Hit Generation and Selection

The goal of drug discovery is to identify new agents for therapeutic use—agents that impart a desired physiological effect and are safe for human consumption.

Early drug discovery focuses on identifying “hits,” compounds that are capable of acting on specific targets to create the desired modulation. For hit generation and selection, researchers screen numerous different compounds to find potential candidates, which they then characterize and test.

First, researchers must select which compounds to examine.

The broadest approach is simply to employ high-throughput screening techniques to scan the entire compound library of thousands and even millions of molecules. Alternatively, drug developers may elect to scan smaller, more focused subsets of compounds in order to save time and resources.

These subsets can include compounds that:

  • Already have data suggesting that they modulate the target
  • Are structurally similar to existing agents that modulate the target
  • Can be artificially designed and synthesized to theoretically modulate the target 

Compound management involves storing, organizing, tracking, and databasing these candidate compounds for easy reference and use. Effective compound management practices not only ease logistical burdens, but also help researchers select only the most relevant compounds for screening.

Second, researchers must decide how to determine the presence or absence of compound-target interactions. This requires assay selection (or assay development, if necessary), and selecting the parameters that will indicate a “hit.” Proper assay development is key to avoiding false positives and false negatives. It is also essential for post-screen hit selection by parsing the generated data and identifying hits with larger effects for downstream analysis.

Hit generation experimentation can be separated into primary and secondary screening. In primary screening, researchers seek evidence for an interaction between the compound and the target. This can be in the form of a measurable ligand-receptor or antibody-antigen interaction, or through quantifying the inhibition or activation of a known downstream effect. Primary screening assay techniques, such as ELISA, flow cytometry, and aequorin assays, usually handle extremely high throughputs and are simple to interpret.

In secondary screening, researchers select leads identified during primary screening for further examination. The goal of secondary screening is to confirm hit veracity, focusing on sensitivity and reliability over throughput. As such, secondary screening commonly uses more complex models—such as cells and tissues—than primary screening, and aims to determine parameters such as site of action and dose response curve.

Given the sheer number of compounds available to researchers today, and the large volume of data that can be rapidly generated using modern high-throughput techniques, hit generation and selection benefit greatly from automation.

The automation of any or all elements of a hit generation and selection workflow helps to not only reduce logistical burdens, but also to improve data accuracy and reproducibility, as well as prevent errors borne from mistakes or confusion.


  • Early drug discovery focuses on identifying and confirming “hits” through screening processes.
  • Numerous compounds are screened using high-throughput and high-sensitivity assay techniques.
  • Compound management and assay development practices are essential to hit generation success.
  • Primary screening aims to establish a target-compound interaction; secondary screening aims to confirm hit veracity.
  • Automating part or all of a hit generation and selection workflow offers considerable scientific and logistical benefits.