Mass Spectrometry Gaining Momentum for Biochemical Assay Development and Screening

The goal of drug discovery is clear: reveal chemical matter that generates the most effective response towards a particular target and/or disease. Drug discovery researchers aim to accomplish this goal in the most cost and time-effective manner while generating quality data to make faster go/no-go decisions.

The 2020 Society for Laboratory Automation and Screening (SLAS) conference is an annual event where researchers present their progress and engineers/scientists showcase innovative technologies, instruments, and approaches to assist drug discovery researchers achieve their goals. Advantages of label-free and high-throughput remained the key themes echoed throughout the scientific sessions and the exhibition floor:

• Label-free assays avoid costly reagents and eliminate false-positive data prevalent in labeled formats, often due to interference from library compound
• High-throughput approaches deliver data faster to accelerate research, taking projects a step closer towards the clinic

When it comes to label-free and high-throughput approaches for biochemical assays, mass spectrometry (MS) is the clear front-runner and continues to gain momentum.

Here are three trends that emerged at SLAS2020 with a focus on biochemical assay development and screening:

Trend 1: Mass spectrometry tips the balance for label-free biochemical assays

SLAS2020 showcased biochemical data generated from conventional liquid chromatography electrospray ionization (ESI) MS instruments, matrix assisted laser desorption ionization (MALDI) MS, and the newest addition, the open port probe (OPP) (also known as Echo-MS) instrument. The MALDI and Echo-MS instruments feature high-throughput capabilities on par with a fluorescent plate reader. This enables big pharma to complete a screen of their 2 million plus compound decks in a reasonable time period. While speed is a clear benefit, researchers also discussed challenges such as sample preparation for high-throughput MS. MALDI and Echo-MS instruments eliminate the tedious liquid chromatography step often affiliated with MS that is responsible for the lower throughput and directly analyze biochemical reaction solutions. However, that means that the buffers, salts, detergents, and other reaction components remain present in MS samples, which lead to ion suppression and negatively impacts data quality. The Echo-MS instrument addresses this by diluting samples—and thereby the analyte of interest as well—nearly 1000 fold in a carrier solvent. While it minimizes ion suppression due to salts and detergents, questions remain over the sensitivity to detect diverse analytes at low concentrations. Alternatively, scientists may eliminate or minimize buffer component concentrations to allow readouts using these rapid MS instruments, a potential scientific sacrifice for speed. For MALDI users, several scientists presented the use of high-density biochip arrays presenting self-assembled monolayers that are tailored to specifically immobilize the ligand of interest from a biochemical reaction. Following immobilization, the biochips are washed to remove salts, detergents, and buffer components prior to MALDI analysis. This approach allows researchers to develop assays according to the target needs, rather than the instrument’s capabilities and limitations.

Trend 2: Complementary approaches becoming popular for hit finding strategies

Historically, high-throughput screening is run with one methodology for the primary screen and integrates orthogonal approaches during the hit confirmation phase.  The trend at SLAS2020 is that companies are utilizing multiple approaches for the initial large screening campaigns. Combinations include MS and fluorescence, and also different MS approaches. Scientists from multiple big pharma companies presented how they are using MALDI and Echo-MS for hit finding efforts, with their full deck collections. Clearly more data will generate higher confidence in progressing hits towards lead optimization. However, it is curious whether there are scientific questions or limitations of one or both approaches that motivates the additional efforts. As more data is presented, we will gain more insight into their full capabilities and limitations to determine which analytes, concentrations, and biochemical activities are best suited for a particular instrument.

Trend 3: High-throughput binding assays needed for proteins and RNA

SLAS2020 featured a new session track in which companies presented screening efforts aimed to reveal small molecules that engage RNA. Whether the target is RNA or a protein, companies are turning to mass spectrometry for high-throughput binding assays. The general assay workflow includes incubating targets (protein or RNA) with small molecules prior to a cleanup step to remove unbound small molecules, after which a second step removes the bound small molecules for subsequent detection by MS. This strategy, termed affinity selection mass spectrometry (ASMS) or automated ligand identification system (ALIS), is often performed in a lower-throughput setting due to the time required for multiple cleanup steps prior to detection. Throughput is increased by testing up to hundreds of small molecules in a single run. Another strategy to improve throughput is integrating a filter plate prior to MALDI analysis. The final readout benefits from the high-throughput MALDI instrument but still requires tedious sample preparation steps. Moreover, how the presence of hundreds of compounds with a single target impacts binding or opportunities to miss weaker, but potentially interesting chemical matter, is a key question. Innovations with self-assembled monolayers provide an alternative ASMS strategy that permit testing fewer compounds per target while still completing large scale screening campaigns in days.

Taken together, SLAS2020 made a strong case for the important role of MS in drug discovery and more companies continue to integrate this powerful approach. Next year, SLAS2021 is poised to further enlighten the drug discovery world on how MS is accelerating drug discovery for new targets, biochemical, and potentially cell-based assays. See you in San Diego in 2021!