High-Throughput Systems Refine Protein Engineering

Automation is revolutionizing analytical testing necessary for recombinant protein discovery and development as the biopharmaceutical industry undergoes the transition from manual, time-intensive methodologies to high-throughput (HT) automated platform processes. This evolution is driven by the increasing global demand for complex recombinant proteins, which are essential for vaccines, monoclonal antibodies, and therapeutic enzymes (1).

Strategic adoption of automation is no longer an operational preference but a necessity for accelerating drug discovery timelines, improving analytical precision, and facilitating real-time quality assurance. Traditional bottlenecks, such as manual microbiological cultures and paper-based documentation, create significant delays in development. Integrated robotic systems and miniaturized analytical tools are vital for optimizing these workflows (2).

How does HT automation improve recombinant protein engineering?

Protein engineering starts with automated computer-based design, where software is used to generate large sets of protein variants that mirror how DNA libraries are created in the laboratory. This approach enables systematic mutation and flexible cloning strategies, followed by sequencing to accurately identify and analyze each variant in the library (3).

In a fully automated strategy, every step from DNA preparation to protein purification and analysis can be integrated into a single workflow. For instance, a robotic setup can verify correct insert sizes using automated restriction digestion and agarose gel electrophoresis (3).

Automation makes the early stages of protein discovery faster and more efficient by enabling researchers to test many conditions at the same time. For example, studies using Escherichia coli expression systems have relied on automated workflows to explore how different fusion tags and growth temperatures affect protein solubility (4).

These studies show that some tags, such as N-utilization substance A and maltose binding protein, tend to produce more soluble protein at lower induction temperatures (around 25° C), while others, like Glutathione S-transferase, often perform better at higher temperatures (up to 37° C). By handling these comparisons in parallel, automated platforms can evaluate hundreds of protein variants each week (3,4).

What core technologies enable automated analytical testing in protein science?

Central to modern automated laboratories are advanced liquid handling stations, which increase accuracy while reducing human error and contamination risks. These robotic stations are divided into specialized platforms, such as DNA handling stations for plasmid extraction and protein science stations for mammalian cell transfection (5).

A notable advancement in screening technology is the development of "robot cookies," or plant cell packs (PCPs). These are prepared from plant cell suspension cultures and cast into 96-well plates for high-throughput screening of recombinant expression constructs (6).

The automation of PCP preparation reduces manual handling efforts, which previously limited throughput to approximately 500 samples per day. Today, integrating liquid handling with robotic centrifuges and plate readers can increase throughput by five-fold to more than 2500 samples per day while reducing costs by more than 50% (6).

Meanwhile, devices such as microfluidic and lab-on-a-chip systems can detect microbial contaminants or process deviations in minutes rather than the hours or days required by traditional culture methods. Rapid microbiological methods allow for real-time or near real-time decision making, which is critical for minimizing batch failures and reducing operational downtime. The ability to acquire data quickly provides immediate control over key process parameters, ensuring consistent product quality (2,7).

Advanced multi-attribute analysis is another cornerstone of automated quality monitoring. This includes the daily monitoring of glycosylation, aglycosylation, and glycation levels, all of which are sensitive to shifts in cell culture conditions. (7,8).

How do automated downstream operations support biomanufacturing scale-up?

Automation is also transforming downstream processing by simplifying how proteins are released and purified. New approaches, such as detergent-based chemical lysis and small-scale purification columns arranged in 96-well plates, make these steps easier to run in parallel (6).

Automated lysis methods rely on repeated liquid handling and gentle shaking to break down cell walls and release recombinant proteins. These techniques are well suited to robotic systems and are often more practical than traditional mechanical methods. The large volumes of data generated during these automated steps can then be analyzed to identify the most important process conditions. This insight helps define reliable operating ranges, often called design spaces, that support efficient scale-up to commercial manufacturing (4,6).

References

1. Furtmann, N.; Schneider, M.; Spindler, N.; et al. An End-to-End Automated Platform Process for High-Throughput Engineering of Next-Generation Multi-Specific Antibody Therapeutics. mAbs 2021, 13 (1). DOI: 10.1080/19420862.2021.1955433
2. Mirasol, F. Miniaturized Analytics Are Transforming Aseptic Bioprocessing. BioPharm Int. 2025, 38 (8), 19–21.
3. Kohl, T.; Schmidt, C.; Wiemann, S.; et al. Automated Production of Recombinant Human Proteins as Resource for Proteome Research. Proteome Sci. 2008, 6, 4. DOI: 10.1186/1477-5956-6-4
4. Norton-Baker, B.; Denton, M. C. R.; Murphy, N. P.; et al. Enabling High-Throughput Enzyme Discovery and Engineering with a Low-Cost, Robot-Assisted Pipeline. Sci Rep 2024, 14, 14449. DOI: 10.1038/s41598-024-64938-0
5. Söllner, S. How Liquid Handler Automation Streamlines Workflows & Boosts Accuracy. Blog Post, dispendix.com. March 11, 2025.
6. Gengenbach, B. B.; Opdensteinen, P.; Buyel, J. F. Robot Cookies – Plant Cell Packs as an Automated High-Throughput Screening Platform Based on Transient Expression. Front. Bioeng. Biotechnol. 2020, 8.
7. Silva, T. C.; Eppink, M.; Ottens, M. Automation and Miniaturization: Enabling Tools for Fast, High-Throughput Process Development in Integrated Continuous Biomanufacturing. J. Chem. Technol. Biotechnol. 2022, 97 (9), 2365–2375. DOI: 10.1002/jctb.6792
8. Dong, J.; Migliore, N.; Mehrman, S. J.; et al. High-Throughput, Automated Protein A Purification Platform with Multiattribute LC–MS Analysis for Advanced Cell Culture Process Monitoring. Anal. Chem. 2016, 88 (17), 8673–8679. DOI: 10.1021/acs.analchem.6b01956