Common challenges when designing bioassays for early drug discovery and how to overcome them
Bioassays are an essential tool for early drug discovery. By helping to identify ‘hit’ compounds that effectively act on a biological target involved in a disease pathway, bioassays underpin key decisions about compound progression. Without a well optimised bioassay, fewer ‘hits’ would be translated into new drugs that could improve patients’ lives.
In previous blogs, we have offered a range of practical advice on bioassay design and development to facilitate reliable data-driven decisions during early drug discovery. Following these key principles and guidelines is a crucial step towards developing successful bioassays, but even then, you are still likely to encounter some obstacles. Below we take a look at some of the most common challenges you might face and offer advice on how to overcome them and discuss some FAQs about bioassay development.
Challenge 1: How should you define a hit compound?
Usually, if the compound has an activity greater than the statistically defined noise of the bioassay, and has shown this same activity consistently when tested multiple times, then you can call it a ‘hit’. But how does this work in practice?
If you screen 1,000 compounds in your bioassay, you can rank them based on their activity. Look to determine the change observed for these compounds, when compared to your controls, and calculate this as a percentage. By plotting this as a distribution of percentage activity (on the x-axis) versus frequency (on the y-axis), you can then logically apply a ‘cut-off’ to identify the active compounds to retest.
If you want to find out more about how to define a ‘hit’ compound and why it’s important to develop appropriate bioassays that can reliably identify a ‘hit’, then why not read our free eBook?
Challenge 2: What plate format and layout should you use for developing bioassays?
The multi-well plates used in bioassays come in different densities (i.e., 6/24/48/96/384/1536-wells), but the format you decide to use will depend on how many compounds you will be testing, and the cost of your reagents. For example, using a 384-well plate format allows you to screen more compounds at a time and decreases the well volume, so you can use your reagents more efficiently and make your experiments more cost-effective.
To find out more about optimising the plate format and layout for your bioassay development, why not take a look at our guidelines? These go into much more detail about how to decide on the optimal plate layout for your controls and test wells and how to miniaturise bioassays from 96- to 384-wells (it’s not as simple as reducing all the reagents by four-fold!).
Challenge 3: What dilutions should you use for a dose-response experiment?
Performing a dose-response experiment of your standard in the bioassay, can give you greater insights into the effects of your compound. But what are the optimum dilutions to use? A good place to start is to use either one in two or half log (1 in 3.16) dilutions. Also determine the maximum compound concentration your bioassay can cope with i.e. the tolerance of the bioassay to the solvent dimethyl sulfoxide (DMSO) to prevent toxicity issues.
If you’d like to discover more tips about how to calculate the compound dilution factors and the maximum bioassay concentration for your system, including what to do if you only have limited information about the compound’s activity, then read our new eBook to find out more.
Here we’ve touched upon just a few of the hurdles you may encounter in bioassay development, and offered key insights into how you can overcome them to drive your drug discovery programmes forward. However, other challenges such as what to do if the Z prime of your bioassay is less than 0.5, or if you can’t access a pharmacological tool or reference compound may also arise.
The future of bioassays in early drug discovery
Ensuring your research makes the biggest impact means staying up-to-date with the current fast pace of innovation in drug discovery. In our eBook, you can read about some of the most exciting emerging bioassay technologies, such as three-dimensional cell culture and acoustic mass spectrometry, that could help you to accelerate the success of your drug discovery programme.