Protein minimization by random fragmentation and selection

Protein-protein interactions are involved in most biological processes and are important targets for drug design. Over the past decade, there has been increased interest in the design of small molecules that mimic functional epitopes of protein inhibitors. BLIP is a 165 amino acid protein that is a potent inhibitor of TEM-1 beta -lactamase (K-i = 0.1 nM). To aid in the dev elopment of new inhibitors of beta -lactamase, the gene encoding BLIP was r andomly fragmented and DNA segments encoding peptides that retain the abili ty to bind TEM-1 beta -lactamase were isolated using phage display. The sel ected peptides revealed a common, overlapping region that includes BLIP res idues C30-D49. Synthesis and binding analysis of the C30-D49 peptide indica te that this peptide inhibits TEM-1 beta -lactamase. Therefore, a peptide d erivative of BLIP that has been reduced in size by 88% compared with wild-t ype BLIP retains the ability to bind and inhibit beta -lactamase.