High-throughput screening (HTS), driven by the great progress in automation technology and combinatorial chemistry, has been widely implemented in drug discovery since the early 1990s and rapidly became one of the major sources of drug leads. Pharmaceutical companies, such as Pfizer and GlaxoSmithKline, were among the early leaders. In the past twenty years or so, many academic institutions joined the ‘screening mania’ and simultaneously, hundreds of screening centers appeared, as molecules available for screening continued to increase. However, in spite of constant increases in research and development (R&D) expenditures, the number of new chemical entities (NCEs) that reached to the market has actually decreased1 and 2. Analyses show that leads originating from HTS are responsible for over 60% of clinical trial failures3 and 4. Nonetheless, the data also indicate that among 58 drugs that were approved between 1991 and 2008, 19 were attributed to HTS5. Without question, HTS is still a feasible approach to drug innovation. The problem becomes one of how to improve the quality of leads arising from drug screening that may result in increased productivity of new molecular entity (NME) entering to the market place.
Since HTS has not substantially improved the drug discovery process and increased R&D spending has not led to a proportionate increase in new drug output, the pharmaceutical industry is looking back to the golden age of phenotype-oriented drug discovery6 and considering ADMET (absorption, distribution, metabolism, excretion and toxicity) of leads at earlier stages in drug development. A potential way to do this is through the use of cell-based assays. Cell-based assays not only obtain potencies of compounds but also detect cytotoxicity, permeability and effects on growth at the same time, which can be viewed as predictors for late development. Cell-based assays accounted for 52.6% of all HTS efforts in 20067 and became more favorable in recent years. However, cell-based assays are generally more complicated than biochemical ones and their performance could be undesirable under certain circumstances. Thus, quality control is of paramount importance and will be discussed in detail below. Although several comprehensive reviews are accessible in the public domain, this article attempts to give key points relevant to carrying out high quality cell-based HTS in a systematic and practical manner with potential problems and solutions highlighted.
Basically, HTS program consists of five parts: target identification, reagent preparation, assay development, compound management and high-throughput screening8. Among them, target identification and reagent preparation are beyond the interest of this review, although both of them are vital for successful HTS. Instead, we will cover topics such as assay development and optimization, compound management and data analysis, as well as hit identification and lead validation. High content screening (HCS), as an important part of cell-based HTS, has attracted significant attention recently because of its multiplexing and functional cell based characteristics9. However, considering the complexity of its data analysis, HCS is not included in this discussion.