Learn about Compound Screening

What is compound screening?

Compound screening is a service that enables rapid screening of thousands of compounds to identify a ‘hit’, or a compound that elicits a desired biochemical effect against a validated target or a phenotypic effect in cells. Compound screening can rapidly assess thousands of potential compounds and narrow down a list of ‘hits’ that can then be evaluated in more detail. Automated compound screening can complete this daunting task in a matter of hours which would otherwise take a team of researchers several days or months of laborious benchwork. There are a few types of compound screening, which we will briefly discuss below:

  • High-throughput screening
  • Focused screening
  • Physiological screening
  • Virtual screening

High-throughput screening:

High-throughput screening is a highly automated process that allows for fast testing of hundreds of thousands of compounds in a library against a target or cell line for a particular biological or chemical effect [1]. The three general steps of high-throughput screening include: 1) Selecting a diverse, relevant library for testing, 2) setting up a suitable automated workflow with a robotics station, and 3) determining the method of acquiring and processing data. High-throughput screening usually occurs in a miniaturized format, such as in a 96-well, 384-well, or other plate format [1]. The miniaturization of the process enabled minute amounts of chemicals or drugs to be used in testing and the automation of the process allowed for a dramatic decrease in the time and labor needed to screen these compounds [1]. In fact, the process of quantitative high-throughput screening (qHTS) added an additional layer of complexity to high-throughput screening: testing varying concentrations of a single compound simultaneously to establish a dose curve [2]. By establishing a dose curve during screening, the rate of false negative and false positive hits has decreased [2]. Overall, high-throughput screening has dramatically improved the process of screening multitudes of compounds in a rapid fashion, helping researchers spend less time on labor-intensive screens and more time on validating intriguing hits.

Focused screening:

While one of the advantages of high-throughput screening is the ability to screen through enormous libraries of compounds, focused screening, as the name suggests, narrows down the library to a smaller fraction of compounds [3]. If there is already some information on a target that suggests certain compounds would react with it in the desired fashion, focused screening allows for testing of a smaller list of compounds [3]. While this method may not work if there is not much data on a target or if the researcher wants to cast a wide net when searching for hits, it can certainly reduce the cost and the timeframe of screening if many compounds can already be eliminated from the initial screening process [3].

Physiological screening:

Another type of specialized screening is physiological screening, in which compounds for testing are selected based on their potential effect in a target organ [3]. For example, many drugs are unable to cross the blood-brain barrier, so eliminating compounds that are unable to cross this barrier would be beneficial if the target organ is the brain. Physiological screening also enables researchers to consider the complex effects a drug or compound would have on the organ as a whole, rather than focusing solely on molecular interactions [3].

Virtual screening:

Virtual screening is a highly sophisticated process that considers the potential interactions of compounds and a target based on the current structural information of the target [3]. Similar to focused screening, this method can be used initially to narrow down a broad list of compounds to a more manageable list of potential compounds, all while conducting initial screens in silico [3].

How can I use compound screening?

Compound screening can be used in a variety of assays, from drug discovery to screening for compounds that target a receptor on cells to induce a signaling pathway. We will briefly discuss applications of compound screening in reporter cell lines, compound screening in drug discovery, as well as some practical considerations, such as timeline and cost for screening assays.

Compound screening in reporter cell lines:

Many compound screens rely on examining the biochemical interaction between a target and a compound. However, other screens utilize cell culture in order to identify hits that affect receptors, ion channels on the cell surface, etc. [3]. Reporter cell lines in particular can prove useful when screening for hits. For example, one study used cells overexpressing a validated target and a biosensor. When a compound in the screen would bind to the target receptor, a cascade of intracellular events resulted in luminescence, which could be measured and quantified in the assay [3,4]. Utilizing this reporter cell line in high-throughput screening enabled researchers to test numerous compounds quickly and simply through the evaluation of luminescence produced in vitro [3,4]. Other studies have used reporter cell lines in compound screening and identified hits by measuring luciferase in common murine and human cell lines [5].

Compound screening in drug discovery:

For every drug that was discovered, there were countless potential compounds that were initially screened out. In the initial stages of drug discovery, compound screening is paramount in finding a few potential hits among thousands of compounds, especially since it already takes over a decade on average from the initial stages of research to the release of new drugs [3]. Compound screening, especially high-throughput screening, has improved the process of screening for potential drugs against targets. Quantitative high-throughput screening for compounds also improves the process, as it allows for screening of multiple concentrations of the drug and can decrease false positives and negatives in screens [2]. An ideal drug binds with high specificity to a target and works at a low concentration to minimize side effects. In this regard, high-throughput screening and quantitative high-throughput screening enable more rapid testing of compounds to find ‘hits’ that can be evaluated in vitro and in vivo.

How many compounds are typically screened in drug discovery?

In drug discovery, on average 200,000 to over 1 million compounds may be screened to narrow down a list of potential hits [3]. Once the list is narrowed after compound screening, select compounds are focused on and validated [3]. However, not every compound library contains over a million compounds to be tested. In fact, focused screening and physiological screening focus on a much smaller initial list, reducing the overall cost and time required for the screen.

What is hit identification and validation in compound screening?

Before a screen can begin, a target must first be identified and validated as biologically relevant to the disease or mechanism researchers aim to affect [3]. Through in vitro and in vivo work, the target should be validated in multiple ways that it plays an important role in the disease or mechanism of interest [3]. Once a target has been validated (or shown that it does play a crucial role in the disease or condition through several assays), then researchers can move on to hit identification. Hit identification narrows down a list of chemical or biological compounds that interact with or have an effect on the validated target in a way that is desired [3]. For example, if the goal was to inhibit the validated target, then compounds that interacted with and inhibited the target would be identified as a ‘hit’ [3]. Compound screening of diverse libraries promotes hit identification rapidly.

How long does compound screening take to complete? How much does compound screening cost?

The cost of compound screening varies at each facility, but typically there is a set charge per well in a plate. The more compounds that are screened against a target and the complexity of the screen can increase the price. Oftentimes, pilot screens or small-scale screens can be completed first to evaluate how well the workflow is set up and the reproducibility of the screen. In general, the cost of a screen will vary for each individual project, but it is possible to find the right screen for your project and budget. High-throughput screening can take anywhere from a week up to a few months depending on the amount of compounds used in the screen and the complexity of the project [6]. Smaller screens or more focused screens using ~10,000 compounds may only take about a week to complete [6]. High-throughput screening with a vast, diverse library of ~1 million compounds can take up to a few months however [6]. In general, it is important to consider the timeframe and budget of each individual project when developing compound screening, as well as the complexity of the screening process (biochemical or reporter cell line assays, etc.).

Conclusions

Utilizing compound screening as a method to quickly test thousands of compounds in small amounts has vastly improved research and early drug discovery. What normally would have taken months of laborious research and large amounts of expensive reagents has now become a highly automated process, saving both time and money. Variations in compound screening—such as focused screens for smaller, knowledge-based screens or quantitative high-throughput screening to generate dose curves for thousands of compounds simultaneously—have enabled researchers to customize compound screening to their experimental needs. The evolution of compound screening has become an integral part of the drug discovery process in industry and allows for faster screening of compounds of interest. Compound screening in reporter cell lines has also proved highly useful when screening for compounds that interact with a receptor or ion channel on the cell surface, while physiological screens provide a more focused examination of compounds that affect a target organ. With a plethora of compound screens available such as Boster Bio’s compound screening service, it is possible to incorporate a customized compound screening assay in your experiments.

References

  • [1] Pereira DA, Williams JA. Origin and evolution of high throughput screening. Br J Pharmacol. 2007;152(1):53-61. doi:10.1038/sj.bjp.0707373
  • [2] Alkhilaiwi F. Conditionally Reprogrammed Cells and Robotic High-Throughput Screening for Precision Cancer Therapy. Front Oncol. 2021;11:761986. doi:10.3389/fonc.2021.761986
  • [3] Hughes J, Rees S, Kalindjian S, Philpott K. Principles of early drug discovery. Br J Pharmacol. 2011;162(6):1239-1249. doi:10.1111/j.1476-5381.2010.01127.x
  • [4] Stables J, Mattheakis LC, Chang R, Rees S. Recombinant aequorin as reporter of changes in intracellular calcium in mammalian cells. Methods Enzymol. 2000;327:456-471. doi:10.1016/s0076-6879(00)27296-0
  • [5] Brustikova K, Sedlak D, Kubikova J, et al. Cell-Based Reporter System for High-Throughput Screening of MicroRNA Pathway Inhibitors and Its Limitations. Front Genet. 2018;9. Accessed July 11, 2022. https://www.frontiersin.org/articles/10.3389/fgene.2018.00045
  • [6] Macarron R, Banks MN, Bojanic D, et al. Impact of high-throughput screening in biomedical research. Nat Rev Drug Discov. 2011;10(3):188-195. doi:10.1038/nrd3368