Combinatorial Chemistry and Peptide Library Methods to Characterize Protein Phosphatases

Abstract

The chapter discusses the combinatorial chemistry and peptide library methods to characterize protein phosphatases. Combinatorial methods provide tools and strategies to quickly generate large numbers of chemically related compounds (libraries). Two aspects of characterizing protein phosphatases are: (1) the assessment of the preferred substrates; and (2) the identification of compounds inhibiting the catalytic activity. The process of characterizing protein phosphatases, using combinatorial library methods is divided in three steps: (1) synthesis of the library; (2) screening of the library; and (3) deducing structure activity relations and identifying consensus or lead structures. Only general considerations for each step are presented, and a number of examples are discussed briefly. The examples presented in this chapter focus on protein tyrosine phosphatases (PTPs). However, the strategies discussed can be applied to related proteins such as serine/threonine protein phosphatases, dual specific protein phosphatases, and also to SH2 or PTB domain containing proteins. Chemical libraries can be based on any chemical scaffold, but the most easily accessible scaffold is linear oligoamides, in particular peptides. In addition, peptides are reasonably good substitutes/models for phosphoproteins, the in vivo targets of protein phosphatases. For these reasons, the synthesis of peptide-, phosphopeptide-, and modified peptide libraries are discussed in the chapter.