Automated Cell-based Assays: Novel tools overcome the barriers to drug discovery success

Automated Cell-based Assays: Novel tools overcome the barriers to drug discovery success

By Helen Stewart-Miller and Kate Tointon

In this article, we look at how commercial products and services are facilitating the automation of cell-based assays to advance drug discovery and accelerate the delivery of new medicines to patients.

Cell-based assays are vital tools in modern drug discovery. Live cell cultures that replicate in vivo physiological conditions enable more reliable predictions about the safety and efficacy of drugs. Cellular assays have traditionally been complex and labour-intensive, however, automated technologies are now streamlining workflows as well as improving assay precision.

The last decade in drug discovery has seen a strong drive towards using in vitro cellular models that better mimic the in vivo environment, such as three-dimensional (3D) and patient-derived models. This is vital for enabling the reliable analysis of drug targets and drug mechanisms of action during early screening, as well as in later drug absorption, metabolism and toxicity studies.

“The drive for greater physiological relevance in drug discovery assays has resulted in a number of key methodological changes over the last decade,” remarks Peter Banks, Scientific Director at BioTek Instruments. “This includes the greater use of human primary cells relative to immortalised cell lines, measuring endogenous expression of drug targets (as opposed to their overexpression) and the use of 3D cellular models involving hydrogels and spheroid aggregation.”

However, complex protocols, extended run times and large numbers of samples make cellbased assays labour-intensive. They also need to be highly sensitive, reproducible and reliable to ensure they produce high quality data. As cellular assays are increasingly used during primary screening, a high-throughput capability is also highly desirable. The automation of cell-based assays has been critical in tackling these challenges.

Increasing the efficiency and productivity of cell-based assays

The automation of cellular assays can benefit every aspect of drug discovery. In the early stages, automation enables cell-based screening of vast compound libraries, which was previously unfeasible with conventional, manual cellular assays. Thanks to automation, more physiologically-relevant data can now be generated at an earlier stage of the drug discovery pipeline, enabling the prioritisation of only the very best compounds from the outset.

In primary screening, automated cell-based assays can help speed up the process of screening compounds against targets. Recent advances in high-content screening (HCS) enable an entire two colour 96-well plate to be scanned and quantified within just five minutes.

“By helping to speed up the profiling of selected compounds against cellular targets, automation offers more opportunities for downstream applications, such as phenotypic screening,” remarks Manuela Beil-Peter, Director Business Sector Liquid Handling and Automation, Analytik Jena. “As a direct consequence of automation, data improves in quantity and quality, which in return provides higher quality assays and, in the end, better drugs.”

Figure 1 The Analytik Jena CyBio FeliX benchtop liquid handling platform

Automated systems can also help to track which compounds have been screened and when facilitating the management of the huge numbers of compounds during primary screening. HCS, for instance, logs all measurements at numerous time points and pharmacological concentrations, and these data can be retrieved at any time during the screening process.

Streamlining complex cellular assays and improving precision

Automation helps to streamline the complex and labour-intensive processes typically involved in cell-based assays, including cell seeding, media and buffer exchange, compound and reagent dispensing and cell washing. Long-term kinetic assays, for example, require time-consuming cell health maintenance over days to weeks. Robotic arms can streamline this process by shuttling microplates from incubators to microplate readers. Such automated procedures help to maximise the efficiency and productivity of laboratories, especially as they provide crucial ‘walk-away’ time and allow assays to be performed during evenings and weekends.

“The development of integrated platforms, new features of multi-mode readers and advances in software analysis tools, are now enabling more complex experimental designs and longer term kinetic studies of cells,” says Dr Cristopher Cowan, Senior Technology Manager at Promega. “These more sophisticated assays are improving the reproducibility and robustness of the data to benefit drug discovery.”

Automated systems can also improve the reliability of the data by reducing the amount of manual handling by technicians. Not only does this eliminate variability associated with human error, it also reduces the risk of contamination, which is more likely to arise through human interactions with equipment. In this way, automated systems ensure the consistent and reproducible performance of cellular assays, especially as they become more sophisticated.

Tackling the challenges of automated cell-based assays

Despite recent advances, adopting automated cellbased assays can still be challenging. Fortunately, these challenges are being overcome by various commercial products and services, some of which are outlined below.

Challenge 1: Adapting automated solutions to meet specific needs

The requirements for automated systems vary widely among different laboratories, making it difficult to adapt them to changing application parameters and environments. Fortunately, systems such as Analytik Jena’s modular CyBio FeliX benchtop liquid handling platform and the Thermo Scientific™ Cytomat™ series of automated cell incubators are fully compatible with a wide range of laboratory automation solutions. This can help to simplify drug discovery workflows, even for very complex applications.

“Every drug discovery project is unique and there is no standard workflow to rely on, so one of the biggest challenges that laboratories face is having to integrate different automated systems and configurations for different projects,” says Rémi Magnan, Associate Director Cellomics & Proteomics at Tecan. “Customised platforms that integrate and configure the different modules can help optimise workflows to meet specific project needs.”

Expert support services such as Tecan Labwerx™ can design and create complex workstations that integrate a wide range of automation systems, such as HCS imagers, multimode readers, flow cytometers, centrifuges, incubators and cell dispensers. The service aims to deliver customised workflows for highly complex projects to dramatically improve the laboratory’s efficiency and productivity.

Figure 2 The Tecan Labwerx expert support service

Challenge 2: The automation of increasingly complex cellular assays

As the complexity of cellular assays increases in drug discovery, so do the challenges associated with automating them. More physiologically-relevant 3D spheroid models, for example, have become a key tool, such as in the booming field of immuno-oncology. Spheroid tumour samples can be used to test which immune-mediated drugs are most efficacious in degrading tumours including, for individual patients’ tumours, to develop personalised cancer-targeting medicines.

However, 3D spheroid proliferation assays can be difficult to automate due to the need to monitor the growth of spheroids kinetically over weeks using microscopy. Additionally, these assays require several different automation processes, including the initial assay set-up of cell seeding into spheroid microplates, automating the periodic imaging of the spheroids, while also maintaining cell health and performing media exchanges.

Three benchtop systems developed by BioTek Instruments are designed to be used in concert to fully automate 3D spheroid proliferation assays. The MultiFlo™ FX Multi-Mode Dispenser can be used to seed cells into spheroid microplates, while the Cytation™ 5 Cell Imaging MultiMode Reader, in conjunction with the BioSpa™ 8 Automated Incubator, provides long-term automated kinetic imaging of the spheroids.

As the Cytation™ 5 is both a digital widefield microscope and a microplate reader, absorbance measurements can be made to assess media pH using the common media additive phenol red. These measurements can be used to identify when to initiate gentle media exchange using the AMX automated module of the MultiFlo FX.

Figure 3 The BioTek Instruments MultiFlo FX Multi-Mode Dispenser

Additionally, rigorously evaluating such complex cellular models can be challenging. One issue that arises from analysing thick 3D spheroid samples is that conventional light-emitting diode light engines are typically not bright enough to completely illuminate their entire depth. This has recently been overcome by the new Thermo Scientific™ CellInsight™ CX7 LZR HCS platform which provides seven independent, solid-state lasers to illuminate thick tissue. The laser light engine provides for shorter exposure times, which further accelerates throughput for large scale projects.

Another key challenge facing labs is the need to use automated systems that are sufficiently flexible to adapt to rapidly changing needs in drug discovery as well as address the industry’s current demands. The Thermo Scientific™ inSPIRE™ Collaborative Laboratory Automation Platform has modular components that allow the optimal configuration for a certain workflow, helping to adapt the automation platform to the specific needs of laboratories as they evolve.

Figure 4 The Thermo Scientific inSPIRE Collaborative Laboratory Automation Platform

Challenge 3: Ensuring expertise and experience in automation

Expertise and experience in automation are among the greatest barriers to implementing automated cell-based assays in drug discovery, particularly those involving more complex processes. Dedicated support service teams can help fill any gaps with their expertise in programming and experience in optimising a variety of automation platforms.

“For more complex automation, it is important to maintain specialist skills within an organisation to ensure the best use is made from the investment in automation,” notes Roger Clark, Group Leader of High Throughput Screening Biology & Head of Compound Management at Charles River. “This includes having key personnel on hand to quickly teach robotic platforms, recover platforms when they malfunction and configure complex cellular readers, to prevent any costly delays to the drug discovery pipeline.”

Charles River’s team of experts provides critical support for automated solutions throughout the drug discovery and development pipeline, from hit identification through to the pre-clinical phases. Similarly, Promega’s team of Global Field Services Scientists will collaborate with customers on-site to optimise and programme assays for high-throughput platforms.

What’s the future of cell-based automation in drug discovery?

Ongoing advances in automated cell-based assays are likely to focus on a variety of existing needs in drug discovery. One such need is for modular devices that can quickly adapt to new laboratory conditions and devices, as well as for more compact systems to enable them to fit into increasingly limited laboratory spaces. Moreover, it is likely that improvements in software will continue to drive data analyses as well as data trending to provide greater analysis capabilities. With every laboratory looking to reduce costs, there will also be continued demand for scalable automated systems that can quickly increase throughput, as well as label-free applications such as matrix-assisted laser desorption/ ionisation (often referred to as MALDI), which avoid the use of expensive fluorescence markers.

“As automation technologies become more collaborative, intuitive and versatile, more researchers will be able to access these tools for cellular assays,” says Dara Grantham Wright, Vice- President and General Manager, Protein and Cell Analysis Business Unit, Life Science Solutions Group, Thermo Fisher Scientific. “This will improve our ability to develop more clinically-relevant models and enhance the overall reproducibility of data, helping to discover new drug classes, personalised treatments and replace conventional animal testing.”

As researchers explore more complex disease types and employ co-culture systems, it is also likely that the resurgence of phenotypic and fragmentbased screening will continue. In addition, the combination of cell biology with virtual simulations and computer learning is set to further advance cellular assays in drug discovery.


Automation is enabling more sophisticated cellbased assays to advance drug discovery. Laboratories can gain numerous benefits from automating cellular assays, including streamlined workflows, increased productivity and enhanced assay precision. While there are still some barriers to their adoption, novel technologies and services are starting to overcome these effectively, accelerating the search for innovative treatments. DDW

This article originally featured in the DDW Summer 2019 Issue

Helen Stewart-Miller is Director of PR Services and Kate Tointon is a Science Writer at BioStrata, a life science specialist marketing agency. The company’s growing team in Cambridge (UK) and Boston (US) includes a significant number of people with deep scientific experience and knowledge. The agency offers a range of services from strategy, branding and message development through to content creation, creative design, digital marketing and public relations.

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