PLoS computational biology 2012-01-01

Molecular evolution of peptide ligands with custom-tailored characteristics for targeting of glycostructures.

Niels Röckendorf, Markus Borschbach, Andreas Frey

Index: PLoS Comput. Biol. 8(12) , e1002800, (2012)

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Abstract

As an advanced approach to identify suitable targeting molecules required for various diagnostic and therapeutic interventions, we developed a procedure to devise peptides with customizable features by an iterative computer-assisted optimization strategy. An evolutionary algorithm was utilized to breed peptides in silico and the "fitness" of peptides was determined in an appropriate laboratory in vitro assay. The influence of different evolutional parameters and mechanisms such as mutation rate, crossover probability, gaussian variation and fitness value scaling on the course of this artificial evolutional process was investigated. As a proof of concept peptidic ligands for a model target molecule, the cell surface glycolipid ganglioside G(M1), were identified. Consensus sequences describing local fitness optima were reached from diverse sets of L- and proteolytically stable D lead peptides. Ten rounds of evolutional optimization encompassing a total of just 4400 peptides lead to an increase in affinity of the peptides towards fluorescently labeled ganglioside G(M1) by a factor of 100 for L- and 400 for D-peptides.