Identification of the cellular targets of bioactive small organic molecules using affinity reagents

Abstract

The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.

Small‐Molecule Mechanism of Action Studies in Caenorhabditis elegans

“…[23] The approach was first tested through the use of a derivative of the macrolide lactone FK506 (1). [24] The natural product, like the structurally related compound rapamycin (2), binds to the immunophilin FKBP12 (FK506 binding protein 12) to generate a small molecule-protein complex.…”

Interplay between the Chemical Space and the Biological Space

“…Note that this tutorial review provides a conceptual framework, supplied with brief descriptions of a few selected examples. Extensive reviews on the studies in this field are available [104][105][106].…”

Perspective on the Discovery and Scientific Impact of p38 MAP Kinase

“…For example, it is now possible to develop affinity reagents that can be used to isolate the target through affinity chromatography, provided that a suitable site on the ligand can be found to add a biotin or other group that can be used to conjugate the molecule to a column. 25,26 Furthermore, the availability of mass spectrometric sequencing methods combined with a database of all the potential human protein sequences derived from translation of the human genome has made identification of potential candidate target proteins considerably easier. 9,10,27,28 The list of potential candidates may be further trimmed through the use of small interfering RNAs (siRNAs) directed toward candidate genes, in the case of inhibition, or overexpression in the case of activation.…”