Tobias Ost, the SVP of Product Development at Nuclera. Ost has 19 years of experience in product development for disruptive NGS and epigenetics tools companies such as Solexa, Illumina and PacBio.
CREDIT: Tobias Ost, Nuclera.
Membrane proteins, including receptors, channels, and transporters, play vital roles in cell signaling, transport, and homeostasis, and are the targets of more than half of all clinically approved drugs. Yet, their structural complexity and hydrophobicity have made them notoriously difficult to produce and study. Cell-free expression systems are now helping to shift that paradigm by offering a faster, more flexible, and less toxic route to producing functional, stable membrane proteins at scale.
Drug Discovery News spoke with Tobias Ost, Senior Vice President of Product Development at Nuclera, to explore how innovations in cell-free protein synthesis, digital microfluidics, and AI-driven construct design are helping overcome persistent bottlenecks and redefining what's possible in membrane protein research.
Why are membrane proteins such critical targets in drug discovery, and what makes them so difficult to study structurally and functionally?
Membrane proteins are vital to life, controlling everything from cellular signaling to transport. As a result, these complex molecules account for more than 60 percent of FDA-approved drug targets, however, they are also among the most difficult proteins to study. Their hydrophobic nature and structural complexity make them challenging to express, stabilize, and analyze. To advance drug discovery, there's a pressing need to make membrane protein production faster, more reliable, and scalable. Membrane protein workflows, such as that added to our eProtein Discovery™ System (Figure 1), are designed to overcome these long-standing obstacles in drug discovery.
Figure 1. The eProtein Discovery membrane protein workflow enables construct design, screening under customizable, membrane-stabilizing cell-free conditions using automated digital microfluidics, and rapid scale-up of stable, functional membrane proteins for any downstream application.
CREDIT: Nuclera
What are the main technical and biological challenges in expressing and stabilizing membrane proteins for structural analysis?
Despite their therapeutic relevance, membrane proteins have long been difficult to work with due to their inherent complexity. Their transmembrane domains are highly hydrophobic, which makes them prone to aggregation or misfolding when removed from their native lipid environments. This instability creates major hurdles for expression, purification, and downstream structural or functional studies.
On top of that, many membrane proteins depend on specific co-factors or lipid compositions to stay properly folded and functional. Combine that with their typically low natural abundance and the limitations of conventional expression systems, and it’s easy to see why membrane proteins have remained so challenging to study.
How does the use of cell-free expression systems compare to traditional cell-based systems for membrane protein production?
For years, researchers have relied on cell-based systems to express membrane proteins, often running into familiar roadblocks. Overexpression can lead to toxic effects in host cells, misfolded proteins, or insoluble aggregates. And when expression does work, purification usually demands painstaking optimization of detergents or membrane mimetics to keep the proteins stable and functional.
We realized early on that squeezing incremental gains from these systems wasn’t enough. To make real progress, we needed to rethink the approach entirely.
That’s where cell-free protein synthesis (CFPS) systems, such as eProtein Discovery™ come in, which bypass the complexities of cellular expression. With this approach, scientists can synthesize proteins directly from DNA templates in vitro, within hours, and without relying on any living cells.
This method puts researchers in full control of the reaction environment. Need to add a specific lipid or detergent to help the protein fold? Go ahead. Want to sidestep toxicity issues? CFPS makes that irrelevant. The flexibility of this system opens the door to producing membrane proteins once considered too complex, unstable, or risky to handle.
How does automated digital microfluidics enhance the efficiency and reproducibility of membrane protein screening and optimization?
The real magic happens when CFPS systems are combined with digital microfluidics (DMF). Using nanoliter-scale droplets, it is possible to perform thousands of parallel reactions with precision and reproducibility. With built-in fluorescence-based monitoring, scientists can rapidly assess protein solubility, yield, and activity — all within a single, hands-free run.
When combined with CFPS, DMF lets researchers explore a wide range of membrane mimetics and expression conditions in parallel, dramatically increasing the odds of finding the right formulation to express and stabilize a given membrane protein. What once required weeks of trial and error can now be accomplished in a single day, with data-rich insights generated in real time.
How does improved access to stable, functional membrane proteins accelerate the identification of novel drug targets?
When researchers can reliably produce functional membrane proteins in less time and with less effort, they’re able to advance more quickly into downstream applications. Whether it’s high-resolution structural studies via cryo-EM, ligand-binding assays, or high-throughput drug screening, systems that integrate CFPS with DMF provide a consistent supply of high-quality proteins tailored for these workflows. This not only improves the likelihood of success in early drug discovery but also helps teams make go/no-go decisions with greater confidence and speed.
What role might rapid membrane protein production play in advancing newer modalities such as PROTACs or molecular glues targeting membrane proteins?
Emerging modalities like PROTACs and molecular glues are expanding the definition of “druggable.” These strategies often depend on a deep structural understanding of protein targets, including membrane proteins that have long been out of reach.
Rapid membrane protein production will help researchers access these targets more reliably. It gives researchers the material they need to validate structure and function, supporting the development of targeted degraders and modulators. This kind of access is key to unlocking therapies that were out of reach just a few years ago.
What’s the most exciting innovation in drug discovery you've seen recently?
What excites us most about this moment is the convergence of technologies like AlphaFold and other AI-based protein prediction models, which are accelerating construct design and de-risking experiments. When paired with CFPS systems, they create a feedback loop that lets researchers move seamlessly from design to data.
This intersection of AI, synthetic biology, and microfluidics is shaping the future of protein science, and we’re proud to be helping lead that transformation.
Where are the greatest untapped opportunities in your area of focus in drug discovery?
There is still vast, untapped potential in membrane protein research. Many disease-relevant targets remain uncharacterized simply because researchers lacked the tools to study them. We believe that with the right technology in place, we can unlock these proteins and reveal entirely new therapeutic possibilities.
Our goal is to democratize access to functional proteins, bringing complex science into reach for more researchers, faster. With a focus on membrane proteins, we’re opening new frontiers, turning once-impossible projects into achievable goals.
