Capillary electrophoresis in drug discovery

The several advantages that capillary electrophoresis (CE) offers in the study of protein folding, protein-ligand and protein-protein interactions, render this methodology appealing in several areas. In this chapter, a specific example is reported, where the use of affinity CE (ACE) in drug discovery is particularly advantageous over other separative and spectroscopic techniques. ACE is an analytical approach in which the migration patterns of interacting molecules in an electric field are recorded and used to identify specific binding and to estimate binding constants. A library of compounds has been tested, in free solution and with minimum sample consumption, for the affinity to two targets previously separated by CE, the native form and the partially structured intermediate of the folding of beta(2)-microglobulin (beta(2)-m) [Chiti et al. (J. Biol. Chem. 276:46714-46721, 2001), Quaglia et al. (Electrophoresis 26:4055-4063, 2005)]. beta(2)-m is an intrinsically amyloidogenic protein, and its tendency to misfold is responsible for dialysis-related amyloidosis, an unavoidable complication of chronic haemodialysed patients. The criteria for choosing the compounds to be screened, the method conditions, and the possible data analysis strategies are detailed and discussed in this chapter.