High-Throughput Affinity-Based Technologies for Small-Molecule Drug Discovery

Abstract

High-throughput affinity-based technologies are rapidly growing in use as primary screening methods in drug discovery. In this review, their principles and applications are described and their impact on small-molecule drug discovery is evaluated. In general, these technologies can be divided into 2 groups: those that detect binding interactions by measuring changes to the protein target and those that detect bound compounds. Technologies detecting binding interactions by focusing on the protein have limited throughput but can reveal mechanistic information about the binding interaction; technologies detecting bound compounds have very high throughput, some even significantly higher than current high-throughput screening technologies, but offer limited information about the binding interaction. In addition, the appropriate use of affinity-based technologies is discussed. Finally, nanotechnology is predicted to generate a significant impact on the future of affinity-based technologies. (Journal of Biomolecular

Small-molecule discovery from DNA-encoded chemical libraries

“…42, 43 Since researchers are often interested in interrogating multiple targets to increase the likelihood of finding a potent and selective ligand, the first constraint restricts the throughput of the method. The second limitation requires purification of library member-target complexes from inactive library members and, when immobilized targets are used, introduces artifacts arising from matrix binding, imprecise control of target concentration, or loss of native target structure.…”

Novel selection methods for DNA-encoded chemical libraries

“…Because DNA can be readily replicated and sequenced, in vitro selections of DNA-encoded chemical libraries offer the major advantage of simultaneously evaluating thousands or even millions of compounds for their ability to interact with target proteins in a single experiment. Selections significantly reduce the amount of compound, target protein, time, and cost required to evaluate a library [14,15]. In addition, selections on such libraries can readily yield structure-activity relationships that inform future medicinal chemistry efforts.…”

Overview of Recent Progress in Protein-Expression Technologies for Small-Molecule Screening

“…55 Affinity tags are also critical for affinity-based screening methodologies that rely on capturing protein-small-molecule complexes to identify hits. 7 One of the most commonly used affinity tags on constructs today is the polyHis tag. Designed more than 25 years ago, the polyHis tag binds to metal-containing matrices and can be eluted with high concentrations of imidazole.…”

“…Lack of efficacy in these downstream assays can occur for many reasons, including limited understanding of disease biology, 3 but any potentially significant differences between the endogenous target and the protein used for screening must also be considered, especially because the properties of the same protein expressed in different systems may not be similar. 4,5 With the rapid proliferation of targets resulting from an explosion of genomic data combined with recent advances in affinity screening technologies that access significantly larger regions of chemical space than traditional screening decks, 6,7 it is critical at the outset of any new screening campaign to consider expression technologies designed to produce proteins that structurally and functionally resemble endogenous targets. Such systems should also be more suitable for production of what have unfortunately been labeled as "challenging" targets, such as those that require complex posttranslational modifications or the presence of cell-type-specific protein partners to fold into their native conformation and multispanning membrane targets.…”