Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing

Abstract

We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg- Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932–936, 2007) with improved ability to inhibit tumor growth. Computer mod- eling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bio- active conformation of CREKA. Because this conforma- tion presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids a -methyl and N -methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incor- porated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabil- ization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can con- verge and lead to useful biomedical advances