produce functional recombinant proteins to support research and therapeutic development in autoimmune disease. For soluble polymeric targets, structure-guided engineering is employed, encompassing linker optimization for IL-17A/IL-17F heterodimer stabilization. For other targets such as the assembly of IL-2 receptor subunits, the incorporation of protein tags is the optimal methodology for recombinant protein production. Finally, by utilizing targeted mutagenesis, oligomerization can be controlled for TL1A disulfide bonds to control oligomerization. With the incorporation of process optimization in culture and purification, the development of hard-to-express recombinant proteins helps preserve native conformation and bioactivity. These are encapsulated into three complementary platforms are implemented to ensure solubility and functional reconstitution: detergent micelles for structural studies, ELISA, and surface plasmon resonance; nanodiscs for detergent-free, cell-based assays; and virus-like particles providing a native membrane context and high immunogenicity. These proteins further enable antibody discovery, including epitope-focused immunogen design, for example, IL-23/IL-12 chimeras to reduce off-target responses. By adhering to Quality-by-Design principles, this closed-loop workflow from structural analysis through application validation ensures maintenance of native functionality, stability, and homogeneity. Collectively, these approaches accelerate drug discovery in autoimmune disease by generating high-quality reagents for mechanistic studies, screening, and therapeutic development, overcoming longstanding production bottlenecks in structurally complex targets.